1,721,004 research outputs found
Bacillus subtilis, a Swiss Army Knife in Science and Biotechnology
No full textNext to Escherichia coli , Bacillus subtilis is the most studied and best understood organism that also serves as a model for many important pathogens. Due to its ability to form heat-resistant spores that can germinate even after very long periods of time, B. subtilis has attracted much scientific interest.ABSTRACT Next to Escherichia coli , Bacillus subtilis is the most studied and best understood organism that also serves as a model for many important pathogens. Due to its ability to form heat-resistant spores that can germinate even after very long periods of time, B. subtilis has attracted much scientific interest. Another feature of B. subtilis is its genetic competence, a developmental state in which B. subtilis actively takes up exogenous DNA. This makes B. subtilis amenable to genetic manipulation and investigation. The bacterium was one of the first with a fully sequenced genome, and it has been subject to a wide variety of genome- and proteome-wide studies that give important insights into many aspects of the biology of B. subtilis . Due to its ability to secrete large amounts of proteins and to produce a wide range of commercially interesting compounds, B. subtilis has become a major workhorse in biotechnology. Here, we review the development of important aspects of the research on B. subtilis with a specific focus on its cell biology and biotechnological and practical applications from vitamin production to concrete healing. The intriguing complexity of the developmental programs of B. subtilis , paired with the availability of sophisticated tools for genetic manipulation, positions it at the leading edge for discovering new biological concepts and deepening our understanding of the organization of bacterial cells.Deutsche Forschungsgemeinschaft https://doi.org/10.13039/501100001659Deutsche Forschungsgemeinschaft https://doi.org/10.13039/501100001659Deutsche Forschungsgemeinschaft https://doi.org/10.13039/501100001659Deutsche Forschungsgemeinschaft https://doi.org/10.13039/50110000165
Author Correction: Lysogenic control of Bacillus subtilis morphology and fitness by Spbetavirus phi3T
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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
Refining the genetic signature of bacterial genotoxin colibactin and its presence in premalignant lesions of colorectal cancer
Full text linkThis work not only defines how colibactin leaves a lasting mutational signature in human cells but also establishes SBS88 as a functional and clinically relevant biomarker of microbial genotoxicity. By integrating microbiology, cancer genomics, and regenerative biology, it contributes to a broader effort to translate mutational signatures into mechanistic insight, prevention strategies, and precision medicine for colorectal cancer
The evolutionary dynamics and functional role of the REPIN-RAYT system in the hut locus of Pseudomonas fluorescens SBW25
Full text linkMobile genetic elements (MGEs) shape bacterial genomes but often degenerate or vanish. In contrast, the REPIN-RAYT system, composed of repetitive extragenic palindromic doublets forming hairpins (REPINs) and REP-associated tyrosine transposases (RAYTs), is widespread and persists. REPINs can form hairpin structures and affect gene regulation, while RAYTs resemble housekeeping genes. The system is thought to provide a fitness benefit, though mechanisms remain unclear. In Chapter 3, I examined the evolutionary dynamics of RAYTs in Pseudomonas fluorescens SBW25 and related strains, focusing on the histidine utilization (hut) locus. I found that horizontal transfer of RAYTs occurs more often than assumed and that RAYTs can associate with multiple REPIN groups. Six REPIN sites in the hut locus were conserved across strains, though sequences varied depending on the RAYT present. In Chapter 4, I tested REPIN function using deletion mutants. Loss of REPIN RH, located between hutH2 and hutTh, caused reduced fitness early in competition but increased fitness later. RT-qPCR indicated that REPIN RH downregulates these genes, explaining the dynamic phenotype. Deletion of RAYTs had no detectable effect. In Chapter 5, I explored the role of hutD, a gene of unclear function. ΔhutD populations evolved for ~200 generations showed increased fitness. Genome sequencing revealed adaptive changes mainly in motility and biofilm genes, suggesting environmental adaptation rather than compensation for hutD loss. Overall, my work shows that REPINs can modulate gene expression and bacterial fitness, and that the REPIN-RAYT system is more dynamic than previously recognized. These findings highlight REPINs as regulatory elements and advance understanding of the hut locus
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
Harnessing predation: the probiotic and antibiotic potential of Bdellovibrio
No full textPredatory bacteria like Bdellovibrio and like organisms (BALOs) are widespread in aquatic and host-associated ecosystems, preying on Gram-negative bacteria. Despite over 60 years of research, their ecological diversity, predation mechanisms, and long-term microbiome roles remain underexplored. Their ability to reduce pathogens and shape microbial communities positions them as promising “living antibiotics.” Chapter 1 explored nine newly isolated host-associated BALOs from the Pseudobdellovibrionaceae family using genomic and microscopy analyses. Several novel Bdellovibrio species and two new genera were identified. Comparative genomics of 250+ core genes supported periplasmic predation as ancestral. Epibiotic strains lacked genes for host-independent growth, indicating that they were obligate predators due to genomic trade-offs. Chapter 2 assessed BALO probiotic potential in C. elegans using two strains: B. krueschi MYbb4 (narrow prey range) and B. tiberii MYbb2 (broad range). Introduced into CeMbio(12) and CeMbio(43) communities, both altered microbiome composition. MYbb4 caused distinct taxonomic shifts; MYbb2 enriched Ochrobactrum. These shifts extended lifespan in low-complexity, nutrient-rich settings. LC-MS and reporter assays confirmed microbial B12 production. Supplementation experiments showed B12 modulates host fertility and lifespan. Chapter 3 developed a three-step assay for antimicrobial resistance in plaque-forming BALOs. Applied to B. bacteriovorus HD100 and B. tiberii MYbb2, it revealed consistent MICs and species-specific profiles: resistance to ciprofloxacin and susceptibility to piperacillin/tazobactam. This offers a reproducible method for BALO-antibiotic combination testing. Together, these findings link BALO genomic diversity to ecological function and therapeutic potential
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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