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Sample records for engineering molecular biology

  1. 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. PMID:27620079

  2. Incorporating Molecular and Cellular Biology into a Chemical Engineering Degree Program

    ERIC Educational Resources Information Center

    O'Connor, Kim C.

    2005-01-01

    There is a growing need for a workforce that can apply engineering principles to molecular based discovery and product development in the biological sciences. To this end, Tulane University established a degree program that incorporates molecular and cellular biology into the chemical engineering curriculum. In celebration of the tenth anniversary…

  3. Introducing Molecular Biology to Environmental Engineers through Development of a New Course.

    ERIC Educational Resources Information Center

    Oerther, Daniel B.

    2002-01-01

    Introduces a molecular biology course designed for environmental engineering majors using 16S ribosomal ribonucleic acid-targeted technology that allows students to identify and study microorganisms in bioreactor environments. (Contains 17 references.) (YDS)

  4. Methods of Genome Engineering: a New Era of Molecular Biology.

    PubMed

    Chugunova, A A; Dontsova, O A; Sergiev, P V

    2016-07-01

    Genome sequencing now progressing much faster than our understanding of the majority of gene functions. Studies of physiological functions of various genes would not be possible without the ability to manipulate the genome. Methods of genome engineering can now be used to inactivate a gene to study consequences, introduce heterologous genes into the genome for scientific and biotechnology applications, create genes coding for fusion proteins to study gene expression, protein localization, and molecular interactions, and to develop animal models of human diseases to find appropriate treatment. Finally, genome engineering might present the possibility to cure hereditary diseases. In this review, we discuss and compare the most important methods for gene inactivation and editing, as well as methods for incorporation of heterologous genes into the genome. PMID:27449613

  5. Molecular-level engineering of THz/IR-sensitive materials for future biological sensing application

    NASA Astrophysics Data System (ADS)

    Woolard, Dwight; Recine, Gregory; Bykhovski, Alexei; Zhang, Weidong

    2010-08-01

    While the unique spectral information associated with chemical and biological molecules within the terahertz frequency regime (~ 3.0-3.0 millimeters) motivates its use for practical sensing applications, limiting factors at the macroscale (weak spectral absorption, broad line widths and masking geometrical effects introduced by the samples) provides motivation for man-engineered sensing materials that allow for the transduction of the spectral information about target molecules from the nanoscale. This brief letter will overview work being performed by our research group to define molecular-level functionality that will be useful for realizing "THz/IR-sensitive" materials. Here the goal is to define switchable molecular components that when incorporated into larger DNA-based nanoscaffolds lead to THz and/or IR regime electronic and/or photonic material properties that are dictated in a predictable manner by novel functionality paradigms. In particular, theoretical modeling and design studies are being performed to engineer organic and biological switches that can be incorporated into DNA-based architectures that enable the precise extraction of nanoscale information (e.g., composition, dynamics, conformation) through electronic/photonic transformations to the macroscale. Hence, these studies seek to define new spectral-based sensing modalities useful for characterizing bio-molecules

  6. 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…

  7. Engineering molecular machines

    NASA Astrophysics Data System (ADS)

    Erman, Burak

    2016-04-01

    Biological molecular motors use chemical energy, mostly in the form of ATP hydrolysis, and convert it to mechanical energy. Correlated thermal fluctuations are essential for the function of a molecular machine and it is the hydrolysis of ATP that modifies the correlated fluctuations of the system. Correlations are consequences of the molecular architecture of the protein. The idea that synthetic molecular machines may be constructed by designing the proper molecular architecture is challenging. In their paper, Sarkar et al (2016 New J. Phys. 18 043006) propose a synthetic molecular motor based on the coarse grained elastic network model of proteins and show by numerical simulations that motor function is realized, ranging from deterministic to thermal, depending on temperature. This work opens up a new range of possibilities of molecular architecture based engine design.

