Science.gov

Sample records for molecular biological application

  1. Application of molecular modeling to biological processing

    NASA Astrophysics Data System (ADS)

    Lowrey, Alfred H.; Famini, George R.; Wick, Charles

    1993-07-01

    Detailed understanding of the molecular basis for biological processes is now available through computational modeling techniques. Advances in computational algorithms and technology allow applications to large biological macromolecules and permits the study of such problems as binding mechanisms, chemical reactivity, structural and conformational effects, and simulations of molecular motions. Recent crystallographic data provides access to detailed structural information that allows analysis and comparison of various computational techniques. Preliminary semiempirical studies on N-acetylneuraminic acid are presented as an example of computational studies on binding mechanisms. N-acetylneuraminic acid is a substituted carbohydrate, which is a recognition site for binding of proteins (i.e., cholera toxin). These calculations provide some insight into electronic effects on bin in a crystal complex and the effect of the molecular charge on hydrogen bonding the crystal complex.

  2. Molecular biology and cytopathology. Principles and applications.

    PubMed

    Schmitt, Fernando C; Vielh, Philippe

    2012-12-01

    Some of the main applications of molecular techniques using cellular materials obtained from tumors by means of non-gynecological exfoliative cytology or fine-needle aspiration are briefly described in this review. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  3. [Application of molecular biological techniques in Taenia identification].

    PubMed

    Li, Yan; Liu, Hang; Yang, Yi-Mei

    2011-10-01

    The traditional identification of Taenia spp. based on morphological features of adult and cysticercus has difficulties in identifying the morphologically similar species. The recent development of molecular techniques provides more scientific ways for distinguishing Taenia species. This paper summarizes the application of molecular biological techniques in the identification of Taenia, such as analysis of DNA sequence, PCR-RFLP and LAMP.

  4. Photoactive molecules for applications in molecular imaging and cell biology.

    PubMed

    Shao, Qing; Xing, Bengang

    2010-08-01

    Photoactive technology has proven successful for non-invasive regulation of biological activities and processes in living cells. With the light-directed generation of biomaterials or signals, mechanisms in cell biology can be investigated at the molecular level with spatial and temporal resolution. In this tutorial review, we aim to introduce the important applications of photoactive molecules for elucidating cell biology on aspects of protein engineering, fluorescence labelling, gene regulation and cell physiological functions.

  5. Structural Biology and Molecular Applications Research

    Cancer.gov

    Part of NCI's Division of Cancer Biology's research portfolio, research and development in this area focuses on enabling technologies, models, and methodologies to support basic and applied cancer research.

  6. Application of Molecular Modeling to Biological Processes

    DTIC Science & Technology

    1993-07-01

    informa- tion. DNA is the storehouse for the information that ultimately governs the synthesis of all biomolecules. It is generally found in the Watson ... Crick double helix . Breakthroughs in computer graphics and simulations have discovered that intercalation of flat aromatic rings is a major mechanism...for mutations.’ 0 Using molecular mechanics, docking studies show that molecules (e.g., acridine) can insert through the edge of the DNA helix . This

  7. Ordinary differential equations with applications in molecular biology.

    PubMed

    Ilea, M; Turnea, M; Rotariu, M

    2012-01-01

    Differential equations are of basic importance in molecular biology mathematics because many biological laws and relations appear mathematically in the form of a differential equation. In this article we presented some applications of mathematical models represented by ordinary differential equations in molecular biology. The vast majority of quantitative models in cell and molecular biology are formulated in terms of ordinary differential equations for the time evolution of concentrations of molecular species. Assuming that the diffusion in the cell is high enough to make the spatial distribution of molecules homogenous, these equations describe systems with many participating molecules of each kind. We propose an original mathematical model with small parameter for biological phospholipid pathway. All the equations system includes small parameter epsilon. The smallness of epsilon is relative to the size of the solution domain. If we reduce the size of the solution region the same small epsilon will result in a different condition number. It is clear that the solution for a smaller region is less difficult. We introduce the mathematical technique known as boundary function method for singular perturbation system. In this system, the small parameter is an asymptotic variable, different from the independent variable. In general, the solutions of such equations exhibit multiscale phenomena. Singularly perturbed problems form a special class of problems containing a small parameter which may tend to zero. Many molecular biology processes can be quantitatively characterized by ordinary differential equations. Mathematical cell biology is a very active and fast growing interdisciplinary area in which mathematical concepts, techniques, and models are applied to a variety of problems in developmental medicine and bioengineering. Among the different modeling approaches, ordinary differential equations (ODE) are particularly important and have led to significant advances

  8. Research Applications of Proteolytic Enzymes in Molecular Biology

    PubMed Central

    Mótyán, János András; Tóth, Ferenc; Tőzsér, József

    2013-01-01

    Proteolytic enzymes (also termed peptidases, proteases and proteinases) are capable of hydrolyzing peptide bonds in proteins. They can be found in all living organisms, from viruses to animals and humans. Proteolytic enzymes have great medical and pharmaceutical importance due to their key role in biological processes and in the life-cycle of many pathogens. Proteases are extensively applied enzymes in several sectors of industry and biotechnology, furthermore, numerous research applications require their use, including production of Klenow fragments, peptide synthesis, digestion of unwanted proteins during nucleic acid purification, cell culturing and tissue dissociation, preparation of recombinant antibody fragments for research, diagnostics and therapy, exploration of the structure-function relationships by structural studies, removal of affinity tags from fusion proteins in recombinant protein techniques, peptide sequencing and proteolytic digestion of proteins in proteomics. The aim of this paper is to review the molecular biological aspects of proteolytic enzymes and summarize their applications in the life sciences. PMID:24970197

  9. [Applications of molecular biology in the wine industry].

    PubMed

    Ramón, D; González-Candelas, L; Pérez-González, J A; González, R; Ventura, L; Sánchez-Torres, P; Vallés, S; Piñaga, F; Gallego, M V; Fernández-Espinar, M T

    1995-03-01

    Population dynamics of natural and inoculated industrial wine fermentations have been studied by using a simple molecular biology technique based on mitochondrial DNA restriction analysis profile. The predominance of the inoculated strain in the inoculated fermentations is obvious. A genetic transformation system has been developed for an industrial wine yeast strain named T73. By using this technique, different fungal hydrolases in this industrial strain have been expressed. Problems and benefits of the application of recombinant DNA techniques in wine yeast strains are also discussed here.

  10. Molecular biology techniques and applications for ocean sensing

    NASA Astrophysics Data System (ADS)

    Zehr, J. P.; Hewson, I.; Moisander, P.

    2009-05-01

    The study of marine microorganisms using molecular biological techniques is now widespread in the ocean sciences. These techniques target nucleic acids which record the evolutionary history of microbes, and encode for processes which are active in the ocean today. Molecular techniques can form the basis of remote instrumentation sensing technologies for marine microbial diversity and ecological function. Here we review some of the most commonly used molecular biological techniques. These techniques include the polymerase chain reaction (PCR) and reverse-transcriptase PCR, quantitative PCR, whole assemblage "fingerprinting" approaches (based on nucleic acid sequence or length heterogeneity), oligonucleotide microarrays, and high-throughput shotgun sequencing of whole genomes and gene transcripts, which can be used to answer biological, ecological, evolutionary and biogeochemical questions in the ocean sciences. Moreover, molecular biological approaches may be deployed on ocean sensor platforms and hold promise for tracking of organisms or processes of interest in near-real time.

  11. NANOPARTICLES AND THEIR APPLICATIONS IN CELL AND MOLECULAR BIOLOGY

    PubMed Central

    Wang, Edina C.; Wang, Andrew Z.

    2013-01-01

    Nanoparticles can be engineered with distinctive compositions, sizes, shapes, and surface chemistries to enable novel techniques in a wide range of biological applications. The unique properties of nanoparticles and their behavior in biological milieu also enable exciting and integrative approaches to studying fundamental biological questions. This review will provide an overview of various types of nanoparticles and concepts of targeting nanoparticles. We will also discuss the advantages and recent applications of using nanoparticles as tools for drug delivery, imaging, sensing, and for the understanding of basic biological processes. PMID:24104563

  12. Applications of molecular biology and genetics in endocrinology.

    PubMed

    Kopp, Peter

    2007-09-01

    To review the growing impact of molecular biology and genetics on clinical endocrinology. Medical literature, databases, and Web sites describing genetics and genomic medicine with relevance for clinical endocrinology were reviewed. Many monogenic disorders can now be explained at the molecular level and the diagnosis can be established through mutational analysis. The ability to establish a molecular diagnosis is relevant for carrier detection and genetic counseling. In contrast to the significant advances in monogenic disorders, the current knowledge about the genetic components contributing to the pathogenesis of complex disorders is still relatively modest and is a major focus of current research efforts. Molecular biology already has an important impact on therapy in endocrine disorders. A broad spectrum of recombinant peptides and proteins are used in daily practice, eg, insulin and insulin analogues. Moreover, the increasingly detailed understanding of the molecular pathogenesis of cancer is leading to the development of novel and more specific inhibitors. While genetic testing has many advantages, it is important that physicians and patients are aware of potential limitations. They include, among others, technical limitations and allelic and nonallelic heterogeneity. These limitations need to be discussed in detail with patients and relatives, and it is often useful to involve a genetic counselor before obtaining informed consent by the individuals undergoing testing. Molecular biology and genetics play an increasingly important role for the diagnosis and therapy of endocrine disorders. Challenges for the future include the elucidation of the genetic components contributing to complex disorders, eg, diabetes mellitus type 2, and the development of cheaper and comprehensive DNA sequencing technologies. Lastly, it is important that there is continuing attention directed towards the ethical, social, and legal aspects surrounding genetic medicine.

  13. Medical and molecular biological application in the FELI

    SciTech Connect

    Nishimura, E.; Ogino, S.; Suzuki, T.

    1995-12-31

    Some of the user`s rooms of the FELI have been equipped for medical and molecular biological research. Main subjects are immunological reaction and cell fusion induced by IR FEL. We are beginning to do the preliminary irradiation experiments. The cultured T lymphocytes (Molt-4, human) are irradiated to FEL at wavelength 6.3{mu}m with the power density approximate 500mW/mm{sup 2} for 10 minutes, in the culture media (RPMI-1640) including 10% fetal bovine serum. Swelling and consequent collapse of the cells can be observed, probably due to abrasion of the cell membranes.

  14. Review and application of group theory to molecular systems biology

    PubMed Central

    2011-01-01

    In this paper we provide a review of selected mathematical ideas that can help us better understand the boundary between living and non-living systems. We focus on group theory and abstract algebra applied to molecular systems biology. Throughout this paper we briefly describe possible open problems. In connection with the genetic code we propose that it may be possible to use perturbation theory to explore the adjacent possibilities in the 64-dimensional space-time manifold of the evolving genome. With regards to algebraic graph theory, there are several minor open problems we discuss. In relation to network dynamics and groupoid formalism we suggest that the network graph might not be the main focus for understanding the phenotype but rather the phase space of the network dynamics. We show a simple case of a C6 network and its phase space network. We envision that the molecular network of a cell is actually a complex network of hypercycles and feedback circuits that could be better represented in a higher-dimensional space. We conjecture that targeting nodes in the molecular network that have key roles in the phase space, as revealed by analysis of the automorphism decomposition, might be a better way to drug discovery and treatment of cancer. PMID:21696623

  15. Review and application of group theory to molecular systems biology.

    PubMed

    Rietman, Edward A; Karp, Robert L; Tuszynski, Jack A

    2011-06-22

    In this paper we provide a review of selected mathematical ideas that can help us better understand the boundary between living and non-living systems. We focus on group theory and abstract algebra applied to molecular systems biology. Throughout this paper we briefly describe possible open problems. In connection with the genetic code we propose that it may be possible to use perturbation theory to explore the adjacent possibilities in the 64-dimensional space-time manifold of the evolving genome. With regards to algebraic graph theory, there are several minor open problems we discuss. In relation to network dynamics and groupoid formalism we suggest that the network graph might not be the main focus for understanding the phenotype but rather the phase space of the network dynamics. We show a simple case of a C6 network and its phase space network. We envision that the molecular network of a cell is actually a complex network of hypercycles and feedback circuits that could be better represented in a higher-dimensional space. We conjecture that targeting nodes in the molecular network that have key roles in the phase space, as revealed by analysis of the automorphism decomposition, might be a better way to drug discovery and treatment of cancer.

  16. Molecular biology and its applications in orthodontics and oral and maxillofacial surgery.

    PubMed

    Ren, Yi-jin

    2005-06-01

    Molecular biology is an exciting, rapidly expanding field, which has enabled enormously greater understanding of the biology of diseases and malfunctions in many fields. It chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interrelationship of DNA, RNA and protein synthesis and how these interactions are regulated. Since the introduction of molecular biology into modern science, numerous other fields have been enabled to go "molecular". Advanced molecular biological techniques showed us new avenue towards finding answers to the questions asked for decades. The first part of this article described the history of molecular biology. It started as a joined discipline of other areas of biology, i.e. genetics and biochemistry in the 1930s and 1940s, and enjoyed its classical period and became institutionalized in the 1950s and 1960s. Major molecular techniques manipulating proteins, DNA and RNA were introduced and their mechanisms were concisely illustrated. The current knowledge of molecular biology and their applications in orthodontic and oral and maxillofacial surgery, i.e. osteoclast differentiation and function, regulation of tooth movement, mechanotransduction/cell-signalling, bone fracture healing, oral cancer as well as craniofacial/dental anomalies and distraction osteogenesis were discussed. Although the problems of introducing molecular technologies are still substantial, it is anticipated that the future of medicine/dentistry will be "molecular": molecular prevention, molecular diagnosis and molecular therapy.

  17. Application of mitochondrial DNA polymorphism to meloidogyne molecular population biology.

    PubMed

    Hyman, B C; Whipple, L E

    1996-09-01

    Recent advances in molecular biology have enabled the genotyping of individual nematodes, facilitating the analysis of genetic variability within and among plant-pathogenic nematode isolates. This review first describes representative examples of how RFLP, RAPD, AFLP, and DNA sequence analysis have been employed to describe populations of several phytonematodes, including the pinewood, burrowing, root-knot, and cyst nematodes. The second portion of this paper evaluates the utility of a size-variable mitochondrial DNA locus to examine the genetic structure of Meloidogyne isolates using two alternate methodologies, variable number tandem repeat (VNTR) and repeat associated poiymorphism (RAP) analysis. VNTR analysis has revealed genetic variation among individual nematodes, whereas RAP may provide useful markers for species and population differentiation.

  18. Applications of Discrete Molecular Dynamics in biology and medicine.

    PubMed

    Proctor, Elizabeth A; Dokholyan, Nikolay V

    2016-04-01

    Discrete Molecular Dynamics (DMD) is a physics-based simulation method using discrete energetic potentials rather than traditional continuous potentials, allowing microsecond time scale simulations of biomolecular systems to be performed on personal computers rather than supercomputers or specialized hardware. With the ongoing explosion in processing power even in personal computers, applications of DMD have similarly multiplied. In the past two years, researchers have used DMD to model structures of disease-implicated protein folding intermediates, study assembly of protein complexes, predict protein-protein binding conformations, engineer rescue mutations in disease-causative protein mutants, design a protein conformational switch to control cell signaling, and describe the behavior of polymeric dispersants for environmental cleanup of oil spills, among other innovative applications.

  19. Zsyntax: a formal language for molecular biology with projected applications in text mining and biological prediction.

    PubMed

    Boniolo, Giovanni; D'Agostino, Marcello; Di Fiore, Pier Paolo

    2010-03-03

    We propose a formal language that allows for transposing biological information precisely and rigorously into machine-readable information. This language, which we call Zsyntax (where Z stands for the Greek word zetaomegaeta, life), is grounded on a particular type of non-classical logic, and it can be used to write algorithms and computer programs. We present it as a first step towards a comprehensive formal language for molecular biology in which any biological process can be written and analyzed as a sort of logical "deduction". Moreover, we illustrate the potential value of this language, both in the field of text mining and in that of biological prediction.

  20. Molecular biology of breast cancer stem cells: potential clinical applications.

    PubMed

    Nguyen, Nam P; Almeida, Fabio S; Chi, Alex; Nguyen, Ly M; Cohen, Deirdre; Karlsson, Ulf; Vinh-Hung, Vincent

    2010-10-01

    Breast cancer stem cells (CSC) have been postulated recently as responsible for failure of breast cancer treatment. The purpose of this study is to review breast CSCs molecular biology with respect to their mechanism of resistance to conventional therapy, and to develop treatment strategies that may improve survival of breast cancer patients. A literature search has identified in vitro and in vivo studies of breast CSCs. Breast CSCs overexpress breast cancer resistance protein (BCRP) which allows cancer cells to transport actively chemotherapy agents out of the cells. Radioresistance is modulated through activation of Wnt signaling pathway and overexpression of genes coding for glutathione. Lapatinib can selectively target HER-2 positive breast CSCs and improves disease-free survival in these patients. Metformin may target basal type breast CSCs. Parthenolide and oncolytic viruses are promising targeting agents for breast CSCs. Future clinical trials for breast cancer should include anti-cancer stem cells targeting agents in addition to conventional chemotherapy. Hypofractionation radiotherapy may be indicated for residual disease post chemotherapy.

  1. Zsyntax: A Formal Language for Molecular Biology with Projected Applications in Text Mining and Biological Prediction

    PubMed Central

    Boniolo, Giovanni; D'Agostino, Marcello; Di Fiore, Pier Paolo

    2010-01-01

    We propose a formal language that allows for transposing biological information precisely and rigorously into machine-readable information. This language, which we call Zsyntax (where Z stands for the Greek word ζωή, life), is grounded on a particular type of non-classical logic, and it can be used to write algorithms and computer programs. We present it as a first step towards a comprehensive formal language for molecular biology in which any biological process can be written and analyzed as a sort of logical “deduction”. Moreover, we illustrate the potential value of this language, both in the field of text mining and in that of biological prediction. PMID:20209084

  2. Molecular biology in physiology

    SciTech Connect

    Chien, S.; Gargus, J.J.

    1987-08-01

    The aim of this symposium on molecular biology in physiology was to introduce molecular biology to physiologists who had relatively little exposure to the new developments in this field, so that they can become conversant on this topic and contribute to the advancement of physiology by incorporating molecular biological approaches as a part of their research arsenal. This report is a review of the symposium, which consisted of two four-part sessions. Each session had four papers. After the discussion of the basic concepts, terminology, and methodology used in molecular biology, it was shown how these basic principles have been applied to the study of the genes encoding two membrane proteins that have important transport functions (band 3 and ATPase). The second half of the symposium consisted of papers on the state-of-the-art developments in the application of molecular biology to the studies of the atrial natriuretic factor and renin genes, adenylate cyclase-coupled adrenergic receptors, acetylcholine receptors and sodium channel, and long-term and short-term memories. The ultimate goal is that these examples will provide an impetus for the opening of new frontiers of research in physiology by taking advantage of the tools developed from recent advances in molecular biology.

  3. Malonate metabolism: biochemistry, molecular biology, physiology, and industrial application.

    PubMed

    Kim, Yu Sam

    2002-09-30

    Malonate is a three-carbon dicarboxylic acid. It is well known as a competitive inhibitor of succinate dehydrogenase. It occurs naturally in biological systems, such as legumes and developing rat brains, which indicates that it may play an important role in symbiotic nitrogen metabolism and brain development. Recently, enzymes that are related to malonate metabolism were discovered and characterized. The genes that encode the enzymes were isolated, and the regulation of their expression was also studied. The mutant bacteria, in which the malonate-metabolizing gene was deleted, lost its primary function, symbiosis, between Rhizobium leguminosarium bv trifolii and clover. This suggests that malonate metabolism is essential in symbiotic nitrogen metabolism, at least in clover nodules. In addition to these, the genes matB and matC have been successfully used for generation of the industrial strain of Streptomyces for the production of antibiotics.

  4. Applications of the Aurora parallel Prolog system to computational molecular biology

    SciTech Connect

    Lusk, E.L.; Overbeek, R.; Mudambi, S.; Szeredi, P.

    1993-09-01

    We describe an investigation into the use of the Aurora parallel Prolog system in two applications within the area of computational molecular biology. The computational requirements were large, due to the nature of the applications, and were large, due to the nature of the applications, and were carried out on a scalable parallel computer the BBN ``Butterfly`` TC-2000. Results include both a demonstration that logic programming can be effective in the context of demanding applications on large-scale parallel machines, and some insights into parallel programming in Prolog.

  5. Data warehousing in molecular biology.

    PubMed

    Schönbach, C; Kowalski-Saunders, P; Brusic, V

    2000-05-01

    In the business and healthcare sectors data warehousing has provided effective solutions for information usage and knowledge discovery from databases. However, data warehousing applications in the biological research and development (R&D) sector are lagging far behind. The fuzziness and complexity of biological data represent a major challenge in data warehousing for molecular biology. By combining experiences in other domains with our findings from building a model database, we have defined the requirements for data warehousing in molecular biology.

  6. Molecular biology of potyviruses.

    PubMed

    Revers, Frédéric; García, Juan Antonio

    2015-01-01

    Potyvirus is the largest genus of plant viruses causing significant losses in a wide range of crops. Potyviruses are aphid transmitted in a nonpersistent manner and some of them are also seed transmitted. As important pathogens, potyviruses are much more studied than other plant viruses belonging to other genera and their study covers many aspects of plant virology, such as functional characterization of viral proteins, molecular interaction with hosts and vectors, structure, taxonomy, evolution, epidemiology, and diagnosis. Biotechnological applications of potyviruses are also being explored. During this last decade, substantial advances have been made in the understanding of the molecular biology of these viruses and the functions of their various proteins. After a general presentation on the family Potyviridae and the potyviral proteins, we present an update of the knowledge on potyvirus multiplication, movement, and transmission and on potyvirus/plant compatible interactions including pathogenicity and symptom determinants. We end the review providing information on biotechnological applications of potyviruses.

  7. Recent advances of molecular toolbox construction expand Pichia pastoris in synthetic biology applications.

    PubMed

    Kang, Zhen; Huang, Hao; Zhang, Yunfeng; Du, Guocheng; Chen, Jian

    2017-01-01

    Pichia pastoris: (reclassified as Komagataella phaffii), a methylotrophic yeast strain has been widely used for heterologous protein production because of its unique advantages, such as readily achievable high-density fermentation, tractable genetic modifications and typical eukaryotic post-translational modifications. More recently, P. pastoris as a metabolic pathway engineering platform has also gained much attention. In this mini-review, we addressed recent advances of molecular toolboxes, including synthetic promoters, signal peptides, and genome engineering tools that established for P. pastoris. Furthermore, the applications of P. pastoris towards synthetic biology were also discussed and prospected especially in the context of genome-scale metabolic pathway analysis.

  8. Double-helical nucleic acids with cross-linked strands: synthesis and applications in molecular biology

    NASA Astrophysics Data System (ADS)

    Antsypovitch, Sergei I.; Oretskaya, Tat'yana S.

    1998-03-01

    Data on the methods employed for cross-linking of DNA strands and for the synthesis of oligonucleotide duplexes with cross-links between strands are summarised. Existing methods are systematised; their advantages and drawbacks are discussed. The examples of applications of DNA duplexes with covalently cross-linked chains for the study of protein-nucleic acid recognition and mechanisms of action of nucleic acid-binding proteins for gaining information about the spatial structure of nucleic acids, and for the solution of other problems of molecular biology are given. The bibliography includes 131 references.

  9. Human papillomavirus molecular biology.

    PubMed

    Harden, Mallory E; Munger, Karl

    Human papillomaviruses are small DNA viruses with a tropism for squamous epithelia. A unique aspect of human papillomavirus molecular biology involves dependence on the differentiation status of the host epithelial cell to complete the viral lifecycle. A small group of these viruses are the etiologic agents of several types of human cancers, including oral and anogenital tract carcinomas. This review focuses on the basic molecular biology of human papillomaviruses. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Expression of exogenous DNA methyltransferases: application in molecular and cell biology.

    PubMed

    Dyachenko, O V; Tarlachkov, S V; Marinitch, D V; Shevchuk, T V; Buryanov, Y I

    2014-02-01

    DNA methyltransferases might be used as powerful tools for studies in molecular and cell biology due to their ability to recognize and modify nitrogen bases in specific sequences of the genome. Methylation of the eukaryotic genome using exogenous DNA methyltransferases appears to be a promising approach for studies on chromatin structure. Currently, the development of new methods for targeted methylation of specific genetic loci using DNA methyltransferases fused with DNA-binding proteins is especially interesting. In the present review, expression of exogenous DNA methyltransferase for purposes of in vivo analysis of the functional chromatin structure along with investigation of the functional role of DNA methylation in cell processes are discussed, as well as future prospects for application of DNA methyltransferases in epigenetic therapy and in plant selection.

  11. Prokaryotic toxin-antitoxin systems--the role in bacterial physiology and application in molecular biology.

    PubMed

    Bukowski, Michal; Rojowska, Anna; Wladyka, Benedykt

    2011-01-01

    Bacteria have developed multiple complex mechanisms ensuring an adequate response to environmental changes. In this context, bacterial cell division and growth are subject to strict control to ensure metabolic balance and cell survival. A plethora of studies cast light on toxin-antitoxin (TA) systems as metabolism regulators acting in response to environmental stress conditions. Many of those studies suggest direct relations between the TA systems and the pathogenic potential or antibiotic resistance of relevant bacteria. Other studies point out that TA systems play a significant role in ensuring stability of mobile genetic material. The evolutionary origin and relations between various TA systems are still a subject of a debate. The impact of toxin-antitoxin systems on bacteria physiology prompted their application in molecular biology as tools allowing cloning of some hard-to-maintain genes, plasmid maintenance and production of recombinant proteins.

  12. Molecular biology of development

    SciTech Connect

    Davidson, E.H.; Firtel, R.A.

    1984-01-01

    This book is a compilation of papers presented at a symposium on the molecular biology of development. Topics discussed include: cytoplasmic localizations and pattern formations, gene expression during oogenesis and early development, developmental expression of gene families molecular aspects of plant development and transformation in whole organisms and cells.

  13. Biological Molecular Machines

    NASA Astrophysics Data System (ADS)

    Kurzyński, Michał

    2007-11-01

    Like small molecules taking part in usual chemical reactions, biological molecular machines perform their functions owing to thermal fluctuations and the only difference consists in more complex and specially organized internal dynamics. It is this dynamics that determines processes of free energy transduction in molecular machines. The case of the actomyosin motor is considered in some detail.

  14. Parameter estimation method for improper fractional models and its application to molecular biological systems.

    PubMed

    Tian, Li-Ping; Liu, Lizhi; Wu, Fang-Xiang

    2010-01-01

    Derived from biochemical principles, molecular biological systems can be described by a group of differential equations. Generally these differential equations contain fractional functions plus polynomials (which we call improper fractional model) as reaction rates. As a result, molecular biological systems are nonlinear in both parameters and states. It is well known that it is challenging to estimate parameters nonlinear in a model. However, in fractional functions both the denominator and numerator are linear in the parameters while polynomials are also linear in parameters. Based on this observation, we develop an iterative linear least squares method for estimating parameters in biological systems modeled by improper fractional functions. The basic idea is to transfer optimizing a nonlinear least squares objective function into iteratively solving a sequence of linear least squares problems. The developed method is applied to the estimation of parameters in a metabolism system. The simulation results show the superior performance of the proposed method for estimating parameters in such molecular biological systems.

  15. Molecular biomimetics: nanotechnology through biology

    NASA Astrophysics Data System (ADS)

    Sarikaya, Mehmet; Tamerler, Candan; Jen, Alex K.-Y.; Schulten, Klaus; Baneyx, François

    2003-09-01

    Proteins, through their unique and specific interactions with other macromolecules and inorganics, control structures and functions of all biological hard and soft tissues in organisms. Molecular biomimetics is an emerging field in which hybrid technologies are developed by using the tools of molecular biology and nanotechnology. Taking lessons from biology, polypeptides can now be genetically engineered to specifically bind to selected inorganic compounds for applications in nano- and biotechnology. This review discusses combinatorial biological protocols, that is, bacterial cell surface and phage-display technologies, in the selection of short sequences that have affinity to (noble) metals, semiconducting oxides and other technological compounds. These genetically engineered proteins for inorganics (GEPIs) can be used in the assembly of functional nanostructures. Based on the three fundamental principles of molecular recognition, self-assembly and DNA manipulation, we highlight successful uses of GEPI in nanotechnology.

  16. Biological and biomimetic molecular machines.

    PubMed

    Huang, Tony J; Juluri, Bala K

    2008-02-01

    The evolution of life facilitates the creation of biological molecular machines. In these so-called 'nanomachines,' nature elegantly shows that when precisely organized and assembled, simple molecular mechanical components can link motions efficiently from the nanometer scale to the macroscopic world, and achieve complex functions such as powering skeletal muscles, synthesizing ATP and producing DNA/RNA. Inspired by nature, researchers are creating artifical molecular machines with tailored structures and properties, with the aim of realizing man-made active nanosystems that operate with the same efficiency and complexity as biological nanomachines. It is anticipated that in the not-too-distant future, unique applications of biological and biomimetic molecular machines will emerge in areas such as biochemical instrumentation and nanomedicine.

  17. Marine molecular biology: an emerging field of biological sciences.

    PubMed

    Thakur, Narsinh L; Jain, Roopesh; Natalio, Filipe; Hamer, Bojan; Thakur, Archana N; Müller, Werner E G

    2008-01-01

    An appreciation of the potential applications of molecular biology is of growing importance in many areas of life sciences, including marine biology. During the past two decades, the development of sophisticated molecular technologies and instruments for biomedical research has resulted in significant advances in the biological sciences. However, the value of molecular techniques for addressing problems in marine biology has only recently begun to be cherished. It has been proven that the exploitation of molecular biological techniques will allow difficult research questions about marine organisms and ocean processes to be addressed. Marine molecular biology is a discipline, which strives to define and solve the problems regarding the sustainable exploration of marine life for human health and welfare, through the cooperation between scientists working in marine biology, molecular biology, microbiology and chemistry disciplines. Several success stories of the applications of molecular techniques in the field of marine biology are guiding further research in this area. In this review different molecular techniques are discussed, which have application in marine microbiology, marine invertebrate biology, marine ecology, marine natural products, material sciences, fisheries, conservation and bio-invasion etc. In summary, if marine biologists and molecular biologists continue to work towards strong partnership during the next decade and recognize intellectual and technological advantages and benefits of such partnership, an exciting new frontier of marine molecular biology will emerge in the future.

  18. Knowledge discovery and system biology in molecular medicine: an application on neurodegenerative diseases.

    PubMed

    Fattore, Matteo; Arrigo, Patrizio

    2005-01-01

    The possibility to study an organism in terms of system theory has been proposed in the past, but only the advancement of molecular biology techniques allow us to investigate the dynamical properties of a biological system in a more quantitative and rational way than before . These new techniques can gave only the basic level view of an organisms functionality. The comprehension of its dynamical behaviour depends on the possibility to perform a multiple level analysis. Functional genomics has stimulated the interest in the investigation the dynamical behaviour of an organism as a whole. These activities are commonly known as System Biology, and its interests ranges from molecules to organs. One of the more promising applications is the 'disease modeling'. The use of experimental models is a common procedure in pharmacological and clinical researches; today this approach is supported by 'in silico' predictive methods. This investigation can be improved by a combination of experimental and computational tools. The Machine Learning (ML) tools are able to process different heterogeneous data sources, taking into account this peculiarity, they could be fruitfully applied to support a multilevel data processing (molecular, cellular and morphological) that is the prerequisite for the formal model design; these techniques can allow us to extract the knowledge for mathematical model development. The aim of our work is the development and implementation of a system that combines ML and dynamical models simulations. The program is addressed to the virtual analysis of the pathways involved in neurodegenerative diseases. These pathologies are multifactorial diseases and the relevance of the different factors has not yet been well elucidated. This is a very complex task; in order to test the integrative approach our program has been limited to the analysis of the effects of a specific protein, the Cyclin dependent kinase 5 (CDK5) which relies on the induction of neuronal

  19. Molecular Models in Biology

    ERIC Educational Resources Information Center

    Goodman, Richard E.

    1970-01-01

    Describes types of molecular models (ball-and-stick, framework, and space-filling) and evaluates commercially available kits. Gives instructions for constructive models from polystyrene balls and pipe-cleaners. Models are useful for class demonstrations although not sufficiently accurate for research use. Illustrations show biologically important…

  20. Molecular Models in Biology

    ERIC Educational Resources Information Center

    Goodman, Richard E.

    1970-01-01

    Describes types of molecular models (ball-and-stick, framework, and space-filling) and evaluates commercially available kits. Gives instructions for constructive models from polystyrene balls and pipe-cleaners. Models are useful for class demonstrations although not sufficiently accurate for research use. Illustrations show biologically important…

  1. MyLabStocks: a web-application to manage molecular biology materials.

    PubMed

    Chuffart, Florent; Yvert, Gaël

    2014-05-01

    Laboratory stocks are the hardware of research. They must be stored and managed with mimimum loss of material and information. Plasmids, oligonucleotides and strains are regularly exchanged between collaborators within and between laboratories. Managing and sharing information about every item is crucial for retrieval of reagents, for planning experiments and for reproducing past experimental results. We have developed a web-based application to manage stocks commonly used in a molecular biology laboratory. Its functionalities include user-defined privileges, visualization of plasmid maps directly from their sequence and the capacity to search items from fields of annotation or directly from a query sequence using BLAST. It is designed to handle records of plasmids, oligonucleotides, yeast strains, antibodies, pipettes and notebooks. Based on PHP/MySQL, it can easily be extended to handle other types of stocks and it can be installed on any server architecture. MyLabStocks is freely available from: https://forge.cbp.ens-lyon.fr/redmine/projects/mylabstocks under an open source licence. © 2014 Laboratoire de Biologie Moleculaire de la Cellule CNRS. Yeast published by John Wiley & Sons, Ltd.

  2. Building DNA nanostructures for molecular computation, templated assembly, and biological applications.

    PubMed

    Rangnekar, Abhijit; LaBean, Thomas H

    2014-06-17

    CONSPECTUS: DNA is a critical biomolecule well-known for its roles in biology and genetics. Moreover, its double-helical structure and the Watson-Crick pairing of its bases make DNA structurally predictable. This predictability enables design and synthesis of artificial DNA nanostructures by suitable programming of the base sequences of DNA strands. Since the advent of the field of DNA nanotechnology in 1982, a variety of DNA nanostructures have been designed and used for numerous applications. In this Account, we discuss the progress made by our lab which has contributed toward the overall advancement of the field. Tile-based DNA nanostructures are an integral part of structural DNA nanotechnology. These structures are formed using several short, chemically synthesized DNA strands by programming their base sequences so that they self-assemble into desired constructs. Design and assembly of several DNA tiles will be discussed in this Account. Tiles include, for example, TX tiles with three parallel, coplanar duplexes, 4 × 4 cross-tiles with four arms, and weave-tiles with weave-like architecture. Another category of tiles we will present involve multiple parallel duplexes that assemble to form closed tubular structures. All of these tile types have been used to form micrometer-scale one- and two-dimensional arrays and lattices. Origami-based structures constitute another category where a long single-stranded DNA scaffold is folded into desired shapes by association with multiple short staple strands. This Account will describe the efforts by our lab in devising new strategies to improve the maximum size of origami structures. The various DNA nanostructures detailed here have been used in a wide variety of different applications. This Account will discuss the use of DNA tiles for logical computation, encoding information as molecular barcodes, and functionalization for patterning of other nanoscale organic and inorganic materials. Consequently, we have used DNA

  3. High molecular weight DNA assembly in vivo for synthetic biology applications.

    PubMed

    Juhas, Mario; Ajioka, James W

    2017-05-01

    DNA assembly is the key technology of the emerging interdisciplinary field of synthetic biology. While the assembly of smaller DNA fragments is usually performed in vitro, high molecular weight DNA molecules are assembled in vivo via homologous recombination in the host cell. Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae are the main hosts used for DNA assembly in vivo. Progress in DNA assembly over the last few years has paved the way for the construction of whole genomes. This review provides an update on recent synthetic biology advances with particular emphasis on high molecular weight DNA assembly in vivo in E. coli, B. subtilis and S. cerevisiae. Special attention is paid to the assembly of whole genomes, such as those of the first synthetic cell, synthetic yeast and minimal genomes.

  4. Calculating the secrets of life: Applications of the mathematical sciences in molecular biology

    SciTech Connect

    Lander, E.S.; Waterman, M.S.

    1995-12-31

    Molecular biology has emerged from the synthesis of two complementary approaches to the study of life-biochemistry and genetics--to become one of the most exciting and vibrant scientific fields at the end of the twentieth century. This book covers the following topic areas: a brief history of the intellectual foundations of modem molecular biology; mapping heredity; seeing conserved signals: using algorithms to detect similarities between biosequences; hearing distant echoes: using extremal statistics to probe evolutionary origins; calibrating the clock: using stochastic processes to measure the rate of evolution; winding the double helix; using geometry, topology, and mechanics of DNA; unwinding the double helix: using differential mechanics to probe conformational changes in DNA; lifting the curtain: using topology to probe the hidden action of enzymes; folding the sheets: using computational methods to predict the structure of proteins.

  5. Quantum Information Biology: From Information Interpretation of Quantum Mechanics to Applications in Molecular Biology and Cognitive Psychology

    NASA Astrophysics Data System (ADS)

    Asano, Masanari; Basieva, Irina; Khrennikov, Andrei; Ohya, Masanori; Tanaka, Yoshiharu; Yamato, Ichiro

    2015-10-01

    We discuss foundational issues of quantum information biology (QIB)—one of the most successful applications of the quantum formalism outside of physics. QIB provides a multi-scale model of information processing in bio-systems: from proteins and cells to cognitive and social systems. This theory has to be sharply distinguished from "traditional quantum biophysics". The latter is about quantum bio-physical processes, e.g., in cells or brains. QIB models the dynamics of information states of bio-systems. We argue that the information interpretation of quantum mechanics (its various forms were elaborated by Zeilinger and Brukner, Fuchs and Mermin, and D' Ariano) is the most natural interpretation of QIB. Biologically QIB is based on two principles: (a) adaptivity; (b) openness (bio-systems are fundamentally open). These principles are mathematically represented in the framework of a novel formalism— quantum adaptive dynamics which, in particular, contains the standard theory of open quantum systems.

  6. Imaging modes of atomic force microscopy for application in molecular and cell biology

    NASA Astrophysics Data System (ADS)

    Dufrêne, Yves F.; Ando, Toshio; Garcia, Ricardo; Alsteens, David; Martinez-Martin, David; Engel, Andreas; Gerber, Christoph; Müller, Daniel J.

    2017-04-01

    Atomic force microscopy (AFM) is a powerful, multifunctional imaging platform that allows biological samples, from single molecules to living cells, to be visualized and manipulated. Soon after the instrument was invented, it was recognized that in order to maximize the opportunities of AFM imaging in biology, various technological developments would be required to address certain limitations of the method. This has led to the creation of a range of new imaging modes, which continue to push the capabilities of the technique today. Here, we review the basic principles, advantages and limitations of the most common AFM bioimaging modes, including the popular contact and dynamic modes, as well as recently developed modes such as multiparametric, molecular recognition, multifrequency and high-speed imaging. For each of these modes, we discuss recent experiments that highlight their unique capabilities.

  7. Imaging modes of atomic force microscopy for application in molecular and cell biology.

    PubMed

    Dufrêne, Yves F; Ando, Toshio; Garcia, Ricardo; Alsteens, David; Martinez-Martin, David; Engel, Andreas; Gerber, Christoph; Müller, Daniel J

    2017-04-06

    Atomic force microscopy (AFM) is a powerful, multifunctional imaging platform that allows biological samples, from single molecules to living cells, to be visualized and manipulated. Soon after the instrument was invented, it was recognized that in order to maximize the opportunities of AFM imaging in biology, various technological developments would be required to address certain limitations of the method. This has led to the creation of a range of new imaging modes, which continue to push the capabilities of the technique today. Here, we review the basic principles, advantages and limitations of the most common AFM bioimaging modes, including the popular contact and dynamic modes, as well as recently developed modes such as multiparametric, molecular recognition, multifrequency and high-speed imaging. For each of these modes, we discuss recent experiments that highlight their unique capabilities.

  8. Molecular biology of testicular germ cell tumors: unique features awaiting clinical application.

    PubMed

    Boublikova, Ludmila; Buchler, Tomas; Stary, Jan; Abrahamova, Jitka; Trka, Jan

    2014-03-01

    Testicular germ cell tumors (TGCTs) are the most common solid tumors in young adult men characterized by distinct biologic features and clinical behavior. Both genetic predispositions and environmental factors probably play a substantial role in their etiology. TGTCs arise from a malignant transformation of primordial germ cells in a process that starts prenatally, is often associated with a certain degree of gonadal dysgenesis, and involves the acquirement of several specific aberrations, including activation of SCF-CKIT, amplification of 12p with up-regulation of stem cell genes, and subsequent genetic and epigenetic alterations. Their embryonic and germ origin determines the unique sensitivity of TGCTs to platinum-based chemotherapy. Contrary to the vast majority of other malignancies, no molecular prognostic/predictive factors nor targeted therapy is available for patients with these tumors. This review summarizes the principal molecular characteristics of TGCTs that could represent a potential basis for development of novel diagnostic and treatment approaches.

  9. Investigating the Postmortem Molecular Biology of Cartilage and its Potential Forensic Applications.

    PubMed

    Bolton, Shawna N; Whitehead, Michael P; Dudhia, Jayesh; Baldwin, Timothy C; Sutton, Raul

    2015-07-01

    This study investigated the postmortem molecular changes that articular cartilage undergoes following burial. Fresh pig trotters were interred in 30-cm-deep graves at two distinct locations exhibiting dissimilar soil environments for up to 42 days. Extracts of the metacarpophalangeal (MCP) and metatarsophalangeal (MTP) joint cartilage from trotters disinterred weekly over 6 weeks were analyzed by Western blot against the monoclonal antibody 2-B-6 to assess aggrecan degradation. In both soil conditions, aggrecan degradation by-products of decreasing molecular size and complexity were observed up to 21 days postmortem. Degradation products were undetected after this time and coincided with MCP/MTP joint exposure to the soil environment. These results show that cartilage proteoglycans undergo an ordered molecular breakdown, the analysis of which may have forensic applications. This model may prove useful for use as a human model and for forensic investigations concerning crimes against animals and the mortality of endangered species.

  10. Declaration of patent applications as financial interests: a survey of practice among authors of papers on molecular biology in Nature.

    PubMed

    Mayer, S

    2006-11-01

    To determine whether authors of scientific publications in molecular biology declare patents and other potential financial interests. Survey of a 6-month sample of papers related to molecular biology in Nature. The esp@cenet worldwide patent search engine was used to search for patents applied for by the authors of scientific papers in Nature that were related to molecular biology and genetics, between January and June 2005. Of the 79 papers considered, four had declared that certain authors had competing financial interests. Seven papers in which no financial interests were declared had authors with patent applications that were based on the research in the paper or were closely related to it. Another paper had two authors with connections to biotechnology companies that were not disclosed. Two thirds of the papers in which authors had patent applications or company affiliations that might be considered to be competing financial interests did not disclose them. Failure to disclose such information may have negative implications on the perception of science in society and on its quality if the possible bias is hidden. Journals should make greater efforts to ensure full disclosure, and scientific institutions should consider failure to disclose financial interests as an example of scientific malpractice. Establishing a register of interests for scientists is one way to increase transparency and openness.

  11. Declaration of patent applications as financial interests: a survey of practice among authors of papers on molecular biology in Nature

    PubMed Central

    Mayer, S

    2006-01-01

    Objectives To determine whether authors of scientific publications in molecular biology declare patents and other potential financial interests. Design Survey of a 6‐month sample of papers related to molecular biology in Nature. Methods The esp@cenet worldwide patent search engine was used to search for patents applied for by the authors of scientific papers in Nature that were related to molecular biology and genetics, between January and June 2005. Results Of the 79 papers considered, four had declared that certain authors had competing financial interests. Seven papers in which no financial interests were declared had authors with patent applications that were based on the research in the paper or were closely related to it. Another paper had two authors with connections to biotechnology companies that were not disclosed. Conclusion Two thirds of the papers in which authors had patent applications or company affiliations that might be considered to be competing financial interests did not disclose them. Failure to disclose such information may have negative implications on the perception of science in society and on its quality if the possible bias is hidden. Journals should make greater efforts to ensure full disclosure, and scientific institutions should consider failure to disclose financial interests as an example of scientific malpractice. Establishing a register of interests for scientists is one way to increase transparency and openness. PMID:17074824

  12. Dynalets: a new method for modelling and compressing biological signals. Applications to physiological and molecular signals.

    PubMed

    Demongeot, Jacques; Hansen, Olivier; Hamie, Ali; Franco, Céline; Sutton, Brian; Cohen, Elie-Paul

    2014-11-01

    The biological information coming from electrophysiologic sensors like ECG, pulse sensor or from molecular signal devices like NMR spectrometry has to be visualized and manipulated in a compressed way for an efficient medical use by clinicians, if stored in scientific data bases or in personalized patient records repositories. Here, we define a new transform called Dynalet based on Liénard ordinary differential equations susceptible to model the mechanism at the source of the studied signal, and we propose to apply this new technique first to the modelling and compression of real biological periodic signals like ECG and pulse rhythm. We consider that the cardiovascular activity results from the summation of cellular oscillators located in the cardiac sinus node and we show that, as a result, the van der Pol oscillator (a particular Liénard system) fits well the ECG signal and the pulse signal. The reconstruction of the original signal (pulse or ECG) using Dynalet transform is then compared with that of Fourier, counting the number of parameters to be set for obtaining an expected signal-to-noise ratio. Then, we apply the Dynalet transform to the modelling and compression of molecular spectra obtained by protein NMR spectroscopy. The reconstruction of the original signal (peak) using Dynalet transform is again compared with that of Fourier. After reconstructing visually the peak, we propose to periodize the signal and give it to hear, the whole process being called the protein "stethoscope".

  13. Molecular biology references.

    PubMed

    2003-05-01

    Many of the units in this manual describe methods and techniques for the cloning, expression, and structural analysis of neural genes and proteins. We assume that users of these protocols have at least some introductory background in recombinant DNA technology (or are working with a collaborator who does); therefore, we have not provided comprehensive coverage of all of these topics, but rather have concentrated on presenting selected techniques that will be of the most interest and use to the general neuroscience laboratory. More comprehensive coverage of these topics can be found in Current Protocols in Molecular Biology (CPMB), which is extensively cross-referenced throughout this manual. These cross-references are summarized in this appendix.

  14. Molecular ferroelectrics: where electronics meet biology

    PubMed Central

    Li, Jiangyu; Liu, Yuanming; Zhang, Yanhang; Cai, Hong-Ling; Xiong, Ren-Gen

    2013-01-01

    In the last several years, we have witnessed significant advances in molecular ferroelectrics, with ferroelectric properties of molecular crystals approaching those of barium titanate. In addition, ferroelectricity has been observed in biological systems, filling an important missing link in bioelectric phenomena. In this perspective, we will present short historical notes on ferroelectrics, followed by overview on the fundamentals of ferroelectricity. Latest development in molecular ferroelectrics and biological ferroelectricity will then be highlighted, and their implications and potential applications will be discussed. We close by noting molecular ferroelectric as an exciting frontier between electronics and biology, and a number of challenges ahead are also noted. PMID:24018952

  15. Molecular ferroelectrics: where electronics meet biology.

    PubMed

    Li, Jiangyu; Liu, Yuanming; Zhang, Yanhang; Cai, Hong-Ling; Xiong, Ren-Gen

    2013-12-28

    In the last several years, we have witnessed significant advances in molecular ferroelectrics, with the ferroelectric properties of molecular crystals approaching those of barium titanate. In addition, ferroelectricity has been observed in biological systems, filling an important missing link in bioelectric phenomena. In this perspective, we will present short historical notes on ferroelectrics, followed by an overview of the fundamentals of ferroelectricity. The latest developments in molecular ferroelectrics and biological ferroelectricity will then be highlighted, and their implications and potential applications will be discussed. We close by noting molecular ferroelectric as an exciting frontier between electronics and biology, and a number of challenges ahead are also described.

  16. Special conference of the American Association for Cancer Research on molecular imaging in cancer: linking biology, function, and clinical applications in vivo.

    PubMed

    Luker, Gary D

    2002-04-01

    The AACR Special Conference on Molecular Imaging in Cancer: Linking Biology, Function, and Clinical Applications In Vivo, was held January 23-27, 2002, at the Contemporary Hotel, Walt Disney World, Orlando, FL. Co-Chairs David Piwnica-Worms, Patricia Price and Thomas Meade brought together researchers with diverse expertise in molecular biology, gene therapy, chemistry, engineering, pharmacology, and imaging to accelerate progress in developing and applying technologies for imaging specific cellular and molecular signals in living animals and humans. The format of the conference was the presentation of research that focused on basic and translational biology of cancer and current state-of-the-art techniques for molecular imaging in animal models and humans. This report summarizes the special conference on molecular imaging, highlighting the interfaces of molecular biology with animal models, instrumentation, chemistry, and pharmacology that are essential to convert the dreams and promise of molecular imaging into improved understanding, diagnosis, and management of cancer.

  17. Molecular biological applications in the diagnosis and control of leishmaniasis and parasite identification.

    PubMed

    Schallig, Henk D F H; Oskam, Linda

    2002-08-01

    Molecular biology is increasingly relevant to the diagnosis and control of infectious diseases. Information on DNA sequences has been extensively exploited for the development of polymerase chain reaction-based assays for the diagnosis of leishmaniasis and the identification of parasite species. It has also led to the use of cloned antigen for serodiagnosis. It is expected that the sequencing of the Leishmania major genome and the genomes of other Leishmania species will enable important progress in further improving diagnosis and control. The ability to use genome data to clone and sequence genes, which, when expressed, provide antigens for vaccine development, will increase the possibilities for rational vaccine development. Moreover, DNA on its own will provide the basis for the development of DNA vaccines that may overcome some of the problems encountered with protein-based vaccines. One of the greatest threats to parasite control is the development of drug resistance in parasites. Knowing the molecular basis of drug resistance and the ability to monitor its development with sensitive and specific DNA-based assays for 'resistance alleles' may aid maintaining the effectiveness of available anti-Leishmania drugs. Finally, techniques such as microarrays and nucleic acid sequence-based amplification will eventually allow rapid screening for specific parasite genotypes and assist in diagnostic and epidemiological studies.

  18. Molecular Biology of Nitrogen Fixation

    ERIC Educational Resources Information Center

    Shanmugam, K. T.; Valentine, Raymond C.

    1975-01-01

    Reports that as a result of our increasing knowledge of the molecular biology of nitrogen fixation it might eventually be possible to increase the biological production of nitrogenous fertilizer from atmospheric nitrogen. (GS)

  19. Molecular Biology of Nitrogen Fixation

    ERIC Educational Resources Information Center

    Shanmugam, K. T.; Valentine, Raymond C.

    1975-01-01

    Reports that as a result of our increasing knowledge of the molecular biology of nitrogen fixation it might eventually be possible to increase the biological production of nitrogenous fertilizer from atmospheric nitrogen. (GS)

  20. Application of cytology and molecular biology in diagnosing premalignant or malignant oral lesions

    PubMed Central

    Mehrotra, Ravi; Gupta, Anurag; Singh, Mamta; Ibrahim, Rahela

    2006-01-01

    Early detection of a premalignant or cancerous oral lesion promises to improve the survival and the morbidity of patients suffering from these conditions. Cytological study of oral cells is a non-aggressive technique that is well accepted by the patient, and is therefore an attractive option for the early diagnosis of oral cancer, including epithelial atypia and squamous cell carcinoma. However its usage has been limited so far due to poor sensitivity and specificity in diagnosing oral malignancies. Lately it has re-emerged due to improved methods and it's application in oral precancer and cancer as a diagnostic and predictive method as well as for monitoring patients. Newer diagnostic techniques such as "brush biopsy" and molecular studies have been developed. Recent advances in cytological techniques and novel aspects of applications of scraped or exfoliative cytology for detecting these lesions and predicting their progression or recurrence are reviewed here. PMID:16556320

  1. Application of cytology and molecular biology in diagnosing premalignant or malignant oral lesions.

    PubMed

    Mehrotra, Ravi; Gupta, Anurag; Singh, Mamta; Ibrahim, Rahela

    2006-03-23

    Early detection of a premalignant or cancerous oral lesion promises to improve the survival and the morbidity of patients suffering from these conditions. Cytological study of oral cells is a non-aggressive technique that is well accepted by the patient, and is therefore an attractive option for the early diagnosis of oral cancer, including epithelial atypia and squamous cell carcinoma. However its usage has been limited so far due to poor sensitivity and specificity in diagnosing oral malignancies. Lately it has re-emerged due to improved methods and it's application in oral precancer and cancer as a diagnostic and predictive method as well as for monitoring patients. Newer diagnostic techniques such as "brush biopsy" and molecular studies have been developed. Recent advances in cytological techniques and novel aspects of applications of scraped or exfoliative cytology for detecting these lesions and predicting their progression or recurrence are reviewed here.

  2. Molecular biology of atherosclerosis

    PubMed Central

    Mannarino, Elmo; Pirro, Matteo

    2008-01-01

    The traditional view of atherosclerosis as a pathological lipid deposition within the artery wall has been redefined by a more complex concept of an ongoing inflammatory disease. The atherosclerotic process is initiated when cardiovascular risk factors, through a chemical, mechanical or immunological insult, activate and/or injury the endothelium, thus contributing to endothelial dysfunction and fragmentation. This triggers a cascade of inflammatory reactions, in which monocytes, macrophages, T lymphocytes, vascular smooth muscle cells actively participate. Particularly, atherosclerotic lesions have been seen to have increased expression of T helper-1 cells together with increased levels of the T helper-1 related pro-inflammatory cytokines. Along with pro-inflammatory cytokines, other molecular factors involved in atherosclerosis appearance, progression and complication include chemokines, growth factors, vasoactive substances, enzymes, apoptosis signals and many others. Many of these molecular factors are both involved as possible markers of the atherosclerotic disease activity and burden, but may also play a crucial role in the pathogenesis of the disease. In recent years, the discovery of progenitor cells of myeloid origin has offered the prospect of merging the most recent theories on the pathogenesis of atherosclerosis with the evolving concept of a role of these progenitor cells in the repair of the injured vessel wall and the neovascularisation of ischemic tissues. This review summarizes current knowledge about the biology of atherosclerosis with emphasis on the mechanisms of endothelial damage and repair and on the concept that the turnover and replacement of endothelial cells is a major determinant in the maintenance of vascular integrity. PMID:22460847

  3. Applications of space-electrophoresis in medicine. [for cellular separations in molecular biology

    NASA Technical Reports Server (NTRS)

    Bier, M.

    1976-01-01

    The nature of electrophoresis is reviewed and potential advances realizable in the field of biology and medicine from a space electrophoresis facility are examined. The ground-based applications of electrophoresis: (1) characterization of an ionized species; (2) determination of the quantitative composition of a complex mixture; and (3) isolation of the components of a mixture, separation achieved on the basis of the difference in transport rates is reviewed. The electrophoresis of living cells is considered, touching upon the following areas: the separation of T and B lymphocytes; the genetic influence on mouse lymphocyte mobilities; the abnormal production of specific and monoclonal immunoproteins; and the study of cancer. Schematic diagrams are presented of three types of electrophoresis apparatus: the column assembly for the static electrophoresis experiment on the Apollo-Soyuz mission, the continuous flow apparatus used in the same mission and a miniaturized electrophoresis apparatus.

  4. Applications of space-electrophoresis in medicine. [for cellular separations in molecular biology

    NASA Technical Reports Server (NTRS)

    Bier, M.

    1976-01-01

    The nature of electrophoresis is reviewed and potential advances realizable in the field of biology and medicine from a space electrophoresis facility are examined. The ground-based applications of electrophoresis: (1) characterization of an ionized species; (2) determination of the quantitative composition of a complex mixture; and (3) isolation of the components of a mixture, separation achieved on the basis of the difference in transport rates is reviewed. The electrophoresis of living cells is considered, touching upon the following areas: the separation of T and B lymphocytes; the genetic influence on mouse lymphocyte mobilities; the abnormal production of specific and monoclonal immunoproteins; and the study of cancer. Schematic diagrams are presented of three types of electrophoresis apparatus: the column assembly for the static electrophoresis experiment on the Apollo-Soyuz mission, the continuous flow apparatus used in the same mission and a miniaturized electrophoresis apparatus.

  5. Inflammatory therapeutic targets in coronary atherosclerosis—from molecular biology to clinical application

    PubMed Central

    Linden, Fabian; Domschke, Gabriele; Erbel, Christian; Akhavanpoor, Mohammadreza; Katus, Hugo A.; Gleissner, Christian A.

    2014-01-01

    Atherosclerosis is the leading cause of death worldwide. Over the past two decades, it has been clearly recognized that atherosclerosis is an inflammatory disease of the arterial wall. Accumulating data from animal experiments have supported this hypothesis, however, clinical applications making use of this knowledge remain scarce. In spite of optimal interventional and medical therapy, the risk for recurrent myocardial infarction remains by about 20% over 3 years after acute coronary syndromes, novel therapies to prevent atherogenesis or treat atherosclerosis are urgently needed. This review summarizes selected potential molecular inflammatory targets that may be of clinical relevance. We also review recent and ongoing clinical trails that target inflammatory processes aiming at preventing adverse cardiovascular events. Overall, it seems surprising that translation of basic science into clinical practice has not been a great success. In conclusion, we propose to focus on specific efforts that promote translational science in order to improve outcome and prognosis of patients suffering from atherosclerosis. PMID:25484870

  6. Applications of DNA Nanomechanical Devices to Molecular Biology and to Programmed Dynamic Motion

    NASA Astrophysics Data System (ADS)

    Liu, Chunhua

    Not merely is DNA a favorable genetic material, but an effective supermolecular subunit for nanoconstruction as well. In structural DNA nanotechnology, rigid branched DNA motifs have been combined with sticky-ended cohesion to build DNA objects, arrays and devices for functional purposes. Reciprocating devices are key features in macroscopic machines. In Chapter II, I report the construction of two reciprocal PX-JX2 devices, wherein the control strands leading to the PX state in one device lead to the JX2 state in the other device, and vice versa. The formation, transformation and reciprocal motions of these two devices are confirmed utilizing gel electrophoresis, and atomic force microscopy. This system is likely to be of use for molecular robotic applications where reciprocal motions are of value in addition its inherent contribution to molecular choreography and molecular aesthetics. Recently, several DNA-based nanomechanical devices have been developed as an attractive tool for fine measurements on nanoscale objects. In Chapter III, I have constructed a device wherein two DNA triple crossover (TX) molecules are connected by a shaft, similar to a previous device that measured the amount of work that can be performed by integration host factor [Shen, W., Bruist, M., Goodman, S. & Seeman, N. C., Angew. Chemie Int. Ed. 43, 4750-4752 (2004)]. In the present case, the binding site on the shaft contains the sequence recognized by apo-SoxR, the apo-form of a protein that is a redox-sensing transcriptional activator; previous data suggest that it distorts its binding site by an amount that corresponds to about two base pairs. A pair of dyes reports the fluorescence resonance energy transfer (FRET) signal between the two TX domains, reflecting changes in the shape of the device upon binding the protein. The TX domains are used to amplify the signal expected from a relatively small distortion of the DNA binding site. From FRET analysis of apo-SoxR binding, the effect of

  7. Teaching Applied Genetics and Molecular Biology to Agriculture Engineers. Application of the European Credit Transfer System

    ERIC Educational Resources Information Center

    Weiss, J.; Egea-Cortines, M.

