A Variety of Nucleic Acid Species Are Sensed by cGAS, Implications for Its Diverse Functions.

Cyclic GMP-AMP synthase (cGAS) recognizes double-stranded DNA (dsDNA) derived from invading pathogens and induces an interferon response via activation of the key downstream adaptor protein stimulator of interferon genes (STING). This is the most classic biological function of the cGAS-STING signaling pathway and is critical for preventing pathogenic microorganism invasion. In addition, cGAS can interact with various types of nucleic acids, including cDNA, DNA : RNA hybrids, and circular RNA, to contribute to a diverse set of biological functions. An increasing number of studies have revealed an important relationship between the cGAS-STING signaling pathway and autophagy, cellular senescence, antitumor immunity, inflammation, and autoimmune diseases. This review details the mechanism of action of cGAS as it interacts with different types of nucleic acids, its rich biological functions, and the potential for targeting this pathway to treat various diseases.

Global Substance Registration System: consistent scientific descriptions for substances related to health.

The US Food and Drug Administration (FDA) and the National Center for Advancing Translational Sciences (NCATS) have collaborated to publish rigorous scientific descriptions of substances relevant to regulated products. The FDA has adopted the global ISO 11238 data standard for the identification of substances in medicinal products and has populated a database to organize the agency's regulatory submissions and marketed products data. NCATS has worked with FDA to develop the Global Substance Registration System (GSRS) and produce a non-proprietary version of the database for public benefit. In 2019, more than half of all new drugs in clinical development were proteins, nucleic acid therapeutics, polymer products, structurally diverse natural products or cellular therapies. While multiple databases of small molecule chemical structures are available, this resource is unique in its application of regulatory standards for the identification of medicinal substances and its robust support for other substances in addition to small molecules. This public, manually curated dataset provides unique ingredient identifiers (UNIIs) and detailed descriptions for over 100 000 substances that are particularly relevant to medicine and translational research. The dataset can be accessed and queried at https://gsrs.ncats.nih.gov/app/substances.

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.

The AMOEBA polarizable atomic multipole force field for nucleic acids is presented. Valence and electrostatic parameters were determined from high-level quantum mechanical data, including structures, conformational energy, and electrostatic potentials, of nucleotide model compounds. Previously derived parameters for the phosphate group and nucleobases were incorporated. A total of over 35 µs of condensed-phase molecular dynamics simulations of DNA and RNA molecules in aqueous solution and crystal lattice were performed to validate and refine the force field. The solution and/or crystal structures of DNA B-form duplexes, RNA duplexes, and hairpins were captured with an average root-mean-squared deviation from NMR structures below or around 2.0 Å. Structural details, such as base pairing and stacking, sugar puckering, backbone and χ-torsion angles, groove geometries, and crystal packing interfaces, agreed well with NMR and/or X-ray. The interconversion between A- and B-form DNAs was observed in ethanol-water mixtures at 328 K. Crystal lattices of B- and Z-form DNA and A-form RNA were examined with simulations. For the RNA tetraloop, single strand tetramers, and HIV TAR with 29 residues, the simulated conformational states, 3 J-coupling, nuclear Overhauser effect, and residual dipolar coupling data were compared with NMR results. Starting from a totally unstacked/unfolding state, the rCAAU tetranucleotide was folded into A-form-like structures during ∼1 µs molecular dynamics simulations.

Medical Devices; Clinical Chemistry and Clinical Toxicology Devices; Classification of the Reagents for Molecular Diagnostic Instrument Test Systems. Final order.

The Food and Drug Administration (FDA or we) is classifying the reagents for molecular diagnostic instrument test systems into class I (general controls). We are taking this action because we have determined that classifying the device into class I (general controls) will provide a reasonable assurance of safety and effectiveness of the device. We believe this action will also enhance patients' access to beneficial innovative devices, in part by reducing regulatory burdens.

The Nucleic Acid Database: new features and capabilities.