  8. Engineering scalable biological systems

    PubMed Central

    2010-01-01

    Synthetic biology is focused on engineering biological organisms to study natural systems and to provide new solutions for pressing medical, industrial and environmental problems. At the core of engineered organisms are synthetic biological circuits that execute the tasks of sensing inputs, processing logic and performing output functions. In the last decade, significant progress has been made in developing basic designs for a wide range of biological circuits in bacteria, yeast and mammalian systems. However, significant challenges in the construction, probing, modulation and debugging of synthetic biological systems must be addressed in order to achieve scalable higher-complexity biological circuits. Furthermore, concomitant efforts to evaluate the safety and biocontainment of engineered organisms and address public and regulatory concerns will be necessary to ensure that technological advances are translated into real-world solutions. PMID:21468204

  9. Ontologies for molecular biology.

    PubMed

    Schulze-Kremer, S

    1998-01-01

    Molecular biology has a communication problem. There are many databases using their own labels and categories for storing data objects and some using identical labels and categories but with a different meaning. A prominent example is the concept "gene" which is used with different semantics by major international genomic databases. Ontologies are one means to provide a semantic repository to systematically order relevant concepts in molecular biology and to bridge the different notions in various databases by explicitly specifying the meaning of and relation between the fundamental concepts in an application domain. Here, the upper level and a database branch of a prospective ontology for molecular biology (OMB) is presented and compared to other ontologies with respect to suitability for molecular biology (http:/(/)igd.rz-berlin.mpg.de/approximately www/oe/mbo.html). PMID:9697223

  10. Philosophical Foundations of Biological Engineering.

    ERIC Educational Resources Information Center

    Johnson, Arthur T.; Phillips, Winfred M.

    1995-01-01

    Discusses a philosophy from which biological engineering curriculums can emerge. Discusses competencies, basic engineering and biological concepts, common courses, interfacing between engineers and biologists, and employment. Contains 28 references. (JRH)

  11. 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.

  12. Graphs in molecular biology

    PubMed Central

    Huber, Wolfgang; Carey, Vincent J; Long, Li; Falcon, Seth; Gentleman, Robert

    2007-01-01

    Graph theoretical concepts are useful for the description and analysis of interactions and relationships in biological systems. We give a brief introduction into some of the concepts and their areas of application in molecular biology. We discuss software that is available through the Bioconductor project and present a simple example application to the integration of a protein-protein interaction and a co-expression network. PMID:17903289

  13. 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…

  14. 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.

  15. Grand challenges for biological engineering

    PubMed Central

    Yoon, Jeong-Yeol; Riley, Mark R

    2009-01-01

    Biological engineering will play a significant role in solving many of the world's problems in medicine, agriculture, and the environment. Recently the U.S. National Academy of Engineering (NAE) released a document "Grand Challenges in Engineering," covering broad realms of human concern from sustainability, health, vulnerability and the joy of living. Biological engineers, having tools and techniques at the interface between living and non-living entities, will play a prominent role in forging a better future. The 2010 Institute of Biological Engineering (IBE) conference in Cambridge, MA, USA will address, in part, the roles of biological engineering in solving the challenges presented by the NAE. This letter presents a brief outline of how biological engineers are working to solve these large scale and integrated problems of our society. PMID:19772647

  16. 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)

  17. Molecular biology and reproduction.

    PubMed

    McDonough, P G

    1999-03-01

    Modern molecular biology has provided unique insights into the fundamental understanding of reproductive disorders and the detection of microorganisms. The remarkable advances in DNA diagnostics have been expedited by the development of polymerase chain reaction (PCR) and the ability to isolate DNA and RNA from many different sources such as blood, saliva, hair roots, microscopic slides, paraffin-embedded tissue sections, clinical swabs, and even cancellous bone. These technical advances have been bolstered by the development of an increasing number of effective screening techniques to scan genomic DNA for unknown point mutations. The continued development of technology will ultimately result in automated DNA (desoxyribonucleic acid) diagnosis for the practicing clinician. The continuing expansion of information concerning the human genome will place an increasing emphasis on bioinformatics and the use of computer software for analyzing DNA sequences. With the automation of DNA diagnosis and the use of small samples (500 nanograms), the direct examination of the DNA of a patient, fetus, or microorganism will emerge as a definitive means of establishing the presence of the specific genetic change that causes disease. A knowledge of the precise pathology at the molecular level has and will provide important insights into the biochemical basis for many human diseases. A firm knowledge of the DNA alterations in disease and expression patterns of specific genes will provide for more directed therapeutic strategies. The refinement of vector technology and nuclear transplantion techniques will provide the opportunity for directed gene therapy to the early human embryo. This presentation is designed to acquaint the reader with current techniques of testing at the DNA level, prototype mutations in the reproductive sciences, new concepts in the molecular mechanisms of disease that affect reproduction, and therapeutic opportunities for the future. It is hoped that future

  18. Biological handbook for engineers

    NASA Technical Reports Server (NTRS)

    1970-01-01

    Microbiological background information is compiled in handbook for engineers and scientists working on bio-related projects. It is intended as aid in - /1/ evaluating effects of engineering procedures on microbial life, /2/ determining effects of decontamination and sterilization on performance of overall systems, and /3/ understanding language of microbiologists.

