186,323 research outputs found
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe 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
Appropriate Similarity Measures for Author Cocitation Analysis
No full textWe 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
No full textWe 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
Dr. Edward P. Wimberly, ITC, July 2011
No full textThis video is a conversation with Dr. Edward P. Wimberly. Dr. Wimberly talks about his book, "No Shame in Wesley's Gospel: A Twenty-First Century Pastoral Gospel". Brad Ost, AUC Woodruff Library, is the interviewer
Author Rights and Scholarly Publishing
No full textOriginally posted at
http://blog.library.gsu.edu/2014/10/24/author-rights-and-scholarly-publishing/</p
Influence Of FtsH Protease On The Medial FtsZ Ring In Escherichia Coli
No full textFtsH is an essential AAA family Zn++ metalloprotease of Escherichia coli, possessing ATPase-dependent chaperon activity and ATP-dependent protease activity. Heat shock transcription factor Sigma32, LpxC, SecY, and bacteriophage protein CII are some of the substrates of FtsH. Although FtsH is known to influence several cellular processes, the role of FtsH in bacterial cell division had not been identified. FtsZ is the principal cell division protein that marks the cell division site at mid-cell by forming a ring structure. Using a pair of ftsH-null and isogenic wild type strain of E. coli, earlier studies in the laboratory had demonstrated that proteolytic function of FtsH is required for the presence of FtsZ rings at mid-cell site. It was also shown that FtsZ is not a substrate for FtsH protease in vivo. In view of these observations, using a pair of ftsH-null and isogenic wild type strain of E. coli, experiments were carried out to find out the mechanism behind the requirement for FtsH protease for the presence of FtsZ ring at mid-cell site. Viability of the cells having ftsH-null status was maintained by a suppressor mutation at another locus, and was found to be comparable to that of isogenic wild type cells.
Immunostaining for FtsZ showed that only 20% cells of ftsH-null strain of E. coli has FtsZ ring at mid-cell site, On the contrary, more than 90% cells of isogenic wild type cells had FtsZ ring at mid-cell site. Live cell imaging with FtsZ-GFP also showed similar results. Low fraction of ftsH-null cells having FtsZ ring was found to be independent of slow growth rate of the cells. Confocal microscopy revealed that ftsH-null cells lacked the normal helical spiral-type structure of FtsZ, unlike the intact FtsZ helices present in isogenic wild type cells. FtsZ protein levels in the membrane and cytoplasmic fractions of ftsH-null cells were found to be same as those in the isogenic wild type cells. Exogenous expression of wild type FtsH in ftsH-null cells could restore FtsZ ring status to normalcy, similar to that in the isogenic wild type cells. However, this restoration could not be accomplished by FtsH mutants, which were lacking in ATP binding, ATPase, or protease activities.
FtsA anchors FtsZ to the membrane and a specific FtsZ/FtsA ratio is known to be critical for cell division. Further, FtsA and/or ZipA are required for the stabilisation of FtsZ ring at mid-cell site. The levels of FtsA were found to be lower by more than 2.5-fold in all the membrane and soluble fractions of ftsH-null cells. The levels of FtsA were found restored to normalcy upon complementation with exogenous expression of FtsH. Low levels of FtsA were not due to the slow growth of ftsH-null cells. Exogenous expression of FtsA or FtsA-GFP restored FtsZ in more than 90% of ftsH-null cells. Moreover, FtsA mutants, which are defective in the interaction with FtsZ, did not restore FtsZ rings to normalcy. The levels of ZipA were found to be same in ftsH-null and isogenic wild type cells. Expression of ZipA or ZipA-GFP could restore FtsZ rings to normalcy in ftsH-null cells. These data showed that low FtsA levels might be the reason for low percentage of cells having FtsZ ring in ftsH-null cells. It implied that ftsH-null cells might have been managing FtsZ ring stabilisation with ZipA, to facilitate septation.
