1,721,024 research outputs found
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
Functional characterization of the eukaryotic-specific conserved features of nuclear RNase P in the yeast <italic>Saccharomyces cerevisiae</italic>.
No full textRNase P is an endoribonuclease responsible for cleavage of the 5' leader of precursor tRNAs (pre-tRNAs). Most forms of RNase P are ribonucleoprotein complexes containing RNA and protein subunits. Bacterial RNase P contains one RNA moiety and one protein subunit, with the RNA subunit by itself capable of cleaving pre-tRNAs in vitro. Eukaryotic nuclear RNase P also has a single RNA molecule, but many more protein subunits. The RNA subunits are relatively conserved in all three kingdoms of life, but structural elements of the RNA are identified that are conserved only in eukaryotes. Eukaryotic RNase P is closely related to another ribonucleoprotein enzyme, RNase MRP, which is involved in 5.8S rRNA maturation. Several protein subunits are common to RNases P and MRP. My thesis research focuses on functional characterization of the eukaryotic-specific features of nuclear RNase P in the yeast Saccharomyces cerevisiae . This work is illustrated in Chapters II and III of my dissertation. Chapter II describes characterization of the eukaryotic-specific conserved elements of the yeast RNase P RNA. Four eukaryotic-specific regions were mutated, and effects of the mutations on cell growth, enzyme function and biogenesis of RNase P were examined. Results suggest that most eukaryotic-specific conserved regions of RNase P RNA are important for holoenzyme assembly, localization and pre-tRNA processing. Chapter III focuses on characterization of the largest common protein subunit of yeast RNase P and MRP, Pop1p. Sequence alignment of Pop1p with its homologs has revealed four conserved regions. Mutations at the highly conserved positions were obtained by randomization mutagenesis, and were screened for conditional growth defects. Most Pop1p mutations affect both pre-tRNA and 5.8S rRNA processing, but a few mutations preferentially weaken only one of the two activities. In many cases, functional defects of RNase P and MRP are consistent with assembly defects of the holoenzymes. Mutations were also obtained that slow RNase P and MRP functions without notably affecting holoenzyme assembly. Taken together this study suggests that Pop1p plays a role in assembly and stability of the RNases P and MRP holoenzymes, but that it also has additional roles in the functions of the enzymes.PhDBiochemistryBiological SciencesMolecular biologyPure SciencesUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/125547/2/3192821.pd
tRNA genes as organizers of genetic information.
No full textThe genome of Saccharomyces cerevisiae contains 274 tRNA genes that are linearly scattered throughout all sixteen chromosomes. In this work, we have found that despite their apparently random distribution, tRNA genes are clustered together at the nucleolus and that this nucleolar localization depends on the active transcription of a tRNA gene. We went on to characterize the effect of this surprising arrangement on transcription near tRNA gene loci. The active transcription of a tRNA gene by RNA polymerase III can antagonize transcription from a linearly adjacent polymerase II promoter, an effect termed tRNA gene mediated (tgm) silencing. We have now identified several mutations in nucleolar proteins that cause tgm silencing to be released. These mutants also show tRNA genes and pre-tRNAs dispersed throughout the nucleoplasm instead of their normal nucleolar localization. Thus, the nucleolar clustering of tRNA genes appears to contribute to tgm silencing. Extensive spatial organization of the S. cerevisiae genome must exist in order to gather these genes, and we investigated whether structural elements were involved in the tRNA gene localization mechanism. After treatment with the microtubule-depolymerizing drug nocodazole, tRNA genes were still clustered together, but the clusters were divorced from the nucleolus. This role for microtubules appears to be unrelated to cell cycle stage, because we found that unsynchronized cells throughout the cell cycle showed tRNA gene signal concentrated at the nucleolus. These observations suggest that microtubules are involved in the nucleolar localization of tRNA gene clusters, which are initially formed by a separate mechanism. To investigate the initial clustering mechanism, we examined the condensin complex, which has been found to bind to tRNA genes along S. cerevisiae chromosomes. Condensin is involved in the compaction of mitotic chromosomes and is concentrated at the nucleolus during anaphase. We have now found that temperature sensitive mutants of condensin subunits are able to release tgm silencing and mislocalize tRNA genes. This work has shown that clustering of the linearly dispersed tRNA genes is a major force in spatial organization of the yeast genome and has provided the first mechanistic insights as to how this clustering is accomplished.PhDBiochemistryBiological SciencesCellular biologyMolecular biologyPure SciencesUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/126428/2/3253277.pd
Mutational analyses of yeast nuclear RNase P.