    2008-01-01

    We have been teaching applied molecular genetics to engineers and adapted the teaching methodology to the European Credit Transfer System. We teach core principles of genetics that are universal and form the conceptual basis of most molecular technologies. The course then teaches widely used techniques and finally shows how different techniques…

  8. Teaching Applied Genetics and Molecular Biology to Agriculture Engineers. Application of the European Credit Transfer System

    ERIC Educational Resources Information Center

    Weiss, J.; Egea-Cortines, M.

    2008-01-01

    We have been teaching applied molecular genetics to engineers and adapted the teaching methodology to the European Credit Transfer System. We teach core principles of genetics that are universal and form the conceptual basis of most molecular technologies. The course then teaches widely used techniques and finally shows how different techniques…

  9. Molecular characteristics versus biological activity

    USGS Publications Warehouse

    Applegate, Vernon C.; Smith, Manning A.; Willeford, Bennett R.

    1967-01-01

    The molecular characteristics of mononitrophenols containing halogens not only play a key role in their biological activity but provide a novel example of selective toxicity among vertebrate animals. It has been reported that efforts to control the parasitic sea lamprey in the Great Lakes are directed at present to the applications of a selective toxicant to streams inhabited by lamprey larvae. Since 1961, the larvicide that has been used almost exclusively in the control program has been 3-trifluoromethyl-4-nitrophenol (TFM). However, this is only one of about 15 closely related compounds, all halogen-containing mononitrophenols, that display a selectively toxic action upon lampreys. Although not all of the halogenated mononitrophenols are selectively toxic to lampreys (in fact, fewer than half of those tested), no other group of related compounds has displayed any useful larvicidal activity except for the substituted nitrosalicylanilides.

  10. Integrating molecular biology into the veterinary curriculum.

    PubMed

    Ryan, Marion T; Sweeney, Torres

    2007-01-01

    The modern discipline of molecular biology is gaining increasing relevance in the field of veterinary medicine. This trend must be reflected in the curriculum if veterinarians are to capitalize on opportunities arising from this field and direct its development toward their own goals as a profession. This review outlines current applications of molecular-based technologies that are relevant to the veterinary profession. In addition, the current techniques and technologies employed within the field of molecular biology are discussed. Difficulties associated with teaching a subject such as molecular biology within a veterinary curriculum can be alleviated by effectively integrating molecular topics throughout the curriculum, pitching the subject at an appropriate depth, and employing varied teaching methods throughout.

  11. Teaching Molecular Biology with Microcomputers.

    ERIC Educational Resources Information Center

    Reiss, Rebecca; Jameson, David

    1984-01-01

    Describes a series of computer programs that use simulation and gaming techniques to present the basic principles of the central dogma of molecular genetics, mutation, and the genetic code. A history of discoveries in molecular biology is presented and the evolution of these computer assisted instructional programs is described. (MBR)

  12. Teaching Molecular Biology with Microcomputers.

    ERIC Educational Resources Information Center

    Reiss, Rebecca; Jameson, David

    1984-01-01

    Describes a series of computer programs that use simulation and gaming techniques to present the basic principles of the central dogma of molecular genetics, mutation, and the genetic code. A history of discoveries in molecular biology is presented and the evolution of these computer assisted instructional programs is described. (MBR)

  13. Molecular plasmonics for biology and nanomedicine

    PubMed Central

    Zheng, Yue Bing; Kiraly, Brian; Weiss, Paul S; Huang, Tony Jun

    2014-01-01

    The optical excitation of surface plasmons in metal nanoparticles leads to nanoscale spatial confinement of electromagnetic fields. The confined electromagnetic fields can generate intense, localized thermal energy and large near-field optical forces. The interaction between these effects and nearby molecules has led to the emerging field known as molecular plasmonics. Recent advances in molecular plasmonics have enabled novel optical materials and devices with applications in biology and nanomedicine. In this article, we categorize three main types of interactions between molecules and surface plasmons: optical, thermal and mechanical. Within the scope of each type of interaction, we will review applications of molecular plasmonics in biology and nanomedicine. We include a wide range of applications that involve sensing, spectral analysis, imaging, delivery, manipulation and heating of molecules, biomolecules or cells using plasmonic effects. We also briefly describe the physical principles of molecular plasmonics and progress in the nanofabrication, surface functionalization and bioconjugation of metal nanoparticles. PMID:22630155

  14. Molecular plasmonics for biology and nanomedicine.

    PubMed

    Zheng, Yue Bing; Kiraly, Brian; Weiss, Paul S; Huang, Tony Jun

    2012-05-01

    The optical excitation of surface plasmons in metal nanoparticles leads to nanoscale spatial confinement of electromagnetic fields. The confined electromagnetic fields can generate intense, localized thermal energy and large near-field optical forces. The interaction between these effects and nearby molecules has led to the emerging field known as molecular plasmonics. Recent advances in molecular plasmonics have enabled novel optical materials and devices with applications in biology and nanomedicine. In this article, we categorize three main types of interactions between molecules and surface plasmons: optical, thermal and mechanical. Within the scope of each type of interaction, we will review applications of molecular plasmonics in biology and nanomedicine. We include a wide range of applications that involve sensing, spectral analysis, imaging, delivery, manipulation and heating of molecules, biomolecules or cells using plasmonic effects. We also briefly describe the physical principles of molecular plasmonics and progress in the nanofabrication, surface functionalization and bioconjugation of metal nanoparticles.

  15. Molecular Biology of Archaebacteria

    DTIC Science & Technology

    1988-03-31

    elucidate at the molecular level some of the features that make archaebacteria unique and distinguish them from eubacteria and eucaryotes. Three types...regulate translation of the mRNA by a mechanism similar to that employed in eubacteria . Thus halophilic archaebacteria retain the same gene order and...possibly also the same regulatory mechanism for controlling ribosomal protein synthesis that is found in eubacteria . Ribosomal protein structure: The

  16. Molecular biology of hearing

    PubMed Central

    Stöver, Timo; Diensthuber, Marc

    2012-01-01

    The inner ear is our most sensitive sensory organ and can be subdivided into three functional units: organ of Corti, stria vascularis and spiral ganglion. The appropriate stimulus for the organ of hearing is sound, which travels through the external auditory canal to the middle ear where it is transmitted to the inner ear. The inner ear houses the hair cells, the sensory cells of hearing. The inner hair cells are capable of mechanotransduction, the transformation of mechanical force into an electrical signal, which is the basic principle of hearing. The stria vascularis generates the endocochlear potential and maintains the ionic homeostasis of the endolymph. The dendrites of the spiral ganglion form synaptic contacts with the hair cells. The spiral ganglion is composed of neurons that transmit the electrical signals from the cochlea to the central nervous system. In recent years there has been significant progress in research on the molecular basis of hearing. An increasing number of genes and proteins related to hearing are being identified and characterized. The growing knowledge of these genes contributes not only to greater appreciation of the mechanism of hearing but also to a deeper understanding of the molecular basis of hereditary hearing loss. This basic research is a prerequisite for the development of molecular diagnostics and novel therapies for hearing loss. PMID:22558056

  17. Forty Years of Ebolavirus Molecular Biology: Understanding a Novel Disease Agent Through the Development and Application of New Technologies.

    PubMed

    Groseth, Allison; Hoenen, Thomas

    2017-01-01

    Molecular biology is a broad discipline that seeks to understand biological phenomena at a molecular level, and achieves this through the study of DNA, RNA, proteins, and/or other macromolecules (e.g., those involved in the modification of these substrates). Consequently, it relies on the availability of a wide variety of methods that deal with the collection, preservation, inactivation, separation, manipulation, imaging, and analysis of these molecules. As such the state of the art in the field of ebolavirus molecular biology research (and that of all other viruses) is largely intertwined with, if not driven by, advancements in the technical methodologies available for these kinds of studies. Here we review of the current state of our knowledge regarding ebolavirus biology and emphasize the associated methods that made these discoveries possible.

  18. The Renormalization Group and Its Applications to Generating Coarse-Grained Models of Large Biological Molecular Systems.

    PubMed

    Koehl, Patrice; Poitevin, Frédéric; Navaza, Rafael; Delarue, Marc

    2017-03-14

    Understanding the dynamics of biomolecules is the key to understanding their biological activities. Computational methods ranging from all-atom molecular dynamics simulations to coarse-grained normal-mode analyses based on simplified elastic networks provide a general framework to studying these dynamics. Despite recent successes in studying very large systems with up to a 100,000,000 atoms, those methods are currently limited to studying small- to medium-sized molecular systems due to computational limitations. One solution to circumvent these limitations is to reduce the size of the system under study. In this paper, we argue that coarse-graining, the standard approach to such size reduction, must define a hierarchy of models of decreasing sizes that are consistent with each other, i.e., that each model contains the information of the dynamics of its predecessor. We propose a new method, Decimate, for generating such a hierarchy within the context of elastic networks for normal-mode analysis. This method is based on the concept of the renormalization group developed in statistical physics. We highlight the details of its implementation, with a special focus on its scalability to large systems of up to millions of atoms. We illustrate its application on two large systems, the capsid of a virus and the ribosome translation complex. We show that highly decimated representations of those systems, containing down to 1% of their original number of atoms, still capture qualitatively and quantitatively their dynamics. Decimate is available as an OpenSource resource.

  19. Molecular biology of sarcomas.

    PubMed

    Gebhardt, M C

    1996-07-01

    There has been a virtual explosion of information relating to the biology of sarcomas with which we as orthopaedists deal. Much more is yet to be learned. These findings will teach us more about the etiology of these tumors. More important, the findings will alter the way in which these tumors are treated. It is unlikely that we will continue to treat osteosarcoma or Ewing's sarcoma patients with currently available drug regimens and surgery or make treatment decisions based on the histologic classification of tumors we know today. If we are to remain active in the management of these patients we must be aware of the findings as they occur. That will ensure both that we remain the primary caretakers of these patients, and that we will continue to be stimulated intellectually by these intriguing scientific investigations.

  20. Rift Valley Fever Virus: Molecular Biologic Studies of the M Segment RNA for Application in Disease Prevention.

    DTIC Science & Technology

    1986-08-01

    AD-A174 610 RIFT VALLEY FEVER VIRUS- MOLECULAR BIOLOGIC STUDIES 6F 1/1 THE M SEGMENT RNA (U) MOLECULAR GENETICS INC MINNETONK~A MN M COLLETT AUG 86...Molecular Genetics , In. DTIC ioso Eron Road East --ELECTE -Minetnka, Minnesota 64 DEC 0 11986 DOD DISTRIBUTION unE"--£ Approved for public release...ForNTIS GRA&I DTIC TAB Contract No. DAMD17-8S-C-6220 U:Iannouned Justiff cat toa_____ Molecular Genetlcs. Inc. 1010 Oran Road East Mlnnetonka, Milnneoota

  1. Book review: Baculovirus Molecular Biology, Second Edition

    USDA-ARS?s Scientific Manuscript database

    The application of cell culture and molecular biology methodologies to the study of baculoviruses has resulted in an explosion of information on this group of insect pathogens. The quantity of the corresponding literature on baculoviruses has reached a level difficult for any one researcher to mast...

  2. Isolation of granulosa cells from follicular fluid; applications in biomedical and molecular biology experiments

    PubMed Central

    Aghadavod, Esmat; Zarghami, Nosratollah; Farzadi, Laya; Zare, Mina; Barzegari, Abolfazl; Movassaghpour, Ali Akbar; Nouri, Mohammad

    2015-01-01

    Background: Recently, a lot of research has been conducted to investigate the molecular mechanisms of the low quality of oocytes with granulosa cells (GCs). GCs are one of the major cell types found in follicular fluid and purification of these cells from the follicular fluid is very important for further studies. Although, there are different techniques of purification, a method for separation of highly-pure and minimally-damaged cells is necessary. In this paper, we presented a novel method for high purification of GCs with a large quantity and high purity. Materials and Methods: Follicular fluid was collected from patients who referred for in vitro fertilization and GCs in follicular fluid were extracted by Ficoll, Percoll and Red blood cell lysing buffer (RLB) methods. Then purity of extracted GCs was assessed by flow cytometry and morphological properties of GCs were observed by differential interference contrast microscopy. The purity of deoxyribonucleic acid and ribonucleic acid extracts was examined by NanoDrop 1000, pre-restriction fragment length polymorphism and electrophoresis techniques. Quality and quantity of extracting GCs were affected during the cell separation procedures. Results: Our results showed that each of purification method can affect quality and quantity of extracted cells. Conclusion: RLB method for extraction of GCs was shown to be a convenient procedure in comparison with Ficoll and Percoll methods. PMID:26918232

  3. Isolation of granulosa cells from follicular fluid; applications in biomedical and molecular biology experiments.

    PubMed

    Aghadavod, Esmat; Zarghami, Nosratollah; Farzadi, Laya; Zare, Mina; Barzegari, Abolfazl; Movassaghpour, Ali Akbar; Nouri, Mohammad

    2015-01-01

    Recently, a lot of research has been conducted to investigate the molecular mechanisms of the low quality of oocytes with granulosa cells (GCs). GCs are one of the major cell types found in follicular fluid and purification of these cells from the follicular fluid is very important for further studies. Although, there are different techniques of purification, a method for separation of highly-pure and minimally-damaged cells is necessary. In this paper, we presented a novel method for high purification of GCs with a large quantity and high purity. Follicular fluid was collected from patients who referred for in vitro fertilization and GCs in follicular fluid were extracted by Ficoll, Percoll and Red blood cell lysing buffer (RLB) methods. Then purity of extracted GCs was assessed by flow cytometry and morphological properties of GCs were observed by differential interference contrast microscopy. The purity of deoxyribonucleic acid and ribonucleic acid extracts was examined by NanoDrop 1000, pre-restriction fragment length polymorphism and electrophoresis techniques. Quality and quantity of extracting GCs were affected during the cell separation procedures. Our results showed that each of purification method can affect quality and quantity of extracted cells. RLB method for extraction of GCs was shown to be a convenient procedure in comparison with Ficoll and Percoll methods.

  4. Uveal melanoma and macular degeneration: molecular biology and potential therapeutic applications.

    PubMed

    Economou, Mario-Alexander

    2008-12-01

    Uveal melanoma is the most common primary intraocular malignant tumor in adults with 30% to 50% of patients that ultimately succumb to metastatic disease, mainly to the liver. (Shields et al. 1991) Although new diagnostic and therapeutic tools have been developed during the most recent years, only the eye conservation rate has been achieved, while the survival rate remains poor. The reason for this liver-homing is largely unknown, but it is conceivable that hepatic environmental factors may be implicated in the growth, dissemination, and progression of this malignancy. The insulin-like growth factor (IGF-1) that binds to the IGF-1 receptor (IGF-1R) is mainly produced in the liver. It has been shown to be crucial for tumor transformation, maintenance of malignant phenotype, promotion of cell growth, and prevention of apoptosis. (Baserga 1995) The hepatocyte growth factor/scatter factor (HGF/SF) is another growth factor produced in the liver and exerts its biological effects through binding to the plasma membrane receptor c-Met. The activation of this receptor by HGF/SF ligand can induce proliferation, motility, adhesion, and invasion of tumor cells. (Cruz et al. 2003) Metastasis is a process involving many components, including tumor cell adhesion, migration, extracellular matrix (ECM) proteolysis, and invasion. The tumor cells undergo intravasation, disperse via the vascular and the lymphatic systems, and finally extravasate to invade the secondary sites. In all these steps, proteolytic enzyme systems are involved, including the matrix metalloproteinase (MMP) system and the plasminogen activation system. The migration of a malignant cell through the ECM and the basement membrane requires proteolytic activities. (Stetler-Stevenson et al. 1993). Efforts to target the IGF-I system has been made with different types of cancer but not with uveal melanoma.

  5. Tetracycline Antibiotics: Mode of Action, Applications, Molecular Biology, and Epidemiology of Bacterial Resistance

    PubMed Central

    Chopra, Ian; Roberts, Marilyn

    2001-01-01

    Tetracyclines were discovered in the 1940s and exhibited activity against a wide range of microorganisms including gram-positive and gram-negative bacteria, chlamydiae, mycoplasmas, rickettsiae, and protozoan parasites. They are inexpensive antibiotics, which have been used extensively in the prophlylaxis and therapy of human and animal infections and also at subtherapeutic levels in animal feed as growth promoters. The first tetracycline-resistant bacterium, Shigella dysenteriae, was isolated in 1953. Tetracycline resistance now occurs in an increasing number of pathogenic, opportunistic, and commensal bacteria. The presence of tetracycline-resistant pathogens limits the use of these agents in treatment of disease. Tetracycline resistance is often due to the acquisition of new genes, which code for energy-dependent efflux of tetracyclines or for a protein that protects bacterial ribosomes from the action of tetracyclines. Many of these genes are associated with mobile plasmids or transposons and can be distinguished from each other using molecular methods including DNA-DNA hybridization with oligonucleotide probes and DNA sequencing. A limited number of bacteria acquire resistance by mutations, which alter the permeability of the outer membrane porins and/or lipopolysaccharides in the outer membrane, change the regulation of innate efflux systems, or alter the 16S rRNA. New tetracycline derivatives are being examined, although their role in treatment is not clear. Changing the use of tetracyclines in human and animal health as well as in food production is needed if we are to continue to use this class of broad-spectrum antimicrobials through the present century. PMID:11381101

  6. Design and construction of a first-generation high-throughput integrated robotic molecular biology platform for bioenergy applications

    USDA-ARS?s Scientific Manuscript database

    The molecular biological techniques for plasmid-based assembly and cloning of gene open reading frames are essential for elucidating the function of the proteins encoded by the genes. These techniques involve the production of full-length cDNA libraries as a source of plasmid-based clones to expres...

  7. Measurement Frontiers in Molecular Biology

    NASA Astrophysics Data System (ADS)

    Laderman, Stephen

    2009-03-01

    Developments of molecular measurements and manipulations have long enabled forefront research in evolution, genetics, biological development and its dysfunction, and the impact of external factors on the behavior of cells. Measurement remains at the heart of exciting and challenging basic and applied problems in molecular and cell biology. Methods to precisely determine the identity and abundance of particular molecules amongst a complex mixture of similar and dissimilar types require the successful design and integration of multiple steps involving biochemical manipulations, separations, physical probing, and data processing. Accordingly, today's most powerful methods for characterizing life at the molecular level depend on coordinated advances in applied physics, biochemistry, chemistry, computer science, and engineering. This is well illustrated by recent approaches to the measurement of DNA, RNA, proteins, and intact cells. Such successes underlie well founded visions of how molecular biology can further assist in answering compelling scientific questions and in enabling the development of remarkable advances in human health. These visions, in turn, are motivating the interdisciplinary creation of even more comprehensive measurements. As a further and closely related consequence, they are motivating innovations in the conceptual and practical approaches to organizing and visualizing large, complex sets of interrelated experimental results and distilling from those data compelling, informative conclusions.

  8. Nanotubes in biological applications.

    PubMed

    Mundra, Ruchir V; Wu, Xia; Sauer, Jeremy; Dordick, Jonathan S; Kane, Ravi S

    2014-08-01

    Researchers over the last few years have recognized carbon nanotubes (CNTs) as promising materials for a number of biological applications. CNTs are increasingly being explored as potent drug carriers for cancer treatment, for biosensing, and as scaffolds for stem cell culture. Moreover, the integration of CNTs with proteins has led to the development of functional nanocomposites with antimicrobial properties. This review aims at understanding the critical role of CNTs in biological applications with a particular emphasis on more recent studies.

  9. Molecular biology of the human brain

    SciTech Connect

    Jones, E.G.

    1988-01-01

    This book examines new methods of molecular biology that are providing valuable insights into the human brain, the genes that govern its assembly and function, and the many genetic defects that cause neurological diseases such as Alzheimer's, Cri du Chat syndrome, Huntington's disease, and bipolar depression disorder. In addition, the book reviews techniques in molecular neurobiological research, including the use of affinity reagents, chimeric receptors, and site-directed mutagenesis in localizing the ion channel and cholinergic binding site, and the application of somatic cell genetics in isolating specific chromosomes or chromosomal segments.

  10. Molecular biology of gastric cancer.

    PubMed

    Cervantes, A; Rodríguez Braun, E; Pérez Fidalgo, A; Chirivella González, I

    2007-04-01

    Despite its decreasing incidence overall, gastric cancer is still a challenging disease. Therapy is based mainly upon surgical resection when the tumour remains localised in the stomach. Conventional chemotherapy may play a role in treating micrometastatic disease and is effective as palliative therapy for recurrent or advanced disease. However, the knowledge of molecular pathways implicated in gastric cancer pathogenesis is still in its infancy and the contribution of molecular biology to the development of new targeted therapies in gastric cancer is far behind other more common cancers such as breast, colon or lung. This review will focus first on the difference of two well defined types of gastric cancer: intestinal and diffuse. A discussion of the cell of origin of gastric cancer with some intriguing data implicating bone marrow derived cells will follow, and a comprehensive review of different genetic alterations detected in gastric cancer, underlining those that may have clinical, therapeutic or prognostic implications.

  11. Molecular biology of nuclear autoantigens.

    PubMed

    Saitta, M R; Keene, J D

    1992-05-01

    This article provides a historical overview of the application of molecular and immunologic techniques to the analysis of autoantigenic structure and function, as well as to autoantibody recognition of protein and nucleic acid autoantigens. Examples presented here illustrate the role of autoantibodies as tools in the elucidation of the autoimmune components of cellular ribonucleoproteins. In turn, the subsequent molecular dissection of autoantigenic ribonucleoproteins has advanced understanding of autoantibody specificities. The nature of autoantibodies reactive with various proteins and nucleic acids will be the subject of the following articles in this issue. Taken together, these studies of antibody-antigen interactions that arise during the autoimmune response have revealed novel mechanisms of molecular recognition within the RNP autoantigens. These findings are of general importance for understanding basic cellular processes and have contributed to our knowledge of the underlying mechanisms of immunoregulatory abnormalities that arise in autoimmune diseases.

  12. [New concepts in molecular biology applied to traslational research].

    PubMed

    Mengual, Lourdes

    2013-06-01

    This chapter intends to introduce the new concepts that have been established in molecular biology over the last years and are being applied in translational research. The chapter is divided in four big blocks, which treat the molecular biology concepts and techniques in relation to DNA, RNA, proteins and metabolites, respectively. Moreover, we give examples of translational application of these new methodologies described.

  13. Molecular biology and the pediatric surgeon: definitions and basic methodology.

    PubMed

    Tagge, E P; Tagge, D U; Chandler, J C; Pitre, B R; Haddad, G; Frankel, A E; Willingham, M C; Garvin, A J; Papas, T S

    1996-08-01

    Molecular biology techniques and their application are becoming increasingly important to the practicing clinician. This article reviews the basics of DNA chemistry and highlights important molecular biology techniques. It will provide a guide for the pediatric surgeon as she/he attempts to integrate this field into everyday practice.

  14. Discovering the intelligence in molecular biology.

    PubMed

    Uberbacher, E

    1995-12-01

    The Third International Conference on Intelligent Systems in Molecular Biology was truly an outstanding event. Computational methods in molecular biology have reached a new level of maturity and utility, resulting in many high-impact applications. The success of this meeting bodes well for the rapid and continuing development of computational methods, intelligent systems and information-based approaches for the biosciences. The basic technology, originally most often applied to 'feasibility' problems, is now dealing effectively with the most difficult real-world problems. Significant progress has been made in understanding protein-structure information, structural classification, and how functional information and the relevant features of active-site geometry can be gleaned from structures by automated computational approaches. The value and limits of homology-based methods, and the ability to classify proteins by structure in the absence of homology, have reached a new level of sophistication. New methods for covariation analysis in the folding of large structures such as RNAs have shown remarkably good results, indicating the long-term potential to understand very complicated molecules and multimolecular complexes using computational means. Novel methods, such as HMMs, context-free grammars and the uses of mutual information theory, have taken center stage as highly valuable tools in our quest to represent and characterize biological information. A focus on creative uses of intelligent systems technologies and the trend toward biological application will undoubtedly continue and grow at the 1996 ISMB meeting in St Louis.

  15. The molecular biology of ilarviruses.

    PubMed

    Pallas, Vicente; Aparicio, Frederic; Herranz, Mari C; Sanchez-Navarro, Jesus A; Scott, Simon W

    2013-01-01

    Ilarviruses were among the first 16 groups of plant viruses approved by ICTV. Like Alfalfa mosaic virus (AMV), bromoviruses, and cucumoviruses they are isometric viruses and possess a single-stranded, tripartite RNA genome. However, unlike these other three groups, ilarviruses were recognized as being recalcitrant subjects for research (their ready lability is reflected in the sigla used to create the group name) and were renowned as unpromising subjects for the production of antisera. However, it was recognized that they shared properties with AMV when the phenomenon of genome activation, in which the coat protein (CP) of the virus is required to be present to initiate infection, was demonstrated to cross group boundaries. The CP of AMV could activate the genome of an ilarvirus and vice versa. Development of the molecular information for ilarviruses lagged behind the knowledge available for the more extensively studied AMV, bromoviruses, and cucumoviruses. In the past 20 years, genomic data for most known ilarviruses have been developed facilitating their detection and allowing the factors involved in the molecular biology of the genus to be investigated. Much information has been obtained using Prunus necrotic ringspot virus and the more extensively studied AMV. A relationship between some ilarviruses and the cucumoviruses has been defined with the recognition that members of both genera encode a 2b protein involved in RNA silencing and long distance viral movement. Here, we present a review of the current knowledge of both the taxonomy and the molecular biology of this genus of agronomically and horticulturally important viruses. Copyright © 2013 Elsevier Inc. All rights reserved.

  16. Design and construction of a first-generation high-throughput integrated robotic molecular biology platform for bioenergy applications.

    PubMed

    Hughes, Stephen R; Butt, Tauseef R; Bartolett, Scott; Riedmuller, Steven B; Farrelly, Philip

    2011-08-01

    The molecular biological techniques for plasmid-based assembly and cloning of gene open reading frames are essential for elucidating the function of the proteins encoded by the genes. High-throughput integrated robotic molecular biology platforms that have the capacity to rapidly clone and express heterologous gene open reading frames in bacteria and yeast and to screen large numbers of expressed proteins for optimized function are an important technology for improving microbial strains for biofuel production. The process involves the production of full-length complementary DNA libraries as a source of plasmid-based clones to express the desired proteins in active form for determination of their functions. Proteins that were identified by high-throughput screening as having desired characteristics are overexpressed in microbes to enable them to perform functions that will allow more cost-effective and sustainable production of biofuels. Because the plasmid libraries are composed of several thousand unique genes, automation of the process is essential. This review describes the design and implementation of an automated integrated programmable robotic workcell capable of producing complementary DNA libraries, colony picking, isolating plasmid DNA, transforming yeast and bacteria, expressing protein, and performing appropriate functional assays. These operations will allow tailoring microbial strains to use renewable feedstocks for production of biofuels, bioderived chemicals, fertilizers, and other coproducts for profitable and sustainable biorefineries.

  17. Molecular biology research in neuropsychiatry: India's contribution.

    PubMed

    Sathyanarayana Rao, T S; Ramesh, B N; Vasudevaraju, P; Rao, K S J

    2010-01-01

    Neuropsychiatric disorders represent the second largest cause of morbidity worldwide. These disorders have complex etiology and patho-physiology. The major lacunae in the biology of the psychiatric disorders include genomics, biomarkers and drug discovery, for the early detection of the disease, and have great application in the clinical management of disease. Indian psychiatrists and scientists played a significant role in filling the gaps. The present annotation provides in depth information related to research contributions on the molecular biology research in neuropsychiatric disorders in India. There is a great need for further research in this direction as to understand the genetic association of the neuropsychiatric disorders; molecular biology has a tremendous role to play. The alterations in gene expression are implicated in the pathogenesis of several neuropsychiatric disorders, including drug addiction and depression. The development of transgenic neuropsychiatric animal models is of great thrust areas. No studies from India in this direction. Biomarkers in neuropsychiatric disorders are of great help to the clinicians for the early diagnosis of the disorders. The studies related to gene-environment interactions, DNA instability, oxidative stress are less studied in neuropsychiatric disorders and making efforts in this direction will lead to pioneers in these areas of research in India. In conclusion, we provided an insight for future research direction in molecular understanding of neuropsychiatry disorders.

  18. The Gene Ontology (GO) project: structured vocabularies for molecular biology and their application to genome and expression analysis.

    PubMed

    Blake, Judith A; Harris, Midori A

    2008-09-01

    Scientists wishing to utilize genomic data have quickly come to realize the benefit of standardizing descriptions of experimental procedures and results for computer-driven information retrieval systems. The focus of the Gene Ontology project is three-fold. First, the project goal is to compile the Gene Ontologies: structured vocabularies describing domains of molecular biology. Second, the project supports the use of these structured vocabularies in the annotation of gene products. Third, the gene product-to-GO annotation sets are provided by participating groups to the public through open access to the GO database and Web resource. This unit describes the current ontologies and what is beyond the scope of the Gene Ontology project. It addresses the issue of how GO vocabularies are constructed and related to genes and gene products. It concludes with a discussion of how researchers can access, browse, and utilize the GO project in the course of their own research. Copyright 2008 by John Wiley & Sons, Inc.

  19. Molecular biology of weed control.

    PubMed

    Gressel, J

    2000-01-01

    The vast commercial effort to utilize chemical and molecular tools to solve weed control problems has had a major impact on the basic biological sciences as well as benefits to agriculture, and the first generation of transgenic products has been successful, while somewhat crude. More sophisticated products are envisaged and expected. Biotechnologically-derived herbicide-resistant crops have been a considerable benefit, yet in some cases there is a risk that the same useful transgenes may introgress into related weeds, specifically the weeds that are hardest to control without such transgenic crops. Biotechnology can also be used to mitigate the risks. Molecular tools should be considered for weed control without the use of, or with less chemicals, whether by enhancing crop competitiveness with weeds for light, nutrients and water, or via allelochemicals. Biocontrol agents may become more effective as well as more safe when rendered hypervirulent yet non-spreading by biotechnology. There might be ways to disperse deleterious transposons throughout weed populations, obviating the need to modify the crops.

  20. Molecular Imaging in Synthetic Biology, and Synthetic Biology in Molecular Imaging.

    PubMed

    Gilad, Assaf A; Shapiro, Mikhail G

    2017-02-17

    Biomedical synthetic biology is an emerging field in which cells are engineered at the genetic level to carry out novel functions with relevance to biomedical and industrial applications. This approach promises new treatments, imaging tools, and diagnostics for diseases ranging from gastrointestinal inflammatory syndromes to cancer, diabetes, and neurodegeneration. As these cellular technologies undergo pre-clinical and clinical development, it is becoming essential to monitor their location and function in vivo, necessitating appropriate molecular imaging strategies, and therefore, we have created an interest group within the World Molecular Imaging Society focusing on synthetic biology and reporter gene technologies. Here, we highlight recent advances in biomedical synthetic biology, including bacterial therapy, immunotherapy, and regenerative medicine. We then discuss emerging molecular imaging approaches to facilitate in vivo applications, focusing on reporter genes for noninvasive modalities such as magnetic resonance, ultrasound, photoacoustic imaging, bioluminescence, and radionuclear imaging. Because reporter genes can be incorporated directly into engineered genetic circuits, they are particularly well suited to imaging synthetic biological constructs, and developing them provides opportunities for creative molecular and genetic engineering.

  1. Preparation of 17β-estradiol surface molecularly imprinted polymers and their application to the analysis of biological samples.

    PubMed

    Zhang, Jing; Wang, Lingling; Han, Yanting

    2013-11-01

    17β-Estradiol (E2) surface molecularly imprinted polymers have been prepared using functionalized monodispersed poly(glycidyl methacrylate-co-ethylene dimethacrylate) beads as a support. The resulting polymers were found to be uniform in size (5 μm), and the surfaces of the microspheres possessed large pore-like structures. A chromatographic experiment demonstrated that the resulting microspheres exhibited high levels of recognition and selectivity toward the target molecule. The particles were employed as a novel sorbent in a molecularly imprinted SPE protocol. A method was then developed involving the combination of the pretreatment with HPLC to determine the levels of estrogen secreted from Michigan Cancer Foundation-7 cells. The obtained results revealed that the extraction recoveries of E2 from real samples were in the range of 73.0-97.5% with RSDs of < 7.5% (n = 3). Calibration curves were established with R values > 0.9996 for concentrations in the range of 0.50-100.00 ng/mL. The LOD of this new method was 0.14 ng/mL. Compared with traditional C18 SPE agents, the particles showed high selectivity and extraction efficiency for E2 in the pretreatment process. The particles could therefore be used to determine trace estrogen in biological samples with a UV detector only.

  2. Biological Applications of Protein Splicing

    PubMed Central

    Vila-Perelló, Miquel; Muir, Tom W.

    2010-01-01

    Protein splicing is a naturally-occurring process in which a protein editor, called an intein, performs a molecular disappearing act by cutting itself out of a host protein in a traceless manner. In the two decades since its discovery, protein splicing has been harnessed for the development of several protein-engineering methods. Collectively, these technologies help bridge the fields of chemistry and biology, allowing hitherto impossible manipulations of protein covalent structure. These tools and their application are the subject of this Primer. PMID:20946979

  3. History of the molecular biology of cytomegaloviruses.

    PubMed

    Stinski, Mark F

    2014-01-01

    The history of the molecular biology of cytomegaloviruses from the purification of the virus and the viral DNA to the cloning and expression of the viral genes is reviewed. A key genetic element of cytomegalovirus (the CMV promoter) contributed to our understanding of eukaryotic cell molecular biology and to the development of lifesaving therapeutic proteins. The study of the molecular biology of cytomegaloviruses also contributed to the development of antivirals to control the viral infection.

  4. Molecular biology for the pediatric surgeon.

    PubMed

    Boulanger, S C; Caty, M G; Glick, P L

    1999-06-01

    Molecular biology is leading a revolution in our understanding, diagnosis, and treatment of disease and will continue to do so. Medicine in the future will require a greater understanding of this field and its methods by medical practitioners. This report reviews the basic aspects of the field including recombinant DNA methods. Of particular importance is how molecular biology will impact pediatric surgeons. Accordingly, the final section of this report briefly reviews the molecular biology of three diseases commonly treated by pediatric surgeons.

  5. Molecular biology of lung cancer.

    PubMed

    Cooper, Wendy A; Lam, David C L; O'Toole, Sandra A; Minna, John D

    2013-10-01

    Lung cancers are characterised by abundant genetic diversity with relatively few recurrent mutations occurring at high frequency. However, the genetic alterations often affect a common group of oncogenic signalling pathways. There have been vast improvements in our understanding of the molecular biology that underpins lung cancer in recent years and this has led to a revolution in the diagnosis and treatment of lung adenocarcinomas (ADC) based on the genotype of an individual's tumour. New technologies are identifying key and potentially targetable genetic aberrations not only in adenocarcinoma but also in squamous cell carcinoma (SCC) of the lung. Lung cancer mutations have been identified in v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS), epidermal growth factor receptor (EGFR), BRAF and the parallel phosphatidylinositol 3-kinase (PI3K) pathway oncogenes and more recently in MEK and HER2 while structural rearrangements in ALK, ROS1 and possibly rearranged during transfection (RET) provide new therapeutic targets. Amplification is another mechanism of activation of oncogenes such as MET in adenocarcinoma, fibroblastgrowth factor receptor 1 (FGFR1) and discoidin domain receptor 2 (DDR2) in SCC. Intriguingly, many of these genetic alternations are associated with smoking status and with particular racial and gender differences, which may provide insight into the mechanisms of carcinogenesis and role of host factors in lung cancer development and progression. The role of tumour suppressor genes is increasingly recognised with aberrations reported in TP53, PTEN, RB1, LKB11 and p16/CDKN2A. Identification of biologically significant genetic alterations in lung cancer that lead to activation of oncogenes and inactivation of tumour suppressor genes has the potential to provide further therapeutic opportunities. It is hoped that these discoveries may make a major contribution to improving outcome for patients with this poor prognosis disease.

  6. 2009 Archaea: Ecology, Metabolism & Molecular Biology GRC

    SciTech Connect

    Furlow, Julie Maupin-

    2009-07-26

    Archaea, one of three major evolutionary lineages of life, are a fascinating and diverse group of microbes with deep roots overlapping those of eukaryotes. The focus of the 'Archaea: Ecology Metabolism & Molecular Biology' GRC conference expands on a number of emerging topics highlighting new paradigms in archaeal metabolism, genome function and systems biology; information processing; evolution and the tree of life; the ecology and diversity of archaea and their viruses; and industrial applications. The strength of this conference lies in its ability to couple a field with a rich history in high quality research with new scientific findings in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

  7. Molecular Biological Methods in Environmental Engineering.

    PubMed

    Zhang, Guocai; Wei, Li; Chang, Chein-Chi; Zhang, Yuhua; Wei, Dong

    2016-10-01

    Bacteria, acting as catalysts, perform the function of degrading pollutants. Molecular biological techniques play an important role in research on the community analysis, the composition and the functions of complex microbial communities. The development of secondary high-throughput pyrosequencing techiniques enhances the understanding of the composition of the microbial community. The literatures of 2015 indicated that 16S rDNA gene as genetic tag is still the important method for bacteria identification and classification. 454 high throughput sequencing and Illumina MiSeq sequencing have been the primary and widely recognized methods to analyze the microbial. This review will provide environmental engineers and microbiologists an overview of important advancements in molecular techniques and highlight the application of these methods in diverse environments.

  8. On anti-portfolio effects in science and technology with application to reaction kinetics, chemical synthesis, and molecular biology

    PubMed Central

    Vlad, Marcel O.; Corlan, Alexandru Dan; Popa, Vlad T.; Ross, John

    2007-01-01

    The portfolio effect is the increase of the stability of a system to random fluctuations with the increase of the number of random state variables due to spreading the risk among these variables; many examples exist in various areas of science and technology. We report the existence of an opposite effect, the decrease of stability to random fluctuations due to an increase of the number of random state variables. For successive industrial or biochemical processes of independent, random efficiencies, the stability of the total efficiency decreases with the increase of the number of processes. Depending on the variables considered, the same process may display both a portfolio as well as an anti-portfolio behavior. In disordered kinetics, the activation energy of a reaction or transport process is the result of a sum of random components. Although the total activation energy displays a portfolio effect, the rate coefficient displays an anti-portfolio effect. For random-channel kinetics, the stability of the total rate coefficient increases with the average number of reaction pathways, whereas the stability of the survival function has an opposite behavior: it decreases exponentially with the increase of the average number of reaction pathways (anti-portfolio effect). In molecular biology, the total rate of a nucleotide substitution displays a portfolio effect, whereas the probability that no substitutions occur displays an anti-portfolio effect, resulting in faster evolutionary processes due to fluctuations. The anti-portfolio effect emerges for products of random variables or equations involving multiplicative convolution products. PMID:18003905

  9. On anti-portfolio effects in science and technology with application to reaction kinetics, chemical synthesis, and molecular biology.

    PubMed

    Vlad, Marcel O; Corlan, Alexandru Dan; Popa, Vlad T; Ross, John

    2007-11-20

    The portfolio effect is the increase of the stability of a system to random fluctuations with the increase of the number of random state variables due to spreading the risk among these variables; many examples exist in various areas of science and technology. We report the existence of an opposite effect, the decrease of stability to random fluctuations due to an increase of the number of random state variables. For successive industrial or biochemical processes of independent, random efficiencies, the stability of the total efficiency decreases with the increase of the number of processes. Depending on the variables considered, the same process may display both a portfolio as well as an anti-portfolio behavior. In disordered kinetics, the activation energy of a reaction or transport process is the result of a sum of random components. Although the total activation energy displays a portfolio effect, the rate coefficient displays an anti-portfolio effect. For random-channel kinetics, the stability of the total rate coefficient increases with the average number of reaction pathways, whereas the stability of the survival function has an opposite behavior: it decreases exponentially with the increase of the average number of reaction pathways (anti-portfolio effect). In molecular biology, the total rate of a nucleotide substitution displays a portfolio effect, whereas the probability that no substitutions occur displays an anti-portfolio effect, resulting in faster evolutionary processes due to fluctuations. The anti-portfolio effect emerges for products of random variables or equations involving multiplicative convolution products.

  10. Biologically effective dose in fractionated molecular radiotherapy—application to treatment of neuroblastoma with 131I-mIBG

    NASA Astrophysics Data System (ADS)

    Mínguez, Pablo; Gustafsson, Johan; Flux, Glenn; Sjögreen Gleisner, Katarina

    2016-03-01

    In this work, the biologically effective dose (BED) is investigated for fractionated molecular radiotherapy (MRT). A formula for the Lea-Catcheside G-factor is derived which takes the possibility of combinations of sub-lethal damage due to radiation from different administrations of activity into account. In contrast to the previous formula, the new G-factor has an explicit dependence on the time interval between administrations. The BED of tumour and liver is analysed in MRT of neuroblastoma with 131I-mIBG, following a common two-administration protocol with a mass-based activity prescription. A BED analysis is also made for modified schedules, when due to local regulations there is a maximum permitted activity for each administration. Modifications include both the simplistic approach of delivering this maximum permitted activity in each of the two administrations, and also the introduction of additional administrations while maintaining the protocol-prescribed total activity. For the cases studied with additional (i.e. more than two) administrations, BED of tumour and liver decreases at most 12% and 29%, respectively. The decrease in BED of the tumour is however modest compared to the two-administration schedule using the maximum permitted activity, where the decrease compared to the original schedule is 47%.

  11. Molecular imprinting: perspectives and applications.

    PubMed

    Chen, Lingxin; Wang, Xiaoyan; Lu, Wenhui; Wu, Xiaqing; Li, Jinhua

    2016-04-21

    Molecular imprinting technology (MIT), often described as a method of making a molecular lock to match a molecular key, is a technique for the creation of molecularly imprinted polymers (MIPs) with tailor-made binding sites complementary to the template molecules in shape, size and functional groups. Owing to their unique features of structure predictability, recognition specificity and application universality, MIPs have found a wide range of applications in various fields. Herein, we propose to comprehensively review the recent advances in molecular imprinting including versatile perspectives and applications, concerning novel preparation technologies and strategies of MIT, and highlight the applications of MIPs. The fundamentals of MIPs involving essential elements, preparation procedures and characterization methods are briefly outlined. Smart MIT for MIPs is especially highlighted including ingenious MIT (surface imprinting, nanoimprinting, etc.), special strategies of MIT (dummy imprinting, segment imprinting, etc.) and stimuli-responsive MIT (single/dual/multi-responsive technology). By virtue of smart MIT, new formatted MIPs gain popularity for versatile applications, including sample pretreatment/chromatographic separation (solid phase extraction, monolithic column chromatography, etc.) and chemical/biological sensing (electrochemical sensing, fluorescence sensing, etc.). Finally, we propose the remaining challenges and future perspectives to accelerate the development of MIT, and to utilize it for further developing versatile MIPs with a wide range of applications (650 references).

  12. Monod and the spirit of molecular biology.

    PubMed

    Morange, Michel

    2015-06-01

    The founders of molecular biology shared views on the place of biology within science, as well as on the relations of molecular biology to Darwinism. Jacques Monod was no exception, but the study of his writings is particularly interesting because he expressed his point of view very clearly and pushed the implications of some of his choices further than most of his contemporaries. The spirit of molecular biology is no longer the same as in the 1960s but, interestingly, Monod anticipated some recent evolutions of this discipline.

  13. Molecular biology of microbial ureases.

    PubMed Central

    Mobley, H L; Island, M D; Hausinger, R P

    1995-01-01

    progress in our understanding of the molecular biology of microbial ureases is reviewed. PMID:7565414

  14. Genetics and molecular biology in laboratory medicine, 1963-2013.

    PubMed

    Whitfield, John B

    2013-01-01

    The past 50 years have seen many changes in laboratory medicine, either as causes or consequences of increases in productivity and expansion of the range of information which can be provided. The drivers and facilitators of change in relation to clinical applications of molecular biology included the need for diagnostic tools for genetic diseases and technical advances such as PCR and sequencing. However, molecular biology techniques have proved to have far wider applications, from detection of infectious agents to molecular characterization of tumors. Journals such as Clinical Chemistry and Laboratory Medicine play an important role in communication of these advances to the laboratory medicine community and in publishing evaluations of their practical value.

  15. Molecular biology of the peptide hormone families.

    PubMed

    Pearson, R K; Anderson, B; Dixon, J E

    1993-12-01

    The application of recombinant molecular biology has lead to remarkable advances in our understanding of the basic mechanisms of cell function in general and of the polarized GI endocrine cell in particular. This article focuses on some of the advances made towards determining the contribution of peptide hormone gene regulation to the regulation of physiological events in the GI tract. Application of these techniques to other subcellular processes involved in peptide hormone physiology such as subcellular trafficing in the regulated secretory pathway and post-translational processing have been equally impressive. For example, many of the key enzymes in the peptide hormone processing cascade have been cloned and are being studied at a molecular level. We have focused this article on the SS and gastrin peptides because of their known physiologic importance and interactions, and the depth of analysis accomplished to date. Studies using SS and gastrin as models have established principals that cover the spectrum of luminal regulation of gene activity to the identification of a single amino acid residue responsible for cAMP induction of SS gene expression. Many genes in the GI endocrine system have been cloned and the article by Dr. Habener (elsewhere in this issue) discusses progress made in understanding the complex regulation of the glucagon gene. We anticipate similar advances in studies of cholecystokinin, secretin, motilin, VIP, pancreatic polypeptide, and neuropeptide Y, whose genes have been cloned and initially characterized. Finally, as outlined in this article, the mechanisms of regulation of a specific gene often differ between sites of expression, even within the GI tract. Direct studies of the subcellular mechanisms regulating gene expression and other processes in GI endocrine cells await novel methods to maintain and propagate these cells. These studies will almost certainly involve new and creative uses of recombinant molecular biology.

  16. Does the Committee Peer Review Select the Best Applicants for Funding? An Investigation of the Selection Process for Two European Molecular Biology Organization Programmes

    PubMed Central

    Bornmann, Lutz; Wallon, Gerlind; Ledin, Anna

    2008-01-01

    Does peer review fulfill its declared objective of identifying the best science and the best scientists? In order to answer this question we analyzed the Long-Term Fellowship and the Young Investigator programmes of the European Molecular Biology Organization. Both programmes aim to identify and support the best post doctoral fellows and young group leaders in the life sciences. We checked the association between the selection decisions and the scientific performance of the applicants. Our study involved publication and citation data for 668 applicants to the Long-Term Fellowship programme from the year 1998 (130 approved, 538 rejected) and 297 applicants to the Young Investigator programme (39 approved and 258 rejected applicants) from the years 2001 and 2002. If quantity and impact of research publications are used as a criterion for scientific achievement, the results of (zero-truncated) negative binomial models show that the peer review process indeed selects scientists who perform on a higher level than the rejected ones subsequent to application. We determined the extent of errors due to over-estimation (type I errors) and under-estimation (type 2 errors) of future scientific performance. Our statistical analyses point out that between 26% and 48% of the decisions made to award or reject an application show one of both error types. Even though for a part of the applicants, the selection committee did not correctly estimate the applicant's future performance, the results show a statistically significant association between selection decisions and the applicants' scientific achievements, if quantity and impact of research publications are used as a criterion for scientific achievement. PMID:18941530

  17. Homology in classical and molecular biology.

    PubMed

    Patterson, C

    1988-11-01

    Hypotheses of homology are the basis of comparative morphology and comparative molecular biology. The kinds of homologous and nonhomologous relations in classical and molecular biology are explored through the three tests that may be applied to a hypothesis of homology: congruence, conjunction, and similarity. The same three tests apply in molecular comparisons and in morphology, and in each field they differentiate eight kinds of relation. These various relations are discussed and compared. The unit or standard of comparison differs in morphology and in molecular biology; in morphology it is the adult or life cycle, but with molecules it is the haploid genome. In morphology the congruence test is decisive in separating homology and nonhomology, whereas with molecular sequence data similarity is the decisive test. Consequences of this difference are that the boundary between homology and nonhomology is not the same in molecular biology as in morphology, that homology and synapomorphy can be equated in morphology but not in all molecular comparisons, and that there is no detected molecular equivalent of convergence. Since molecular homology may reflect either species phylogeny or gene phylogeny, there are more kinds of homologous relation between molecular sequences than in morphology. The terms paraxenology and plerology are proposed for two of these kinds--respectively, the consequence of multiple xenology and of gene conversion.

  18. Molecular biology of lung cancer: clinical implications.

    PubMed

    Larsen, Jill E; Minna, John D

    2011-12-01

    Lung cancer is a heterogeneous disease clinically, biologically, histologically, and molecularly. Understanding the molecular causes of this heterogeneity, which might reflect changes occurring in different classes of epithelial cells or different molecular changes occurring in the same target lung epithelial cells, is the focus of current research. Identifying the genes and pathways involved, determining how they relate to the biological behavior of lung cancer, and their utility as diagnostic and therapeutic targets are important basic and translational research issues. This article reviews current information on the key molecular steps in lung cancer pathogenesis, their timing, and clinical implications. Published by Elsevier Inc.

  19. The Molecular Biology Capstone Assessment: A Concept Assessment for Upper-Division Molecular Biology Students

    ERIC Educational Resources Information Center

    Couch, Brian A.; Wood, William B.; Knight, Jennifer K.

    2015-01-01

    Measuring students' conceptual understandings has become increasingly important to biology faculty members involved in evaluating and improving departmental programs. We developed the Molecular Biology Capstone Assessment (MBCA) to gauge comprehension of fundamental concepts in molecular and cell biology and the ability to apply these concepts in…

  20. The Molecular Biology Capstone Assessment: A Concept Assessment for Upper-Division Molecular Biology Students

    ERIC Educational Resources Information Center

    Couch, Brian A.; Wood, William B.; Knight, Jennifer K.

    2015-01-01

    Measuring students' conceptual understandings has become increasingly important to biology faculty members involved in evaluating and improving departmental programs. We developed the Molecular Biology Capstone Assessment (MBCA) to gauge comprehension of fundamental concepts in molecular and cell biology and the ability to apply these concepts in…

  1. Genetics and molecular biology of breast cancer

    SciTech Connect

    King, M.C.; Lippman, M.

    1992-12-31

    This volume contains the abstracts of oral presentations and poster sessions presented at the Cold Springs Harbor Meeting on Cancer Cells, this meeting entitled Genetics and Molecular Biology of Breast Cancer.

  2. Applications of Molecular Imaging

    PubMed Central

    Galbán, Craig; Galbán, Stefanie; Van Dort, Marcian; Luker, Gary D.; Bhojani, Mahaveer S.; Rehemtualla, Alnawaz; Ross, Brian D.

    2015-01-01

    Today molecular imaging technologies play a central role in clinical oncology. The use of imaging techniques in early cancer detection, treatment response and new therapy development is steadily growing and has already significantly impacted clinical management of cancer. In this chapter we will overview three different molecular imaging technologies used for the understanding of disease biomarkers, drug development, or monitoring therapeutic outcome. They are (1) optical imaging (bioluminescence and fluorescence imaging) (2) magnetic resonance imaging (MRI), and (3) nuclear imaging (e.g, single photon emission computed tomography (SPECT) and positron emission tomography (PET)). We will review the use of molecular reporters of biological processes (e.g. apoptosis and protein kinase activity) for high throughput drug screening and new cancer therapies, diffusion MRI as a biomarker for early treatment response and PET and SPECT radioligands in oncology. PMID:21075334

  3. Seeing the Unseen: Molecular Visualization in Biology

    ERIC Educational Resources Information Center

    Finnan, Jeff; Taylor-Papp, Kim; Duran, Mesut

    2005-01-01

    In high school biology, students are challenged by many molecular concepts and structures. They meander through a number of molecular structures, some in macromolecular form: carbohydrates, amino acids, fatty acids, nucleotides. Student difficulties arise in part from inability to visualize what they can't easily see. Students struggle moving from…

  4. Emerging molecular approaches in stem cell biology.

    PubMed

    Jaishankar, Amritha; Vrana, Kent

    2009-04-01

    Stem cells are characterized by their ability to self-renew and differentiate into multiple adult cell types. Although substantial progress has been made over the last decade in understanding stem cell biology, recent technological advances in molecular and systems biology may hold the key to unraveling the mystery behind stem cell self-renewal and plasticity. The most notable of these advances is the ability to generate induced pluripotent cells from somatic cells. In this review, we discuss our current understanding of molecular similarities and differences among various stem cell types. Moreover, we survey the current state of systems biology and forecast future needs and direction in the stem cell field.

  5. [Physical methods and molecular biology].

    PubMed

    Serdiuk, I N

    2009-01-01

    The review is devoted to the description of the current state of physical and chemical methods used for studying the structural and functional bases of living processes. Special attention is focused on the physical methods that have opened a new page in the research of the structure of biological macromolecules. They include primarily the methods of detecting and manipulating single molecules using optical and magnetic traps. New physical methods, such as two-dimensional infrared spectroscopy, fluorescence correlation spectroscopy and magnetic resonance microscopy are also analyzed briefly in the review. The path that physics and biology have passed for the latest 55 years shows that there is no single method providing all necessary information on macromolecules and their interactions. Each method provides its space-time view of the system. All physical methods are complementary. It is just complementarity that is the fundamental idea justifying the existence in practice of all physical methods, whose description is the aim of the review.

  6. Singlet molecular oxygen generated by biological hydroperoxides.

    PubMed

    Miyamoto, Sayuri; Martinez, Glaucia R; Medeiros, Marisa H G; Di Mascio, Paolo

    2014-10-05

    The chemistry behind the phenomenon of ultra-weak photon emission has been subject of considerable interest for decades. Great progress has been made on the understanding of the chemical generation of electronically excited states that are involved in these processes. Proposed mechanisms implicated the production of excited carbonyl species and singlet molecular oxygen in the mechanism of generation of chemiluminescence in biological system. In particular, attention has been focused on the potential generation of singlet molecular oxygen in the recombination reaction of peroxyl radicals by the Russell mechanism. In the last ten years, our group has demonstrated the generation of singlet molecular oxygen from reactions involving the decomposition of biologically relevant hydroperoxides, especially from lipid hydroperoxides in the presence of metal ions, peroxynitrite, HOCl and cytochrome c. In this review we will discuss details on the chemical aspects related to the mechanism of singlet molecular oxygen generation from different biological hydroperoxides.

  7. Molecular biology of pancreatic cancer

    PubMed Central

    Zavoral, Miroslav; Minarikova, Petra; Zavada, Filip; Salek, Cyril; Minarik, Marek

    2011-01-01

    In spite of continuous research efforts directed at early detection and treatment of pancreatic cancer, the outlook for patients affected by the disease remains dismal. With most cases still being diagnosed at advanced stages, no improvement in survival prognosis is achieved with current diagnostic imaging approaches. In the absence of a dominant precancerous condition, several risk factors have been identified including family history, chronic pancreatitis, smoking, diabetes mellitus, as well as certain genetic disorders such as hereditary pancreatitis, cystic fibrosis, familial atypical multiple mole melanoma, and Peutz–Jeghers and Lynch syndromes. Most pancreatic carcinomas, however, remain sporadic. Current progress in experimental molecular techniques has enabled detailed understanding of the molecular processes of pancreatic cancer development. According to the latest information, malignant pancreatic transformation involves multiple oncogenes and tumor-suppressor genes that are involved in a variety of signaling pathways. The most characteristic aberrations (somatic point mutations and allelic losses) affect oncogenes and tumor-suppressor genes within RAS, AKT and Wnt signaling, and have a key role in transcription and proliferation, as well as systems that regulate the cell cycle (SMAD/DPC, CDKN2A/p16) and apoptosis (TP53). Understanding of the underlying molecular mechanisms should promote development of new methodology for early diagnosis and facilitate improvement in current approaches for pancreatic cancer treatment. PMID:21734801

  8. Synthetic biology platform technologies for antimicrobial applications.

    PubMed

    Braff, Dana; Shis, David; Collins, James J

    2016-10-01

    The growing prevalence of antibiotic resistance calls for new approaches in the development of antimicrobial therapeutics. Likewise, improved diagnostic measures are essential in guiding the application of targeted therapies and preventing the evolution of therapeutic resistance. Discovery platforms are also needed to form new treatment strategies and identify novel antimicrobial agents. By applying engineering principles to molecular biology, synthetic biologists have developed platforms that improve upon, supplement, and will perhaps supplant traditional broad-spectrum antibiotics. Efforts in engineering bacteriophages and synthetic probiotics demonstrate targeted antimicrobial approaches that can be fine-tuned using synthetic biology-derived principles. Further, the development of paper-based, cell-free expression systems holds promise in promoting the clinical translation of molecular biology tools for diagnostic purposes. In this review, we highlight emerging synthetic biology platform technologies that are geared toward the generation of new antimicrobial therapies, diagnostics, and discovery channels.

  9. BIOLOGICAL FORMATION OF MOLECULAR HYDROGEN.

    PubMed

    GRAY, C T; GEST, H

    1965-04-09

    From a general standpoint, the formation of molecular hydrogen can be considered a device for disposal of electrons released in metabolic oxidations. We presume that this means of performing anaerobic oxidations is of ancient origin and that the hydrogen-evolving system of strict anaerobes represents a primitive form of cytochrome oxidase, which in aerobes effects the terminal step of respiration, namely the disposal of electrons by combination with molecular oxygen. We further assume that the original pattern of reactions leading to H(2) production has become modified in various ways (with respect to both mechanisms and functions) during the course of biochemical evolution, and we believe that this point of view suggests profitable approaches for clarifying a number of problems in the intermediary metabolism of microorganisms which produce or utilize H(2). Of special general importance in this connection is the basic problem of defining more precisely the fundamental elements in the regulatory control of anaerobic energy metabolism. Among the more specific aspects awaiting further elucidation are: the relations between formation of H(2) and use of H(2) as a primary reductant for biosynthetic purposes; the various forms of direct and indirect interactions between hydrogenase and N(2) reduction systems; and the transitional stages between anaerobic and aerobic energy-metabolism patterns of facultative organisms.

