Template Structure Research Articles

Reconciling bathymetric and stratigraphic expressions of submarine channel geometry

Modern submarine channels form distinctive morphological features on the seafloor and play a critical role in shaping the marine sedimentary record. Recent studies have captured the extremely diverse range of cross-sectional geometries in submarine channels from bathymetric data, which typically display aspect ratios markedly different to the stratigraphic record of ancient submarine channels. Here, we compare and reconcile the relationship between the geomorphic expression of submarine channels as observed on the seafloor and the geometry of their stratigraphic bodies as mapped in seismic-reflection data, using the Niger Delta slope an exemplar. For the same channels, our data allows us to contrast the distribution of widths, depths, and aspect ratios from bathymetric data and at two hierarchical scales in the underlying stratigraphy – the channel element and channel system scale. Channel characteristics are also contextualised with respect to two key variables, the underlying structural template and the relative timescale for which the studied systems have been active. Analysis of the seafloor bankfull geometries highlights substantial variability with widths ranging from ∼300 m to ∼4 km and aspect ratios from ∼10:1–100:1. In contrast, the geometry of stratigraphic channel element bodies remains remarkably consistent across the three channels with widths ∼480–620 m and aspect ratios of ∼9:1. At channel system scale stratigraphic width is comparable to that seen in the bathymetric data, but with aspect ratios of 6–23:1. Our results therefore highlight a marked disparity in the cross-sectional geometries on the present-day seafloor and for their associated channels in the stratigraphic record. We demonstrate that a large part of the disparity between modern and ancient submarine channel geometries may be explained by post-abandonment modification of the seabed channels where there is reduced Holocene activity and we argue this effect likely plays a role in the differences seen in global data sets. These results have significant implications for the use of bankfull process analogues when applied to bathymetric data to estimate submarine channel flow characteristics.

Paramecium: RNA sequence-structure phylogenetics.

Organisms classified as members of the genus Paramecium belong to the best-known group of single-celled eukaryotes. Nevertheless, the phylogeny within the genus Paramecium has been discussed and revisited in recent decades and remains partly unresolved. By applying an RNA sequence-structure approach, we attempt to increase accuracy and robustness of phylogenetic trees. For each individual 18S and internal transcribed spacer 2 (ITS2) sequence, a putative secondary structure was predicted through homology modelling. While searching for a structural template, we found, in contrast to the available literature, that the ITS2 molecule consists of three helices in members of the genus Paramecium and four helices in members of the genus Tetrahymena. Two sequencestructure neighbor-joining overall trees were reconstructed with (1) more than 400 taxa (ITS2) and (2) more than 200 taxa (18S). For smaller subsets, neighbor-joining, maximum-parsimony, and maximum-likelihood analyses were executed using sequence-structure information simultaneously. Based on a combined data set (ITS2+18S rDNA) a well-supported tree was reconstructed with bootstrap values over 50 in at least one of the applied analyses. Our results are in general agreement with those published in the available literature based on multi-gene analyses. Our study supports the simultaneous use of sequence-structure data to reconstruct accurate and robust phylogenetic trees.

Abstract 3424: Template-assisted covalent modification of DCAF16 enables BRD4 molecular glue degraders

