Dihedral-based segment identification and classification of biopolymers II: polynucleotides.

In an accompanying paper (Nagy, G.; Oostenbrink, C. Dihedral-based segment identification and classification of biopolymers I: Proteins. J. Chem. Inf. Model. 2013, DOI: 10.1021/ci400541d), we introduce a new algorithm for structure classification of biopolymeric structures based on main-chain dihedral angles. The DISICL algorithm (short for DIhedral-based Segment Identification and CLassification) classifies segments of structures containing two central residues. Here, we introduce the DISICL library for polynucleotides, which is based on the dihedral angles ε, ζ, and χ for the two central residues of a three-nucleotide segment of a single strand. Seventeen distinct structural classes are defined for nucleotide structures, some of which--to our knowledge--were not described previously in other structure classification algorithms. In particular, DISICL also classifies noncanonical single-stranded structural elements. DISICL is applied to databases of DNA and RNA structures containing 80,000 and 180,000 segments, respectively. The classifications according to DISICL are compared to those of another popular classification scheme in terms of the amount of classified nucleotides, average occurrence and length of structural elements, and pairwise matches of the classifications. While the detailed classification of DISICL adds sensitivity to a structure analysis, it can be readily reduced to eight simplified classes providing a more general overview of the secondary structure in polynucleotides.

Dihedral-based segment identification and classification of biopolymers I: proteins.

A new structure classification scheme for biopolymers is introduced, which is solely based on main-chain dihedral angles. It is shown that by dividing a biopolymer into segments containing two central residues, a local classification can be performed. The method is referred to as DISICL, short for Dihedral-based Segment Identification and Classification. Compared to other popular secondary structure classification programs, DISICL is more detailed as it offers 18 distinct structural classes, which may be simplified into a classification in terms of seven more general classes. It was designed with an eye to analyzing subtle structural changes as observed in molecular dynamics simulations of biomolecular systems. Here, the DISICL algorithm is used to classify two databases of protein structures, jointly containing more than 10 million segments. The data is compared to two alternative approaches in terms of the amount of classified residues, average occurrence and length of structural elements, and pair wise matches of the classifications by the different programs. In an accompanying paper (Nagy, G.; Oostenbrink, C. Dihedral-based segment identification and classification of biopolymers II: Polynucleotides. J. Chem. Inf. Model. 2013, DOI: 10.1021/ci400542n), the analysis of polynucleotides is described and applied. Overall, DISICL represents a potentially useful tool to analyze biopolymer structures at a high level of detail.

Nanocellulose-based composites and bioactive agents for food packaging.

Global environmental concern, regarding the use of petroleum-based packaging materials, is encouraging researchers and industries in the search for packaging materials from natural biopolymers. Bioactive packaging is gaining more and more interest not only due to its environment friendly nature but also due to its potential to improve food quality and safety during packaging. Some of the shortcomings of biopolymers, such as weak mechanical and barrier properties can be significantly enhanced by the use of nanomaterials such as nanocellulose (NC). The use of NC can extend the food shelf life and can also improve the food quality as they can serve as carriers of some active substances, such as antioxidants and antimicrobials. The NC fiber-based composites have great potential in the preparation of cheap, lightweight, and very strong nanocomposites for food packaging. This review highlights the potential use and application of NC fiber-based nanocomposites and also the incorporation of bioactive agents in food packaging.

Análisis de las polihidroxialcanoato sintasas (PhaC1 y PhaC2) en una cepa de Pseudomonas fluorescens IBUN S1602, aislada en suelos colombianos / Analysis of polyhydroxyalkanoate synthases (PhaC1 and PhaC2) in a strain of Pseudomonas fluorescens IBUN S1602 isolated from Colombian soil

La cepa Pseudomonas fluorescens IBUN S1602 conforma el grupo de aislamientos provenientes de suelos colombianos de caña de azúcar, que acumula polihidrioxialcanoato (PHA), fue seleccionada como promisoria para escalamiento comercial por tener afinidad por sustratos alternativos y económicos como el glicerol, aceites usados, suero de leche, entre otros. Dada la importancia de la enzima sintasa en la síntesis de los PHAs, en el presente trabajo se realizó el análisis molecular de los genes phaC1 y phaC2 que codifican las enzimas sintasas tipo II (PhaC1 y PhaC2). Para la obtención de los amplímeros requeridos en la secuenciación, se utilizó la técnica de PCR bajo condiciones estandarizadas para iniciadores diseñados reportados en las bases de datos. Se identificaron dos fragmentos de 1680 pb y 1683 pb correspondientes a phaC1 y phaC2. El análisis comparativo de las secuencias proteicas resultantes de estos genes demuestra que la sintasa IBUN S1602 contiene la región α/β hidrolasa y 8 residuos de aminoácidos conservados, que son características de las sintasas examinadas a nivel mundial. Se analizó la estructura enzimática a nivel primario y se predijo la secundaria. Se concluyó que las sintasas de la cepa Pseudomonas fluorescens IBUN S1602 presentan alta homología con las sintasas tipo II que se reportan para Pseudomonas. Los resultados obtenidos contribuyen al entendimiento básico de la biosíntesis de PHA, la cual permitirá, en un futuro, el aumento de la calidad de PHA debida a la modulación del nivel de sintasa que se exprese en un organismo recombinante, con el fin de variar el peso molecular del biopolímero, propiedad esencial en el estudio de aplicaciones industriales.

