bluuebunny/crossref_metadata_2025_split huggingface dataset:
On rational maps from a general surface in to surfaces of general type
Authors: Guerra Lucio , Pirola Gian Pietro 
Published: May 2008

Abstract
We study dominant rational maps from a general surface in to surfaces of general type. We prove restrictions on the target surfaces, and special properties of these rational maps. We show that for small degree the general surface has no such map. Moreover a slight improvement of a result of Catanese, on the number of moduli of a surface of general type, is also obtained.
Distinctive morphological features, life-cycle phases and seasonal variations in subtropical populations ofDictyota dichotoma(Dictyotales, Phaeophyceae)
Authors: Tronholm Ana , Sansón Marta , Afonso-Carrillo Julio , De Clerck Olivier 
Published: May 2008

AbstractAlthough it has been suggested that the distribution ofDictyota dichotomais probably restricted to the European Atlantic Ocean and the Mediterranean Sea, its occurrence in the Canary Islands (new southernmost distribution limit) is confirmed by nuclear ribosomal sequence data (LSU rDNA). Even thoughD. dichotomahas been described and illustrated prominently in early studies of brown algae, the species remains difficult to characterize due to considerable morphological plasticity. An exhaustive analysis of several quantitative characters confirms significant morphological variation both seasonally and between life-cycle phases. The species may be characterized in the Canary Islands only by the following qualitative features: erect thallus attached by a single holdfast, subdichotomous branches always of similar width, straight terminal segments and smooth margins and an entirely unilayered medulla. In the Canary Islands,D. dichotomais an aseasonal annual with at least three overlapping generations in which sporophytes and gametophytes grow simultaneously. Thallus life span seems to be less than 3 months. The species occurs throughout the year, but as cryptic microthalli in autumn. Two abundance peaks were detected with the maximum value in February (6.2 thalli m-2). The optimum reproductive stage (88.3% fertile specimens) occurred in winter and the maximum vegetative stage (maximum thallus length: 18.6 cm) in summer. Sporophytes outnumbered gametophytes throughout the year, with ratios decreasing from 13.2±1.1 in winter to 1.9±0.2 in summer. Gametophytes made up to 25% of the population and fertile thalli were always dominant. The populations from the Canaries exhibited a temporal displacement compared to northern populations with the favorable period in the coldest season (winter) and the resting period in the warmest season (autumn).
Laurencia caduciramulosa(Ceramiales, Rhodophyta) from the Canary Islands, Spain: a new record for the eastern Atlantic Ocean
Authors: Cassano Valéria , Candelaria Gil-Rodríguez Maria , Sentíes Abel , Toyota Fujii Mutue 
Published: May 2008

AbstractLaurencia caduciramulosais recorded for the first time for the eastern Atlantic Ocean off Tenerife, Canary Islands, Spain. The specimens were collected in 2006, growing epilithically in the lower intertidal zone on moderately exposed rocky shores. This species is characterized by reduced size, a well-developed stolon-like basal system and erect axes with abundant deciduous branchlets that function as propagules, except on the uppermost portions of the branches, where they form crowns of branchlets. As in all other reports of this species, gametangia and sporangia were not observed. This study expands the geographical distribution ofL. caduciramulosato the eastern Atlantic Ocean.
Analysis of theDrosophila melanogasterTestes Transcriptome Reveals Coordinate Regulation of Paralogous Genes
Authors: Mikhaylova Lyudmila M , Nguyen Kimberly , Nurminsky Dmitry I 
Published: May 2008

AbstractGene duplications have been broadly implicated in the generation of testis-specific genes. To perform a comprehensive analysis of paralogous testis-biased genes, we characterized the testes transcriptome of Drosophila melanogaster by comparing gene expression in testes vs. ovaries, heads, and gonadectomized males. A number of the identified 399 testis-biased genes code for the known components of mature sperm. Among the detected 69 genes downregulated in testes, a large fraction is required for viability. By analyzing paralogs of testis-biased genes, we identified “co-regulated” paralogous pairs in which both genes are testis biased, “anti-regulated” pairs in which one paralog is testis biased and the other downregulated in testes, and “neutral” pairs in which one paralog is testis biased and the other constitutively expressed. The numbers of identified co-regulated and anti-regulated pairs were higher than expected by chance. Testis-biased genes included in these pairs show decreased frequency of lethal mutations, suggesting their specific role in male reproduction. These genes also show exceptionally high interspecific variability of expression in comparison between D. melanogaster and the closely related D. simulans. Further, interspecific changes in testis bias of expression are generally correlated within the co-regulated pairs and are anti-correlated within the anti-regulated pairs, suggesting coordinated regulation within both types of paralogous gene pairs.
Linkage Disequilibrium Under Genetic Hitchhiking in Finite Populations
Authors: Pfaffelhuber P , Lehnert A , Stephan W 
Published: May 2008

