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Algorithms for the search of amino acid patterns in nucleic acid sequences.

Some algorithms are described for the search of regions in a nucleic acid sequence that, when translated into amino acids, are homologous to a given amino acid pattern. All algorithms are modifications of the dynamic programming method for sequence comparison such that the translation of codons is taken into account. One of the algorithms has been implemented as a FORTRAN 77 program. The program operates on files that follow the format of the EMBL Nucleotide Sequence Data Library.

Amino Acid Sequence

Multiple sequence alignment with hierarchical clustering.

An algorithm is presented for the multiple alignment of sequences, either proteins or nucleic acids, that is both accurate and easy to use on microcomputers. The approach is based on the conventional dynamic-programming method of pairwise alignment. Initially, a hierarchical clustering of the sequences is performed using the matrix of the pairwise alignment scores. The closest sequences are aligned creating groups of aligned sequences. Then close groups are aligned until all sequences are aligned in one group. The pairwise alignments included in the multiple alignment form a new matrix that is used to produce a hierarchical clustering. If it is different from the first one, iteration of the process can be performed. The method is illustrated by an example: a global alignment of 39 sequences of cytochrome c.

Algorithms

An RNA secondary structure workbench.

A multiple approach to the study of RNA secondary structure is described which provides for the independent drawing of structures using base-pairing lists, for the generation of local structures in the form of hairpins, and for the generation of global structures by both Monte Carlo and dynamic programming methodologies. User-adjustable parameters provide for limiting the size of hairpin loops, bulges and inner loops, and constraints can be imposed relative to position-dependent base pairing.

Algorithms

Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information.

This paper presents a new computer method for folding an RNA molecule that finds a conformation of minimum free energy using published values of stacking and destabilizing energies. It is based on a dynamic programming algorithm from applied mathematics, and is much more efficient, faster, and can fold larger molecules than procedures which have appeared up to now in the biological literature. Its power is demonstrated in the folding of a 459 nucleotide immunoglobulin gamma 1 heavy chain messenger RNA fragment. We go beyond the basic method to show how to incorporate additional information into the algorithm. This includes data on chemical reactivity and enzyme susceptibility. We illustrate this with the folding of two large fragments from the 16S ribosomal RNA of Escherichia coli.

Base Composition

Crystallographic studies of a calcium binding lysozyme from equine milk at 2.5 A resolution.

The crystal structure of a calcium binding equine lysozyme has been determined at 2.5 A resolution by means of molecular replacement. The energy minimized equine lysozyme as the starting model, was refined with the molecular dynamics program, X-PLOR, and the R factor of the current model was found to be 24% without any water molecules. The conformation of the calcium binding loop is similar to that of alpha-lactalbumin. The profiles of backbone atomic displacements throughout the lysozyme and alpha-lactalbumin superfamilies are comparable as well as their homologous tertiary structures.

Amino Acid Sequence

Search for the stable state of a short chain in a molecular field.

A general approach is developed to search for stable structures of short chain fragments (e.g. of loops or bound oligopeptides) in a given molecular field. This molecular field is produced by the remaining part of a globule or by any other surface with a defined spatial structure. The fragment must be short enough to have no pronounced long-range interactions within itself. The method is illustrated by calculation of the 3-D structures of two loops of bovine pancreatic trypsin inhibitor (BPTI). Computations are based on a lattice model of conformational space and on strict and fast algorithms of 1-D statistical mechanics and dynamic programming (which are very similar in essence). This makes a search of oligopeptide structures only several times (and not several orders of magnitude) longer than that of a dipeptide.

Algorithms

A new approach to the design of a sequence with the highest affinity for a molecular surface.

We describe an algorithm to design the primary structures for peptides which must have the strongest binding to a given molecular surface. This problem cannot be solved by a direct combinatorial sorting, because of an enormous number of possible primary and spatial structures. The approach to solve this problem is to describe a state of each residue by two variables: (i) amino acid type and (ii) 3-D coordinate, and to minimize binding energy over all these variables simultaneously. For short chains which have no long-range interactions within themselves, this minimization can be done easily and efficiently by dynamic programming. We also discuss the problem of how to estimate specificity of binding and how to deduce a sequence with maximal specificity for a given surface. We show that this sequence can be deduced by the same algorithm after some modification of energetic parameters.

Algorithms

Investigating milk-derived extracellular vesicles as mediators of maternal stress and environmental intervention.