Abstract Molecular glue degraders have emerged as a powerful class of small-molecule therapeutics, as demonstrated by the clinical successes of thalidomide analogs in the treatment of hematological malignancies. These small molecules act by recruiting ubiquitin ligases to disease-relevant proteins, resulting in neosubstrate ubiquitination and degradation. To date, only a small number of ubiquitin ligase - neosubstrate interactions have been exploited by molecular glue degraders, limiting the targeting scope of this therapeutic modality. Covalent chemistry, which confers high binding affinity and the ability of targeting shallow binding sites, can expand the addressable protein interfaces for molecular glue degraders. In this study, we identified a new class of BRD4 covalent molecular glue degraders (GNE-0011, TMX-4137, MMH-252, MMH-272) by derivatizing electrophiles on the solvent-facing side of a non-degradative BRD4 inhibitor, JQ1. These degraders recruit the ubiquitin ligase CUL4DCAF16 to BRD4 via a novel, trans-labeling mechanism we term “template-assisted covalent modification.” These covalent small molecules have only weak reactivity to DCAF16 in the absence of BRD4. However, BRD4 binding allows its BD2 domain, in complex with DCAF16, to serve as a structural template to boost the covalent modification of these degraders to DCAF16. This leads to efficient BRD4-degrader-DCAF16 ternary complex formation and subsequent BRD4 degradation. We solved the cryo-electron microscopy structure of the DDB1-DCAF16 ligase complex bound to BRD4(BD2) and MMH-272, demonstrating that DCAF16 and BRD4(BD2) have pre-existing structural complementarity which optimally orients the reactive moiety of MMH-272 for DCAF16 covalent modification. We performed systematic mutagenesis screens of both DCAF16 and BRD4(BD2) to characterize the drug-induced interaction, discovering that Cys58 of DCAF16 is modified by covalent warheads and is critical for the activity of these degraders, and that His437 of BRD4(BD2) and its adjacent residues are important for a stable interaction with DCAF16. Analysis of a chemical series revealed that the covalent reactivity of these small molecules is required for degradation, and that the degree of reactivity can tune the potency and specificity of the degraders. Our work highlights a new class of BRD4 molecular glue degraders that are enabled by the template-assisted covalent modification of DCAF16. The templated reactivity is likely to exist in other covalent small molecules that engage complementary protein interfaces, and this trans-labeling mechanism can be exploited to develop covalent drugs with more precisely controlled reactivity. Moreover, our findings demonstrate that the decoration of solvent-exposed electrophiles to protein-binding small molecules has great potential to enable discovery and optimization of novel molecular glue degraders. Citation Format: Yen-Der Li, Michelle W. Ma, Muhammad Murtaza Hassan, Kedar Puvar, Mingxing Teng, Brittany Sandoval, Ryan Lumpkin, Scott B. Ficarro, Michelle Y. Wang, Shawn Xu, Brian J. Groendyke, Logan H. Sigua, Isidoro Tavares, Charles Zou, Jonathan M. Tsai, Paul M. Park, Hojong Yoon, Radosław P. Nowak, Jarrod A. Marto, Jun Qi, Katherine A. Donovan, Mikołaj Słabicki, Nathanael S. Gray, Eric S. Fischer, Benjamin L. Ebert. Template-assisted covalent modification of DCAF16 enables BRD4 molecular glue degraders [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3424.

In silico annotation of a hypothetical protein from Listeria monocytogenes EGD-e unfolds a toxin protein of the type II secretion system.

The gram-positive bacterium Listeria monocytogenes is an important foodborne intracellular pathogen that is widespread in the environment. The functions of hypothetical proteins (HP) from various pathogenic bacteria have been successfully annotated using a variety of bioinformatics strategies. In this study, a HP Imo0888 (NP_464414.1) from the Listeria monocytogenes EGD-e strain was annotated using several bioinformatics tools. Various techniques, including CELLO, PSORTb, and SOSUIGramN, identified the candidate protein as cytoplasmic. Domain and motif analysis revealed that the target protein is a PemK/MazFlike toxin protein of the type II toxin-antitoxin system (TAS) which was consistent with BLASTp analysis. Through secondary structure analysis, we found the random coil to be the most frequent. The Alpha Fold 2 Protein Structure Prediction Database was used to determine the three-dimensional (3D) structure of the HP using the template structure of a type II TAS PemK/MazF family toxin protein (DB ID_AFDB: A0A4B9HQB9) with 99.1% sequence identity. Various quality evaluation tools, such as PROCHECK, ERRAT, Verify 3D, and QMEAN were used to validate the 3D structure. Following the YASARA energy minimization method, the target protein's 3D structure became more stable. The active site of the developed 3D structure was determined by the CASTp server. Most pathogens that harbor TAS create a crucial risk to human health. Our aim to annotate the HP Imo088 found in Listeria could offer a chance to understand bacterial pathogenicity and identify a number of potential targets for drug development.