Real time RT-PCR showed that the levels of ftsA mRNA and those of all the other fts genes, except ftsZ, in the 16-gene dcw cluster, were found to be low in ftsH-null cells. Moreover, real time RT-PCR using specific primers designed for multiple promoters of ftsZ and for the RNaseE processing site, just upstream of ftsZ, showed that the levels of transcripts of the genes upstream to RNaseE site were significantly low and that the levels of ftsZ transcripts, which were downstream to RNaseE site, were unaffected. On the contrary, the levels of mRNAs of fts genes, such as ftsE, ftsX, ftsN, and zipA that were located at another part of the genome, were normal in ftsH-null cells. These observations suggested that the reason for the low levels of FtsA protein might be low levels of ftsA mRNA. In addition, the low levels of other fts mRNAs from the dcw cluster, and probably of the respective proteins, might contribute to the slow growth of ftsH-null cells.
The ftsH null strains also showed less compact nucleoids and the nucleoids did not look bilobular. This data suggested that there may be some defect in the compaction of nucleoids in ftsH-null cells. On the contrary, isogenic wild type cells, when grown slow like the growth of ftsH-null cells, had no defect in nucleoid compaction and looked bilobular. The proper compaction of nucleoids could be restored only by wild type FtsH, but not by the protease mutant of FtsH. These observations suggest that proteolytic activity of FtsH might be required for the proper compaction of nucleoids, which in turn might have influence on the placement of FtsZ ring at mid-cell site.
In parallel, different percentage of silver stained single-dimension SDS-PAGE showed conspicuous difference in the protein profiles of the membrane and soluble fractions of ftsH-null cells, in comparison to those of isogenic wild type cells. FtsZ co-immuno precipitation (CoIP) of total cell lysates of ftsH-null and isogenic wild type cells showed differential interaction of two proteins, the outer membrane protein A (OmpA) and a 50 kDa protein, between the two strains. The level of OmpA was 2.5-fold high in ftsH-null cells, in comparison to that in isogenic wild type cells. However, overexpression of ompA in isogenic wild type cells did not have any effect on FtsZ rings in isogenic wild type cells. Two-dimensional gel electrophoresis for membrane and soluble fractions of ftsH-null cells, in comparison with that of isogenic wild type cells, showed that several proteins in each fraction were either present or absent between these two strains. Most of these proteins were then identified using MALDI-TOF / LC –MS methods. Identification of these proteins, which were present differentially between ftsH-null and isogenic wild type cells, has revealed existence of many more hitherto unidentified potential substrates of FtsH and therefore cell processes, which FtsH may influence
Structural, Functional And Transcriptional Analysis Of Nucleoside Diphosphate Kinase From Mycobacterium Smegmatis mc2 155
No full textMaintenance of the levels of nucleoside triphosphates (NTPs) as well as their corresponding deoxy derivatives (dNTPs) is crucial to all growth and developmental processes. The enzyme nucleoside diphosphate kinase (NDK) utilises an autophosporylated enzyme intermediate to catalyse the transfer of 5’ terminal phosphate from NTPs (mostly ATP) to nucleoside diphosphates (NDPs) via a reversible mechanism as given below.
N1TP + NDK ↔N1DP+ −NDK-His* (1)
N2DP + NDK-His* P ↔N2TP + NDK−His. (2) In the γ-phosphoryl group transfer, the highly conserved His 117 active site residue becomes autocatalytically phosphorylated, in the enzyme intermediate (NDK-H*). This phosphoryl group is transferred to ribo-or deoxyribonucleotides (N2DP) in a substrate non-specific manner. In addition to its fundamental role in nucleotide metabolism, NDP kinase is also involved in a number of cellular regulatory functions such as growth and developmental control, tumor metastasis suppression, signal transduction and so on. From mycobacterial genera, NDK of Mycobacterium tuberculosis (MtNDK) has been crystallised, structure was solved and biochemical functions were elucidated. However, there has not been any such study on the NDK of Mycobacterium smegmatis, except on the possible interaction with other proteins which modulates the NTP synthesising activity of MsNDK, towards specific NTPs. M. smegmatis, being a saprophytic, fast growing and non-pathogenic mycobacterium that is widely used as an experimental model mycobacterial system to study various biological processes in mycobacteria, it was thought appropriate to study NDK from this organism.
The outcome of current study is presented in five chapters. The First Chapter gives a detailed introduction on the structural and functional aspects of NDK from diverse organisms, from bacteria to humans.
