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PubMed1996

Compact encoding strategies for DNA sequence similarity search.

Determining whether two DNA sequences are similar is an essential component of DNA sequence analysis. Dynamic programming is the algorithm of choice if computational time is not the most important consideration. Heuristic search tools, such as BLAST, are computationally more efficient, but they may miss some of the sequence similarities (Altschul et al., 1990). These tools often use common k-tuples (words) between the two sequences to determine anchor points for the alignment, and spend most of their computational time extending the alignment beyond these anchor points. We discuss and provide a DNA sequence similarity search implementation (called SENSEI) that improves upon the performance of BLASTN by almost an order of magnitude for comparable sensitivity. This improvement is a result of using compactly encoded scoring tables for k-tuples, encoding bases with a single bit, filtering the sequence to remove the simple sequence repeats using XNUN, and masking the known species-specific repeats in the query sequence. To reduce memory requirements, especially for large genomic DNA query sequences, we recommend generating the neighborhood words from the target sequence at run-time, instead of generating them by preprocessing the query sequence.

Base Sequence↗
PubMed1997

Hierarchical protein structure superposition using both secondary structure and atomic representations.

The structural comparison of proteins has become increasingly important as a means to identify protein motifs and fold families. In this paper we present a new algorithm for the comparison of proteins based on a hierarchy of structural representations, from the secondary structure level to the atomic level. Our technique represents alpha-helices and beta-strands as vectors and uses a set of seven scoring functions to compare pairs of vectors from different proteins. The scores obtained are used in a dynamic programming algorithm that finds the best local alignment of the two sets of vectors. The second step in our algorithm is based on the atomic coordinates of the protein structures and improves the initial vector alignment by iteratively minimizing the RMSD between pairs of nearest atoms from the two proteins. We refine the final alignment by determining a core of well aligned atoms and minimizing the RMSD of this core. In a comparison of our method to Holm and Sander's DALI algorithm, our program was able to detect structural similarity at the same level as DALI. We also performed searches of a representative set of the Protein Data Bank (PDB) using our program and detected structurally similarity between several distantly related proteins.

Algorithms↗
PubMed1997

Integrating database homology in a probabilistic gene structure model.

We present an improved stochastic model of genes in DNA, and describe a method for integrating database homology into the probabilistic framework. A generalized hidden Markov model (GHMM) describes the grammar of a legal parse of a DNA sequence. Probabilities are estimated for gene features by using dynamic programming to combine information from multiple sensors. We show how matches to homologous sequences from a database can be integrated into the probability estimation by interpreting the likelihood of a sequence in terms of the bit-cost to encode a sequence given a homology match. We also demonstrate how homology matches in protein databases can be exploited to help identify splice sites. Our experiments show significant improvements in the sensitivity and specificity of gene structure identification when these new features are added to our gene-finding system, Genie. Experimental results in tests using a standard set of annotated genes showed that Genie identified 95% of coding nucleotides correctly with a specificity of 91%, and 77% of exons were identified exactly.

Algorithms↗
PubMed1998

Process models for production of beta-lactam antibiotics.

Great progress has been made in the modelling of biotechnical processes using filamentous microorganisms. This paper deals with cultivations of Penicillium chrysogenum for the production of Penicillin and of Acremonium chrysogenum for the production of Cephalosporin C. The properties of the processes and the existing models are reviewed. Models are presented for both processes that consider aspects which are important for industrial cultivation. The process model for Penicillin production is based on a detailed morphological description of growth of hyphal filaments and pellets. The model allows for simulation of the production process including the preculture and considering the inhomogenous pellet population. It opens new possibilities for understanding the complex kinetics of the process and improvement of its control. The structured segregated model for Cephalosporin C production considers soy oil as second carbon source besides sugar. The application of the model for dynamic optimization of feeding strategies by Iterative Dynamic Programming is demonstrated. As an alternative approach, modelling of the Cephalosporin production by an artificial neural network is discussed.

Acremonium↗
PubMed1998

Sequence assembly validation by multiple restriction digest fragment coverage analysis.

DNA sequence analysis depends on the accurate assembly of fragment reads for the determination of a consensus sequence. This report examines the possibility of analyzing multiple, independent restriction digests as a method for testing the fidelity of sequence assembly. A dynamic programming algorithm to determine the maximum likelihood alignment of error prone electrophoretic mobility data to the expected fragment mobilities given the consensus sequence and restriction enzymes is derived and used to assess the likelihood of detecting rearrangements in genomic sequencing projects. The method is shown to reliably detect errors in sequence fragment assembly without the necessity of making reference to an overlying physical map. An html form-based interface is available at http:/(/)www.ibc.wustl.edu/services/validate. html.