  10. [Molecular biology methods in immunohematology].

    PubMed

    Tournamille, C

    2013-05-01

    The molecular basis of almost all antigens of the 33 blood group systems are known. These knowledge and the advent of the PCR technology have allowed the DNA-based genotyping in order to predict the presence or absence of a blood group antigen on the cell membrane of red blood cells. DNA genotyping is required in cases where red blood cells patient cannot be used for serological typing either after a recent transfusion or because of the presence of autoantibodies on the red blood cells. Numerous DNA assays are available to detect any nucleotide polymorphism on the genes encoding blood group antigens. The technologies have improved to answer quickly to any case of transfusion emergency and to limit the risk of DNA contamination in a molecular diagnostic laboratory. Some technologies are ready for high-throughput blood group genotyping. They will be used in the future to obtain a fully typed blood group card of each donor but also to detect blood donors with rare phenotypes to register them to the Banque Nationale de Sang de Phénotype Rare (BNSPR).

  11. The nucleic acid revolution continues - will forensic biology become forensic molecular biology?

    PubMed

    Gunn, Peter; Walsh, Simon; Roux, Claude

    2014-01-01

    Molecular biology has evolved far beyond that which could have been predicted at the time DNA identity testing was established. Indeed we should now perhaps be referring to "forensic molecular biology." Aside from DNA's established role in identifying the "who" in crime investigations, other developments in medical and developmental molecular biology are now ripe for application to forensic challenges. The impact of DNA methylation and other post-fertilization DNA modifications, plus the emerging role of small RNAs in the control of gene expression, is re-writing our understanding of human biology. It is apparent that these emerging technologies will expand forensic molecular biology to allow for inferences about "when" a crime took place and "what" took place. However, just as the introduction of DNA identity testing engendered many challenges, so the expansion of molecular biology into these domains will raise again the issues of scientific validity, interpretation, probative value, and infringement of personal liberties. This Commentary ponders some of these emerging issues, and presents some ideas on how they will affect the conduct of forensic molecular biology in the foreseeable future.

  12. The nucleic acid revolution continues – will forensic biology become forensic molecular biology?

    PubMed Central

    Gunn, Peter; Walsh, Simon; Roux, Claude

    2014-01-01

    Molecular biology has evolved far beyond that which could have been predicted at the time DNA identity testing was established. Indeed we should now perhaps be referring to “forensic molecular biology.” Aside from DNA’s established role in identifying the “who” in crime investigations, other developments in medical and developmental molecular biology are now ripe for application to forensic challenges. The impact of DNA methylation and other post-fertilization DNA modifications, plus the emerging role of small RNAs in the control of gene expression, is re-writing our understanding of human biology. It is apparent that these emerging technologies will expand forensic molecular biology to allow for inferences about “when” a crime took place and “what” took place. However, just as the introduction of DNA identity testing engendered many challenges, so the expansion of molecular biology into these domains will raise again the issues of scientific validity, interpretation, probative value, and infringement of personal liberties. This Commentary ponders some of these emerging issues, and presents some ideas on how they will affect the conduct of forensic molecular biology in the foreseeable future. PMID:24634675

  13. Biological spectra analysis: Linking biological activity profiles to molecular structure

    PubMed Central

    Fliri, Anton F.; Loging, William T.; Thadeio, Peter F.; Volkmann, Robert A.

    2005-01-01

    Establishing quantitative relationships between molecular structure and broad biological effects has been a longstanding challenge in science. Currently, no method exists for forecasting broad biological activity profiles of medicinal agents even within narrow boundaries of structurally similar molecules. Starting from the premise that biological activity results from the capacity of small organic molecules to modulate the activity of the proteome, we set out to investigate whether descriptor sets could be developed for measuring and quantifying this molecular property. Using a 1,567-compound database, we show that percent inhibition values, determined at single high drug concentration in a battery of in vitro assays representing a cross section of the proteome, provide precise molecular property descriptors that identify the structure of molecules. When broad biological activity of molecules is represented in spectra form, organic molecules can be sorted by quantifying differences between biological spectra. Unlike traditional structure–activity relationship methods, sorting of molecules by using biospectra comparisons does not require knowledge of a molecule's putative drug targets. To illustrate this finding, we selected as starting point the biological activity spectra of clotrimazole and tioconazole because their putative target, lanosterol demethylase (CYP51), was not included in the bioassay array. Spectra similarity obtained through profile similarity measurements and hierarchical clustering provided an unbiased means for establishing quantitative relationships between chemical structures and biological activity spectra. This methodology, which we have termed biological spectra analysis, provides the capability not only of sorting molecules on the basis of biospectra similarity but also of predicting simultaneous interactions of new molecules with multiple proteins. PMID:15625110

  14. Molecular biology of epilepsy genes.

    PubMed

    Williams, Charles A; Battaglia, Agatino

    2013-06-01

    Multifactorial inheritance is the most important model accounting for the genetic behavior of the common epilepsies. Important to this model is the concept that many cumulative or synergistic risk genes ultimately lead to a threshold effect. Sophisticated molecular testing indicates that the common epilepsies are very polygenic without evidence of any single gene having even a mild-to-modest risk effect. However, enrichment of copy number variants in cohorts of individuals with epilepsy indicates that certain structural changes in the genome can confer significant risk for epilepsy. The mechanisms whereby copy number variants confer this effect are not yet known. The study of epilepsy due to single gene defects however has helped clarify certain seizure mechanisms. For example, discoveries using animal models of SCN1A or ARX mutations implicate a predominant role for interneurons due to disturbed GABAergic function. It is hoped that future genetic and neurobiological studies will provide better insight into how multiple genes contribute to the common epilepsies.

  15. Physics and the origins of molecular biology.

    PubMed

    Holliday, Robin

    2006-08-01

    Bohr, Delbrück and Schrödinger were physicists who had important influences on biology in the second half of the twentieth century. They thought that future studies of the gene might reveal new principles or paradoxes, analogous to the wave/particle paradox of light propagation, or even new physical laws. This stimulated several physicists to enter the field of biology. Delbrück founded the bacteriophage group which provided one of the roots of molecular biology. Another was X-ray crystallography which led to the discovery of DNA structure. The strength and success of molecular biology came from the many interactions between geneticists, physicists, chemists and biochemists. It was also characterized by a powerful combination of theoretical and experimental approaches.

  16. Molecular Mechanism of Biological Proton Transport

    SciTech Connect

    Pomes, R.

    1998-09-01

    Proton transport across lipid membranes is a fundamental aspect of biological energy transduction (metabolism). This function is mediated by a Grotthuss mechanism involving proton hopping along hydrogen-bonded networks embedded in membrane-spanning proteins. Using molecular simulations, the authors have explored the structural, dynamic, and thermodynamic properties giving rise to long-range proton translocation in hydrogen-bonded networks involving water molecules, or water wires, which are emerging as ubiquitous H{sup +}-transport devices in biological systems.

  17. Frontiers of NMR in Molecular Biology

    SciTech Connect

    1999-08-25

    NMR spectroscopy is expanding the horizons of structural biology by determining the structures and describing the dynamics of blobular proteins in aqueous solution, as well as other classes of proteins including membrane proteins and the polypeptides that form the aggregates diagnostic of prion and amyloid diseases. Significant results are also emerging on DNA and RNA oligomers and their complexes with proteins. This meeting focused attention on key structural questions emanating from molecular biology and how NMR spectroscopy can be used to answer them.

  18. Dictyostelium discoideum: Molecular approaches to cell biology

    SciTech Connect

    Spudich, J.A.

    1987-01-01

    The central point of this book is to present Dictyostelium as a valuable eukaryotic organism for those interested in molecular studies that require a combined biochemical, structural, and genetic approach. The book is not meant to be a comprehensive compilation of all methods involving Dictyostelium, but instead is a selective set of chapters that demonstrates the utility of the organism for molecular approaches to interesting cell biological problems.

  19. Biological (Molecular and Cellular) Markers of Toxicity.

    DTIC Science & Technology

    1991-12-15

    other mammals (Farber, 1987). Therefore, if we are to understand in any depth the processes by which environnental chemicals exhibit genotoxicity ... effectiveness to detect and quantitate biological responses at the molecular level to the action of genotoxic agenst. Particular emphasis was placed on the...Task 3. The short-term responses of the molecular markers as suitable biomarkers to estimate exposure and predict cellular effects to genotoxic

  20. Molecular Biology and Physiology of Methanogenic Archaebacteria

    DTIC Science & Technology

    1989-06-27

    study the biochemistry, genetics , and molecular biology of the thermophilic autotroph Methanobacterium thermoautotrophicum. DNA from antimetabolite...pH 7) [6]. A putatively anabolic enzyme converted to a catabolic role would be of interest. IV. Prospects. A basis for progress in the genetics and...which will be pursued and described. New molecular techniques, such as additive transformation, can be applied to our genetic system. 11 Our

  1. Application of culture culture-independent molecular biology based methods to evaluate acetic acid bacteria diversity during vinegar processing.

    PubMed

    Ilabaca, Carolina; Navarrete, Paola; Mardones, Pamela; Romero, Jaime; Mas, Albert

    2008-08-15

    Acetic acid bacteria (AAB) are considered fastidious microorganisms because they are difficult to isolate and cultivate. Different molecular approaches were taken to detect AAB diversity, independently of their capacity to grow in culture media. Those methods were tested in samples that originated during traditional vinegar production. Bacterial diversity was assessed by analysis of 16S rRNA gene, obtained by PCR amplifications of DNA extracted directly from the acetification container. Bacterial composition was analyzed by RFLP-PCR of 16S rRNA gene, Temporal Temperature Gradient Gel Electrophoresis (TTGE) separation of amplicons containing region V3-V5 of 16S rRNA gene and cloning of those amplicons. TTGE bands and clones were grouped based on their electrophoretic pattern similarity and sequenced to be compared with reference strains. The main microorganism identified in vinegar was Acetobacter pasteurianus, which at the end of the acetification process was considered to be the only microorganism present. The diversity was the highest at 2% acetic acid, where indefinite species of Gluconacetobacter xylinus/europaeus/intermedius were also present.

  2. Synthetic biology for therapeutic applications.

    PubMed

    Abil, Zhanar; Xiong, Xiong; Zhao, Huimin

    2015-02-02

    Synthetic biology is a relatively new field with the key aim of designing and constructing biological systems with novel functionalities. Today, synthetic biology devices are making their first steps in contributing new solutions to a number of biomedical challenges, such as emerging bacterial antibiotic resistance and cancer therapy. This review discusses some synthetic biology approaches and applications that were recently used in disease mechanism investigation and disease modeling, drug discovery and production, as well as vaccine development and treatment of infectious diseases, cancer, and metabolic disorders.

  3. Synthetic Biology for Therapeutic Applications

    PubMed Central

    2015-01-01

    Synthetic biology is a relatively new field with the key aim of designing and constructing biological systems with novel functionalities. Today, synthetic biology devices are making their first steps in contributing new solutions to a number of biomedical challenges, such as emerging bacterial antibiotic resistance and cancer therapy. This review discusses some synthetic biology approaches and applications that were recently used in disease mechanism investigation and disease modeling, drug discovery and production, as well as vaccine development and treatment of infectious diseases, cancer, and metabolic disorders. PMID:25098838

  4. Molecular Biology and Biotechnology of Bacteriophage

    NASA Astrophysics Data System (ADS)

    Onodera, Kazukiyo

    The development of the molecular biology of bacteriophage such as T4, lambda and filamentous phages was described and the process that the fundamental knowledge obtained in this field has subsequently led us to the technology of phage display was introduced.

  5. Rabies vaccine. Developments employing molecular biology methods.

    PubMed

    Paolazzi, C C; Pérez, O; De Filippo, J

    1999-04-01

    Rabies vaccines produced by means of molecular biology are described. Recombinant vaccines employing either viruses as vectors (vaccinia, adenovirus, poxvirus, baculovirus, plant viruses) or a plasmid vector carrying the rabies virus glycoprotein gene are discussed. Synthetic peptide technology directed to rabies vaccine production is also presented.

  6. Molecular Biology and Prevention of Endometrial Cancer

    DTIC Science & Technology

    2009-07-01

    of the oral contraceptive pill (OCP). Project 1: Objectives completed and data previously submitted with 2004 report. Data published this past year...molecular aberrations associated with endometrial carcinogenesis and the biologic mechanisms underlying the protective effect of oral contraceptive (OC...not been altered appreciably. Despite the known protective effect of oral contraceptives , little has been learned regarding the underlying mechanism

  7. Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology

    SciTech Connect

    Taylor, Ronald C.

    1991-11-01

    This thesis involved the construction of (1) a grammar that incorporates knowledge on base invariancy and secondary structure in a molecule and (2) a parser engine that uses the grammar to position bases into the structural subunits of the molecule. These concepts were combined with a novel pinning technique to form a tool that semi-automates insertion of a new species into the alignment for the 16S rRNA molecule (a component of the ribosome) maintained by Dr. Carl Woese`s group at the University of Illinois at Urbana. The tool was tested on species extracted from the alignment and on a group of entirely new species. The results were very encouraging, and the tool should be substantial aid to the curators of the 16S alignment. The construction of the grammar was itself automated, allowing application of the tool to alignments for other molecules. The logic programming language Prolog was used to construct all programs involved. The computational linguistics approach used here was found to be a useful way to attach the problem of insertion into an alignment.

  8. Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology

    SciTech Connect

    Taylor, R.C.

    1991-11-01

    This thesis involved the construction of (1) a grammar that incorporates knowledge on base invariancy and secondary structure in a molecule and (2) a parser engine that uses the grammar to position bases into the structural subunits of the molecule. These concepts were combined with a novel pinning technique to form a tool that semi-automates insertion of a new species into the alignment for the 16S rRNA molecule (a component of the ribosome) maintained by Dr. Carl Woese's group at the University of Illinois at Urbana. The tool was tested on species extracted from the alignment and on a group of entirely new species. The results were very encouraging, and the tool should be substantial aid to the curators of the 16S alignment. The construction of the grammar was itself automated, allowing application of the tool to alignments for other molecules. The logic programming language Prolog was used to construct all programs involved. The computational linguistics approach used here was found to be a useful way to attach the problem of insertion into an alignment.

  9. Molecular profiles to biology and pathways: a systems biology approach.

    PubMed

    Van Laere, Steven; Dirix, Luc; Vermeulen, Peter

    2016-06-16

    Interpreting molecular profiles in a biological context requires specialized analysis strategies. Initially, lists of relevant genes were screened to identify enriched concepts associated with pathways or specific molecular processes. However, the shortcoming of interpreting gene lists by using predefined sets of genes has resulted in the development of novel methods that heavily rely on network-based concepts. These algorithms have the advantage that they allow a more holistic view of the signaling properties of the condition under study as well as that they are suitable for integrating different data types like gene expression, gene mutation, and even histological parameters.

  10. [Endophenotypes: the molecular biology point of view].

    PubMed

    Belzeaux, R; Ibrahim, E C; Cermolacce, M; Fakra, E; Azorin, J M

    2012-12-01

    Endophenotypes are proposed for a better understanding of the molecular substrate underlying psychiatric disorders vulnerability. In this review, we discuss key points of the definition of endophenotypes from the molecular biology point of view. First, we examine the concept of heritability of endophenotype, which does not directly explain the molecular mechanisms responsible for the studied disorder Indeed, we discuss the necessity to better decipher the functional role of polymorphisms associated to endophenotypes, especially if those endophenotypes would be assigned a clinical and biological value. The complexity of endophenotypes definition and use in psychiatric research is also illustrated by the complexity of the human genome organization and gene networks as well as by the gene x environment interactions and also the possible existence of phenocopies.

  11. APPLICATION OF PROTEOMICS TO NEUTROPHIL BIOLOGY

    PubMed Central

    Luerman, Gregory C.; Uriarte, Silvia M.; Rane, Madhavi J.; McLeish, Kenneth R.

    2009-01-01

    Polymorphonuclear leukocytes or neutrophils are a primary effector cell of the innate immune system and contribute to the development of adaptive immunity. Neutrophils participate in both the initiation and resolution of inflammatory responses through a series of highly coordinated molecular and phenotypic changes. To accomplish these changes, neutrophils express numerous receptors and use multiple overlapping and redundant signal transduction pathways. Dysregulation of the activation or resolution pathways plays a role in a number of human diseases. A comprehensive understanding of the regulation of neutrophil responses can be provided by high throughput proteomic technologies and sophisticated computational analysis. The first steps in the application of proteomics to understanding neutrophil biology have been taken. Here we review the application of expression, structural, and functional proteomic studies to neutrophils. Although defining the complex molecular events associated with neutrophil activation is in the early stages, the data generated to date suggest that proteomic technologies will dramatically enhance our understanding of neutrophil biology. PMID:19580889

  12. Clinical applications in molecular imaging.

    PubMed

    Heneweer, Carola; Grimm, Jan

    2011-02-01

    Molecular imaging is aimed at the noninvasive in vivo characterization and measurement of processes at a cellular and molecular level with clinical imaging methods. Contrast agents are constructed to target markers that are specific either for certain diseases or for functional states of specialized tissues. Efforts are currently focused mainly on processes involved in angiogenesis, inflammation, and apoptosis. Cell tracking is performed for diagnostic purposes as well as for monitoring of novel cell therapies. Visualization of these processes would provide more precise information about disease expansion as well as treatment response, and could lead to a more individualized therapy for patients. Many attempts have shown promising results in preclinical studies; however, translation into the clinic remains a challenge. This applies especially to paediatrics because of more stringent safety concerns and the low prevalence of individual diseases. The most promising modalities for clinical translation are nuclear medicine methods (positron emission tomography [PET] and single photon emission CT [SPECT]) due to their high sensitivity, which allows concentrations below biological activity. However, special dose consideration is required for any application of ionizing radiation especially in children. While very little has been published on molecular imaging in a paediatric patient population beyond fluorodeoxyglucose (FDG)-PET and metaiodobenzylguanidine (MIBG) tracers, this review will attempt to discuss approaches that we believe have promise for paediatric imaging. These will include agents that already reached clinical trials as well as preclinical developments with high potential for clinical application.

  13. The Use of Multiscale Molecular Simulations in Understanding a Relationship between the Structure and Function of Biological Systems of the Brain: The Application to Monoamine Oxidase Enzymes.

    PubMed

    Vianello, Robert; Domene, Carmen; Mavri, Janez

    2016-01-01

    HIGHLIGHTS Computational techniques provide accurate descriptions of the structure and dynamics of biological systems, contributing to their understanding at an atomic level.Classical MD simulations are a precious computational tool for the processes where no chemical reactions take place.QM calculations provide valuable information about the enzyme activity, being able to distinguish among several mechanistic pathways, provided a carefully selected cluster model of the enzyme is considered.Multiscale QM/MM simulation is the method of choice for the computational treatment of enzyme reactions offering quantitative agreement with experimentally determined reaction parameters.Molecular simulation provide insight into the mechanism of both the catalytic activity and inhibition of monoamine oxidases, thus aiding in the rational design of their inhibitors that are all employed and antidepressants and antiparkinsonian drugs. Aging society and therewith associated neurodegenerative and neuropsychiatric diseases, including depression, Alzheimer's disease, obsessive disorders, and Parkinson's disease, urgently require novel drug candidates. Targets include monoamine oxidases A and B (MAOs), acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and various receptors and transporters. For rational drug design it is particularly important to combine experimental synthetic, kinetic, toxicological, and pharmacological information with structural and computational work. This paper describes the application of various modern computational biochemistry methods in order to improve the understanding of a relationship between the structure and function of large biological systems including ion channels, transporters, receptors, and metabolic enzymes. The methods covered stem from classical molecular dynamics simulations to understand the physical basis and the time evolution of the structures, to combined QM, and QM/MM approaches to probe the chemical mechanisms of enzymatic

  14. The Use of Multiscale Molecular Simulations in Understanding a Relationship between the Structure and Function of Biological Systems of the Brain: The Application to Monoamine Oxidase Enzymes

    PubMed Central

    Vianello, Robert; Domene, Carmen; Mavri, Janez

    2016-01-01

    HIGHLIGHTS Computational techniques provide accurate descriptions of the structure and dynamics of biological systems, contributing to their understanding at an atomic level.Classical MD simulations are a precious computational tool for the processes where no chemical reactions take place.QM calculations provide valuable information about the enzyme activity, being able to distinguish among several mechanistic pathways, provided a carefully selected cluster model of the enzyme is considered.Multiscale QM/MM simulation is the method of choice for the computational treatment of enzyme reactions offering quantitative agreement with experimentally determined reaction parameters.Molecular simulation provide insight into the mechanism of both the catalytic activity and inhibition of monoamine oxidases, thus aiding in the rational design of their inhibitors that are all employed and antidepressants and antiparkinsonian drugs. Aging society and therewith associated neurodegenerative and neuropsychiatric diseases, including depression, Alzheimer's disease, obsessive disorders, and Parkinson's disease, urgently require novel drug candidates. Targets include monoamine oxidases A and B (MAOs), acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and various receptors and transporters. For rational drug design it is particularly important to combine experimental synthetic, kinetic, toxicological, and pharmacological information with structural and computational work. This paper describes the application of various modern computational biochemistry methods in order to improve the understanding of a relationship between the structure and function of large biological systems including ion channels, transporters, receptors, and metabolic enzymes. The methods covered stem from classical molecular dynamics simulations to understand the physical basis and the time evolution of the structures, to combined QM, and QM/MM approaches to probe the chemical mechanisms of enzymatic

  15. Molecularly imprinted polymers for biomedical and biotechnological applications

    NASA Astrophysics Data System (ADS)

    Dmitrienko, E. V.; Pyshnaya, I. A.; Martyanov, O. N.; Pyshnyi, D. V.

    2016-05-01

    This survey covers main advances in the preparation and application of molecularly imprinted polymers which are capable of specific recognition of biologically active compounds. The principles underlying the production of highly efficient and template-specific molecularly imprinted polymers are discussed. The focus is on the imprinting of highly structured macromolecular and supramolecular templates. The existing and potential applications of molecularly imprinted polymers in various fields of chemistry and molecular biology are considered. The bibliography includes 261 references.

  16. Molecular knots in biology and chemistry

    NASA Astrophysics Data System (ADS)

    Lim, Nicole C. H.; Jackson, Sophie E.

    2015-09-01

    Knots and entanglements are ubiquitous. Beyond their aesthetic appeal, these fascinating topological entities can be either useful or cumbersome. In recent decades, the importance and prevalence of molecular knots have been increasingly recognised by scientists from different disciplines. In this review, we provide an overview on the various molecular knots found in naturally occurring biological systems (DNA, RNA and proteins), and those created by synthetic chemists. We discuss the current knowledge in these fields, including recent developments in experimental and, in some cases, computational studies which are beginning to shed light into the complex interplay between the structure, formation and properties of these topologically intricate molecules.

  17. Molecular neurodegeneration: basic biology and disease pathways.

    PubMed

    Vassar, Robert; Zheng, Hui

    2014-09-23

    The field of neurodegeneration research has been advancing rapidly over the past few years, and has provided intriguing new insights into the normal physiological functions and pathogenic roles of a wide range of molecules associated with several devastating neurodegenerative disorders, including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, frontotemporal dementia, Huntington's disease, and Down syndrome. Recent developments have also facilitated initial efforts to translate preclinical discoveries toward novel therapeutic approaches and clinical trials in humans. These recent developments are reviewed in the current Review Series on "Molecular Neurodegeneration: Basic Biology and Disease Pathways" in a number of state-of-the-art manuscripts that cover themes presented at the Third International Conference on Molecular Neurodegeneration: "Basic biology and disease pathways" held in Cannes, France, September, 2013.

  18. 2004 Reversible Associations in Structure & Molecular Biology

    SciTech Connect

    Edward Eisenstein Nancy Ryan Gray

    2005-03-23

    The Gordon Research Conference (GRC) on 2004 Gordon Research Conference on Reversible Associations in Structure & Molecular Biology was held at Four Points Sheraton, CA, 1/25-30/2004. The Conference was well attended with 82 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students.

  19. Cellular and Molecular Biological Approaches to Interpreting Ancient Biomarkers

    NASA Astrophysics Data System (ADS)

    Newman, Dianne K.; Neubauer, Cajetan; Ricci, Jessica N.; Wu, Chia-Hung; Pearson, Ann

    2016-06-01

    Our ability to read the molecular fossil record has advanced significantly in the past decade. Improvements in biomarker sampling and quantification methods, expansion of molecular sequence databases, and the application of genetic and cellular biological tools to problems in biomarker research have enabled much of this progress. By way of example, we review how attempts to understand the biological function of 2-methylhopanoids in modern bacteria have changed our interpretation of what their molecular fossils tell us about the early history of life. They were once thought to be biomarkers of cyanobacteria and hence the evolution of oxygenic photosynthesis, but we now believe that 2-methylhopanoid biosynthetic capacity originated in the Alphaproteobacteria, that 2-methylhopanoids are regulated in response to stress, and that hopanoid 2-methylation enhances membrane rigidity. We present a new interpretation of 2-methylhopanes that bridges the gap between studies of the functions of 2-methylhopanoids and their patterns of occurrence in the rock record.

  20. Coarse-Grained Models Reveal Functional Dynamics – II. Molecular Dynamics Simulation at the Coarse-Grained Level – Theories and Biological Applications

    PubMed Central

    Chng, Choon-Peng; Yang, Lee-Wei

    2008-01-01

    Molecular dynamics (MD) simulation has remained the most indispensable tool in studying equilibrium/non-equilibrium conformational dynamics since its advent 30 years ago. With advances in spectroscopy accompanying solved biocomplexes in growing sizes, sampling their dynamics that occur at biologically interesting spatial/temporal scales becomes computationally intractable; this motivated the use of coarse-grained (CG) approaches. CG-MD models are used to study folding and conformational transitions in reduced resolution and can employ enlarged time steps due to the absence of some of the fastest motions in the system. The Boltzmann-Inversion technique, heavily used in parameterizing these models, provides a smoothed-out effective potential on which molecular conformation evolves at a faster pace thus stretching simulations into tens of microseconds. As a result, a complete catalytic cycle of HIV-1 protease or the assembly of lipid-protein mixtures could be investigated by CG-MD to gain biological insights. In this review, we survey the theories developed in recent years, which are categorized into Folding-based and Molecular-Mechanics-based. In addition, physical bases in the selection of CG beads/time-step, the choice of effective potentials, representation of solvent, and restoration of molecular representations back to their atomic details are systematically discussed. PMID:19812774

  1. Molecular biomimetics: GEPI-based biological routes to technology.

    PubMed

    Tamerler, Candan; Khatayevich, Dmitriy; Gungormus, Mustafa; Kacar, Turgay; Oren, E Emre; Hnilova, Marketa; Sarikaya, Mehmet

    2010-01-01

    In nature, the viability of biological systems is sustained via specific interactions among the tens of thousands of proteins, the major building blocks of organisms from the simplest single-celled to the most complex multicellular species. Biomolecule-material interaction is accomplished with molecular specificity and efficiency leading to the formation of controlled structures and functions at all scales of dimensional hierarchy. Through evolution, Mother Nature developed molecular recognition by successive cycles of mutation and selection. Molecular specificity of probe-target interactions, e.g., ligand-receptor, antigen-antibody, is always based on specific peptide molecular recognition. Using biology as a guide, we can now understand, engineer, and control peptide-material interactions and exploit them as a new design tool for novel materials and systems. We adapted the protocols of combinatorially designed peptide libraries, via both cell surface or phage display methods; using these we select short peptides with specificity to a variety of practical materials. These genetically engineered peptides for inorganics (GEPI) are then studied experimentally to establish their binding kinetics and surface stability. The bound peptide structure and conformations are interrogated both experimentally and via modeling, and self-assembly characteristics are tested via atomic force microscopy. We further engineer the peptide binding and assembly characteristics using a computational biomimetics approach where bioinformatics based peptide-sequence similarity analysis is developed to design higher generation function-specific peptides. The molecular biomimetic approach opens up new avenues for the design and utilization of multifunctional molecular systems in a wide-range of applications from tissue engineering, disease diagnostics, and therapeutics to various areas of nanotechnology where integration is required among inorganic, organic and biological materials. Here, we

  2. Shaping Biological Knowledge: Applications in Proteomics

    PubMed Central

    Chichester, C.; Gonnet, P.; Jaillet, O.; Kappus, S.; Nikitin, F.; Roland, P.; Rossier, G.; Truong, L.; Appel, R.

    2004-01-01

    The central dogma of molecular biology has provided a meaningful principle for data integration in the field of genomics. In this context, integration reflects the known transitions from a chromosome to a protein sequence: transcription, intron splicing, exon assembly and translation. There is no such clear principle for integrating proteomics data, since the laws governing protein folding and interactivity are not quite understood. In our effort to bring together independent pieces of information relative to proteins in a biologically meaningful way, we assess the bias of bioinformatics resources and consequent approximations in the framework of small-scale studies. We analyse proteomics data while following both a data-driven (focus on proteins smaller than 10 kDa) and a hypothesis-driven (focus on whole bacterial proteomes) approach. These applications are potentially the source of specialized complements to classical biological ontologies. PMID:18629073

  3. Electron scattering from molecules and molecular aggregates of biological relevance

    NASA Astrophysics Data System (ADS)

    Gorfinkiel, Jimena D.; Ptasinska, Sylwia

    2017-09-01

    In this Topical Review we survey the current state of the art in the study of low energy electron collisions with biologically relevant molecules and molecular clusters. We briefly describe the methods and techniques used in the investigation of these processes and summarise the results obtained so far for DNA constituents and their model compounds, amino acids, peptides and other biomolecules. The applications of the data obtained is briefly described as well as future required developments.

  4. Enhanced sampling techniques in molecular dynamics simulations of biological systems.

    PubMed

    Bernardi, Rafael C; Melo, Marcelo C R; Schulten, Klaus

    2015-05-01

    Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. New Tools and New Biology: Recent Miniaturized Systems for Molecular and Cellular Biology

    PubMed Central

    Hamon, Morgan; Hong, Jong Wook

    2013-01-01

    Recent advances in applied physics and chemistry have led to the development of novel microfluidic systems. Microfluidic systems allow minute amounts of reagents to be processed using μm-scale channels and offer several advantages over conventional analytical devices for use in biological sciences: faster, more accurate and more reproducible analytical performance, reduced cell and reagent consumption, portability, and integration of functional components in a single chip. In this review, we introduce how microfluidics has been applied to biological sciences. We first present an overview of the fabrication of microfluidic systems and describe the distinct technologies available for biological research. We then present examples of microsystems used in biological sciences, focusing on applications in molecular and cellular biology. PMID:24305843

  6. Biocompatible Quantum Dots for Biological Applications

    PubMed Central

    Rosenthal, Sandra J.; Chang, Jerry C.; Kovtun, Oleg; McBride, James R.; Tomlinson, Ian D.

    2011-01-01

    Semiconductor quantum dots are quickly becoming a critical diagnostic tool for discerning cellular function at the molecular level. Their high brightness, long-lasting, sizetunable, and narrow luminescence set them apart from conventional fluorescence dyes. Quantum dots are being developed for a variety of biologically oriented applications, including fluorescent assays for drug discovery, disease detection, single protein tracking, and intracellular reporting. This review introduces the science behind quantum dots and describes how they are made biologically compatible. Several applications are also included, illustrating strategies toward target specificity, and are followed by a discussion on the limitations of quantum dot approaches. The article is concluded with a look at the future direction of quantum dots. PMID:21276935

  7. Biocompatible Quantum Dots for Biological Applications

    SciTech Connect

    Rosenthal, Sandra; Chang, Jerry; Kovtun, Oleg; McBride, James; Tomlinson, Ian

    2011-01-01

    Semiconductor quantum dots are quickly becoming a critical diagnostic tool for discerning cellular function at the molecular level. Their high brightness, long-lasting, size-tunable, and narrow luminescence set them apart from conventional fluorescence dyes. Quantum dots are being developed for a variety of biologically oriented applications, including fluorescent assays for drug discovery, disease detection, single protein tracking, and intracellular reporting. This review introduces the science behind quantum dots and describes how they are made biologically compatible. Several applications are also included, illustrating strategies toward target specificity, and are followed by a discussion on the limitations of quantum dot approaches. The article is concluded with a look at the future direction of quantum dots.

  8. Image informatics in systems biology applications

    NASA Astrophysics Data System (ADS)

    Wong, Stephen T. C.

    2005-02-01

    Digital optical microscopy, coupled with parallel processing and a large arsenal of labeling techniques, offers tremendous values to localize, identify, and characterize cells and molecules. This generates many image informatics challenges in requiring new algorithms and tools to extract, classify, correlate, and model image features and content from massive amounts of cellular and molecular images acquired. Image informatics aims to fill this gap. Coupling automated microscopy and image analysis with biostatistical and data mining techniques to provide a system biologic approach in studying the cells, the basic unit of life, potentially leads to many exciting applications in life and health sciences. In this presentation, we describe certain new system biology applications enabled by image informatics technology.

  9. Phenomenological and molecular models of biological proton transfers.

    PubMed

    Bertrand, Patrick

    2004-01-01

    In this paper, the main models describing the transfer of a proton in a molecular system are presented. Models valid when the intersite coupling is weak (non-adiabatic and electronically adiabatic regimes) and strong (adiabatic regime) are described. We distinguish molecular models in which the rate constant is obtained by considering explicitly various degrees of freedom of the system and simpler, phenomenological models built to account for the kinetic isotope effect. The relations between the various models are discussed. Their application to specific systems is illustrated by several studies reported in the literature, with a special emphasis on biological systems.

  10. Biological Applications of Cryogenic Detectors

    SciTech Connect

    Friedrich, S

    2003-12-03

    High energy resolution and broadband efficiency are enabling the use of cryogenic detectors in biological research. Two areas where they have found initial application are X-ray absorption spectroscopy (XAS) and time-of-flight mass spectrometry (TOF-MS). In synchrotron-based fluorescence-detected XAS cryogenic detectors are used to examine the role of metals in biological systems by measuring their oxidation states and ligand symmetries. In time-of-flight mass spectrometry cryogenic detectors increase the sensitivity for biomolecule detection and identification for masses above {approx}50 kDa, and thus enable TOF-MS on large protein complexes or even entire viruses. More recently, cryogenic detectors have been proposed as optical sensors for fluorescence signals from biomarkers. We discuss the potential for cryogenic detectors in biological research, as well as the challenges the technology faces.

  11. 2011 Archaea: Ecology, Metabolism, & Molecular Biology

    SciTech Connect

    Keneth Stedman

    2011-08-05

    Archaea, one of three major evolutionary lineages of life, are a fascinating and diverse group of microbes with deep roots overlapping those of eukaryotes. The focus of the 'Archaea: Ecology Metabolism & Molecular Biology' GRC conference expands on a number of emerging topics highlighting new paradigms in archaeal metabolism, genome function and systems biology; information processing; evolution and the tree of life; the ecology and diversity of archaea and their viruses. The strength of this conference lies in its ability to couple a field with a rich history in high quality research with new scientific findings in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

  12. The Molecular Biology of Brain Metastasis

    PubMed Central

    Rahmathulla, Gazanfar; Toms, Steven A.; Weil, Robert J.

    2012-01-01

    Metastasis to the central nervous system (CNS) remains a major cause of morbidity and mortality in patients with systemic cancers. Various crucial interactions between the brain environment and tumor cells take place during the development of the cancer at its new location. The rapid expansion in molecular biology and genetics has advanced our knowledge of the underlying mechanisms involved, from invasion to final colonization of new organ tissues. Understanding the various events occurring at each stage should enable targeted drug delivery and individualized treatments for patients, with better outcomes and fewer side effects. This paper summarizes the principal molecular and genetic mechanisms that underlie the development of brain metastasis (BrM). PMID:22481931

  13. Genetics and molecular biology of hypotension

    NASA Technical Reports Server (NTRS)

    Robertson, D.

    1994-01-01

    Major strides in the molecular biology of essential hypertension are currently underway. This has tended to obscure the fact that a number of inherited disorders associated with low blood pressure exist and that these diseases may have milder and underrecognized phenotypes that contribute importantly to blood pressure variation in the general population. This review highlights some of the gene products that, if abnormal, could cause hypotension in some individuals. Diseases due to abnormalities in the catecholamine enzymes are discussed in detail. It is likely that genetic abnormalities with hypotensive phenotypes will be as interesting and diverse as those that give rise to hypertensive disorders.

  14. Genetics and molecular biology of hypotension

    NASA Technical Reports Server (NTRS)

    Robertson, D.

    1994-01-01

    Major strides in the molecular biology of essential hypertension are currently underway. This has tended to obscure the fact that a number of inherited disorders associated with low blood pressure exist and that these diseases may have milder and underrecognized phenotypes that contribute importantly to blood pressure variation in the general population. This review highlights some of the gene products that, if abnormal, could cause hypotension in some individuals. Diseases due to abnormalities in the catecholamine enzymes are discussed in detail. It is likely that genetic abnormalities with hypotensive phenotypes will be as interesting and diverse as those that give rise to hypertensive disorders.

  15. 2007 Archaea: Ecology, Metabolism and Molecular Biology

    SciTech Connect

    Imke Schroeder Nancy Ryan Gray

    2008-09-18

    The Archaea are a fascinating and diverse group of prokaryotic organisms with deep roots overlapping those of eukaryotes. The focus of this GRC conference, 'Archaea: Ecology Metabolism & Molecular Biology', expands on a number of emerging topics highlighting the evolution and composition of microbial communities and novel archaeal species, their impact on the environment, archaeal metabolism, and research that stems from sequence analysis of archaeal genomes. The strength of this conference lies in its ability to couple reputable areas with new scientific topics in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

  16. Molecular biology of human muscle disease

    SciTech Connect

    Dunne, P.W.; Epstein, H.F. )

    1991-01-01

    The molecular revolution that is transforming the entire biomedical field has had far-reaching impact in its application to inherited human muscle disease. The gene for Duchenne muscular dystrophy was one of the first cloned without knowledge of the defective protein product. This success was based upon the availability of key chromosomal aberrations that provided molecular landmarks for the disease locus. Subsequent discoveries regarding the mode of expression for this gene, the structure and localization of its protein product dystrophin, and molecular diagnosis of affected and carrier individuals constitute a paradigm for investigation of human genetics. Finding the gene for myotonic muscular dystrophy is requiring the brute force approach of cloning several million bases of DNA, identifying expressed sequences, and characterizing candidate genes. The gene that causes hypertrophic cardiomyopathy has been found serendipitously to be one of the genetic markers on chromosome 14, the {beta} myosin heavy chain.

  17. Applications of docking and molecular dynamic studies on the search for new drugs against the biological warfare agents Bacillus anthracis and Yersinia pestis.

    PubMed

    França, Tanos Celmar Costa; Guimarães, Ana Paula; Cortopassi, Wilian Augusto; Oliveira, Aline Alves; Ramalho, Teodorico Castro

    2013-12-01

    The fear of biological warfare agents (BWA) use by terrorists is the major concern of the security agencies and health authorities worldwide today. The non-existence of vaccines or drugs against most BWA and the possibility of genetic modified strains has turned the search for new drugs to a state of urgency. Fast in silico techniques are, therefore, perfect tools for this task once they can quickly provide structures of several new lead compounds for further experimental work. Here we try to present a mini-review on docking and molecular dynamics simulations studies applied to the drug design against the BWA Bacillus anthracis and Yersinia pestis.

  18. Effective application of the methanol-based PreservCyt(™) fixative and the Cellient(™) automated cell block processor to diagnostic cytopathology, immunocytochemistry, and molecular biology.

    PubMed

    van Hemel, Bettien M; Suurmeijer, Albert J H

    2013-08-01

    quality of DNA and RNA in Cellient(™) cell blocks allowed sensitive and specific molecular biologic analysis, in particular FISH and PCR. Copyright © 2013 Wiley Periodicals, Inc.

  19. Rhabdomyosarcoma: Advances in Molecular and Cellular Biology.

    PubMed

    Sun, Xin; Guo, Wei; Shen, Jacson K; Mankin, Henry J; Hornicek, Francis J; Duan, Zhenfeng

    2015-01-01

    Rhabdomyosarcoma (RMS) is the most common soft tissue malignancy in childhood and adolescence. The two major histological subtypes of RMS are alveolar RMS, driven by the fusion protein PAX3-FKHR or PAX7-FKHR, and embryonic RMS, which is usually genetically heterogeneous. The prognosis of RMS has improved in the past several decades due to multidisciplinary care. However, in recent years, the treatment of patients with metastatic or refractory RMS has reached a plateau. Thus, to improve the survival rate of RMS patients and their overall well-being, further understanding of the molecular and cellular biology of RMS and identification of novel therapeutic targets are imperative. In this review, we describe the most recent discoveries in the molecular and cellular biology of RMS, including alterations in oncogenic pathways, miRNA (miR), in vivo models, stem cells, and important signal transduction cascades implicated in the development and progression of RMS. Furthermore, we discuss novel potential targeted therapies that may improve the current treatment of RMS.

  20. Enhanced Sampling Techniques in Molecular Dynamics Simulations of Biological Systems

    PubMed Central

    Bernardi, Rafael C.; Melo, Marcelo C. R.; Schulten, Klaus

    2014-01-01

    Background Molecular Dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. Scope of review In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Major Conclusions Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. General Significance Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. PMID:25450171

  1. Current dichotomy between traditional molecular biological and omic research in cancer biology and pharmacology.

    PubMed

    Reinhold, William C

    2015-12-10

    There is currently a split within the cancer research community between traditional molecular biological hypothesis-driven and the more recent "omic" forms or research. While the molecular biological approach employs the tried and true single alteration-single response formulations of experimentation, the omic employs broad-based assay or sample collection approaches that generate large volumes of data. How to integrate the benefits of these two approaches in an efficient and productive fashion remains an outstanding issue. Ideally, one would merge the understandability, exactness, simplicity, and testability of the molecular biological approach, with the larger amounts of data, simultaneous consideration of multiple alterations, consideration of genes both of known interest along with the novel, cross-sample comparisons among cell lines and patient samples, and consideration of directed questions while simultaneously gaining exposure to the novel provided by the omic approach. While at the current time integration of the two disciplines remains problematic, attempts to do so are ongoing, and will be necessary for the understanding of the large cell line screens including the Developmental Therapeutics Program's NCI-60, the Broad Institute's Cancer Cell Line Encyclopedia, and the Wellcome Trust Sanger Institute's Cancer Genome Project, as well as the the Cancer Genome Atlas clinical samples project. Going forward there is significant benefit to be had from the integration of the molecular biological and the omic forms or research, with the desired goal being improved translational understanding and application.

  2. [Von Willebrand disease. Molecular biology and diagnosis].

    PubMed

    Hernández-Zamora, Edgar; Zavala-Hernández, Cesar; Quintana-González, Sandra; Reyes-Maldonado, Elba

    2015-01-01

    Von Willebrand disease is the most common inherited disorder of the coagulation proteins in humans. There are three types: 1, 2A, 2B, 2N, 2M and 3. It is associated with mutations on chromosome 12 in the region p13.2, encoding the von Willebrand factor (VWF), which is synthesized in endothelial cells and megakaryocytes. The VWF gene has been characterised using molecular biology techniques, which have acquired an important role in diagnosis von Willebrand disease, as well as in the investigation of alterations in other genes, which may be involved in regulating the synthesis, processing, and secretion of VWF. However, there are still no strategies to integrate the molecular biology diagnostic tests available. Analysis of VWF multimers is a methodology that meets the characteristics for diagnosis, but it is not easy to standardise. Considering that even in tertiary centres in our country, von Willebrand patients do not have a definitive diagnosis, it is necessary to implement these methodologies to study and improve diagnosis. Von Willebrand disease is highly heterogeneous due to the molecular mechanisms that produce the various clinical and laboratory phenotypes. In Mexico there are few studies related to this disease; therefore it is essential to conduct a comprehensive study including clinical, basic, and special testing laboratory tests, in order to establish a correct diagnosis, develop new therapeutic approaches, and offer the appropriate medical care and genetic counselling. Copyright © 2015 Academia Mexicana de Cirugía A.C. Published by Masson Doyma México S.A. All rights reserved.

  3. The molecular biology capstone assessment: a concept assessment for upper-division molecular biology students.

    PubMed

    Couch, Brian A; Wood, William B; Knight, Jennifer K

    2015-03-02

    Measuring students' conceptual understandings has become increasingly important to biology faculty members involved in evaluating and improving departmental programs. We developed the Molecular Biology Capstone Assessment (MBCA) to gauge comprehension of fundamental concepts in molecular and cell biology and the ability to apply these concepts in novel scenarios. Targeted at graduating students, the MBCA consists of 18 multiple-true/false (T/F) questions. Each question consists of a narrative stem followed by four T/F statements, which allows a more detailed assessment of student understanding than the traditional multiple-choice format. Questions were iteratively developed with extensive faculty and student feedback, including validation through faculty reviews and response validation through student interviews. The final assessment was taken online by 504 students in upper-division courses at seven institutions. Data from this administration indicate that the MBCA has acceptable levels of internal reliability (α=0.80) and test-retest stability (r=0.93). Students achieved a wide range of scores with a 67% overall average. Performance results suggest that students have an incomplete understanding of many molecular biology concepts and continue to hold incorrect conceptions previously documented among introductory-level students. By pinpointing areas of conceptual difficulty, the MBCA can provide faculty members with guidance for improving undergraduate biology programs.

  4. The Molecular Biology Capstone Assessment: A Concept Assessment for Upper-Division Molecular Biology Students

    PubMed Central

    Couch, Brian A.; Wood, William B.; Knight, Jennifer K.

    2015-01-01

    Measuring students’ conceptual understandings has become increasingly important to biology faculty members involved in evaluating and improving departmental programs. We developed the Molecular Biology Capstone Assessment (MBCA) to gauge comprehension of fundamental concepts in molecular and cell biology and the ability to apply these concepts in novel scenarios. Targeted at graduating students, the MBCA consists of 18 multiple-true/false (T/F) questions. Each question consists of a narrative stem followed by four T/F statements, which allows a more detailed assessment of student understanding than the traditional multiple-choice format. Questions were iteratively developed with extensive faculty and student feedback, including validation through faculty reviews and response validation through student interviews. The final assessment was taken online by 504 students in upper-division courses at seven institutions. Data from this administration indicate that the MBCA has acceptable levels of internal reliability (α = 0.80) and test–retest stability (r = 0.93). Students achieved a wide range of scores with a 67% overall average. Performance results suggest that students have an incomplete understanding of many molecular biology concepts and continue to hold incorrect conceptions previously documented among introductory-level students. By pinpointing areas of conceptual difficulty, the MBCA can provide faculty members with guidance for improving undergraduate biology programs. PMID:25713098

  5. Nanoporous membranes for medical and biological applications

    PubMed Central

    Adiga, Shashishekar P; Jin, Chunmin; Curtiss, Larry A; Monteiro-Riviere, Nancy A.; Narayan, Roger J

    2013-01-01

    Synthetic nanoporous materials have numerous potential biological and medical applications that involve sorting, sensing, isolating and releasing biological molecules. Nanoporous systems engineered to mimic natural filtration systems are actively being developed for use in smart implantable drug delivery systems, bioartificial organs, and other novel nano-enabled medical devices. Recent advances in nanoscience have made it possible to precisely control the morphology as well as physical and chemical properties of the pores in nanoporous materials that make them increasingly attractive for regulating and sensing transport at the molecular level. In this work, an overview of nanoporous membranes for biomedical applications is given. Various in vivo and in vitro membrane applications, including biosensing, biosorting, immunoisolation and drug delivery, are presented. Different types of nanoporous materials and their fabrication techniques are discussed with an emphasis on membranes with ordered pores. Desirable properties of membranes used in implantable devices, including biocompatibility and antibiofouling behavior, are discussed. The use of surface modification techniques to improve the function of nanoporous membranes is reviewed. Despite the extensive research carried out in fabrication, characterization, and modeling of nanoporous materials, there are still several challenges that must be overcome in order to create synthetic nanoporous systems that behave similarly to their biological counterparts. PMID:20049818

  6. NASA Applications of Molecular Nanotechnology

    NASA Technical Reports Server (NTRS)

    Globus, Al; Bailey, David; Han, Jie; Jaffe, Richard; Levit, Creon; Merkle, Ralph; Srivastava, Deepak

    1998-01-01

    Laboratories throughout the world are rapidly gaining atomically precise control over matter. As this control extends to an ever wider variety of materials, processes and devices, opportunities for applications relevant to NASA's missions will be created. This document surveys a number of future molecular nanotechnology capabilities of aerospace interest. Computer applications, launch vehicle improvements, and active materials appear to be of particular interest. We also list a number of applications for each of NASA's enterprises. If advanced molecular nanotechnology can be developed, almost all of NASA's endeavors will be radically improved. In particular, a sufficiently advanced molecular nanotechnology can arguably bring large scale space colonization within our grasp.

  7. Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut?

    PubMed

    De Backer, Philippe; De Waele, Danny; Van Speybroeck, Linda

    2010-03-01

    The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.

  8. Teaching Molecular Biological Techniques in a Research Content

    ERIC Educational Resources Information Center

    Stiller, John W.; Coggins, T. Chad

    2006-01-01

    Molecular biological methods, such as the polymerase chain reaction (PCR) and gel electrophoresis, are now commonly taught to students in introductory biology courses at the college and even high school levels. This often includes hands-on experience with one or more molecular techniques as part of a general biology laboratory. To assure that most…

  9. Teaching Molecular Biological Techniques in a Research Content

    ERIC Educational Resources Information Center

    Stiller, John W.; Coggins, T. Chad

    2006-01-01

    Molecular biological methods, such as the polymerase chain reaction (PCR) and gel electrophoresis, are now commonly taught to students in introductory biology courses at the college and even high school levels. This often includes hands-on experience with one or more molecular techniques as part of a general biology laboratory. To assure that most…

  10. Orthogonal optical force separation simulation of particle and molecular species mixtures under direct current electroosmotic driven flow for applications in biological sample preparation.

    PubMed

    Staton, Sarah J R; Terray, Alex; Collins, Greg E; Hart, Sean J

    2013-04-01

    Presented here are the results from numerical simulations applying optical forces orthogonally to electroosmotically induced flow containing both molecular species and particles. Simulations were conducted using COMSOL v4.2a Multiphysics® software including the particle tracking module. The study addresses the application of optical forces to selectively remove particulates from a mixed sample stream that also includes molecular species in a pinched flow microfluidic device. This study explores the optimization of microfluidic cell geometry, magnitude of the applied direct current electric field, EOF rate, diffusion, and magnitude of the applied optical forces. The optimized equilibrium of these various contributing factors aids in the development of experimental conditions and geometry for future experimentation as well as directing experimental expectations, such as diffusional losses, separation resolution, and percent yield. The result of this work generated an optimized geometry with flow conditions leading to negligible diffusional losses of the molecular species while also being able to produce particle removal at near 100% levels. An analytical device, such as the one described herein with the capability to separate particulate and molecular species in a continuous, high-throughput fashion would be valuable by minimizing sample preparation and integrating gross sample collection seamlessly into traditional analytical detection methods.

  11. A National Comparison of Biochemistry and Molecular Biology Capstone Experiences

    ERIC Educational Resources Information Center

    Aguanno, Ann; Mertz, Pamela; Martin, Debra; Bell, Ellis

    2015-01-01

    Recognizing the increasingly integrative nature of the molecular life sciences, the "American Society for Biochemistry and Molecular Biology" (ASBMB) recommends that Biochemistry and Molecular Biology (BMB) programs develop curricula based on concepts, content, topics, and expected student outcomes, rather than courses. To that end,…

  12. A National Comparison of Biochemistry and Molecular Biology Capstone Experiences

    ERIC Educational Resources Information Center

    Aguanno, Ann; Mertz, Pamela; Martin, Debra; Bell, Ellis

    2015-01-01

    Recognizing the increasingly integrative nature of the molecular life sciences, the "American Society for Biochemistry and Molecular Biology" (ASBMB) recommends that Biochemistry and Molecular Biology (BMB) programs develop curricula based on concepts, content, topics, and expected student outcomes, rather than courses. To that end,…

  13. Biological applications of graphene oxide

    SciTech Connect

    Gürel, Hikmet Hakan; Salmankurt, Bahadır

    2016-03-25

    Graphene as a 2D material has unique chemical and electronic properties. Because of its unique physical, chemical, and electronic properties, its interesting shape and size make it a promising nanomaterial in many biological applications. However, the lower water-solubility and the irreversible aggregation due to the strong π-π stacking hinder the wide application of graphene nanosheets in biomedical field. Thus, graphene oxide (GO), one derivative of graphene, has been used more frequently in the biological system owing to its relatively higher water solubility and biocompatibility. Recently, it has been demonstrated that nanomaterials with different functional groups on the surface can be used to bind the drug molecules with high affinity. GO has different functional groups such as H, OH and O on its surface; it can be a potential candidate as a drug carrier. The interactions of biomolecules and graphene like structures are long-ranged and very weak. Development of new techniques is very desirable for design of bioelectronics sensors and devices. In this work, we present first-principles spin polarized calculations within density functional theory to calculate effects of charging on DNA/RNA nucleobases on graphene oxide. It is shown that how modify structural and electronic properties of nucleobases on graphene oxide by applied charging.

  14. Laboratory techniques in plant molecular biology taught with UniformMu insertion alleles of maize

    USDA-ARS?s Scientific Manuscript database

    An undergraduate course - Laboratory Techniques in Plant Molecular Biology - was organized around our research application of UniformMu insertion alleles to investigate mitochondrial functions in plant reproduction. The course objectives were to develop students’ laboratory, record keeping, bioinfor...

  15. [From bioinformatics to systems biology: account of the 12th international conference on intelligent systems in molecular biology].

    PubMed

    Ivakhno, S S

    2004-01-01

    The paper reviews the 12th International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004 that was held in Glasgow, UK, during July 31-August 4. A number of talks, papers and software demos from the conference in bioinformatics, genomics, proteomics, transcriptomics and systems biology are described. Recent applications of liquid chromatography - tandem mass spectrometry, comparative genomics and DNA microarrays are given along with the discussion of bioinformatics curricular in higher education.

  16. Molecular biology of cantharidin in cancer cells.

    PubMed

    Rauh, Rolf; Kahl, Stefan; Boechzelt, Herbert; Bauer, Rudolf; Kaina, Bernd; Efferth, Thomas

    2007-07-04

    Herbal medicine is one of the forms of traditional medical practice. Traditional Chinese medicine (TCM) and traditional Vietnamese medicine (TVM) are well-known for their long-standing tradition of herbal medicine. Secreted by many species of blister beetle, most notably by the 'Spanish fly' (Lytta vesicatoria), cantharidin inhibits protein phosphatases 1 and 2A (PP1, PP2A). Blister beetle has been used in Asian traditional medicine to treat Molluscum contagiosum virus (MCV) infections and associated warts, and is now also used for cancer treatment. A combination of both genomic and postgenomic techniques was used in our studies to identify candidate genes affecting sensitivity or resistance to cantharidin. Cantharidin was not found to be related to multidrug resistance phenotype, suggesting its potential usefulness for the treatment of refractory tumors. Oxidative stress response genes diminish the activity of cantharidin by inducing DNA strand breaks which may be subject to base excision repair and induce apoptosis in a p53- and Bcl2-dependent manner. Cantharidin is one of many natural products used in traditional Chinese medicine and traditional Vietnamese medicine for cancer treatment. Combined methods of pharmaceutical biology and molecular biology can help elucidate modes of action of these natural products.

  17. Biological (molecular and cellular) markers of toxicity

    SciTech Connect

    Shugart, L.R.

    1990-10-01

    The overall objective of this study is to evaluate the use of the small aquarium fish, Japanese Medaka (Oryzias latipes), as a predictor of potential genotoxicity following exposure to carcinogens. This will be accomplished by quantitatively investigating the early molecular events associated with genotoxicity of various tissues of Medaka subsequent to exposure of the organism to several known carcinogens, such as diethylnitrosamine (DEN) and benzo(a)pyrene (BaP). Because of the often long latent period between initial contact with certain chemical and physical agents in our environment and subsequent expression of deleterious health or ecological impact, the development of sensitive methods for detecting and estimating early exposure is needed so that necessary interventions can ensue. A promising biological endpoint for detecting early exposure to damaging chemicals is the interaction of these compounds with cellular macromolecules such as Deoxyribonucleic acids (DNA). This biological endpoint assumes significance because it can be one of the critical early events leading eventually to adverse effects (neoplasia) in the exposed organism.

  18. 2010 Plant Molecular Biology Gordon Research Conference

    SciTech Connect

    Michael Sussman

    2010-07-23

    The Plant Molecular Biology Conference has traditionally covered a breadth of exciting topics and the 2010 conference will continue in that tradition. Emerging concerns about food security have inspired a program with three main themes: (1) genomics, natural variation and breeding to understand adaptation and crop improvement, (2) hormonal cross talk, and (3) plant/microbe interactions. There are also sessions on epigenetics and proteomics/metabolomics. Thus this conference will bring together a range of disciplines, will foster the exchange of ideas and enable participants to learn of the latest developments and ideas in diverse areas of plant biology. The conference provides an excellent opportunity for individuals to discuss their research because additional speakers in each session will be selected from submitted abstracts. There will also be a poster session each day for a two-hour period prior to dinner. In particular, this conference plays a key role in enabling students and postdocs (the next generation of research leaders) to mingle with pioneers in multiple areas of plant science.

  19. Myeloproliferative neoplasms: Current molecular biology and genetics.

    PubMed

    Saeidi, Kolsoum

    2016-02-01

    Myeloproliferative neoplasms (MPNs) are clonal disorders characterized by increased production of mature blood cells. Philadelphia chromosome-negative MPNs (Ph-MPNs) consist of polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). A number of stem cell derived mutations have been identified in the past 10 years. These findings showed that JAK2V617F, as a diagnostic marker involving JAK2 exon 14 with a high frequency, is the best molecular characterization of Ph-MPNs. Somatic mutations in an endoplasmic reticulum chaperone, named calreticulin (CALR), is the second most common mutation in patients with ET and PMF after JAK2 V617F mutation. Discovery of CALR mutations led to the increased molecular diagnostic of ET and PMF up to 90%. It has been shown that JAK2V617F is not the unique event in disease pathogenesis. Some other genes' location such as TET oncogene family member 2 (TET2), additional sex combs-like 1 (ASXL1), casitas B-lineage lymphoma proto-oncogene (CBL), isocitrate dehydrogenase 1/2 (IDH1/IDH2), IKAROS family zinc finger 1 (IKZF1), DNA methyltransferase 3A (DNMT3A), suppressor of cytokine signaling (SOCS), enhancer of zeste homolog 2 (EZH2), tumor protein p53 (TP53), runt-related transcription factor 1 (RUNX1) and high mobility group AT-hook 2 (HMGA2) have also identified to be involved in MPNs phenotypes. Here, current molecular biology and genetic mechanisms involved in MNPs with a focus on the aforementioned factors is presented.