The Nucleic Acid Database (NDB) (http://ndbserver.rutgers.edu) is a web portal providing access to information about 3D nucleic acid structures and their complexes. In addition to primary data, the NDB contains derived geometric data, classifications of structures and motifs, standards for describing nucleic acid features, as well as tools and software for the analysis of nucleic acids. A variety of search capabilities are available, as are many different types of reports. This article describes the recent redesign of the NDB Web site with special emphasis on new RNA-derived data and annotations and their implementation and integration into the search capabilities.

Comparison of viremia of type II porcine reproductive and respiratory syndrome virus in naturally infected pigs by zip nucleic acid probe-based real-time PCR.

BACKGROUND: Porcine reproductive and respiratory syndrome virus (PRRSV) is a RNA virus with high genetic variation. This virus causes significant economic losses in most pig-producing countries. The clinical presentation of PRRSV ranges from asymptomatic to devastating. In this study, we developed a sensitive and specific zip nucleic acid probe-based real-time PCR assay to evaluate the viremia of natural PRRSV-infected pigs in Taiwan. Serum samples were collected from 577 pigs aged 5-12 weeks. These include 444 clinically healthy pigs and 133 symptomatic pigs were confirmed to have porcine respiratory disease complex (PRDC). RESULTS: Viremia was quantified in 79 of the 444 (17.8%) clinically healthy pigs and in 112 of the 133 (84.2%) PRDC cases. Viremias were significantly more common in pigs with PRDC compared with the clinically healthy pigs (P <0.0001). These results suggest that a high viral load is a major feature of PRRSV-affected pigs. CONCLUSIONS: ZNA probe-based real-time PCR can be a useful tool to diagnose symptomatic and asymptomatic PRRSV-infected pigs. The presence of this marker in a sample of animals with high PRRSV loads (>10(4.2) PRRSV genomes/µl of serum) seems to indicate that it correlates with the presence of PRDC in pigs.

An extended IUPAC nomenclature code for polymorphic nucleic acids.

UNLABELLED: The International Union of Pure and Applied Chemistry (IUPAC) code specified nearly 25 years ago provides a nomenclature for incompletely specified nucleic acids. However, no system currently exists that allows for the informatics representation of the relative abundance at polymorphic nucleic acids (e.g. single nucleotide polymorphisms) in a single specified character, or a string of characters. Here, I propose such an information code as a natural extension to the IUPAC nomenclature code, and present some potential uses and limitations to such a code. The primary anticipated use of this extended nomenclature code is to assist in the representation of the rapidly growing space of information in human genetic variation. CONTACT: johnsonad2@nhlbi.nih.gov SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Simplicity, function, and legibility in an enhanced ambigraphic nucleic acid notation.

We previously showed that an ambigraphic nucleic acid notation, based on symmetrical lowercase Roman characters, permits users to complement DNA by physically rotating the sequence text 180 degrees . This article describes an enhanced ambigraphic notation, which uses concept-related symbol design, rather than the arbitrary set of symbols that constitute the Roman alphabet, to logically encode the four DNA bases and 11 ambiguity characters. As ambigrams, the symbols continue to permit the rapid derivation of complementary sequences and visualization of palindromic DNA. In addition, the new AmbiScript notation uses legibility principles to support the identification of sequence polymorphism and improves writing efficiency by requiring fewer strokes per character than the International Union of Pure and Applied Chemistry (IUPAC) notation.

Molecular methods for assessing insect parasitism.

Determining insect parasitism rates is problematic due to the small size and lack of useful distinguishing morphological characters of many parasitoid taxa. To solve this problem, entomologists have employed one of four general methods to detect parasitoid protein or nucleic acid markers: serological assay; random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR); allozyme electrophoresis; or specific PCR. Serological methods, especially with monoclonal antibodies, are unrivalled for specificity, enabling discrimination at the stage as well as species level. However, they have not found favour with many workers, possibly due to complexity and expense. RAPD-PCR has been widely used, but can only be recommended for restricted applications because of its poor reproducibility. Allozyme electrophoresis provides reproducible detection and discrimination of closely related species. Specific-PCR is highly specific and reproducible, and also has the shortest latency for detection, usually 24 h or less after parasitization. The substantial existing literature on allozyme electrophoresis and specific PCR is used to support recommendations on what are apt to be fruitful enzyme systems or genomic regions for detecting and discriminating parasitoids in untried parasitoid-host assemblages.