The strain Pseudomonas fluorescens IBUN S1602 forms the group of isolates from colombian sugarcane soil´s, which accumulates polyhydroxyalkanoate biopolymer (PHA) and was selected as promising for commercial scale by having affinity for economic and alternative substrates such as glycerol, oils, whey, among others. Given the importance of the synthase enzyme in the synthesis of PHAs, was realized the molecular analysis of genes phaC1 and phaC2 which encode type II synthases (PhaC1 y PhaC2). To obtain the amplimers required in the sequencing, was used the PCR technique under standardized conditions for primers designed based on the updated review in databases. Were identified two fragments of 1680 bp and 1683 bp for phaC1 and phaC2. Comparative analysis of the resulting protein sequences of these genes shows that the IBUN S1602 synthases containing the region α/β hydrolase and 8 conserved amino acid residues that are characteristic of synthases examined worldwide. Enzyme structure was analyzed at the primary level and was predicted the secondary. It is concluded that synthase strain Pseudomonas fluorescens IBUN S1602 has high homology with type II synthases that are reported for Pseudomonas. The results contribute to basic understanding of the biosynthesis of PHA, and will allow in the future, increasing the quality of PHA due to modulation of the level of synthase is expressed in a recombinant organism, in order to vary the weight molecular biopolymer, an essential property in the study of industrial applications.

Bromoisobutyramide as an intermolecular surface binder for the preparation of free-standing biopolymer assemblies.

Bromoisobutyramide (BrIBAM)-modified silica templates facilitate the formation of bio-functional thin films made of a range of biopolymers (e.g., polypeptides, nucleic acids or polysaccharides). Upon template removal, non-covalent free-standing biopolymeric assemblies (e.g., hollow capsules or replicated spheres and fibers) are formed without the need for covalent cross-linking.

BioExtract server--an integrated workflow-enabling system to access and analyze heterogeneous, distributed biomolecular data.

Many in silico investigations in bioinformatics require access to multiple, distributed data sources and analytic tools. The requisite data sources may include large public data repositories, community databases, and project databases for use in domain-specific research. Different data sources frequently utilize distinct query languages and return results in unique formats, and therefore researchers must either rely upon a small number of primary data sources or become familiar with multiple query languages and formats. Similarly, the associated analytic tools often require specific input formats and produce unique outputs which make it difficult to utilize the output from one tool as input to another. The BioExtract Server (http://bioextract.org) is a Web-based data integration application designed to consolidate, analyze, and serve data from heterogeneous biomolecular databases in the form of a mash-up. The basic operations of the BioExtract Server allow researchers, via their Web browsers, to specify data sources, flexibly query data sources, apply analytic tools, download result sets, and store query results for later reuse. As a researcher works with the system, their "steps" are saved in the background. At any time, these steps can be preserved long-term as a workflow simply by providing a workflow name and description.

[Classification and the composition of food fibers].

Fiber promotes the contractions that keep food moving through the intestine. Also, high-fiber foods expand the inside walls of the colon and eases the passage of waste. The food and fiber research was conducted. In the article, the classification and the composition of food fibers are presented. Multifunctional properties of food fiber in the process of digestion are discussed. The physiological value of food fibers for the human organism is stressed. Diets high in fiber during the entire life are recommended. If a person can't consume enough fiber in diet alone, certain stool softening and bulking agents are recommended. They can be very useful in preventing and treating digestive tract disorders. The analysis of high fiber food sources and world production and consumption of food fiber is also presented.

Natural-origin polymers as carriers and scaffolds for biomolecules and cell delivery in tissue engineering applications.

The present paper intends to overview a wide range of natural-origin polymers with special focus on proteins and polysaccharides (the systems more inspired on the extracellular matrix) that are being used in research, or might be potentially useful as carriers systems for active biomolecules or as cell carriers with application in the tissue engineering field targeting several biological tissues. The combination of both applications into a single material has proven to be very challenging though. The paper presents also some examples of commercially available natural-origin polymers with applications in research or in clinical use in several applications. As it is recognized, this class of polymers is being widely used due to their similarities with the extracellular matrix, high chemical versatility, typically good biological performance and inherent cellular interaction and, also very significant, the cell or enzyme-controlled degradability. These biocharacteristics classify the natural-origin polymers as one of the most attractive options to be used in the tissue engineering field and drug delivery applications.