  20. Genetics and molecular biology of deafness. Update.

    PubMed

    Grundfast, K M; Siparsky, N; Chuong, D

    2000-12-01

    This article discusses the latest research in the molecular biology and genetics of hearing impairment and its importance to otolaryngologists. Recent research has led to the discovery of many of the genes and gene products that are responsible for hereditary hearing impairment. State mandated screening of newborn infants for hearing loss ensures that a large number of hearing-impaired children will be detected at a very early age. Additionally, these children often will be referred to the otolaryngologist for evaluation of the hearing impairment. It is the otolaryngologist who must gather a detailed family history and perform a thorough physical examination to fully assess the cause of the hearing impairment. In taking the family history, it is important to note that the diagnosis of a hereditary hearing impairment often involves the evaluation of a large-sized family that has a history of hearing disorders. A history of an affected individual in a small family does not necessarily support a diagnosis of hearing impairment in later affected offspring because of the small sample size. Often, a hearing impairment that is part of a syndrome may not be detected because the physical findings associated with a syndrome are subtle in a young infant. For example, the white forelock seen in patients with Waardenburg's syndrome type I cannot be visualized in the infant who lacks hair. Additionally, some patients with syndromic hearing impairment do not present with physical findings, but rather they exhibit abnormal laboratory studies. Additional points to remember include the following: As infectious iatrogenic causes of hearing impairment decrease, the relative incidence of hereditary hearing impairment will increase. Hereditary hearing impairment can present as an isolated finding, or in association with a number of anomalies recognizable as a syndrome. The study of genetics and molecular biology has led to the identification of genes associated with hearing impairment

  1. [The molecular biology of distraction osteogenesis].

    PubMed

    Boulétreau, P; Longaker, M T

    2004-02-01

    Distraction osteogenesis has become a mainstay in bone engineering and the recent application of this technique to the membranous craniofacial skeleton has significantly improved our armamentarium for reconstructive craniomaxillofacial procedures. However, if the biomechanical, histological and ultrastructural changes associated with distraction osteogenesis have been widely described, the molecular mechanisms governing the formation of new bone in the interfragmental gap of gradually distracted bone segments remain largely unclear. Recently, our laboratory has described a rat mandibular distraction model that provides an excellent environment for deciphering the molecular mechanisms that mediate distraction osteogenesis. In this Article, we present the hypotheses and current research that have furthered our knowledge of the molecular mechanisms that govern distraction osteogenesis. Recent studies have implicated a growing number of cytokines that are intimately involved in the regulation of bone synthesis and turnover. The gene regulation of numerous cytokines (Transforming Growth Factor-B, Bone Morphogenetic Proteins, Insulin-like Growth Factor-1, Fibroblast Growth Factor-2) during distraction osteogenesis have been best characterized and will be discussed in this text. We believe that novel systems like the rat model will facilitate our understanding of the biomolecular mechanisms that mediate membranous distraction osteogenesis and will ultimately guide the development of targeted-strategies designed to accelerate bone healing.

  2. Third international congress of plant molecular biology: Molecular biology of plant growth and development

    SciTech Connect

    Hallick, R.B.

    1995-02-01

    The Congress was held October 6-11, 1991 in Tucson with approximately 3000 scientists attending and over 300 oral presentations and 1800 posters. Plant molecular biology is one of the most rapidly developing areas of the biological sciences. Recent advances in the ability to isolate genes, to study their expression, and to create transgenic plants have had a major impact on our understanding of the many fundamental plant processes. In addition, new approaches have been created to improve plants for agricultural purposes. This is a book of presentation and posters from the conference.

  3. Molecular dynamics simulations: advances and applications

    PubMed Central

    Hospital, Adam; Goñi, Josep Ramon; Orozco, Modesto; Gelpí, Josep L

    2015-01-01

    Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed. PMID:26604800

  4. Single-molecule fluorescence resonance energy transfer in molecular biology.

    PubMed

    Sasmal, Dibyendu K; Pulido, Laura E; Kasal, Shan; Huang, Jun

    2016-12-08

    Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful technique for studying the conformation dynamics and interactions of individual biomolecules. In this review, we describe the concept and principle of smFRET, illustrate general instrumentation and microscopy settings for experiments, and discuss the methods and algorithms for data analysis. Subsequently, we review applications of smFRET in protein conformational changes, ion channel open-close properties, receptor-ligand interactions, nucleic acid structure regulation, vesicle fusion, and force induced conformational dynamics. Finally, we discuss the main limitations of smFRET in molecular biology.

  5. Deep-UV biological imaging by lanthanide ion molecular protection

    PubMed Central

    Kumamoto, Yasuaki; Fujita, Katsumasa; Smith, Nicholas Isaac; Kawata, Satoshi

    2015-01-01

    Deep-UV (DUV) light is a sensitive probe for biological molecules such as nucleobases and aromatic amino acids due to specific absorption. However, the use of DUV light for imaging is limited because DUV can destroy or denature target molecules in a sample. Here we show that trivalent ions in the lanthanide group can suppress molecular photodegradation under DUV exposure, enabling a high signal-to-noise ratio and repetitive DUV imaging of nucleobases in cells. Underlying mechanisms of the photodegradation suppression can be excitation relaxation of the DUV-absorptive molecules due to energy transfer to the lanthanide ions, and/or avoiding ionization and reactions with surrounding molecules, including generation of reactive oxygen species, which can modify molecules that are otherwise transparent to DUV light. This approach, directly removing excited energy at the fundamental origin of cellular photodegradation, indicates an important first step towards the practical use of DUV imaging in a variety of biological applications. PMID:26819825

  6. Molecular biology of breast tumors and prognosis.

    PubMed

    Baldassarre, Gustavo; Belletti, Barbara

    2016-01-01

    Breast cancer is the most common cancer among women worldwide. Great scientific, economical, and organizational efforts are in place to understand the causes of onset, identify the critical molecular players of progression, and define new lines of intervention providing more benefits and less toxicity. These efforts have certainly not been vain, since overall survival, especially in specific subsets of breast cancer, has greatly improved during the last decades. At present, breast cancer patients' treatment and care have reached a high standard of quality, and currently one of the most urgent needs resides in the necessity to better distinguish the tumors that need to be more aggressively treated and identify the best therapeutic option tailored to each patient. This objective will be achievable only if the information clarifying the biology of breast cancer can be successfully transferred to the clinic. A common effort by scientists and clinicians toward this integration and toward the use of multidisciplinary approaches will be necessary to reach this important goal.

  7. [The molecular biology of hepatitis C virus].

    PubMed

    Koutsoudakis, George; Forns, Xavier; Pérez-Del-Pulgar, Sofía

    2013-04-01

    Since the discovery of the hepatitis C virus (HCV), a plethora of experimental models have evolved, allowing the virus's life cycle and the pathogenesis of associated liver diseases to be investigated. These models range from inoculation of cultured cells with serum from patients with hepatitis C to the use of surrogate models for the study of specific stages of the HCV life cycle: retroviral pseudoparticles for the study of HCV entry, replicons for the study of HCV replication, and the HCV cell culture model, which reproduces the entire life cycle (replication and production of infectious particles). The use of these tools has been and remains crucial to identify potential therapeutic targets in the different stages of the virus's life cycle and to screen new antiviral drugs. A clear example is the recent approval of two viral protease inhibitors (boceprevir and telaprevir) in combination with pegylated interferon and ribavirin for the treatment of chronic hepatitis C. This review analyzes the advances made in the molecular biology of HCV and highlights possible candidates as therapeutic targets for the treatment of HCV infection.

  8. 2003 Archaea: Ecology, Metabolism and Molecular Biology

    SciTech Connect

    Richard F. Shand

    2004-09-21

    The Gordon Research Conference (GRC) on 2003 Archaea: Ecology, Metabolism and Molecular Biology was held at Proctor Academy, Andover, NH from August 3-8, 2003. The Conference was well-attended with 150 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students. In designing the formal speakers program, emphasis was placed on current unpublished research and discussion of the future target areas in this field. There was a conscious effort to stimulate lively discussion about the key issues in the field today. Time for formal presentations was limited in the interest of group discussions. In order that more scientists could communicate their most recent results, poster presentation time was scheduled. Attached is a copy of the formal schedule and speaker program and the poster program. In addition to these formal interactions, ''free time'' was scheduled to allow informal discussions. Such discussions are fostering new collaborations and joint efforts in the field. I want to personally thank you for your support of this Conference. As you know, in the interest of promoting the presentation of unpublished and frontier-breaking research, Gordon Research Conferences does not permit publication of meeting proceedings. If you wish any further details, please feel free to contact me. Thank you, Dr. Richard F. Shand, 2003 Conference Chair.

  9. Diagnosis of Dermatophytosis Using Molecular Biology.

    PubMed

    Verrier, Julie; Monod, Michel

    2017-02-01

    Identification of fungi in dermatological samples using PCR is reliable and provides significantly improved results in comparison with cultures. It is possible to identify the infectious agent when negative results are obtained from cultures. In addition, identification of the infectious agent can be obtained in 1 day. Conventional and real-time PCR methods used for direct fungus identification in collected samples vary by DNA extraction methods, targeted DNA and primers, and the way of analysing the PCR products. The choice of a unique method in a laboratory is complicated because the results expected from skin and hair sample analysis are different from those expected in cases of onychomycosis. In skin and hair samples, one dermatophyte among about a dozen possible species has to be identified. In onychomycosis, the infectious agents are mainly Trichophyton rubrum and, to a lesser extent, Trichophyton interdigitale, but also moulds insensitive to oral treatments used for dermatophytes, which renders fungal identification mandatory. The benefits obtained with the use of PCR methods for routine analysis of dermatological samples have to be put in balance with the relative importance of getting a result in a short time, the price of molecular biology reagents and equipment, and especially the time spent conducting laboratory manipulations.

  10. Zika virus genome biology and molecular pathogenesis.

    PubMed

    Wang, Anyou; Thurmond, Stephanie; Islas, Leonel; Hui, Kingyung; Hai, Rong

    2017-03-22

    Zika virus (ZIKV) is an emerging RNA virus in the widespread Flavivirus genus. Recently, ZIKV has rapidly spread around the world and has been implicated in human disease, including neurological disorders, triggering public and scientific attention. Understanding how ZIKV causes disease is the highest priority, yet little is known about this virus. Here we examine the currently published data from ZIKV studies to provide the latest understanding of ZIKV genome biology and molecular pathogenesis. The ZIKV genome evolved rapidly from the Flavivirus genus and diverged from the members of this genus, even within the dengue virus cluster to which ZIKV belongs. Genome variations and divergences also exist among ZIKV strains/isolates. These genome divergences might account for the uniqueness of Zika disease. ZIKV infection activates not only the antiviral immune response but also the pro-inflammatory responses associated with disease symptoms. Strikingly, ZIKV activates protein complexes that are functionally associated with disease process, such as glial cell activation and proliferation (for example, Toll-like receptors), apoptosis and cell death, and inflammation. The activation of these complexes may critically contribute to Zika disease. The novel insights into ZIKV genome divergence and disease mechanisms summarized in this review will help accelerate the development of anti-ZIKV strategies.

  11. Reviewe: Genetics and genomics in equine exercise physiology: an overview of the new applications of molecular biology as positive and negative markers of performance and health.

    PubMed

    Barrey, E

    2010-11-01

    Equine breeding selection has been developed by applying quantitative genetic methods for calculating the heritability of the complex traits such as performance in racing or sport competitions. With the great development of biotechnologies, equine molecular genetics has come of age. The recent sequencing of the equine genome by an international consortium was a major advance that will impact equine genomics in the near future. With the rapid progress in equine genetics, new applications in early performance evaluation and the detection of disease markers become available. Many new biomolecular tools will change management of horse selection, disease diagnosis and treatment. The purpose of this review is to present new developments in equine genetics and genomics for performance evaluation and health markers after a short summary of the previous knowledge about the genetic components of the exercise performance traits.

  12. [Tools of molecular biology, what can be expected from them?].

    PubMed

    Delpech, M

    1993-01-01

    The techniques of molecular biology represent a new tool for research and diagnosis. They have been used routinely since the middle 80s. The first applications were mainly in hereditary diseases. These techniques investigated an information and not direct biological activity and so new strategies had to be developed. Two techniques have played key roles. They are Southern's method which enables the detection of specific sequences among DNA fragments in any individual within a few days, and the method of in vitro selective amplification (PCR) which is the equivalent of cloning a sequence of several hundred pairs of bases in any individual in less than 3 hours. In hereditary diseases, molecular biological techniques enable diagnosis of the genetic abnormality responsible for the condition, even when the defect is not known. To this end, two strategies are available. The first, and the most satisfactory, is the direct strategy of characterising the genetic defect itself. This is possible when the mutation is a major alteration of the DNA molecule such as a deletion, an insertion or a recombination or when the mutation is isolated and known. In other cases, an indirect approach may be used which consists of determining whether the subject has received normal or defective chromosomes from his or her parents. The identification of good or bad chromosomes is based on the study of DNA markers: polymorphism. The indirect strategy can only be used under certain conditions: presence of an index case, informativity of polymorphisms, complete family study.(ABSTRACT TRUNCATED AT 250 WORDS)

  13. Dissecting the Molecular Mechanisms of Neurodegenerative Diseases through Network Biology.

    PubMed

    Santiago, Jose A; Bottero, Virginie; Potashkin, Judith A

    2017-01-01

    Neurodegenerative diseases are rarely caused by a mutation in a single gene but rather influenced by a combination of genetic, epigenetic and environmental factors. Emerging high-throughput technologies such as RNA sequencing have been instrumental in deciphering the molecular landscape of neurodegenerative diseases, however, the interpretation of such large amounts of data remains a challenge. Network biology has become a powerful platform to integrate multiple omics data to comprehensively explore the molecular networks in the context of health and disease. In this review article, we highlight recent advances in network biology approaches with an emphasis in brain-networks that have provided insights into the molecular mechanisms leading to the most prevalent neurodegenerative diseases including Alzheimer's (AD), Parkinson's (PD) and Huntington's diseases (HD). We discuss how integrative approaches using multi-omics data from different tissues have been valuable for identifying biomarkers and therapeutic targets. In addition, we discuss the challenges the field of network medicine faces toward the translation of network-based findings into clinically actionable tools for personalized medicine applications.

  14. A Diagnostic Assessment for Introductory Molecular and Cell Biology

    ERIC Educational Resources Information Center

    Shi, Jia; Wood, William B.; Martin, Jennifer M.; Guild, Nancy A.; Vicens, Quentin; Knight, Jennifer K.

    2010-01-01

    We have developed and validated a tool for assessing understanding of a selection of fundamental concepts and basic knowledge in undergraduate introductory molecular and cell biology, focusing on areas in which students often have misconceptions. This multiple-choice Introductory Molecular and Cell Biology Assessment (IMCA) instrument is designed…

  15. A Diagnostic Assessment for Introductory Molecular and Cell Biology

    ERIC Educational Resources Information Center

    Shi, Jia; Wood, William B.; Martin, Jennifer M.; Guild, Nancy A.; Vicens, Quentin; Knight, Jennifer K.

    2010-01-01

    We have developed and validated a tool for assessing understanding of a selection of fundamental concepts and basic knowledge in undergraduate introductory molecular and cell biology, focusing on areas in which students often have misconceptions. This multiple-choice Introductory Molecular and Cell Biology Assessment (IMCA) instrument is designed…

  16. Digital Learning Material for Model Building in Molecular Biology

    ERIC Educational Resources Information Center

    Aegerter-Wilmsen, Tinri; Janssen, Fred; Hartog, Rob; Bisseling, Ton

    2005-01-01

    Building models to describe processes forms an essential part of molecular biology research. However, in molecular biology curricula little attention is generally being paid to the development of this skill. In order to provide students the opportunity to improve their model building skills, we decided to develop a number of digital cases about…

  17. Commentary: Biochemistry and Molecular Biology Educators Launch National Network

    ERIC Educational Resources Information Center

    Bailey, Cheryl; Bell, Ellis; Johnson, Margaret; Mattos, Carla; Sears, Duane; White, Harold B.

    2010-01-01

    The American Society of Biochemistry and Molecular Biology (ASBMB) has launched an National Science Foundation (NSF)-funded 5 year project to support biochemistry and molecular biology educators learning what and how students learn. As a part of this initiative, hundreds of life scientists will plan and develop a rich central resource for…

  18. Commentary: Biochemistry and Molecular Biology Educators Launch National Network

    ERIC Educational Resources Information Center

    Bailey, Cheryl; Bell, Ellis; Johnson, Margaret; Mattos, Carla; Sears, Duane; White, Harold B.

    2010-01-01

    The American Society of Biochemistry and Molecular Biology (ASBMB) has launched an National Science Foundation (NSF)-funded 5 year project to support biochemistry and molecular biology educators learning what and how students learn. As a part of this initiative, hundreds of life scientists will plan and develop a rich central resource for…

  19. Digital Learning Material for Model Building in Molecular Biology

    ERIC Educational Resources Information Center

    Aegerter-Wilmsen, Tinri; Janssen, Fred; Hartog, Rob; Bisseling, Ton

    2005-01-01

    Building models to describe processes forms an essential part of molecular biology research. However, in molecular biology curricula little attention is generally being paid to the development of this skill. In order to provide students the opportunity to improve their model building skills, we decided to develop a number of digital cases about…

  20. Support of the IMA summer program molecular biology. Final report

    SciTech Connect

    Friedman, A.

    1995-08-01

    The revolutionary progress in molecular biology within the last 30 years opens the way to full understanding of the molecular structures and mechanisms of living organisms. The mathematical sciences accompany and support much of the progress achieved by experiment and computation, as well as provide insight into geometric and topological properties of biomolecular structure and processes. The 4 week program at the IMA brought together biologists and mathematicians leading researchers, postdocs, and graduate students. It focused on genetic mapping and DNA sequencing, followed by biomolecular structure and dynamics. High-resolution linkage maps of genetic marker were discussed extensively in relation to the human genome project. The next level of DNA mapping is physical mapping, consisting of overlapping clones spanning the genome. These maps are extremely useful for genetic analysis. They provide the material for less redundant sequencing and for detailed searches for a gene among other things. This topic was also extensively studied by the participants. From there, the program moved to consider protein structure and dynamics; this is a broad field with a large array of interesting topics. It is of key importance in answering basic scientific questions about the nature of all living organisms, and has practical biomedical applications. The major subareas of structure prediction and classification, techniques and heuristics for the simulation of protein folding, and molecular dynamics provide a rich problem domain where mathematics can be helpful in analysis, modeling, and simulation. One of the important problems in molecular biology is the three-dimensional structure of proteins, DNA and RNA in the cell, and the relationship between structure and function. The program helped increased the understanding of the topology of cellular DNA, RNA and proteins and the various life-sustaining mechanisms used by the cell which modify this molecular topology.

  1. Bibliometric analysis of original molecular biology research in anaesthesia.

    PubMed

    Schreiber, K; Girard, T; Kindler, C H

    2004-10-01

    Molecular biology has expanded the horizons of anaesthesia during the last 20 years and has led to an increase of basic science articles that are published in the specialised anaesthetic journals or originate in anaesthetic institutions. We searched for and analysed the specific features, such as year of publication, publishing journal, and country of origin, of all such molecular biology articles stored in the MEDLINE database during the period 1986-2002. We identified 1265 original articles that used molecular biology techniques; 223 (18%) of these articles were published in anaesthetic journals and 1042 (82%) articles in 556 other biomedical journals. While in the late 1980s only a few molecular biology articles were published each year by anaesthetic institutions, worldwide this number reached approximately 200 basic science articles by the end of 2002. The USA clearly dominates the field of anaesthesia with respect to molecular biology research with 839 (66%) such articles.

  2. Molecular Biology and Pathogenicity of Mycoplasmas

    PubMed Central

    Razin, Shmuel; Yogev, David; Naot, Yehudith

    1998-01-01

    The recent sequencing of the entire genomes of Mycoplasma genitalium and M. pneumoniae has attracted considerable attention to the molecular biology of mycoplasmas, the smallest self-replicating organisms. It appears that we are now much closer to the goal of defining, in molecular terms, the entire machinery of a self-replicating cell. Comparative genomics based on comparison of the genomic makeup of mycoplasmal genomes with those of other bacteria, has opened new ways of looking at the evolutionary history of the mycoplasmas. There is now solid genetic support for the hypothesis that mycoplasmas have evolved as a branch of gram-positive bacteria by a process of reductive evolution. During this process, the mycoplasmas lost considerable portions of their ancestors’ chromosomes but retained the genes essential for life. Thus, the mycoplasmal genomes carry a high percentage of conserved genes, greatly facilitating gene annotation. The significant genome compaction that occurred in mycoplasmas was made possible by adopting a parasitic mode of life. The supply of nutrients from their hosts apparently enabled mycoplasmas to lose, during evolution, the genes for many assimilative processes. During their evolution and adaptation to a parasitic mode of life, the mycoplasmas have developed various genetic systems providing a highly plastic set of variable surface proteins to evade the host immune system. The uniqueness of the mycoplasmal systems is manifested by the presence of highly mutable modules combined with an ability to expand the antigenic repertoire by generating structural alternatives, all compressed into limited genomic sequences. In the absence of a cell wall and a periplasmic space, the majority of surface variable antigens in mycoplasmas are lipoproteins. Apart from providing specific antimycoplasmal defense, the host immune system is also involved in the development of pathogenic lesions and exacerbation of mycoplasma induced diseases. Mycoplasmas are

  3. The molecular biology in wound healing & non-healing wound.

    PubMed

    Qing, Chun

    2017-08-01

    The development of molecular biology and other new biotechnologies helps us to recognize the wound healing and non-healing wound of skin in the past 30 years. This review mainly focuses on the molecular biology of many cytokines (including growth factors) and other molecular factors such as extracellular matrix (ECM) on wound healing. The molecular biology in cell movement such as epidermal cells in wound healing was also discussed. Moreover many common chronic wounds such as pressure ulcers, leg ulcers, diabetic foot wounds, venous stasis ulcers, etc. usually deteriorate into non-healing wounds. Therefore the molecular biology such as advanced glycation end products (AGEs) and other molecular factors in diabetes non-healing wounds were also reviewed. Copyright © 2017 Daping Hospital and the Research Institute of Surgery of the Third Military Medical University. Production and hosting by Elsevier B.V. All rights reserved.

  4. Molecular biology of pancreatic cancer: how useful is it in clinical practice?

    PubMed

    Sakorafas, George H; Smyrniotis, Vasileios

    2012-07-10

    During the recent two decades dramatic advances of molecular biology allowed an in-depth understanding of pancreatic carcinogenesis. It is currently accepted that pancreatic cancer has a genetic component. The real challenge is now how these impressive advances could be used in clinical practice. To critically present currently available data regarding clinical application of molecular biology in pancreatic cancer. Reports about clinical implications of molecular biology in patients with pancreatic cancer were retrieved from PubMed. These reports were selected on the basis of their clinical relevance, and the data of their publication (preferentially within the last 5 years). Emphasis was placed on reports investigating diagnostic, prognostic, and therapeutic implications. Molecular biology can be used to identify individuals at high-risk for pancreatic cancer development. Intensive surveillance is indicated in these patients to detect pancreatic neoplasia ideally at a preinvasive stage, when curative resection is still possible. Molecular biology can also be used in the diagnosis of pancreatic cancer, with molecular analysis on samples of biologic material, such as serum or plasma, duodenal fluid or preferentially pure pancreatic juice, pancreatic cells or tissue, and stools. Molecular indices have also prognostic significance. Finally, molecular biology may have therapeutic implications by using various therapeutic approaches, such as antiangiogenic factors, purine synthesis inhibitors, matrix metalloproteinase inhibitors, factors modulating tumor-stroma interaction, inactivation of the hedgehog pathway, gene therapy, oncolytic viral therapy, immunotherapy (both passive as well as active) etc. Molecular biology may have important clinical implications in patients with pancreatic cancer and represents one of the most active areas on cancer research. Hopefully clinical applications of molecular biology in pancreatic cancer will expand in the future, improving the

  5. Thermophilic molds: Biology and applications.

    PubMed

    Singh, Bijender; Poças-Fonseca, Marcio J; Johri, B N; Satyanarayana, Tulasi

    2016-11-01

    Thermophilic molds thrive in a variety of natural habitats including soils, composts, wood chip piles, nesting materials of birds and other animals, municipal refuse and others, and ubiquitous in their distribution. These molds grow in simple media containing carbon and nitrogen sources and mineral salts. Polyamines are synthesized in these molds and the composition of lipids varies considerably, predominantly containing palmitic, oleic and linoleic acids with low levels of lauric, palmiotoleic and stearic acids. Thermophilic molds are capable of efficiently degrading organic materials by secreting thermostable enzymes, which are useful in the bioremediation of industrial wastes and effluents that are rich in oil, heavy metals, anti-nutritional factors such as phytic acid and polysaccharides. Thermophilic molds synthesize several antimicrobial substances and biotechnologically useful miscellaneous enzymes. The analysis of genomes of thermophilic molds reveals high G:C contents, shorter introns and intergenic regions with lesser repetitive sequences, and further confirms their ability to degrade agro-residues efficiently. Genetic engineering has aided in ameliorating the characteristics of the enzymes of thermophilic molds. This review is aimed at focusing on the biology of thermophilic molds with emphasis on recent developments in the analysis of genomes, genetic engineering and potential applications.

  6. Molecular biological enhancement of coal biodesulfurization

    SciTech Connect

    Litchfield, J.H.; Zupancic, T.J.; Kittle, J.D. Jr.; Baker, B.; Palmer, D.T.; Traunero, C.G.; Wyza, R.E.; Schweitzer, A.; Conkle, H.N. ); Chakravarty, L.; Tuovinen, O.H. )

    1992-10-08

    Progress is reported in understanding Thiobacillus molecular biology, specifically in the area of vector development. At the initiation of this program, the basic elements needed for performing genetic engineering in T. ferrooxidans were either not yet developed. Improved techniques are described which will make it easier to construct and analyze the genetic structure and metabolism of recombinant T. ferrooxidans. The metabolism of the model organic sulfur compound dibenzothiophene (DBT) by certain heterotrophic bacteria was confirmed and characterized. Techniques were developed to analyze the metabolites of DBT, so that individual 4S pathway metabolites could be distinguished. These techniques are expected to be valuable when engineering organic sulfur metabolism in Thiobacillus. Strain isolation techniques were used to develop pure cultures of T. ferrooxidans seven of which were assessed as potential recombinant hosts. The mixotrophic strain T. coprinus was also characterized for potential use as an electroporation host. A family of related Thiobacillus plasmids was discovered in the seven strains of P. ferrooxidans mentioned above. One of these plasmids, pTFI91, was cloned into a pUC-based plasmid vector, allowing it to propagate in E. coli. A key portion of the cloned plasmid was sequenced. This segment, which is conserved in all of the related plasmids characterized, contains the vegetative origin of DNA replication, and fortuitously, a novel insertion sequence, designated IS3091. The sequence of the DNA origin revealed that these Thiobacillus plasmids represent a unique class of replicons not previously described. The potentially useful insertion sequence IS3091 was identified as a new member of a previously undefined family of insertion sequences which include the E. coli element IS30.

  7. Towards molecular computers that operate in a biological environment

    NASA Astrophysics Data System (ADS)

    Kahan, Maya; Gil, Binyamin; Adar, Rivka; Shapiro, Ehud

    2008-07-01

    Even though electronic computers are the only computer species we are accustomed to, the mathematical notion of a programmable computer has nothing to do with electronics. In fact, Alan Turing’s notional computer [L.M. Turing, On computable numbers, with an application to the entcheidungsproblem, Proc. Lond. Math. Soc. 42 (1936) 230-265], which marked in 1936 the birth of modern computer science and still stands at its heart, has greater similarity to natural biomolecular machines such as the ribosome and polymerases than to electronic computers. This similarity led to the investigation of DNA-based computers [C.H. Bennett, The thermodynamics of computation - Review, Int. J. Theoret. Phys. 21 (1982) 905-940; A.M. Adleman, Molecular computation of solutions to combinatorial problems, Science 266 (1994) 1021-1024]. Although parallelism, sequence specific hybridization and storage capacity, inherent to DNA and RNA molecules, can be exploited in molecular computers to solve complex mathematical problems [Q. Ouyang, et al., DNA solution of the maximal clique problem, Science 278 (1997) 446-449; R.J. Lipton, DNA solution of hard computational problems, Science 268 (1995) 542-545; R.S. Braich, et al., Solution of a 20-variable 3-SAT problem on a DNA computer, Science 296 (2002) 499-502; Liu Q., et al., DNA computing on surfaces, Nature 403 (2000) 175-179; D. Faulhammer, et al., Molecular computation: RNA solutions to chess problems, Proc. Natl. Acad. Sci. USA 97 (2000) 1385-1389; C. Mao, et al., Logical computation using algorithmic self-assembly of DNA triple-crossover molecules, Nature 407 (2000) 493-496; A.J. Ruben, et al., The past, present and future of molecular computing, Nat. Rev. Mol. Cell. Biol. 1 (2000) 69-72], we believe that the more significant potential of molecular computers lies in their ability to interact directly with a biochemical environment such as the bloodstream and living cells. From this perspective, even simple molecular computations may have

  8. [Biological characteristics of calliphoridae and its application in forensic medicine].

    PubMed

    Zhao, Boa; Wen, Charn; Qi, Li-Li; Wang, He; Wang, Ji

    2013-12-01

    Diptera Calliphoridae is the first major kind of flies that appears on the decomposed corpses. In forensic entomology, according to the living characteristics of Calliphoridae flies, we could accurately estimate postmortem interval (PMI) in a murder or unidentified case and could provide useful clues to solve the case. This paper introduces the characteristics of the biology and morphology of Diptera Calliphoridae, and reviews the combined application of forensic entomology, molecular biology, mathematical morphology and toxicology.

  9. Molecular Biology of Pediatric Hydrocephalus and Hydrocephalus-related Diseases

    PubMed Central

    YAMASAKI, Mami; KANEMURA, Yonehiro

    2015-01-01

    We are beginning to understand the molecular biology of hydrocephalus and its related diseases. X-linked hydrocephalus (XLH), holoprosencephaly (HPE), Dandy–Walker malformation (DWM), and neural tube defect (NTD) can all be discussed with respect to their available molecular genetics knowledge base and its clinical applications. XLH is single gene disorder caused by mutations in the neural cell adhesion molecule-encoding L1CAM (L1) gene. Our knowledge of the molecular basis of XLH is already being applied clinically in disease diagnosis, disease classification, and prenatal diagnosis. However, the molecular mechanism underlying XLH-related hydrocephalus still needs to be clarified. Sixteen causative genes for HPE have been identified, of which mutations are most often found in SHH, ZIC2, SIX3, and TGIF. Genetic interactions, gene complexity, and the wide variety of HPE phenotypes and genotypes are topics for future study. For DWM, two important loci, 3q24, which includes the FOXC1 gene, and 6q25.3, which includes the ZIC1 and ZIC4 genes, were recently identified as causative areas. The planar cell polarity (PCP) genes CELSR1, CELSR2, VANGL1, and VANGL2 have been implicated in NTD; these genes have roles in neural tube closure and ependymal ciliary movement. PMID:26227058

  10. Molecularly Imprinted Nanomaterials for Sensor Applications

    PubMed Central

    Irshad, Muhammad; Iqbal, Naseer; Mujahid, Adnan; Afzal, Adeel; Hussain, Tajamal; Sharif, Ahsan; Ahmad, Ejaz; Athar, Muhammad Makshoof

    2013-01-01

    Molecular imprinting is a well-established technology to mimic antibody-antigen interaction in a synthetic platform. Molecularly imprinted polymers and nanomaterials usually possess outstanding recognition capabilities. Imprinted nanostructured materials are characterized by their small sizes, large reactive surface area and, most importantly, with rapid and specific analysis of analytes due to the formation of template driven recognition cavities within the matrix. The excellent recognition and selectivity offered by this class of materials towards a target analyte have found applications in many areas, such as separation science, analysis of organic pollutants in water, environmental analysis of trace gases, chemical or biological sensors, biochemical assays, fabricating artificial receptors, nanotechnology, etc. We present here a concise overview and recent developments in nanostructured imprinted materials with respect to various sensor systems, e.g., electrochemical, optical and mass sensitive, etc. Finally, in light of recent studies, we conclude the article with future perspectives and foreseen applications of imprinted nanomaterials in chemical sensors. PMID:28348356

  11. Central Equipment Facility for Molecular Marine Biology

    DTIC Science & Technology

    1990-03-07

    used. Projects supported include marine symbiosis (Haygood, Felback), cell biology (Vacquier), pressure adaptation in marine bacteria (Bartlett), population genetics and evolution of marine organisms (Perrin, Newman).

  12. Fundamental approaches in molecular biology for communication sciences and disorders.

    PubMed

    Bartlett, Rebecca S; Jetté, Marie E; King, Suzanne N; Schaser, Allison; Thibeault, Susan L

    2012-08-01

    This contemporary tutorial will introduce general principles of molecular biology, common deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein assays and their relevance in the field of communication sciences and disorders. Over the past 2 decades, knowledge of the molecular pathophysiology of human disease has increased at a remarkable pace. Most of this progress can be attributed to concomitant advances in basic molecular biology and, specifically, the development of an ever-expanding armamentarium of technologies for analysis of DNA, RNA, and protein structure and function. Details of these methodologies, their limitations, and examples from the communication sciences and disorders literature are presented. Results/Conclusions The use of molecular biology techniques in the fields of speech, language, and hearing sciences is increasing, facilitating the need for an understanding of molecular biology fundamentals and common experimental assays.

  13. Nanoparticle fluorescence based technology for biological applications.

    PubMed

    Chen, Wei

    2008-03-01

    Fluorescence is widely used in biological detection and imaging. The emerging luminescent nanoparticles or quantum dots provide a new type of biological agents that can improve these applications. The advantages of luminescent nanoparticles for biological applications include their high quantum yield, color availability, good photo-stability, large surface-to-volume ratio, surface functionality, and small size. In this review article, we first introduce quantum size confinement, photoluminescence and upconversion luminescence of nanoparticles, then describe the preparation and conjugation of water soluble nanoparticles and introduce the applications of luminescence nanoparticles for in vitro and in vivo imaging, fluorescence resonance energy based detection, and the applications of luminescence nanoparticles for photodynamic activation.

  14. Assessment of knowledge of participants on basic molecular biology techniques after 5-day intensive molecular biology training workshops in Nigeria.

    PubMed

    Yisau, J I; Adagbada, A O; Bamidele, T; Fowora, M; Brai, B I C; Adebesin, O; Bamidele, M; Fesobi, T; Nwaokorie, F O; Ajayi, A; Smith, S I

    2017-02-01

    The deployment of molecular biology techniques for diagnosis and research in Nigeria is faced with a number of challenges, including the cost of equipment and reagents coupled with the dearth of personnel skilled in the procedures and handling of equipment. Short molecular biology training workshops were conducted at the Nigerian Institute of Medical Research (NIMR), to improve the knowledge and skills of laboratory personnel and academics in health, research, and educational facilities. Five-day molecular biology workshops were conducted annually between 2011 and 2014, with participants drawn from health, research facilities, and the academia. The courses consisted of theoretical and practical sessions. The impact of the workshops on knowledge and skill acquisition was evaluated by pre- and post-tests which consisted of 25 multiple choice and other questions. Sixty-five participants took part in the workshops. The mean knowledge of molecular biology as evaluated by the pre- and post-test assessments were 8.4 (95% CI 7.6-9.1) and 13.0 (95 CI 11.9-14.1), respectively. The mean post-test score was significantly greater than the mean pre-test score (p < 0.0001). The five-day molecular biology workshop significantly increased the knowledge and skills of participants in molecular biology techniques. © 2017 by The International Union of Biochemistry and Molecular Biology, 2017.

  15. Advances in the cellular and molecular biology of angiogenesis.

    PubMed

    Egginton, Stuart; Bicknell, Roy

    2011-12-01

    Capillaries have been recognized for over a century as one of the most important components in regulating tissue oxygen transport, and their formation or angiogenesis a pivotal element of tissue remodelling during development and adaptation. Clinical interest stems from observations that both excessive and inadequate vascular growth plays a major role in human diseases, and novel developments in treatments for cancer and eye disease increasingly rely on anti-angiogenic therapies. Although the discovery of VEGF (vascular endothelial growth factor) provided the first clue for specificity of signalling in endothelial cell activation, understanding the integrative response that drives angiogenesis requires a much broader perspective. The Advances in the Cellular and Molecular Biology of Angiogenesis meeting brought together researchers at the forefront of this rapidly moving field to provide an update on current understanding, and the most recent insights into molecular and cellular mechanisms of vascular growth. The plenary lecture highlighted the integrative nature of the angiogenic process, whereas invited contributions from basic and clinician scientists described fundamental mechanisms and disease-associated issues of blood vessel formation, grouped under a number of themes to aid discussion. These articles will appeal to academic, clinical and pharmaceutical scientists interested in the molecular and cellular basis of angiogenesis, their modulation or dysfunction in human diseases, and application of these findings towards translational medicine.

  16. Computer Analogies: Teaching Molecular Biology and Ecology.

    ERIC Educational Resources Information Center

    Rice, Stanley; McArthur, John

    2002-01-01

    Suggests that computer science analogies can aid the understanding of gene expression, including the storage of genetic information on chromosomes. Presents a matrix of biology and computer science concepts. (DDR)

  17. Cell and molecular biology of Chlamydomonas

    SciTech Connect

    Not Available

    1988-01-01

    This document contains only the abstracts of 92 presentations on the biology of Chlamydomonas. Topics include gene transformations, gene regulation, biosynthetic pathways, cell surfaces, circadian clocks, and the development and structure of the flagellar apparatus. (TEM)

  18. Cell and molecular mechanics of biological materials

    NASA Astrophysics Data System (ADS)

    Bao, G.; Suresh, S.

    2003-11-01

    Living cells can sense mechanical forces and convert them into biological responses. Similarly, biological and biochemical signals are known to influence the abilities of cells to sense, generate and bear mechanical forces. Studies into the mechanics of single cells, subcellular components and biological molecules have rapidly evolved during the past decade with significant implications for biotechnology and human health. This progress has been facilitated by new capabilities for measuring forces and displacements with piconewton and nanometre resolutions, respectively, and by improvements in bio-imaging. Details of mechanical, chemical and biological interactions in cells remain elusive. However, the mechanical deformation of proteins and nucleic acids may provide key insights for understanding the changes in cellular structure, response and function under force, and offer new opportunities for the diagnosis and treatment of disease. This review discusses some basic features of the deformation of single cells and biomolecules, and examines opportunities for further research.

  19. Computer Analogies: Teaching Molecular Biology and Ecology.

    ERIC Educational Resources Information Center

    Rice, Stanley; McArthur, John

    2002-01-01

    Suggests that computer science analogies can aid the understanding of gene expression, including the storage of genetic information on chromosomes. Presents a matrix of biology and computer science concepts. (DDR)

  20. Molecular communication among biological nanomachines: a layered architecture and research issues.

    PubMed

    Nakano, Tadashi; Suda, Tatsuya; Okaie, Yutaka; Moore, Michael J; Vasilakos, Athanasios V

    2014-09-01

    Molecular communication is an emerging communication paradigm for biological nanomachines. It allows biological nanomachines to communicate through exchanging molecules in an aqueous environment and to perform collaborative tasks through integrating functionalities of individual biological nanomachines. This paper develops the layered architecture of molecular communication and describes research issues that molecular communication faces at each layer of the architecture. Specifically, this paper applies a layered architecture approach, traditionally used in communication networks, to molecular communication, decomposes complex molecular communication functionality into a set of manageable layers, identifies basic functionalities of each layer, and develops a descriptive model consisting of key components of the layer for each layer. This paper also discusses open research issues that need to be addressed at each layer. In addition, this paper provides an example design of targeted drug delivery, a nanomedical application, to illustrate how the layered architecture helps design an application of molecular communication. The primary contribution of this paper is to provide an in-depth architectural view of molecular communication. Establishing a layered architecture of molecular communication helps organize various research issues and design concerns into layers that are relatively independent of each other, and thus accelerates research in each layer and facilitates the design and development of applications of molecular communication.

  1. Biomarkers of Aging: From Function to Molecular Biology.

    PubMed

    Wagner, Karl-Heinz; Cameron-Smith, David; Wessner, Barbara; Franzke, Bernhard

    2016-06-02

    Aging is a major risk factor for most chronic diseases and functional impairments. Within a homogeneous age sample there is a considerable variation in the extent of disease and functional impairment risk, revealing a need for valid biomarkers to aid in characterizing the complex aging processes. The identification of biomarkers is further complicated by the diversity of biological living situations, lifestyle activities and medical treatments. Thus, there has been no identification of a single biomarker or gold standard tool that can monitor successful or healthy aging. Within this short review the current knowledge of putative biomarkers is presented, focusing on their application to the major physiological mechanisms affected by the aging process including physical capability, nutritional status, body composition, endocrine and immune function. This review emphasizes molecular and DNA-based biomarkers, as well as recent advances in other biomarkers such as microRNAs, bilirubin or advanced glycation end products.

  2. Biomarkers of Aging: From Function to Molecular Biology

    PubMed Central

    Wagner, Karl-Heinz; Cameron-Smith, David; Wessner, Barbara; Franzke, Bernhard

    2016-01-01

    Aging is a major risk factor for most chronic diseases and functional impairments. Within a homogeneous age sample there is a considerable variation in the extent of disease and functional impairment risk, revealing a need for valid biomarkers to aid in characterizing the complex aging processes. The identification of biomarkers is further complicated by the diversity of biological living situations, lifestyle activities and medical treatments. Thus, there has been no identification of a single biomarker or gold standard tool that can monitor successful or healthy aging. Within this short review the current knowledge of putative biomarkers is presented, focusing on their application to the major physiological mechanisms affected by the aging process including physical capability, nutritional status, body composition, endocrine and immune function. This review emphasizes molecular and DNA-based biomarkers, as well as recent advances in other biomarkers such as microRNAs, bilirubin or advanced glycation end products. PMID:27271660

  3. The extracellular matrix of plants: Molecular, cellular and developmental biology

    SciTech Connect

    1996-12-31

    A symposium entitled ``The Extracellular Matrix of Plants: Molecular, Cellular and Developmental Biology was held in Tamarron, Colorado, March 15--21, 1996. The following topics were explored in addresses by 43 speakers: structure and biochemistry of cell walls; biochemistry, molecular biology and biosynthesis of lignin; secretory pathway and synthesis of glycoproteins; biosynthesis of matrix polysaccharides, callose and cellulose; role of the extracellular matrix in plant growth and development; plant cell walls in symbiosis and pathogenesis.

  4. Debaryomyces hansenii: A Model System for Marine Molecular Biology

    DTIC Science & Technology

    1991-05-30

    System for Marine Molecular Biology PERIOD OF PERFORMANCE: June 1, 1990 to May 30, 1991 RESEARCH OBJECTIVE: To establish Debaryomyces hansenii as a model...Analysis of 17s rRNA gene from the marine yeast Debaryomyces hansenii . In preparation for Current Genetics. TRAINING ACTIVITIES Two graduate students, one...Institution: University of California, Santa Barbara. Grant Title: Debaryomyces hansenii : A Model System for Marine Molecular Biology. Period of

  5. Analysis application in biological field and prediction of human diseases with dual luminescence molecular of 3.5-generations polyamidoamine dendrimers-porphyrin

    NASA Astrophysics Data System (ADS)

    Liu, Jia-Ming; Lin, Chang-Qing; Lin, Shao-Qin; Lin, Li-Ping; Wang, Xin-Xing; Zheng, Mei-Xia; Zhang, Bin

    2010-09-01

    A new phosphorescence-labelling reagent (3.5-G-D-P labelling reagent) was developed, based on 3.5-generation polyamidoamine dendrimers (3.5-G-D) as internal acceptor to capture porphyrin (P) molecular. In the disturber of heavy atom, 3.5-G-D-P could emit room temperature phosphorescence (RTP) of 3.5-G-D and P on the surface of polyamide membrane (PAM), respectively. Products (3.5-G-D-P-WGA) of 3.5-G-D-P labelling triticum vulgaris lectin (WGA) could emit strong and stable RTP signal on the surface of PAM, and it also could take specific affinity adsorption reaction (AA) with alkaline phosphatase (ALP). The product of the AA reaction (3.5-G-D-P-WGA-ALP) could keep the RTP characteristics of 3.5-G-D-P very well, and the Δ Ip of the system was linear correlation to the content of ALP. The Δ Ip of the system with Tween-80 was once for P and twice for 3.5-G-D more than that without Tween-80. Thus, the affinity adsorption solid substrate-room temperature phosphorimetry (AA-SS-RTP) for the determination of trace ALP has been established using Tween-80-3.5-G-D-P to label WGA. The detection limit (LD) of this method was 0.12 fg spot -1 for 3.5-G-D and 0.18 fg spot -1 for P with direct method, 0.14 fg spot -1 for 3.5-G-D and 0.17 fg spot -1 for P with sandwich method, respectively, and the sensitivity was obviously high. This research showed that either using 3.5-G-D or P excitation/emission wavelength to determine the content of ALP in human serum, the results were coincided with ELISA, and the flexibility of AA-SS-RTP was obviously improved and the applicability was wider. Meanwhile, the reaction mechanism of determining ALP by direct method AA-SS-RTP was discussed.

  6. How synthetic biology will reconsider natural bioluminescence and its applications.

    PubMed

    Reeve, Benjamin; Sanderson, Theo; Ellis, Tom; Freemont, Paul

    2014-01-01

    As our understanding of natural biological systems grows, so too does our ability to alter and rebuild them. Synthetic biology is the application of engineering principles to biology in order to design and construct novel biological systems for specific applications. Bioluminescent organisms offer a treasure trove of light-emitting enzymes that may have applications in many areas of bioengineering, from biosensors to lighting. A few select bioluminescent organisms have been well researched and the molecular and genetic basis of their luminescent abilities elucidated, with work underway to understand the basis of luminescence in many others. Synthetic biology will aim to package these light-emitting systems as self-contained biological modules, characterize their properties, and then optimize them for use in other chassis organisms. As this catalog of biological parts grows, synthetic biologists will be able to engineer complex biological systems with the ability to emit light. These may use luminescence for an array of disparate functions, from providing illumination to conveying information or allowing communication between organisms.

  7. The molecular biology of Bluetongue virus replication.

    PubMed

    Patel, Avnish; Roy, Polly

    2014-03-01

    The members of Orbivirus genus within the Reoviridae family are arthropod-borne viruses which are responsible for high morbidity and mortality in ruminants. Bluetongue virus (BTV) which causes disease in livestock (sheep, goat, cattle) has been in the forefront of molecular studies for the last three decades and now represents the best understood orbivirus at a molecular and structural level. The complex nature of the virion structure has been well characterised at high resolution along with the definition of the virus encoded enzymes required for RNA replication; the ordered assembly of the capsid shell as well as the protein and genome sequestration required for it; and the role of host proteins in virus entry and virus release. More recent developments of Reverse Genetics and Cell-Free Assembly systems have allowed integration of the accumulated structural and molecular knowledge to be tested at meticulous level, yielding higher insight into basic molecular virology, from which the rational design of safe efficacious vaccines has been possible. This article is centred on the molecular dissection of BTV with a view to understanding the role of each protein in the virus replication cycle. These areas are important in themselves for BTV replication but they also indicate the pathways that related viruses, which includes viruses that are pathogenic to man and animals, might also use providing an informed starting point for intervention or prevention.

  8. Computer-Based Semantic Network in Molecular Biology: A Demonstration.

    ERIC Educational Resources Information Center

    Callman, Joshua L.; And Others

    This paper analyzes the hardware and software features that would be desirable in a computer-based semantic network system for representing biology knowledge. It then describes in detail a prototype network of molecular biology knowledge that has been developed using Filevision software and a Macintosh computer. The prototype contains about 100…

  9. Computer-Based Semantic Network in Molecular Biology: A Demonstration.

    ERIC Educational Resources Information Center

    Callman, Joshua L.; And Others

    This paper analyzes the hardware and software features that would be desirable in a computer-based semantic network system for representing biology knowledge. It then describes in detail a prototype network of molecular biology knowledge that has been developed using Filevision software and a Macintosh computer. The prototype contains about 100…

  10. Fundamental Approaches in Molecular Biology for Communication Sciences and Disorders

    ERIC Educational Resources Information Center

    Bartlett, Rebecca S.; Jette, Marie E.; King, Suzanne N.; Schaser, Allison; Thibeault, Susan L.

    2012-01-01

    Purpose: This contemporary tutorial will introduce general principles of molecular biology, common deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein assays and their relevance in the field of communication sciences and disorders. Method: Over the past 2 decades, knowledge of the molecular pathophysiology of human disease has…

  11. Fundamental Approaches in Molecular Biology for Communication Sciences and Disorders

    ERIC Educational Resources Information Center

    Bartlett, Rebecca S.; Jette, Marie E.; King, Suzanne N.; Schaser, Allison; Thibeault, Susan L.

    2012-01-01

    Purpose: This contemporary tutorial will introduce general principles of molecular biology, common deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein assays and their relevance in the field of communication sciences and disorders. Method: Over the past 2 decades, knowledge of the molecular pathophysiology of human disease has…

  12. Concepts and Skills in the Biochemistry/Molecular Biology Lab

    ERIC Educational Resources Information Center

    Boyer, Rodney

    2003-01-01

    Most colleges and universities throughout the world now offer a Biochemistry/Molecular Biology (BMB) lab course that is designed for undergraduate students in the molecular life sciences, chemistry, and related fields. To best serve our students, we must introduce them to the most current concepts, skills, and methods available. Suggestions for…

  13. Micropropagation, genetic engineering, and molecular biology of Populus

    Treesearch

    N. B. Klopfenstein; Y. W. Chun; M. -S. Kim; M. A. Ahuja; M. C. Dillon; R. C. Carman; L. G. Eskew

    1997-01-01

    Thirty-four Populus biotechnology chapters, written by 85 authors, are comprised in 5 sections: 1) in vitro culture (micropropagation, somatic embryogenesis, protoplasts, somaclonal variation, and germplasm preservation); 2) transformation and foreign gene expression; 3) molecular biology (molecular/genetic characterization); 4) biotic and abiotic resistance (disease,...

  14. Using a Computer Animation to Teach High School Molecular Biology

    ERIC Educational Resources Information Center

    Rotbain, Yosi; Marbach-Ad, Gili; Stavy, Ruth

    2008-01-01

    We present an active way to use a computer animation in secondary molecular genetics class. For this purpose we developed an activity booklet that helps students to work interactively with a computer animation which deals with abstract concepts and processes in molecular biology. The achievements of the experimental group were compared with those…

  15. The Macromolecular Concept and the Origins of Molecular Biology

    ERIC Educational Resources Information Center

    Olby, Robert

    1970-01-01

    Traces the origins of molecular biology to the work of 19th century biophysicists, ultrastructurists and collodial chemists. The development of the Aggregate Theory,and its overthrow by the Macromolecule Concept is described. Research in molecular genetics in the pre-second world war period, and the effects of the war on it, are briefly reviewed.…

  16. Using a Computer Animation to Teach High School Molecular Biology

    ERIC Educational Resources Information Center

    Rotbain, Yosi; Marbach-Ad, Gili; Stavy, Ruth

    2008-01-01

    We present an active way to use a computer animation in secondary molecular genetics class. For this purpose we developed an activity booklet that helps students to work interactively with a computer animation which deals with abstract concepts and processes in molecular biology. The achievements of the experimental group were compared with those…

  17. [Progress in molecular biology of a semi-mangrove, Millettia pinnata].

    PubMed

    Huang, Jianzi; Zhang, Wanke; Huang, Rongfeng; Zheng, Yizhi

    2015-04-01

    Millettia pinnata L. is a leguminous tree with great potential in biodiesel applications and also a typical semi-mangrove. In this review, we presented several aspects about the recent research progress in molecular biology of M. pinnata. We descrived several types of molecular markers used to assess the genetic diversity and phylogeny of this species, genome and transcriptome analyses based on high-throughput sequencing platform accomplished for this species, and several gene and genomic sequences of this species isolated for further research. Finally, based on the current research progress, we proposed some orientations for future molecular biology research on M. pinnata.

  18. Immunochemical methods in cell and molecular biology

    SciTech Connect

    Mayer, R.J.; Walker, J.H.

    1987-01-01

    This book presents immuno-chemical techniques for isolating and analysing a wide variety of biological products. CONTENTS: Introduction, Polyclonal Antiserum Production;Polyclonal Antiserum Processing;Uses of Polyclonal Antisera. Production and Use of Monoclonal Antibodies;Synthetic Petpides: A New Development in Protein Immunochemistry;and Technical Supplement.

  19. Methods in molecular biology: plant cytogenetics

    USDA-ARS?s Scientific Manuscript database

    Cytogenetic studies have contributed greatly to our understanding of genetics, biology, reproduction, and evolution. From early studies in basic chromosome behavior the field has expanded enabling whole genome analysis to the manipulation of chromosomes and their organization. This book covers a ran...

  20. Synthetic biology: programming cells for biomedical applications.

    PubMed

    Hörner, Maximilian; Reischmann, Nadine; Weber, Wilfried

    2012-01-01

    The emerging field of synthetic biology is a novel biological discipline at the interface between traditional biology, chemistry, and engineering sciences. Synthetic biology aims at the rational design of complex synthetic biological devices and systems with desired properties by combining compatible, modular biological parts in a systematic manner. While the first engineered systems were mainly proof-of-principle studies to demonstrate the power of the modular engineering approach of synthetic biology, subsequent systems focus on applications in the health, environmental, and energy sectors. This review describes recent approaches for biomedical applications that were developed along the synthetic biology design hierarchy, at the level of individual parts, of devices, and of complex multicellular systems. It describes how synthetic biological parts can be used for the synthesis of drug-delivery tools, how synthetic biological devices can facilitate the discovery of novel drugs, and how multicellular synthetic ecosystems can give insight into population dynamics of parasites and hosts. These examples demonstrate how this new discipline could contribute to novel solutions in the biopharmaceutical industry.

  1. Molecular biological enhancement of coal biodesulfurization

    SciTech Connect

    Kilbane, J.J. II; Bielaga, B.A.

    1991-12-01

    The overall objective of this project was to use molecular genetics to develop strains of bacteria with enhanced ability to remove sulfur from coal, and to obtain data that will allow the performance and economics of a coal biodesulfurization process to be predicted. (VC)

  2. Molecular biological enhancement of coal biodesulfurization

    SciTech Connect

    Bielaga, B.A.; Kilbane, J.J.

    1990-04-01

    The overall objectives of this project is to use Molecular Genetics to develop strains of bacteria (esp. Rhodococcus) with enhanced ability to remove sulfur from coal, and to obtain data that will allow the performance and economics of a coal biodesulfurization process to be predicted. 5 figs.

  3. Siderophores for molecular imaging applications.

    PubMed

    Petrik, Milos; Zhai, Chuangyan; Haas, Hubertus; Decristoforo, Clemens

    2017-01-01

    This review covers publications on siderophores applied for molecular imaging applications, mainly for radionuclide-based imaging. Siderophores are low molecular weight chelators produced by bacteria and fungi to scavenge essential iron. Research on these molecules has a continuing history over the past 50 years. Many biomedical applications have been developed, most prominently the use of the siderophore desferrioxamine (DFO) to tackle iron overload related diseases. Recent research described the upregulation of siderophore production and transport systems during infection. Replacing iron in siderophores by radionuclides, the most prominent Ga-68 for PET, opens approaches for targeted imaging of infection; the proof of principle has been reported for fungal infections using (68)Ga-triacetylfusarinine C (TAFC). Additionally, fluorescent siderophores and therapeutic conjugates have been described and may be translated to optical imaging and theranostic applications. Siderophores have also been applied as bifunctional chelators, initially DFO as chelator for Ga-67 and more recently for Zr-89 where it has become the standard chelator in Immuno-PET. Improved DFO constructs and bifunctional chelators based on cyclic siderophores have recently been developed for Ga-68 and Zr-89 and show promising properties for radiopharmaceutical development in PET. A huge potential from basic biomedical research on siderophores still awaits to be utilized for clinical and translational imaging.

  4. Mathematical biology modules based on modern molecular biology and modern discrete mathematics.

    PubMed

    Robeva, Raina; Davies, Robin; Hodge, Terrell; Enyedi, Alexander

    2010-01-01

    We describe an ongoing collaborative curriculum materials development project between Sweet Briar College and Western Michigan University, with support from the National Science Foundation. We present a collection of modules under development that can be used in existing mathematics and biology courses, and we address a critical national need to introduce students to mathematical methods beyond the interface of biology with calculus. Based on ongoing research, and designed to use the project-based-learning approach, the modules highlight applications of modern discrete mathematics and algebraic statistics to pressing problems in molecular biology. For the majority of projects, calculus is not a required prerequisite and, due to the modest amount of mathematical background needed for some of the modules, the materials can be used for an early introduction to mathematical modeling. At the same time, most modules are connected with topics in linear and abstract algebra, algebraic geometry, and probability, and they can be used as meaningful applied introductions into the relevant advanced-level mathematics courses. Open-source software is used to facilitate the relevant computations. As a detailed example, we outline a module that focuses on Boolean models of the lac operon network.

  5. Mathematical Biology Modules Based on Modern Molecular Biology and Modern Discrete Mathematics

    PubMed Central

    Davies, Robin; Hodge, Terrell; Enyedi, Alexander

    2010-01-01

    We describe an ongoing collaborative curriculum materials development project between Sweet Briar College and Western Michigan University, with support from the National Science Foundation. We present a collection of modules under development that can be used in existing mathematics and biology courses, and we address a critical national need to introduce students to mathematical methods beyond the interface of biology with calculus. Based on ongoing research, and designed to use the project-based-learning approach, the modules highlight applications of modern discrete mathematics and algebraic statistics to pressing problems in molecular biology. For the majority of projects, calculus is not a required prerequisite and, due to the modest amount of mathematical background needed for some of the modules, the materials can be used for an early introduction to mathematical modeling. At the same time, most modules are connected with topics in linear and abstract algebra, algebraic geometry, and probability, and they can be used as meaningful applied introductions into the relevant advanced-level mathematics courses. Open-source software is used to facilitate the relevant computations. As a detailed example, we outline a module that focuses on Boolean models of the lac operon network. PMID:20810955

  6. Applications of microfluidics in quantitative biology.

    PubMed

    Bai, Yang; Gao, Meng; Wen, Lingling; He, Caiyun; Chen, Yuan; Liu, Chenli; Fu, Xiongfei; Huang, Shuqiang

    2017-10-04

    Quantitative biology is dedicated to taking advantage of quantitative reasoning and advanced engineering technologies to make biology more predictable. Microfluidics, as an emerging technique, provides new approaches to precisely control fluidic conditions on small scales and collect data in high-throughput and quantitative manners. In this review, we present the relevant applications of microfluidics to quantitative biology based on two major categories (channel-based microfluidics and droplet-based microfluidics), and their typical features. We also envision some other microfluidic techniques that may not be employed in quantitative biology right now, but have great potential in the near future. This article is protected by copyright. All rights reserved.

