1,720,983 research outputs found
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Regulation of class II pilin gene expression in Neisseria meningitidis
Full text linkNeisseria meningitidis expresses multi-component organelles called Type four pili (Tfp), which are key virulence factors involved in interactions with host cells. Pilin (PilE) is the main component of Tfp and N. meningitidis can express either class I pilins that undergo antigenic variation or class II pilins, which are highly conserved. The region upstream of the pilE gene contains two putative promoters which are recognised by distinct sigma factors: sigma70 family and sigmaN. We aimed to investigate regulation of class II pilE by characterising the role of multiple sigma factors in class II pilE transcription.
We confirmed the presence of conserved sigma70 family- and sigmaN-dependent promoter sequences in a large collection of meningococcal genomes. We show that the promoters are functional in E. coli, however in N. meningitidis PilE expression under steady state is initiated from the sigma70 family-dependent promoter. Furthermore, neither the absence nor overexpression of sigmaN had any effect on pilin levels in N. meningitidis which indicates that sigmaN does not contribute to class II pilin regulation, and also suggests that sigmaN does not function as a -12/-24 sequence-dependent activator. Strikingly, Neisseria elongata sigma N, which is known to function as an activator of pilE in commensal N. elongata, was able to reduce meningococcal pilin expression. The negative effect exerted by N. elongata sigmaN on class II pilin expression raises a possibility that in pathogenic Neisseria the sigma-dependent network responsible for the expression of pilE has been modified to maintain Tfp expression, considering their key role in colonisation and pathogenesis.
Studying transcription patterns of virulence factors offers an interesting possibility to understand features that define pathogenic Neisseria. We analysed sigmaH regulon in N. meningitidis by RNA sequencing and our results suggest that sigmaH might be implicated in the response to diverse stimuli including the canonical heat shock response.
In summary, results presented here provide new insights into class II pilE regulation and the role of sigmaH in N. meningitidis. Future work will focus on identifying signalling networks that govern pilE expression in response to environmental stimuli and will explore the sigma factor cross-talk in pathogenic Neisseria. This will expand our knowledge of meningococcal adaptation to niches within the host.</p
The interplay between plasmids in Shigella sonnei
Full text linkShigella sonnei causes bacillary dysentery in higher-income countries, with emerging antimicrobial resistance spread by plasmids. My thesis aimed to investigate the interplay between S. sonnei pINV, which is required for virulence, and resistance plasmids. pRES, a naturally occurring 114 kbp conjugative resistance plasmid, was used as an exemplar to investigate the transfer the 228 kbp virulence plasmid pINV, which was previously considered non-mobilisable.
pRES belongs to incompatibility group IncB/O/K/Z and is stably maintained during laboratory culture. The co-existence of pINV and pRES does not affect their maintenance within a bacterial population. pRES is a conjugative plasmid which can mobilises a 5.1 kbp colicin-E1 encoding plasmid as well as pINV. During pINV transfer, pINV and pRES form a single 334 kbp fusion plasmid, and/or hybrid plasmids, via RecA-dependent and -independent recombination, and insertion sequence transposition. Copies of IS21 on pINV and pRES, and a conserved 199 bp region (199R) downstream of the plasmid replicons were detected at the pINV/pRES junctions in fusion and hybrid molecules.
The 199R is conserved in plasmids from IncFII and IncI-complex groups in S. sonnei which replicate unidrectionally. The sequence includes the single-stranded initiation site for synthesis of the leading strand during plasmid replication. Removal of the 199R increases pINV and pRES loss. The first 99 bp of the 199R (99O) overlaps with a previously described 218 bp (218B) deletion on the R1 plasmid, which involves the terR site for replication termination. Deletion of 218B or 99O also increases plasmid loss. RNAfold prediction suggest that the 99O can form secondary structures when single-stranded. SNPs were introduced into the 99O, disrupting these structures and increasing plasmid loss, corresponding to the degree of disruption. Secondary structures in the 199R might influence plasmid replication and inter-plasmid recombination, contributing to the mosaic architecture of many plasmids
Variations on the Author
Full text link“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
Interactions between Neisseria meningitidis and galectin-3
Full text linkGalectins are beta-galactoside animal lectins which possess similar carbohydrate recognition domains and have important roles in the development and regulation of innate and adaptive immunity. Galectins have been previously shown to modulate inflammatory responses to bacterial infections, however nothing is known about the functions of different galectins during meningococcal disease.
Here I describe the interaction between galectins, in particular galectin-3, and Neisseria meningitidis, a commensal of the human respiratory tract that occasionally causes septicaemia and meningitis. Immunohistochemical analyses showed that expression of galectin-3, but not galectin-1 and galectin-8, is increased in tissues of mice following challenge with N. meningitidis; furthermore, galectin-3 staining co-localises with the bacterium in tissues from patients with meningococcal disease.
The molecular basis of interaction between N. meningitidis and exogenous galectin-3 was investigated by identifying both the bacterial structures and the regions of galectin-3 involved. Binding of galectin-3 to N. meningitidis was shown to be dependent on bacterial lipopolysaccharide (LPS), while inhibition assays with lactose and the use of truncated versions of galectin-3 demonstrated that the C-terminal carbohydrate recognition domain is necessary, but not sufficient, for the interaction. Furthermore, the biological consequences of interaction of bacteria with galectin-3 were investigated. Exogenous galectin-3 did not affect adhesion of N. meningitidis to epithelial cells, but increased the attachment of bacteria to phagocytic cells; silencing of galectin-3 expression in phagocytes did not alter the interaction of N. meningitidis with cells.
In summary, galectin-3 binds to N. meningitidis via LPS and affects meningococcal interaction with phagocytic cells. The potential role of galectin-3 in pathogen recognition is discussed
Characterization of pilE antisense RNA in Neisseria meningitidis
Full text linkExpression of Type four pili is important for colonization and virulence in Neisseria meningitidis, which is a major causative agent of bacterial meningitis and septicaemia. Pili mediate adhesion, twitching motility, DNA uptake, and can be subject to phase and antigenic variation (Av). Pilin expression and Av may be modulated in response to environmental cues; however, the mechanisms of regulation are still unclear.
This work demonstrates the identification of a novel cis-encoded RNA on the antisense (AS) strand of pilE, which encodes the major pilin subunit. The AS promoter is conserved in different N. meningitidis isolates, suggesting that the AS RNA may play an important role N. meningitidis biology. By Northern blot and strand-specific qRT-PCR, the AS transcript was shown to be expressed during specific conditions, namely after overnight growth and in response to salt stress. The AS RNA was found to encompass sequences antisense to the entire pilE coding sequence and 5' untranslated region, and extends to a promoter upstream of pilE that drives expression of a G4 small RNA that is important for pilin Av.
Noncoding RNAs are increasingly recognized as important regulators of gene expression in bacteria. AS RNAs often modulate expression of the sense mRNA, however in this study, overexpression or deletion of the AS RNA had no significant effect on pilE transcript or pilin levels despite its long stretch of complementarity to the pilE mRNA. Potential trans targets were also investigated by performing RNAseq analysis to identify differentially expressed genes in the absence of the AS RNA. Expression of the AS RNA was found to reduce the frequency of pilE variation. The possible influence of the AS RNA on G4 small RNA transcription was investigated by examining its effect on the levels of G4 small RNA and RNA:DNA hybrids. Although technical issues prevented us from obtaining definitive results, our findings suggest the AS RNA forms RNA:DNA hybrids, adding an additional layer of complexity of molecular processes in the pilE locus of N. meningitidis.</p
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe 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
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe 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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