Prospects for biopolymer production in plants.

It is likely that during this century polymers based on renewable materials will gradually replace industrial polymers based on petrochemicals. This chapter gives an overview of the current status of research on plant biopolymers that are used as a material in non-food applications. We cover technical and scientific bottlenecks in the production of novel or improved materials, and the potential of using transgenic or alternative crops in overcoming these bottlenecks. Four classes of biopolymers will be discussed: starch, proteins, natural rubber, and poly-beta-hydroxyalkanoates. Renewable polymers produced by chemical polymerization of monomers derived from sugars, vegetable oil, or proteins, are not considered here.

A framework for scientific data modeling and automated software development.

MOTIVATION: The lack of standards for storage and exchange of data is a serious hindrance for the large-scale data deposition, data mining and program interoperability that is becoming increasingly important in bioinformatics. The problem lies not only in defining and maintaining the standards, but also in convincing scientists and application programmers with a wide variety of backgrounds and interests to adhere to them. RESULTS: We present a UML-based programming framework for the modeling of data and the automated production of software to manipulate that data. Our approach allows one to make an abstract description of the structure of the data used in a particular scientific field and then use it to generate fully functional computer code for data access and input/output routines for data storage, together with accompanying documentation. This code can be generated simultaneously for different programming languages from a single model, together with, for example for format descriptions and I/O libraries XML and various relational databases. The framework is entirely general and could be applied in any subject area. We have used this approach to generate a data exchange standard for structural biology and analysis software for macromolecular NMR spectroscopy. AVAILABILITY: The framework is available under the GPL license, the data exchange standard with generated subroutine libraries under the LGPL license. Both may be found at http://www.ccpn.ac.uk; http://sourceforge.net/projects/ccpn CONTACT: ccpn@mole.bio.cam.ac.uk.

Ligand Depot: a data warehouse for ligands bound to macromolecules.

UNLABELLED: Ligand Depot is an integrated data resource for finding information about small molecules bound to proteins and nucleic acids. The initial release (version 1.0, November, 2003) focuses on providing chemical and structural information for small molecules found as part of the structures deposited in the Protein Data Bank. Ligand Depot accepts keyword-based queries and also provides a graphical interface for performing chemical substructure searches. A wide variety of web resources that contain information on small molecules may also be accessed through Ligand Depot. AVAILABILITY: Ligand Depot is available at http://ligand-depot.rutgers.edu/. Version 1.0 supports multiple operating systems including Windows, Unix, Linux and the Macintosh operating system. The current drawing tool works in Internet Explorer, Netscape and Mozilla on Windows, Unix and Linux.

Electrophoretic data classification for phylogenetics and biostatistics.

SUMMARY: This paper presents ClassMaker, a macro of MS Excel able to classify continuous data of molecular weight data as binary (1/0) values. The output is represented by a binary matrix, which can be introduced in every software application for phylogenetics or multivariate statistics. This application is designed in order to be a link between image analysis programs and statistical or phylogenetic applications, in order to produce a complete series of free programs able to carry out the complete analysis from the gel to the dendrogram. AVAILABILITY: ClassMaker is freely available from http://www.agr.unipg.it/cardinali/index.html, where a list of the URLs from which programs of image analysis, statistics and phylogenetics can be freely downloaded.

Dynamics of living polymers.

We study theoretically the dynamics of living polymers which can add and subtract monomer units at their live chain ends. The classic example is ionic living polymerization. In equilibrium, a delicate balance is maintained in which each initiated chain has a very small negative average growth rate ("velocity") just sufficient to negate the effect of growth rate fluctuations. This leads to an exponential molecular weight distribution (MWD) with mean N. After a small perturbation of relative amplitude epsilon, e.g. a small temperature jump, this balance is destroyed: the velocity acquires a boost greatly exceeding its tiny equilibrium value. For epsilon > epsilonc approximately equal to 1/N(1/2) the response has 3 stages: (1) Coherent chain growth or shrinkage, leaving a highly non-linear hole or peak in the MWD at small chain lengths. During this episode, lasting time tau(fast) approximately N, the MWD's first moment and monomer concentration m relax very close to equilibrium. (2) Hole-filling (or peak decay) after tau(fill) approximately epsilon2N2. The absence or surfeit of small chains is erased. (3) Global MWD shape relaxation after tau(slow) approximately N2. By this time second and higher MWD moments have relaxed. During episodes (2) and (3) the fast variables (N, m) are enslaved to the slowly varying number of free initiators (chains of zero length). Thus fast variables are quasi-statically fine-tuned to equilibrium. The outstanding feature of these dynamics is their ultrasensitivity: despite the perturbation's linearity, the response is non-linear until the late episode (3). For very small perturbations, epsilon < epsilonc, response remains non-linear but with a less dramatic peak or hole during episode (1). Our predictions are in agreement with viscosity measurements on the most widely studied system, alpha-methylstyrene.

