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Reported herein is the first total synthesis of the poly‐pseudoindoxyl natural product baphicacanthcusine A. The synthesis leverages the oxidative rearrangement of indoles to pseudoindoxyls to install vicinal pseudoindoxyl heterocycles in a diastereoselective manner. Key steps include an acid‐mediated cyclization/indole transposition, two diastereoselective oxidative ring contractions, and a site‐selective C−H oxygenation. The synthesis of the oxidation precursors was guided by recognition of an element of hidden symmetry. This work provides a foundation for the chemical synthesis of other poly‐pseudoindoxyl alkaloids. [ABSTRACT FROM AUTHOR]

An improved practical and efficient procedure for the synthesis of non-racemic unnatural α-amino acids through a stereocontrolled rearrangement is reported. Carboxylic acids are converted into azanyl esters RCO2 NHBoc followed by an iron-catalyzed 1,3-nitrogen migration to provide non-racemic α-amino acids in an asymmetric (α-monosubstituted α-amino acids) or enantioconvergent fashion (α,α-disubstituted α-amino acids). Under optimized conditions using a fluorinated chiral iron catalyst and 2,2,6,6-tetramethylpiperidine as the base in a solvent mixture of 1,2-dichlorobenzene and CHCl3 , enantioselectivities of up to 98% ee were obtained. Such high ee values are important for practical purposes, allowing the direct use of many of the obtained N-Boc-protected α-amino acids for subsequent applications. [ABSTRACT FROM AUTHOR]

The genome organization of woodpeckers has several distinctive features e.g., an uncommon accumulation of repetitive sequences, enlarged Z chromosomes, and atypical diploid numbers. Despite the large diversity of species, there is a paucity of detailed cytogenomic studies for this group and we thus aimed to rectify this. Genome organization patterns and hence evolutionary change in the microchromosome formation of four species (Colaptes campestris, Veniliornis spilogaster, Melanerpes candidus, and Picumnus nebulosus) was established through fluorescence in situ hybridization using bacterial artificial chromosomes originally derived from Gallus gallus and Taeniopygia guttata. Findings suggest that P. nebulosus (2n = 110), which was described for the first time, had the most basal karyotype among species of Picidae studied here, and probably arose as a result of fissions of avian ancestral macrochromosomes. We defined a new chromosomal number for V. spilogaster (2n = 88) and demonstrated microchromosomal rearrangements involving C. campestris plus a single, unique hitherto undescribed rearrangement in V. spilogaster. This comprised an inversion after a fusion involving the ancestral microchromosome 12 (homologous to chicken microchromosome 12). We also determined that the low diploid number of M. candidus is related to microchromosome fusions. Woodpeckers thus exhibit significantly rearranged karyotypes compared to the putative ancestral karyotype. [ABSTRACT FROM AUTHOR]

A carbon‐rich molecule is synthesized, which mainly contains conjugated sp2 and sp hybridized carbon centers. Alkenyl and alkynyl binding sites are arranged such that this compound serves as ligand to a binuclear metal unit with a RhI─RhI bond. Furthermore, CH units are placed in proximity to the metal centers. The dicationic complex [Rh2(bipy)2{Ph2Ptrop(C≡CCy)2}]2+(OTf−)2 allows to study possible responses of the carbon‐framework to redox reactions as well as deprotonation reactions. All products are, whenever possible, characterized by X‐ray diffraction (XRD) methods, NMR and EPR spectroscopy as well as electrochemical methods. It is shown that the carbon skeleton of the ligand framework undergoes C─C bond rearrangement reactions of remarkable diversity. In combination with DFT (density functional theory) studies, these results allow to gain insight into the electronic structure changes caused by metal sites in a carbon‐rich environment, which may be of relevance for the properties of metal particles on carbon support materials when they are exposed to hydrogen, electrons, or protons. [ABSTRACT FROM AUTHOR]

