Alignments of biomolecular contact maps

Abstract

Alignments of discrete objects can be constructed in a very general setting as super-objects from which the constituent objects are recovered by means of projections. Here, we focus on contact maps, i.e. undirected graphs with an ordered set of vertices. These serve as natural discretizations of RNA and protein structures. In the general case, the alignment problem for vertex-ordered graphs is NP-complete. In the special case of RNA secondary structures, i.e. crossing-free matchings, however, the alignments have a recursive structure. The alignment problem then can be solved by a variant of the Sankoff algorithm in polynomial time. Moreover, the tree or forest alignments of RNA secondary structure can be understood as the alignments of ordered edge sets.

Antioxidant Microgels Support Peroxide‐Challenged Hepatic Cells

“…Alginate is an FDA approved polysaccharide used for a variety of applications as outlined by Lee and Mooney, [ 39 ] and has previously been used by us to successfully fabricate ACs appropriate for interfacing with biological cells. [ 10,13,21,22 ] The PtNPs or EUK‐B were dispersed in an alginate solution made from a mixture of low and high molecular weight alginate, with high α‐ l ‐guluronate content. Specifically, alginate was directly dissolved in the stock solution of PtNPs, which corresponded to a PtNP concentration of ≈1 mg mL −1 , while dissolved alginate was added to a solution of EUK‐B, resulting in an EUK‐B concentration of ≈0.5 mg mL −1 .…”

“…[ 9 ] For example, ACs capable of communicating and exchanging chemical information with mammalian cells have recently been demonstrated with alginate‐based ACs capable of eavesdropping on the hepatic activity of HepG2 cells, by releasing sender molecules that react with a conversion product from the hepatocytes, and in turn convert the product to luminescence. [ 10 ] Further, giant unilamellar vesicle (GUV)‐based ACs producing H 2 O 2 by encapsulated catalysis were demonstrated, with H 2 O 2 utilized by red blood cells as peroxidase agents to convert Amplex Red to resorufin, [ 11 ] and brain‐derived neurotrophic factor producing ACs to drive differentiation of neural stem cells. [ 12 ] Additionally, ACs capable of providing a supportive, therapeutic function to mammalian cell counterparts include the use of alginate‐based ACs loaded with matrix vesicles (purified from cell culture) co‐cultured with osteoblasts for enhanced biomineralization; [ 13 ] combating excitotoxicity in neuroblastoma cells with polystyrene‐based ACs loaded with platinum nanoparticles that remove exogenous hydrogen peroxide (H 2 O 2 ) and ammonia; [ 14,15 ] microsphere‐based artificial stem cells that release Tβ4‐exosomes to improve the angiogenic capacity of coronary endothelial cells; [ 16 ] prototissue of nitric oxide (NO) producing GUVs capable of relaxing rat blood vessels ex vivo; [ 17 ] ACs producing insulin precursor/insulin under hyperglycemic conditions to promote glucose uptake in MCF‐7 cells; [ 18 ] erythrocyte membrane fragment coated coacervates producing NO for blood vessel vasodilation in rabbits, [ 19 ] and proangiogenic GUV‐based ACs expressing a fibroblast growth factor which when suspended in matrigel and injected into mice, enables blood venule infiltration.…”

Bi-alignments with affine gaps costs

“…These were studied here because the corresponding optimization problems can be solved exactly by means of relatively simple dynamic programming algorithms. In a more general setting, one may want to consider as an alignment of contact structures [ 45 ] or as an alignment of ordered sequences of 3D points, e.g. scored in terms of euclidean distances [ 46 , 47 ].…”

A Computational Design of siRNA in SARS-CoV-2 Spike Glycoprotein Gene and Its Binding Capability toward mRNA

“…The barrier Server software was accessed at this link: http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/barriers. cgi [45][46]. The Vienna dot-bracket annotation of 2D data annotation was applied in this pipeline.…”