The Combinatorial Fusion Cascade to Generate the Standard Genetic Code

Combinatorial fusion cascade was proposed as a transition stage between prebiotic chemistry and early forms of life. The combinatorial fusion cascade consists of three stages: eight initial complimentary pairs of amino acids, four protocodes, and the standard genetic code. The initial complimentary pairs and the protocodes are divided into dominant and recessive entities. The transitions between these stages obey the same combinatorial fusion rules for all amino acids. The combinatorial fusion cascade mathematically describes the codon assignments in the standard genetic code. It explains the availability of amino acids with the even and odd numbers of codons, the appearance of stop codons, inclusion of novel canonical amino acids, exceptional high numbers of codons for amino acids arginine, leucine, and serine, and the temporal order of amino acid inclusion into the genetic code. The temporal order of amino acids within the cascade is congruent with the consensus temporal order previously derived from the similarities between the available hypotheses. The control over the combinatorial fusion cascades would open the road for a novel technology to develop artificial microorganism

Combinatorial Fusion Rules to Describe Codon Assignment in the Standard Genetic Code

We propose combinatorial fusion rules that describe the codon assignment in the standard genetic code simply and uniformly for all canonical amino acids. These rules become obvious if the origin of the standard genetic code is considered as a result of a fusion of four protocodes: Two dominant AU and GC protocodes and two recessive AU and GC protocodes. The biochemical meaning of the fusion rules consists of retaining the complementarity between cognate codons of the small hydrophobic amino acids and large charged or polar amino acids within the protocodes. The proto tRNAs were assembled in form of two kissing hairpins with 9-base and 10-base loops in the case of dominant protocodes and two 9-base loops in the case of recessive protocodes. The fusion rules reveal the connection between the stop codons, the non-canonical amino acids, pyrrolysine and selenocysteine, and deviations in the translation of mitochondria. Using fusion rules, we predicted the existence of additional amino acids that are essential for the development of the standard genetic code. The validity of the proposed partition of the genetic code into dominant and recessive protocodes is considered referring to state-of-the-art hypotheses. The formation of two aminoacyl-tRNA synthetase classes is compatible with four-protocode partition

Soundness-preserving composition of synchronously and asynchronously interacting workflow net components

In this paper, we propose a compositional approach to construct formal models of complex distributed systems with several synchronously and asynchronously interacting components. A system model is obtained from a composition of individual component models according to requirements on their interaction. We represent component behavior using workflow nets - a class of Petri nets. We propose a general approach to model and compose synchronously and asynchronously interacting workflow nets. Through the use of Petri net morphisms and their properties, we prove that this composition of workflow nets preserves component correctness.Comment: Preprint of the paper submitted to "Fundamenta Informaticae

Discovering Hierarchical Process Models: an Approach Based on Events Clustering

Process mining is a field of computer science that deals with discovery and analysis of process models based on automatically generated event logs. Currently, many companies use this technology for optimization and improving their processes. However, a discovered process model may be too detailed, sophisticated and difficult for experts to understand. In this paper, we consider the problem of discovering a hierarchical business process model from a low-level event log, i.e., the problem of automatic synthesis of more readable and understandable process models based on information stored in event logs of information systems. Discovery of better structured and more readable process models is intensively studied in the frame of process mining research from different perspectives. In this paper, we present an algorithm for discovering hierarchical process models represented as two-level workflow nets. The algorithm is based on predefined event ilustering so that the cluster defines a sub-process corresponding to a high-level transition at the top level of the net. Unlike existing solutions, our algorithm does not impose restrictions on the process control flow and allows for concurrency and iteration

Die Botschaft von LUCA — der letzte universelle gemeinsame Vorfahre

The standard genetic code is the only reliable information about the first living cell on Earth called the last universal common ancestor – LUCA. The central mystery of the genetic code is the assignment of the canonical amino acids to the codons – base triplets. Simple and uniform combinatorial rules indicate that the standard genetic code arose during the fusion of four primordial single base-pair codes

Renaissance Distribution for Statistically Failed Experiments

Much of the experimental data, especially in life sciences, is considered to be useless if it demonstrates a large standard deviation from the mean value. The Renaissance distribution, as presented in this study, allows one to extract true values from such statistical data with large noise. To obtain proof of the Renaissance distribution, high-throughput synthesis of deep substitutions for a target amino acid sequence was performed, and the known epitope was identified in assay with human serum antibodies. In addition, the Renaissance distribution was shown to approach the epitope affinity maturation by the deep alanine substitution. The Renaissance distribution may have an impact in the development of novel specific drugs

Diaqua­bis­(propane-1,3-diamine)­copper(II) bis­[diamminetetra­kis­(thio­cyanato-κN)chromate(III)] dimethyl sulfoxide octa­solvate

The ionic title complex, [Cu(C3H10N2)2(H2O)2][Cr(NCS)4(NH3)2]·8C2H6OS, consists of complex [Cu(dipr)2(H2O)2]2+ copper cations (dipr is propane-1,3-diamine), complex [Cr(NCS)4(NH3)2]− anions and uncoord­inated solvent dimethyl sulfoxide (DMSO) mol­ecules. All the metal atoms lie on crystallographic centers of symmetry. The cations are connected to the anions through N—H⋯O hydrogen bonds between the NH3 mol­ecules of the anion and the water mol­ecules of the cation. The DMSO mol­ecules are involved in hydrogen-bonded linkage of the [Cr(NCS)4(NH3)2]− anions into supra­molecular chains through bridging O atoms. A network of hydrogen bonds as well as short S⋯S contacts [3.5159 (12) and 3.4880 (12) Å] between the NCS groups of the complex anions link the mol­ecules into a three-dimensional supra­molecular network

Resemblance-Ranking Peptide Library to Screen for Binders to Antibodies on a Peptidomic Scale

This article belongs to the Special Issue Exploiting the Multitarget and Repositioned Drugs Approac