Parental communication signals are transmitted through nursing and critically shape neurodevelopmental trajectories. Mirroring some well characterized effects of gestational challenges in rodents, maternal immune activation (MIA) during the lactational period disrupts maternal physiology, decreases lipid content, and is associated with adverse neurobehavioral outcomes in offspring. This occurs without MIA significantly affecting maternal care. While gestational MIA models are responsive to environmental interventions, which beneficially alter maternal milk composition and associated offspring outcomes, the bioactive mediators in milk underlying resilience remain poorly understood. Milk-derived extracellular vesicles (MEVs) transport and deposit biologically active cargo, including microRNAs (miRNAs) that induce post-translational regulation of candidate mRNA in the nursing offspring's tissues and cells. Using a rat model, we show that lactational MIA alters MEV-miRNA cargo and the expression of hippocampal miRNAs in offspring. Several miRNAs in MEVs were also found in the hippocampus of matching offspring. Remarkably, the miRNA changes in MEVs and the neonatal hippocampus were rescued when dams were raised in an enriched environment, suggesting environmental enrichment protected from the effects of MIA. This was supported by the behavioral phenotype. RNA-seq of adult offspring hippocampus showed long-term transcriptional changes associated with the gene targets of early-life regulated miRNAs. Our results position MEV-miRNA as dynamic programming signals by which maternal experience is communicated to offspring, encoding both stress-induced and protective cues that influence development. This suggests that breastfeeding interventions can regulate the genetic cargo of the milk, programming the life of developing infants.

Journal Article

k-mer-based Upstream Preprocessing of long reads for Isoform Discovery.

Eukaryotic genes can encode multiple protein isoforms based on alternative splicing of their transcribed regions. Most modern novel isoform discovery methods function by identifying and assembling exon splice junctions from an RNA-seq sample. However, splice junctions can only be accurately annotated with time-intensive dynamic programming alignment. This manuscript introduces KuPID, a method for preprocessing long RNA-seq reads with the goal of better identifying novel isoform transcripts. KuPID utilizes k-mer sketching as a prefilter to quickly pseudo-align reads to known reference isoforms. Full alignment need only then be applied to reads that are most relevant to isoform discovery. Not only does KuPID speed up the discovery pipeline, it also increases downstream accuracy by filtering out extraneous reads. KuPID preprocessing simultaneously increases the f1 accuracy of isoform discovery pipelines by up to 11.6 points while decreasing the runtime by a factor of 2-3×;. An optional mode permits a KuPID sample to be paired with both isoform discovery and transcript quantification.

Journal Article

Temporal feature extraction and clustering analysis of electromyographic linear envelopes in gait studies.

A technique for automatically clustering linear envelopes of the EMG during gait has been developed which uses a temporal feature representation and a maximum peak matching scheme. This new technique provides a viable way to define compact and meaningful EMG waveform features. The envelope matching is performed by dynamic programming, providing qualitatively the largest numbers of matched peaks and quantitatively a minimum distance measurement. The resulting averaged EMG profiles have low statistical variation and can serve as templates for EMG comparison and further classification.

Algorithms

Numerical experiments with a new differentiation filter.

A dynamic programming filter which provides estimates of the first and second derivative of empirical displacement data is investigated numerically. This filter uses a weighted least squares criteria in estimating the derivatives. The filter equations are presented together with several numerical examples. These examples are taken from references that proposed other techniques.

Biomechanical Phenomena

Automated detection of the tongue surface in sequences of ultrasound images.

An image processing system has been developed for a Macintosh II personal computer. It is designed to process sequences of sagittal tongue sections that are digitized in real time and stored in standard tagged image file format (TIFF). The successive processing steps are: (a) a low-pass filter for noise reduction, (b) a resampling of the sector of interest in polar coordinates, (c) a matched filter (vertical differentiator) for the enhancement of the tissue/air interface in the surface region of the tongue, and (d) an extraction of border points by searching for an optimal radial path along the angular dimension. This latter task is achieved by dynamic programming, which has the following advantages. First, due to the use of a global criterion to guide the detection, it is very robust. Second, as a result of certain restrictions of the allowable transitions, the extracted contours are smooth. Finally, the method permits the specification of particular predefined contour points. This system was implemented in a program that can handle image sequences in a fully automatic mode. Results obtained using ultrasound data are presented.

Humans

Conformational study of the cembranoid sarcophytol A, a potent anti-tumor-promoter.