Algorithms↗
PubMed1998

Curve matching on brain surfaces using Frenet distances.

This paper describes methods for diffeomorphic matching of curves on brain surfaces. Distances between curves are defined by Frenet representation via speed, curvature, and torsion. The curvematching algorithm is based on bipartite graph matching, with weights defined by the Frenet distance over diffeomorphic maps of one curve onto the other (Sedgewick [1983]: Algorithms). We follow Khaneja ([1996]: Statistics and Geometry of Cortical Features) and define fundus curves on the brain surfaces as extremal curvature lines generated using dynamic programming. Examples are shown for fundus curve matchings on macaque brain surfaces.

Algorithms↗
PubMed2006

A stretching program increases the dynamic passive length and passive resistive properties of the calf muscle-tendon unit of unconditioned younger women.

This study examined the effects of a 6-week stretching program on the dynamic passive elastic properties of the calf muscle-tendon unit (MTU) of unconditioned younger women. After random assignment of 12 women (age 18-31 years) to a stretching group (SG) or to a control group (CG), six subjects in the SG and four subjects in the CG completed the study. For the initial tests, a Kin-Com dynamometer moved the ankle from plantarflexion to maximal dorsiflexion (DF) with negligible surface EMG activity in the soleus, gastrocnemius and tibialis anterior muscles. Angular displacement, passive resistive torque, area under the curve (passive elastic energy) and stiffness variables were reduced from the passive DF torque curves. The SG then completed ten static wall stretches held 15 s each, five times a week for 6 weeks, the CG did not. The tests were repeated and the changes between the tests and retests were examined for group differences (Mann-Whitney U). The SG had significant increases in the maximal passive DF angle (7 degrees +/- 4 degrees ), maximal passive DF torque (11.2 +/- 8.3 N m), full stretch range of motion (23 degrees +/- 24 degrees ), full stretch mean torque (3.4 +/- 2.1 N m), and area under the full stretch curve (22.7 +/- 23.5 degrees N m) compared to the CG (P < or = 0.019). The passive stiffness did not change significantly. The results showed that a stretching program for unconditioned calf MTUs increased the maximal DF angle and length extensibility, as well as the passive resistive properties throughout the full stretch range of motion. The adaptations within the calf MTU provide evidence that stretching enhances the dynamic passive length and passive resistive properties in unconditioned younger women.

Adaptation, Physiological↗
PubMed2004

Assessment of an optimized dog-culling program in the dynamics of canine Leishmania transmission.

In Brazil, zoonotic visceral leishmaniasis (ZVL) control programs based on the mass elimination of seropositive dogs have failed to reduce the number of leishmaniasis cases. However, these programs have been done under sub-optimal conditions. We studied a cohort of dogs in an urban area in Brazil to determine, whether a dog-culling program optimized with: (i) replacement of a relatively low-sensitivity indirect immune-fluorescent test on blood eluate by a more sensitive enzyme-linked immunosorbent assay on serum blood samples; (ii) shortening of the time interval from serodiagnosis to removal of dogs; (iii) screening a high proportion of the dog population could reduce the incidence of canine Leishmania infection (CLI). The study ran from December 1997 to July 2000, with four follow-up assessments performed at approximately 8-month intervals. All dogs seropositive for anti-Leishmania antibodies were promptly eliminated. A large number of new dogs immigrated to the study area throughout the study period. They comprised 43.8-49.8% of the cohort at each follow-up assessment, and upto 15% of them already had Leishmania infection. Overall, 42 news cases of CLI were identified, for a crude incidence rate of 11.8 cases per 100 dog-years (95% CI 8.6-15.6). In the first, second, third and fourth follow-up assessments the incidence rates were 8.2 (95% CI 3.0-17.9), 12.2 (95% CI 6.3-21.2), 16.4 (95% CI 8.5-28.6) and 13.6 (95% CI 7.1-23.8), respectively. There was no statistically significant change in these rates throughout the study period. Our results suggest that dog-culling programs do not reduce the incidence of CLI, even with an optimized intervention. Possible reasons for this failure include: currently available serologic methods lack sufficient sensitivity and/or specificity to accurately identify all infected dogs warranting removal in order to prevent Leishmania transmission; destroyed dogs are immediately replaced by susceptible puppies, and quite often, by already infected dogs; and other reservoirs may be involved in maintaining canine infection. Further efforts on ZVL control should be directed to developing new strategies or to testing control methods already in place with properly designed trials.

Animals↗
PubMedDate not supplied

Building integrated approaches for the proteomics of complex, dynamic systems: NIH programs in technology and infrastructure development.