In situ modification of LiMn3/4Fe1/4PO4/C cathode realized by hierarchical porous α-LiAlO2 as channel for lithium-ion batteries

In view of the lower electronic and ionic conductivity of LiMnPO4 cathode materials, we use α-LiAlO2 solid electrolyte with pore structure to compound LiMn3/4Fe1/4PO4/C solid solution on the basis of Mn site doped Fe, forming a conductive connection network between them. Using anode aluminum oxide as porous structure template, a series of LiMn3/4Fe1/4PO4/C@α-LiAlO2 nano composites are constructed by hydrothermal in-situ deposition and subsequent heat treatment. Through the first-principles calculation, it is found that the modification of α-LiAlO2 leads to an increase in the number of states near Fermi level, and the adjustment energy band width affects the electronic conductivity of LiMn3/4Fe1/4PO4 electrode. When the content of α-LiAlO2 is 6 wt%, the electronic structure of LiMn3/4Fe1/4PO4@α-LiAlO2 composite is the best and has the best performance. This material material exhibits a better specific discharge capacity, that is, 142.6, 137.7, 130.3, 117.1, 100.6, 79.2 and 68.5 mAh·g−1 at 0.5C, 2C, 4C, 8C, 10C, 15C and 20C, respectively. In addition, its DLi + is 2.02 × 10−12 cm2·s−1, which is an order of magnitude higher than that of other α-LiAlO2-containing electrodes. Hence, it is significant in cathode for lithium-ion batteries to reasonably design multi-functional hybrid materials.

In silico characterization of the psilocybin biosynthesis pathway

Nearly all mushrooms of the Psilocybe genus contain the natural product psilocybin, which is a psychoactive alkaloid derived from l-tryptophan. Considering their use in ancient times, as well as their psychedelic properties, these mushrooms have re-emerged with psychotherapeutic potential for treating depression, which has triggered increased pharmaceutical interest. However, the psilocybin biosynthesis pathway was only recently defined and, as such, little exists in the way of structural data. Accordingly, the aim of this study was to structurally characterize this pathway by generating homology models for the four Psilocybe cubensis enzymes involved in psilocybin biosynthesis (PsiD, a decarboxylase; PsiH, a monooxygenase; PsiK, a phosphotransferase; PsiM, a methyltransferase). Following initial model generation and alignment with the identified structural templates, repeated refinement of the models was carried out using secondary structure prediction, geometry evaluation, energy minimization, and molecular dynamics simulations in water. The final models were then evaluated using molecular docking interactions with their substrates, i.e., psilocybin precursors (l-tryptophan, tryptamine, 4-hydroxytryptamine, and norbaeocystin/baeocystin), all of which generated feasible binding modes for the expected biotransformation. Further plausibility of the psilocybin → aeruginascin, 4-hydroxytryptamine → norpsilocin, and tryptamine → N,N-dimethyltryptamine conversions, all mediated by the generated model for PsiM, suggests valid routes of formation for these key secondary metabolites. The structural characterization of these enzymes and their binding modes which emerged from this study can lead to a better understanding of psilocybin synthesis, thereby paving the way for the development of novel substrates and selective inhibitors, as well as improved biotechnological manipulation and production of psilocybin in vitro.

Design, Synthesis, and Insecticidal and Fungicidal Activities of Ether/Oxime-ether Containing Isoxazoline Derivatives

The existing agricultural insecticides have developed drug resistance from long-term use. Isoxazoline derivatives are new insecticides discovered in the 21st century. Because of their unique insecticidal mechanism, high selectivity, safety, and no significant cross resistance with the existing pesticides on the market, they have become a hot spot in the field of pesticide research. Herein, a series of novel isoxazoline derivatives containing ether and oxime-ether structures were designed and synthesized by a scaffold-hopping strategy using the pesticide fluralaner as a template structure. Through the investigation of insecticidal activity and the systematic structure-activity relationship, a series of compounds with high insecticidal activities were found, and compounds I-4, II-9, and II-13 with LC50 values of 0.00008-0.00036 mg/L against diamondback moth emerged as novel insecticide candidates. These compounds also exhibited broad spectrum fungicidal activities against 14 plant fungi. The current work provides a reference for the design of new isoxazoline compounds based on the scaffold-hopping strategy.