  19. Nucleic acids and molecular biology

    SciTech Connect

    Eckstein, F.; Lilley, D.M.J.

    1988-01-01

    Molecular biology has always been a discipline of rapid development. Despite this the authors are presently experiencing a period of unprecedented proliferation of information in nucleic acid studies and molecular biology. These areas are intimately interwoven, so that each influences the other to their mutual benefit. The rapid growth in information leads to ever-increasing specialization. The authors present the series Nucleic Acids and Molecular Biology. It comprises focused review articles by active researchers who report on the newest developments in their areas of particular interest.

  20. 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)

  1. 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. PMID:18393670

  2. 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

  3. Synthetic biology meets tissue engineering.

    PubMed

    Davies, Jamie A; Cachat, Elise

    2016-06-15

    Classical tissue engineering is aimed mainly at producing anatomically and physiologically realistic replacements for normal human tissues. It is done either by encouraging cellular colonization of manufactured matrices or cellular recolonization of decellularized natural extracellular matrices from donor organs, or by allowing cells to self-organize into organs as they do during fetal life. For repair of normal bodies, this will be adequate but there are reasons for making unusual, non-evolved tissues (repair of unusual bodies, interface to electromechanical prostheses, incorporating living cells into life-support machines). Synthetic biology is aimed mainly at engineering cells so that they can perform custom functions: applying synthetic biological approaches to tissue engineering may be one way of engineering custom structures. In this article, we outline the 'embryological cycle' of patterning, differentiation and morphogenesis and review progress that has been made in constructing synthetic biological systems to reproduce these processes in new ways. The state-of-the-art remains a long way from making truly synthetic tissues, but there are now at least foundations for future work. PMID:27284030

  4. Molecular biology of pancreatic cancer.

    PubMed

    Belda-Iniesta, Cristóbal; Ibáñez de Cáceres, Immaculada; Barriuso, Jorge; de Castro Carpeño, Javier; González Barón, Manuel; Feliú, Jaime

    2008-09-01

    Pancreatic cancer is a leading cause of cancer death. This devastating disease has the horrible honour of close to equal incidence and mortality rates. Late diagnosis and a constitutive resistance to every chemotherapy approach are responsible for this scenario. However, molecular biology tools in cooperation with translational efforts have dissected several secrets that underlie pancreatic cancer. Progressive acquisition of malignant, invasive phenotypes from pre-malignant lesions, recent revelations on core signalling pathways and new targeted designed trials offer a better future for pancreatic cancer patients. This review will summarise recent advances in the molecular biology of pancreatic cancer. PMID:18796369

  5. [Knowledgebases in postgenomic molecular biology].

    PubMed

    Lisitsa, A V; Shilov, B V; Evdokimov, P A; Gusev, S A

    2010-01-01

    Knowledgebases can become an effective tool essentially raising quality of information retrieval in molecular biology, promoting the development of new methods of education and forecasting of the biomedical R&D. Knowledge-based technologies should induce "paradigm shift" in the life science due to integrative focusing of research groups towards the challenges of postgenomic era. This paper debates concept of the knowledgebase, which exploits web usage mining to personalize the access of molecular biologist to the Internet resources. PMID:21328913

  6. Fluctuation as a tool of biological molecular machines.

    PubMed

    Yanagida, Toshio

    2008-01-01

    The mechanism for biological molecular machines is different from that of man-made ones. Recently single molecule measurements and other experiments have revealed unique operations where biological molecular machines exploit thermal fluctuation in response to small inputs of energy or signals to achieve their function. Understanding and applying this mechanism to engineering offers new artificial machine designs. PMID:18583025

  7. Molecular Processes in Biological Thermosensation

    PubMed Central

    Digel, I.; Kayser, P.; Artmann, G. M.

