Search results for "recte"
showing 10 items of 463 documents
Adjacency matrices of random digraphs: singularity and anti-concentration
2017
Let ${\mathcal D}_{n,d}$ be the set of all $d$-regular directed graphs on $n$ vertices. Let $G$ be a graph chosen uniformly at random from ${\mathcal D}_{n,d}$ and $M$ be its adjacency matrix. We show that $M$ is invertible with probability at least $1-C\ln^{3} d/\sqrt{d}$ for $C\leq d\leq cn/\ln^2 n$, where $c, C$ are positive absolute constants. To this end, we establish a few properties of $d$-regular directed graphs. One of them, a Littlewood-Offord type anti-concentration property, is of independent interest. Let $J$ be a subset of vertices of $G$ with $|J|\approx n/d$. Let $\delta_i$ be the indicator of the event that the vertex $i$ is connected to $J$ and define $\delta = (\delta_1, …
Effect of substitutions of key residues on the stability and the insecticidal activity of Vip3Af from Bacillus thuringiensis
2021
Modern agriculture demands for more sustainable agrochemicals to reduce the environmental and health impact. The whole process of the discovery and development of new active substances or control agents is sorely slow and expensive. Vegetative insecticidal proteins (Vip3) from Bacillus thuringiensis are specific toxins against caterpillars with a potential capacity to broaden the range of target pests. Site-directed mutagenesis is one of the most approaches used to test hypotheses on the role of different amino acids on the structure and function of proteins. To gain a better understanding of the role of key amino acid residues of Vip3A proteins, we have generated 12 mutants of the Vip3Af1 …
Epigenetic and Genetic Contributions to Adaptation in Chlamydomonas
2017
Epigenetic modifications, such as DNA methylation or histone modifications, can be transmitted between cellular or organismal generations. However, there are no experiments measuring their role in adaptation, so here we use experimental evolution to investigate how epigenetic variation can contribute to adaptation. We manipulated DNA methylation and histone acetylation in the unicellular green alga Chlamydomonas reinhardtii both genetically and chemically to change the amount of epigenetic variation generated or transmitted in adapting populations in three different environments (salt stress, phosphate starvation, and high CO2) for two hundred asexual generations. We find that reducing the …
Rigid Core and Flexible Terminus
2012
The structure of the major light-harvesting chlorophyll a/b complex (LHCII) was analyzed by pulsed EPR measurements and compared with the crystal structure. Site-specific spin labeling of the recombinant protein allowed the measurement of distance distributions over several intra- and intermolecular distances in monomeric and trimeric LHCII, yielding information on the protein structure and its local flexibility. A spin label rotamer library based on a molecular dynamics simulation was used to take the local mobility of spin labels into account. The core of LHCII in solution adopts a structure very similar or identical to the one seen in crystallized LHCII trimers with little motional freed…
Viral fitness determines the magnitude of transcriptomic and epigenomic reprograming of defense responses in plants
2020
Although epigenetic factors may influence the expression of defense genes in plants, their role in antiviral responses and the impact of viral adaptation and evolution in shaping these interactions are still poorly explored. We used two isolates of turnip mosaic potyvirus with varying degrees of adaptation to Arabidopsis thaliana to address these issues. One of the isolates was experimentally evolved in the plant and presented increased load and virulence relative to the ancestral isolate. The magnitude of the transcriptomic responses was larger for the evolved isolate and indicated a role of innate immunity systems triggered by molecular patterns and effectors in the infection process. Sev…
Implications of the EFSA Scientific Opinion on Site Directed Nucleases 1 and 2 for Risk Assessment of Genome-Edited Plants in the EU
2021
Genome editing is a set of techniques for introducing targeted changes in genomes. It may be achieved by enzymes collectively called site-directed nucleases (SDN). Site-specificity of SDNs is provided either by the DNA binding domain of the protein molecule itself or by RNA molecule(s) that direct SDN to a specific site in the genome. In contrast to transgenesis resulting in the insertion of exogenous DNA, genome editing only affects specific endogenous sequences. Therefore, multiple jurisdictions around the world have exempted certain types of genome-edited organisms from national biosafety regulations completely, or on a case-by-case basis. In the EU, however, the ruling of the Court of J…
Distributed Adaptive Consensus Tracking Control of Uncertain High-order Nonlinear Systems under Directed Graph Condition
2018
In this paper, we investigate the output consensus tracking problem for a class of high-order nonlinear systems subjected to unknown parameters and uncertain external disturbances. A novel backstepping based distributed adaptive control scheme is presented under the directed communication status. For the subsystems without direct access to time-varying desired trajectory, local estimators are introduced and the corresponding adaptive laws are designed in a totally distributed fashion. With the presented scheme, the assumption on linearly parameterized reference signal and the information exchange operation of subsystem inputs in the existing results are no longer needed. It is shown that al…
Variable neighborhood descent for the incremental graph drawing
2017
Abstract Graphs are used to represent reality in several areas of knowledge. Drawings of graphs have many applications, from project scheduling to software diagrams. The main quality desired for drawings of graphs is readability, and crossing reduction is a fundamental aesthetic criterion for a good representation of a graph. In this paper we target the edge crossing reduction in the context of incremental graph drawing, in which we want to preserve the layout of a graph over successive drawings. We propose a hybrid method based on the GRASP (Greedy Randomized Adaptive Search Procedure) and VND (Variable Neighborhood Descent) methodologies and compare it with previous methods via simulation.
Evaluation of an amino acid residue critical for the specificity and activity of human Gb3/CD77 synthase
2016
Human Gb3/CD77 synthase (α1,4-galactosyltransferase) is the only known glycosyltransferase that changes acceptor specificity because of a point mutation. The enzyme, encoded by A4GALT locus, is responsible for biosynthesis of Gal(α1–4)Gal moiety in Gb3 (CD77, Pk antigen) and P1 glycosphingolipids. We showed before that a single nucleotide substitution c.631C > G in the open reading frame of A4GALT, resulting in replacement of glutamine with glutamic acid at position 211 (substitution p. Q211E), broadens the enzyme acceptor specificity, so it can not only attach galactose to another galactose but also to N-acetylgalactosamine. The latter reaction leads to synthesis of NOR antigens, which are…
Engineering of a DNA Polymerase for Direct m6A Sequencing
2017
Methods for the detection of RNA modifications are of fundamental importance for advancing epitranscriptomics. N6-methyladenosine (m6A) is the most abundant RNA modification in mammalian mRNA and is involved in the regulation of gene expression. Current detection techniques are laborious and rely on antibody-based enrichment of m6A-containing RNA prior to sequencing, since m6A modifications are generally "erased" during reverse transcription (RT). To overcome the drawbacks associated with indirect detection, we aimed to generate novel DNA polymerase variants for direct m6A sequencing. Therefore, we developed a screen to evolve an RT-active KlenTaq DNA polymerase variant that sets a mark for…