AbstractThe model of genetic hitchhiking predicts a reduction in sequence diversity at a neutral locus closely linked to a beneficial allele. In addition, it has been shown that the same process results in a specific pattern of correlations (linkage disequilibrium) between neutral polymorphisms along the chromosome at the time of fixation of the beneficial allele. During the hitchhiking event, linkage disequilibrium on either side of the beneficial allele is built up whereas it is destroyed across the selected site. We derive explicit formulas for the expectation of the covariance measure D and standardized linkage disequilibrium $\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{{\sigma}}_{D}^{2}\) \end{document}$ between a pair of polymorphic sites. For our analysis we use the approximation of a star-like genealogy at the selected site. The resulting expressions are approximately correct in the limit of large selection coefficients. Using simulations we show that the resulting pattern of linkage disequilibrium is quickly—i.e., in &lt;0.1N generations—destroyed after the fixation of the beneficial allele for moderately distant neutral loci, where N is the diploid population size.
A Statistical Model for Testing the Pleiotropic Control of Phenotypic Plasticity for a Count Trait
Authors: Ma Chang-Xing , Yu Qibin , Berg Arthur , Drost Derek , Novaes Evandro , Fu Guifang , Yap John Stephen , Tan Aixin , Kirst Matias , Cui Yuehua , Wu Rongling 
Published: May 2008

Abstract
The differences of a phenotypic trait produced by a genotype in response to changes in the environment are referred to as phenotypic plasticity. Despite its importance in the maintenance of genetic diversity via genotype-by-environment interactions, little is known about the detailed genetic architecture of this phenomenon, thus limiting our ability to predict the pattern and process of microevolutionary responses to changing environments. In this article, we develop a statistical model for mapping quantitative trait loci (QTL) that control the phenotypic plasticity of a complex trait through differentiated expressions of pleiotropic QTL in different environments. In particular, our model focuses on count traits that represent an important aspect of biological systems, controlled by a network of multiple genes and environmental factors. The model was derived within a multivariate mixture model framework in which QTL genotype-specific mixture components are modeled by a multivariate Poisson distribution for a count trait expressed in multiple clonal replicates. A two-stage hierarchic EM algorithm is implemented to obtain the maximum-likelihood estimates of the Poisson parameters that specify environment-specific genetic effects of a QTL and residual errors. By approximating the number of sylleptic branches on the main stems of poplar hybrids by a Poisson distribution, the new model was applied to map QTL that contribute to the phenotypic plasticity of a count trait. The statistical behavior of the model and its utilization were investigated through simulation studies that mimic the poplar example used. This model will provide insights into how genomes and environments interact to determine the phenotypes of complex count traits.
Gene Expression Profiling of Flagellar Disassembly in Chlamydomonas reinhardtii
Authors: Chamberlain Kara L , Miller Steven H , Keller Laura R 
Published: May 2008

Abstract
Flagella are sensory organelles that interact with the environment through signal transduction and gene expression networks. We used microarray profiling to examine gene regulation associated with flagellar length change in the green alga Chlamydomonas reinhardtii. Microarrays were probed with fluorescently labeled cDNAs synthesized from RNA extracted from cells before and during flagellar assembly or disassembly. Evaluation of the gene expression profiles identified &gt;100 clones showing at least a twofold change in expression during flagellar length changes. Products of these genes are associated not only with flagellar structure and motility but also with other cellular responses, including signal transduction and metabolism. Expression of specific genes from each category was further characterized at higher resolution by using quantitative real-time PCR (qRT–PCR). Analysis and comparison of the gene expression profiles coupled to flagellar assembly and disassembly revealed that each process involves a new and uncharacterized whole-cell response to flagellar length changes. This analysis lays the groundwork for a more comprehensive understanding of the cellular and molecular networks regulating flagellar length changes.
AnALMT1Gene Cluster Controlling Aluminum Tolerance at theAlt4Locus of Rye (Secale cerealeL.)
Authors: Collins N C , Shirley N J , Saeed M , Pallotta M , Gustafson J P 
Published: May 2008