Highly selective butyrylcholinesterase inhibitors related to Amaryllidaceae alkaloids - Design, synthesis, and biological evaluation

Butyrylcholinesterase (BChE) is one of the most frequently implicated enzymes in the advanced stage of Alzheimer's disease (AD). As part of our endeavors to develop new drug candidates for AD, we have focused on natural template structures, namely the Amaryllidaceae alkaloids carltonine A and B endowed with high BChE selectivity. Herein, we report the design, synthesis, and in vitro evaluation of 57 novel highly selective human BChE (hBChE) inhibitors. Most synthesized compounds showed hBChE inhibition potency ranging from micromolar to low nanomolar scale. Compounds that revealed BChE inhibition below 100 nM were selected for detailed biological investigation. The CNS-targeted profile of the presented compounds was confirmed theoretically by calculating the BBB score algorithm, these data were corroborated by determining the permeability in vitro using PAMPA-assay for the most active derivatives. The study highlighted compounds 87 (hBChE IC50 = 3.8 ± 0.2 nM) and 88 (hBChE IC50 = 5.7 ± 1.5 nM) as the top-ranked BChE inhibitors. Compounds revealed negligible cytotoxicity for the human neuroblastoma (SH-SY5Y) and hepatocellular carcinoma (HepG2) cell lines compared to BChE inhibitory potential. A crystallographic study was performed to inspect the binding mode of compound 87, revealing essential interactions between 87 and hBChE active site. In addition, multidimensional QSAR analyses were applied to determine the relationship between chemical structures and biological activity in a dataset of designed agents. Compound 87 is a promising lead compound with potential implications for treating the late stages of AD.

Dual fluorescence output aptamer sensing of cortisol in Cushing syndrome samples assisted by tandem hybridization chain reaction

Accurate and sensitive detection of serum free cortisol has been a challenge for precise diagnosis and assessment of Cushing syndrome (CS). The present study described a dual fluorescent homogeneous cortisol aptasensor based on the tandem hybridization chain reaction (HCR) amplification strategy. The system used split G-quadruplex (G4)/thioflavin T (ThT) complexes and dsDNA-templated copper nanoparticles (Cu NPs) as signal reporters. The cortisol binds its aptamer, inhibiting the triggering of HCRs between the aptamer and the four hairpin structures (H1-H4), thereby inhibiting the generation of the dsDNA template and G4 structure. Under optimized conditions, the limit of detection (LOD) was 3 fg/mL for G4/ThT and 2.5 fg/mL for Cu NPs, with a linear range of 1 fg/mL-100 pg/mL, indicating high specificity to various potential interfering substances. This method was used to determine cortisol levels in 54 clinical blood samples. Cortisol levels in clinical samples detected by this method agreed well with those obtained by the electrochemiluminescence immunoassay (ECL-IA) kit and radiological findings. We could distinguish CS from healthy controls and other patients using this approach, with 0.94 of the area under the receiver operating characteristic curve (AUC). This cortisol quantification method was 100% specific and 83.3% sensitive. This sensing strategy has shown great potential as an additional diagnostic tool for cortisol-related disorders.

Rejuvenating the [1, 2, 3]-triazolo [1,5-a]quinoxalin-4(5H)-one scaffold: Synthesis and derivatization in a sustainable guise and preliminary antimicrobial evaluation.

The [1,2,3]-triazolo [1,5-a] quinoxalin-4(5H)-one scaffold and its analogues triazole-fused heterocyclic compounds are relevant structural templates in both natural and synthetic biologically active compounds. However, their medicinal chemistry applications are often limited due to the lack of synthetic protocols combining straightforward generation of the central core while also allowing extensive decoration activity for drug discovery purposes. Herein, we report a "refreshed" synthesis of the [1,2,3]-triazolo [1,5-a]quinoxalin-4(5H)-one core, encompassing the use of eco-compatible catalysts and reaction conditions. We have also performed a sustainable and extensive derivatization campaign at both the endocyclic amide nitrogen and the ester functionality, comprehensively exploring the reaction scope and overcoming some of the previously reported difficulties in introducing functional groups on this structural template. Finally, we unveiled a preliminary biological investigation for the newly generated chemical entities. Our assessment of the compounds on different bacterial species (two S. aureus strains, three P. aeruginosa strains, K. pneumonia), and two fungal C. albicans strains, as well as the evaluation of their activity on S. epidermidis biofilm formation, foster further optimization for the retrieved hit compounds 9, 14, and 20.