Proteomics technology and methods remain inadequate. Technological constraints contribute to an artificially static view of complex biological systems and a barrier between quantitative and interaction studies. Several NIH programs combine proteomics technology development with research on challenging biological problems to drive progress. A new initiative of the NIH Roadmap focuses on characterization of dynamic systems. The success of these programs will be judged by their impact on relevant biological problems.

Biomedical Research↗
PubMed1996

The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules.

A new program for molecular dynamics (MD) simulation and energy refinement of biological macromolecules, OPAL, is introduced. Combined with the supporting program TRAJEC for the analysis of MD trajectories, OPAL affords high efficiency and flexibility for work with different force fields, and offers a user-friendly interface and extensive trajectory analysis capabilities. Salient features are computational speeds of up to 1.5 GFlops on vector supercomputers such as the NEC SX-3, ellipsoidal boundaries to reduce the system size for studies in explicit solvents, and natural treatment of the hydrostatic pressure. Practical applications of OPAL are illustrated with MD simulations of pure water, energy minimization of the NMR structure of the mixed disulfide of a mutant E. coli glutaredoxin with glutathione in different solvent models, and MD simulations of a small protein, pheromone Er-2, using either instantaneous or time-averaged NMR restraints, or no restraints.

Computer Simulation↗
PubMed2005

Near and far field contamination modeling in a large scale enclosure: Fire Dynamics Simulator comparisons with measured observations.

The occurrence of a fire, no matter how small, often exposes objects to significant levels of contamination from the products of combustion. The production and dispersal of these contaminants has been an issue of relevance in the field of fire science for many years, though little work has been done to examine the contamination levels accumulated within an enclosure some time after an incident. This phenomenon is of great importance when considering the consequences associated with even low level contamination of sensitive materials, such as food, pharmaceuticals, clothing, electrical equipment, etc. Not only does such exposure present a localized hazard, but also the shipment of contaminated goods places distant recipients at risk. It is the intent of this paper to use a well-founded computational fluid dynamic (CFD) program, the Fire Dynamics Simulator (FDS), a large eddy simulation (LES) code developed by National Institute of Standards and Technology (NIST), to model smoke dispersion in order to assess the subject of air contamination and post fire surface contamination in a warehouse facility. Measured results are then compared with the results from the FDS model. Two components are examined: the production rate of contaminates and the trajectory of contaminates caused by the forced ventilation conditions. Each plays an important role in determining the extent to which the products of combustion are dispersed and the levels to which products are exposed to the contaminants throughout the enclosure. The model results indicate a good first-order approximation to the measured surface contamination levels. The proper application of the FDS model can provide a cost and time efficient means of evaluating contamination levels within a defined volume.

Computer Simulation↗
PubMed2026

From immature to mature epithelium: unveiling structural dynamics and transcriptional programs in rainbow trout intestinal barrier.

The intestinal epithelium is crucial for nutrient absorption, immune defense, and barrier function in farmed fish. However, the molecular mechanisms underlying its development and maturation in salmonids remain poorly characterized, hindering our ability to address pervasive gut health challenges in aquaculture. In this study, we use the RTgutGC cell line to implement an epithelial maturation model with the aim of characterizing the global transcriptional program in rainbow trout (Oncorhynchus mykiss). We evaluated in vitro culture conditions to generate a polarized epithelial barrier with high transepithelial electrical resistance (TEER&#x2009;=&#x2009;75.8 &#x3a9;&#x2009;&#xd7;&#x2009;cm2), low permeability (6.2&#x2009;&#xd7;&#x2009;10-6&#xa0;cm/s), and well-defined apical specializations, including microvilli-like structures and clusters of these structures (brush border). Comparative transcriptomic profiling between immature (7&#xa0;days post-seeding, dps) and mature (28 dps) epithelia revealed 3,817 differentially expressed genes (DEGs). Functional enrichment analysis showed that maturation was characterized by the downregulation of proliferative and ribosomal pathways and the concerted upregulation of processes critical for barrier function, including transmembrane transport, proteolysis, cell adhesion, extracellular matrix organization, and tight junction assembly. We identified a core set of 60 genes indicators of epithelial maturation, encompassing solute transporters (slc26a6, slc43a2), tight junction proteins (tjp1, cldn1, cldn3, cldn5, cldn18, among others), and structural components essential for microvilli formation and polarization (cdhr5b, pard6a). By integrating ultrastructural, functional, and transcriptomic data, this study established a framework for future mechanistic investigations into gut development and maturation in vitro. This set of mature epithelium indicators has diverse applications, such as the design of nutritional and pharmacological interventions to improve gut health and resilience in farmed fish.

Animals↗