AbstractAluminum toxicity is a major problem in agriculture worldwide. Among the cultivated Triticeae, rye (Secale cereale L.) is one of the most Al tolerant and represents an important potential source of Al tolerance for improvement of wheat. The Alt4 Al-tolerance locus of rye contains a cluster of genes homologous to the single-copy Al-activated malate transporter (TaALMT1) Al-tolerance gene of wheat. Tolerant (M39A-1-6) and intolerant (M77A-1) rye haplotypes contain five and two genes, respectively, of which two (ScALMT1-M39.1 and ScALMT1-M39.2) and one (ScALMT1-M77.1) are highly expressed in the root tip, typically the main site of plant Al tolerance/susceptibility. All three transcripts are upregulated by exposure to Al. High-resolution genetic mapping identified two resistant lines resulting from recombination within the gene cluster. These recombinants exclude all genes flanking the gene cluster as candidates for controlling Alt4 tolerance, including a homolog of the barley HvMATE Al-tolerance gene. In the recombinants, one hybrid gene containing a chimeric open reading frame and the ScALMT1-M39.1 gene each appeared to be sufficient to provide full tolerance. mRNA splice variation was observed for two of the rye ALMT1 genes and in one case, was correlated with a ∼400-bp insertion in an intron.
FER1 and FER2 Encoding Two Ferritin Complexes in Chlamydomonas reinhardtii Chloroplasts Are Regulated by Iron
Authors: Long Joanne C , Sommer Frederik , Allen Michael D , Lu Shu-Fen , Merchant Sabeeha S 
Published: May 2008

Abstract
Two unlinked genes FER1 and FER2 encoding ferritin subunits were identified in the Chlamydomonas genome. An improved FER2 gene model, built on the basis of manual sequencing and incorporation of unplaced reads, indicated 49% identity between the ferritin subunits. Both FER1 and FER2 transcripts are increased in abundance as iron nutrition is decreased but the pattern for each gene is distinct. Using subunit-specific antibodies, we monitored expression at the protein level. In response to low iron, ferritin1 subunits and the ferritin1 complex are increased in parallel to the increase in FER1 mRNA. Nevertheless, the iron content of the ferritin1 complex is decreased. This suggests that increased expression results in increased capacity for iron binding in the chloroplast of iron-limited cells, which supports a role for ferritin1 as an iron buffer. On the other hand, ferritin2 abundance is decreased in iron-deprived cells, indicative of the operation of iron-nutrition-responsive regulation at the translational or post-translational level for FER2. Both ferritin subunits are plastid localized but ferritin1 is quantitatively recovered in soluble extracts of cells while ferritin2 is found in the particulate fraction. Partial purification of the ferritin1 complex indicates that the two ferritins are associated in distinct complexes and do not coassemble. The ratio of ferritin1 to ferritin2 is 70:1 in iron-replete cells, suggestive of a more dominant role of ferritin1 in iron homeostasis. The Volvox genome contains orthologs of each FER gene, indicating that the duplication of FER genes and potential diversification of function occurred prior to the divergence of species in the Volvocales.
Analysis of Chromatin Structure of Genes Silenced by Heterochromatin in Trans
Authors: Nisha Parul , Plank Jennifer L , Csink Amy K 
Published: May 2008