Magnetic Iron Oxide Nanoneedles with Hierarchical Structure for Controllable Catalytic Activity of 4-Nitrophenol Reduction.

Catalyst systems with high catalytic activity and sustainability are highly desirable. Here, we report a design for catalytic composites with a hierarchical structure in which polydopamine (PD), multi-metallic nanocatalysts and iron oxide nanoneedles are successively deposited on a magnetic core. PD layers with various thicknesses are coated onto the magnetic core and serve as a template by which to take up multi-metallic nanocatalysts such as Au, Ag and Pt nanoparticles. The iron oxide nanoneedles act as spacers, preventing the nanocomposite from aggregating and increasing the surface area of the composite. The distinctive structures of the controllable template, the multi-metallic catalysts and needle-like layers enable the rapid migration of reactive ionic species and enhance catalytic ability via the synergistic effect of the multi-metallic nanocatalysts and iron oxide nanoneedles. Moreover, due to the strong magnetic property of the catalytic nanocomposites, they can be easily recovered with an external magnet and reused. Our hierarchical nanocomposites for recyclable nanocatalysts provide a new design concept for highly efficient catalysts.

Are Deep Learning Structural Models Sufficiently Accurate for Virtual Screening? Application of Docking Algorithms to AlphaFold2 Predicted Structures.

Machine learning-based protein structure prediction algorithms, such as RosettaFold and AlphaFold2, have greatly impacted the structural biology field, arousing a fair amount of discussion around their potential role in drug discovery. While there are few preliminary studies addressing the usage of these models in virtual screening, none of them focus on the prospect of hit-finding in a real-world virtual screen with a model based on low prior structural information. In order to address this, we have developed an AlphaFold2 version where we exclude all structural templates with more than 30% sequence identity from the model-building process. In a previous study, we used those models in conjunction with state-of-the-art free energy perturbation methods and demonstrated that it is possible to obtain quantitatively accurate results. In this work, we focus on using these structures in rigid receptor-ligand docking studies. Our results indicate that using out-of-the-box Alphafold2 models is not an ideal scenario for virtual screening campaigns; in fact, we strongly recommend to include some post-processing modeling to drive the binding site into a more realistic holo model.

Design of 2-amino-6-methyl-pyrimidine benzoic acids as ATP competitive casein kinase-2 (CK2) inhibitors using structure- and fragment-based design, docking and molecular dynamic simulation studies

ABSTRACT Overexpression of casein kinase-2 (CK2) has been implicated in several carcinomas, mainly lung, prostate and acute myeloid leukaemia. The smaller nucleotide pocket compared to related kinases provides a great opportunity to discover newer ATP-competitive CK2 inhibitors. In this study, we have employed an integrated structure- and fragment-based design strategy to design 2-amino-6-methyl-pyrimidine benzoic acids as ATP-competitive CK2 inhibitors. A statistically significant four features-based E-pharmacophore (ARRR) model was used to screen 780,092 molecules. Further, the retrieved hits were considered for molecular docking study to identify essential binding interactions. At the same time, fragment-based virtual screening was performed using a dataset of 1,542,397 fragments. The identified hits and fragments were used as structure templates to rationalize the design of 2-amino-6-methyl-pyrimidine benzoic acids as newer CK2 inhibitors. Finally, the binding interactions of the designed hits were identified using an induced fit docking (IFD) study, and their stability was estimated by a molecular dynamics (MD) simulation study of 100 ns.

Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMR.

Peptides and proteins containing non-canonical amino acids (ncAAs) are a large and important class of biopolymers. They include non-ribosomally synthesised peptides, post-translationally modified proteins, expressed or synthesised proteins containing unnatural amino acids, and peptides and proteins that are chemically modified. Here, we describe a general procedure for generating atomic descriptions required to incorporate ncAAs within popular NMR structure determination software such as CYANA, CNS, Xplor-NIH and ARIA. This procedure is made publicly available via the existing Automated Topology Builder (ATB) server (https://atb.uq.edu.au, last access: 17 February 2023) with all submitted ncAAs stored in a dedicated database. The described procedure also includes a general method for linking of sidechains of amino acids from CYANA templates. To ensure compatibility with other systems, atom names comply with IUPAC guidelines. In addition to describing the workflow, 3D models of complex natural products generated by CYANA are presented, including vancomycin. In order to demonstrate the manner in which the templates for ncAAs generated by the ATB can be used in practice, we use a combination of CYANA and CNS to solve the structure of a synthetic peptide designed to disrupt Alzheimer-related protein-protein interactions. Automating the generation of structural templates for ncAAs will extend the utility of NMR spectroscopy to studies of more complex biomolecules, with applications in the rapidly growing fields of synthetic biology and chemical biology. The procedures we outline can also be used to standardise the creation of structural templates for any amino acid and thus have the potential to impact structural biology more generally.