Conformational analysis of the marine cembranoid sarcophytol A (1a), a potent anti-tumor promoter, was carried out using a newly introduced molecular mechanic and molecular dynamic program Discover. Four minimum-energy conformations were derived, in accordance with a previous results of the epoxidation of 1a, which afforded 7R,8R/7S,8S- and 11R,12R/11S,12S-epoxide pairs. The most stable conformation was the one having C-19 and C-20 directed opposite to C-18, with respect to the average plane of the fourteen-membered ring. X-Ray crystallography of sarcophytol A alpha-methoxy-alpha-trifluoromethylphenylacetate (1c) was carried out simultaneously. This confirmed the 14S absolute configuration of 1a but the conformation of crystalline 1c did not correspond to any of the four minimum-energy conformers of 1a.

Crystallization

[A rapid method of searching for homology of nucleic acid sequences].

A new method of the homology search between DNA sequences was suggested. This method may be used to find extensive and not strong homologies with point mutations and deletions. The computer time to compare sequences is less than dynamic program algorithms at least by four orders of magnitude. It makes possible to use the method for homology search all over the nucleotide bank by personal computers. Some results of homology search are presented.

Algorithms

Induction of common patterns of polypeptide synthesis and phosphorylation by calcium and 12-O-tetradecanoylphorbol-13-acetate in mouse epidermal cell culture.

Terminal differentiation can be induced in cultured basal cells by either increasing the Ca2+ level in the medium from 0.05 to 1.4 mM or by exposure to the tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA). If Ca2+ and TPA act by a common mechanism, then a common pattern of protein synthesis and/or phosphorylation would be expected. Computer-assisted analysis of radioactively labeled polypeptides separated by two-dimensional-polyacrylamide gel electrophoresis was utilized to study protein synthesis and phosphorylation. Within 1 h of increasing the Ca2+ level in the medium, the synthesis of 57 polypeptides was altered by 2-fold or more. Similarly, exposure to TPA for 1 h affected the synthesis of 106 polypeptides. Sixteen polypeptides were affected by both Ca2+ and TPA; the synthesis of nine was increased and seven was decreased, with changes in the same direction for both effectors. By 4 h, the synthesis of 32 polypeptides was similarly modulated by both Ca2+ and TPA. Only one polypeptide which was increased at 1 h was still elevated at 4 h. These results suggest that a common dynamic program of protein synthesis, likely to be related to terminal keratinocyte differentiation, is induced by both Ca2+ and TPA. Overall phosphorylation of epidermal proteins was increased after 30 min of TPA treatment, but was not increased by Ca2+ at this time. Keratin polypeptides were heavily phosphorylated in low Ca2+ medium, but the level or pattern of phosphorylation of these proteins was not altered by either Ca2+ or TPA. Although phosphorylation of a minor polypeptide (pI 5.1/Mr 45,000) was increased 2-3-fold by both Ca2+ and TPA, most of the specific protein phosphorylation changes induced in keratinocytes by Ca2+ and TPA appear to be unique. Thus, if protein phosphorylation is an early signal for epidermal differentiation by each effector, only a single apparent common substrate is involved and multiple kinases are activated. Alternatively, substrate specificity of a single kinase may be differentially altered by each effector.

Animals

Redistribution of arterial blood flow in metastases-bearing livers after infusion of degradable starch microspheres.

Changes in intrahepatic arterial blood flow after intraarterial injection of degradable starch microspheres (DSM) were studied in four patients undergoing hepatic arterial chemotherapy. All four livers contained metastases, three from colorectal cancer and one from melanoma. Using a CT scanner with a dynamic program, 8 mm liver sections were studied in each patient before and after the DSM infusion (180(-6) in 3 min). Density plots were obtained from 12 tumoral and 12 parenchymal areas after 5 ml push arterial injections of nonionic contrast medium. The areas under the curves (ID) were calculated. The ID after DSM infusion was reduced by 94% in a single hyperdense colorectal metastasis and by a mean of c. 82% in ten parenchymal areas. By contrast, nine hypodense colorectal metastases showed an average ID decrease of c. 156%. The ID of two melanoma metastases was reduced after DSM (-48% and -68%), while the ID of two matched parenchymal areas showed an approximately similar degree of increase (+36% and +64%). Since ID after contrast injection can be assumed to be a function of blood volume, mutual changes of parenchymal and tumoral blood flow appear to take place in metastases-bearing liver after arterial infusion of DSM. This phenomenon may be of diagnostic and therapeutic value for intraarterial chemotherapy of liver tumors.

Antineoplastic Agents

[Tasks in planning biological experiments].

The paper describes certain cases of using mathematical methods in the planning of biological experiments. The paper presents an algorithm of the distribution of the experimental data based on dynamic programming. The paper discusses an application of computer-aided calculations for the formation of homogeneous groups of experimental and control tests.

Animals