GapCoder automates the use of indel characters in phylogenetic analysis.

BACKGROUND: Several ways of incorporating indels into phylogenetic analysis have been suggested. Simple indel coding has two strengths: (1) biological realism and (2) efficiency of analysis. In the method, each indel with different start and/or end positions is considered to be a separate character. The presence/absence of these indel characters is then added to the data set. ALGORITHM: We have written a program, GapCoder to automate this procedure. The program can input PIR format aligned datasets, find the indels and add the indel-based characters. The output is a NEXUS format file, which includes a table showing what region each indel characters is based on. If regions are excluded from analysis, this table makes it easy to identify the corresponding indel characters for exclusion. DISCUSSION: Manual implementation of the simple indel coding method can be very time-consuming, especially in data sets where indels are numerous and/or overlapping. GapCoder automates this method and is therefore particularly useful during procedures where phylogenetic analyses need to be repeated many times, such as when different alignments are being explored or when various taxon or character sets are being explored. GapCoder is currently available for Windows from http://www.home.duq.edu/~youngnd/GapCoder.

Taxonomy workbench.

UNLABELLED: At advanced stages of working with user-defined protein and gene sequence collections, it is frequently necessary to link these data to the taxonomic tree and to extract subsets in accordance with taxonomic considerations. Since no general automatic tools had been available, this was a tedious manual effort. Our taxonomy workbench allows processing of sequence sets, mapping of these sets onto the taxonomic tree, collection of taxonomic subsets from them and printing of the whole tree or some part of it. As a side effect, the system enables queries to and navigation within the taxonomy database. AVAILABILITY: An implementation of the taxonomy workbench is accessible for public use as a www-service at http://mendel.imp.univie.ac.at/taxonomy/. Software components for the command-line and for the www-version are available on request. CONTACT: Georg.Schneider@nt.imp.univie.ac.at; Frank.Eisenhaber@nt.imp.univie.ac.at SUPPLEMENTARY INFORMATION: Documentation for the taxonomy workbench can be accessed at http://mendel.imp.univie.ac.at/taxonomy/help.html.

TrExML: a maximum-likelihood approach for extensive tree-space exploration.

MOTIVATION: Maximum-likelihood analysis of nucleotide and amino acid sequences is a powerful approach for inferring phylogenetic relationships and for comparing evolutionary hypotheses. Because it is a computationally demanding and time-consuming process, most algorithms explore only a minute portion of tree-space, with the emphasis on finding the most likely tree while ignoring the less likely, but not significantly worse, trees. However, when such trees exist, it is equally important to identify them to give due consideration to the phylogenetic uncertainty. Consequently, it is necessary to change the focus of these algorithms such that near optimal trees are also identified. RESULTS: This paper presents the Advanced Stepwise Addition Algorithm for exploring tree-space and two algorithms for generating all binary trees on a set of sequences. The Advanced Stepwise Addition Algorithm has been implemented in TrExML, a phylogenetic program for maximum-likelihood analysis of nucleotide sequences. TrExML is shown to be more effective at finding near optimal trees than a similar program, fastDNAml, implying that TrExML offers a better approach to account for phylogenetic uncertainty than has previously been possible. A program, TreeGen, is also described; it generates binary trees on a set of sequences allowing for extensive exploration of tree-space using other programs. AVAILABILITY: TreeGen, TrExML, and the sequence data used to test the programs are available from the following two WWW sites: http://whitetail.bemidji.msus. edu/trexml/and http://jcsmr.anu.edu.au/dmm/humgen.+ ++html.

Validation of nuclear magnetic resonance structures of proteins and nucleic acids: hydrogen geometry and nomenclature.

