Comparison of biochemical and molecular genetic approaches for identification of environmental strains

In order to confirm the taxonomic position of environmental strains determined based on their biochemical, cultural, and morphological characteristics, molecular genetic identification was carried out. A number of problems in identification of microorganisms were shown to be associated with contamination of the cultures in the course of isolation. Advantages of a comprehensive approach—combining 16S rRNA gene sequencing with a set of biochemical, cultural, and morphological parameters—for identification of microorganisms isolated from environmental objects and clinical samples are discussed.     

Scrapie: uncertainties, biology and molecular approaches

The study of the biology of scrapie in sheep is irretrievably associated with the genetics of the PrP gene in sheep. Control of susceptibility and resistance is so closely linked to certain alleles of the sheep PrP gene that no review on scrapie can avoid PrP genetics. Before the importance of PrP protein was discovered and before the influence of the gene itself on disease incidence was understood, it was clear there were some sheep which were more susceptible to natural scrapie than others and that this feature was heritable. These early observations have led to the development and use of PrP genotyping in sheep in what is probably the biggest genetic selection process ever attempted. The accompanying increase in surveillance has also discovered a novel type of scrapie, the subject of much speculation about its origin.     

Combining genetic and biochemical approaches to identify functional molecular contact points

Protein-protein interactions are required for many viral and cellular functions and are potential targets for novel therapies. Here we detail a series of genetic and biochemical techniques used in combination to find an essential molecular contact point on the duck hepatitis B virus polymerase. These techniques include differential immunoprecipitation, mutagenesis and peptide competition. The strength of these techniques is their ability to identify contact points on intact proteins or protein complexes employing functional assays. This approach can be used to aid identification of putative binding sites on proteins and protein complexes which are resistant to characterization by other methods.     

The biology of coral metamorphosis: molecular responses of larvae to inducers of settlement and metamorphosis

Like many other cnidarians, corals undergo metamorphosis from a motile planula larva to a sedentary polyp. In some sea anemones such as Nematostella this process is a smooth transition requiring no extrinsic stimuli, but in many corals it is more complex and is cue-driven. To better understand the molecular events underlying coral metamorphosis, competent larvae were treated with either a natural inducer of settlement (crustose coralline algae chips/extract) or LWamide, which bypasses the settlement phase and drives larvae directly into metamorphosis. Microarrays featuring > 8000 Acropora unigenes were used to follow gene expression changes during the 12 h period after these treatments, and the expression patterns of specific genes, selected on the basis of the array experiments, were investigated by in situ hybridization. Three patterns of expression were common—an aboral pattern restricted to the searching/settlement phase, a second phase of aboral expression corresponding to the beginning of the development of the calicoblastic ectoderm and continuing after metamorphosis, and a later orally-restricted pattern.     

Synthetic biology approaches to improve biocatalyst identification in metagenomic library screening

There is a growing demand for enzymes with improved catalytic performance or tolerance to process‐specific parameters, and biotechnology plays a crucial role in the development of biocatalysts for use in industry, agriculture, medicine and energy generation. Metagenomics takes advantage of the wealth of genetic and biochemical diversity present in the genomes of microorganisms found in environmental samples, and provides a set of new technologies directed towards screening for new catalytic activities from environmental samples with potential biotechnology applications. However, biased and low level of expression of heterologous proteins in Escherichia coli together with the use of non‐optimal cloning vectors for the construction of metagenomic libraries generally results in an extremely low success rate for enzyme identification. The bottleneck arising from inefficient screening of enzymatic activities has been addressed from several perspectives; however, the limitations related to biased expression in heterologous hosts cannot be overcome by using a single approach, but rather requires the synergetic implementation of multiple methodologies. Here, we review some of the principal constraints regarding the discovery of new enzymes in metagenomic libraries and discuss how these might be resolved by using synthetic biology methods.     

Digital reviews in molecular biology: approaches to structured digital publication

MOTIVATION: It is widely appreciated that it is no longer possible for biomedical research scientists to keep up with as much of what is published in their field as they ought. One solution to this problem is to increase the efficiency of information use by moving away from the classical browsing model for scientific information dissemination towards an information on demand model which would allow researchers to access information quickly and efficiently only as they need it. The most common approach to this goal has been to use information retrieval technology to improve access to text databases of biomedical information. We are interested in exploring an alternative; encoding this information for storage in structured databases for efficient retrieval. RESULTS: Two small databases described here are test beds for development of structured digital publication software; the Tumor Gene Database, containing information about genes which are the sites for cancer-causing mutations, and the Mammary Transgene Database, containing information about expression of transgenes in agriculturally important animals. Both have been successfully searched by users and edited by curators via the World Wide Web.     

Systems biology approaches to study the molecular effects of caloric restriction and polyphenols on aging processes

Worldwide population is aging, and a large part of the growing burden associated with age-related conditions can be prevented or delayed by promoting healthy lifestyle and normalizing metabolic risk factors. However, a better understanding of the pleiotropic effects of available nutritional interventions and their influence on the multiple processes affected by aging is needed to select and implement the most promising actions. New methods of analysis are required to tackle the complexity of the interplay between nutritional interventions and aging, and to make sense of a growing amount of -omics data being produced for this purpose. In this paper, we review how various systems biology-inspired methods of analysis can be applied to the study of the molecular basis of nutritional interventions promoting healthy aging, notably caloric restriction and polyphenol supplementation. We specifically focus on the role that different versions of network analysis, molecular signature identification and multi-omics data integration are playing in elucidating the complex mechanisms underlying nutrition, and provide some examples on how to extend the application of these methods using available microarray data.