Abstract
While heterochromatic gene silencing in cis is often accompanied by nucleosomal compaction, characteristic histone modifications, and recruitment of heterochromatin proteins, little is known concerning genes silenced by heterochromatin in trans. An insertion of heterochromatic satellite DNA in the euchromatic brown (bw) gene of Drosophila melanogaster results in bwDominant (bwD), which can inactivate loci on the homolog by relocation near the centric heterochromatin (trans-inactivation). Nucleosomal compaction was found to accompany trans-inactivation, but stereotypical heterochromatic histone modifications were mostly absent on silenced reporter genes. HP1 was enriched on trans-inactivated reporter constructs and this enrichment was more pronounced on adult chromatin than on larval chromatin. Interestingly, this HP1 enrichment in trans was unaccompanied by an increase in the 2MeH3K9 mark, which is generally thought to be the docking site for HP1 in heterochromatin. However, a substantial increase in the 2MeH3K9 mark was found on or near the bwD satellite insertion in cis, but did not spread further. These observations suggest that the interaction of HP1 with chromatin in cis is fundamentally different from that in trans. Our molecular data agree well with the differential phenotypic effect on bwD trans-inactivation of various genes known to be involved in histone modification and cis gene silencing.
The Drosophila Gap Gene giant Has an Anterior Segment Identity Function Mediated Through disconnected and teashirt
Authors: Sanders Lisa R , Patel Mukund , Mahaffey James W 
Published: May 2008

Abstract
The C2H2 zinc-finger-containing transcription factors encoded by the disconnected (disco) and teashirt (tsh) genes contribute to the regionalization of the Drosophila embryo by establishing fields in which specific Homeotic complex (Hom-C) proteins can function. In Drosophila embryos, disco and the paralogous disco-related (disco-r) are expressed throughout most of the epidermis of the head segments, but only in small patches in the trunk segments. Conversely, tsh is expressed extensively in the trunk segments, with little or no accumulation in the head segments. Little is known about the regulation of these genes; for example, what limits their expression to these domains? Here, we report the regulatory effects of gap genes on the spatial expression of disco, disco-r, and tsh during Drosophila embryogenesis. The data shed new light on how mutations in giant (gt) affect patterning within the anterior gt domain, demonstrating homeotic function in this domain. However, the homeosis does not occur through altered expression of the Hom-C genes but through changes in the regulation of disco and tsh.
The Effect of Chromosome Geometry on Genetic Diversity
Authors: Marri Pradeep Reddy , Harris Leigh K , Houmiel Kathryn , Slater Steven C , Ochman Howard 
Published: May 2008

Abstract
Although organisms with linear chromosomes must solve the problem of fully replicating their chromosome ends, this chromosome configuration has emerged repeatedly during bacterial evolution and is evident in three divergent bacterial phyla. The benefit usually ascribed to this topology is the ability to boost genetic variation through increased recombination. But because numerous processes can impact linkage disequilibrium, such an effect is difficult to assess by comparing across bacterial taxa that possess different chromosome topologies. To test directly the contribution of chromosome architecture to genetic diversity and recombination, we examined sequence variation in strains of Agrobacterium Biovar 1, which are unique among sequenced bacteria in having both a circular and a linear chromosome. Whereas the allelic diversity among strains is generated principally by mutations, intragenic recombination is higher within genes situated on the circular chromosome. In contrast, recombination between genes is, on average, higher on the linear chromosome, but it occurs at the same rate as that observed between genes mapping to the distal portion of the circular chromosome. Collectively, our findings indicate that chromosome topology does not contribute significantly to either allelic or genotypic diversity and that the evolution of linear chromosomes is not based on a facility to recombine.
On the Evolution and Expression of Chlamydomonas reinhardtii Nucleus-Encoded Transfer RNA Genes
Authors: Cognat Valérie , Deragon Jean-Marc , Vinogradova Elizaveta , Salinas Thalia , Remacle Claire , Maréchal-Drouard Laurence 
Published: May 2008

Abstract
In Chlamydomonas reinhardtii, 259 tRNA genes were identified and classified into 49 tRNA isoaccepting families. By constructing phylogenetic trees, we determined the evolutionary history for each tRNA gene family. The majority of the tRNA sequences are more closely related to their plant counterparts than to animals ones. Northern experiments also permitted us to show that at least one member of each tRNA isoacceptor family is transcribed and correctly processed in vivo. A short stretch of T residues known to be a signal for termination of polymerase III transcription was found downstream of most tRNA genes. It allowed us to propose that the vast majority of the tRNA genes are expressed and to confirm that numerous tRNA genes separated by short spacers are indeed cotranscribed. Interestingly, in silico analyses and hybridization experiments show that the cellular tRNA abundance is correlated with the number of tRNA genes and is adjusted to the codon usage to optimize translation efficiency. Finally, we studied the origin of SINEs, short interspersed elements related to tRNAs, whose presence in Chlamydomonas is exceptional. Phylogenetic analysis strongly suggests that tRNAAsp-related SINEs originate from a prokaryotic-type tRNA either horizontally transferred from a bacterium or originally present in mitochondria or chloroplasts.
Genomewide Analysis of Box C/D and Box H/ACA snoRNAs in Chlamydomonas reinhardtii Reveals an Extensive Organization Into Intronic Gene Clusters
Authors: Chen Chun-Long , Chen Chong-Jian , Vallon Olivier , Huang Zhan-Peng , Zhou Hui , Qu Liang-Hu 
Published: May 2008