States and changes-of-state in the semantics of result roots

A major challenge for event structural theories that decompose verbs into event templates and roots relates to the syntactic distribution of roots and what types of event structures roots can be integrated into. Ontological Approaches propose roots fall into semantic classes, such as manner versus result, which determine root distribution (Rappaport Hovav and Levin 1998, 2010). Free Distribution Approaches, in contrast, hold that root distribution is not constrained by semantic content and roots are free to integrate into various types of event structures (Borer 2005; Acedo-Matellán and Mateu 2014). We focus on two different classes of verbs classified as result verbs in Rappaport Hovav and Levin’s (1998, 2010) sense and their ability to appear in resultative constructions. We build on Beavers and Koontz-Garboden’s (2012, 2020) proposal that the roots underlying these verbs fall into two classes: property concept roots, which denote relations between individuals and states, and change-of-state roots, which on our proposal, denote relations between individuals and events of change. We show that change-of-state roots, but not property concept roots, are able to appear in the modifier position of resultative constructions by providing naturally occurring examples of such resultatives. Combining the proposed lexical semantics of these two classes of roots with a reformulation of an Ontological Approach solely dependent on a root’s semantic type, we show that this analysis makes novel and accurate predictions about the possibility of the two classes of roots appearing in resultative constructions and the range of interpretations available when change-of-state roots are integrated into resultative event structure templates.

Integrating comparative modeling and accelerated simulations reveals conformational and energetic basis of actomyosin force generation

Muscle contraction is performed by arrays of contractile proteins in the sarcomere. Serious heart diseases, such as cardiomyopathy, can often be results of mutations in myosin and actin. Direct characterization of how small changes in the myosin-actin complex impact its force production remains challenging. Molecular dynamics (MD) simulations, although capable of studying protein structure-function relationships, are limited owing to the slow timescale of the myosin cycle as well as a lack of various intermediate structures for the actomyosin complex. Here, employing comparative modeling and enhanced sampling MD simulations, we show how the human cardiac myosin generates force during the mechanochemical cycle. Initial conformational ensembles for different myosin-actin states are learned from multiple structural templates with Rosetta. This enables us to efficiently sample the energy landscape of the system using Gaussian accelerated MD. Key myosin loop residues, whose substitutions are related to cardiomyopathy, are identified to form stable or metastable interactions with the actin surface. We find that the actin-binding cleft closure is allosterically coupled to the myosin motor core transitions and ATP-hydrolysis product release from the active site. Furthermore, a gate between switch I and switch II is suggested to control phosphate release at the prepowerstroke state. Our approach demonstrates the ability to link sequence and structural information to motor functions.

Synthetic peptides for the precise transportation of proteins of interests to selectable subcellular areas.

Proteins, as gifts from nature, provide structure, sequence, and function templates for designing biomaterials. As first reported here, one group of proteins called reflectins and derived peptides were found to present distinct intracellular distribution preferences. Taking their conserved motifs and flexible linkers as Lego bricks, a series of reflectin-derivates were designed and expressed in cells. The selective intracellular localization property leaned on an RMs (canonical conserved reflectin motifs)-replication-determined manner, suggesting that these linkers and motifs were constructional fragments and ready-to-use building blocks for synthetic design and construction. A precise spatiotemporal application demo was constructed in the work by integrating RLNto2 (as one representative of a synthetic peptide derived from RfA1) into the Tet-on system to effectively transport cargo peptides into nuclei at selective time points. Further, the intracellular localization of RfA1 derivatives was spatiotemporally controllable with a CRY2/CIB1 system. At last, the functional homogeneities of either motifs or linkers were verified, which made them standardized building blocks for synthetic biology. In summary, the work provides a modularized, orthotropic, and well-characterized synthetic-peptide warehouse for precisely regulating the nucleocytoplasmic localization of proteins.