AbstractMitochondrial DNA is a valuable tool for population genetics and evolutionary studies in a wide range of organisms. With advancements in sequencing techniques, it’s now possible to gain deeper insights into this molecule. By understanding how many genes there are, how they’re organized within the molecule, identifying the presence of spacers, and analyzing the composition of the D-Loop, we can better grasp the rearrangements that play a crucial role in the evolutionary dynamics of mitochondrial DNA. Additionally, phylogenetic analyses benefit significantly from having access to a larger pool of mtDNA genes. This wealth of genetic information allows for the establishment of evolutionary relationships with greater accuracy than ever before, providing a more robust framework than analyses based on a limited number of genes. Studies on mitogenomes belonging to the family Formicidae have proven promising, enabling the identification of gene rearrangements and enhancing our understanding of the internal relationships within the group. Despite this, the number of mitogenomes available for the subfamily Ponerinae is still limited, and here we present for the first time the complete mitogenome of Odontomachus. Our data reveal a gene duplication event in Formicidae, the first involving trnV, and new gene arrangements involving the trnM–trnI–trnQ and trnW–trnC–trnY clusters, suggesting a possible synapomorphy for the genus. Our phylogenetic analysis using the PCGs available for Formicidae supports the monophyly of the subfamily Ponerinae and sheds light on the relationship between Odontomachus and Pachycondyla. [ABSTRACT FROM AUTHOR]

When studying signal reconstruction, the frames are often selected in advance as encoding tools. However, in practical applications, this encoding frame may be subject to attacks by intermediaries and generate errors. To solve this problem, in this paper, the erasure recovery matrices for data erasures and rearrangements are analyzed. Unlike the previous research, first of all, we introduce a kind of frame and its erasure recovery matrix M so that M I , Λ = I m × m , where I m × m is a unit matrix. In this case, we do not need to invert the matrix of the frame operator and the erasure recovery matrix, and this greatly simplifies reconstruction problems and calculations. Then three different construction algorithms of the above erasure recovery matrix M and the frame are proposed, and each of them has advantages. Furthermore, some restrictions on M so that the constructed frame and erasure recovery matrix M can recover coefficients from rearrangements are imposed. We prove that in some cases, the above M and frame can recover coefficients stably from m rearrangements. [ABSTRACT FROM AUTHOR]

2‐Acetonaphthones, which bear an alkenyl group tethered to its C1 carbon atom via an oxygen atom, were found to undergo an enantioselective intramolecular ortho photocycloaddition reaction. A chiral oxazaborolidine Lewis acid leads to a bathochromic absorption shift of the substrate and enables an efficient enantioface differentiation. Visible light irradiation (λ=450 nm) triggers the reaction which is tolerant of various groups at almost any position except carbon atom C8 (16 examples, 53–99 % yield, 80–97 % ee). Consecutive reactions were explored including a sensitized rearrangement to tetrahydrobiphenylenes, which occurred with full retention of configuration. Evidence was collected that the catalytic photocycloaddition occurs via triplet intermediates, and the binding mode of the acetonaphthone to the chiral Lewis acid was elucidated by DFT calculations. [ABSTRACT FROM AUTHOR]

This article discusses the use of glycosyl radicals in the epimerisation of carbohydrates, specifically focusing on d-mannopyranosyl fluorides. The authors provide experimental evidence and theoretical calculations to support their findings, highlighting the importance of β-configuration in achieving l-hexose selectivity. The article also describes the synthesis of α- and β-configured d-mannopyranosyl fluorides and their potential applications in the synthesis of rare sugars. The document provides detailed experimental procedures and characterization data for the compounds synthesized in the study, which can be valuable for researchers studying similar compounds. [Extracted from the article]

In this paper we prove a comparison result for a class of Dirichlet boundary problems whose model is$ \left\{ \begin{array}{ll} -\Delta u = {\beta}|\nabla u|^q +c u + f &\rm{in\;} \Omega \\ u = 0&\rm{su\;} \partial \Omega \,, \end{array} \right. $where $ \Omega $ is an open bounded subset of $ {{\mathbb R}^N} $, $ N>2 $. We also prove an existence and uniqueness result for weak solution to these problems. [ABSTRACT FROM AUTHOR]