    2008-01-01

    Since thermal gradients are almost everywhere, thermosensation could represent one of the oldest sensory transduction processes that evolved in organisms. There are many examples of temperature changes affecting the physiology of living cells. Almost all classes of biological macromolecules in a cell (nucleic acids, lipids, proteins) can present a target of the temperature-related stimuli. This review discusses some features of different classes of temperature-sensing molecules as well as molecular and biological processes that involve thermosensation. Biochemical, structural, and thermodynamic approaches are applied in the paper to organize the existing knowledge on molecular mechanisms of thermosensation. Special attention is paid to the fact that thermosensitive function cannot be assigned to any particular functional group or spatial structure but is rather of universal nature. For instance, the complex of thermodynamic, structural, and functional features of hemoglobin family proteins suggests their possible accessory role as “molecular thermometers”. PMID:20130806

  8. Biosilica: Molecular Biology, Biochemistry and Function in Demosponges as well as its Applied Aspects for Tissue Engineering.

    PubMed

    Wang, Xiaohong; Schröder, Heinz C; Wiens, Matthias; Schloßmacher, Ute; Müller, Werner E G

    2012-01-01

    Biomineralization, biosilicification in particular (i.e. the formation of biogenic silica, SiO(2)), has become an exciting source of inspiration for the development of novel bionic approaches following 'nature as model'. Siliceous sponges are unique among silica-forming organisms in their ability to catalyze silica formation using a specific enzyme termed silicatein. In this study, we review the present state of knowledge on silicatein-mediated 'biosilica' formation in marine demosponges, the involvement of further molecules in silica metabolism and their potential applications in nano-biotechnology and bio-medicine. While most forms of multicellular life have developed a calcium-based skeleton, a few specialized organisms complement their body plan with silica. Only sponges (phylum Porifera) are able to polymerize silica enzymatically mediated in order to generate massive siliceous skeletal elements (spicules) during a unique reaction, at ambient temperature and pressure. During this biomineralization process (i.e. biosilicification), hydrated, amorphous silica is deposited within highly specialized sponge cells, ultimately resulting in structures that range in size from micrometres to metres. This peculiar phenomenon has been comprehensively studied in recent years, and in several approaches, the molecular background was explored to create tools that might be employed for novel bioinspired biotechnological and biomedical applications. Thus, it was discovered that spiculogenesis is mediated by the enzyme silicatein and starts intracellularly. The resulting silica nanoparticles fuse and subsequently form concentric lamellar layers around a central protein filament, consisting of silicatein and the scaffold protein silintaphin-1. Once the growing spicule is extruded into the extracellular space, it obtains final size and shape. Again, this process is mediated by silicatein and silintaphin-1/silintaphin-1, in combination with other molecules such as galectin and

  9. 7th Annual Systems Biology Symposium: Systems Biology and Engineering

    SciTech Connect

    Galitski, Timothy P.

    2008-04-01

    Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology has been hosted by the Institute for Systems Biology in Seattle, Washington, since 2002. The annual two-day event gathers the most influential researchers transforming biology into an integrative discipline investingating complex systems. Engineering and application of new technology is a central element of systems biology. Genome-scale, or very small-scale, biological questions drive the enigneering of new technologies, which enable new modes of experimentation and computational analysis, leading to new biological insights and questions. Concepts and analytical methods in engineering are now finding direct applications in biology. Therefore, the 2008 Symposium, funded in partnership with the Department of Energy, featured global leaders in "Systems Biology and Engineering."

  10. Molecular biology of malignant gliomas.

    PubMed

    Belda-Iniesta, Cristóbal; de Castro Carpeño, Javier; Casado Sáenz, Enrique; Cejas Guerrero, Paloma; Perona, Rosario; González Barón, Manuel