  7. METHODS IN MOLECULAR BIOLOGY: ASSAYING CHROMATIN SIRTUINS

    PubMed Central

    Silberman, Dafne M.; Sebastian, Carlos; Mostoslavsky, Raul

    2015-01-01

    Summary Most of the sirtuins’ nuclear substrates indentified so far are histones or other chromatin-associated proteins and, thus, it is of special relevance the development of good biochemical techniques to analyze the biology of these proteins in the context of chromatin. Here, we describe several of the chromatin-based techniques to identify sirtuins’ substrates, including a chromatin immunoprecipitation (ChIP) protocol, an acid-extraction protocol, and a nucleosomal immunoprecipitation protocol to analyze putative sirtuin chromatin interactors. PMID:24014405

  8. [Molecular biology for sarcoma: useful or necessary?].

    PubMed

    Neuville, Agnès; Coindre, Jean-Michel; Chibon, Frédéric

    2015-01-01

    Sarcomas are a heterogeneous group of tumors. Their diagnosis is based on morphology and immunohistochemical profile, with categories of tumors according to the type of tissue that they resemble. Nevertheless, for several tumors, cellular origin is unknown. Molecular analysis performed in recent years allowed, combining histophenotype and genomics, better classifying such sarcomas, individualizing new entities and grouping some tumors. Simple and recurrent genetic alterations, such as translocation, mutation, amplification, can be identified in one of two sarcomas and appear as new diagnostic markers. Their identification in specialized laboratories in molecular pathology of sarcomas is often useful and sometimes necessary for a good diagnosis, leading to a heavy and multidisciplinary multi-step treatment. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  9. Biological (molecular and cellular) markers of toxicity

    SciTech Connect

    McCarthy, J.F.

    1990-04-01

    The overall objective of this study is to evaluate the use of the small aquarium fish, Japanese Medaka, as a predictor of potential genotoxicity following exposure to carcinogens. This will be accomplished by quantitatively investigating the early molecular events associated with genotoxicity of various tissues of Medaka subsequent to exposure of the organism to several known carcinogens, such as diethylnitrosamine (DEN) and benzo(a)pyrene (BaP). 11 refs., 1 fig., 1 tab.

  10. The molecular biology of distraction osteogenesis.

    PubMed

    Bouletreau, Pierre J; Warren, Stephen M; Longaker, Michael T

    2002-02-01

    Distraction osteogenesis has become a mainstay in bone tissue engineering and has significantly improved our armamentarium for reconstructive craniomaxillofacial procedures. However, although the biomechanical, histological, and ultrastructural changes associated with distraction osteogenesis have been widely described, the molecular mechanisms governing the formation of new bone in the interfragmental gap of gradually distracted bone segments remain largely unclear. Recently, a rat model of mandibular distraction was described that provides an excellent environment for deciphering the molecular mechanisms that mediate distraction osteogenesis. This article presents the hypotheses and current research that have furthered knowledge of the molecular mechanisms that govern distraction osteogenesis. Recent studies have implicated a growing number of cytokines that are intimately involved in the regulation of bone synthesis and turnover. The gene regulation of numerous cytokines (transforming growth factor-beta1, -beta2, -beta3, bone morphogenetic proteins, insulin-like growth factor-1, fibroblast growth factor-2) and extracellular matrix proteins (osteonectin, osteopontin) during distraction osteogenesis have been best characterized and are discussed in this article. It is believed that understanding the biomolecular mechanisms that mediate membranous distraction osteogenesis may guide the development of targeted strategies designed to improve distraction osteogenesis and accelerate bone healing.

  11. Applications in biology and condensed matter physics

    NASA Astrophysics Data System (ADS)

    Faruqi, A. R.

    1991-12-01

    Position-sensitive detectors are a vital research tool in many areas of structural and molecular biology and condensed matter physics. The present review is mainly restricted to structural information obtained by X-ray scattering and diffraction and in DNA sequence analysis using autoradiography. Film has traditionally played the most important role, and for many applications is still the best medium for recording data, but advances in various types of detector technology has made them attractive, and in some cases essential alternatives. The requirements imposed by experiments vary a great deal and can be very demanding in terms of detector performance, e.g. in terms of count rates, particularly for synchrotron radiation, dynamic range, spatial resolution, ability to do time-resolved measurements on a millisecond time scale, differential and integral linearity and resistance to radiation damage. A brief review of detector properties will be presented and how they are matched in different cases with the experimental requirements along with a small selection of recent results and what new developments are needed to cope with the new generation of storage rings now under construction.

  12. Information theory applications for biological sequence analysis.

    PubMed

    Vinga, Susana

    2014-05-01

    Information theory (IT) addresses the analysis of communication systems and has been widely applied in molecular biology. In particular, alignment-free sequence analysis and comparison greatly benefited from concepts derived from IT, such as entropy and mutual information. This review covers several aspects of IT applications, ranging from genome global analysis and comparison, including block-entropy estimation and resolution-free metrics based on iterative maps, to local analysis, comprising the classification of motifs, prediction of transcription factor binding sites and sequence characterization based on linguistic complexity and entropic profiles. IT has also been applied to high-level correlations that combine DNA, RNA or protein features with sequence-independent properties, such as gene mapping and phenotype analysis, and has also provided models based on communication systems theory to describe information transmission channels at the cell level and also during evolutionary processes. While not exhaustive, this review attempts to categorize existing methods and to indicate their relation with broader transversal topics such as genomic signatures, data compression and complexity, time series analysis and phylogenetic classification, providing a resource for future developments in this promising area.

  13. Aptamers and Their Biological Applications

    PubMed Central

    Song, Kyung-Mi; Lee, Seonghwan; Ban, Changill

    2012-01-01

    Recently, aptamers have attracted the attention of many scientists, because they not only have all of the advantages of antibodies, but also have unique merits, such as thermal stability, low cost, and unlimited applications. In this review, we present the reasons why aptamers are known as alternatives to antibodies. Furthermore, several types of in vitro selection processes, including nitrocellulose membrane filtration, affinity chromatography, magnetic bead, and capillary electrophoresis-based selection methods, are explained in detail. We also introduce various applications of aptamers for the diagnosis of diseases and detection of small molecules. Numerous analytical techniques, such as electrochemical, colorimetric, optical, and mass-sensitive methods, can be utilized to detect targets, due to convenient modifications and the stability of aptamers. Finally, several medical and analytical applications of aptamers are presented. In summary, aptamers are promising materials for diverse areas, not just as alternatives to antibodies, but as the core components of medical and analytical equipment. PMID:22368488

  14. Microgravity research in plant biological systems: Realizing the potential of molecular biology

    NASA Technical Reports Server (NTRS)

    Lewis, Norman G.; Ryan, Clarence A.

    1993-01-01

    The sole all-pervasive feature of the environment that has helped shape, through evolution, all life on Earth is gravity. The near weightlessness of the Space Station Freedom space environment allows gravitational effects to be essentially uncoupled, thus providing an unprecedented opportunity to manipulate, systematically dissect, study, and exploit the role of gravity in the growth and development of all life forms. New and exciting opportunities are now available to utilize molecular biological and biochemical approaches to study the effects of microgravity on living organisms. By careful experimentation, we can determine how gravity perception occurs, how the resulting signals are produced and transduced, and how or if tissue-specific differences in gene expression occur. Microgravity research can provide unique new approaches to further our basic understanding of development and metabolic processes of cells and organisms, and to further the application of this new knowledge for the betterment of humankind.

  15. Molecularly imprinted materials: synthesis, properties, applications

    NASA Astrophysics Data System (ADS)

    Lisichkin, Georgii V.; Krutyakov, Yu A.

    2006-10-01

    This review is devoted to the method of molecular imprinting. The physicochemical fundamentals and mechanisms of covalent and non-covalent molecular imprinting aimed at the development of organic polymeric sorbents capable of molecular recognition are considered. Attention is focused on the preparation of molecular imprints on mineral supports. The mechanisms of molecular recognition in adsorption are discussed. Application fields of materials with molecular imprints are briefly surveyed.

  16. Database Transformations for Biological Applications

    SciTech Connect

    Overton, C.; Davidson, S. B.; Buneman, P.; Tannen, V.

    2001-04-11

    The goal of this project was to develop tools to facilitate data transformations between heterogeneous data sources found throughout biomedical applications. Such transformations are necessary when sharing data between different groups working on related problems as well as when querying data spread over different databases, files and software analysis packages.

  17. A comprehensive experiment for molecular biology: Determination of single nucleotide polymorphism in human REV3 gene using PCR-RFLP.

    PubMed

    Zhang, Xu; Shao, Meng; Gao, Lu; Zhao, Yuanyuan; Sun, Zixuan; Zhou, Liping; Yan, Yongmin; Shao, Qixiang; Xu, Wenrong; Qian, Hui

    2017-02-01

    Laboratory exercise is helpful for medical students to understand the basic principles of molecular biology and to learn about the practical applications of molecular biology. We have designed a lab course on molecular biology about the determination of single nucleotide polymorphism (SNP) in human REV3 gene, the product of which is a subunit of DNA polymerase ζ and SNPs in this gene are associated with altered susceptibility to cancer. This newly designed experiment is composed of three parts, including genomic DNA extraction, gene amplification by PCR, and genotyping by RFLP. By combining these activities, the students are not only able to learn a series of biotechniques in molecular biology, but also acquire the ability to link the learned knowledge with practical applications. This comprehensive experiment will help the medical students improve the conceptual understanding of SNP and the technical understanding of SNP detection. © 2017 by The International Union of Biochemistry and Molecular Biology, 2017.

  18. Asymmetry at the molecular level in biology

    NASA Astrophysics Data System (ADS)

    Johnson, Louise N.

    2005-10-01

    Naturally occurring biological molecules are made of homochiral building blocks. Proteins are composed of L-amino acids (and not D-amino acids); nucleic acids such as DNA have D-ribose sugars (and not L-ribose sugars). It is not clear why nature selected a particular chirality. Selection could have occurred by chance or as a consequence of basic physical chemistry. Possible proposals, including the contribution of the parity violating the weak nuclear force, are discussed together with the mechanisms by which this very small contribution might be amplified. Homochirality of the amino acids has consequences for protein structure. Helices are right handed and beta sheets have a left-hand twist. When incorporated into the tertiary structure of a protein these chiralities limit the topologies of connections between helices and sheets. Polypeptides comprised of D-amino acids can be synthesized chemically and have been shown to adopt stable structures that are the mirror image of the naturally occurring L-amino acid polypeptides. Chirality is important in drug design. Three examples are discussed: penicillin; the CD4 antagonistic peptides; and thalidomide. The absolute hand of a biological structure can only be established by X-ray crystallographic methods using the technique of anomalous scattering.

  19. Luciferase Genes as Reporter Reactions: How to Use Them in Molecular Biology?

    PubMed

    Cevenini, L; Calabretta, M M; Calabria, D; Roda, A; Michelini, E

    2016-01-01

    : The latest advances in molecular biology have made available several biotechnological tools that take advantage of the high detectability and quantum efficiency of bioluminescence (BL), with an ever-increasing number of novel applications in environmental, pharmaceutical, food, and forensic fields. Indeed, BL proteins are being used to develop ultrasensitive binding assays and cell-based assays, thanks to their high detectability and to the availability of highly sensitive BL instruments. The appealing aspect of molecular biology tools relying on BL reactions is their general applicability in both in vitro assays, such as cell cultures or purified proteins, and in vivo settings, such as in whole-animal BL imaging. The aim of this chapter is to provide the reader with an overview of state-of-the-art bioluminescent tools based on luciferase genes, highlighting molecular biology strategies that have been applied so far, together with some selected examples.

  20. The molecular biology of WHO grade I astrocytomas.

    PubMed

    Marko, Nicholas F; Weil, Robert J

    2012-12-01

    World Health Organization (WHO) grade I astrocytomas include pilocytic astrocytoma (PA) and subependymal giant cell astrocytoma (SEGA). As technologies in pharmacologic neo-adjuvant therapy continue to progress and as molecular characteristics are progressively recognized as potential markers of both clinically significant tumor subtypes and response to therapy, interest in the biology of these tumors has surged. An updated review of the current knowledge of the molecular biology of these tumors is needed. We conducted a Medline search to identify published literature discussing the molecular biology of grade I astrocytomas. We then summarized this literature and discuss it in a logical framework through which the complex biology of these tumors can be clearly understood. A comprehensive review of the molecular biology of WHO grade I astrocytomas is presented. The past several years have seen rapid progress in the level of understanding of PA in particular, but the molecular literature regarding both PA and SEGA remains nebulous, ambiguous, and occasionally contradictory. In this review we provide a comprehensive discussion of the current understanding of the chromosomal, genomic, and epigenomic features of both PA and SEGA and provide a logical framework in which these data can be more readily understood.

  1. Systems biology of molecular chaperone networks.

    PubMed

    Csermely, Péter; Korcsmáros, Tamás; Kovács, István A; Szalay, Máté S; Soti, Csaba

    2008-01-01

    Molecular chaperones are not only fascinating molecular machines that help the folding, refolding, activation or assembly of other proteins, but also have a number of functions. These functions can be understood only by considering the emergent properties of cellular networks--and that of chaperones as special network constituents. As a notable example for the network-related roles of chaperones they may act as genetic buffers stabilizing the phenotype of various cells and organisms, and may serve as potential regulators of evolvability. Why are chaperones special in the context of cellular networks? Chaperones: (1) have weak links, i.e. low affinity, transient interactions with most of their partners; (2) connect hubs, i.e. act as 'masterminds' of the cell being close to several centre proteins with a lot of neighbours; and (3) are in the overlaps of network modules, which confers upon them a special regulatory role. Importantly, chaperones may uncouple or even quarantine modules of protein-protein interaction networks, signalling networks, genetic regulatory networks and membrane organelle networks during stress, which gives an additional chaperone-mediated protection for the cell at the network-level. Moreover, chaperones are essential to rebuild inter-modular contacts after stress by their low affinity, 'quasi-random' sampling of the potential interaction partners in different cellular modules. This opens the way to the chaperone-regulated modular evolution of cellular networks, and helps us to design novel therapeutic and anti-ageing strategies.

  2. Panel 4: Recent advances in otitis media in molecular biology, biochemistry, genetics, and animal models.

    PubMed

    Li, Jian-Dong; Hermansson, Ann; Ryan, Allen F; Bakaletz, Lauren O; Brown, Steve D; Cheeseman, Michael T; Juhn, Steven K; Jung, Timothy T K; Lim, David J; Lim, Jae Hyang; Lin, Jizhen; Moon, Sung-Kyun; Post, J Christopher

    2013-04-01

    Otitis media (OM) is the most common childhood bacterial infection and also the leading cause of conductive hearing loss in children. Currently, there is an urgent need for developing novel therapeutic agents for treating OM based on full understanding of molecular pathogenesis in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. To provide a state-of-the-art review concerning recent advances in OM in the areas of molecular biology, biochemistry, genetics, and animal model studies and to discuss the future directions of OM studies in these areas. A structured search of the current literature (since June 2007). The authors searched PubMed for published literature in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. Over the past 4 years, significant progress has been made in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. These studies brought new insights into our understanding of the molecular and biochemical mechanisms underlying the molecular pathogenesis of OM and helped identify novel therapeutic targets for OM. Our understanding of the molecular pathogenesis of OM has been significantly advanced, particularly in the areas of inflammation, innate immunity, mucus overproduction, mucosal hyperplasia, middle ear and inner ear interaction, genetics, genome sequencing, and animal model studies. Although these studies are still in their experimental stages, they help identify new potential therapeutic targets. Future preclinical and clinical studies will help to translate these exciting experimental research findings into clinical applications.

  3. Evolution of egg coats: linking molecular biology and ecology.

    PubMed

    Shu, Longfei; Suter, Marc J-F; Räsänen, Katja

    2015-08-01

    One central goal of evolutionary biology is to explain how biological diversity emerges and is maintained in nature. Given the complexity of the phenotype and the multifaceted nature of inheritance, modern evolutionary ecological studies rely heavily on the use of molecular tools. Here, we show how molecular tools help to gain insight into the role of egg coats (i.e. the extracellular structures surrounding eggs and embryos) in evolutionary diversification. Egg coats are maternally derived structures that have many biological functions from mediating fertilization to protecting the embryo from environmental hazards. They show great molecular, structural and functional diversity across species, but intraspecific variability and the role of ecology in egg coat evolution have largely been overlooked. Given that much of the variation that influences egg coat function is ultimately determined by their molecular phenotype, cutting-edge molecular tools (e.g. proteomics, glycomics and transcriptomics), combined with functional assays, are needed for rigorous inferences on their evolutionary ecology. Here, we identify key research areas and highlight emerging molecular techniques that can increase our understanding of the role of egg coats in the evolution of biological diversity, from adaptation to speciation.

  4. Xenopus laevis in Developmental and Molecular Biology.

    ERIC Educational Resources Information Center

    Dawid, Igor B.; Sargent, Thomas D.

    1988-01-01

    Discusses the advantages of Xenopus laevis as an experimental animal in the study of embryogenesis in vertebrates. Summarizes the contributions of this system to the analysis of ribosomal and 5S RNA genes, and the diverse and highly productive applications of the oocyte injection technology. (RT)

  5. Xenopus laevis in Developmental and Molecular Biology.

    ERIC Educational Resources Information Center

    Dawid, Igor B.; Sargent, Thomas D.

    1988-01-01

    Discusses the advantages of Xenopus laevis as an experimental animal in the study of embryogenesis in vertebrates. Summarizes the contributions of this system to the analysis of ribosomal and 5S RNA genes, and the diverse and highly productive applications of the oocyte injection technology. (RT)

  6. Micro and nanotechnology for biological and biomedical applications.

    PubMed

    Lim, Chwee Teck; Han, Jongyoon; Guck, Jochen; Espinosa, Horacio

    2010-10-01

    This special issue contains some of the current state-of-the-art development and use of micro and nanotechnological tools, devices and techniques for both biological and biomedical research and applications. These include nanoparticles for bioimaging and biosensing, optical and biophotonic techniques for probing diseases at the nanoscale, micro and nano-fabricated tools for elucidating molecular mechanisms of mechanotransduction in cell and molecular biology and cell separation microdevices and techniques for isolating and enriching targeted cells for disease detection and diagnosis. Although some of these works are still at the research stage, there is no doubt that some of the important outcomes will eventually see actual biomedical applications in the not too distant future.

  7. Overview of selected molecular biological databases

    SciTech Connect

    Rayl, K.D.; Gaasterland, T.

    1994-11-01

    This paper presents an overview of the purpose, content, and design of a subset of the currently available biological databases, with an emphasis on protein databases. Databases included in this summary are 3D-ALI, Berlin RNA databank, Blocks, DSSP, EMBL Nucleotide Database, EMP, ENZYME, FSSP, GDB, GenBank, HSSP, LiMB, PDB, PIR, PKCDD, ProSite, and SWISS-PROT. The goal is to provide a starting point for researchers who wish to take advantage of the myriad available databases. Rather than providing a complete explanation of each database, we present its content and form by explaining the details of typical entries. Pointers to more complete ``user guides`` are included, along with general information on where to search for a new database.

  8. Cellular and molecular biology of neuronal dystonin.

    PubMed

    Ferrier, Andrew; Boyer, Justin G; Kothary, Rashmi

    2013-01-01

    Neuronal dystonin isoforms are giant cytoskeletal cross-linking proteins capable of interacting with actin and microtubule networks, protein complexes, membrane-bound organelles and cellular membranes. In the neuromuscular system, dystonin proteins are involved in maintaining cytoarchitecture integrity and have more recently been ascribed roles in other cellular processes such as organelle structure and intracellular transport. Loss of dystonin expression in mice results in a profound sensory ataxia termed dystonia musculorum (dt), which is attributed to the degeneration of sensory nerves. This chapter provides a comprehensive overview of the dystonin gene, the structure of encoded proteins, biological functions of neuronal dystonin isoforms, and known roles of dystonin in dt pathogenesis and human disease. Copyright © 2013 Elsevier Inc. All rights reserved.

  9. pGLO Mutagenesis: A Laboratory Procedure in Molecular Biology for Biology Students

    ERIC Educational Resources Information Center

    Bassiri, Eby A.

    2011-01-01

    A five-session laboratory project was designed to familiarize or increase the laboratory proficiency of biology students and others with techniques and instruments commonly used in molecular biology research laboratories and industries. In this project, the EZ-Tn5 transposon is used to generate and screen a large number of cells transformed with…

  10. pGLO Mutagenesis: A Laboratory Procedure in Molecular Biology for Biology Students

    ERIC Educational Resources Information Center

    Bassiri, Eby A.

    2011-01-01

    A five-session laboratory project was designed to familiarize or increase the laboratory proficiency of biology students and others with techniques and instruments commonly used in molecular biology research laboratories and industries. In this project, the EZ-Tn5 transposon is used to generate and screen a large number of cells transformed with…

  11. Molecular biology of testicular germ cell tumors.

    PubMed

    Gonzalez-Exposito, R; Merino, M; Aguayo, C

    2016-06-01

    Testicular germ cell tumors (TGCTs) are the most common solid tumors in young adult men. They constitute a unique pathology because of their embryonic and germ origin and their special behavior. Genetic predisposition, environmental factors involved in their development and genetic aberrations have been under study in many works throughout the last years trying to explain the susceptibility and the transformation mechanism of TGCTs. Despite the high rate of cure in this type of tumors because its particular sensitivity to cisplatin, there are tumors resistant to chemotherapy for which it is needed to find new therapies. In the present work, it has been carried out a literature review on the most important molecular aspects involved in the onset and development of such tumors, as well as a review of the major developments regarding prognostic factors, new prognostic biomarkers and the possibility of new targeted therapies.

  12. Comparative molecular modelling of biologically active sterols

    NASA Astrophysics Data System (ADS)

    Baran, Mariusz; Mazerski, Jan

    2015-04-01

    Membrane sterols are targets for a clinically important antifungal agent - amphotericin B. The relatively specific antifungal action of the drug is based on a stronger interaction of amphotericin B with fungal ergosterol than with mammalian cholesterol. Conformational space occupied by six sterols has been defined using the molecular dynamics method to establish if the conformational features correspond to the preferential interaction of amphotericin B with ergosterol as compared with cholesterol. The compounds studied were chosen on the basis of structural features characteristic for cholesterol and ergosterol and on available experimental data on the ability to form complexes with the antibiotic. Statistical analysis of the data obtained has been performed. The results show similarity of the conformational spaces occupied by all the sterols tested. This suggests that the conformational differences of sterol molecules are not the major feature responsible for the differential sterol - drug affinity.

  13. [Molecular biology of von Willebrand disease].

    PubMed

    Melo-Nava, Brenda; Peñaloza, Rosenda

    2007-01-01

    Von Willebrand Factor (VWF) is a large multimeric glycoprotein expressed in the megakaryocytes and endothelial cells of all vertebrates. It participates fundamentally in the primary and secondary hemostasis because it induces the adhesion of platelets to vascular subendothelium and promotes aggregation of platelets when blood vessels and capillaries are damaged. In addition, VWF links to factor VIII which avoids its proteolysis. The deficiency or the inadequate synthesis of the VWF causes von Willebrand disease (VWD), which is the most common hereditary bleeding disorder in humans principally from mucous and cutaneous sites. VWD is difficult to detect with accuracy due to interrelation among VWF with different components of hemostasis, although it is performed by different tests of haemostatic system, and the basic mechanisms in VWD are herein emphasized. The diagnosis of VWD is difficult due to the heterogeneous manifestation of the disease, which also complicates its classification. This article focuses on the molecular aspects of the disease and discusses their possible clinical implications.

  14. Teaching molecular genetics: Chapter 1--Background principles and methods of molecular biology.

    PubMed

    Knoers, Nine V A M; Monnens, Leo A H

    2006-02-01

    In this first chapter of the series "Teaching molecular genetics," an introduction to molecular genetics is presented. We describe the structure of DNA and genes and explain in detail the central dogma of molecular biology, that is, the flow of genetic information from DNA via RNA to polypeptide (protein). In addition, several basic and frequently used general molecular tools, such as restriction enzymes, Southern blotting, DNA amplification and sequencing are discussed, in order to lay the foundations for the forthcoming chapters.

  15. From atom to brain: applications of molecular imaging to neurosurgery.

    PubMed

    Taghva, Alexander; Khalessi, Alexander A; Kim, Paul E; Liu, Charles Y; Apuzzo, Michael L J

    2010-05-01

    Molecular imaging is a field born out of the happy marriage of molecular biology and radiology. The first installment of this two-part series on molecular imaging demonstrated basic principles for practitioners in the field of the neurosciences. This installment seeks to provide some illustrative examples, insights, and specific applications to the neurosciences. The fields of functional neurosurgery including the treatment of neuropsychiatric disorders, novel treatments and imaging of tumors, neuroregenerative medicine, and nanotechnology in vascular disorders are covered. Finally, we give some parting thoughts on the future of molecular imaging, including advances in the imaging of neurodegenerative disorders. Published by Elsevier Inc.

  16. Molecular and biological hallmarks of ageing.

    PubMed

    Aunan, J R; Watson, M M; Hagland, H R; Søreide, K

    2016-01-01

    Ageing is the inevitable time-dependent decline in physiological organ function that eventually leads to death. Age is a major risk factor for many of the most common medical conditions, such as cardiovascular disease, cancer, diabetes and Alzheimer's disease. This study reviews currently known hallmarks of ageing and their clinical implications. A literature search of PubMed/MEDLINE was conducted covering the last decade. Average life expectancy has increased dramatically over the past century and is estimated to increase even further. Maximum longevity, however, appears unchanged, suggesting a universal limitation to the human organism. Understanding the underlying molecular processes of ageing and health decline may suggest interventions that, if used at an early age, can prevent, delay, alleviate or even reverse age-related diseases. Hallmarks of ageing can be grouped into three main categories. The primary hallmarks cause damage to cellular functions: genomic instability, telomere attrition, epigenetic alterations and loss of proteostasis. These are followed by antagonistic responses to such damage: deregulated nutrient sensing, altered mitochondrial function and cellular senescence. Finally, integrative hallmarks are possible culprits of the clinical phenotype (stem cell exhaustion and altered intercellular communication), which ultimately contribute to the clinical effects of ageing as seen in physiological loss of reserve, organ decline and reduced function. The sum of these molecular hallmarks produces the clinical picture of the elderly surgical patient: frailty, sarcopenia, anaemia, poor nutrition and a blunted immune response system. Improved understanding of the ageing processes may give rise to new biomarkers of risk or prognosis, novel treatment targets and translational approaches across disciplines that may improve outcomes. © 2016 BJS Society Ltd Published by John Wiley & Sons Ltd.

  17. The molecular biology of WHO grade II gliomas.

    PubMed

    Marko, Nicholas F; Weil, Robert J

    2013-02-01

    The WHO grading scheme for glial neoplasms assigns Grade II to 5 distinct tumors of astrocytic or oligodendroglial lineage: diffuse astrocytoma, oligodendroglioma, oligoastrocytoma, pleomorphic xanthoastrocytoma, and pilomyxoid astrocytoma. Although commonly referred to collectively as among the "low-grade gliomas," these 5 tumors represent molecularly and clinically unique entities. Each is the subject of active basic research aimed at developing a more complete understanding of its molecular biology, and the pace of such research continues to accelerate. Additionally, because managing and predicting the course of these tumors has historically proven challenging, translational research regarding Grade II gliomas continues in the hopes of identifying novel molecular features that can better inform diagnostic, prognostic, and therapeutic strategies. Unfortunately, the basic and translational literature regarding the molecular biology of WHO Grade II gliomas remains nebulous. The authors' goal for this review was to present a comprehensive discussion of current knowledge regarding the molecular characteristics of these 5 WHO Grade II tumors on the chromosomal, genomic, and epigenomic levels. Additionally, they discuss the emerging evidence suggesting molecular differences between adult and pediatric Grade II gliomas. Finally, they present an overview of current strategies for using molecular data to classify low-grade gliomas into clinically relevant categories based on tumor biology.

  18. Plant synthetic biology for molecular engineering of signalling and development

    PubMed Central

    Nemhauser, Jennifer L.; Torii, Keiko U.

    2016-01-01

    Molecular genetic studies of model plants in the past few decades have identified many key genes and pathways controlling development, metabolism and environmental responses. Recent technological and informatics advances have led to unprecedented volumes of data that may uncover underlying principles of plants as biological systems. The newly emerged discipline of synthetic biology and related molecular engineering approaches is built on this strong foundation. Today, plant regulatory pathways can be reconstituted in heterologous organisms to identify and manipulate parameters influencing signalling outputs. Moreover, regulatory circuits that include receptors, ligands, signal transduction components, epigenetic machinery and molecular motors can be engineered and introduced into plants to create novel traits in a predictive manner. Here, we provide a brief history of plant synthetic biology and significant recent examples of this approach, focusing on how knowledge generated by the reference plant Arabidopsis thaliana has contributed to the rapid rise of this new discipline, and discuss potential future directions. PMID:27249346

  19. Intelligent Systems for Molecular Biology: review of the first international conference.

    PubMed

    Clark, D A; Rawlings, C J

    1994-04-01

    This review provides a description of the background to the first international conference on Intelligent Systems for Molecular Biology and a problem-oriented overview of the papers presented. It focuses on genome analysis, gene identification, protein and RNA structure prediction and function, the modelling of biochemical pathways and data and knowledge bases. The range and quality of papers indicates that intelligent systems is emerging as an important sub-field of computational applications in the biological sciences.

  20. Single nanoparticle detectors for biological applications

    NASA Astrophysics Data System (ADS)

    Yurt, Abdulkadir; Daaboul, George G.; Connor, John H.; Goldberg, Bennett B.; Selim Ünlü, M.

    2012-01-01

    Nanoparticle research has become increasingly important in the context of bioscience and biotechnology. Practical use of nanoparticles in biology has significantly advanced our understanding about biological processes in the nanoscale as well as led to many novel diagnostic and therapeutic applications. Besides, synthetic and natural nanoparticles are of concern for their potential adverse effect on human health. Development of novel detection and characterization tools for nanoparticles will impact a broad range of disciplines in biological research from nanomedicine to nanotoxicology. In this article, we discuss the recent progress and future directions in the area of single nanoparticle detectors with an emphasis on their biological applications. A brief critical overview of electrical and mechanical detection techniques is given and a more in-depth discussion of label-free optical detection techniques is presented.

  1. Phage integrases: biology and applications.

    PubMed

    Groth, Amy C; Calos, Michele P

    2004-01-16

    Phage integrases are enzymes that mediate unidirectional site-specific recombination between two DNA recognition sequences, the phage attachment site, attP, and the bacterial attachment site, attB. Integrases may be grouped into two major families, the tyrosine recombinases and the serine recombinases, based on their mode of catalysis. Tyrosine family integrases, such as lambda integrase, utilize a catalytic tyrosine to mediate strand cleavage, tend to recognize longer attP sequences, and require other proteins encoded by the phage or the host bacteria. Phage integrases from the serine family are larger, use a catalytic serine for strand cleavage, recognize shorter attP sequences, and do not require host cofactors. Phage integrases mediate efficient site-specific recombination between two different sequences that are relatively short, yet long enough to be specific on a genomic scale. These properties give phage integrases growing importance for the genetic manipulation of living eukaryotic cells, especially those with large genomes such as mammals and most plants, for which there are few tools for precise manipulation of the genome. Integrases of the serine family have been shown to work efficiently in mammalian cells, mediating efficient integration at introduced att sites or native sequences that have partial identity to att sites. This reaction has applications in areas such as gene therapy, construction of transgenic organisms, and manipulation of cell lines. Directed evolution can be used to increase further the affinity of an integrase for a particular native sequence, opening up additional applications for genomic modification.

  2. Photoactivatable fluorophores and techniques for biological imaging applications

    PubMed Central

    Zheng, Genhua

    2013-01-01

    Photoactivatable fluorophores (PAFs) are powerful imaging probes for tracking molecular and cellular dynamics with high spatiotemporal resolution in biological systems. Recent developments in biological microscopy have raised new demands for engineering new PAFs with improved properties such as high two photon excitation efficiency, reversibility, cellular delivery and targeting. Here we review the history and some of the recent developments in this area, emphasizing our efforts in developing a new class of caged coumarins and related imaging methods for studying dynamic cell-cell communication through gap junction channels, and in extending the application of these caged coumarins to new areas including spatiotemporal control of microRNA activity in vivo. PMID:22252510

  3. Quantum metrology and its application in biology

    NASA Astrophysics Data System (ADS)

    Taylor, Michael A.; Bowen, Warwick P.

    2016-02-01

    Quantum metrology provides a route to overcome practical limits in sensing devices. It holds particular relevance to biology, where sensitivity and resolution constraints restrict applications both in fundamental biophysics and in medicine. Here, we review quantum metrology from this biological context, focusing on optical techniques due to their particular relevance for biological imaging, sensing, and stimulation. Our understanding of quantum mechanics has already enabled important applications in biology, including positron emission tomography (PET) with entangled photons, magnetic resonance imaging (MRI) using nuclear magnetic resonance, and bio-magnetic imaging with superconducting quantum interference devices (SQUIDs). In quantum metrology an even greater range of applications arise from the ability to not just understand, but to engineer, coherence and correlations at the quantum level. In the past few years, quite dramatic progress has been seen in applying these ideas into biological systems. Capabilities that have been demonstrated include enhanced sensitivity and resolution, immunity to imaging artefacts and technical noise, and characterization of the biological response to light at the single-photon level. New quantum measurement techniques offer even greater promise, raising the prospect for improved multi-photon microscopy and magnetic imaging, among many other possible applications. Realization of this potential will require cross-disciplinary input from researchers in both biology and quantum physics. In this review we seek to communicate the developments of quantum metrology in a way that is accessible to biologists and biophysicists, while providing sufficient details to allow the interested reader to obtain a solid understanding of the field. We further seek to introduce quantum physicists to some of the central challenges of optical measurements in biological science. We hope that this will aid in bridging the communication gap that exists

  4. Encapsulins: molecular biology of the shell.

    PubMed

    Nichols, Robert J; Cassidy-Amstutz, Caleb; Chaijarasphong, Thawatchai; Savage, David F

    2017-10-01

    Compartmentalization is both a fundamental principle of cellular organization and an emerging theme in prokaryotic biology. Work in the past few decades has shown that protein-based organelles called microcompartments enhance the function of encapsulated cargo proteins. More recently, the repertoire of known prokaryotic organelles has expanded beyond microcompartments to include a new class of smaller proteinaceous compartments, termed nanocompartments (also known as encapsulins). Nanocompartments are icosahedral capsids that are smaller and less complex than microcompartments. Encapsulins are formed by a single species of shell protein that self-assembles and typically encapsulates only one type of cargo protein. Significant progress has been made in understanding the structure of nanocompartment shells and the loading of cargo to the interior. Recent analysis has also demonstrated the prevalence of encapsulin genes throughout prokaryotic genomes and documented a large diversity of cargo proteins with a variety of novel functions, suggesting that nanocompartments play an important role in many microbes. Here we review the current understanding of encapsulin structure and function and highlight exciting open questions of physiological significance.

  5. Application of STED microscopy to cell biology questions.

    PubMed

    Revelo, Natalia H; Rizzoli, Silvio O

    2015-01-01

    The increasing interest in "seeing" the molecular environment in biological systems has led to the recent quest for breaking the diffraction barrier in far-field fluorescence microscopy. The first nanoscopy method successfully applied to conventional biological probes was stimulated emission depletion microscopy (STED). It is based on a physical principle that instantly delivers diffraction-unlimited images, with no need for further computational processing: the excitation laser beam is overlaid with a doughnut-shaped depleting beam that switches off previously excited fluorophores, thereby resulting in what is effectively a smaller imaging volume. In this chapter we give an overview of several applications of STED microscopy to biological questions. We explain technical aspects of sample preparation and image acquisition that will help in obtaining good diffraction-unlimited pictures. We also present embedding techniques adapted for ultrathin sectioning, which allow optimal 3D resolutions in virtually all biological preparations.

  6. [Molecular biology of haemostasis: fibrinogen, factor XIII].

    PubMed

    Meyer, M

    2004-05-01

    Genetic defects of fibrinogen are caused by a broad spectrum of mutations in one of the three structural genes FGA, FGB and FGG. They result in complete or partial lack of plasma fibrinogen (a- or hypofibrinogenaemia) or in structural abnormalities affecting protein function (dysfibrinogenaemia). In contrast to afibrinogenaemia mainly caused by nonsense, frameshift, and splice site mutations resulting in substantially truncated polypeptide chains (mainly Aalpha), in hypo- and dysfibrinogenaemias missense mutations lead to the exchange of single amino acids as dominating underlying defect. In the cases with quantitative disorders, bleeding with various degrees of severity is generally observed. Dysfibrinogenaemia is associated with both bleeding or thrombosis or even a combination of haemorrhagic and thromboembolic symptoms. About one half of the dysfibrinogenaemic cases is clinically asymptomatic. The plasmatic factor XIII (FXIII) is a heterotetramer composed of two A and two B subunits encoded by two different genes. FXIII deficiency is associated with bleeding, wound dehiscence and recurrent spontaneous abortions. The most frequent form is caused by defects in the A subunit with a broad spectrum of underlying mutations. Defects of the B subunit are very rare and were molecularly elucidated in only a few cases.

  7. Cellular and Molecular Biology of Airway Mucins

    PubMed Central

    Lillehoj, Erik P.; Kato, Kosuke; Lu, Wenju; Kim, Kwang C.

    2017-01-01

    Airway mucus constitutes a thin layer of airway surface liquid with component macromolecules that covers the luminal surface of the respiratory tract. The major function of mucus is to protect the lungs through mucociliary clearance of inhaled foreign particles and noxious chemicals. Mucus is comprised of water, ions, mucin glycoproteins, and a variety of other macromolecules, some of which possess anti-microbial, anti-protease, and anti-oxidant activities. Mucins comprise the major protein component of mucus and exist as secreted and cell-associated glycoproteins. Secreted, gel-forming mucins are mainly responsible for the viscoelastic property of mucus, which is crucial for effective mucociliary clearance. Cell-associated mucins shield the epithelial surface from pathogens through their extracellular domains and regulate intracellular signaling through their cytoplasmic regions. However, neither the exact structures of mucin glycoproteins, nor the manner through which their expression is regulated, are completely understood. This chapter reviews what is currently known about the cellular and molecular properties of airway mucins. PMID:23445810

  8. Epidemiology and molecular biology of Barrett esophagus.

    PubMed

    Casson, Alan G; Williams, Lara; Guernsey, Duane L

    2005-01-01

    Over the past three decades, there has been a marked change in the epidemiology of esophageal malignancy, with an increasing incidence of esophageal adenocarcinoma. The reasons for this are largely unknown and remain controversial, but several lifestyle risk factors have been proposed, including gastroesophageal reflux disease (GERD). It is hypothesized that chronic GERD results in acute mucosal injury, promotes cellular proliferation, and induces specialized columnar metaplasia (Barrett esophagus). Progression of Barrett esophagus to invasive adenocarcinoma is reflected histologically by the metaplasia-dysplasia-carcinoma sequence. Dysplasia is widely regarded as the precursor of invasive cancer, and high-grade dysplasia in Barrett epithelium is frequently associated with esophageal adenocarcinoma. Although several molecular alterations have been described in Barrett esophagus, it is anticipated that relatively few will prove to be clinically useful. To date, biomarkers which currently appear to predict the progression of Barrett esophagus to invasive malignancy include aneuploidy, loss of heterozygosity of 17p (implicating the p53 tumor suppressor gene), and cyclin D1 protein overexpression, and with further validation, will most likely be incorporated into routine clinical practice. It is anticipated that models incorporating objective scores of sociodemographic and lifestyle risk factors (ie, age, gender, body mass index), severity of reflux symptoms, endoscopic and histologic findings, and an assessment of a panel of biomarkers will be developed to further define subsets of patients with Barrett esophagus at increased risk for malignant progression, thereby permitting the development of more rational endoscopic surveillance and screening programs.

  9. Scanned probe microscope for biological applications

    NASA Astrophysics Data System (ADS)

    Baiburin, Vil B.; Konnov, Nikolai P.; Shcherbakov, Anatolyi A.; Malakhaeva, Alina N.; Zadnova, Svetlana P.; Volkov, Yuri P.

    1997-12-01

    In our biophysical laboratory has been developed a new scanned probe microscope (SPM) for biological application. The SPM allows to investigate a biological samples' surface by means of three different near field microscopes: scanning tunneling microscope (STM), atomic force microscope (AFM) and near field scanning optical microscope (NSOM). The SPM is very rigid and can be operated in ordinary laboratory without any vibration isolation. The scanning area of the microscope is about 10 by 10 micrometers. Some different biological objects were visualized by means of the SPM viz. bacteria (E. Coli, plague, cholera, staphylococcus), macromolecules (DNA, plague proteins) and phage (T2).

  10. Molecular Phenotyping Combines Molecular Information, Biological Relevance, and Patient Data to Improve Productivity of Early Drug Discovery.

    PubMed

    Drawnel, Faye Marie; Zhang, Jitao David; Küng, Erich; Aoyama, Natsuyo; Benmansour, Fethallah; Araujo Del Rosario, Andrea; Jensen Zoffmann, Sannah; Delobel, Frédéric; Prummer, Michael; Weibel, Franziska; Carlson, Coby; Anson, Blake; Iacone, Roberto; Certa, Ulrich; Singer, Thomas; Ebeling, Martin; Prunotto, Marco

    2017-05-18

    Today, novel therapeutics are identified in an environment which is intrinsically different from the clinical context in which they are ultimately evaluated. Using molecular phenotyping and an in vitro model of diabetic cardiomyopathy, we show that by quantifying pathway reporter gene expression, molecular phenotyping can cluster compounds based on pathway profiles and dissect associations between pathway activities and disease phenotypes simultaneously. Molecular phenotyping was applicable to compounds with a range of binding specificities and triaged false positives derived from high-content screening assays. The technique identified a class of calcium-signaling modulators that can reverse disease-regulated pathways and phenotypes, which was validated by structurally distinct compounds of relevant classes. Our results advocate for application of molecular phenotyping in early drug discovery, promoting biological relevance as a key selection criterion early in the drug development cascade. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. A decade of molecular cell biology: achievements and challenges.

    PubMed

    Akhtar, Asifa; Fuchs, Elaine; Mitchison, Tim; Shaw, Reuben J; St Johnston, Daniel; Strasser, Andreas; Taylor, Susan; Walczak, Claire; Zerial, Marino

    2011-09-23

    Nature Reviews Molecular Cell Biology celebrated its 10-year anniversary during this past year with a series of specially commissioned articles. To complement this, here we have asked researchers from across the field for their insights into how molecular cell biology research has evolved during this past decade, the key concepts that have emerged and the most promising interfaces that have developed. Their comments highlight the broad impact that particular advances have had, some of the basic understanding that we still require, and the collaborative approaches that will be essential for driving the field forward.

  12. Molecular Biology of STLV-III and HTLV-IV

    DTIC Science & Technology

    1990-08-22

    proviral clones to assess heterogeneity in a given virus population. The modifications to the standard Sanger method are: 1 . An increased primer-to...IIi AD-A228 929 il~t COP, A CONTRACT NO: DAND17-87-C-7187 TITLE: MOLECULAR BIOLOGY OF STLV-III AND HTLV -IV PRINCIPAL INVESTIGATOR: Joseph Sodroski...21702-5012 63105A 63105H29 AC 072 11. TITLE (Include Security Clasification) Molecular Biology of STLV-III and HTLV -IV 12. PERSONAL AUTHOR(S) Joseph

  13. Molecular Biology of STLV-III and HTLV-IV

    DTIC Science & Technology

    1989-08-10

    AD-A228 948 DTIC FILE COpy AD C3NTRACT NO: DAMD17-87-C-7187 TITLE: MOLECULAR BIOLOGY OF STLV-III AND HTLV -IV PRINCIPAL INVESTIGATOR: Joseph Sodroski...NO.Frederick, Maryland 21702-5012 63105A 63105H29 AC 072 11. TITLE (Include Security Classification) Molecular Biology of STLV-III and HTLV -IV 12...FROM7/ 1 /88 TO6/-.10 891 1989 August 10 I 17 16. SUPPLEMENTARY NOTATION 17. COSATI CODES L1ISUBJECT TERMS (Co €ki ’ orrreve f tfnrcessar endfNiti" y b/ck

  14. Multispectral optical tweezers for molecular diagnostics of single biological cells

    NASA Astrophysics Data System (ADS)

    Butler, Corey; Fardad, Shima; Sincore, Alex; Vangheluwe, Marie; Baudelet, Matthieu; Richardson, Martin

    2012-03-01

    Optical trapping of single biological cells has become an established technique for controlling and studying fundamental behavior of single cells with their environment without having "many-body" interference. The development of such an instrument for optical diagnostics (including Raman and fluorescence for molecular diagnostics) via laser spectroscopy with either the "trapping" beam or secondary beams is still in progress. This paper shows the development of modular multi-spectral imaging optical tweezers combining Raman and Fluorescence diagnostics of biological cells.

  15. Molecular biology and genetic engineering in nitrogen fixation.

    PubMed

    Dos Santos, Patricia C

    2011-01-01

    Biological nitrogen fixation is a complex and tightly regulated process limited to a group of prokaryotic species known as diazotrophs. Among well-studied diazotrophs, Azotobacter vinelandii is the best studied for its convenience of aerobic growth, its high levels of nitrogenase expression, and its genetic tractability. This chapter includes protocols and strategies in the molecular biology and genetic engineering of A. vinelandii that have been used as valuable tools for advancing studies on the biosynthesis, mechanism, and regulation of nitrogen fixation.

  16. Where statistics and molecular microarray experiments biology meet.

    PubMed

    Kelmansky, Diana M

    2013-01-01

    This review chapter presents a statistical point of view to microarray experiments with the purpose of understanding the apparent contradictions that often appear in relation to their results. We give a brief introduction of molecular biology for nonspecialists. We describe microarray experiments from their construction and the biological principles the experiments rely on, to data acquisition and analysis. The role of epidemiological approaches and sample size considerations are also discussed.

  17. Imaging mass spectrometry: Molecular microscopy for the new age of biology and medicine.

    PubMed

    Caprioli, Richard M

    2016-06-01

    Imaging mass spectrometry provides a powerful tool for monitoring and discovery of molecular processes in the spatial domain in tissues for research and practical applications in both biology and medicine. This technology directly measures molecular compounds in tissues without the use of target-specific reagents such as antibodies, is applicable to a wide variety of analytes, and can provide spatial resolutions below the single cell level. Importantly, it has paradigm shifting capabilities in clinical applications, especially for anatomic pathology. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Hepatitis B virus molecular biology and pathogenesis

    PubMed Central

    Lamontagne, R. Jason; Bagga, Sumedha; Bouchard, Michael J.

    2016-01-01

    As obligate intracellular parasites, viruses need a host cell to provide a milieu favorable to viral replication. Consequently, viruses often adopt mechanisms to subvert host cellular signaling processes. While beneficial for the viral replication cycle, virus-induced deregulation of host cellular signaling processes can be detrimental to host cell physiology and can lead to virus-associated pathogenesis, including, for oncogenic viruses, cell transformation and cancer progression. Included among these oncogenic viruses is the hepatitis B virus (HBV). Despite the availability of an HBV vaccine, 350–500 million people worldwide are chronically infected with HBV, and a significant number of these chronically infected individuals will develop hepatocellular carcinoma (HCC). Epidemiological studies indicate that chronic infection with HBV is the leading risk factor for the development of HCC. Globally, HCC is the second highest cause of cancer-associated deaths, underscoring the need for understanding mechanisms that regulate HBV replication and the development of HBV-associated HCC. HBV is the prototype member of the Hepadnaviridae family; members of this family of viruses have a narrow host range and predominately infect hepatocytes in their respective hosts. The extremely small and compact hepadnaviral genome, the unique arrangement of open reading frames, and a replication strategy utilizing reverse transcription of an RNA intermediate to generate the DNA genome are distinguishing features of the Hepadnaviridae. In this review, we provide a comprehensive description of HBV biology, summarize the model systems used for studying HBV infections, and highlight potential mechanisms that link a chronic HBV-infection to the development of HCC. For example, the HBV X protein (HBx), a key regulatory HBV protein that is important for HBV replication, is thought to play a cofactor role in the development of HBV-induced HCC, and we highlight the functions of HBx that may

  19. Human papillomavirus molecular biology and disease association

    PubMed Central

    Egawa, Nagayasu; Griffin, Heather; Kranjec, Christian; Murakami, Isao

    2015-01-01

    Summary Human papillomaviruses (HPVs) have evolved over millions of years to propagate themselves in a range of different animal species including humans. Viruses that have co‐evolved slowly in this way typically cause chronic inapparent infections, with virion production in the absence of apparent disease. This is the case for many Beta and Gamma HPV types. The Alpha papillomavirus types have however evolved immunoevasion strategies that allow them to cause persistent visible papillomas. These viruses activate the cell cycle as the infected epithelial cell differentiates in order to create a replication competent environment that allows viral genome amplification and packaging into infectious particles. This is mediated by the viral E6, E7, and E5 proteins. High‐risk E6 and E7 proteins differ from their low‐risk counterparts however in being able to drive cell cycle entry in the upper epithelial layers and also to stimulate cell proliferation in the basal and parabasal layers. Deregulated expression of these cell cycle regulators underlies neoplasia and the eventual progression to cancer in individuals who cannot resolve high‐risk HPV infection. Most work to date has focused on the study of high‐risk HPV types such as HPV 16 and 18, which has led to an understanding of the molecular pathways subverted by these viruses. Such approaches will lead to the development of better strategies for disease treatment, including targeted antivirals and immunotherapeutics. Priorities are now focused toward understanding HPV neoplasias at sites other than the cervix (e.g. tonsils, other transformation zones) and toward understanding the mechanisms by which low‐risk HPV types can sometimes give rise to papillomatosis and under certain situations even cancers. Copyright © 2015 John Wiley & Sons, Ltd. PMID:25752814

  20. Biological applications of nanoscale materials

    NASA Astrophysics Data System (ADS)

    Liang, Chi-Hui

    2007-12-01

    The objective of my research work is to synthesize, characterize, design, and apply nanocrystals for biomedical use. Gold nanoparticles were synthesized in the presence of chitosan via reduction of HAuCl4 with sodium borohydride. The average particle size of gold nanoparticles was significantly affected with the concentration of chitosan added and was ranged between 5 and 30 nm. The gold-chitosan nanocomposites were formed by adsorbing chitosan molecules on the gold nanoparticles. CdSe/ZnS quantum dots were prepared by a solution phase synthetic method. A new route for the phase transfer of CdSe/ZnS quantum dots from non-polar solvents into aqueous solution was developed using hydrophobically modified polysaccharides, both chitosan and alginate. In addition, it was shown that CdSe/ZnS based polysaccharide nanoparticles effectively inhibited the proliferation of human ovarian cancer cell line SKOV-3 in vitro. The findings suggest that CdSe/ZnS quantum dot based polysaccharide nanoparticles not only act as a long-term biomarker but also have potential value in cancer therapy. A novel method for extracting magnetite nanoparticles from magnetotactic bacteria was developed by using co-surfactant. The problem of mass cultivation was solved by growing AMB-1 in Ca2+-alginate microbeads. To apply magnetotactic bacterial in biomedical applications, uptake of chitosan-capped CdSe/ZnS quantum dots on magnetotactic bacteria and introducing fluorescent magnetotactic bacteria into mouse macrophage cells was achieved. A general strategy is described which allows for constructing multifunctional magnetic nanocomposites based on bacterial magnetite nanoparticles. Specifically, core-shell structures of bacterial magnetite-CdSe ZnS and bacterial magnetite-gold nanocomplexes have been built in this way. Furthermore, design and synthesis multimodal contrast agents which are ultrasound and photoacoustic active are achieved by utilizing biocompatible gold nanorods self assembling on

  1. 2D molecular graphics: a flattened world of chemistry and biology.

    PubMed

    Zhou, Peng; Shang, Zhicai

    2009-05-01

    Molecular graphics provides an intuitive way for representation, modeling and analysis of complex chemical and biological systems. It is now widely used in the theoretical chemistry, structural biology, molecular modeling and drug design communities. Traditional molecular graphics techniques mainly dedicate to showing molecular architectures at three-dimensional (3D) level. However, in some occasions the two-dimensional (2D) representation of molecular configurations, profiles, behaviors and interactions may be more readily acceptable for audiences, especially when we need to describe abstract information in a straightforward way or to present numerous data in schematic diagrams. In recent years, 2D representation methods/tools have been developed rapidly for various purposes, ranging from the aesthetic depiction of atomic arrangement for small organic molecules to schematic layout of complicated nonbonding network across the biomolecular binding interfaces, and have received considerable interest in the fields of chemistry, biology and medicine. In this article we first propose the term of 2D molecular graphics to cover the spectrum of 2D representing chemical and biological systems, we also give a comprehensive review on the methods, tools and applications of 2D molecular graphics.

  2. Applications of recombinant DNA technology in gastrointestinal medicine and hepatology: basic paradigms of molecular cell biology. Part B: eukaryotic gene transcription and post-transcriptional RNA processing.

    PubMed

    Wild, G E; Papalia, P; Ropeleski, M J; Faria, J; Thomson, A B

    2000-04-01

    The transcription of DNA into RNA is the primary level at which gene expression is controlled in eukaryotic cells. Eukaryotic gene transcription involves several different RNA polymerases that interact with a host of transcription factors to initiate transcription. Genes that encode proteins are transcribed into messenger RNA (mRNA) by RNA polymerase II. Ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs) are transcribed by RNA polymerase I and III, respectively. The production of each mRNA in human cells involves complex interactions of proteins (ie, trans-acting factors) with specific sequences on the DNA (ie, cis-acting elements). Cis-acting elements are short base sequences adjacent to or within a particular gene. While the regulation of transcription is a pivotal step in the control of gene expression, a variety of molecular events, collectively known as 'RNA processing' add an additional level of control of gene expression in eukaryotic cells. (Pour le résumé, voir page suivante)

  3. Functionalized Nanodiamonds for Biological and Medical Applications.

    PubMed

    Lai, Lin; Barnard, Amanda S

    2015-02-01

    Nanodiamond is a promising material for biological and medical applications, owning to its relatively inexpensive and large-scale synthesis, unique structure, and superior optical properties. However, most biomedical applications, such as drug delivery and bio-imaging, are dependent upon the precise control of the surfaces, and can be significantly affected by the type, distribution and stability of chemical funtionalisations of the nanodiamond surface. In this paper, recent studies on nanodiamonds and their biomedical applications by conjugating with different chemicals are reviewed, while highlighting the critical importance of surface chemical states for various applications.

  4. Fluorescence interferometry: principles and applications in biology.

    PubMed

    Bilenca, Alberto; Cao, Jing; Colice, Max; Ozcan, Aydogan; Bouma, Brett; Raftery, Laurel; Tearney, Guillermo

    2008-01-01

    The use of fluorescence radiation is of fundamental importance for tackling measurement problems in the life sciences, with recent demonstrations of probing biological systems at the nanoscale. Usually, fluorescent light-based tools and techniques use the intensity of light waves, which is easily measured by detectors. However, the phase of a fluorescence wave contains subtle, but no less important, information about the wave; yet, it has been largely unexplored. Here, we introduce the concept of fluorescence interferometry to allow the measurement of phase information of fluorescent light waves. In principle, fluorescence interferometry can be considered a unique form of optical low-coherence interferometry that uses fluorophores as a light source of low temporal coherence. Fluorescence interferometry opens up new avenues for developing new fluorescent light-based imaging, sensing, ranging, and profiling methods that to some extent resemble interferometric techniques based on white light sources. We propose two experimental realizations of fluorescence interferometry that detect the interference pattern cast by the fluorescence fields. This article discusses their measurement capabilities and limitations and compares them with those offered by optical low-coherence interferometric schemes. We also describe applications of fluorescence interferometry to imaging, ranging, and profiling tasks and present experimental evidences of wide-field cross-sectional imaging with high resolution and large range of depth, as well as quantitative profiling with nanometer-level precision. Finally, we point out future research directions in fluorescence interferometry, such as fluorescence tomography of whole organisms and the extension to molecular interferometry by means of quantum dots and bioluminescence.

  5. Planetary Biology and Microbial Ecology: Molecular Ecology and the Global Nitrogen cycle

    NASA Technical Reports Server (NTRS)

    Nealson, Molly Stone (Editor); Nealson, Kenneth H. (Editor)

    1993-01-01

    This report summarizes the results of the Planetary Biology and Molecular Ecology's summer 1991 program, which was held at the Marine Biological Laboratory in Woods Hole, Massachusetts. The purpose of the interdisciplinary PBME program is to integrate, via lectures and laboratory work, the contributions of university and NASA scientists and student interns. The goals of the 1991 program were to examine several aspects of the biogeochemistry of the nitrogen cycle and to teach the application of modern methods of molecular genetics to field studies of organisms. Descriptions of the laboratory projects and protocols and abstracts and references of the lectures are presented.

  6. Cell and molecular biology of epidermal growth factor receptor.

    PubMed

    Ceresa, Brian P; Peterson, Joanne L

    2014-01-01

    The epidermal growth factor receptor (EGFR) has been one of the most intensely studied cell surface receptors due to its well-established roles in developmental biology, tissue homeostasis, and cancer biology. The EGFR has been critical for creating paradigms for numerous aspects of cell biology, such as ligand binding, signal transduction, and membrane trafficking. Despite this history of discovery, there is a continual stream of evidence that only the surface has been scratched. New ways of receptor regulation continue to be identified, each of which is a potential molecular target for manipulating EGFR signaling and the resultant changes in cell and tissue biology. This chapter is an update on EGFR-mediated signaling, and describes some recent developments in the regulation of receptor biology.

  7. Signature molecular descriptor : advanced applications.

    SciTech Connect

    Visco, Donald Patrick, Jr.

