1,721,509 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
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
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
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Designing Genetic Circuits for Memory and Communication
Full text linkThe goal of synthetic biology is to allow the rapid design of organisms that can find diverse uses in environmental remediation, chemical production, or human health. Genetic engineering has traditionally been done by trial and error, but synthetic biology seeks to apply engineering principles and build complex circuits by rationally composing genetic parts together. We envision engineering microbes to form spatial communities for applications such as programmable tissues. We present novel circuit designs for memory and communication, which are basic building blocks for programming these behaviors. Our memory device uses molecular sequestration instead of cooperativity that was used in almost all previously built synthetic switches. In addition, our design allows predictable tuning of the switching boundaries and enables the rapid design of custom bistable switches that can function as a set-reset latch. We also present designs for contact-based communication by utilizing the recently discovered contact-dependent inhibition (CDI) system. Such a communication channel could allow programmed spatial features with micron-scale resolution, which can be advantageous compared to existing communication methods that rely on diffusible molecules. We present two strategies for harnessing the CDI system. In the first method, we fuse a small transcriptional activator to the protein that is delivered during CDI. In the second method, we exploit the known biology that the delivered domain can co-localize two other proteins. We use this co-localization effect to trigger an increase in activity from a split enzyme, and design an ultrasensitive response to the small number of molecules delivered during the CDI process. While we were not able to show control of gene expression in touching E. coli cells, we believe that our circuit designs can guide future engineering efforts
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Iterative library generation and FACS screening for increased production of the pharmaceutical precursor L-DOPA in yeast
Full text linkOptimizing microbial hosts for large-scale production of valuable metabolites has two main challenges: (i) maximizing the expression and function of the proteins needed to perform the desired reactions; and, (ii) adapting host metabolism to support these new reactions and remove unwanted or toxic side products. Although considerable effort has been focused on the first challenge, the methodology developed and described in this dissertation addresses the second challenge. As a test case, I sought to increase production of L-DOPA, a pharmaceutically-relevant metabolite and precursor to the benzylisoquinoline (BIA) class of medicinal molecules, in the yeast S. cerevisiae. Production of L-DOPA and derived BIAs in yeast can be accomplished through the action of CYP76AD1, a heterologously-expressed cytochrome P450 enzyme from beet. Hence, I sought to devise strategies for isolating strain variants that carry genome modifications that improve CYP76AD1-dependent L-DOPA production. My approach was based on the assumption that endogenous factors in yeast restrain or impede this process. To perform multiple rounds of mutagenesis and screening, we constructed an in vitro barcoded transposon-disruption library. This library was introduced and integrated into the host genome by homologous recombination. The resulting variants were screened using a biosensor in which L-DOPA produced by the cells is converted to a fluorescent derivative via the action of the enzyme DOPA dioxygenase (DOD). Thus, I was able to use high-throughput fluorescence-activated cell sorting (FACS) to enrich for the desired variants. I conducted this approach, iteratively, for three rounds, i.e. improved strains obtained from the preceding rounds were transformed with the transposon-disruption library and re-screened. In the first two rounds of screening, I identified deletions that improved biosensor compartmentalization and, consequently, improved the reliability of the read-out for L-DOPA production. In the final round, I discovered that deletion of the gene encoding a heme oxygenase (HMX1) that is localized to the endoplasmic reticulum and involved in heme degradation increased both total cellular heme content and L-DOPA production (as monitored by measuring its derivative dopamine as a proxy). I demonstrated further that deleting HMX1 may represent a general strategy for improving the performance of heterologous P450 enzymes in yeast because the absence of Hmx1 also enhanced the ability of a second P450 enzyme, BM3, to generate its product
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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Development and Application of High-Throughput Technologies to Study Gene Function in Soil Bacteria
