Search results for "Computational Biology"
showing 7 items of 1237 documents
Absolute quantification of noncoding RNA by microscale thermophoresis
2019
Abstract Accurate quantification of the copy numbers of noncoding RNA has recently emerged as an urgent problem, with impact on fields such as RNA modification research, tissue differentiation, and others. Herein, we present a hybridization‐based approach that uses microscale thermophoresis (MST) as a very fast and highly precise readout to quantify, for example, single tRNA species with a turnaround time of about one hour. We developed MST to quantify the effect of tRNA toxins and of heat stress and RNA modification on single tRNA species. A comparative analysis also revealed significant differences to RNA‐Seq‐based quantification approaches, strongly suggesting a bias due to tRNA modifica…
BioImageXD: an open, general-purpose and high-throughput image-processing platform
2012
BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes. We demonstrate its performance in a study of integrin clustering in response to selected inhibitors.
Distinctive attributes for predicted secondary structures at terminal sequences of non-classically secreted proteins from proteobacteria
2008
Abstract C- and N-terminal sequences (64 amino acid residues each) of 89 non-classically secreted type I, type III and type IV proteins (Swiss-Prot/TrEMBL) from proteobacteria were transformed into predicted secondary structures. Multivariate analysis of variance (MANOVA) confirmed the significance of location (C- or N-termini) and secretion type as essential factors in respect of quantitative representations of structured (a-helices, b-strands) and unstructured (coils) elements. The profiles of secondary structures were transcripted using unequal property values for helices, strands and coils and corresponding numerical vectors (independent variables) were subjected to multiple discriminan…
IDPlanT: the Italian database of plant translocation
2021
IDPlanT is the Italian Database of Plant Translocation, an initiative of the Nature Conservation Working Group of the Italian Botanical Society. IDPlanT currently includes 185 plant translocations. The establishment of a national database on plant translocation is a key step forward in data sharing and techniques improvement in this field of plant conservation. Supplemental data for this article is available online at https://doi.org/10.1080/11263504.2021.1985004.
Model organisms and their application in environmental epigenetics
2020
Abstract Epigenetic mechanisms operate at the interface between the environment and the genome of a given organism. More particularly, they convert environmental stimuli as diverse as chemical pollutants, nutritional components, temperature changes, and social conditions into changes in the chromatin landscape, which influence gene expression in the absence of alterations in the DNA sequence, ultimately leading to phenotype adaptation and diversification. The use of experimental model organisms in epigenetics research allows for the careful manipulation of environmental factors in order to understand how they mechanistically modulate the establishment, maintenance, and inheritance of epigen…
Baculovirus display strategies: Emerging tools for eukaryotic libraries and gene delivery
2004
Recombinant baculoviruses have been extensively used as vectors for abundant expression of a large variety of foreign proteins in insect cell cultures. The appeal of the system lies essentially in easy cloning techniques and virus propagation combined with the eukaryotic post-translational modification machinery of the insect cell. Recently, a novel molecular biology tool was established by the development of baculovirus surface display, using different strategies for presentation of foreign peptides and proteins on the surface of budded virions. This eukaryotic display system enables presentation of large complex proteins on the surface of baculovirus particles and has thereby become a ver…
Modeling multipartite virus evolution: the genome formula facilitates rapid adaptation to heterogeneous environments
2020
Multipartite viruses have two or more genome segments, and package different segments into different particle types. Although multipartition is thought to have a cost for virus transmission, its benefits are not clear. Recent experimental work has shown that the equilibrium frequency of viral genome segments, the setpoint genome formula (SGF), can be unbalanced and host-species dependent. These observations have reinvigorated the hypothesis that changes in genome-segment frequencies can lead to changes in virus-gene expression that might be adaptive. Here we explore this hypothesis by developing models of bipartite virus infection, leading to a threefold contribution. First, we show that th…