A statistical analysis is reported of 1,200 of the 1,404 nuclear magnetic resonance (NMR)-derived protein and nucleic acid structures deposited in the Protein Data Bank (PDB) before 1999. Excluded from this analysis were the entries not yet fully validated by the PDB and the more than 100 entries that contained < 95% of the expected hydrogens. The aim was to assess the geometry of the hydrogens in the remaining structures and to provide a check on their nomenclature. Deviations in bond lengths, bond angles, improper dihedral angles, and planarity with respect to estimated values were checked. More than 100 entries showed anomalous protonation states for some of their amino acids. Approximately 250,000 (1.7%) atom names differed from the consensus PDB nomenclature. Most of the inconsistencies are due to swapped prochiral labeling. Large deviations from the expected geometry exist for a considerable number of entries, many of which are average structures. The most common causes for these deviations seem to be poor minimization of average structures and an improper balance between force-field constraints for experimental and holonomic data. Some specific geometric outliers are related to the refinement programs used. A number of recommendations for biomolecular databases, modeling programs, and authors submitting biomolecular structures are given.

Application of multivariate data analysis methods to comparative molecular field analysis (CoMFA) data: proton affinities and pKa prediction for nucleic acids components.

Multivariate data analysis methods (Principal Component Analysis (PCA) and Partial Least Squares (PLS)) are applied to the analysis of the CoMFA (Comparative Molecular Field Analysis) data for several nucleic acids components. The data set includes nitrogenated bases, nucleosides, linear nucleotides, 3', 5'-cyclic nucleotides and oligonucleotides. PCA is applied to study the structure of the CoMFA data and to detect possible outliers in the data set. PLS is applied to correlate the CoMFA data with either calculated AM1 proton affinities or with experimental pKa values. The possibility of making a prediction of pKa values directly from 3D structures of the monomers for polynucleotides is also shown. The influence of the superposition criteria and of conformational changes along the glycosidic bond on the pKa prediction are studied as well.

Phylogenetic reconstruction using an unsupervised growing neural network that adopts the topology of a phylogenetic tree.

We propose a new type of unsupervised, growing, self-organizing neural network that expands itself by following the taxonomic relationships that exist among the sequences being classified. The binary tree topology of this neutral network, contrary to other more classical neural network topologies, permits an efficient classification of sequences. The growing nature of this procedure allows to stop it at the desired taxonomic level without the necessity of waiting until a complete phylogenetic tree is produced. This novel approach presents a number of other interesting properties, such as a time for convergence which is, approximately, a lineal function of the number of sequences. Computer simulation and a real example show that the algorithm accurately finds the phylogenetic tree that relates the data. All this makes the neural network presented here an excellent tool for phylogenetic analysis of a large number of sequences.

Neural networks for molecular sequence classification.

A neural network classification method has been developed as an alternative approach to the search/organization problem of large molecular databases. Two artificial neural systems have been implemented on a Cray supercomputer for rapid protein/nucleic acid sequence classifications. The neural networks used are three-layered, feed-forward networks that employ back-propagation learning algorithm. The molecular sequences are encoded into neural input vectors by applying an n-gram hashing method or a SVD (singular value decomposition) method. Once trained with known sequences in the molecular databases, the neural system becomes an associative memory capable of classifying unknown sequences based on the class information embedded in its neural interconnections. The protein system, which classifies proteins into PIR (Protein Identification Resource) superfamilies, showed a 82% to a close to 100% sensitivity at a speed that is about an order of magnitude faster than other search methods. The pilot nucleic acid system, which classifies ribosomal RNA sequences according to phylogenetic groups, has achieved a 100% classification accuracy. The system could be used to reduce the database search time and help organize the molecular sequence databases. The tool is generally applicable to any databases that are organized according to family relationships.

StrateGene: object-oriented programming in molecular biology.

This paper describes some of the ways that object-oriented programming methodologies have been used to represent and manipulate biological information in a working application. When running on a Xerox 1100 series computer, StrateGene functions as a genetic engineering workstation for the management of information about cloning experiments. It represents biological molecules, enzymes, fragments, and methods as classes, subclasses, and members in a hierarchy of objects. These objects may have various attributes, which themselves can be defined and classified. The attributes and their values can be passed from the classes of objects down to the subclasses and members. The user can modify the objects and their attributes while using them. New knowledge and changes to the system can be incorporated relatively easily. The operations on the biological objects are associated with the objects themselves. This makes it easier to invoke them correctly and allows generic operations to be customized for the particular object.