Full text linkBacteria that reside in terrestrial soils are abundant, metabolically diverse, and display complex and dynamic interactions with each other and with their environments. The combined effect of their functions has shaped our planet, most notably powering the global carbon, nitrogen and oxygen cycles, setting the stage for the emergence of human life on Earth [1]. Since then, the study and application of soil bacterial functions has advanced our society and technologies, for example in the use of nitrifiers to restore depleted crop soils [2], or the discovery of new antibiotics to cure infectious diseases [3]. Now, as we are beset by the accumulated consequences of rapid human development (i.e. climate change, overpopulation, environmental toxicity, loss of biodiversity, disruptions in food production) soil bacteria may hold the key to our endurance [4]. Understanding what soil bacteria do, and how they do it, has never been more important. The diverse functions of soil bacteria are encoded by an equally diverse gene set. This limits how much we can extrapolate functional genetics from one bacterium to another. A recent evaluation of protein homology-based annotation methods found that 52% of the genes in an average bacterial genome can be annotated, and in some cases only 14% could be identified [5]. Notably, less researched and newly discovered taxa tended to have a lower proportion of annotated genes [5]. A separate study used low-coverage next-generation sequence data to estimate the size of the soil metagenome at 100 million genes [6]. While some of these genes are encoded by the Eukarya and Archaea found in the soil, there is no doubt that there are many soil bacterial genes that remain poorly understood. I proposed to tackle these gaps in our knowledge through the development and application of high-throughput functional genomics technologies to study gene function in soil bacteria. First, I sought to query gene functions encoded by any clonable DNA by extending the functionality of Dub-seq (dual barcoded shotgun expression library sequencing), our group’s method for rapidly phenotyping gain-of-function mutants in Escherichia coli [7]. I built Dub-seq libraries that express randomly sheared genome fragments from 26 medically, agriculturally and industrially important strains spanning the bacterial tree of life in E. coli. Separately, I developed protocols for cloning DNA from single amplified genomes (SAGs), motivated by the possibility of interrogating gene functions in uncultured bacteria. Second, I investigated adapting three high-throughput functional genomics methods–RB-TnSeq (random barcode transposon-site sequencing) [8], CRISPRi [9,10] and Dub-seq–to the study of gene functions in Streptomyces, a large, ubiquitous and metabolically diverse taxon of soil bacteria. I had the most success with the Dub-seq approach, combining a recently published inducible promoter [11] and T7 RNA polymerase [12] for inducible and processive heterologous DNA expression in Streptomyces. Third, I applied RB-TnSeq to investigate the genetic determinants of sensitivity to tailocins in soil Pseudomonas isolates. Tailocins are an understudied class of bacteriocins that evolutionarily and morphologically resemble tailed bacteriophages. My mutant screens identified O-specific antigen (OSA) composition and display as the most important factors in sensitivity to our tailocins. Additionally, the screens suggested lipopolysaccharide thinning as a mechanism by which resistant strains can become more sensitive to tailocins. My data can be summarized as reinforcing a model that lipopolysaccharide molecules can act as either a receptor for, or shield against, tailocin binding and killing. The work described in this dissertation represents multiple efforts to shrink gaps in our knowledge of soil bacteria gene functions. The tools I developed can provide experimental access, in high-throughput, to new bacterial phenotypes. My work with Streptomyces provides a set of good practices for high-throughput phenotyping coupled to next-generation sequencing in this recalcitrant taxon. Finally, my investigations on tailocins provides novel insight into a specialized form of bacterial competition, and additionally informs the potential use of tailocins in microbiome manipulation and antibacterial therapy
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Interactions of Microbes in Communities
Full text linkGroups of microorganisms sharing an environment (microbial communities) are ubiquitous in nature. Microbial communities provide essential ecosystem services to other life on Earth by e.g., participating in global biogeochemical processes or interacting with a host’s immune system. Such microbes compete for scarce resources, modify an environment for their own purposes, actively war, and occasionally cooperate. Though numerous studies have surveyed the diversity of microbial life in different environments, few have determined the ways in which members of microbial communities interact with one another. Understanding the ways and means by which microbes interact is essential if we are to understand how microbial communities form, persist, and change over time. Knowledge of these processes will allow us to rationally design microbial communities to perform useful functions and predict how our actions might shift the balance of microbes in a community, and thus affect its function. In this work, we develop and apply novel methods for understanding microbial interactions
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