Abstract
Chlamydomonas reinhardtii is a unicellular green alga, the lineage of which diverged from that of land plants &gt;1 billion years ago. Using the powerful small nucleolar RNA (snoRNA) mining platform to screen the C. reinhardtii genome, we identified 322 snoRNA genes grouped into 118 families. The 74 box C/D families can potentially guide methylation at 96 sites of ribosomal RNAs (rRNAs) and snRNAs, and the 44 box H/ACA families can potentially guide pseudouridylation at 62 sites. Remarkably, 242 of the snoRNA genes are arranged into 76 clusters, of which 77% consist of homologous genes produced by small local tandem duplications. At least 70 snoRNA gene clusters are found within introns of protein-coding genes. Although not exhaustive, this analysis reveals that C. reinhardtii has the highest number of intronic snoRNA gene clusters among eukaryotes. The prevalence of intronic snoRNA gene clusters in C. reinhardtii is similar to that of rice but in contrast with the one-snoRNA-per-intron organization of vertebrates and fungi and with that of Arabidopsis thaliana in which only a few intronic snoRNA gene clusters were identified. This analysis of C. reinhardtii snoRNA gene organization shows the functional importance of introns in a single-celled organism and provides evolutionary insight into the origin of intron-encoded RNAs in the plant lineage.
A Linkage Map of the Zebra FinchTaeniopygia guttataProvides New Insights Into Avian Genome Evolution
Authors: Stapley J , Birkhead T R , Burke T , Slate J 
Published: May 2008

AbstractPasseriformes are the largest order of birds and one of the most widely studied groups in evolutionary biology and ecology. Until recently genomic tools in passerines relied on chicken genomic resources. Here we report the construction and analysis of a whole-genome linkage map for the zebra finch (Taeniopygia guttata) using a 354-bird pedigree. The map contains 876 SNPs dispersed across 45 linkage groups and we found only a few instances of interchromosomal rearrangement between the zebra finch and the chicken genomes. Interestingly, there was a greater than expected degree of intrachromosomal rearrangements compared to the chicken, suggesting that gene order is not conserved within avian chromosomes. At 1068 cM the map is approximately only one quarter the length of the chicken linkage map, providing further evidence that the chicken has an unusually high recombination rate. Male and female linkage-map lengths were similar, suggesting no heterochiasmy in the zebra finch. This whole-genome map is the first for any passerine and a valuable tool for the zebra finch genome sequence project and for studies of quantitative trait loci.
Sex and Deleterious Mutations
Authors: Gordo Isabel , Campos Paulo R A 
Published: May 2008

Abstract
The evolutionary advantage of sexual reproduction has been considered as one of the most pressing questions in evolutionary biology. While a pluralistic view of the evolution of sex and recombination has been suggested by some, here we take a simpler view and try to quantify the conditions under which sex can evolve given a set of minimal assumptions. Since real populations are finite and also subject to recurrent deleterious mutations, this minimal model should apply generally to all populations. We show that the maximum advantage of recombination occurs for an intermediate value of the deleterious effect of mutations. Furthermore we show that the conditions under which the biggest advantage of sex is achieved are those that produce the fastest fitness decline in the corresponding asexual population and are therefore the conditions for which Muller's ratchet has the strongest effect. We also show that the selective advantage of a modifier of the recombination rate depends on its strength. The quantification of the range of selective effects that favors recombination then leads us to suggest that, if in stressful environments the effect of deleterious mutations is enhanced, a connection between sex and stress could be expected, as it is found in several species.