    2010-04-01

    In this work we report on the development of the Signature Molecular Descriptor (or Signature) for use in the solution of inverse design problems as well as in highthroughput screening applications. The ultimate goal of using Signature is to identify novel and non-intuitive chemical structures with optimal predicted properties for a given application. We demonstrate this in three studies: green solvent design, glucocorticoid receptor ligand design and the design of inhibitors for Factor XIa. In many areas of engineering, compounds are designed and/or modified in incremental ways which rely upon heuristics or institutional knowledge. Often multiple experiments are performed and the optimal compound is identified in this brute-force fashion. Perhaps a traditional chemical scaffold is identified and movement of a substituent group around a ring constitutes the whole of the design process. Also notably, a chemical being evaluated in one area might demonstrate properties very attractive in another area and serendipity was the mechanism for solution. In contrast to such approaches, computer-aided molecular design (CAMD) looks to encompass both experimental and heuristic-based knowledge into a strategy that will design a molecule on a computer to meet a given target. Depending on the algorithm employed, the molecule which is designed might be quite novel (re: no CAS registration number) and/or non-intuitive relative to what is known about the problem at hand. While CAMD is a fairly recent strategy (dating to the early 1980s), it contains a variety of bottlenecks and limitations which have prevented the technique from garnering more attention in the academic, governmental and industrial institutions. A main reason for this is how the molecules are described in the computer. This step can control how models are developed for the properties of interest on a given problem as well as how to go from an output of the algorithm to an actual chemical structure. This report

  8. Multifunctional Glyconanoparticles : Applications in Biology and Biomedicine

    NASA Astrophysics Data System (ADS)

    Penadés, Soledad; de La Fuente, Jesus M.; Barrientos, África G.; Clavel, Caroline; Martínez-Ávila, Olga; Alcántara, David

    The design and preparation of complex bio-functional glyconanoparticles (GNPs) and their application as polyvalent tools to study and intervene in carbohydrate mediated biological interactions are highlighted. As examples, the preparation and study of GNPs as anti-adhesion agents in inhibition of metastasis, as potential microbicides for blocking HIV-1 infection, or as anti-cancer vaccines are also discussed. In addition, magnetic glyconanoparticles for application in cellular labelling and magnetic resonance imaging (MRI) are also reviewed.

  9. Biological networks 101: computational modeling for molecular biologists.

    PubMed

    Scholma, Jetse; Schivo, Stefano; Urquidi Camacho, Ricardo A; van de Pol, Jaco; Karperien, Marcel; Post, Janine N

    2014-01-01

    Computational modeling of biological networks permits the comprehensive analysis of cells and tissues to define molecular phenotypes and novel hypotheses. Although a large number of software tools have been developed, the versatility of these tools is limited by mathematical complexities that prevent their broad adoption and effective use by molecular biologists. This study clarifies the basic aspects of molecular modeling, how to convert data into useful input, as well as the number of time points and molecular parameters that should be considered for molecular regulatory models with both explanatory and predictive potential. We illustrate the necessary experimental preconditions for converting data into a computational model of network dynamics. This model requires neither a thorough background in mathematics nor precise data on intracellular concentrations, binding affinities or reaction kinetics. Finally, we show how an interactive model of crosstalk between signal transduction pathways in primary human articular chondrocytes allows insight into processes that regulate gene expression.

  10. A Biochemistry and Molecular Biology Course for Secondary School Teachers

    ERIC Educational Resources Information Center

    Fernandez-Novell, J. M.; Cid, E.; Gomis, R.; Barbera, A.; Guinovart, J. J.

    2004-01-01

    This article describes a course for reinforcing the knowledge of biochemistry in secondary school science teachers. The Department of Biochemistry and Molecular Biology of the University of Barcelona designed a course to bring these teachers up to date with this discipline. In addition to updating their knowledge of biochemistry and molecular…

  11. A Streamlined Molecular Biology Module for Undergraduate Biochemistry Labs

    ERIC Educational Resources Information Center

    Muth, Gregory W.; Chihade, Joseph W.

    2008-01-01

    Site-directed mutagenesis and other molecular biology techniques, including plasmid manipulation and restriction analysis, are commonly used tools in the biochemistry research laboratory. In redesigning our biochemistry lab curricula, we sought to integrate these techniques into a term-long, project-based course. In the module presented here,…

  12. A Streamlined Molecular Biology Module for Undergraduate Biochemistry Labs

    ERIC Educational Resources Information Center

    Muth, Gregory W.; Chihade, Joseph W.

    2008-01-01

    Site-directed mutagenesis and other molecular biology techniques, including plasmid manipulation and restriction analysis, are commonly used tools in the biochemistry research laboratory. In redesigning our biochemistry lab curricula, we sought to integrate these techniques into a term-long, project-based course. In the module presented here,…

  13. Web Based Learning Support for Experimental Design in Molecular Biology.

    ERIC Educational Resources Information Center

    Wilmsen, Tinri; Bisseling, Ton; Hartog, Rob

    An important learning goal of a molecular biology curriculum is a certain proficiency level in experimental design. Currently students are confronted with experimental approaches in textbooks, in lectures and in the laboratory. However, most students do not reach a satisfactory level of competence in the design of experimental approaches. This…

  14. An Inquiry-based Introduction to Molecular Biology.

    ERIC Educational Resources Information Center

    Levy, Foster

    2000-01-01

    Presents investigative approaches to teaching molecular biology. Emphasizes a deductive determination of the nature of nucleic acids visualized in a gel, and a comparison of different genomes. Asks why students should take it on faith that what they view on a gel is DNA. (SAH)

  15. Frontiers in nuclear medicine symposium: Nuclear medicine & molecular biology

    SciTech Connect

    1995-04-01

    This document contains the abstracts from the American College of Nuclear Physicians 1993 Fall Meeting entitled, `Frontiers in Nuclear Medicine Symposium: Nuclear Medicine and Molecular Biology`. This meeting was sponsored by the US DOE, Office of Health and Environmental Research, Office of Energy Research. The program chairman was Richard C. Reba, M.D.

  16. Gene Concepts in Higher Education Cell and Molecular Biology Textbooks

    ERIC Educational Resources Information Center

    Albuquerque, Pitombo Maiana; de Almeida, Ana Maria Rocha; El-Hani, Nino Charbel

    2008-01-01

    Despite being a landmark of 20th century biology, the "classical molecular gene concept," according to which a gene is a stretch of DNA encoding a functional product, which may be a single polypeptide or RNA molecule, has been recently challenged by a series of findings (e.g., split genes, alternative splicing, overlapping and nested…

  17. Assessing Practical Laboratory Skills in Undergraduate Molecular Biology Courses

    ERIC Educational Resources Information Center

    Hunt, Lynne; Koenders, Annette; Gynnild, Vidar

    2012-01-01

    This study explored a new strategy of assessing laboratory skills in a molecular biology course to improve: student effort in preparation for and participation in laboratory work; valid evaluation of learning outcomes; and students' employment prospects through provision of evidence of their skills. Previously, assessment was based on written…

  18. A Biochemistry and Molecular Biology Course for Secondary School Teachers

    ERIC Educational Resources Information Center

    Fernandez-Novell, J. M.; Cid, E.; Gomis, R.; Barbera, A.; Guinovart, J. J.

    2004-01-01

    This article describes a course for reinforcing the knowledge of biochemistry in secondary school science teachers. The Department of Biochemistry and Molecular Biology of the University of Barcelona designed a course to bring these teachers up to date with this discipline. In addition to updating their knowledge of biochemistry and molecular…

  19. Proceedings: Second international conference on intelligent systems for molecular biology

    SciTech Connect

    Altman, R.; Brutlag, D.; Karp, P.; Lathrop, R.; Searls, D.

    1994-12-31

    This volume provided full papers for presentations at the Second International Conference on Intelligent Systems for Molecular Biology held August 14-17, 1994 at Stanford University, Stanford, California. Each individual paper has been separately abstracted and indexed for the database.

  20. Progress in nucleic acid research and molecular biology

    SciTech Connect

    Cohn, W.E. . Biology Div.); Moldave, K. )

    1989-01-01

    This book contain the proceedings on progress in nucleic acid research and molecular biology. Topics covered include: polynucleotide-protein cross-links induced by ultraviolet light and their use for structural investigation of nucleoproteins; left-handed Z-DNA and genetic recombination, and structure and function of signal recognition particle RNA.

  1. Teaching Introductory Cell & Molecular Biology: A Historical and Empirical Approach.

    ERIC Educational Resources Information Center

    Posner, Herbert B.

    1996-01-01

    Describes the reorganized introductory cell and molecular biology lecture course at the State University of New York at Binghamton that was designed to address the issues of lack of active student participation and the stress put on memorization rather than analytical skills. Emphasizes teaching the subject historically and empirically…

  2. An Inquiry-based Introduction to Molecular Biology.

    ERIC Educational Resources Information Center

    Levy, Foster

    2000-01-01

    Presents investigative approaches to teaching molecular biology. Emphasizes a deductive determination of the nature of nucleic acids visualized in a gel, and a comparison of different genomes. Asks why students should take it on faith that what they view on a gel is DNA. (SAH)

  3. Assessing Practical Laboratory Skills in Undergraduate Molecular Biology Courses

    ERIC Educational Resources Information Center

    Hunt, Lynne; Koenders, Annette; Gynnild, Vidar

    2012-01-01

    This study explored a new strategy of assessing laboratory skills in a molecular biology course to improve: student effort in preparation for and participation in laboratory work; valid evaluation of learning outcomes; and students' employment prospects through provision of evidence of their skills. Previously, assessment was based on written…

  4. The molecular biology of the olive fly comes of age

    PubMed Central

    2014-01-01

    were shown to be differentially expressed in the female and male reproductive systems analyzed. Finally, the expression profile of the embryonic serendipity-α locus and the pre-apoptotic head involution defective gene were analyzed during embryonic developmental stages. Conclusions Several years of molecular studies on the olive fly can now be combined with new information from whole transcriptome analyses and lead to a deep understanding of the biology of this notorious insect pest. This is a prerequisite for the development of novel embryonic lethality female sexing strains for successful SIT efforts which, combined with improved mass-reared conditions, give new hope for efficient SIT applications for the olive fly. PMID:25472866

  5. Single molecular biology: coming of age in DNA replication.

    PubMed

    Liu, Xiao-Jing; Lou, Hui-Qiang

    2017-09-20

    DNA replication is an essential process of the living organisms. To achieve precise and reliable replication, DNA polymerases play a central role in DNA synthesis. Previous investigations have shown that the average rates of DNA synthesis on the leading and lagging strands in a replisome must be similar to avoid the formation of significant gaps in the nascent strands. The underlying mechanism has been assumed to be coordination between leading- and lagging-strand polymerases. However, Kowalczykowski's lab members recently performed single molecule techniques in E. coli and showed the real-time behavior of a replisome. The leading- and lagging-strand polymerases function stochastically and independently. Furthermore, when a DNA polymerase is paused, the helicase slows down in a self-regulating fail-safe mechanism, akin to a ''dead-man's switch''. Based on the real-time single-molecular observation, the authors propose that leading- and lagging-strand polymerases synthesize DNA stochastically within a Gaussian distribution. Along with the development and application of single-molecule techniques, we will witness a new age of DNA replication and other biological researches.

  6. [Progress in molecular biology study of DNA computer].

    PubMed

    Zhang, Zhi-Zhou; Zhao, Jian; He, Lin

    2003-09-01

    DNA (deoxyribonucleotide acids) computer is an emerging new study area that basically combines molecular biology study of DNA molecules and computational study on how to employ these specific molecules to calculate. In 1994 Adleman described his pioneering research on DNA computing in Science. This is the first experimental report on DNA computer study. In 2001 Benenson et al published a paper in Nature regarding a programmable and autonomous DNA computing device. Because of its Turing-like functions, the device is regarded as another milestone progress for DNA computer study. The main features of DNA computer are massively parallel computing ability and potential enormous data storage capacity. Comparing with conventional electronic computers, DNA molecules provide conceptually a revolution in computing, and more and more implications have been found in various disciplines. DNA computer studies have brought great progress not only in its own computing mechanisms, but also in DNA manipulation technologies especially nano-technology. This article presents the basic principles of DNA computer, its applications, its important relationship with genomic research and our comments on all above issues.

  7. Liquid Crystalline Materials for Biological Applications.

    PubMed

    Lowe, Aaron M; Abbott, Nicholas L

    2012-03-13

    Liquid crystals have a long history of use as materials that respond to external stimuli (e.g., electrical and optical fields). More recently, a series of investigations have reported the design of liquid crystalline materials that undergo ordering transitions in response to a range of biological interactions, including interactions involving proteins, nucleic acids, viruses, bacteria and mammalian cells. A central challenge underlying the design of liquid crystalline materials for such applications is the tailoring of the interface of the materials so as to couple targeted biological interactions to ordering transitions. This review describes recent progress toward design of interfaces of liquid crystalline materials that are suitable for biological applications. Approaches addressed in this review include the use of lipid assemblies, polymeric membranes containing oligopeptides, cationic surfactant-DNA complexes, peptide-amphiphiles, interfacial protein assemblies and multi-layer polymeric films.

  8. [Applications of synthetic biology in materials science].

    PubMed

    Zhao, Tianxin; Zhong, Chao

    2017-03-25

    Materials are the basis for human being survival and social development. To keep abreast with the increasing needs from all aspects of human society, there are huge needs in the development of advanced materials as well as high-efficiency but low-cost manufacturing strategies that are both sustainable and tunable. Synthetic biology, a new engineering principle taking gene regulation and engineering design as the core, greatly promotes the development of life sciences. This discipline has also contributed to the development of material sciences and will continuously bring new ideas to future new material design. In this paper, we review recent advances in applications of synthetic biology in material sciences, with the focus on how synthetic biology could enable synthesis of new polymeric biomaterials and inorganic materials, phage display and directed evolution of proteins relevant to materials development, living functional materials, engineered bacteria-regulated artificial photosynthesis system as well as applications of gene circuits for material sciences.

  9. Applications of nanoparticles in biology and medicine

    PubMed Central

    Salata, OV

    2004-01-01

    Nanomaterials are at the leading edge of the rapidly developing field of nanotechnology. Their unique size-dependent properties make these materials superior and indispensable in many areas of human activity. This brief review tries to summarise the most recent developments in the field of applied nanomaterials, in particular their application in biology and medicine, and discusses their commercialisation prospects. PMID:15119954

  10. A Computer Applications Course for Biology Students.

    ERIC Educational Resources Information Center

    Ralph, Charles L.

    1989-01-01

    Describes a computer applications course developed for undergraduate biology students (primarily sophomores) to teach word processing, database and spreadsheet programs, graphing programs, telecommunications, and file transfer procedures. AppleWorks software is discussed, course content is explained, and the microcomputer laboratory is described.…

  11. Molecular Biology of Gallbladder Cancer: Potential Clinical Implications

    PubMed Central

    Andrén-Sandberg, Åke

    2012-01-01

    Gallbladder cancer (GBC) is a common malignancy of the biliary tract and involves the changes in multiple oncogenes and multiple genetic genes. Since over the past decade there has been an advance in the knowledge of the genetic basis of cancer, mainly as a result of the rapid progression of molecular technology; however, conventional therapeutic approaches have not had much impact on the course of this aggressive neoplasm. Knowledge of the molecular biology of GBC is rapidly growing. Genetic alterations in GBC include adenosine triphosphate-binding cassette transporter ABCG8, membrane-bound enzyme ADAM-17 of multi-functional gene family, and other genes including p53, COX2, XPC, and RASSF1A. The advances in molecular biology have potential implications for the detection of this disease, using Synuclein-gamma, Syndecan-1, glycoprotein 72 (TAG-72), tumor endothelial marker 8 protein (TEM8) and TNF-alpha. The use of these molecular diagnostic methods is of clinical importance for the gene replacement therapy, genetic prodrug activation therapy, and antisense immunology technology for the treatment of malignancy. The author reviewed recent publications on PubMed, and summarized molecular biology of GBC, with an emphasis on features of potential clinical implications for diagnosis and management. PMID:23112962

  12. tRNA--the golden standard in molecular biology.

    PubMed

    Barciszewska, Mirosława Z; Perrigue, Patrick M; Barciszewski, Jan

    2016-01-01

    Transfer RNAs (tRNAs) represent a major class of RNA molecules. Their primary function is to help decode a messenger RNA (mRNA) sequence in order to synthesize protein and thus ensures the precise translation of genetic information that is imprinted in DNA. The discovery of tRNA in the late 1950's provided critical insight into a genetic machinery when little was known about the central dogma of molecular biology. In 1965, Robert Holley determined the first nucleotide sequence of alanine transfer RNA (tRNA(Ala)) which earned him the 1968 Nobel Prize in Physiology or Medicine. Today, tRNA is one of the best described and characterized biological molecules. Here we review some of the key historical events in tRNA research which led to breakthrough discoveries and new developments in molecular biology.

  13. Practices and exploration on competition of molecular biological detection technology among students in food quality and safety major.

    PubMed

    Chang, Yaning; Peng, Yuke; Li, Pengfei; Zhuang, Yingping

    2017-07-08

    With the increasing importance in the application of the molecular biological detection technology in the field of food safety, strengthening education in molecular biology experimental techniques is more necessary for the culture of the students in food quality and safety major. However, molecular biology experiments are not always in curricula of Food quality and safety Majors. This paper introduced a project "competition of molecular biological detection technology for food safety among undergraduate sophomore students in food quality and safety major", students participating in this project needed to learn the fundamental molecular biology experimental techniques such as the principles of molecular biology experiments and genome extraction, PCR and agarose gel electrophoresis analysis, and then design the experiments in groups to identify the meat species in pork and beef products using molecular biological methods. The students should complete the experimental report after basic experiments, write essays and make a presentation after the end of the designed experiments. This project aims to provide another way for food quality and safety majors to improve their knowledge of molecular biology, especially experimental technology, and enhances them to understand the scientific research activities as well as give them a chance to learn how to write a professional thesis. In addition, in line with the principle of an open laboratory, the project is also open to students in other majors in East China University of Science and Technology, in order to enhance students in other majors to understand the fields of molecular biology and food safety. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):343-350, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

  14. [Molecular biology in myelodysplastic syndromes and acute myeloid leukemias "smoldering"].

    PubMed

    Martinelli, Giovanni; Sartor, Chiara; Papayannidis, Cristina; Iacobucci, Ilaria; Paolini, Stefania; Clissa, Cristina; Ottaviani, Emanuela; Finelli, Carlo

    2014-03-01

    Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal hematopoietic disorders of the myeloid lineage characterized by peripheral cytopenias and frequent leukemic evolution. MDS differ for clinical presentation, disease behavior and progression and this is the reflection of remarkable variability at molecular level. To this moment disease diagnosis is still dependent on bone marrow morphology that, although high concordance rates among experts are reported, remains subjective. Karyotype analysis is mandatory but diagnosis may be difficult in presence of normal karyotype or non-informative cytogenetics. Standardized molecular markers are needed to better define diagnosis, prediction of disease progression and prognosis. Furthermore, a molecular biology analysis could provide an important therapeutic tool towards tailored therapy and new insights in the disease's biology.

  15. Membrane curvature in cell biology: An integration of molecular mechanisms.

    PubMed

    Jarsch, Iris K; Daste, Frederic; Gallop, Jennifer L

    2016-08-15

    Curving biological membranes establishes the complex architecture of the cell and mediates membrane traffic to control flux through subcellular compartments. Common molecular mechanisms for bending membranes are evident in different cell biological contexts across eukaryotic phyla. These mechanisms can be intrinsic to the membrane bilayer (either the lipid or protein components) or can be brought about by extrinsic factors, including the cytoskeleton. Here, we review examples of membrane curvature generation in animals, fungi, and plants. We showcase the molecular mechanisms involved and how they collaborate and go on to highlight contexts of curvature that are exciting areas of future research. Lessons from how membranes are bent in yeast and mammals give hints as to the molecular mechanisms we expect to see used by plants and protists.

  16. Membrane curvature in cell biology: An integration of molecular mechanisms

    PubMed Central

    Daste, Frederic

    2016-01-01

    Curving biological membranes establishes the complex architecture of the cell and mediates membrane traffic to control flux through subcellular compartments. Common molecular mechanisms for bending membranes are evident in different cell biological contexts across eukaryotic phyla. These mechanisms can be intrinsic to the membrane bilayer (either the lipid or protein components) or can be brought about by extrinsic factors, including the cytoskeleton. Here, we review examples of membrane curvature generation in animals, fungi, and plants. We showcase the molecular mechanisms involved and how they collaborate and go on to highlight contexts of curvature that are exciting areas of future research. Lessons from how membranes are bent in yeast and mammals give hints as to the molecular mechanisms we expect to see used by plants and protists. PMID:27528656

  17. Mammalian synthetic biology: emerging medical applications.

    PubMed

    Kis, Zoltán; Pereira, Hugo Sant'Ana; Homma, Takayuki; Pedrigi, Ryan M; Krams, Rob

    2015-05-06

    In this review, we discuss new emerging medical applications of the rapidly evolving field of mammalian synthetic biology. We start with simple mammalian synthetic biological components and move towards more complex and therapy-oriented gene circuits. A comprehensive list of ON-OFF switches, categorized into transcriptional, post-transcriptional, translational and post-translational, is presented in the first sections. Subsequently, Boolean logic gates, synthetic mammalian oscillators and toggle switches will be described. Several synthetic gene networks are further reviewed in the medical applications section, including cancer therapy gene circuits, immuno-regulatory networks, among others. The final sections focus on the applicability of synthetic gene networks to drug discovery, drug delivery, receptor-activating gene circuits and mammalian biomanufacturing processes.

  18. Mammalian synthetic biology: emerging medical applications

    PubMed Central

    Kis, Zoltán; Pereira, Hugo Sant'Ana; Homma, Takayuki; Pedrigi, Ryan M.; Krams, Rob

    2015-01-01

    In this review, we discuss new emerging medical applications of the rapidly evolving field of mammalian synthetic biology. We start with simple mammalian synthetic biological components and move towards more complex and therapy-oriented gene circuits. A comprehensive list of ON–OFF switches, categorized into transcriptional, post-transcriptional, translational and post-translational, is presented in the first sections. Subsequently, Boolean logic gates, synthetic mammalian oscillators and toggle switches will be described. Several synthetic gene networks are further reviewed in the medical applications section, including cancer therapy gene circuits, immuno-regulatory networks, among others. The final sections focus on the applicability of synthetic gene networks to drug discovery, drug delivery, receptor-activating gene circuits and mammalian biomanufacturing processes. PMID:25808341

  19. Selective extraction of proteins and other macromolecules from biological samples using molecular imprinted polymers.

    PubMed

    Stevenson, Derek; El-Sharif, Hazim F; Reddy, Subrayal M

    2016-11-01

    The accurate determination of intact macromolecules in biological samples, such as blood, plasma, serum, urine, tissue and feces is a challenging problem. The increased interest in macromolecules both as candidate drugs and as biomarkers for diagnostic purposes means that new method development approaches are needed. This review charts developments in the use of molecularly imprinted polymers first for small-molecular-mass compounds then for proteins and other macromolecules. Examples of the development of molecularly imprinted polymers for macromolecules are highlighted. The two main application areas to date are sensors and separation science, particularly SPE. Examples include peptides and polypeptides, lysozyme, hemoglobin, ovalbumin, bovine serum albumin and viruses.

  20. Molecular Imaging with MRI: Potential Application in Pancreatic Cancer

    PubMed Central

    Chen, Chen; Wu, Chang Qiang; Chen, Tian Wu; Tang, Meng Yue; Zhang, Xiao Ming

    2015-01-01

    Despite the variety of approaches that have been improved to achieve a good understanding of pancreatic cancer (PC), the prognosis of PC remains poor, and the survival rates are dismal. The lack of early detection and effective interventions is the main reason. Therefore, considerable ongoing efforts aimed at identifying early PC are currently being pursued using a variety of methods. In recent years, the development of molecular imaging has made the specific targeting of PC in the early stage possible. Molecular imaging seeks to directly visualize, characterize, and measure biological processes at the molecular and cellular levels. Among different imaging technologies, the magnetic resonance (MR) molecular imaging has potential in this regard because it facilitates noninvasive, target-specific imaging of PC. This topic is reviewed in terms of the contrast agents for MR molecular imaging, the biomarkers related to PC, targeted molecular probes for MRI, and the application of MRI in the diagnosis of PC. PMID:26579537

  1. Mechanistic modeling confronts the complexity of molecular cell biology.

    PubMed

    Phair, Robert D

    2014-11-05

    Mechanistic modeling has the potential to transform how cell biologists contend with the inescapable complexity of modern biology. I am a physiologist-electrical engineer-systems biologist who has been working at the level of cell biology for the past 24 years. This perspective aims 1) to convey why we build models, 2) to enumerate the major approaches to modeling and their philosophical differences, 3) to address some recurrent concerns raised by experimentalists, and then 4) to imagine a future in which teams of experimentalists and modelers build-and subject to exhaustive experimental tests-models covering the entire spectrum from molecular cell biology to human pathophysiology. There is, in my view, no technical obstacle to this future, but it will require some plasticity in the biological research mind-set.

  2. Mimicking Biological Delivery Through Feedback-Controlled Drug Release Systems Based on Molecular Imprinting

    PubMed Central

    Kryscio, David R.; Peppas, Nicholas A.

    2015-01-01

    Intelligent drug delivery systems (DDS) are able to rapidly detect a biological event and respond appropriately by releasing a therapeutic agent; thus, they are advantageous over their conventional counterparts. Molecular imprinting is a promising area that generates a polymeric network which can selectively recognize a desired analyte. This field has been studied for a variety of applications over a long period of time, but only recently has it been investigated for biomedical and pharmaceutical applications. Recent work in the area of molecularly imprinted polymers in drug delivery highlights the potential of these recognitive networks as environmentally responsive DDS that can ultimately lead to feedback controlled recognitive release systems. PMID:26500352

  3. A diagnostic assessment for introductory molecular and cell biology.

    PubMed

    Shi, Jia; Wood, William B; Martin, Jennifer M; Guild, Nancy A; Vicens, Quentin; Knight, Jennifer K

    2010-01-01

    We have developed and validated a tool for assessing understanding of a selection of fundamental concepts and basic knowledge in undergraduate introductory molecular and cell biology, focusing on areas in which students often have misconceptions. This multiple-choice Introductory Molecular and Cell Biology Assessment (IMCA) instrument is designed for use as a pre- and posttest to measure student learning gains. To develop the assessment, we first worked with faculty to create a set of learning goals that targeted important concepts in the field and seemed likely to be emphasized by most instructors teaching these subjects. We interviewed students using open-ended questions to identify commonly held misconceptions, formulated multiple-choice questions that included these ideas as distracters, and reinterviewed students to establish validity of the instrument. The assessment was then evaluated by 25 biology experts and modified based on their suggestions. The complete revised assessment was administered to more than 1300 students at three institutions. Analysis of statistical parameters including item difficulty, item discrimination, and reliability provides evidence that the IMCA is a valid and reliable instrument with several potential uses in gauging student learning of key concepts in molecular and cell biology.

  4. A Diagnostic Assessment for Introductory Molecular and Cell Biology

    PubMed Central

    Wood, William B.; Martin, Jennifer M.; Guild, Nancy A.; Vicens, Quentin; Knight, Jennifer K.

    2010-01-01

    We have developed and validated a tool for assessing understanding of a selection of fundamental concepts and basic knowledge in undergraduate introductory molecular and cell biology, focusing on areas in which students often have misconceptions. This multiple-choice Introductory Molecular and Cell Biology Assessment (IMCA) instrument is designed for use as a pre- and posttest to measure student learning gains. To develop the assessment, we first worked with faculty to create a set of learning goals that targeted important concepts in the field and seemed likely to be emphasized by most instructors teaching these subjects. We interviewed students using open-ended questions to identify commonly held misconceptions, formulated multiple-choice questions that included these ideas as distracters, and reinterviewed students to establish validity of the instrument. The assessment was then evaluated by 25 biology experts and modified based on their suggestions. The complete revised assessment was administered to more than 1300 students at three institutions. Analysis of statistical parameters including item difficulty, item discrimination, and reliability provides evidence that the IMCA is a valid and reliable instrument with several potential uses in gauging student learning of key concepts in molecular and cell biology. PMID:21123692

  5. Molecular biology: the key to personalised treatment in radiation oncology?

    PubMed

    Hirst, D G; Robson, T

    2010-09-01

    We know considerably more about what makes cells and tissues resistant or sensitive to radiation than we did 20 years ago. Novel techniques in molecular biology have made a major contribution to our understanding at the level of signalling pathways. Before the "New Biology" era, radioresponsiveness was defined in terms of physiological parameters designated as the five Rs. These are: repair, repopulation, reassortment, reoxygenation and radiosensitivity. Of these, only the role of hypoxia proved to be a robust predictive and prognostic marker, but radiotherapy regimens were nonetheless modified in terms of dose per fraction, fraction size and overall time, in ways that persist in clinical practice today. The first molecular techniques were applied to radiobiology about two decades ago and soon revealed the existence of genes/proteins that respond to and influence the cellular outcome of irradiation. The subsequent development of screening techniques using microarray technology has since revealed that a very large number of genes fall into this category. We can now obtain an adequately robust molecular signature, predicting for a radioresponsive phenotype using gene expression and proteomic approaches. In parallel with these developments, functional magnetic resonance imaging (fMRI) and positron emission tomography (PET) can now detect specific biological molecules such as haemoglobin and glucose, so revealing a 3D map of tumour blood flow and metabolism. The key to personalised radiotherapy will be to extend this capability to the proteins of the molecular signature that determine radiosensitivity.

  6. Molecular biology of the primitive neuroectodermal tumor: a review.

    PubMed

    Raffel, C

    1999-08-15

    In terms of its molecular biology and molecular genetics, medulloblastoma is the most thoroughly studied of the pediatric brain tumors. Alterations in chromosome 17, usually an isochromosome 17q, are the most common cytogenetic abnormalities. Similarly, deletion of the short arm of one 17 chromosome, the result of formation of an iso17q, is the most common molecular biological abnormality found. The gene or genes important in the development of medulloblastoma found on chromsome 17 have not yet been identified. Both a tumor suppressor gene and an oncogene have been identified that may play a role in the development of this tumor type. The Patched (PTC) tumor suppressor gene is inactivated in approximately 15% of medulloblatomas; this alteration may be specific to the desmoplastic variant. Oncogenic mutations in the beta-catenin gene are found in a small subset of medulloblastomas. Both of these genes play central roles in developmental pathways. Prognosis in this tumor type has been related to the level of expression of the neurotrophin receptor trkC. In this review, these and other molecular biological and genetic findings are discussed with respect to the development of medulloblastoma.

  7. Porphyrin Microparticles for Biological and Biomedical Applications

    NASA Astrophysics Data System (ADS)

    Huynh, Elizabeth

    Lipids are one of the critical building blocks of life, forming the plasma membrane of cells. In addition, porphyrins also play an equally important role in life, for example, through carrying oxygen in blood. The importance of both these components is evident through the biological and biomedical applications of supramolecular structures generated from lipids and porphyrins. This thesis investigates new porphyrin microparticles based on porphyrin-lipid architecture and their potential applications in biology and medicine. In Chapter 1, a background on lipid and porphyrin-based supramolecular structures is presented and design considerations for generating multifunctional agents. Chapter 2 describes the generation of a monolayer porphyrin microparticle as a dual-modal ultrasound and photoacoustic contrast agent and subsequently, a trimodal ultrasound, photoacoustic and fluorescence contrast agent. Chapter 3 examines the optical and morphological response of these multimodality ultrasound-based contrast agents to low frequency, high duty cycle ultrasound that causes the porphyrin microparticles to convertinto nanoparticles. Chapter 4 examines the generation of bilayer micrometer-sized porphyrin vesicles and their properties. Chapter 5 presents a brief summary and potential future directions. Although these microscale structures are similar in structure, the applications of these structures greatly differ with potential applications in biology and also imaging and therapy of disease. This thesis aims to explore and demonstrate the potential of new simplified, supramolecular structures based on one main building block, porphyrin-lipid.

  8. International Conference on Intelligent Systems for Molecular Biology (ISMB)

    SciTech Connect

    Goldberg, Debra; Hibbs, Matthew; Kall, Lukas; Komandurglayavilli, Ravikumar; Mahony, Shaun; Marinescu, Voichita; Mayrose, Itay; Minin, Vladimir; Neeman, Yossef; Nimrod, Guy; Novotny, Marian; Opiyo, Stephen; Portugaly, Elon; Sadka, Tali; Sakabe, Noboru; Sarkar, Indra; Schaub, Marc; Shafer, Paul; Shmygelska, Olena; Singer, Gregory; Song, Yun; Soumyaroop, Bhattacharya; Stadler, Michael; Strope, Pooja; Su, Rong; Tabach, Yuval; Tae, Hongseok; Taylor, Todd; Terribilini, Michael; Thomas, Asha; Tran, Nam; Tseng, Tsai-Tien; Vashist, Akshay; Vijaya, Parthiban; Wang, Kai; Wang, Ting; Wei, Lai; Woo, Yong; Wu, Chunlei; Yamanishi, Yoshihiro; Yan, Changhui; Yang, Jack; Yang, Mary; Ye, Ping; Zhang, Miao

    2009-12-29

    The Intelligent Systems for Molecular Biology (ISMB) conference has provided a general forum for disseminating the latest developments in bioinformatics on an annual basis for the past 13 years. ISMB is a multidisciplinary conference that brings together scientists from computer science, molecular biology, mathematics and statistics. The goal of the ISMB meeting is to bring together biologists and computational scientists in a focus on actual biological problems, i.e., not simply theoretical calculations. The combined focus on "intelligent systems" and actual biological data makes ISMB a unique and highly important meeting, and 13 years of experience in holding the conference has resulted in a consistently well organized, well attended, and highly respected annual conference. The ISMB 2005 meeting was held June 25-29, 2005 at the Renaissance Center in Detroit, Michigan. The meeting attracted over 1,730 attendees. The science presented was exceptional, and in the course of the five-day meeting, 56 scientific papers, 710 posters, 47 Oral Abstracts, 76 Software demonstrations, and 14 tutorials were presented. The attendees represented a broad spectrum of backgrounds with 7% from commercial companies, over 28% qualifying for student registration, and 41 countries were represented at the conference, emphasizing its important international aspect. The ISMB conference is especially important because the cultures of computer science and biology are so disparate. ISMB, as a full-scale technical conference with refereed proceedings that have been indexed by both MEDLINE and Current Contents since 1996, bridges this cultural gap.

  9. The molecular biology of ear development - "Twenty years are nothing".

    PubMed

    Giraldez, Fernando; Fritzsch, Bernd

    2007-01-01

    Views of classical biological problems changed dramatically with the rise of molecular biology as a common framework. It was indeed the new language of life sciences. Molecular biology increasingly moved us towards a unified view of developmental genetics as ideas and techniques were imported to vertebrates from other biological systems where genetics was in a more advanced state. The ultimate advance has been the ability to actually perform genetic manipulations in vertebrate organisms that were almost unthinkable before. During the last two decades these technical advances entered into and affected the research on ear development. These events are still very recent and have been with us for no longer than two decades, which is the reason for the title of this article. This new scenario forms the basis of the current and productive work of many laboratories, and this is what this Special Issue of The International Journal of Developmental Biology wants to show, presenting a snapshot of insights at the beginning of the 21st Century. In this article, we give an overview of the topics that are addressed in this Ear Development Special Issue, and also we take the opportunity to informally dig into the genealogy of some of those topics, trying to link the current work with some classical work of the past.

  10. Quasielastic neutron scattering in biology: Theory and applications

    DOE PAGES

    Vural, Derya; Hu, Xiaohu; Lindner, Benjamin; ...

    2016-06-15

    Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrations, localized diffusion and transitions between energy minima. In biological systems, such as proteins and membranes, these relaxation processes are of considerable physical interest. We review here recent methodological advances and applications of quasielastic neutron scattering (QENS) in biology, concentrating on the role of molecular dynamics simulation in generating data with which neutron profiles can be unambiguously interpreted. We examine the use of massively-parallel computers in calculating scattering functions, and the application of Markov state modeling. The decomposition of MD-derived neutron dynamic susceptibilities is described, and the use of thismore » in combination with NMR spectroscopy. We discuss dynamics at very long times, including approximations to the infinite time mean-square displacement and nonequilibrium aspects of single-protein dynamics. Lastly, we examine how neutron scattering and MD can be combined to provide information on lipid nanodomains.« less

  11. Quasielastic neutron scattering in biology: Theory and applications

    SciTech Connect

    Vural, Derya; Hu, Xiaohu; Lindner, Benjamin; Jain, Nitin; Miao, Yinglong; Cheng, Xiaolin; Liu, Zhuo; Hong, Liang; Smith, Jeremy C.

    2016-06-15

    Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrations, localized diffusion and transitions between energy minima. In biological systems, such as proteins and membranes, these relaxation processes are of considerable physical interest. We review here recent methodological advances and applications of quasielastic neutron scattering (QENS) in biology, concentrating on the role of molecular dynamics simulation in generating data with which neutron profiles can be unambiguously interpreted. We examine the use of massively-parallel computers in calculating scattering functions, and the application of Markov state modeling. The decomposition of MD-derived neutron dynamic susceptibilities is described, and the use of this in combination with NMR spectroscopy. We discuss dynamics at very long times, including approximations to the infinite time mean-square displacement and nonequilibrium aspects of single-protein dynamics. Lastly, we examine how neutron scattering and MD can be combined to provide information on lipid nanodomains.

  12. Molecular biology of pancreatic cancer: potential clinical implications.

    PubMed

    Sakorafas, G H; Tsiotos, G G

    2001-01-01

    The development of cancer involves the accumulation of genetic changes. Over the past decade there has a been spectacular advance in the knowledge of the genetic basis of cancer, mainly as a result of the rapid progression of molecular technology. Pancreatic cancer is one of the most lethal cancers. Conventional therapeutic approaches have not had much impact on the course of this aggressive neoplasm. Knowledge of the molecular biology of pancreatic cancer has grown rapidly. Genetic alterations in pancreatic cancer include oncogene mutations (most commonly K-ras mutations), and tumour suppressor gene alterations (mainly p53, p16, DCC, etc.). These advances have potential implications for the management of this deadly disease. Identification of a hereditary genetic predisposition to pancreatic cancer has led to the formation of pancreatic cancer registries around the world, with voluntary screening of patients and siblings for the hereditary genetic defect. Asymptomatic population screening remains unrealistic, but the recognition of subpopulations at increased risk from pancreatic cancer, along with novel and sensitive detection techniques, means that targeted population screening is a step closer. Intensive research is performed in specialist laboratories to improve the diagnostic approach in patients with pancreatic cancer. The use of such molecular diagnostic methods is likely to expand. Molecular biology may also have a great impact on the treatment of pancreatic cancer, and many therapeutic approaches are being evaluated in clinical trials, including gene replacement therapy, genetic prodrug activation therapy, antisense immunology and peptide technology. The 'molecular age' has the promise of delivering still better results. This review summarises recent data relating to the molecular biology of pancreatic cancer, with emphasis on features that may be of clinical significance for diagnosis and/or therapy.

  13. Time scale of diffusion in molecular and cellular biology

    NASA Astrophysics Data System (ADS)

    Holcman, D.; Schuss, Z.

    2014-05-01

    Diffusion is the driver of critical biological processes in cellular and molecular biology. The diverse temporal scales of cellular function are determined by vastly diverse spatial scales in most biophysical processes. The latter are due, among others, to small binding sites inside or on the cell membrane or to narrow passages between large cellular compartments. The great disparity in scales is at the root of the difficulty in quantifying cell function from molecular dynamics and from simulations. The coarse-grained time scale of cellular function is determined from molecular diffusion by the mean first passage time of molecular Brownian motion to a small targets or through narrow passages. The narrow escape theory (NET) concerns this issue. The NET is ubiquitous in molecular and cellular biology and is manifested, among others, in chemical reactions, in the calculation of the effective diffusion coefficient of receptors diffusing on a neuronal cell membrane strewn with obstacles, in the quantification of the early steps of viral trafficking, in the regulation of diffusion between the mother and daughter cells during cell division, and many other cases. Brownian trajectories can represent the motion of a molecule, a protein, an ion in solution, a receptor in a cell or on its membrane, and many other biochemical processes. The small target can represent a binding site or an ionic channel, a hidden active site embedded in a complex protein structure, a receptor for a neurotransmitter on the membrane of a neuron, and so on. The mean time to attach to a receptor or activator determines diffusion fluxes that are key regulators of cell function. This review describes physical models of various subcellular microdomains, in which the NET coarse-grains the molecular scale to a higher cellular-level, thus clarifying the role of cell geometry in determining subcellular function.

  14. Machine Learning for Biological Trajectory Classification Applications

    NASA Technical Reports Server (NTRS)

    Sbalzarini, Ivo F.; Theriot, Julie; Koumoutsakos, Petros

    2002-01-01

    Machine-learning techniques, including clustering algorithms, support vector machines and hidden Markov models, are applied to the task of classifying trajectories of moving keratocyte cells. The different algorithms axe compared to each other as well as to expert and non-expert test persons, using concepts from signal-detection theory. The algorithms performed very well as compared to humans, suggesting a robust tool for trajectory classification in biological applications.

  15. Scanning Tip Microscopy With Applications To Biology

    NASA Astrophysics Data System (ADS)

    Sarid, Dror; Thall, Edmond H.; Iams, Douglas A.; Ingle, Jeffery T.; Henson, Tammy D.; Lee, Y. C.; Bell, L. Stephen

    1989-06-01

    Scanning tunneling microscopy and atomic force microscopy, denoted here scanning tip microscopy, are two powerful novel techniques for imaging surfaces with atomic resolution. We describe the underlying principles of these two techniques with special emphasis on an instrument developed in our laboratory that uses a laser diode to detect minute deflections of a tip as it raster scans the surface of a sample. Applications of these techniques to research in biology are assessed and their relative merits discussed.

  16. Molecular biology of thermosensory transduction in C. elegans.

    PubMed

    Aoki, Ichiro; Mori, Ikue

    2015-10-01

    As the environmental temperature prominently influences diverse biological aspects of the animals, thermosensation and the subsequent information processing in the nervous system has attracted much attention in biology. Thermotaxis in the nematode Caenorhabditis elegans is an ideal behavioral paradigm by which to address the molecular mechanism underlying thermosensory transduction. Molecular genetic analysis in combination with other physiological and behavioral studies revealed that sensation of ambient temperature is mediated mainly by cyclic guanosine monophosphate (cGMP) signaling in thermosensory neurons. The information of the previously perceived temperature is also stored within the thermosensory neurons, and the consequence of the comparison between the past and the present temperature is conveyed to the downstream interneurons to further regulate the motor-circuits that encode the locomotion.

  17. Grete Kellenberger-Gujer: Molecular biology research pioneer.

    PubMed

    Citi, Sandra; Berg, Douglas E

    2016-01-01

    Grete Kellenberger-Gujer was a Swiss molecular biologist who pioneered fundamental studies of bacteriophage in the mid-20(th) century at the University of Geneva. Her life and career stories are reviewed here, focusing on her fundamental contributions to our early understanding of phage biology via her insightful analyses of phenomena such as the lysogenic state of a temperate phage (λ), genetic recombination, radiation's in vivo consequences, and DNA restriction-modification; on her creative personality and interactions with peers; and how her academic advancement was affected by gender, societal conditions and cultural attitudes of the time. Her story is important scientifically, putting into perspective features of the scientific community from just before the molecular biology era started through its early years, and also sociologically, in illustrating the numerous "glass ceilings" that, especially then, often hampered the advancement of creative women.

  18. Grete Kellenberger-Gujer: Molecular biology research pioneer

    PubMed Central

    Citi, Sandra; Berg, Douglas E.

    2016-01-01

    ABSTRACT Grete Kellenberger-Gujer was a Swiss molecular biologist who pioneered fundamental studies of bacteriophage in the mid-20th century at the University of Geneva. Her life and career stories are reviewed here, focusing on her fundamental contributions to our early understanding of phage biology via her insightful analyses of phenomena such as the lysogenic state of a temperate phage (λ), genetic recombination, radiation's in vivo consequences, and DNA restriction-modification; on her creative personality and interactions with peers; and how her academic advancement was affected by gender, societal conditions and cultural attitudes of the time. Her story is important scientifically, putting into perspective features of the scientific community from just before the molecular biology era started through its early years, and also sociologically, in illustrating the numerous “glass ceilings” that, especially then, often hampered the advancement of creative women. PMID:27607140

  19. Molecular and cellular biology of small-bowel mucosa.

    PubMed

    Kitchen, Paul A.; Walters, Julian R.F.

    2001-03-01

    Study of the molecular and cellular biology of the small-intestinal mucosa is providing insights into the remarkable properties of this unique tissue. With its structured pattern of cell proliferation, differentiation, and apoptosis, and its ability to adapt following exposure to luminal nutrients or injury from surgery or pathogens, it functions in a regulated but responsive manner. We review recent publications on factors affecting development, gene expression, cell turnover, and adaptation.

  20. In focus: molecular and cell biology research in China.

    PubMed

    Yao, Xuebiao; Li, Dangsheng; Pei, Gang

    2013-09-01

    An interactive, intellectual environment with good funding opportunities is essential for the development and success of basic research. The fast-growing economy and investment in science, together with a visionary plan, have attracted foreign scholars to work in China, motivated world-class Chinese scientists to return and strengthened the country's international collaborations. As a result, molecular and cell biology research in China has evolved rapidly over the past decade.

  1. Free molecular biological software available from the EMBL file server.

    PubMed

    Fuchs, R

    1990-04-01

    A new service provided by EMBL (EMBL Software File Server) is described that will make free molecular biology software available to anyone with computer network access. MS-DOS, Apple Macintosh and VAX/VMX are supported at the moment. The programs will be delivered by normal electronic mail; conversion mechanisms will transform binary files to ASCII to allow mail transfer. This service will also help authors to distribute their software conveniently.

  2. Rattlesnake Neurotoxin Structure, Mechanism of Action, Immunology and Molecular Biology

    DTIC Science & Technology

    1992-09-10

    Aird, S. D., and Kaiser, I. I. (1988) Physiological and immunological properties of small myotoxins from -Zhe venom of the midget faded rattlesnake ...AD-A258 669 AD RATTLESNAKE NEUROTOXIN STRUCTURE, MECHANISM OF ACTION, IMMUNOLOGY AND MOLECULAR BIOLOGY FINAL REPORT D TIC IVAN I. KAISER ELECTE S DEC...u m_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 6 2 7 8 7 A I 6 2 7 8 7 A 8 7 7 I A A [ ~A 3 1 7 8 2 1 (u) Rattlesnake neurotoxin structure

  3. Rattlesnake Neurotoxin Structure, Mechanism of Action, Immunology and Molecular Biology

    DTIC Science & Technology

    1990-09-01

    from the venom of the midget faded . rattlesnake (Crotalus viridis concolor . Toxicon 2&, 319- 323. Rehm, H. and Betz, H. (1982) Binding of B...8217determined. It was shown to have great similarity to the basic subunits of related toxins from the venoms of the South American and midget faded ...AD-A228 003 CONTRACT NO.: DAMD17-89-C-9007 TITLE: RATTLESNAKE NEUROTOXIN STRUCTURE, MECHANISM OF ACTION, IMMUNOLOGY AND MOLECULAR BIOLOGY PRINCIPAL

  4. TOPICAL REVIEW: Carbon nanotubes for biological and biomedical applications

    NASA Astrophysics Data System (ADS)

    Yang, Wenrong; Thordarson, Pall; Gooding, J. Justin; Ringer, Simon P.; Braet, Filip

    2007-10-01

    Ever since the discovery of carbon nanotubes, researchers have been exploring their potential in biological and biomedical applications. The recent expansion and availability of chemical modification and bio-functionalization methods have made it possible to generate a new class of bioactive carbon nanotubes which are conjugated with proteins, carbohydrates, or nucleic acids. The modification of a carbon nanotube on a molecular level using biological molecules is essentially an example of the 'bottom-up' fabrication principle of bionanotechnology. The availability of these biomodified carbon nanotube constructs opens up an entire new and exciting research direction in the field of chemical biology, finally aiming to target and to alter the cell's behaviour at the subcellular or molecular level. This review covers the latest advances of bio-functionalized carbon nanotubes with an emphasis on the development of functional biological nano-interfaces. Topics that are discussed herewith include methods for biomodification of carbon nanotubes, the development of hybrid systems of carbon nanotubes and biomolecules for bioelectronics, and carbon nanotubes as transporters for a specific delivery of peptides and/or genetic material to cells. All of these current research topics aim at translating these biotechnology modified nanotubes into potential novel therapeutic approaches.

  5. Biological Moleculars: Have Most of Our Problems Already Been Solved?

    NASA Technical Reports Server (NTRS)

    Downey, James P.; Rose, M. Franklin (Technical Monitor)

    2000-01-01

    Evolution has resulted in biological machinery that engineers have great reason to envy and at present can only poorly mimic. This is not just a curiosity as biological systems perform many functions that are desired industrial processes. Examples include photosynthesis, chemosynthesis, energy storage, low temperature chemical conversion, reproducible manufacture of chemical compounds, etc. The bases of biological machinery are the proteins and nucleic acids that comprise living organisms. Each molecule functions as a part of a biological machine. In many cases the molecule can be properly regarded as a stand alone machine of its own. Concepts and methods for harnessing the power of biological molecules exist but are often overlooked in the industrial world. Some are old and appear crude but are quite effective, e.g. the fermentation of grains and fruits. Currently, there is a revolution in progress regarding the harnessing biological processes. These include techniques such as genetic manipulation via polymerase chain reaction, forced evolution also known as evolution in a test tube, determination of molecular structure, and combinatorial chemistry. The following is a brief discussion on how these processes are performed and how they may relate to industrial and aerospace processes.

  6. Biological Moleculars: Have Most of Our Problems Already Been Solved?

    NASA Technical Reports Server (NTRS)

    Downey, James P.; Rose, M. Franklin (Technical Monitor)

    2000-01-01

    Evolution has resulted in biological machinery that engineers have great reason to envy and at present can only poorly mimic. This is not just a curiosity as biological systems perform many functions that are desired industrial processes. Examples include photosynthesis, chemosynthesis, energy storage, low temperature chemical conversion, reproducible manufacture of chemical compounds, etc. The bases of biological machinery are the proteins and nucleic acids that comprise living organisms. Each molecule functions as a part of a biological machine. In many cases the molecule can be properly regarded as a stand alone machine of its own. Concepts and methods for harnessing the power of biological molecules exist but are often overlooked in the industrial world. Some are old and appear crude but are quite effective, e.g. the fermentation of grains and fruits. Currently, there is a revolution in progress regarding the harnessing biological processes. These include techniques such as genetic manipulation via polymerase chain reaction, forced evolution also known as evolution in a test tube, determination of molecular structure, and combinatorial chemistry. The following is a brief discussion on how these processes are performed and how they may relate to industrial and aerospace processes.

  7. Protocols, practices, and the reproduction of technique in molecular biology.

    PubMed

    Lynch, Michael

    2002-06-01

    Protocols are one of the main organizational resources in molecular biology. They are written instructions that specify ingredients, equipment, and sequences of steps for making technical preparations. Some protocols are published in widely used manuals, while others are hand-written variants used by particular laboratories and individual technicians. It is widely understood, both in molecular biology and in social studies of science, that protocols do not describe exactly what practitioners do in the laboratory workplace. In social studies of science, the difference between protocols and the actual practices of doing them often is used to set up ironic contrasts between 'messy' laboratory practices and the appearance of technical order. Alternatively, in ethnomethodological studies of work, the difference is examined as a constitutive feature, both of the lived-work of doing technical projects, and of the administrative work of regulating and evaluating such projects. The present article takes its point of departure from ethnomethodology, and begins with a discussion of local problems with performing molecular biology protocols on specific occasions. The discussion then moves to particular cases in criminal law in which defense attorneys cross-examine forensic technicians and lab administrators. In these interrogations, the distinction between protocols and actual practices animates the dialogue and becomes consequential for judgments in the case at hand. The article concludes with a discussion of administrative science: the work of treating protocols and paper trails as proxies for actual 'scientific' practices.

  8. Imaging mass spectrometry with nuclear microprobes for biological applications

    NASA Astrophysics Data System (ADS)

    Nakata, Y.; Yamada, H.; Honda, Y.; Ninomiya, S.; Seki, T.; Aoki, T.; Matsuo, J.

    2009-06-01

    A mass spectrometric technique using nuclear microprobes is presented in this paper for biological applications. In recent years, imaging mass spectrometry has become an increasingly important technique for visualizing the spatial distribution of molecular species in biological tissues and cells. However, due to low yields of large molecular ions, the conventional secondary ion mass spectrometry (SIMS), that uses keV primary ion beams, is typically applied for imaging of either elements or low mass compounds. In this study, we performed imaging mass spectrometry using MeV ion beams collimated to about 10 μm, and successfully obtained molecular ion images from plant and animal cell sections. The molecular ion imaging of the pollen section showed high intensities of PO3- ions in the pollen cytoplasm, compared to the pollen wall, and indicated the heterogeneous distribution in the cytoplasm. The 3T3-L1 cell image revealed the high intensity of PO3- ions, in particular from the cell nucleus. The result showed that not only the individual cell, but also the cell nucleus could be identified with the present imaging technique.

  9. Physical and chemical mechanisms in molecular radiation biology

    SciTech Connect

    Glass, W.A.; Varma, M.N.

    1991-01-01

    Through its Radiological and Chemical Physics Program, the Department of Energy (DOE) has been a primary source of funding for research in radiation physics and radiochemistry, supporting a wide range of explorations of the link between physical, chemical and biological events. This book is a series of articles by authors working within this field, most of whom have been central to the DOE-sponsored research. The opening papers focus on radiological physics; the second section covers radiation chemistry in a discussion that extends from the initial energy transfer to the production of intermediate chemical species and DNA damage. The third section explores the link between the physical and chemical events and the production of biological effects. Finally the book closes with a series of papers on molecular radiation biology.

  10. Panel 4: Recent Advances in Otitis Media in Molecular Biology, Biochemistry, Genetics, and Animal Models

    PubMed Central

    Li, Jian-Dong; Hermansson, Ann; Ryan, Allen F.; Bakaletz, Lauren O.; Brown, Steve D.; Cheeseman, Michael T.; Juhn, Steven K.; Jung, Timothy T. K.; Lim, David J.; Lim, Jae Hyang; Lin, Jizhen; Moon, Sung-Kyun; Post, J. Christopher

    2014-01-01

    Background Otitis media (OM) is the most common childhood bacterial infection and also the leading cause of conductive hearing loss in children. Currently, there is an urgent need for developing novel therapeutic agents for treating OM based on full understanding of molecular pathogenesis in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. Objective To provide a state-of-the-art review concerning recent advances in OM in the areas of molecular biology, biochemistry, genetics, and animal model studies and to discuss the future directions of OM studies in these areas. Data Sources and Review Methods A structured search of the current literature (since June 2007). The authors searched PubMed for published literature in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. Results Over the past 4 years, significant progress has been made in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. These studies brought new insights into our understanding of the molecular and biochemical mechanisms underlying the molecular pathogenesis of OM and helped identify novel therapeutic targets for OM. Conclusions and Implications for Practice Our understanding of the molecular pathogenesis of OM has been significantly advanced, particularly in the areas of inflammation, innate immunity, mucus overproduction, mucosal hyperplasia, middle ear and inner ear interaction, genetics, genome sequencing, and animal model studies. Although these studies are still in their experimental stages, they help identify new potential therapeutic targets. Future preclinical and clinical studies will help to translate these exciting experimental research findings into clinical applications. PMID:23536532

  11. Molecular imaging applications for immunology.

    PubMed

    Hildebrandt, Isabel Junie; Gambhir, Sanjiv Sam

    2004-05-01

    The use of multimodality molecular imaging has recently facilitated the study of molecular and cellular events in living subjects in a noninvasive and repetitive manner to improve the diagnostic capability of traditional assays. The noninvasive imaging modalities utilized for both small animal and human imaging include positron emission tomography (PET), single photon emission computed tomography (SPECT), magnetic resonance imaging (MRI), ultrasound, and computed tomography (CT). Techniques specific to small-animal imaging include bioluminescent imaging (BIm) and fluorescent imaging (FIm). Molecular imaging permits the study of events within cells, the examination of cell trafficking patterns that relate to inflammatory diseases and metastases, and the ability to rapidly screen new drug treatments for distribution and effectiveness. In this paper, we will review the current field of molecular imaging assays (especially those utilizing PET and BIm modalities) and examine how they might impact animal models and human disease in the field of clinical immunology.

  12. A comparative cellular and molecular biology of longevity database.

    PubMed

    Stuart, Jeffrey A; Liang, Ping; Luo, Xuemei; Page, Melissa M; Gallagher, Emily J; Christoff, Casey A; Robb, Ellen L

    2013-10-01

    Discovering key cellular and molecular traits that promote longevity is a major goal of aging and longevity research. One experimental strategy is to determine which traits have been selected during the evolution of longevity in naturally long-lived animal species. This comparative approach has been applied to lifespan research for nearly four decades, yielding hundreds of datasets describing aspects of cell and molecular biology hypothesized to relate to animal longevity. Here, we introduce a Comparative Cellular and Molecular Biology of Longevity Database, available at ( http://genomics.brocku.ca/ccmbl/ ), as a compendium of comparative cell and molecular data presented in the context of longevity. This open access database will facilitate the meta-analysis of amalgamated datasets using standardized maximum lifespan (MLSP) data (from AnAge). The first edition contains over 800 data records describing experimental measurements of cellular stress resistance, reactive oxygen species metabolism, membrane composition, protein homeostasis, and genome homeostasis as they relate to vertebrate species MLSP. The purpose of this review is to introduce the database and briefly demonstrate its use in the meta-analysis of combined datasets.

  13. A national comparison of biochemistry and molecular biology capstone experiences.

    PubMed

    Aguanno, Ann; Mertz, Pamela; Martin, Debra; Bell, Ellis

    2015-01-01

    Recognizing the increasingly integrative nature of the molecular life sciences, the American Society for Biochemistry and Molecular Biology (ASBMB) recommends that Biochemistry and Molecular Biology (BMB) programs develop curricula based on concepts, content, topics, and expected student outcomes, rather than courses. To that end, ASBMB conducted a series of regional workshops to build a BMB Concept Inventory containing validated assessment tools, based on foundational and discipline-specific knowledge and essential skills, for the community to use. A culminating activity, which integrates the educational experience, is often part of undergraduate molecular life science programs. These "capstone" experiences are commonly defined as an attempt to measure student ability to synthesize and integrate acquired knowledge. However, the format, implementation, and approach to outcome assessment of these experiences are quite varied across the nation. Here we report the results of a nation-wide survey on BMB capstone experiences and discuss this in the context of published reports about capstones and the findings of the workshops driving the development of the BMB Concept Inventory. Both the survey results and the published reports reveal that, although capstone practices do vary, certain formats for the experience are used more frequently and similarities in learning objectives were identified. The use of rubrics to measure student learning is also regularly reported, but details about these assessment instruments are sparse in the literature and were not a focus of our survey. Finally, we outline commonalities in the current practice of capstones and suggest the next steps needed to elucidate best practices.

