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Advances in schistosome genomics
No full textIn Spring 2004, the first draft of the 270 Mb genome of Schistosoma mansoni will be released. This sequence is based on the assembly and annotation of a >7.5-fold coverage, shotgun sequencing project. The key stages involved in the international collaborative efforts that have led to the generation of these sequencing data for the parasite S. mansoni are discussed here
Novel Computational Methods for the Comparison of Leishmania Genomes and Transcriptomes
No full textLeishmania is a genus of protozoan parasites and the causative agent of Leishmaniasis. Twenty-one infectious species have been identified, with many previously being investigated by DNA and RNA-sequencing. However, significant genetic variation has prevented the comparison of this data across Leishmania species. Gene orthology grouping fails to compare over 70% of Leishmania genes’ expression across multiple species because of this variation. Here, we describe a novel method to reliably compare the genomes and transcriptomes of multiple Leishmania. This method produces a hybrid genome from the genetic sequence of any Leishmania species, while containing the rich sequence annotations of the L. major reference genome. In a demonstrative analysis, our approach allowed the comparison of 87% of genes in L. major against 5 other Leishmania species. Significant genetic variation was found to prevent comparison of many virulence-implicated genes, including surface antigens (e.g. amastins), cysteine proteases, and HSP-83. Within genes that could be compared, parasite transcriptomes segregated primarily by developmental stage (promastigote and amastigote). Transcriptomes secondarily separated by species. Genes upregulated in infection across all Leishmania were identified and included surface amastins, methyltransferases, and an apoptosis inhibition factor. Downregulated genes showed significantly greater sequence conservation than upregulated genes and comprised paraflagellar, flagellar, and HSP-70 proteins among others. The transcriptome differences between the clinical manifestations of leishmaniasis were additionally characterized. Taken together, these results provide much needed insight into the shared Leishmania pathway of infection and survival.College of Computer, Mathematical, and Natural Science
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Interplay of human macrophage response and natural resistance of infection by L. (V.) panamensis to pentavalent antimony.
No full textMacrophages are the principal host cells of Leishmania spp. in human infection and play a critical role in controlling infection and enabling parasite survival and persistence. Nevertheless, understanding of drug resistance in leishmaniasis has primarily focused on the parasite. This investigation provides evidence of the significant differential macrophage response to ex vivo infection with clinical strains of L. (V.) panamensis naturally resistant (zymodeme 2.3/zym 2.3) or sensitive (zymodeme 2.2/zym 2.2) to antimonial drug, and the distinct effect of this drug on the activation of macrophages. Transcriptome analysis of infected monocyte-derived macrophages from healthy donors revealed significant interferon and cytokine signaling in response to zym 2.3 strains compared to zym 2.2 strains. Furthermore, in the presence of antimony, macrophages infected with zym 2.3 strains, but not with zym 2.2 strains, significantly increased the expression of genes associated with M-CSF-generated macrophages (M-MØ, anti-inflammatory). Notably, macrophages infected with zym 2.3 strains exhibited elevated expression of genes associated with control of inflammatory and microbicidal response, such as the IDO1/IL4I1-Kyn-AHR pathways and superoxide dismutase, and downregulation of transporters like ABC and AQP, compared to macrophages infected with zym 2.2 strains. Remarkably, the majority of these pathways remained upregulated even in the presence of the strong modulatory effect of antimonial drug. Together, these findings demonstrate that the initial and specific parasite-host interaction influences the ex vivo macrophage response to antimony. Identification of key pathways in macrophage responses associated with natural resistance to this antileishmanial, enhances understanding of host-response mechanisms in the outcome of Leishmania infection and response to treatment
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Evolution of non-LTR retrotransposons in the trypanosomatid genomes: Leishmania major has lost the active elements
Get PDFThe ingi and L1Tc non-LTR retrotransposons - which constitute the ingi clade - are abundant in the genome of the trypanosomatid species Trypanosoma brucei and Trypanosoma cruzi, respectively. The corresponding retroelements, however, are not present in the genome of a closely related trypanosomatid, Leishmania major. To study the evolution of non-LTR retrotransposons in trypanosomatids, we have analyzed all ingi/L1Tc elements and highly degenerate ingi/L1Tc-related sequences identified in the recently completed T. brucei, T. cruzi and L. major genomes. The coding sequences of 242 degenerate ingi/L1Tc-related elements (DIREs) in all three genomes were reconstituted by removing the numerous frame shifts. Three independent phylogenetic analyses conducted on the conserved domains encoded by these elements show that all DIREs, including the 52 L. major DIREs, form a monophyletic group belonging to the ingi clade. This indicates that the trypanosomatid ancestor contained active mobile elements that have been retained in the Trypanosoma species, but were lost from L. major genome, where only remnants (DIRE) are detectable. All 242 DIREs analyzed group together according to their species origin with the exception of 11 T. cruzi DIREs which are close to the T. brucei ingi/DIRE families. Considering the absence of known horizontal transfer between the African T. brucei and the South-American T. cruzi, this suggests that this group of elements evolved at a lower rate when compared to the other trypanosomatid elements. Interestingly, the only nucleotide sequence conserved between ingi and L1Tc (the first 79 residues) is also present at the 5′-extremity of all the full length DIREs and suggests a possible role for this conserved motif, as well as for DIREs.Fil: Bringaud, Frédéric. Universite Victor Segalen Bordeaux Ii; FranciaFil: Ghedin, Elodie. The Institute for Genomic Research; Estados Unidos. The George Washington University; Estados UnidosFil: Blandin, Gaëlle. The Institute for Genomic Research; Estados UnidosFil: Bartholomeu, Daniella C.. The Institute for Genomic Research; Estados UnidosFil: Caler, Elisabet. The Institute for Genomic Research; Estados UnidosFil: Levin, Mariano Jorge. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina. Universidad de Buenos Aires; ArgentinaFil: Baltz, Théo. Universite Victor Segalen Bordeaux Ii; FranciaFil: El Sayed, Najib M.. The George Washington University; Estados Unidos. The Institute for Genomic Research; Estados Unido
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