Typology and Modeling Profiles of Moving-Class Process-Entity Interactions: Core Types, Relationships, Constraints and Subschemas

Most of scientific research that are immediately concerned with the development of domain digital models, to one degree or another, is aimed at the derivation of reference conceptual and logical constructions covering all pertinent classes of interactions in which real-world objects with concomitant constraints can be involved. This work is directed to forming the core of a structural template that models facts — instances of associates that arise during the movement (transportation) of freights. The multiple alternatives and high variability of any processes logic, including moving-class processes, make their complete unification problematic. Nevertheless, one can come down to process modeling from a system-wide perspective, focusing on the capture of universal permanent processes components, such as source and output sets of objects, associations and constraints. The reality exhibits examples of hierarchical coherence of any classes of generalized processes, which in their sequential development break up into several self-sufficient processes distributed between organizational, calendar and implementation phases. The main focus of the work is on the sequential (from simple to complex) configuration of the structural core of process-entity interactions in the organizational phase, covering route segments, transport and freights, as well as the study of constraints on permissible instances of links incoming into the corresponding associative complex. Conceptual diagrams are presented in simplified and thorough formats. In a simplified format, multi-valued dependencies are modeled by means of weak entities and relators. In a thorough format, weak entities and relators have been replaced with documentary types, the structures of which contain an eXhaustive set of information about all objects, including auXiliary ones that are involved in interactions. The paper also considers the influence of the environment that is represented by classifying sets on the content of bounded relationships operating between the entity and process types. We have ascertained, formalized and described all constraints appearing in the organizational phase of generalized transport process including new constraint kind — split dependent link, resulting from the formation of cycles in conceptual constructions. Similar cycles contain and link together split, entity and (or) process types.

Isothermal exponential amplification reactions triggered by circular templates (cEXPAR) targeting miRNA.

Isothermal exponential amplification reaction (EXPAR) is an emerging amplification technique that is most frequently used to amplify microRNA (miRNA). However, EXPAR also exhibits non-specific background amplification in the absence of the targeted sequence, which limits the attainable assay sensitivity of EXPAR. A novel modified isothermal EXPAR based on circular amplification templates (cEXPAR) was developed in this study. The circular template consists of two same linear fragments that complement the target sequence, and these two linear fragments are separated by two nicking agent recognition sequences (NARS). Compared with the linear structure template, this circular template allows DNA or RNA fragments to be randomly paired with two repeated sequences and can be successfully amplified. This reaction system developed in this study could rapidly synthesize short oligonucleotide fragments (12-22bp) through simultaneous nicking and displacement reactions. Highly sensitive chain reactions can be specifically triggered by as low as a single copy of target molecule, and non-specific amplification can be effectively eliminated in this optimized system. Moreover, the proposed approach applied to miRNA test can discriminate single-nucleotide variations between miRNAs. The newly developed cEXPAR assay provides a useful alternative tool for rapid, sensitive, and highly specific detection of miRNAs.

Recognition of “Oxygen-/Water-Fueled” PET-RAFT Protocol Matched to Covalent Organic Frameworks

The reactive oxygen species (ROS)-mediated photoinduced electron transfer reversible addition-fragmentation chain transfer (PET-RAFT) process is an attractive tool to enhance the oxygen tolerance of radical polymerization systems. In this paper, we investigate the relationship between the covalent organic framework (COF) structure and polymerization performance based on the O2•–/H2O system by modulating the COF at atomic and molecular levels. We combine density functional theory (DFT) calculations and experiments to clarify the “oxygen-/water-fueled” PET-RAFT polymerization mechanism and identify the key steps of the protocol. Based on the modulation of the TD-1 COF template structure, the relatively efficient charge–hole separation efficiency allows the matching of TD-2 COF and TD-3 COF with the O2•–/H2O system to achieve high-quality RAFT polymerization, providing insights into the rational design and development of catalytic systems with better performance.