  14. Molecular biology in studies of oceanic primary production

    SciTech Connect

    LaRoche, J.; Falkowski, P.G. ); Geider, R. . Coll. of Marine Studies)

    1992-01-01

    Remote sensing and the use of moored in situ instrumentation has greatly improved our ability to measure phytoplankton chlorophyll and photosynthesis on global scales with high temporal resolution. However, the interpretation of these measurements and their significance with respect to the biogeochemical cycling of carbon relies on their relationship with physiological and biochemical processes in phytoplankton. For example, the use of satellite images of surface chlorophyll to estimate primary production is often based on the functional relationship between photosynthesis and irradiance. A variety of environmental factors such as light, temperature, nutrient availability affect the photosynthesis/irradiance (P vs I) relationship in phytoplankton. We present three examples showing how molecular biology can be used to provide basic insight into the factors controlling primary productivity at three different levels of complexity: 1. Studies of light intensity regulation in unicellular alga show how molecular biology can help understand the processing of environmental cues leading to the regulation of photosynthetic gene expression. 2. Probing of the photosynthetic apparatus using molecular techniques can be used to test existing mechanistic models derived from the interpretation of physiological and biophysical measurements. 3. Exploratory work on the expression of specific proteins during nutrient-limited growth of phytoplankton may lead to the identification and production of molecular probes for field studies.

  15. Recent science and its exploration: the case of molecular biology.

    PubMed

    Rheinberger, Hans-Jörg

    2009-03-01

    This paper is about the interaction and the intertwinement between history of science as a historical process and history of science as the historiography of this process, taking molecular biology as an example. In the first part, two historical shifts are briefly characterized that appear to have punctuated the emergence of molecular biology between the 1930s and the 1980s, one connected to a new generation of analytical apparatus, the other to properly molecular tools. The second part concentrates on the historiography of this development. Basically, it distinguishes three phases. The first phase was largely dominated by accounts of the actors themselves. The second coincided with the general 'practical turn' in history of science at large, and today's historical appropriations of the molecularization of the life sciences appear to be marked by the changing disciplinary status of the science under review. In a closing remark, an argument is made for differentiating between long-range, middle-range and short-range perspectives in dealing with the history of the sciences.

  16. Molecular biology in studies of oceanic primary production

    SciTech Connect

    LaRoche, J.; Falkowski, P.G.; Geider, R.

    1992-07-01

    Remote sensing and the use of moored in situ instrumentation has greatly improved our ability to measure phytoplankton chlorophyll and photosynthesis on global scales with high temporal resolution. However, the interpretation of these measurements and their significance with respect to the biogeochemical cycling of carbon relies on their relationship with physiological and biochemical processes in phytoplankton. For example, the use of satellite images of surface chlorophyll to estimate primary production is often based on the functional relationship between photosynthesis and irradiance. A variety of environmental factors such as light, temperature, nutrient availability affect the photosynthesis/irradiance (P vs I) relationship in phytoplankton. We present three examples showing how molecular biology can be used to provide basic insight into the factors controlling primary productivity at three different levels of complexity: 1. Studies of light intensity regulation in unicellular alga show how molecular biology can help understand the processing of environmental cues leading to the regulation of photosynthetic gene expression. 2. Probing of the photosynthetic apparatus using molecular techniques can be used to test existing mechanistic models derived from the interpretation of physiological and biophysical measurements. 3. Exploratory work on the expression of specific proteins during nutrient-limited growth of phytoplankton may lead to the identification and production of molecular probes for field studies.

  17. Defining the molecular biology of inflammatory breast cancer.

    PubMed

    Charafe-Jauffret, Emmanuelle; Tarpin, Carole; Viens, Patrice; Bertucci, François

    2008-02-01

    Inflammatory breast cancer (IBC) is a rare, but aggressive form of breast cancer. Despite the progress related to the introduction of primary combination chemotherapy (CT) to the multimodality treatment regimen, the prognosis of IBC remains poor with long-term survival inferior to 50%. Until recently, IBC remained understudied at the molecular level. In the past 10 years, advances have been made in the molecular characterization of the disease. Recently, the use of experimental models and new high-throughput molecular profiling technologies have led to the identification of genes or pathways potentially involved in disease development, which might represent new clinically relevant targets. The aim of this review is to present and discuss what is known about the biology of this particularly aggressive form of breast cancer and to discuss how this knowledge could improve its management.

  18. Biological applications of rare-earth based nanoparticles.

    PubMed

    Bouzigues, Cedric; Gacoin, Thierry; Alexandrou, Antigoni

    2011-11-22

    Biomedicine and cell and molecular biology require powerful imaging techniques of the single molecule scale to the whole organism, either for fundamental science or diagnosis. These applications are however often limited by the optical properties of the available probes. Moreover, in cell biology, the measurement of the cell response with spatial and temporal resolution is a central instrumental problem. This has been one of the main motivations for the development of new probes and imaging techniques either for biomolecule labeling or detection of an intracellular signaling species. The weak photostability of genetically encoded probes or organic dyes has motivated the interest for different types of nanoparticles for imaging such as quantum dots, nanodiamonds, dye-doped silica particles, or metallic nanoparticles. One of the most active fields of research in the past decade has thus been the development of rare-earth based nanoparticles, whose optical properties and low cytotoxicity are promising for biological applications. Attractive properties of rare-earth based nanoparticles include high photostability, absence of blinking, extremely narrow emission lines, large Stokes shifts, long lifetimes that can be exploited for retarded detection schemes, and facile functionalization strategies. The use of specific ions in their compositions can be moreover exploited for oxidant detection or for implementing potent contrast agents for magnetic resonance imaging. In this review, we present these different applications of rare-earth nanoparticles for biomolecule detection and imaging in vitro, in living cells or in small animals. We highlight how chemical composition tuning and surface functionalization lead to specific properties, which can be used for different imaging modalities. We discuss their performances for imaging in comparison with other probes and to what extent they could constitute a central tool in the future of molecular and cell biology. © 2011 American

  19. Genomic Signal Processing: Predicting Basic Molecular Biological Principles

    NASA Astrophysics Data System (ADS)

    Alter, Orly

    2005-03-01

    Advances in high-throughput technologies enable acquisition of different types of molecular biological data, monitoring the flow of biological information as DNA is transcribed to RNA, and RNA is translated to proteins, on a genomic scale. Future discovery in biology and medicine will come from the mathematical modeling of these data, which hold the key to fundamental understanding of life on the molecular level, as well as answers to questions regarding diagnosis, treatment and drug development. Recently we described data-driven models for genome-scale molecular biological data, which use singular value decomposition (SVD) and the comparative generalized SVD (GSVD). Now we describe an integrative data-driven model, which uses pseudoinverse projection (1). We also demonstrate the predictive power of these matrix algebra models (2). The integrative pseudoinverse projection model formulates any number of genome-scale molecular biological data sets in terms of one chosen set of data samples, or of profiles extracted mathematically from data samples, designated the ``basis'' set. The mathematical variables of this integrative model, the pseudoinverse correlation patterns that are uncovered in the data, represent independent processes and corresponding cellular states (such as observed genome-wide effects of known regulators or transcription factors, the biological components of the cellular machinery that generate the genomic signals, and measured samples in which these regulators or transcription factors are over- or underactive). Reconstruction of the data in the basis simulates experimental observation of only the cellular states manifest in the data that correspond to those of the basis. Classification of the data samples according to their reconstruction in the basis, rather than their overall measured profiles, maps the cellular states of the data onto those of the basis, and gives a global picture of the correlations and possibly also causal coordination of

  20. Biological applications of synchrotron radiation infrared spectromicroscopy.

    PubMed

    Marcelli, Augusto; Cricenti, Antonio; Kwiatek, Wojciech M; Petibois, Cyril

    2012-01-01

    Extremely brilliant infrared (IR) beams provided by synchrotron radiation sources are now routinely used in many facilities with available commercial spectrometers coupled to IR microscopes. Using these intense non-thermal sources, a brilliance two or three order of magnitude higher than a conventional source is achievable through small pinholes (<10 μm) with a high signal to-noise ratio. IR spectroscopy is a powerful technique to investigate biological systems and offers many new imaging opportunities. The field of infrared biological imaging covers a wide range of fundamental issues and applied researches such as cell imaging or tissue imaging. Molecular maps with a spatial resolution down to the diffraction limit may be now obtained with a synchrotron radiation IR source also on thick samples. Moreover, changes of the protein structure are detectable in an IR spectrum and cellular molecular markers can be identified and used to recognize a pathological status of a tissue. Molecular structure and functions are strongly correlated and this aspect is particularly relevant for imaging. We will show that the brilliance of synchrotron radiation IR sources may enhance the sensitivity of a molecular signal obtained from small biosamples, e.g., a single cell, containing extremely small amounts of organic matter. We will also show that SR IR sources allow to study chemical composition and to identify the distribution of organic molecules in cells at submicron resolution is possible with a high signal-to-noise ratio. Moreover, the recent availability of two-dimensional IR detectors promises to push forward imaging capabilities in the time domain. Indeed, with a high current synchrotron radiation facility and a Focal Plane Array the chemical imaging of individual cells can be obtained in a few minutes. Within this framework important results are expected in the next years using synchrotron radiation and Free Electron Laser (FEL) sources for spectro-microscopy and spectral

  1. Biological Properties and Therapeutic Applications of Propolis.

    PubMed

    Sforcin, José M

    2016-06-01

    Propolis is a resinous material collected by bees from bud and exudates of the plants, mixed with bee enzymes, pollen and wax. In this review, the biological properties of propolis and some therapeutic applications are discussed. The same biological activities have been investigated until today, using samples from different geographic regions. Thus, the study of the biological properties of a given sample should always be associated with its chemical composition and botanical source, representing a particular sample of a given geographic area, exploring its biological potential and the role of its constituents. Efforts have been carried out to explain propolis' mechanisms of action in vivo and in vitro, but the majority of propolis' targets and actions are still unclear. The number of formulations containing propolis and patents have increased, although propolis extracts have been used deliberately with different recommendations, not always mentioning the chemical composition, vegetal source and the methods of extraction. Clinical studies will help to obtain criterious recommendations in view of the expected outcomes. Further investigation should explore the effects of common compounds found in the samples from all over the world in an attempt to standardize the research on propolis and to obtain new drugs. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  2. Developing luminescent silver nanodots for biological applications.

    PubMed

    Choi, Sungmoon; Dickson, Robert M; Yu, Junhua

    2012-03-07

    Though creation and characterization of water soluble luminescent silver nanodots were achieved only in the past decade, a large variety of emitters in diverse scaffolds have been reported. Photophysical properties approach those of semiconductor quantum dots, but relatively small sizes are retained. Because of these properties, silver nanodots are finding ever-expanding roles as probes and biolabels. In this critical review we revisit the studies on silver nanodots in inert environments and in aqueous solutions. The recent advances detailing their chemical and physical properties of silver nanodots are highlighted with an effort to decipher the relations between their chemical/photophysical properties and their structures. The primary results about their biological applications are discussed here as well, especially relating to their chemical and photophysical behaviours in biological environments (216 references).

  3. Marine Carotenoids: Biological Functions and Commercial Applications

    PubMed Central

    Vílchez, Carlos; Forján, Eduardo; Cuaresma, María; Bédmar, Francisco; Garbayo, Inés; Vega, José M.

    2011-01-01

    Carotenoids are the most common pigments in nature and are synthesized by all photosynthetic organisms and fungi. Carotenoids are considered key molecules for life. Light capture, photosynthesis photoprotection, excess light dissipation and quenching of singlet oxygen are among key biological functions of carotenoids relevant for life on earth. Biological properties of carotenoids allow for a wide range of commercial applications. Indeed, recent interest in the carotenoids has been mainly for their nutraceutical properties. A large number of scientific studies have confirmed the benefits of carotenoids to health and their use for this purpose is growing rapidly. In addition, carotenoids have traditionally been used in food and animal feed for their color properties. Carotenoids are also known to improve consumer perception of quality; an example is the addition of carotenoids to fish feed to impart color to farmed salmon. PMID:21556162

  4. Biomimetic smart interface materials for biological applications.

    PubMed

    Sun, Taolei; Qing, Guangyan

    2011-03-25

    Controlling the surface chemical and physical properties of materials and modulating the interfacial behaviors of biological entities, e.g., cells and biomolecules, are central tasks in the study of biomaterials. In this context, smart polymer interface materials have recently attracted much interest in biorelated applications and have broad prospects due to the excellent controllability of their surface properties by external stimuli. Among such materials, poly(N-isopropylacrylamide) and its copolymer films are especially attractive due to their reversible hydrogen-bonding-mediated reversible phase transition, which mimics natural biological processes. This platform is promising for tuning surface properties or to introduce novel biofunctionalities via copolymerization with various functional units and/or combination with other materials. Important progress in this field in recent years is highlighted. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Marine carotenoids: biological functions and commercial applications.

    PubMed

    Vílchez, Carlos; Forján, Eduardo; Cuaresma, María; Bédmar, Francisco; Garbayo, Inés; Vega, José M

    2011-03-03

    Carotenoids are the most common pigments in nature and are synthesized by all photosynthetic organisms and fungi. Carotenoids are considered key molecules for life. Light capture, photosynthesis photoprotection, excess light dissipation and quenching of singlet oxygen are among key biological functions of carotenoids relevant for life on earth. Biological properties of carotenoids allow for a wide range of commercial applications. Indeed, recent interest in the carotenoids has been mainly for their nutraceutical properties. A large number of scientific studies have confirmed the benefits of carotenoids to health and their use for this purpose is growing rapidly. In addition, carotenoids have traditionally been used in food and animal feed for their color properties. Carotenoids are also known to improve consumer perception of quality; an example is the addition of carotenoids to fish feed to impart color to farmed salmon.

  6. [Molecular Biology on the Mechanisms of Autism Spectrum Disorder for Clinical Psychiatrists].

    PubMed

    Makinodan, Manabu

    2015-01-01

    While, in general, a certain number of clinical psychiatrists might not be familiar with molecular biology, the mechanisms of mental illnesses have been uncovered by molecular biology for decades. Among mental illnesses, even biological psychiatrists and neuroscientists have paid less attention to the biological treatment of autism spectrum disorder (ASD) than Alzheimer's disease and schizophrenia since ASD has been regarded as a developmental disorder that was seemingly untreatable. However, multifaceted methods of molecular biology have revealed the mechanisms that would lead to the medication of ASD. In this article, how molecular biology dissects the pathobiology of ASD is described in order to announce the possibilities of biological treatment for clinical psychiatrists.

  7. A plea for more theory in molecular biology.

    PubMed

    Wolkenhauer, O; Mesarović, M; Wellstead, P

    2007-01-01

    The integrationist principles of systems theory have proven hugely successful in the physical sciences and engineering. It is an underlying assumption made in the systems approach to biology that they can also be used to understand biological phenomena at the level of an entire organism or organ. Within this holistic vision, the vast majority of systems biology research projects investigate phenomena at the level of the cell, with the belief that unifying principles established at the most basic level can establish a framework within which we may understand phenomena at higher levels of organization. In this spirit, and to use a celestial analogy, if a disease--effecting an organ or entire body--is our universe of discourse, then the cell is the star we gaze at. In building an understanding of disease and the effect of drugs, systems biology makes an implicit assumption about direct causal entailment between cell function and physiology. A skeptic might argue that this is about the same as trying to predict the world economy from observations made at a local supermarket. However, assuming for the moment that the money and hope we are investing in molecular biology, genomics, and systems biology is justified, how should this amazing intellectual achievement be possible? In this chapter we argue that an essential tool to progress is a systems theory that allows biological objects and their operational characteristics to be captured in a succinct yet general form. Armed with this conceptual framework, we construct mathematical representations of standard cellular and intercellular functions which can be integrated to describe more general processes of cell complexes, and potentially entire organs.

  8. Vibrio natriegens as a fast-growing host for molecular biology.

    PubMed

    Weinstock, Matthew T; Hesek, Eric D; Wilson, Christopher M; Gibson, Daniel G

    2016-10-01

    A rapidly growing bacterial host would be desirable for a range of routine applications in molecular biology and biotechnology. The bacterium Vibrio natriegens has the fastest growth rate of any known organism, with a reported doubling time of <10 min. We report the development of genetic tools and methods to engineer V. natriegens and demonstrate the advantages of using these engineered strains in common biotech processes.

  9. Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology

    PubMed Central

    2012-01-01

    Background An important question in the analysis of biochemical data is that of identifying subsets of molecular variables that may jointly influence a biological response. Statistical variable selection methods have been widely used for this purpose. In many settings, it may be important to incorporate ancillary biological information concerning the variables of interest. Pathway and network maps are one example of a source of such information. However, although ancillary information is increasingly available, it is not always clear how it should be used nor how it should be weighted in relation to primary data. Results We put forward an approach in which biological knowledge is incorporated using informative prior distributions over variable subsets, with prior information selected and weighted in an automated, objective manner using an empirical Bayes formulation. We employ continuous, linear models with interaction terms and exploit biochemically-motivated sparsity constraints to permit exact inference. We show an example of priors for pathway- and network-based information and illustrate our proposed method on both synthetic response data and by an application to cancer drug response data. Comparisons are also made to alternative Bayesian and frequentist penalised-likelihood methods for incorporating network-based information. Conclusions The empirical Bayes method proposed here can aid prior elicitation for Bayesian variable selection studies and help to guard against mis-specification of priors. Empirical Bayes, together with the proposed pathway-based priors, results in an approach with a competitive variable selection performance. In addition, the overall procedure is fast, deterministic, and has very few user-set parameters, yet is capable of capturing interplay between molecular players. The approach presented is general and readily applicable in any setting with multiple sources of biological prior knowledge. PMID:22578440

  10. Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology.

    PubMed

    Hill, Steven M; Neve, Richard M; Bayani, Nora; Kuo, Wen-Lin; Ziyad, Safiyyah; Spellman, Paul T; Gray, Joe W; Mukherjee, Sach

    2012-05-11

    An important question in the analysis of biochemical data is that of identifying subsets of molecular variables that may jointly influence a biological response. Statistical variable selection methods have been widely used for this purpose. In many settings, it may be important to incorporate ancillary biological information concerning the variables of interest. Pathway and network maps are one example of a source of such information. However, although ancillary information is increasingly available, it is not always clear how it should be used nor how it should be weighted in relation to primary data. We put forward an approach in which biological knowledge is incorporated using informative prior distributions over variable subsets, with prior information selected and weighted in an automated, objective manner using an empirical Bayes formulation. We employ continuous, linear models with interaction terms and exploit biochemically-motivated sparsity constraints to permit exact inference. We show an example of priors for pathway- and network-based information and illustrate our proposed method on both synthetic response data and by an application to cancer drug response data. Comparisons are also made to alternative Bayesian and frequentist penalised-likelihood methods for incorporating network-based information. The empirical Bayes method proposed here can aid prior elicitation for Bayesian variable selection studies and help to guard against mis-specification of priors. Empirical Bayes, together with the proposed pathway-based priors, results in an approach with a competitive variable selection performance. In addition, the overall procedure is fast, deterministic, and has very few user-set parameters, yet is capable of capturing interplay between molecular players. The approach presented is general and readily applicable in any setting with multiple sources of biological prior knowledge.

  11. Extracting evidence from forensic DNA analyses: future molecular biology directions.

    PubMed

    Budowle, Bruce; van Daal, Angela

    2009-04-01

    Molecular biology tools have enhanced the capability of the forensic scientist to characterize biological evidence to the point where it is feasible to analyze minute samples and achieve high levels of individualization. Even with the forensic DNA field's maturity, there still are a number of areas where improvements can be made. These include: enabling the typing of samples of limited quantity and quality; using genetic information and novel markers to provide investigative leads; enhancing automation with robotics, different chemistries, and better software tools; employing alternate platforms for typing DNA samples; developing integrated microfluidic/microfabrication devices to process DNA samples with higher throughput, faster turnaround times, lower risk of contamination, reduced labor, and less consumption of evidentiary samples; and exploiting high-throughput sequencing, particularly for attribution in microbial forensics cases. Knowledge gaps and new directions have been identified where molecular biology will likely guide the field of forensics. This review aims to provide a roadmap to guide those interested in contributing to the further development of forensic genetics.

  12. Naumovozyma castellii: an alternative model for budding yeast molecular biology.

    PubMed

    Karademir Andersson, Ahu; Cohn, Marita

    2017-03-01

    Naumovozyma castellii (Saccharomyces castellii) is a member of the budding yeast family Saccharomycetaceae. It has been extensively used as a model organism for telomere biology research and has gained increasing interest as a budding yeast model for functional analyses owing to its amenability to genetic modifications. Owing to the suitable phylogenetic distance to S. cerevisiae, the whole genome sequence of N. castellii has provided unique data for comparative genomic studies, and it played a key role in the establishment of the timing of the whole genome duplication and the evolutionary events that took place in the subsequent genomic evolution of the Saccharomyces lineage. Here we summarize the historical background of its establishment as a laboratory yeast species, and the development of genetic and molecular tools and strains. We review the research performed on N. castellii, focusing on areas where it has significantly contributed to the discovery of new features of molecular biology and to the advancement of our understanding of molecular evolution. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  13. Molecular Imprinting of Macromolecules for Sensor Applications

    PubMed Central

    Saylan, Yeşeren; Yilmaz, Fatma; Özgür, Erdoğan; Derazshamshir, Ali; Yavuz, Handan; Denizli, Adil

    2017-01-01

    Molecular recognition has an important role in numerous living systems. One of the most important molecular recognition methods is molecular imprinting, which allows host compounds to recognize and detect several molecules rapidly, sensitively and selectively. Compared to natural systems, molecular imprinting methods have some important features such as low cost, robustness, high recognition ability and long term durability which allows molecularly imprinted polymers to be used in various biotechnological applications, such as chromatography, drug delivery, nanotechnology, and sensor technology. Sensors are important tools because of their ability to figure out a potentially large number of analytical difficulties in various areas with different macromolecular targets. Proteins, enzymes, nucleic acids, antibodies, viruses and cells are defined as macromolecules that have wide range of functions are very important. Thus, macromolecules detection has gained great attention in concerning the improvement in most of the studies. The applications of macromolecule imprinted sensors will have a spacious exploration according to the low cost, high specificity and stability. In this review, macromolecules for molecularly imprinted sensor applications are structured according to the definition of molecular imprinting methods, developments in macromolecular imprinting methods, macromolecular imprinted sensors, and conclusions and future perspectives. This chapter follows the latter strategies and focuses on the applications of macromolecular imprinted sensors. This allows discussion on how sensor strategy is brought to solve the macromolecules imprinting. PMID:28422082

  14. Molecular Imprinting of Macromolecules for Sensor Applications.

    PubMed

    Saylan, Yeşeren; Yilmaz, Fatma; Özgür, Erdoğan; Derazshamshir, Ali; Yavuz, Handan; Denizli, Adil

    2017-04-19

    Molecular recognition has an important role in numerous living systems. One of the most important molecular recognition methods is molecular imprinting, which allows host compounds to recognize and detect several molecules rapidly, sensitively and selectively. Compared to natural systems, molecular imprinting methods have some important features such as low cost, robustness, high recognition ability and long term durability which allows molecularly imprinted polymers to be used in various biotechnological applications, such as chromatography, drug delivery, nanotechnology, and sensor technology. Sensors are important tools because of their ability to figure out a potentially large number of analytical difficulties in various areas with different macromolecular targets. Proteins, enzymes, nucleic acids, antibodies, viruses and cells are defined as macromolecules that have wide range of functions are very important. Thus, macromolecules detection has gained great attention in concerning the improvement in most of the studies. The applications of macromolecule imprinted sensors will have a spacious exploration according to the low cost, high specificity and stability. In this review, macromolecules for molecularly imprinted sensor applications are structured according to the definition of molecular imprinting methods, developments in macromolecular imprinting methods, macromolecular imprinted sensors, and conclusions and future perspectives. This chapter follows the latter strategies and focuses on the applications of macromolecular imprinted sensors. This allows discussion on how sensor strategy is brought to solve the macromolecules imprinting.

  15. Molecular dynamics simulations and applications in computational toxicology and nanotoxicology.

    PubMed

    Selvaraj, Chandrabose; Sakkiah, Sugunadevi; Tong, Weida; Hong, Huixiao

    2017-08-24

    Nanotoxicology studies toxicity of nanomaterials and has been widely applied in biomedical researches to explore toxicity of various biological systems. Investigating biological systems through in vivo and in vitro methods is expensive and time taking. Therefore, computational toxicology, a multi-discipline field that utilizes computational power and algorithms to examine toxicology of biological systems, has gained attractions to scientists. Molecular dynamics (MD) simulations of biomolecules such as proteins and DNA are popular for understanding of interactions between biological systems and chemicals in computational toxicology. In this paper, we review MD simulation methods, protocol for running MD simulations and their applications in studies of toxicity and nanotechnology. We also briefly summarize some popular software tools for execution of MD simulations. Copyright © 2017. Published by Elsevier Ltd.

  16. Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations.

    PubMed

    Dal Peraro, Matteo; Ruggerone, Paolo; Raugei, Simone; Gervasio, Francesco Luigi; Carloni, Paolo

    2007-04-01

    Density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations describe the time evolution of molecular systems without resorting to a predefined potential energy surface. CPMD and hybrid molecular mechanics/CPMD schemes have recently enabled the calculation of redox properties of electron transfer proteins in their complex biological environment. They provided structural and spectroscopic information on novel platinum-based anticancer drugs that target DNA, also setting the basis for the construction of force fields for the metal lesion. Molecular mechanics/CPMD also lead to mechanistic hypotheses for a variety of metalloenzymes. Recent advances that increase the accuracy of DFT and the efficiency of investigating rare events are further expanding the domain of CPMD applications to biomolecules.

  17. Fluorescence applications in molecular neurobiology

    PubMed Central

    Taraska, Justin W.; Zagotta, William N.

    2012-01-01

    Summary Macromolecules drive the complex behavior of neurons. For example, channels and transporters control the movements of ions across membranes, SNAREs direct the fusion of vesicles at the synapse, and motors move cargo throughout the cell. Understanding the structure, assembly, and conformational movements of these and other neuronal proteins is essential to understanding the brain. Developments in fluorescence have allowed the architecture and dynamics of proteins to be studied in real time and in a cellular context with great accuracy. In this review, we cover classic and recent methods for studying protein structure, assembly, and dynamics with fluorescence. These methods include fluorescence and luminescence resonance energy transfer, single molecule bleaching analysis, intensity measurements, co-localization microscopy, electron transfer, and bi-molecular complementation analysis. We present the principles of these methods, highlight recent work that uses the methods, and discuss a framework for interpreting results as they apply to molecular neurobiology. PMID:20434995

  18. Biodiversity: molecular biological domains, symbiosis and kingdom origins

    NASA Technical Reports Server (NTRS)

    Margulis, L.

    1992-01-01

    The number of extant species of organisms is estimated to be from fewer than 3 to more than 30 x 10(6) (May, 1992). Molecular biology, comparative genetics and ultrastructural analyses provide new insights into evolutionary relationships between these species, including increasingly precise ideas of how species and higher taxa have evolved from common ancestors. Accumulation of random mutations and large macromolecular sequence change in all organisms since the Proterozoic Eon has been importantly supplemented by acquisition of inherited genomes ('symbiogenesis'). Karyotypic alterations (polyploidization and karyotypic fissioning) have been added to these other mechanisms of species origin in plants and animals during the Phanerozoic Eon. The new evolution concepts (coupled with current rapid rates of species extinction and ignorance of the extent of biodiversity) prompted this analysis of the field of systematic biology and its role in the reorganization of extant species into higher taxa. Two superkingdoms (= Domains: Prokaryotae and Eukaryotae) and five kingdoms (Monera = Procaryotae or Bacteria; Protoctista: algae, amoebae, ciliates, foraminifera, oomycetes, slime molds, etc.; Mychota: 'true' fungi; Plantae: one phylum (division) of bryophytes and nine phyla of tracheophytes; and Animalia) are recognized. Two subkingdoms comprise the monera: the great diverse lineages are Archaebacteria and Eubacteria. The criteria for classification using molecular, ultrastructural and genetic data for this scheme are mentioned. For the first time since the nineteenth century, logical, technical definitions for each group are given with their time of appearance as inferred from the fossil record in the primary scientific literature. This classification scheme, which most closely reflects the evolutionary history, molecular biology, genetics and ultrastructure of extant life, requires changes in social organization of biologists, many of whom as botanists and zoologists, still

  19. Biodiversity: molecular biological domains, symbiosis and kingdom origins.

    PubMed

    Margulis, L

    1992-01-01

    The number of extant species of organisms is estimated to be from fewer than 3 to more than 30 x 10(6) (May, 1992). Molecular biology, comparative genetics and ultrastructural analyses provide new insights into evolutionary relationships between these species, including increasingly precise ideas of how species and higher taxa have evolved from common ancestors. Accumulation of random mutations and large macromolecular sequence change in all organisms since the Proterozoic Eon has been importantly supplemented by acquisition of inherited genomes ('symbiogenesis'). Karyotypic alterations (polyploidization and karyotypic fissioning) have been added to these other mechanisms of species origin in plants and animals during the Phanerozoic Eon. The new evolution concepts (coupled with current rapid rates of species extinction and ignorance of the extent of biodiversity) prompted this analysis of the field of systematic biology and its role in the reorganization of extant species into higher taxa. Two superkingdoms (= Domains: Prokaryotae and Eukaryotae) and five kingdoms (Monera = Procaryotae or Bacteria; Protoctista: algae, amoebae, ciliates, foraminifera, oomycetes, slime molds, etc.; Mychota: 'true' fungi; Plantae: one phylum (division) of bryophytes and nine phyla of tracheophytes; and Animalia) are recognized. Two subkingdoms comprise the monera: the great diverse lineages are Archaebacteria and Eubacteria. The criteria for classification using molecular, ultrastructural and genetic data for this scheme are mentioned. For the first time since the nineteenth century, logical, technical definitions for each group are given with their time of appearance as inferred from the fossil record in the primary scientific literature. This classification scheme, which most closely reflects the evolutionary history, molecular biology, genetics and ultrastructure of extant life, requires changes in social organization of biologists, many of whom as botanists and zoologists, still

  20. Molecular Mechanisms of Biological Aging in Intervertebral Discs

    PubMed Central

    Vo, Nam V.; Hartman, Robert A.; Patil, Prashanti R.; Risbud, Makarand V.; Kletsas, Dimitris; Iatridis, James C.; Hoyland, Judith A.; Le Maitre, Christine L.; Sowa, Gwendolyn A.; Kang, James D.

    2016-01-01

    Advanced age is the greatest risk factor for the majority of human ailments, including spine-related chronic disability and back pain, which stem from age-associated intervertebral disc degeneration (IDD). Given the rapid global rise in the aging population, understanding the biology of intervertebral disc aging in order to develop effective therapeutic interventions to combat the adverse effects of aging on disc health is now imperative. Fortunately, recent advances in aging research have begun to shed light on the basic biological process of aging. Here we review some of these insights and organize the complex process of disc aging into three different phases to guide research efforts to understand the biology of disc aging. The objective of this review is to provide an overview of the current knowledge and the recent progress made to elucidate specific molecular mechanisms underlying disc aging. In particular, studies over the last few years have uncovered cellular senescence and genomic instability as important drivers of disc aging. Supporting evidence comes from DNA repair-deficient animal models that show increased disc cellular senescence and accelerated disc aging. Additionally, stress-induced senescent cells have now been well documented to secrete catabolic factors, which can negatively impact the physiology of neighboring cells and ECM. These along with other molecular drivers of aging are reviewed in depth to shed crucial insights into the underlying mechanisms of age-related disc degeneration. We also highlight molecular targets for novel therapies and emerging candidate therapeutics that may mitigate age-associated IDD. PMID:26890203

  1. Biodiversity: molecular biological domains, symbiosis and kingdom origins

    NASA Technical Reports Server (NTRS)

    Margulis, L.

    1992-01-01

    The number of extant species of organisms is estimated to be from fewer than 3 to more than 30 x 10(6) (May, 1992). Molecular biology, comparative genetics and ultrastructural analyses provide new insights into evolutionary relationships between these species, including increasingly precise ideas of how species and higher taxa have evolved from common ancestors. Accumulation of random mutations and large macromolecular sequence change in all organisms since the Proterozoic Eon has been importantly supplemented by acquisition of inherited genomes ('symbiogenesis'). Karyotypic alterations (polyploidization and karyotypic fissioning) have been added to these other mechanisms of species origin in plants and animals during the Phanerozoic Eon. The new evolution concepts (coupled with current rapid rates of species extinction and ignorance of the extent of biodiversity) prompted this analysis of the field of systematic biology and its role in the reorganization of extant species into higher taxa. Two superkingdoms (= Domains: Prokaryotae and Eukaryotae) and five kingdoms (Monera = Procaryotae or Bacteria; Protoctista: algae, amoebae, ciliates, foraminifera, oomycetes, slime molds, etc.; Mychota: 'true' fungi; Plantae: one phylum (division) of bryophytes and nine phyla of tracheophytes; and Animalia) are recognized. Two subkingdoms comprise the monera: the great diverse lineages are Archaebacteria and Eubacteria. The criteria for classification using molecular, ultrastructural and genetic data for this scheme are mentioned. For the first time since the nineteenth century, logical, technical definitions for each group are given with their time of appearance as inferred from the fossil record in the primary scientific literature. This classification scheme, which most closely reflects the evolutionary history, molecular biology, genetics and ultrastructure of extant life, requires changes in social organization of biologists, many of whom as botanists and zoologists, still

  2. Biological effects of high molecular weight lignin derivatives.

    PubMed

    Pessala, Piia; Schultz, Eija; Kukkola, Jukka; Nakari, Tarja; Knuutinen, Juha; Herve, Sirpa; Paasivirta, Jaakko

    2010-10-01

    A number of high molecular weight (HMW) lignin derivatives possessing varied chemical properties were screened for their biological effects in order to obtain more information on the possible structural features of HMW lignin-related effects. The studied compounds were both commercial and in-house extracted lignin derivatives. Bioassays used include reverse electron transport (RET), Vibrio fischeri, Daphnia magna, and juvenile rainbow trout (Oncorhynchus mykiss) hepatocytes. The studied lignin derivatives inhibited the in vitro systems and luminescence of V. fischeri bacteria to some extent-daphnids were not affected. It seems that, at least in the RET assay, certain pH-dependent functional groups in lignin may be of importance regarding the biological effects.

  3. Diagnosis of Whipple's disease using molecular biology techniques.

    PubMed

    Cosme, Ángel; Ojeda, Evelia; Muñagorri, Ana I; Gaminde, Eduardo; Bujanda, Luis; Larzabal, Mikel; Gil, Inés

    2011-04-01

    The diagnosis of Whipple's disease (WD) is based on the existence of clinical signs and symptoms compatible with the disease and in the presence of PAS-positive diastase-resistant granules in the macrophages of the small intestine. If there is suspicion of the disease but no histological findings or only isolated extraintestinal manifestations, species-specific PCR using different sequences of the T. whippleii genome from different tissue types and biological fluids is recommended.This study reports two cases: the first patient had diarrhea and the disease was suspected after an endoscopic examination of the ileum, while the second patient had multi-systemic manifestations,particularly abdominal, thoracic, and peripheral lymphadenopathies. In both cases, the diagnosis was confirmed using molecular biology techniques to samples from the small intestine or from a retroperineal lymph node, respectively.

  4. Emerging diagnostic and therapeutic molecular imaging applications in vascular disease

    PubMed Central

    Eraso, Luis H; Reilly, Muredach P; Sehgal, Chandra; Mohler, Emile R

    2013-01-01

    Assessment of vascular disease has evolved from mere indirect and direct measurements of luminal stenosis to sophisticated imaging methods to depict millimeter structural changes of the vasculature. In the near future, the emergence of multimodal molecular imaging strategies may enable robust therapeutic and diagnostic (‘theragnostic’) approaches to vascular diseases that comprehensively consider structural, functional, biological and genomic characteristics of the disease in individualized risk assessment, early diagnosis and delivery of targeted interventions. This review presents a summary of recent preclinical and clinical developments in molecular imaging and theragnostic applications covering diverse atherosclerosis events such as endothelial activation, macrophage infammatory activity, plaque neovascularization and arterial thrombosis. The main focus is on molecular targets designed for imaging platforms commonly used in clinical medicine including magnetic resonance, computed tomography and positron emission tomography. A special emphasis is given to vascular ultrasound applications, considering the important role this imaging platform plays in the clinical and research practice of the vascular medicine specialty. PMID:21310769

  5. Teaching cell and molecular biology for gender equity.

    PubMed

    Sible, Jill C; Wilhelm, Dayna E; Lederman, Muriel

    2006-01-01

    Science, technology, engineering, and math (STEM) fields, including cell biology, are characterized by the "leaky pipeline" syndrome in which, over time, women leave the discipline. The pipeline itself and the pond into which it empties may not be neutral. Explicating invisible norms, attitudes, and practices by integrating social studies of science into science education may be the necessary first step in helping female students persist in STEM disciplines. In 2003 and 2004, a sophomore Cell and Molecular Biology course at Virginia Tech (Blacksburg, VA) was taught integrating social studies of science with standard material. The course was successfully implemented, teaching students factual content while increasing awareness of the cultures of science and their self-confidence in engaging with the subject. Course evaluation data indicated that females in particular perceived greater gains in logical thinking and problem-solving abilities than females in a traditional cell biology course. Consistent with K-12 studies, males in this class were likely to view scientists as male only, whereas females viewed scientists as male and female. This pilot project demonstrates that social studies can be integrated successfully in a cell biology course. Longitudinal studies of this cohort of students will indicate whether this approach contributes to the retention of women in the field.

  6. Biologic Therapy and Novel Molecular Targets of Severe Asthma.

    PubMed

    Pepper, Amber N; Renz, Harald; Casale, Thomas B; Garn, Holger

    Treatment options for severe or uncontrolled asthma are increasing, especially pertaining to novel biologic therapies. The 2 primary asthma endotypes, T2 high and T2 low, are defined by the level of type 2 T helper and innate lymphoid cell activity and mediators. Most therapies for severe asthma target T2 high asthma, including the 3 biologics approved for use in the United States and Europe: omalizumb, mepolizumb, and reslizumab. Other biologics, with various molecular targets, are under investigation. Unfortunately, treatment options for T2 low asthma are limited. Although these therapies may improve asthma symptoms, exacerbation rates, and lung function parameters, they have not been shown to modify the disease process or provide lasting benefits after discontinuation. Biomarkers identified thus far to help guide individualized therapy in severe asthma are helpful, but imperfect discriminators for picking the best option for individual patients. This review will discuss the mechanisms of action, indications, and therapeutic effects of currently available and emerging biologics for the treatment of severe or uncontrolled asthma. Copyright © 2017 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  7. Teaching Cell and Molecular Biology for Gender Equity

    PubMed Central

    Wilhelm, Dayna E.; Lederman, Muriel

    2006-01-01

    Science, technology, engineering, and math (STEM) fields, including cell biology, are characterized by the “leaky pipeline” syndrome in which, over time, women leave the discipline. The pipeline itself and the pond into which it empties may not be neutral. Explicating invisible norms, attitudes, and practices by integrating social studies of science into science education may be the necessary first step in helping female students persist in STEM disciplines. In 2003 and 2004, a sophomore Cell and Molecular Biology course at Virginia Tech (Blacksburg, VA) was taught integrating social studies of science with standard material. The course was successfully implemented, teaching students factual content while increasing awareness of the cultures of science and their self-confidence in engaging with the subject. Course evaluation data indicated that females in particular perceived greater gains in logical thinking and problem-solving abilities than females in a traditional cell biology course. Consistent with K–12 studies, males in this class were likely to view scientists as male only, whereas females viewed scientists as male and female. This pilot project demonstrates that social studies can be integrated successfully in a cell biology course. Longitudinal studies of this cohort of students will indicate whether this approach contributes to the retention of women in the field. PMID:17012214

  8. Electrophoretic gel image analysis software for the molecular biology laboratory.

    PubMed

    Redman, T; Jacobs, T

    1991-06-01

    We present GelReader 1.0, a microcomputer program designed to make precision, digital analysis of one-dimensional electrophoretic gels accessible to the molecular biology laboratory of modest means. Images of electrophoretic gels are digitized via a desktop flatbed scanner from instant photographs, autoradiograms or chromogenically stained blotting media. GelReader is then invoked to locate lanes and bands and generate a report of molecular weights of unknowns, based on specified sets of standards. Frequently used standards can be stored in the program. Lanes and bands can be added or removed, based upon users' subjective preferences. A unique lane histogram feature facilitates precise manual addition of bands missed by the software. Image enhancement features include palette manipulation, histogram equalization, shadowing and magnification. The user interface strikes a balance between program autonomy and user intervention, in recognition of the variability in electrophoretic gel quality and users' analytical needs.

  9. The human glucocorticoid receptor: molecular basis of biologic function.

    PubMed

    Nicolaides, Nicolas C; Galata, Zoi; Kino, Tomoshige; Chrousos, George P; Charmandari, Evangelia

    2010-01-01

    The characterization of the subfamily of steroid hormone receptors has enhanced our understanding of how a set of hormonally derived lipophilic ligands controls cellular and molecular functions to influence development and help achieve homeostasis. The glucocorticoid receptor (GR), the first member of this subfamily, is a ubiquitously expressed intracellular protein, which functions as a ligand-dependent transcription factor that regulates the expression of glucocorticoid-responsive genes. The effector domains of the GR mediate transcriptional activation by recruiting coregulatory multi-subunit complexes that remodel chromatin, target initiation sites, and stabilize the RNA-polymerase II machinery for repeated rounds of transcription of target genes. This review summarizes the basic aspects of the structure and actions of the human (h) GR, and the molecular basis of its biologic functions.

  10. Molecular Requirements for the Biological Activity of Ethylene 1

    PubMed Central

    Burg, Stanley P.; Burg, Ellen A.

    1967-01-01

    The molecular requirements for ethylene action were investigated using the pea straight growth test. Biological activity requires an unsaturated bond adjacent to a terminal carbon atom, is inversely related to molecular size, and is decreased by substitutions which lower the electron density in the unsaturated position. Evidence is presented that ethylene binds to a metal containing receptor site. CO2 is a competitive inhibitor of ethylene action, and prevents high concentrations of auxin (which stimulate ethylene formation) from retarding the elongation of etiolated pea stem sections. It is suggested that CO2 delays fruit ripening by displacing the ripening hormone, ethylene, from its receptor site. Binding of ethylene to the receptor site is also impeded when the O2 concentration is lowered, and this may explain why fruit ripening is delayed at low O2 tensions. PMID:16656478

  11. The Human Glucocorticoid Receptor: Molecular Basis of Biologic Function

    PubMed Central

    Nicolaides, Nicolas C.; Galata, Zoi; Kino, Tomoshige; Chrousos, George P.; Charmandari, Evangelia

    2009-01-01

    The characterization of the subfamily of steroid hormone receptors has enhanced our understanding of how a set of hormonally derived lipophilic ligands controls cellular and molecular functions to influence development and help achieve homeostasis. The glucocorticopid receptor (GR), the first member of this subfamily, is a ubiquitously expressed intracellular protein, which functions as a ligand-dependent transcription factor that regulates the expression of glucocorticoid-responsive genes. The effector domains of the GR mediate transcriptional activation by recruiting coregulatory multi-subunit complexes that remodel chromatin, target initiation sites, and stabilize the RNA polymerase II machinery for repeated rounds of transcription of target genes. This review summarizes the basic aspects of the structure and of the human (h) GR, and the molecular basis of its biologic function. PMID:19818358

  12. Molecular genetics of glioblastomas: defining subtypes and understanding the biology.

    PubMed

    Renault, Ilana Zalcberg; Golgher, Denise

    2015-02-01

    Despite comprehensive therapy, which includes surgery, radiotherapy, and chemotherapy, the prognosis of glioblastoma multiforme is very poor. Diagnosed individuals present an average of 12 to 18 months of life. This article provides an overview of the molecular genetics of these tumors. Despite the overwhelming amount of data available, so far little has been translated into real benefits for the patient. Because this is such a complex topic, the goal is to point out the main alterations in the biological pathways that lead to tumor formation, and how this can contribute to the development of better therapies and clinical care.

  13. Molecular biology, epidemiology, and the elusive nature of pancreatitis.

    PubMed

    Tenner, Scott

    2015-03-05

    The myriad of presentations of pancreatitis can cause confusion and controversy among clinicians affecting the diagnosis, treatment, and research of patients with these disorders. Although the disease is best thought of as a spectrum with classic presentations, the underlying pathophysiologic reasons for the differences in manifestations remains unknown. In this issue of the Journal, LaRusch and colleagues provide an elegant study combining epidemiology and molecular biology to explain why some patients with pancreatitis develop fibrosis chronic pancreatitis. The implications of the findings add to the growing request to support large multidisciplinary, combined genetic, and epidemiologic studies in pancreatic disease.

  14. Mutants of Arabidopsis as tools for physiology and molecular biology

    SciTech Connect

    Somerville, C.R.; Artus, N.; Browse, J.; Caspar, T.; Estelle, M.; Haughn, G.; Kunst, L.; Martinez, J.; McCourt, P.; Moffatt, B.

    1986-04-01

    The authors discuss the importance of developing a facile system for genetic analysis in higher plants which can be used to approach problems specific to plant biology in much the same way that molecular genetic approaches have been used in other classes of organisms such as yeast and Drosophila. Toward this end, they have developed methods for the isolation and analysis of mutants of Arabidopsis with specific alterations in photosynthesis, photorespiration, starch metabolism, lipid metabolism, purine metabolism, amino acid metabolism and phytohormone responses. The utility of this collection of mutants for studying problems in physiology and biochemistry is illustrated with selected examples.

  15. Dictionary of microbiology and molecular biology. 2nd ed

    SciTech Connect

    Singleton, P.; Sainsbury, D.

    1988-01-01

    A newly revised edition of the standard reference for microbiology and molecular biology. Includes a multitude of new terms and designations which, although widely used in the literature, are seldom defined outside the book or paper in which they first appeared. Also accounts for the changes in the meanings of older terms brought about by advances in knowledge. Definition of all terms reflects their actual usage in current journals and texts, and also given (where appropriate) are former meanings, alternative meanings, and synonyms. Includes terms from such fields as mycology, protozoology, virology, etc.

  16. A complex systems approach to computational molecular biology

    SciTech Connect

    Lapedes, A. |

    1993-09-01

    We report on the containing research program at Santa Fe Institute that applies complex systems methodology to computational molecular biology. Two aspects are stressed here are the use of co-evolving adaptive neutral networks for determining predictable protein structure classifications, and the use of information theory to elucidate protein structure and function. A ``snapshot`` of the current state of research in these two topics is presented, representing the present state of two major research thrusts in the program of Genetic Data and Sequence Analysis at the Santa Fe Institute.

  17. How restriction enzymes became the workhorses of molecular biology

    PubMed Central

    Roberts, Richard J.

    2005-01-01

    Restriction enzymes have proved to be invaluable for the physical mapping of DNA. They offer unparalleled opportunities for diagnosing DNA sequence content and are used in fields as disparate as criminal forensics and basic research. In fact, without restriction enzymes, the biotechnology industry would certainly not have flourished as it has. The first experiments demonstrating the utility of restriction enzymes were carried out by Danna and Nathans and reported in 1971. This pioneering study set the stage for the modern practice of molecular biology in which restriction enzymes are ubiquitous tools, although they are often taken for granted. PMID:15840723

  18. Stress and breast cancer: from epidemiology to molecular biology

    PubMed Central

    2011-01-01

    Stress exposure has been proposed to contribute to the etiology of breast cancer. However, the validity of this assertion and the possible mechanisms involved are not well established. Epidemiologic studies differ in their assessment of the relative contribution of stress to breast cancer risk, while physiological studies propose a clear connection but lack the knowledge of intracellular pathways involved. The present review aims to consolidate the findings from different fields of research (including epidemiology, physiology, and molecular biology) in order to present a comprehensive picture of what we know to date about the role of stress in breast cancer development. PMID:21575279

  19. Progress in nucleic acid research and molecular biology

    SciTech Connect

    Cohn, W.E.; Moldave, K.

    1988-01-01

    Complementary Use of Chemical Modification and Site-Directed Mutagenesis to Probe Structure-Activity Relationships in Enzymes. Mechanisms of the Antiviral Action of Inteferons. Modulation of Cellular Genes by Oncogenes. DNA Damage Produced by Ionizing Radiation in Mammalian Cells: Identities, Mechanisms of Formation, and Reparability. Human Ferritin Gene Expression. Molecular Biology of the Insulin Receptor. Cap-Binding Proteins of Eukaryotic Messenger RNA: Functions in Initiation and Control of Translation. Physical Monitoring of Meiotic and Mitotic Recombination in Yeast. Early Signals Underlying the Induction of the c-fos and c-myc Genes in Quiescent Fibroblasts: Studies with Bombesin and Other Growth Factors. Each chapter includes references.

  20. Building bridges between cellular and molecular structural biology.

    PubMed

    Patwardhan, Ardan; Brandt, Robert; Butcher, Sarah J; Collinson, Lucy; Gault, David; Grünewald, Kay; Hecksel, Corey; Huiskonen, Juha T; Iudin, Andrii; Jones, Martin L; Korir, Paul K; Koster, Abraham J; Lagerstedt, Ingvar; Lawson, Catherine L; Mastronarde, David; McCormick, Matthew; Parkinson, Helen; Rosenthal, Peter B; Saalfeld, Stephan; Saibil, Helen R; Sarntivijai, Sirarat; Solanes Valero, Irene; Subramaniam, Sriram; Swedlow, Jason R; Tudose, Ilinca; Winn, Martyn; Kleywegt, Gerard J

    2017-07-06

    The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

  1. Possibility of Microchip Electrophoresis for Biological Application

    NASA Astrophysics Data System (ADS)

    Kataoka, Masatoshi; Kido, Jun-Ichi; Shinohara, Yasuo

    Microchip electrophoresis has recently attracted much attention in the field of nuclear acid analysis due to its high efficiency, ease of operation, low consumption of samples and reagents, and relatively low costs. Nucleic acid fragments are separated by capillary electrophoresis in a chip with microfabricated channels, with automated detection as well as on-line data evaluation. Microfabricated devices are forecast to be fundamental to the postgenome era, especially in the field of genetics and medicine. However, although there are many reports of the use of these instruments to evaluate standard DNA, DNA ladders, PCR products, and commercially available plasmid digests, little information is available their use with biological material. In this report, we showed the accuracy of sizing and quantification of endonuclease-digested plasmid DNA. We also showed the feasibility of on-microchip endonuclease treatment of plasmid DNA and sequential analysis as an additional application for DNA analysis. Furthermore, to evaluate the possibility of microchip electrophoresis for biological application, the results of the examination of blood sugar in human plasma and mitochondrial membrane potential were shown.

  2. Conducting polymer nanostructures for biological applications

    NASA Astrophysics Data System (ADS)

    Berdichevsky, Yevgeny

    A novel polypyrrole nanowire actuator was fabricated and characterized, representing a completely new approach to the design of nanoscale mechanically active components (nanomachines). This design paradigm takes advantage of the fact that unique properties of polypyrrole allow development of mechanically active nanostructures capable of operating in aqueous salt solutions with many potential applications biology and medicine. Template synthesis technique was used to electropolymerize polypyrrole nanowires in the nanoporous alumina templates. Commercial alumina filters were used both "as is" and patterned with microbeads to reduce the open pore density, along with anodized alumina prepared as a thin film on a semiconductor substrate. The ability of the nanowires to expand and contract with applied voltage was then evaluated with scanning electron microscopy and high-resolution optical microscopy. It was confirmed that the nanowires can function as nanoactuators, which is a significant advance in developing nanomechanical structures. Polypyrrole nanoactuators are electrically controlled, rather than relying on changing the chemical composition of solution, can be easily synthesized in parallel and in high numbers without requiring e-beam lithography, and can operate in aqueous salt solutions at biologically-relevant pH. Furthermore, the speed of polypyrrole actuators depends on their size due to diffusion limitations, and nanoactuators are therefore able to operate at higher speeds that micro- or macro-sized devices. The development of these nanoactuators paves the way for mimicking the function of biological actuators such as cilia, creation of controllable membranes, small particle manipulation, cellular nanomechanical probes, and many other biomedical applications. Furthermore, the same technology and process flow used for fabrication of nanoactuators was also used to create nanosensors for detection of electrochemically oxidizable neurotransmitters such as

  3. [Molecular biology of biological clock--genetic regulation of circadian rhythm and sleep].

    PubMed

    Kume, Kazuhiko

    2006-07-01

    Circadian rhythm is a universal biological property functioning in most living species on the earth from bacteria and plants to animals. The molecular mechanisms creating this rhythm have recently been elucidated and the transcriptional feedback loop regulation of 'clock genes' is regarded as essential for all species studied so far. Both mammals and insects share the similar clock genes, which highlights the long conservation of circadian rhythm at the genetic level. Sleep and arousal cycles in mammals are known to be regulated by both homeostatic and circadian processes, but the genetic machinery for sleep regulation is still unclear. Recently, it has been reported that insects also have sleep-like behavior, and we showed that insects use dopamine as a regulator of their sleep/arousal cycling, which strongly suggests the similarity of arousal regulation between insects and mammals at the molecular level. In this review, these recent advancements of the molecular understanding of circadian rhythm and sleep/arousal regulation are outlined.

  4. In vitro biological evaluation of high molecular weight hyperbranched polyglycerols.

    PubMed

    Kainthan, Rajesh Kumar; Hester, Samuel R; Levin, Elena; Devine, Dana V; Brooks, Donald Elliott

    2007-11-01

    Low molecular weight hyperbranched polyglycerols are highly water soluble and biocompatible polyether polyols, which can be synthesized in a controlled manner with narrow polydispersity. Recently we reported the synthesis and characterization of very high molecular weight (Mn up to 700,000) and narrowly polydispersed polyglycerols which could be potentially used as alternatives to high generation dendrimers which are difficult to make. A detailed biocompatibility testing of these polymers conducted in vitro is reported here. The in vitro studies include hemocompatibility testing for effects on coagulation (prothrombin time (PT), activated partial thromboplastin time (APTT), plasma recalcification time (PRT), thrombelastograph parameters (TEG)), complement activation, platelet activation, red blood cell aggregation and cytotoxicity. Results from these studies show that these high molecular weight polyglycerols are highly biocompatible and are potential candidates for various applications in nanobiotechnology and in nanomedicine. Moreover these polymers are thermally and oxidatively stable.

  5. Applications of Chitin and Its Derivatives in Biological Medicine

    PubMed Central

    Park, Bae Keun; Kim, Moon-Moo

    2010-01-01

    Chitin and its derivatives—as a potential resource as well as multiple functional substrates—have generated attractive interest in various fields such as biomedical, pharmaceutical, food and environmental industries, since the first isolation of chitin in 1811. Moreover, chitosan and its chitooligosaccharides (COS) are degraded products of chitin through enzymatic and acidic hydrolysis processes; and COS, in particular, is well suited for potential biological application, due to the biocompatibility and nontoxic nature of chitosan. In this review, we investigate the current bioactivities of chitin derivatives, which are all correlated with their biomedical properties. Several new and cutting edge insights here may provide a molecular basis for the mechanism of chitin, and hence may aid its use for medical and pharmaceutical applications. PMID:21614199

  6. G-Quadruplexes: Prediction, Characterization, and Biological Application.

    PubMed

    Kwok, Chun Kit; Merrick, Catherine J

    2017-10-01

    Guanine (G)-rich sequences in nucleic acids can assemble into G-quadruplex structures that involve G-quartets linked by loop nucleotides. The structural and topological diversity of G-quadruplexes have attracted great attention for decades. Recent methodological advances have advanced the identification and characterization of G-quadruplexes in vivo as well as in vitro, and at a much higher resolution and throughput, which has greatly expanded our current understanding of G-quadruplex structure and function. Accumulating knowledge about the structural properties of G-quadruplexes has helped to design and develop a repertoire of molecular and chemical tools for biological applications. This review highlights how these exciting methods and findings have opened new doors to investigate the potential functions and applications of G-quadruplexes in basic and applied biosciences. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. [Molecular and cellular biological analysis on cancer cachexia syndrome].

    PubMed

    Mukaiyama, T

    2001-07-01

    About half of patients with cancer will suffer from wasting syndrome, called cancer cachexia, which shows abnormality of homeostasis, nutrition, endocrine function, metabolism, immunity et al. This syndrome is characterized with anorexia and weight loss caused by degradation of skeletal muscle and adipose tissue. Progressive weight loss is responsible not only for a poor quality of life and poor response to anti-cancer drug, but also shorter survival time comparing patient without weight loss. Various factors have been found as mediators of this syndrome base on the development of immunology, biochemistry and molecular and cellular biology. These include several cytokines, proteolysis-inducing factor (PIF), lipid-mobilizing factor (LMF), apoptosis-inducing factor and another factors. Recentry, molecular biological analysis makes clear more detail mechanisms of cancer cachexia syndrome, for example, ubiqutin/proteasome pathway, activation of nuclear transcriptional factors and others. These progresses will contribute not only to establish new treatment but also to carry out "order-made palliative oncology" using DNA-chip and/or Protein-chip in near future.

  8. The role of molecular biology in veterinary parasitology.

    PubMed

    Prichard, R; Tait, A

    2001-07-12

    The tools of molecular biology are increasingly relevant to veterinary parasitology. The sequencing of the complete genomes of Caenorhabditis elegans and other helminths and protozoa is allowing great advances in studying the biology, and improving diagnosis and control of parasites. Unique DNA sequences provide very high levels of specificity for the diagnosis and identification of parasite species and strains, and PCR allows extremely high levels of sensitivity. New techniques, such as the use of uniquely designed molecular beacons and DNA microarrays will eventually allow rapid screening for specific parasite genotypes and assist in diagnostic and epidemiological studies of veterinary parasites. The ability to use genome data to clone and sequence genes which when expressed will provide antigens for vaccine screening and receptors and enzymes for mechanism-based chemotherapy screening will increase our options for parasite control. In addition, DNA vaccines can have desirable characteristics, such as sustained stimulation of the host immune system compared with protein based vaccines. One of the greatest threats to parasite control has been the development of drug resistance in parasites. Our knowledge of the basis of drug resistance and our ability to monitor its development with highly sensitive and specific DNA-based assays for 'resistance'-alleles will help maintain the effectiveness of existing antiparasitic drugs and provide hope that we can maintain control of parasitic disease outbreaks.

  9. [Clinical, morphological and molecular biological characteristics of the aging eye].