Electronic supplementary material

The online version of this article (doi:10.1007/s12263-015-0508-9) contains supplementary material, which is available to authorized users.     

Elucidating the molecular mechanisms underlying cellular response to biophysical cues using synthetic biology approaches

ABSTRACT

The use of synthetic surfaces and materials to influence and study cell behavior has vastly progressed our understanding of the underlying molecular mechanisms involved in cellular response to physicochemical and biophysical cues. Reconstituting cytoskeletal proteins and interfacing them with a defined microenvironment has also garnered deep insight into the engineering mechanisms existing within the cell. This review presents recent experimental findings on the influence of several parameters of the extracellular environment on cell behavior and fate, such as substrate topography, stiffness, chemistry and charge. In addition, the use of synthetic environments to measure physical properties of the reconstituted cytoskeleton and their interaction with intracellular proteins such as molecular motors is discussed, which is relevant for understanding cell migration, division and structural integrity, as well as intracellular transport. Insight is provided regarding the next steps to be taken in this interdisciplinary field, in order to achieve the global aim of artificially directing cellular response.     

Complementary approaches of cytogenetics and molecular biology to the taxonomy and study of speciation processes in lemurs

The lemurs, prosimian primates of Madagascar, constitute a zoological group containing numerous species and subspecies. Their taxonomy remains controversial. Depending on the authors and the techniques they have used, the number of species varies between 39 and 52. In addition, although a monophyletic origin of the settlement of Madagascar is the most commonly held opinion, recent studies based on molecular biology do not exclude two independent colonization events, one involving Daubentonia and a second giving rise to the other lemurs. 1 .     

Dialectics, systems biology and embryonic induction

A hallmark of embryonic development is the temporal-spatial continuum of cell-cell interactions, which gives rise to the trajectory of progressive cell differentiations. Despite the great reductionists' success in dissecting the mechanistic basis of developmental processes, the call for more holistic system theories never ceased during the last century. Various system theories were proposed to provide a more adequate understanding of biological systems, including development. Although widely ignored by modern biology, the first systematic system theory was Hegel's dialectics. Here I examine the process of embryonic induction as elaborated by Hans Spemann in the light of dialectics. I conclude that embryonic induction and its underlying molecular mechanisms can be re-interpreted in terms of Hegel's dialectics. The example highlights that despite its shortcomings, dialectics can be of heuristic value as a theory of systems biology.     

Characteristics of the energy-transducing NADH-quinone oxidoreductase ofParacoccus denitrificans as revealed by biochemical,biophysical, and molecular biological approaches

A comparison of the mitochondrial NADH-ubiquinone oxidoreductase and the energy-transducing NADH-quinone oxidoreductase (NDH-1) ofParacoccus denitrificans revealed that both systems have similar electron-transfer and energy-transduction pathways. In addition, both complexes are sensitive to the same inhibitors and contain similar electron carriers, suggesting that theParacoccus NDH-1 may serve as a useful model system for the study of the human enzyme complex. The gene cluster encoding theParacoccus NDH-1 has been cloned and sequenced. It is composed of 18,106 base pairs and contains 14 structural genes and six unidentified reading frames (URFs). The structural genes, URFs, and their polypeptides have been characterized. We also discuss nucleotide sequences which are believed to play a role in the regulation of the NDH-1 gene cluster andParacoccus NDH-1 subunits which may contain the binding sites of substrates and/or electron carriers.     

生物信息学在A型流感病毒研究中的应用

生物信息学是随着人类基因组计划(Human genome project,HGP)的启动而发展起来的一门新兴学科。1995年,在HGP第一个五年总结报告中,给出了较为完整的定义:生物信息学是一门交叉科     

Comparison of different biochemical and molecular methods for the identification of Vibrio parahaemolyticus

AIMS: Multicentre evaluation of biochemical and molecular methods for the identification of Vibrio parahaemolyticus. METHODS AND RESULTS: For the biochemical identification methods, API 20E and API 20NE and Alsina's scheme were evaluated in intra- and interlaboratory tests in order to determine the accuracy and concordance of each method. Both in intra- and interlaboratory tests, the Alsina's scheme showed the highest sensitivity (86% of correct identifications in the interlaboratory test). False-positive results were obtained by all methods (specificity was 95% for API 20E, 73% for API 20NE and 84% for Alsina's scheme) and concordance varied from 65% of API 20NE to 84% of API 20E. For the molecular identifications, polymerase chain reaction (PCR) for the detection of toxR gene, tl gene and pR72H fragment were tested on 30 strains by two laboratories. The PCR for toxR showed the highest inclusivity (96%), exclusivity (100%) and concordance (97%). CONCLUSIONS: Among the biochemical identification methods tested, the Alsina's scheme gave more reliable results; however, in order to avoid false-positive results, all the biochemical identifications should be confirmed by means of molecular methods. SIGNIFICANCE AND IMPACT OF THE STUDY: Availability of an efficient identification method of Vibrio parahaemolyticus to use in official control of fisheries products.     

Cytochemical and immunological approaches to plant cell biology

Book Review

Cytochemical and immunological approaches to plant cell biologyE.L. Vigil and C. Hawes (Eds.), Academic Press, 1989. 152 pages. £14.95. ISBN 0-12-721930-7     

Systems and synthetic biology approaches to cell division

Cells proliferate by division into similar daughter cells, a process that lies at the heart of cell biology. Extensive research on cell division has led to the identification of the many components and control elements of the molecular machinery underlying cellular division. Here we provide a brief review of prokaryotic and eukaryotic cell division and emphasize how new approaches such as systems and synthetic biology can provide valuable new insight.