Abstract A carbon‐rich molecule is synthesized, which mainly contains conjugated sp2 and sp hybridized carbon centers. Alkenyl and alkynyl binding sites are arranged such that this compound serves as ligand to a binuclear metal unit with a RhI─RhI bond. Furthermore, CH units are placed in proximity to the metal centers. The dicationic complex [Rh2(bipy)2{Ph2Ptrop(C≡CCy)2}]2+(OTf−)2 allows to study possible responses of the carbon‐framework to redox reactions as well as deprotonation reactions. All products are, whenever possible, characterized by X‐ray diffraction (XRD) methods, NMR and EPR spectroscopy as well as electrochemical methods. It is shown that the carbon skeleton of the ligand framework undergoes C─C bond rearrangement reactions of remarkable diversity. In combination with DFT (density functional theory) studies, these results allow to gain insight into the electronic structure changes caused by metal sites in a carbon‐rich environment, which may be of relevance for the properties of metal particles on carbon support materials when they are exposed to hydrogen, electrons, or protons.

Abstract Background Large deletions and duplications within the low-density lipoprotein receptor (LDLR) gene make up approximately 10% of LDLR pathogenic variants found in Czech patients with familial hypercholesterolemia. The goal of this study was to test the hypothesis that all probands with each rearrangement share identical breakpoints inherited from a common ancestor and to determine the role of Alu repetitive elements in the generation of these rearrangements. Methods The breakpoint sequence was determined by PCR amplification and Sanger sequencing. To confirm the breakpoint position, an NGS analysis was performed. Haplotype analysis of common LDLR variants was performed using PCR and Sanger sequencing. Results The breakpoints of 8 rearrangements within the LDLR gene were analysed, including the four most common LDLR rearrangements in the Czech population (number of probands ranging from 8 to 28), and four less common rearrangements (1–4 probands). Probands with a specific rearrangement shared identical breakpoint positions and haplotypes associated with the rearrangement, suggesting a shared origin from a common ancestor. All breakpoints except for one were located inside an Alu element. In 6 out of 8 breakpoints, there was high homology (≥ 70%) between the two Alu repeats in which the break occurred. Conclusions The most common rearrangements of the LDLR gene in the Czech population likely arose from one mutational event. Alu elements likely played a role in the generation of the majority of rearrangements inside the LDLR gene.

Sulfenyl imidinium salts are a virtually unexplored class of intermediates in organic chemistry. Herein, we demonstrate how sulfonium rearrangements can be deployed to access these versatile synthetic intermediates, bearing three contiguous (and congested) stereogenic centers, with high levels of selectivity. The synthetic value of the scaffold was unraveled by selective transformations into a range of building blocks, including 1,4‐dicarbonyl derivatives and sulfonolactones. [ABSTRACT FROM AUTHOR]

Collinolactone A is a microbial specialized metabolite with a unique 6‐10‐7 tricyclic bislactone skeleton which was isolated from Streptomyces bacteria. The unusual cyclodecatriene motif features dynamic interconversions of two rotamers. Given the biological profiling of collinolactone A as neuroprotective agent, semisynthetic modifications represent an invaluable strategy to enhance its efficacy. Since understanding conformations and reactions of bioactive substances is crucial for rational structure‐based design and synthesis of derivatives, we conducted computational studies on conformational behavior as well as experiments on thermal and acid induced rearrangements of the cyclodecatriene. Experimental conformer ratios of collinolactone A and its biosynthetic ketolactone precursor are well reproduced by computations at the PW6B95‐D3/def2‐QZVPP//r2SCAN‐3c level. Upon heating collinolactone A in anhydrous dioxane at 100 °C, three collinolactone B stereoisomers exhibiting enollactone structures form via Cope rearrangements. Our computations predict the energetic preference for a boat‐like transition state in agreement with the stereochemical outcome of the main reaction pathway. Constriction of the ten‐membered ring forms collinolactone C with four annulated rings and an exocyclic double bond. Computations and semisynthetic experiments demonstrate strong preference for an acid‐catalyzed reaction pathway over an alternative Alder‐ene route to collinolactone C with a prohibitive reaction barrier, again in line with stereochemical observations. [ABSTRACT FROM AUTHOR]