    PubMed

    Böhm, M R R; Thomasen, H; Parnitzke, F; Steuhl, K-P

    2017-02-01

    The physiological aging of the eye is associated with loss of visual function. Age-related changes of the eye can result in ophthalmological diseases. The aim of this article is to display morphological, histological and molecular biological alterations of the aging eye. A web-based search and review of the literature for aging of the visual system including cornea, lens, vitreous humor, retina, retinal pigment epithelium (RPE), choroidea and optic nerve were carried out. The most important results related to morphological, histological and molecular biological changes are summarized. Age-related, morphological alterations can be found in preretinal structures, e. g. cornea, lens and vitreous humor, as well as neuronal structures, such as the retina. In addition to negligible clinical signs of the aging eye, there are clinically relevant changes which can develop into pathological ophthalmological diseases. These transitions from age-related alterations to relevant ophthalmological diseases, e. g. age-related macular degeneration and glaucoma are continuous. An understanding of aging could provide predictive factors to detect the conversion of physiological aging into pathological conditions. The derivation of physiological markers or new approaches to detection and treatment of disease-related entities associated with the risk factor aging are desirable. Translational approaches in clinical and basic science are necessary to provide new therapeutic options for relevant ophthalmological diseases in the future.

  10. Ependymomas of the adult: molecular biology and treatment.

    PubMed

    Rudà, Roberta; Gilbert, Mark; Soffietti, Riccardo

    2008-12-01

    To review state of art and relevant advances in the molecular biology and management of ependymomas of the adult. Ependymomas of the adult are uncommon neoplasms of the central nervous system, and may occur either in the brain or the spinal cord. Compared with intracranial ependymomas, spinal ependymomas are less frequent and exhibit a better prognosis. Studies performed on genetic changes in ependymoma provide some insight into the pathogenesis and prognostic markers and yield new therapeutic targets, particularly focused on signal transduction modulators. The majority of studies have shown a major impact of extent of resection; thus, a complete resection must be performed, whenever possible, at first surgery or at reoperation. Involved field radiotherapy is recommended for anaplastic or incompletely resected grade II tumors. Craniospinal irradiation is reserved for metastatic disease. Chemotherapy is not advocated as primary treatment, and is best utilized as salvage treatment for patients failing surgery and radiotherapy. Owing to the rarity of the disease, the literature regarding ependymomas in adults is scarce and limited to retrospective series. Thus, the level of evidence regarding therapeutic strategies is low and universally accepted guidelines are lacking. Molecular biology studies suggest some potential new therapeutic targets.

  11. Errant life, molecular biology, and biopower: Canguilhem, Jacob, and Foucault.

    PubMed

    Talcott, Samuel

    2014-01-01

    This paper considers the theoretical circumstances that urged Michel Foucault to analyse modern societies in terms of biopower. Georges Canguilhem's account of the relations between science and the living forms an essential starting point for Foucault's own later explorations, though the challenges posed by the molecular revolution in biology and François Jacob's history of it allowed Foucault to extend and transform Canguilhem's philosophy of error. Using archival research into his 1955-1956 course on "Science and Error," I show that, for Canguilhem, it is inauthentic to treat a living being as an error, even if living things are capable of making errors in the domain of knowledge. The emergent molecular biology in the 1960s posed a grave challenge, however, since it suggested that individuals could indeed be errors of genetic reproduction. The paper discusses how Canguilhem and Foucault each responded to this by examining, among other texts, their respective reviews of Jacob's The Logic of the Living. For Canguilhem this was an opportunity to reaffirm the creativity of life in the living individual, which is not a thing to be evaluated, but the source of values. For Foucault, drawing on Jacob's work, this was the opportunity to develop a transformed account of valuation by posing biopower as the DNA of society. Despite their disagreements, the paper examines these three authors as different iterations of a historical epistemology attuned to errancy, error, and experimentation.

  12. The emerging molecular biology toolbox for the study of long noncoding RNA biology.

    PubMed

    Fok, Ezio T; Scholefield, Janine; Fanucchi, Stephanie; Mhlanga, Musa M

    2017-10-01

    Long noncoding RNAs (lncRNAs) have been implicated in many biological processes. However, due to the unique nature of lncRNAs and the consequential difficulties associated with their characterization, there is a growing disparity between the rate at which lncRNAs are being discovered and the assignment of biological function to these transcripts. Here we present a molecular biology toolbox equipped to help dissect aspects of lncRNA biology and reveal functionality. We outline an approach that begins with a broad survey of genome-wide, high-throughput datasets to identify potential lncRNA candidates and then narrow the focus on specific methods that are well suited to interrogate the transcripts of interest more closely. This involves the use of imaging-based strategies to validate these candidates and observe the behaviors of these transcripts at single molecule resolution in individual cells. We also describe the use of gene editing tools and interactome capture techniques to interrogate functionality and infer mechanism, respectively. With the emergence of lncRNAs as important molecules in healthy and diseased cellular function, it remains crucial to deepen our understanding of their biology.

  13. Fluorescence applications in molecular neurobiology.

    PubMed

    Taraska, Justin W; Zagotta, William N

    2010-04-29

    Macromolecules drive the complex behavior of neurons. For example, channels and transporters control the movements of ions across membranes, SNAREs direct the fusion of vesicles at the synapse, and motors move cargo throughout the cell. Understanding the structure, assembly, and conformational movements of these and other neuronal proteins is essential to understanding the brain. Developments in fluorescence have allowed the architecture and dynamics of proteins to be studied in real time and in a cellular context with great accuracy. In this review, we cover classic and recent methods for studying protein structure, assembly, and dynamics with fluorescence. These methods include fluorescence and luminescence resonance energy transfer, single-molecule bleaching analysis, intensity measurements, colocalization microscopy, electron transfer, and bimolecular complementation analysis. We present the principles of these methods, highlight recent work that uses the methods, and discuss a framework for interpreting results as they apply to molecular neurobiology.

  14. The biochemistry and molecular biology of xenobiotic polymer degradation by microorganisms.

    PubMed

    Kawai, Fusako

    2010-01-01

    Research on microbial degradation of xenobiotic polymers has been underway for more than 40 years. It has exploited a new field not only in applied microbiology but also in environmental microbiology, and has greatly contributed to polymer science by initiating the design of biodegradable polymers. Owing to the development of analytical tools and technology, molecular biological and biochemical advances have made it possible to prospect for degrading microorganisms in the environment and to determine the mechanisms involved in biodegradation when xenobiotic polymers are introduced into the environment and are exposed to microbial attack. In this review, the molecular biological and biochemical aspects of the microbial degradation of xenobiotic polymers are summarized, and possible applications of potent microorganisms, enzymes, and genes in environmental biotechnology are suggested.

  15. Biological Application of Synchrotron Radiation: from Artem Alikhanyan to Nowadays

    NASA Astrophysics Data System (ADS)

    Vazina, A. A.

    Considerable progress in the development of structural biology me-thods has been achieved recently due to the use of synchrotron radiation. The purpose of this leaflet is to display a dual aspect of the field of biological and medical application of synchrotron radiation: first, some basic programs of structural biology, and second, programs aimed at medical applications.

  16. 3D printed microfluidics for biological applications.

    PubMed

    Ho, Chee Meng Benjamin; Ng, Sum Huan; Li, King Ho Holden; Yoon, Yong-Jin

    2015-01-01

    The term "Lab-on-a-Chip," is synonymous with describing microfluidic devices with biomedical applications. Even though microfluidics have been developing rapidly over the past decade, the uptake rate in biological research has been slow. This could be due to the tedious process of fabricating a chip and the absence of a "killer application" that would outperform existing traditional methods. In recent years, three dimensional (3D) printing has been drawing much interest from the research community. It has the ability to make complex structures with high resolution. Moreover, the fast building time and ease of learning has simplified the fabrication process of microfluidic devices to a single step. This could possibly aid the field of microfluidics in finding its "killer application" that will lead to its acceptance by researchers, especially in the biomedical field. In this paper, a review is carried out of how 3D printing helps to improve the fabrication of microfluidic devices, the 3D printing technologies currently used for fabrication and the future of 3D printing in the field of microfluidics.

  17. Holism and life manifestations: molecular and space-time biology.

    PubMed

    Krecek, J

    2010-01-01

    Appeals of philosophers to look for new concepts in sciences are being met with a weak response. Limited attention is paid to the relation between synthetic and analytic approach in solving problems of biology. An attempt is presented to open a discussion on a possible role of holism. The term "life manifestations" is used in accordance with phenomenology. Multicellular creatures maintain milieu intérieur to keep an aqueous milieu intracellulair in order to transform the energy of nutrients into the form utilizable for driving cellular life manifestations. Milieu intérieur enables to integrate this kind of manifestations into life manifestations of the whole multicellular creatures. The integration depends on a uniqueness and uniformity of the genome of cells, on their mutual recognition and adherence. The processes of ontogenetic development represent the natural mode of integration of cellular life manifestations. Functional systems of multicellular creatures are being established by organization of integrable cells using a wide range of developmental processes. Starting from the zygote division the new being displays all properties of a whole creature, although its life manifestations vary. Therefore, the whole organism is not only more than its parts, as supposed by holism, but also more than developmental stages of its life manifestations. Implicitly, the units of whole multicellular creature are rather molecular and developmental events than the cells per se. Holism, taking in mind the existence of molecular and space-time biology, could become a guide in looking for a new mode of the combination of analytical and synthetic reasoning in biology.

  18. Transmission electron microscopy in molecular structural biology: A historical survey.

    PubMed

    Harris, J Robin

    2015-09-01

    In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented.

  19. Embryonic stem cell biology: insights from molecular imaging.

    PubMed

    Sallam, Karim; Wu, Joseph C

    2010-01-01

    Embryonic stem (ES) cells have therapeutic potential in disorders of cellular loss such as myocardial infarction, type I diabetes and neurodegenerative disorders. ES cell biology in living subjects was largely poorly understood until incorporation of molecular imaging into the field. Reporter gene imaging works by integrating a reporter gene into ES cells and using a reporter probe to induce a signal detectable by normal imaging modalities. Reporter gene imaging allows for longitudinal tracking of ES cells within the same host for a prolonged period of time. This has advantages over postmortem immunohistochemistry and traditional imaging modalities. The advantages include expression of reporter gene is limited to viable cells, expression is conserved between generations of dividing cells, and expression can be linked to a specific population of cells. These advantages were especially useful in studying a dynamic cell population such as ES cells and proved useful in elucidating the biology of ES cells. Reporter gene imaging identified poor integration of differentiated ES cells transplanted into host tissue as well as delayed donor cell death as reasons for poor long-term survival in vivo. This imaging technology also confirmed that ES cells indeed have immunogenic properties that factor into cell survival and differentiation. Finally, reporter gene imaging improved our understanding of the neoplastic risk of undifferentiated ES cells in forming teratomas. Despite such advances, much remains to be understood about ES cell biology to translate this technology to the bedside, and reporter gene imaging will certainly play a key role in formulating this understanding.

  20. Black Molecular Adsorber Coatings for Spaceflight Applications

    NASA Technical Reports Server (NTRS)

    Abraham, Nithin Susan; Hasegawa, Mark Makoto; Straka, Sharon A.

    2014-01-01

    The molecular adsorber coating is a new technology that was developed to mitigate the risk of on-orbit molecular contamination on spaceflight missions. The application of this coating would be ideal near highly sensitive, interior surfaces and instruments that are negatively impacted by outgassed molecules from materials, such as plastics, adhesives, lubricants, epoxies, and other similar compounds. This current, sprayable paint technology is comprised of inorganic white materials made from highly porous zeolite. In addition to good adhesion performance, thermal stability, and adsorptive capability, the molecular adsorber coating offers favorable thermal control characteristics. However, low reflectivity properties, which are typically offered by black thermal control coatings, are desired for some spaceflight applications. For example, black coatings are used on interior surfaces, in particular, on instrument baffles for optical stray light control. Similarly, they are also used within light paths between optical systems, such as telescopes, to absorb light. Recent efforts have been made to transform the white molecular adsorber coating into a black coating with similar adsorptive properties. This result is achieved by optimizing the current formulation with black pigments, while still maintaining its adsorption capability for outgassing control. Different binder to pigment ratios, coating thicknesses, and spray application techniques were explored to develop a black version of the molecular adsorber coating. During the development process, coating performance and adsorption characteristics were studied. The preliminary work performed on black molecular adsorber coatings thus far is very promising. Continued development and testing is necessary for its use on future contamination sensitive spaceflight missions.

  1. Black molecular adsorber coatings for spaceflight applications

    NASA Astrophysics Data System (ADS)

    Abraham, Nithin S.; Hasegawa, Mark M.; Straka, Sharon A.

    2014-09-01

    The molecular adsorber coating is a new technology that was developed to mitigate the risk of on-orbit molecular contamination on spaceflight missions. The application of this coating would be ideal near highly sensitive, interior surfaces and instruments that are negatively impacted by outgassed molecules from materials, such as plastics, adhesives, lubricants, epoxies, and other similar compounds. This current, sprayable paint technology is comprised of inorganic white materials made from highly porous zeolite. In addition to good adhesion performance, thermal stability, and adsorptive capability, the molecular adsorber coating offers favorable thermal control characteristics. However, low reflectivity properties, which are typically offered by black thermal control coatings, are desired for some spaceflight applications. For example, black coatings are used on interior surfaces, in particular, on instrument baffles for optical stray light control. Similarly, they are also used within light paths between optical systems, such as telescopes, to absorb light. Recent efforts have been made to transform the white molecular adsorber coating into a black coating with similar adsorptive properties. This result is achieved by optimizing the current formulation with black pigments, while still maintaining its adsorption capability for outgassing control. Different binder to pigment ratios, coating thicknesses, and spray application techniques were explored to develop a black version of the molecular adsorber coating. During the development process, coating performance and adsorption characteristics were studied. The preliminary work performed on black molecular adsorber coatings thus far is very promising. Continued development and testing is necessary for its use on future contamination sensitive spaceflight missions.

  2. Detection of biological threats. A challenge for directed molecular evolution.

    PubMed

    Petrenko, Valery A; Sorokulova, Iryna B

    2004-08-01

    The probe technique originated from early attempts of Anton van Leeuwenhoek to contrast microorganisms under the microscope using plant juices, successful staining of tubercle bacilli with synthetic dyes by Paul Ehrlich and discovery of a stain for differentiation of gram-positive and gram-negative bacteria by Hans Christian Gram. The technique relies on the principle that pathogens have unique structural features, which can be recognized by specifically labeled organic molecules. A hundred years of extensive screening efforts led to discovery of a limited assortment of organic probes that are used for identification and differentiation of bacteria. A new challenge--continuous monitoring of biological threats--requires long lasting molecular probes capable of tight specific binding of pathogens in unfavorable conditions. To respond to the challenge, probe technology is being revolutionized by utilizing methods of combinatorial chemistry, phage display and directed molecular evolution. This review describes how molecular evolution methods are applied for development of peptide, antibody and phage probes, and summarizes the author's own data on development of landscape phage probes against Salmonella typhimurium. The performance of the probes in detection of Salmonella is illustrated by a precipitation test, enzyme-linked immunosorbent assay (ELISA), fluorescence-activated cell sorting (FACS) and fluorescent, optical and electron microscopy.

  3. Molecular biology of insect sodium channels and pyrethroid resistance.

    PubMed

    Dong, Ke; Du, Yuzhe; Rinkevich, Frank; Nomura, Yoshiko; Xu, Peng; Wang, Lingxin; Silver, Kristopher; Zhorov, Boris S

    2014-07-01

    Voltage-gated sodium channels are essential for the initiation and propagation of the action potential in neurons and other excitable cells. Because of their critical roles in electrical signaling, sodium channels are targets of a variety of naturally occurring and synthetic neurotoxins, including several classes of insecticides. This review is intended to provide an update on the molecular biology of insect sodium channels and the molecular mechanism of pyrethroid resistance. Although mammalian and insect sodium channels share fundamental topological and functional properties, most insect species carry only one sodium channel gene, compared to multiple sodium channel genes found in each mammalian species. Recent studies showed that two posttranscriptional mechanisms, alternative splicing and RNA editing, are involved in generating functional diversity of sodium channels in insects. More than 50 sodium channel mutations have been identified to be responsible for or associated with knockdown resistance (kdr) to pyrethroids in various arthropod pests and disease vectors. Elucidation of molecular mechanism of kdr led to the identification of dual receptor sites of pyrethroids on insect sodium channels. Many of the kdr mutations appear to be located within or close to the two receptor sites. The accumulating knowledge of insect sodium channels and their interactions with insecticides provides a foundation for understanding the neurophysiology of sodium channels in vivo and the development of new and safer insecticides for effective control of arthropod pests and human disease vectors.

  4. Molecular Biology of Insect Sodium Channels and Pyrethroid Resistance

    PubMed Central

    Dong, Ke; Du, Yuzhe; Rinkevich, Frank; Nomura, Yoshiko; Xu, Peng; Wang, Lingxin; Silver, Kristopher; Zhorov, Boris S.

    2015-01-01

    Voltage-gated sodium channels are essential for the initiation and propagation of the action potential in neurons and other excitable cells. Because of their critical roles in electrical signaling, sodium channels are targets of a variety of naturally occurring and synthetic neurotoxins, including several classes of insecticides. This review is intended to provide an update on the molecular biology of insect sodium channels and the molecular mechanism of pyrethroid resistance. Although mammalian and insect sodium channels share fundamental topological and functional properties, most insect species carry only one sodium channel gene, compared to multiple sodium channel genes found in each mammalian species. Recent studies showed that two posttranscriptional mechanisms, alternative splicing and RNA editing, are involved in generating functional diversity of sodium channels in insects. More than 50 sodium channel mutations have been identified to be responsible for or associated with knockdown resistance (kdr) to pyrethroids in various arthropod pests and disease vectors. Elucidation of molecular mechanism of kdr led to the identification of dual receptor sites of pyrethroids on insect sodium channels. Most of the kdr mutations appear to be located within or close to the two receptor sites. The accumulating knowledge of insect sodium channels and their interactions with insecticides provides a foundation for understanding the neurophysiology of sodium channels in vivo and the development of new and safer insecticides for effective control of arthropod pests and human disease vectors. PMID:24704279

  5. Flavonoids: biosynthesis, biological functions, and biotechnological applications

    PubMed Central

    Falcone Ferreyra, María L.; Rius, Sebastián P.; Casati, Paula

    2012-01-01

    Flavonoids are widely distributed secondary metabolites with different metabolic functions in plants. The elucidation of the biosynthetic pathways, as well as their regulation by MYB, basic helix-loop-helix (bHLH), and WD40-type transcription factors, has allowed metabolic engineering of plants through the manipulation of the different final products with valuable applications. The present review describes the regulation of flavonoid biosynthesis, as well as the biological functions of flavonoids in plants, such as in defense against UV-B radiation and pathogen infection, nodulation, and pollen fertility. In addition, we discuss different strategies and achievements through the genetic engineering of flavonoid biosynthesis with implication in the industry and the combinatorial biosynthesis in microorganisms by the reconstruction of the pathway to obtain high amounts of specific compounds. PMID:23060891

  6. Molecular Imprinting Applications in Forensic Science.

    PubMed

    Yılmaz, Erkut; Garipcan, Bora; Patra, Hirak K; Uzun, Lokman

    2017-03-28

    Producing molecular imprinting-based materials has received increasing attention due to recognition selectivity, stability, cast effectiveness, and ease of production in various forms for a wide range of applications. The molecular imprinting technique has a variety of applications in the areas of the food industry, environmental monitoring, and medicine for diverse purposes like sample pretreatment, sensing, and separation/purification. A versatile usage, stability and recognition capabilities also make them perfect candidates for use in forensic sciences. Forensic science is a demanding area and there is a growing interest in molecularly imprinted polymers (MIPs) in this field. In this review, recent molecular imprinting applications in the related areas of forensic sciences are discussed while considering the literature of last two decades. Not only direct forensic applications but also studies of possible forensic value were taken into account like illicit drugs, banned sport drugs, effective toxins and chemical warfare agents in a review of over 100 articles. The literature was classified according to targets, material shapes, production strategies, detection method, and instrumentation. We aimed to summarize the current applications of MIPs in forensic science and put forth a projection of their potential uses as promising alternatives for benchmark competitors.

  7. Molecular Imprinting Applications in Forensic Science

    PubMed Central

    Yılmaz, Erkut; Garipcan, Bora; Patra, Hirak K.; Uzun, Lokman

    2017-01-01

    Producing molecular imprinting-based materials has received increasing attention due to recognition selectivity, stability, cast effectiveness, and ease of production in various forms for a wide range of applications. The molecular imprinting technique has a variety of applications in the areas of the food industry, environmental monitoring, and medicine for diverse purposes like sample pretreatment, sensing, and separation/purification. A versatile usage, stability and recognition capabilities also make them perfect candidates for use in forensic sciences. Forensic science is a demanding area and there is a growing interest in molecularly imprinted polymers (MIPs) in this field. In this review, recent molecular imprinting applications in the related areas of forensic sciences are discussed while considering the literature of last two decades. Not only direct forensic applications but also studies of possible forensic value were taken into account like illicit drugs, banned sport drugs, effective toxins and chemical warfare agents in a review of over 100 articles. The literature was classified according to targets, material shapes, production strategies, detection method, and instrumentation. We aimed to summarize the current applications of MIPs in forensic science and put forth a projection of their potential uses as promising alternatives for benchmark competitors. PMID:28350333

  8. Molecular Subgroup of Primary Prostate Cancer Presenting with Metastatic Biology.

    PubMed

    Walker, Steven M; Knight, Laura A; McCavigan, Andrena M; Logan, Gemma E; Berge, Viktor; Sherif, Amir; Pandha, Hardev; Warren, Anne Y; Davidson, Catherine; Uprichard, Adam; Blayney, Jaine K; Price, Bethanie; Jellema, Gera L; Steele, Christopher J; Svindland, Aud; McDade, Simon S; Eden, Christopher G; Foster, Chris; Mills, Ian G; Neal, David E; Mason, Malcolm D; Kay, Elaine W; Waugh, David J; Harkin, D Paul; Watson, R William; Clarke, Noel W; Kennedy, Richard D

    2017-10-01

    Approximately 4-25% of patients with early prostate cancer develop disease recurrence following radical prostatectomy. To identify a molecular subgroup of prostate cancers with metastatic potential at presentation resulting in a high risk of recurrence following radical prostatectomy. Unsupervised hierarchical clustering was performed using gene expression data from 70 primary resections, 31 metastatic lymph nodes, and 25 normal prostate samples. Independent assay validation was performed using 322 radical prostatectomy samples from four sites with a mean follow-up of 50.3 months. Molecular subgroups were identified using unsupervised hierarchical clustering. A partial least squares approach was used to generate a gene expression assay. Relationships with outcome (time to biochemical and metastatic recurrence) were analysed using multivariable Cox regression and log-rank analysis. A molecular subgroup of primary prostate cancer with biology similar to metastatic disease was identified. A 70-transcript signature (metastatic assay) was developed and independently validated in the radical prostatectomy samples. Metastatic assay positive patients had increased risk of biochemical recurrence (multivariable hazard ratio [HR] 1.62 [1.13-2.33]; p=0.0092) and metastatic recurrence (multivariable HR=3.20 [1.76-5.80]; p=0.0001). A combined model with Cancer of the Prostate Risk Assessment post surgical (CAPRA-S) identified patients at an increased risk of biochemical and metastatic recurrence superior to either model alone (HR=2.67 [1.90-3.75]; p<0.0001 and HR=7.53 [4.13-13.73]; p<0.0001, respectively). The retrospective nature of the study is acknowledged as a potential limitation. The metastatic assay may identify a molecular subgroup of primary prostate cancers with metastatic potential. The metastatic assay may improve the ability to detect patients at risk of metastatic recurrence following radical prostatectomy. The impact of adjuvant therapies should be assessed in

  9. DNA tetrahedron nanostructures for biological applications: biosensors and drug delivery.

    PubMed

    Xie, Nuli; Liu, Shiyuan; Yang, Xiaohai; He, Xiaoxiao; Huang, Jin; Wang, Kemin

    2017-09-08

    With the rapid development of DNA nanotechnology, various DNA nanostructures with different shapes and sizes have been self-assembled using "bottom-up" fabrication strategies and applied to a wide range of fields such as biosensors, drug delivery and tools for molecular biology. As a classical and simple polyhedron, DNA tetrahedron can be easily synthesised by a one-step assembly. Due to the excellent biocompatibility and cellular permeability, it provides a universal and promising platform to construct a series of biosensors and drug delivery systems for living cells studies. Moreover, the high programmability of DNA tetrahedron determines its capability to perform artful design and combine with other materials. Herein, we review and summarise the development and applications of DNA tetrahedron in living cell studies. We mainly focus on two parts, cellular biosensors for the detection of nucleic acids, proteins, small molecules and cancer cells and drug delivery systems for chemotherapy, immunotherapy, photodynamic therapy and gene silencing. With the rapid progress in DNA tetrahedron as well as DNA nanotechnology, new avenues and opportunities have opened up in analytical chemistry, molecular biology and medicine.

  10. [Non oncologic applications of molecular targeted therapies].

    PubMed

    Khaled, Wassef; de la Motte Rouge, Thibault; Amirault, Jean-Christophe; Vignot, Stéphane

    2012-10-01

    Significant improvements in the knowledge of cancer biology have permitted the development of new molecular targeted therapies. Meanwhile, a better understanding of the physiology of various non-cancerous diseases has allowed developing these agents in other areas. This review intends to illustrate these perspectives through examples corresponding to different strategies of molecular-targeted therapies : use of a monoclonal antibody binding a receptor (rituximab and rheumatoid arthritis) or a ligand (bevacizumab and age-related macular degeneration), tyrosine kinase inhibitor (imatinib and systemic sclerosis) or inhibitor of cytoplasmic signal transduction pathways (immunosuppressive and antiproliferative effects of mammalian target of rapamycin [mTOR] inhibitors). Clinical results can draw today what could become molecular medicine of tomorrow.

  11. Molecular imaging of prostate cancer: translating molecular biology approaches into the clinical realm.

    PubMed

    Vargas, Hebert Alberto; Grimm, Jan; F Donati, Olivio; Sala, Evis; Hricak, Hedvig

    2015-05-01

    The epidemiology of prostate cancer has dramatically changed since the introduction of prostate-specific antigen (PSA) screening in the 1980's. Most prostate cancers today are detected at early stages of the disease and are considered 'indolent'; however, some patients' prostate cancers demonstrate a more aggressive behaviour which leads to rapid progression and death. Increasing understanding of the biology underlying the heterogeneity that characterises this disease has led to a continuously evolving role of imaging in the management of prostate cancer. Functional and metabolic imaging techniques are gaining importance as the impact on the therapeutic paradigm has shifted from structural tumour detection alone to distinguishing patients with indolent tumours that can be managed conservatively (e.g., by active surveillance) from patients with more aggressive tumours that may require definitive treatment with surgery or radiation. In this review, we discuss advanced imaging techniques that allow direct visualisation of molecular interactions relevant to prostate cancer and their potential for translation to the clinical setting in the near future. The potential use of imaging to follow molecular events during drug therapy as well as the use of imaging agents for therapeutic purposes will also be discussed. • Advanced imaging techniques allow direct visualisation of molecular interactions in prostate cancer. • MRI/PET, optical and Cerenkov imaging facilitate the translation of molecular biology. • Multiple compounds targeting PSMA expression are currently undergoing clinical translation. • Other targets (e.g., PSA, prostate-stem cell antigen, GRPR) are in development.

  12. Sleeping Beauty transposition: from biology to applications.

    PubMed

    Narayanavari, Suneel A; Chilkunda, Shreevathsa S; Ivics, Zoltán; Izsvák, Zsuzsanna

    2017-02-01

    Sleeping Beauty (SB) is the first synthetic DNA transposon that was shown to be active in a wide variety of species. Here, we review studies from the last two decades addressing both basic biology and applications of this transposon. We discuss how host-transposon interaction modulates transposition at different steps of the transposition reaction. We also discuss how the transposon was translated for gene delivery and gene discovery purposes. We critically review the system in clinical, pre-clinical and non-clinical settings as a non-viral gene delivery tool in comparison with viral technologies. We also discuss emerging SB-based hybrid vectors aimed at combining the attractive safety features of the transposon with effective viral delivery. The success of the SB-based technology can be fundamentally attributed to being able to insert fairly randomly into genomic regions that allow stable long-term expression of the delivered transgene cassette. SB has emerged as an efficient and economical toolkit for safe and efficient gene delivery for medical applications.

  13. Graphene for Environmental and Biological Applications

    NASA Astrophysics Data System (ADS)

    Sreeprasad, T. S.; Pradeep, T.

    2012-08-01

    The latest addition to the nanocarbon family, graphene, has been proclaimed to be the material of the century. Its peculiar band structure, extraordinary thermal and electronic conductance and room temperature quantum Hall effect have all been used for various applications in diverse fields ranging from catalysis to electronics. The difficulty to synthesize graphene in bulk quantities was a limiting factor of it being utilized in several fields. Advent of chemical processes and self-assembly approaches for the synthesis of graphene analogues have opened-up new avenues for graphene based materials. The high surface area and rich abundance of functional groups present make chemically synthesized graphene (generally known as graphene oxide (GO) and reduced graphene oxide (RGO) or chemically converted graphene) an attracting candidate in biotechnology and environmental remediation. By functionalizing graphene with specific molecules, the properties of graphene can be tuned to suite applications such as sensing, drug delivery or cellular imaging. Graphene with its high surface area can act as a good adsorbent for pollutant removal. Graphene either alone or in combination with other materials can be used for the degradation or removal of a large variety of contaminants through several methods. In this review some of the relevant efforts undertaken to utilize graphene in biology, sensing and water purification are described. Most recent efforts have been given precedence over older works, although certain specific important examples of the past are also mentioned.

  14. Implementation and Assessment of a Molecular Biology and Bioinformatics Undergraduate Degree Program

    ERIC Educational Resources Information Center

    Pham, Daphne Q. -D.; Higgs, David C.; Statham, Anne; Schleiter, Mary Kay

    2008-01-01

    The Department of Biological Sciences at the University of Wisconsin-Parkside has developed and implemented an innovative, multidisciplinary undergraduate curriculum in Molecular Biology and Bioinformatics (MBB). The objective of the MBB program is to give students a hands-on facility with molecular biology theories and laboratory techniques, an…

  15. Implementation and Assessment of a Molecular Biology and Bioinformatics Undergraduate Degree Program

    ERIC Educational Resources Information Center

    Pham, Daphne Q. -D.; Higgs, David C.; Statham, Anne; Schleiter, Mary Kay

    2008-01-01

    The Department of Biological Sciences at the University of Wisconsin-Parkside has developed and implemented an innovative, multidisciplinary undergraduate curriculum in Molecular Biology and Bioinformatics (MBB). The objective of the MBB program is to give students a hands-on facility with molecular biology theories and laboratory techniques, an…

  16. Accelerating molecular modeling applications with graphics processors.

    PubMed

    Stone, John E; Phillips, James C; Freddolino, Peter L; Hardy, David J; Trabuco, Leonardo G; Schulten, Klaus

    2007-12-01

    Molecular mechanics simulations offer a computational approach to study the behavior of biomolecules at atomic detail, but such simulations are limited in size and timescale by the available computing resources. State-of-the-art graphics processing units (GPUs) can perform over 500 billion arithmetic operations per second, a tremendous computational resource that can now be utilized for general purpose computing as a result of recent advances in GPU hardware and software architecture. In this article, an overview of recent advances in programmable GPUs is presented, with an emphasis on their application to molecular mechanics simulations and the programming techniques required to obtain optimal performance in these cases. We demonstrate the use of GPUs for the calculation of long-range electrostatics and nonbonded forces for molecular dynamics simulations, where GPU-based calculations are typically 10-100 times faster than heavily optimized CPU-based implementations. The application of GPU acceleration to biomolecular simulation is also demonstrated through the use of GPU-accelerated Coulomb-based ion placement and calculation of time-averaged potentials from molecular dynamics trajectories. A novel approximation to Coulomb potential calculation, the multilevel summation method, is introduced and compared with direct Coulomb summation. In light of the performance obtained for this set of calculations, future applications of graphics processors to molecular dynamics simulations are discussed.

  17. Single-molecule experiments in biological physics: methods and applications.

    PubMed

    Ritort, F

    2006-08-16

    I review single-molecule experiments (SMEs) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SMEs it is possible to manipulate molecules one at a time and measure distributions describing molecular properties, characterize the kinetics of biomolecular reactions and detect molecular intermediates. SMEs provide additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SMEs it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level, emphasizing the importance of SMEs to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SMEs from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOTs), magnetic tweezers (MTs), biomembrane force probes (BFPs) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation) and proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SMEs to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.

  18. Obstructive renal injury: from fluid mechanics to molecular cell biology

    PubMed Central

    Ucero, Alvaro C; Gonçalves, Sara; Benito-Martin, Alberto; Santamaría, Beatriz; Ramos, Adrian M; Berzal, Sergio; Ruiz-Ortega, Marta; Egido, Jesus; Ortiz, Alberto

    2010-01-01

    Urinary tract obstruction is a frequent cause of renal impairment. The physiopathology of obstructive nephropathy has long been viewed as a mere mechanical problem. However, recent advances in cell and systems biology have disclosed a complex physiopathology involving a high number of molecular mediators of injury that lead to cellular processes of apoptotic cell death, cell injury leading to inflammation and resultant fibrosis. Functional studies in animal models of ureteral obstruction using a variety of techniques that include genetically modified animals have disclosed an important role for the renin-angiotensin system, transforming growth factor-β1 (TGF-β1) and other mediators of inflammation in this process. In addition, high throughput techniques such as proteomics and transcriptomics have identified potential biomarkers that may guide clinical decision-making. PMID:24198613

  19. Obstructive renal injury: from fluid mechanics to molecular cell biology.

    PubMed

    Ucero, Alvaro C; Gonçalves, Sara; Benito-Martin, Alberto; Santamaría, Beatriz; Ramos, Adrian M; Berzal, Sergio; Ruiz-Ortega, Marta; Egido, Jesus; Ortiz, Alberto

    2010-04-22

    Urinary tract obstruction is a frequent cause of renal impairment. The physiopathology of obstructive nephropathy has long been viewed as a mere mechanical problem. However, recent advances in cell and systems biology have disclosed a complex physiopathology involving a high number of molecular mediators of injury that lead to cellular processes of apoptotic cell death, cell injury leading to inflammation and resultant fibrosis. Functional studies in animal models of ureteral obstruction using a variety of techniques that include genetically modified animals have disclosed an important role for the renin-angiotensin system, transforming growth factor-β1 (TGF-β1) and other mediators of inflammation in this process. In addition, high throughput techniques such as proteomics and transcriptomics have identified potential biomarkers that may guide clinical decision-making.

  20. Molecular biological characterization of equine surfactant protein A.

    PubMed

    Hospes, R; Hospes, B I L; Reiss, I; Bostedt, H; Gortner, L

    2002-12-01

    In the following, we describe the isolation and sequencing of the equine surfactant protein A (Sp-A) as found in both the cDNA and the genomic DNA. We found a length of the cDNA sequence of 747 bp (base pairs), in translation into amino acids of 248. Compared with the known molecular biological facts about Sp-A in other species, the cDNA sequence obtained showed highest homology with that of sheep (85.01%). The genomic DNA of equine Sp-A, as in other species, includes three introns. There were no hints for the existence of two different Sp-A genes. These results should form the basis for a better understanding of respiratory failure in foals and adult horses, and also lead to further studies on this item.

  1. Vascular remodelling and molecular biology: new concepts and therapeutic possibilities.

    PubMed

    Agrotis, A; Bobik, A

    1996-05-01

    1. Over the past decade major advances in molecular cell biology have greatly increased our understanding of the way in which many growth factor genes are expressed and regulated. This knowledge is currently being translated into investigations of the cardiovascular system. 2. Two growth factor families appear to play particularly important roles, the fibroblast growth factors and the transforming growth factors-beta. These are multifunctional growth factors capable of remodelling the vasculature through their effects on cell migration, proliferation and matrix formation. 3. An understanding of their regulation, properties and nature of their receptors is providing novel insights into the physiology and pathobiology of the vasculature. It is also providing highly specific targets for future therapy.

  2. Molecular biology and inhibitors of hepatitis A virus.

    PubMed

    Debing, Yannick; Neyts, Johan; Thibaut, Hendrik Jan

    2014-09-01

    Hepatitis A virus (HAV) is a faeco-orally transmitted picornavirus and is one of the main causes of acute hepatitis worldwide. An overview of the molecular biology of HAV is presented with an emphasis on recent findings. Immune evasion strategies and a possible correlation between HAV and atopy are discussed as well. Despite the availability of efficient vaccines, antiviral drugs targeting HAV are required to treat severe cases of fulminant hepatitis, contain outbreaks, and halt the potential spread of vaccine-escape variants. Additionally, such drugs could be used to shorten the period of illness and decrease associated economical costs. Several known inhibitors of HAV with various mechanisms of action will be discussed. Since none of these molecules is readily useable in the clinic and since the availability of an anti-HAV drug would be of clinical importance, increased efforts should be targeted toward discovery and development of such antivirals.

  3. Emerging applications of small angle solution scattering in structural biology.

    PubMed

    Chaudhuri, Barnali N

    2015-03-01

    Small angle solution X-ray and neutron scattering recently resurfaced as powerful tools to address an array of biological problems including folding, intrinsic disorder, conformational transitions, macromolecular crowding, and self or hetero-assembling of biomacromolecules. In addition, small angle solution scattering complements crystallography, nuclear magnetic resonance spectroscopy, and other structural methods to aid in the structure determinations of multidomain or multicomponent proteins or nucleoprotein assemblies. Neutron scattering with hydrogen/deuterium contrast variation, or X-ray scattering with sucrose contrast variation to a certain extent, is a convenient tool for characterizing the organizations of two-component systems such as a nucleoprotein or a lipid-protein assembly. Time-resolved small and wide-angle solution scattering to study biological processes in real time, and the use of localized heavy-atom labeling and anomalous solution scattering for applications as FRET-like molecular rulers, are amongst promising newer developments. Despite the challenges in data analysis and interpretation, these X-ray/neutron solution scattering based approaches hold great promise for understanding a wide variety of complex processes prevalent in the biological milieu.

  4. Emerging applications of small angle solution scattering in structural biology

    PubMed Central

    Chaudhuri, Barnali N

    2015-01-01

    Small angle solution X-ray and neutron scattering recently resurfaced as powerful tools to address an array of biological problems including folding, intrinsic disorder, conformational transitions, macromolecular crowding, and self or hetero-assembling of biomacromolecules. In addition, small angle solution scattering complements crystallography, nuclear magnetic resonance spectroscopy, and other structural methods to aid in the structure determinations of multidomain or multicomponent proteins or nucleoprotein assemblies. Neutron scattering with hydrogen/deuterium contrast variation, or X-ray scattering with sucrose contrast variation to a certain extent, is a convenient tool for characterizing the organizations of two-component systems such as a nucleoprotein or a lipid-protein assembly. Time-resolved small and wide-angle solution scattering to study biological processes in real time, and the use of localized heavy-atom labeling and anomalous solution scattering for applications as FRET-like molecular rulers, are amongst promising newer developments. Despite the challenges in data analysis and interpretation, these X-ray/neutron solution scattering based approaches hold great promise for understanding a wide variety of complex processes prevalent in the biological milieu. PMID:25516491

  5. Molecular synchronization, the Kai system, and biological oscillators

    NASA Astrophysics Data System (ADS)

    Lubensky, David K.

    2008-03-01

    In most textbook examples, oscillations in cell biology are driven by the periodic creation and destruction of one or more chemical species. The past few years, however, have seen growing interest in a different sort of oscillator. In these systems, the total concentrations of the major protein components are constant, but the molecules move sequentially through a cycle of different states (e.g. covalent modifications). Macroscopic oscillations appear when the progress of the many individual molecules becomes synchronized. The recently-characterized cyanobacterial circadian clock provides a particularly elegant example of such molecular synchronization. Remarkably, with only the 3 proteins KaiA, KaiB, and KaiC, a ˜24 hour oscillation in KaiC phosphorylation can be reconstituted in vitro. We can thus dissect this biochemical circuit in almost unprecedented detail. Here, we give an overview of the Kai system and its relationship to other oscillators. We begin with a review of the major experimental facts about the Kai system, emphasizing possible mechanisms to synchronize KaiC phosphorylation. We then examine in more detail models in which this synchronization occurs through sequestration of KaiA via differential affinity: KaiA, which stimulates KaiC phosphorylation, has a higher affinity for KaiC during certain stages of the phosphorylation cycle; as long as some KaiC molecules at these stages are present in the reaction mixture, they bind all the available KaiA, thereby preventing the other KaiC's from being phosphorylated and proceeding through the cycle. We also discuss the implications of this mechanism for phenomena such as temperature compensation. Finally, we suggest that, in light of lessons learned from the Kai system, a number of other biological oscillators can fruitfully be viewed as examples of molecular synchronization.

  6. [Etiologic diagnosis in meningitis and encephalitis molecular biology techniques].

    PubMed

    Conca, Natalia; Santolaya, María Elena; Farfan, Mauricio J; Cofré, Fernanda; Vergara, Alejandra; Salazar, Liliana; Torres, Juan Pablo

    2016-01-01

    The aetiological study of infections of the central nervous system has traditionally been performed using bacterial cultures and, more recently, using polymerase chain reaction (PCR) for herpes simplex virus (HSV). Bacterial cultures may not have good performance, especially in the context of patients who have received antibiotics prior to sampling, and a request for HSV only by PCR reduces the information to only one aetiological agent. The aim of this study is to determine the infectious causes of meningitis and encephalitis, using traditional microbiology and molecular biology to improve the aetiological diagnosis of these diseases. A prospective study was conducted on 19 patients with suspected meningitis, admitted to the Luis Calvo Mackenna Hospital in Santiago, Chile, from March 1, 2011 to March 30, 2012. After obtaining informed consent, the CSF samples underwent cytochemical study, conventional culture, multiplex PCR for the major producing bacterial meningitis (N. meningitidis, S. pneumoniae, H. influenzae), real-time single PCR for HSV-1 and 2, VZV, EBV, CMV, HHV-6 and enterovirus. Clinical and epidemiological data were also collected from the clinical records. Of the 19 patients analysed, 2 were diagnosed by conventional methods and 7 by adding molecular biology (increase to 37%). Three patients had meningitis due to S. pneumoniae, one due to Enterobacter cloacae, 2 patients meningoencephalitis HSV-1, and one VZV meningitis. The addition of PCR to conventional diagnostic methods in CNS infections increases the probability of finding the causal agent. This allows a more adequate, timely and rational management of the disease. Copyright © 2014. Publicado por Elsevier España, S.L.U.

  7. Blood stasis syndrome in Japan and its molecular biological analysis.

    PubMed

    Goto, Hirozo

    2014-07-01

    Blood stasis syndrome is one of the pathological concepts of Oriental traditional medicine. In Oriental traditional medicine, blood is thought of as not only blood but also as a living component of the body. In fact, blood stasis syndrome is related to not just circulation disorders but dermatological and gynecological and other diseases. In Japan, the concept of blood stasis syndrome is based on the past literature, for instance, Synopsis of Golden Chamber (Jin Kui Yao Lue), etc. There are many signs of this syndrome, such as a dry mouth, fullness of the abdomen and rough skin. However, the levels of importance of these signs had been unclear. Therefore, in order to determine the levels of seriousness, a scoring system of blood stasis syndrome was made based on multivariate analysis by Dr. Terasawa (Terasawa's Blood Stasis Score). Using the scoring system, we have studied blood stasis syndrome mainly related to blood circulation using modern techniques of analysis. From the results, we found that patients with blood stasis syndrome showed hemorheological abnormalities, and an improvement in these abnormalities was shown after administration of removing-blood stasis formulae. Furthermore, we have studied blood stasis syndrome from the point of view of molecular biology. We searched for the specific protein expression in blood stasis syndrome by proteomic analysis, and found no specific protein expression. However, there may be a possibility of developing a diagnostic algorithm for blood stasis by construction of a decision tree. During the past few years, as one of the molecular biological factors affecting blood stasis syndrome, we have been studying hypoxia inducible factor, which is located in the upstream of many genes. Above all, blood stasis syndrome is more than just circulatory deficit but encompasses the pathological concept of constant multilateral change in the living body.

  8. Ribosome-independent biosynthesis of biologically active peptides: Application of synthetic biology to generate structural diversity.

    PubMed

    Giessen, Tobias W; Marahiel, Mohamed A

    2012-07-16

    Peptide natural products continue to play an important role in modern medicine as last-resort treatments of many life-threatening diseases, as they display many interesting biological activities ranging from antibiotic to antineoplastic. A large fraction of these microbial natural products is assembled by ribosome-independent mechanisms. Progress in sequencing technology and the mechanistic understanding of secondary metabolite pathways has led to the discovery of many formerly cryptic natural products and a molecular understanding of their assembly. Those advances enable us to apply protein and metabolic engineering approaches towards the manipulation of biosynthetic pathways. In this review we discuss the application potential of both templated and non-templated pathways as well as chemoenzymatic strategies for the structural diversification and tailoring of peptide natural products. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  9. The role of molecular biology in the biomonitoring of human exposure to chemicals.

    PubMed

    Muñoz, Balam; Albores, Arnulfo

    2010-11-12

    Exposure to different substances in an occupational environment is of utmost concern to global agencies such as the World Health Organization and the International Labour Organization. Interest in improving work health conditions, particularly of those employees exposed to noxious chemicals, has increased considerably and has stimulated the search for new, more specific and selective tests. Recently, the field of molecular biology has been indicated as an alternative technique for monitoring personnel while evaluating work-related pathologies. Originally, occupational exposure to environmental toxicants was assessed using biochemical techniques to determine the presence of higher concentrations of toxic compounds in blood, urine, or other fluids or tissues; results were used to evaluate potential health risk. However, this approach only estimates the presence of a noxious chemical and its effects, but does not prevent or diminish the risk. Molecular biology methods have become very useful in occupational medicine to provide more accurate and opportune diagnostics. In this review, we discuss the role of the following common techniques: (1) Use of cell cultures; (2) evaluation of gene expression; (3) the "omic" sciences (genomics, transcriptomics, proteomics and metabolomics) and (4) bioinformatics. We suggest that molecular biology has many applications in occupational health where the data can be applied to general environmental conditions.

  10. The Role of Molecular Biology in the Biomonitoring of Human Exposure to Chemicals

    PubMed Central

    Muñoz, Balam; Albores, Arnulfo

    2010-01-01

    Exposure to different substances in an occupational environment is of utmost concern to global agencies such as the World Health Organization and the International Labour Organization. Interest in improving work health conditions, particularly of those employees exposed to noxious chemicals, has increased considerably and has stimulated the search for new, more specific and selective tests. Recently, the field of molecular biology has been indicated as an alternative technique for monitoring personnel while evaluating work-related pathologies. Originally, occupational exposure to environmental toxicants was assessed using biochemical techniques to determine the presence of higher concentrations of toxic compounds in blood, urine, or other fluids or tissues; results were used to evaluate potential health risk. However, this approach only estimates the presence of a noxious chemical and its effects, but does not prevent or diminish the risk. Molecular biology methods have become very useful in occupational medicine to provide more accurate and opportune diagnostics. In this review, we discuss the role of the following common techniques: (1) Use of cell cultures; (2) evaluation of gene expression; (3) the “omic” sciences (genomics, transcriptomics, proteomics and metabolomics) and (4) bioinformatics. We suggest that molecular biology has many applications in occupational health where the data can be applied to general environmental conditions. PMID:21151453

  11. Animal models and the molecular biology of hepadnavirus infection.

    PubMed

    Mason, William S

    2015-04-01

    Australian antigen, the envelope protein of hepatitis B virus (HBV), was discovered in 1967 as a prevalent serum antigen in hepatitis B patients. Early electron microscopy (EM) studies showed that this antigen was present in 22-nm particles in patient sera, which were believed to be incomplete virus. Complete virus, much less abundant than the 22-nm particles, was finally visualized in 1970. HBV was soon found to infect chimpanzees, gorillas, orangutans, gibbon apes, and, more recently, tree shrews (Tupaia belangeri) and cynomolgus macaques (Macaca fascicularis). This restricted host range placed limits on the kinds of studies that might be performed to better understand the biology and molecular biology of HBV and to develop antiviral therapies to treat chronic infections. About 10 years after the discovery of HBV, this problem was bypassed with the discovery of viruses related to HBV in woodchucks, ground squirrels, and ducks. Although unlikely animal models, their use revealed the key steps in hepadnavirus replication and in the host response to infection, including the fact that the viral nuclear episome is the ultimate target for immune clearance of transient infections and antiviral therapy of chronic infections. Studies with these and other animal models have also suggested interesting clues into the link between chronic HBV infection and hepatocellular carcinoma. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

  12. Embryology meets molecular biology: Deciphering the apical ectodermal ridge.

    PubMed

    Verheyden, Jamie M; Sun, Xin

    2017-09-15

    More than sixty years ago, while studying feather tracks on the shoulder of the chick embryo, Dr. John Saunders used Nile Blue dye to stain the tissue. There, he noticed a darkly stained line of cells that neatly rims the tip of the growing limb bud. Rather than ignoring this observation, he followed it up by removing this tissue and found that it led to a striking truncation of the limb skeletons. This landmark experiment marks the serendipitous discovery of the apical ectodermal ridge (AER), the quintessential embryonic structure that drives the outgrowth of the limb. Dr. Saunders continued to lead the limb field for the next fifty years, not just through his own work, but also by inspiring the next generation of researchers through his infectious love of science. Together, he and those who followed ushered in the discovery of fibroblast growth factor (FGF) as the AER molecule. The seamless marriage of embryology and molecular biology that led to the decoding of the AER serves as a shining example of how discoveries are made for the rest of the developmental biology field. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Molecular Biology and Infection of Hepatitis E Virus

    PubMed Central

    Nan, Yuchen; Zhang, Yan-Jin

    2016-01-01

    Hepatitis E virus (HEV) is a viral pathogen transmitted primarily via fecal-oral route. In humans, HEV mainly causes acute hepatitis and is responsible for large outbreaks of hepatitis across the world. The case fatality rate of HEV-induced hepatitis ranges from 0.5 to 3% in young adults and up to 30% in infected pregnant women. HEV strains infecting humans are classified into four genotypes. HEV strains from genotypes 3 and 4 are zoonotic, whereas those from genotypes 1 and 2 have no known animal reservoirs. Recently, notable progress has been accomplished for better understanding of HEV biology and infection, such as chronic HEV infection, in vitro cell culture system, quasi-enveloped HEV virions, functions of the HEV proteins, mechanism of HEV antagonizing host innate immunity, HEV pathogenesis and vaccine development. However, further investigation on the cross-species HEV infection, host tropism, vaccine efficacy, and HEV-specific antiviral strategy is still needed. This review mainly focuses on molecular biology and infection of HEV and offers perspective new insight of this enigmatic virus. PMID:27656178

  14. Molecular biology of endometriosis: from aromatase to genomic abnormalities.

    PubMed

    Bulun, Serdar E; Monsivais, Diana; Kakinuma, Toshiyuki; Furukawa, Yuichi; Bernardi, Lia; Pavone, Mary Ellen; Dyson, Matthew

    2015-05-01

    Endometriosis has been initially described as the presence of ectopic endometrial tissue on pelvic organs or in extrapelvic sites; and this has been used as its key pathologic feature ever since. Endometriosis responds to fluctuations in estrogen and progesterone by growth and inflammation, leading to pain aggravated by menses. It was proposed that pelvic endometriosis primarily originate from retrograde menstruation of a critical number of eutopic endometrial cells with stem characteristics. This postulate is supported by the molecular defects found in ectopic endometriotic tissue. Genome-wide differences in CpG methylation between eutopic endometrial and endometriotic stromal cells are present. Defective CpG methylation affecting several genes that encode key transcription factors such as GATA6, steroidogenic factor-1, and estrogen receptor-β in endometriosis gives rise to overproduction of local estrogen and prostaglandins and suppression of progesterone receptor. Progesterone receptor deficiency leads to progesterone resistance, resulting in decreased retinol uptake and retinoic acid production and altered retinoic acid action. These molecular defects collectively give rise to poor cellular differentiation, enhanced survival, and increased inflammation, which are the biological hallmarks of endometriotic tissue.

  15. Molecular Skin Surface-Based Transformation Visualization between Biological Macromolecules

    PubMed Central

    Cheng, Holun; Huang, Jing; Gao, Zhigang

    2017-01-01

    Molecular skin surface (MSS), proposed by Edelsbrunner, is a C2 continuous smooth surface modeling approach of biological macromolecules. Compared to the traditional methods of molecular surface representations (e.g., the solvent exclusive surface), MSS has distinctive advantages including having no self-intersection and being decomposable and transformable. For further promoting MSS to the field of bioinformatics, transformation between different MSS representations mimicking the macromolecular dynamics is demanded. The transformation process helps biologists understand the macromolecular dynamics processes visually in the atomic level, which is important in studying the protein structures and binding sites for optimizing drug design. However, modeling the transformation between different MSSs suffers from high computational cost while the traditional approaches reconstruct every intermediate MSS from respective intermediate union of balls. In this study, we propose a novel computational framework named general MSS transformation framework (GMSSTF) between two MSSs without the assistance of union of balls. To evaluate the effectiveness of GMSSTF, we applied it on a popular public database PDB (Protein Data Bank) and compared the existing MSS algorithms with and without GMSSTF. The simulation results show that the proposed GMSSTF effectively improves the computational efficiency and is potentially useful for macromolecular dynamic simulations.

  16. Molecular codes in biological and chemical reaction networks.

    PubMed

    Görlich, Dennis; Dittrich, Peter

    2013-01-01

    Shannon's theory of communication has been very successfully applied for the analysis of biological information. However, the theory neglects semantic and pragmatic aspects and thus cannot directly be applied to distinguish between (bio-) chemical systems able to process "meaningful" information from those that do not. Here, we present a formal method to assess a system's semantic capacity by analyzing a reaction network's capability to implement molecular codes. We analyzed models of chemical systems (martian atmosphere chemistry and various combustion chemistries), biochemical systems (gene expression, gene translation, and phosphorylation signaling cascades), an artificial chemistry, and random reaction networks. Our study suggests that different chemical systems possess different semantic capacities. No semantic capacity was found in the model of the martian atmosphere chemistry, the studied combustion chemistries, and highly connected random networks, i.e. with these chemistries molecular codes cannot be implemented. High semantic capacity was found in the studied biochemical systems and in random reaction networks where the number of second order reactions is twice the number of species. We conclude that our approach can be applied to evaluate the information processing capabilities of a chemical system and may thus be a useful tool to understand the origin and evolution of meaningful information, e.g. in the context of the origin of life.

  17. Molecular biology of normal melanocytes and melanoma cells.

    PubMed

    Bandarchi, Bizhan; Jabbari, Cyrus Aleksandre; Vedadi, Ali; Navab, Roya

    2013-08-01

    Malignant melanoma is one of the most aggressive malignancies in humans and is responsible for 60-80% of deaths from skin cancers. The 5-year survival of patients with metastatic malignant melanoma is about 14%. Its incidence has been increasing in the white population over the past two decades. The mechanisms leading to malignant transformation of melanocytes and melanocytic lesions are poorly understood. In developing malignant melanoma, there is a complex interaction of environmental and endogenous (genetic) factors, including: dysregulation of cell proliferation, programmed cell death (apoptosis) and cell-to-cell interactions. The understanding of genetic alterations in signalling pathways of primary and metastatic malignant melanoma and their interactions may lead to therapeutics modalities, including targeted therapies, particularly in advanced melanomas that have high mortality rates and are often resistant to chemotherapy and radiotherapy. Our knowledge regarding the molecular biology of malignant melanoma has been expanding. Even though several genes involved in melanocyte development may also be associated with melanoma cell development, it is still unclear how a normal melanocyte becomes a melanoma cell. This article reviews the molecular events and recent findings associated with malignant melanoma.

  18. Molecularly imprinted polymers for 5-fluorouracil release in biological fluids.

    PubMed

    Puoci, Francesco; Iemma, Francesca; Cirillo, Giuseppe; Picci, Nevio; Matricardi, Pietro; Alhaiqu, Franco

    2007-04-18

    The aim of this work was to investigate the possibility of employing Molecularly Imprinted Polymers (MIPs) as a controlled release device for 5-fluorouracil (5-FU) in biological fluids, especially gastrointestinal ones, compared to Non Imprinted Polymers (NIPs). MIPs were synthesized using methacrylic acid (MAA) as functional monomer and ethylene glycol dimethacrylate (EGDMA) as crosslinking agent. The capacity of the polymer to recognize and to bind the template selectively in both organic and aqueous media was evaluated. An in vitro release study was performed both in gastrointestinal and in plasma simulating fluids. The imprinted polymers bound much more 5-Fu than the corresponding non-imprinted ones and showed a controlled/sustained drug release, with MIPs release rate being indeed much more sustained than that obtained from NIPs. These polymers represent a potential valid system for drug delivery and this study indicates that the selective binding characteristic of molecularly imprinted polymers is promising for the preparation of novel controlled release drug dosage form.

  19. mRNA capping: biological functions and applications

    PubMed Central

    Ramanathan, Anand; Robb, G. Brett; Chan, Siu-Hong

    2016-01-01

    The 5′ m7G cap is an evolutionarily conserved modification of eukaryotic mRNA. Decades of research have established that the m7G cap serves as a unique molecular module that recruits cellular proteins and mediates cap-related biological functions such as pre-mRNA processing, nuclear export and cap-dependent protein synthesis. Only recently has the role of the cap 2′O methylation as an identifier of self RNA in the innate immune system against foreign RNA has become clear. The discovery of the cytoplasmic capping machinery suggests a novel level of control network. These new findings underscore the importance of a proper cap structure in the synthesis of functional messenger RNA. In this review, we will summarize the current knowledge of the biological roles of mRNA caps in eukaryotic cells. We will also discuss different means that viruses and their host cells use to cap their RNA and the application of these capping machineries to synthesize functional mRNA. Novel applications of RNA capping enzymes in the discovery of new RNA species and sequencing the microbiome transcriptome will also be discussed. We will end with a summary of novel findings in RNA capping and the questions these findings pose. PMID:27317694

  20. Quasielastic neutron scattering in biology: Theory and applications.

    PubMed

    Vural, Derya; Hu, Xiaohu; Lindner, Benjamin; Jain, Nitin; Miao, Yinglong; Cheng, Xiaolin; Liu, Zhuo; Hong, Liang; Smith, Jeremy C

    2017-01-01

    Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrations, localized diffusion and transitions between energy minima. In biological systems, such as proteins and membranes, these relaxation processes are of considerable physical interest. We review here recent methodological advances and applications of quasielastic neutron scattering (QENS) in biology, concentrating on the role of molecular dynamics simulation in generating data with which neutron profiles can be unambiguously interpreted. We examine the use of massively-parallel computers in calculating scattering functions, and the application of Markov state modeling. The decomposition of MD-derived neutron dynamic susceptibilities is described, and the use of this in combination with NMR spectroscopy. We discuss dynamics at very long times, including approximations to the infinite time mean-square displacement and nonequilibrium aspects of single-protein dynamics. Finally, we examine how neutron scattering and MD can be combined to provide information on lipid nanodomains. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.