Production and mass transfer characteristics of non-Newtonian biopolymers for biomedical applications.

The market for microbial biopolymers is currently expanding to include several emerging biomedical applications. Specifically, these applications are drug delivery and wound healing. A fundamental understanding of the key fermentation parameters is necessary in order to optimize the production of these biopolymers. Considering that most microbial biopolymer systems exhibit non-Newtonian rheology, oxygen mass transfer can be an important parameter to optimize and control. In this article, we present a critical review of recent advances in rheological and mass transfer characteristics of selected biopolymers of commercial interest in biomedical applications.

Fermentation of chicory fructo-oligosaccharides in mixtures of different degrees of polymerization by three strains of bifidobacteria.

We estimated and compared the action of three selected strains of bifidobacteria in a semi-synthetic medium for different degrees of polymerization of fructo-oligosaccharides contained in three commercial products derived from chicory inulin: Fibrulose F97 (shorter chains), Fibruline Instant (native chains), Fibruline LC (longer chains). Biomass and production of lactate and acetate were greater when the substrate contained mostly shorter chain fructo-oligosaccharides. Shorter chains were first to be consumed, and one strain could use longer chains. As the degree of polymerization increased, residual fructo-oligosaccharides increased after growth of the strains, and the rate of consumption of fructo-oligosaccharides decreased.

Predicting properties of intrinsically unstructured proteins.

There is increasing evidence that intrinsically unstructured proteins or protein domains have important biological functions. These types of proteins may be productively analyzed using polymer theory developed to predict global physical properties of polymers. In these theories molecular detail is "coarse grained" out of the models, and replaced with a small number of parameters that characterize the polymer. This reduction in complexity allows extremely large systems to be studied. In the case of simulations, the time scales accessible also increase significantly. Here we discuss the application of polymer theory to unstructured proteins, and consider how to classify proteins within a polymer framework. We then review polymer theory that is relevant to predicting functionally important properties, such as radius of gyration, height of a polymer brush and force required to compress a polymer brush.

Interspecific comparison in the frequency of concerted evolution at the polyubiquitin gene locus.

The polyubiquitin gene, encoding tandemly repeated multiple ubiquitins, constitutes a uniquitin gene subfamily. It has been demonstrated that polyubiquitin genes are subject to concerted evolution; namely, the individual ubiquitin coding units contained within a polyubiquitin gene are more similar to one another than they are to the ubiquitin coding units in the orthologous gene from other species. However there has been no comprehensive study on the concerted evolution of polyubiquitin genes in a wide range of species, because the relationships (orthologous or paralogous) among multiple polyubiquitin genes from different species have not been extensively analyzed yet. In this report, we present the results of analyzing the nucleotide sequence of polyubiquitin genes of mammals, available in the DDBJ/EMBL/GenBank nucleotide sequence databases, in which we found that there are two groups of polyubiquitin genes in an orthologous relationship. Based on this result, we analyzed the concerted evolution of the polyubiquitin gene in various species and compared the frequency of concerted evolutionary events interspecifically by taking into consideration that the rate of synonymous substitution at the polyubiquitin gene locus may vary depending on species. We found that the concerted evolutionary events in polyubiquitin genes have been more frequent in rats and Chinese hamsters than those in humans, cows, and sheep. The guinea pig polyubiquitin gene was an intermediate example. The frequency of concerted evolution in the mouse gene was unexpectedly low compared to that of other rodent genes.

Pattern recognition and classification of images of biological macromolecules using artificial neural networks.

The goal of this work was to analyze an image data set and to detect the structural variability within this set. Two algorithms for pattern recognition based on neural networks are presented, one that performs an unsupervised classification (the self-organizing map) and the other a supervised classification (the learning vector quantization). The approach has a direct impact in current strategies for structural determination from electron microscopic images of biological macromolecules. In this work we performed a classification of both aligned but heterogeneous image data sets as well as basically homogeneous but otherwise rotationally misaligned image populations, in the latter case completely avoiding the typical reference dependency of correlation-based alignment methods. A number of examples on chaperonins are presented. The approach is computationally fast and robust with respect to noise. Programs are available through ftp.