Background: Large deletions and duplications within the low-density lipoprotein receptor (LDLR) gene make up approximately 10% of LDLR pathogenic variants found in Czech patients with familial hypercholesterolemia. The goal of this study was to test the hypothesis that all probands with each rearrangement share identical breakpoints inherited from a common ancestor and to determine the role of Alu repetitive elements in the generation of these rearrangements. Methods: The breakpoint sequence was determined by PCR amplification and Sanger sequencing. To confirm the breakpoint position, an NGS analysis was performed. Haplotype analysis of common LDLR variants was performed using PCR and Sanger sequencing. Results: The breakpoints of 8 rearrangements within the LDLR gene were analysed, including the four most common LDLR rearrangements in the Czech population (number of probands ranging from 8 to 28), and four less common rearrangements (1–4 probands). Probands with a specific rearrangement shared identical breakpoint positions and haplotypes associated with the rearrangement, suggesting a shared origin from a common ancestor. All breakpoints except for one were located inside an Alu element. In 6 out of 8 breakpoints, there was high homology (≥ 70%) between the two Alu repeats in which the break occurred. Conclusions: The most common rearrangements of the LDLR gene in the Czech population likely arose from one mutational event. Alu elements likely played a role in the generation of the majority of rearrangements inside the LDLR gene. [ABSTRACT FROM AUTHOR]

Boronate rearrangements, such as the Matteson and Petasis reactions, are valuable metal‐free reactions for the transfer of the carbo group on boron to intramolecular electrophilic sites. However, only highly reactive electrophiles are suitable, and ketones are too inactive for those boronate rearrangements due to the high energy barriers. We disclose here the 1,3‐boronate rearrangement to ketones, for which a high energy barrier (44.9 kcal/mol) is prohibitory for thermal reactions in the ground state. The reaction is enabled by the key keto‐enol‐boronate bidentate complex formation in situ, which absorbs visible light to reach the excited state for the chemoselective 1,3‐boronate rearrangement to ketones. Experimental and computational investigations exclude free radical intermediates from organoboronates. The aryl, alkenyl, and alkyl boronic acids react with various 1,3‐diketones driven by visible light irradiation to construct structurally diverse β‐keto tertiary alcohols under metal‐free conditions. The reaction demonstrates substrate diversity with 58 examples, yields up to 98 %, and it is suitable for gram‐scale synthesis. [ABSTRACT FROM AUTHOR]

When studying signal reconstruction, the frames are often selected in advance as encoding tools. However, in practical applications, this encoding frame may be subject to attacks by intermediaries and generate errors. To solve this problem, in this paper, the erasure recovery matrices for data erasures and rearrangements are analyzed. Unlike the previous research, first of all, we introduce a kind of frame and its erasure recovery matrix M so that MI,Λ=Im×m, where Im×m is a unit matrix. In this case, we do not need to invert the matrix of the frame operator and the erasure recovery matrix, and this greatly simplifies reconstruction problems and calculations. Then three different construction algorithms of the above erasure recovery matrix M and the frame are proposed, and each of them has advantages. Furthermore, some restrictions on M so that the constructed frame and erasure recovery matrix M can recover coefficients from rearrangements are imposed. We prove that in some cases, the above M and frame can recover coefficients stably from m rearrangements.

Seagrasses are ideal for studying plant adaptation to marine environments. In this study, the mitochondrial (mt) and chloroplast (cp) genomes of Ruppia sinensis were sequenced. The results showed an extensive gene loss in seagrasses, including a complete loss of cp-rpl19 genes in Zosteraceae, most cp-ndh genes in Hydrocharitaceae, and mt-rpl and mt-rps genes in all seagrasses, except for the mt-rpl16 gene in Phyllospadix iwatensis. Notably, most ribosomal protein genes were lost in the mt and cp genomes. The deleted cp genes were not transferred to the mt genomes through horizontal gene transfer. Additionally, a significant DNA transfer between seagrass organelles was found, with the mt genomes of Zostera containing numerous sequences from the cp genome. Rearrangement analyses revealed an unreported inversion of the cp genome in R. sinensis. Moreover, four positively selected genes (atp8 , nad5 , atp4 , and ccmFn) and five variable regions (matR , atp4 , atp8 , rps7 , and ccmFn) were identified. • The first mitochondrial (mt) genome of R. sinensis. • Horizontal gene transfer showed that the deleted cp genes were not transferred to the mt genomes. • Rearrangement analyses revealed an unreported large inversion in the cp genome of R. sinensis. • Four positively selected genes and five variable regions were identified. [ABSTRACT FROM AUTHOR]