Chapter 2. Molecular Cloning, Expression and Characterisation of Biochemical Activities of Nucleoside Diphosphate Kinase from Mycobacterium smegmatis mc 155
The research work starts with the molecular cloning, overexpression, purification, and characterisation of biochemical activities of recombinant MsNDK protein. In brief, ndk gene from M. smegmatis (Msndk) has been cloned, efficiently overexpressed as a soluble 6xHis-tagged recombinant protein, purified through affinity chromatography, and its biochemical characterisation for ATPase, GTPase and NTP synthesising activities have been demonstrated. Catalytic mutant of MsNDK, MsNDK-H117Q, was generated using site-directed mutagenesis approach and H117 was shown to be essential for the catalytic activity. Further experiments revealed that it is the same H117 that is required for mediating autophosphorylation as well, which is an intermediate in the transphosphorylation reaction of NDK.
Chapter 3. Characterisation of Oligomerisation Property of M. smegmatis Nucleoside Diphosphate Kinase: the Possible Role of Hydrogen Bond and Hydrophobic Interactions
The present study revealed that presence of homodimer of MsNDK could be observed in the presence of heat and SDS. Chemical cross-linking experiments revealed that MsNDK forms dimer, tetramer and hexamer. Homology modeling of MsNDK on the MtNDK crystal structure supported the existence of hexamer as three homodimers. Gln 17, Ser 24 and Glu 27 were found to be positioned at the dimer interface. Mutations on these residues did not abolish the stability of the respective mutant dimers in the presence of SDS and heat. Modeled structure of MsNDK revealed the existence of hydrophobic interactions at the dimer interface. In silico approach helped in mapping the existence of hydrophobic interactions at the dimer interface as two consecutive β-strands. Exposure of hydrophobic residues, using organic solvent methanol, abolished the dimer completely, indicating the vital role of hydrophobic interactions in the dimer stability. In solution, the native MsNDK was found to be a hexamer. Chapter 4. Mycobacterial Nucleoside Diphosphate Kinase Functions as GTPase Activating Protein for Mycobacterial Cytokinetic Protein FtsZ In Vitro
Mammalian, plant, and bacterial NDKs can function as GTPase activating protein (GAP) for small G proteins namely, p21 Ras, Rad, and Rho-GTPases in animals and Pra1, Pra2, and GPA1 in Arabidopsis thaliana in vitro. We examined whether NDK of
M. tuberculosis (MtNDK) can function as GAP in vitro for the cytokinetic protein FtsZ of Mycobacterium tuberculosis (MtFtsZ), which is a protein with a classical G-protein fold, possessing GTP-binding and GTPase activities (like G proteins). Both MtNDK and MsNDK could function as GAP for MtFtsZ and FtsZ of M. smegmatis (MsFtsZ) respectively in vitro. Similarly, MtNDK could function as GAP for MsFtsZ and reciprocally MsNDK could function as GAP from MtFtsZ. Interaction of NDK with respective FtsZ could be observed. Physiological implications of GAP activity of NDK on FtsZ are discussed.
Chapter 5. Transcriptional Analyses of Nucleoside Diphosphate Kinase Gene of
Mycobacterium smegmatis mc 155
Although there are studies on the structural and functional aspects of NDK, there are not many studies available on the transcriptional analysis of nucleoside diphosphate kinase (NDK) gene expression in general and nothing in particular in mycobacterial systems. Therefore we studied the transcriptional analysis of expression of Msndk gene, in order to map the Transcriptional Start Site (TSS), identification of promoter elements, and elucidated of transcriptional activity of the promoters. Expression of Msndk gene was analysed in exponential growth phase and under two different stress conditions wherein DNA replication gets arrested. Hydroxy Urea (HU), which reduce dNTP pools by inhibiting ribonucleotide reductase and Phenethyl Alcohol (PEA), which affects membrane structure resulting in DNA replication arrest, were used. Two transcripts and their promoter elements were mapped and their promoter activities were demonstrated. The profile of transcripts was found to be identical under the three different conditions examined
Mapping the Discipline of the Olympic Games An Author-Cocitation Analysis
No full textThe authors conducted an author cocitation analysis on prominent authors writing about the Olympics during the 1990s. Author cocitation is an established bibliometric technique that can be used to measure the relative similarities of topics written about by the cited authors. This enables a visual representation of the “intellectual space” of the discipline, in this case the Olympics, to be created for the period under review. So core and peripheral research areas are identified, along with their major contributors. The representation appears as a two-dimensional cluster-enhanced map. Subject expertise was then applied to the results to place labels on the generated clusters of authors and their topics
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