1,720,963 research outputs found
The Evolution of Flavin-Binding Photoreceptors: An Ancient Chromophore Serving Trendy Blue-Light Sensors
No full textPhotoreceptor flavoproteins of the LOV, BLUF, and cryptochrome
families are ubiquitous among the three domains of life and are configured as UVA/blue-light systems not only in plants—their original arena—but also in prokaryotes and microscopic algae. Here, we review these proteins’ structure and function, their biological roles, and their evolution and impact in the living world, and underline their growing application in biotechnologies. We present novel developments such as the interplay of light and redox stimuli, emerging enzymatic and biological functions, lessons on evolution from picoalgae, metagenomics analysis, and optogenetics applications
Distance-tree analysis, distribution and co-presence of bilin- and flavin-binding prokaryotic photoreceptors for visible light
No full textIn recent years it has become increasingly evident that prokaryotic organisms can sense and react to light
stimuli via a variety of photosensory receptors and signal transduction pathways. There are two main
superfamilies of non-membrane-bound photoreceptors: the bilin-binding phytochrome-related proteins
based on GAF (cGMP-specific phosphodiesterases, cyanobacterial adenylate cyclases, and transcription
activator FhlA) domains (bilin-GAF proteins), and the flavin-binding proteins (FL-Blues), photoperceptive
thanks to their LOV (Light, Oxygen and Voltage) and BLUF (Blue Light sensing Using Flavins) domains. In
this manuscript we present a comprehensive scenario of the existence of bilin-GAF, LOV and BLUF proteins
in the prokaryotic world and inspect possible phylogenetic pathways, also defining novel criteria for
identifying gene (and protein) sequences based on experimentally assessed photochemical events. As a
whole we have inspected almost 2000 proteins recovered in 985 bacteria and 16 archaea. For LOV and
BLUF proteins, ten and, respectively, twelve superconserved amino acids have been identified, which
were used as criterion for selection. A similarly strict parameter cannot be applied to the more variegate
family of bilin-GAF domains. The co-presence of bilin-GAF and FL-Blues occurs in 22% of the analyzed
bacteria, with emphasis on the bilin-GAF/LOV co-presence in cyanobacteria and of bilin-GAF/BLUF in the
Bacteroidetes/Chlorobi group. For construction of phylogeny/distance-trees we used the neighboringmethod
to obtain a branching pattern, limited to photosensing domains. We observed that in many
cases organisms belonging to the same phylum are neighbors, but clustering mostly occurs according to
the type of functional domain associated with the photosensing modules
From Plant Infectivity to Growth Patterns: The Role of Blue-Light Sensing in the Prokaryotic World
No full textFlavin-based photoreceptor proteins of the LOV (Light, Oxygen, and Voltage) and BLUF (Blue Light sensing Using Flavins) superfamilies are ubiquitous among the three life domains and are essential blue-light sensing systems, not only in plants and algae, but also in prokaryotes. Here we review their biological roles in the prokaryotic world and their evolution pathways. An unexpected large number of bacterial species possess flavin-based photosensors, amongst which are important human and plant pathogens. Still, few cases are reported where the activity of blue-light sensors could be correlated to infectivity and/or has been shown to be involved in the activation of specific genes, resulting in selective growth patterns. Metagenomics and bio-informatic analysis have only recently been initiated, but signatures are beginning to emerge that allow definition of a bona fide LOV or BLUF domain, aiming at better selection criteria for novel blue-light sensors. We also present here, for the first time, the phylogenetic tree for archaeal LOV domains that have reached a statistically significant number but have not at all been investigated thus far
Metagenome-based Screening Reveals Worldwide Distribution of LOV-Domain Proteins
No full textMetagenomes from various environments were screened for
sequences homologous to light, oxygen, voltage (LOV)-domain
proteins. LOV domains are flavin binding, blue–light (BL)-
sensitive photoreceptors present in 10–15% of deposited prokaryotic
genomes. The LOV domain has been selected, since BL
is an ever present and sometimes harmful environmental factor
for microbial communities. The majority of the metagenome
material originated from the Sargasso Sea Project and from
open-ocean sampling. In total, more than 40 million open reading
frames were investigated for LOV-domain sequences. Most
sequences were identified from aquatic material, but they were
also found in metagenomes from soil and extreme environments,
e.g. hypersaline ponds, acidic mine drainage or wastewater
treatment facilities. A total of 578 LOV domains was assigned
by three criteria: (1) the highly conserved core region, (2) the
presence of minimally 14 essential amino acids and (3) a minimal
length of 80 amino acids. More than three quarters of these
identified genes showed a sequence divergence of more than 20%
from database-deposited LOV domains from known organisms,
indicating the large variation of this photoreceptor motif. The
broad occurrence of LOV domains in metagenomes emphasizes
their important physiological role for light-induced signal
transduction, stress adaptation and survival mechanisms
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
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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