Plasmids are a key vector of antibiotic resistance, but the current bioinformatics toolkit is not well suited to tracking them. The rapid structural changes seen in plasmid genomes present considerable challenges to evolutionary and epidemiological analysis. Typical approaches are either low resolution (replicon typing) or use shared k-mer content to define a genetic distance. However, this distance can both overestimate plasmid relatedness by ignoring rearrangements, and underestimate by over-penalizing gene gain/loss. Therefore a model is needed which captures the key components of how plasmid genomes evolve structurally - through gene/block gain or loss, and rearrangement. A secondary requirement is to prevent promiscuous transposable elements (TEs) leading to over-clustering of unrelated plasmids. We choose the 'Double Cut and Join Indel' (DCJ-Indel) model, in which plasmids are studied at a coarse level, as a sequence of signed integers (representing genes or aligned blocks), and the distance between two plasmids is the minimum number of rearrangement events or indels needed to transform one into the other. We show how this gives much more meaningful distances between plasmids. We introduce a software workflow pling (https://github.com/iqbal-lab-org/pling), which uses the DCJ-Indel model, to calculate distances between plasmids and then cluster them. In our approach, we combine containment distances and DCJ-Indel distances to build a TE-aware plasmid network. We demonstrate superior performance and interpretability to other plasmid clustering tools on the 'Russian Doll' dataset and a hospital transmission dataset.

This paper provides comparison results for general factor models with respect to the supermodular and directionally convex order. These results extend and strengthen previous ordering results from the literature concerning certain classes of mixture models as mixtures of multivariate normals, multivariate elliptic and exchangeable models to general factor models. For the main results, we first strengthen some known orthant ordering results for the multivariate ▪ -product of the specifications, which represents the copula of the factor model, to the stronger notion of the supermodular ordering. The stronger comparison results are based on classical rearrangement results and in particular are rendered possible by some involved constructions of transfers as arising from mass transfer theory. The ordering results for ▪ -products are then extended to factor models with general conditional dependencies. As a consequence of the ordering results, we derive worst case scenarios in relevant classes of factor models allowing, in particular, interesting applications to deriving sharp bounds in financial and insurance risk models. The results and methods of this paper are a further indication of the particular effectiveness of Sklar's copula notion. [ABSTRACT FROM AUTHOR]

Mitochondrial DNA is a valuable tool for population genetics and evolutionary studies in a wide range of organisms. With advancements in sequencing techniques, it's now possible to gain deeper insights into this molecule. By understanding how many genes there are, how they're organized within the molecule, identifying the presence of spacers, and analyzing the composition of the D-Loop, we can better grasp the rearrangements that play a crucial role in the evolutionary dynamics of mitochondrial DNA. Additionally, phylogenetic analyses benefit significantly from having access to a larger pool of mtDNA genes. This wealth of genetic information allows for the establishment of evolutionary relationships with greater accuracy than ever before, providing a more robust framework than analyses based on a limited number of genes. Studies on mitogenomes belonging to the family Formicidae have proven promising, enabling the identification of gene rearrangements and enhancing our understanding of the internal relationships within the group. Despite this, the number of mitogenomes available for the subfamily Ponerinae is still limited, and here we present for the first time the complete mitogenome of Odontomachus . Our data reveal a gene duplication event in Formicidae, the first involving trnV , and new gene arrangements involving the trnM-trnI-trnQ and trnW-trnC-trnY clusters, suggesting a possible synapomorphy for the genus. Our phylogenetic analysis using the PCGs available for Formicidae supports the monophyly of the subfamily Ponerinae and sheds light on the relationship between Odontomachus and Pachycondyla .