No full textRibonuclease P (RNase P) is an ubiquitous endoribonuclease that cleaves precursor transfer RNA molecules to form mature 5\sp\prime termini. Unlike other ribozymes, it does not recognize its substrates by base-pairing but rather by recognition of conserved tertiary structures in the tRNAs. RNase P is a metalloenzyme, requiring magnesium ions as cofactors for catalysis. In both prokaryotes and eukaryotes the enzyme exists as a ribonucleoprotein, but the eubacterial RNA moieties are catalytic alone in vitro, demonstrating that the RNA is responsible far substrate recognition and catalysis. This dissertation investigates the functional contributions of structural elements of the RNA subunit of yeast nuclear RNase P. Using the yeast Saccharomyces cerevisiae as model system, mutagenesis techniques and in vivo complementation were used to identify regions of the RNA that are essential for function in vivo. Previous phylogenetic studies revealed a high conservation of secondary structure in yeast RNase P RNAs. To correlate this observed conservation with function, in vivo complementation experiments were performed using heterologous yeast RNase P RNAs. The results identified sequences and structures in the RNA that are not essential for interaction with species-specific proteins, processing or localization, and suggested other positions that may be candidates for such processes. Based on these observations, a series of highly conserved sequences and structures that could have important functional roles were analyzed by directed mutagenesis. Results from deletion experiments showed good correlation with our predictions since structures which sequences are not conserved proved not to be essential for function. Highly conserved nucleotides that are invariant between eubacterial and yeast RNase P were also investigated by randomization mutagenesis. Some mutations gave conditional growth mutants. These were used to study the effects of the mutations in different aspects of RNase P function. Through partial purification of mutant holoenzymes it was also possible to inspect enzyme function in vitro. Kinetic analyses have revealed that a highly conserved subdomain in the RNA is involved in catalysis, possibly by coordinating magnesium ion cofactors at the cleavage site.PhDBiological ChemistryUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/105005/1/9624703.pdfDescription of 9624703.pdf : Restricted to UM users only
The study of nuclear ribonuclease P in <italic>Saccharomyces cerevisiae</italic> using novel RNA affinity tags.
No full textRibonuclease P (RNase P) is the enzyme responsible for a cleavage of the 5' leaders of pre-tRNAs in all living organisms. In the yeast Saccharomyces cerevisiae, nuclear RNase P consists of one RNA (RPR1 RNA) and nine protein subunits. RPR1 RNA is initially transcribed as a precursor and subsequently processed into a mature form. Defects in subunit assembly have been associated with a failure of RPR1 RNA to be processed from the precursor to mature form. In order to understand the holoenzyme subunit assembly, the studies in this dissertation address the nature of the precursor form of RNase P (pre-RNase P). Instead of using a long, multistep chromatographic purification of RNase P, which could lead to degradation and loss of the enzymatic activity, a rapid and specific affinity isolation of the enzyme is strongly preferred. However, the RNA affinity ligands for detection and isolation of RNAs or ribonucleoproteins have been lacking. In this study, two small RNA tags have been identified through in vitro selection. These tags bind specifically to Sephadex or streptavidin, and the binding to their targets can be disrupted under mild conditions with either dextran or d-biotin, respectively. This useful feature allows specific isolation and recovery of the tagged RNAs or ribonucleoproteins with intact structures and activity. To isolate RNase P, RPR1 RNA was tagged at various positions with the Sephadex-binding RNA, enabling a rapid and specific affinity isolation of either pre- or mature-RNase P. Pre-RNase P was found to be as active in pre-tRNA cleavage in vitro as mature-RNase P. Its protein subunit composition was also similar to that of mature-RNase P, except that very little Pop3p and Rpr2p could be detected relative to the other subunits. Further depletion of these two subunits did not affect RPR1 RNA maturation even though they are required for RNase P function in vivo. In situ hybridization showed that pre-RNase P RNA was localized primarily in the nucleolus, indicating that the assembly is likely to occur there. The finding that pre-RNase P was enzymatically active suggests that, in addition to being the precursor, it might have an in vivo catalytic role for either pre-tRNAs or other unidentified substrates.PhDBiochemistryBiological SciencesMolecular biologyPure SciencesUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/123287/2/3068971.pd
Biochemical and genetic analyses of the structure and function of the ribonucleoprotein enzyme, RNase P.
No full textRibonuclease P (RNase P) is a ribonucleoprotein metalloenzyme responsible for processing 5' leaders of tRNA transcripts. Eukaryotic nuclear RNase P from Saccharomyces cerevisiae is composed of an RNA subunit and nine protein subunits. RNase P structure, RNA-protein interactions, and reaction kinetics were investigated. The P10/11--P12 RNA subdomain of yeast RNase P RNA contains a conserved motif that is critical for efficient catalysis and magnesium utilization. Solution structure analysis verified the phylogenetic structure of this RNA domain and implicated several of the conserved nucleotides in magnesium-dependent structure changes. It is likely that this portion of the RNase P RNA serves to coordinate magnesium ions necessary for efficient catalysis. The P3 RNA subdomain of RNase P is unique to the eukaryotic enzyme and has been implicated in nucleolar localization of RNase P RNA. This subdomain contains substantial intraspecies conservation with RNase MRP RNA, suggesting an interaction with a common protein subunit. Four conserved nucleotides in the P3 domain were randomized and temperature sensitive clones were isolated. RNase P RNA maturation and tRNA processing were monitored at permissive and non-permissive conditions. Accumulation of pre-RPR1 RNA and unprocessed tRNA precursors was observed at the non-permissive temperature. Therefore, alteration of P3 structure led to phenotypes characteristic of RNase P holoenzyme assembly defects. This domain appears necessary for cellular localization of the enzyme; for its processing and assembly and/or for directing enzyme to substrate processing locales. Finally, substrate recognition elements outside the mature tRNA domain have been investigated. Eukaryotic pre-tRNAs go through a series of reactions required for maturation, the first being cleavage by RNase P. The eukaryotic enzyme encounters primary tRNAs containing leader and trailer sequences. The effects of these sequences on RNase P recognition were investigated by kinetic measurements and calculation of apparent inhibition constants. Leader-trailer pairing considerably hampered substrate recognition and the 3' trailer sequence was found to have a strong, positive interaction with RNase P. These studies have helped elucidate fundamental RNA-based chemistry and determine how RNase P fits into complex processing pathways critical to cellular RNA maturation and protein synthesis.PhDBiochemistryBiological SciencesMolecular biologyPure SciencesUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/132506/2/9963928.pd
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
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