    2006-09-01

    Gliomas are the most common primary brain tumours. In keeping with the degree of aggressiveness, gliomas are divided into four grades, with different biological behaviour. Furthermore, as different gliomas share a predominant histological appearance, the final classification includes both, histological features and degree of malignancy. For example, gliomas of astrocytic origin (astrocytomas) are classified into pilocytic astrocytoma (grade I), astrocytoma (grade II), anaplastic astrocytoma (grade III) and glioblastoma multiforme (GMB) (grade IV). Tumors derived from oligodendrocytes include grade II (oliogodendrogliomas) and grade III neoplasms (oligoastrocytoma). Each subtype has a specific prognosis that dictates the clinical management. In this regard, a patient diagnosed with an oligodendroglioma totally removed has 10-15 years of potential survival. On the opposite site, patients carrying a glioblastoma multiforme usually die within the first year after the diagnosis is made. Therefore, different approaches are needed in each case. Obviously, prognosis and biological behaviour of malignant gliomas are closely related and supported by the different molecular background that possesses each type of glioma. Furthermore, the ability that allows several low-grade gliomas to progress into more aggressive tumors has allowed cancer researchers to elucidate several pathways implicated in molecular biology of these devastating tumors. In this review, we describe classical pathways involved in human malignant gliomas with special focus with recent advances, such as glioma stem-like cells and expression patterns from microarray studies. PMID:17005465

  11. 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. PMID:18299181

  12. 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. PMID:23809923

  13. Consistent design schematics for biological systems: standardization of representation in biological engineering

    PubMed Central

    Matsuoka, Yukiko; Ghosh, Samik; Kitano, Hiroaki

    2009-01-01

    The discovery by design paradigm driving research in synthetic biology entails the engineering of de novo biological constructs with well-characterized input–output behaviours and interfaces. The construction of biological circuits requires iterative phases of design, simulation and assembly, leading to the fabrication of a biological device. In order to represent engineered models in a consistent visual format and further simulating them in silico, standardization of representation and model formalism is imperative. In this article, we review different efforts for standardization, particularly standards for graphical visualization and simulation/annotation schemata adopted in systems biology. We identify the importance of integrating the different standardization efforts and provide insights into potential avenues for developing a common framework for model visualization, simulation and sharing across various tools. We envision that such a synergistic approach would lead to the development of global, standardized schemata in biology, empowering deeper understanding of molecular mechanisms as well as engineering of novel biological systems. PMID:19493898

  14. 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.

  15. Network Reverse Engineering Approach in Synthetic Biology

    NASA Astrophysics Data System (ADS)

    Zhang, Haoqian; Liu, Ao; Lu, Yuheng; Sheng, Ying; Wu, Qianzhu; Yin, Zhenzhen; Chen, Yiwei; Liu, Zairan; Pan, Heng; Ouyang, Qi

    2013-12-01

    Synthetic biology is a new branch of interdisciplinary science that has been developed in recent years. The main purpose of synthetic biology is to apply successful principles that have been developed in electronic and chemical engineering to develop basic biological functional modules, and through rational design, develop man-made biological systems that have predicted useful functions. Here, we discuss an important principle in rational design of functional biological circuits: the reverse engineering design. We will use a research project that was conducted at Peking University for the International Genetic Engineering Machine Competition (iGEM) to illustrate the principle: synthesis a cell which has a semi-log dose-response to the environment. Through this work we try to demonstrate the potential application of network engineering in synthetic biology.

  16. Molecular engineering of polymersome surface topology.

    PubMed

    Ruiz-Pérez, Lorena; Messager, Lea; Gaitzsch, Jens; Joseph, Adrian; Sutto, Ludovico; Gervasio, Francesco Luigi; Battaglia, Giuseppe

    2016-04-01

    Biological systems exploit self-assembly to create complex structures whose arrangements are finely controlled from the molecular to mesoscopic level. We report an example of using fully synthetic systems that mimic two levels of self-assembly. We show the formation of vesicles using amphiphilic copolymers whose chemical nature is chosen to control both membrane formation and membrane-confined interactions. We report polymersomes with patterns that emerge by engineering interfacial tension within the polymersome surface. This allows the formation of domains whose topology is tailored by chemical synthesis, paving the avenue to complex supramolecular designs functionally similar to those found in viruses and trafficking vesicles. PMID:27152331

  17. Molecular engineering of polymersome surface topology

    PubMed Central

    Ruiz-Pérez, Lorena; Messager, Lea; Gaitzsch, Jens; Joseph, Adrian; Sutto, Ludovico; Gervasio, Francesco Luigi; Battaglia, Giuseppe

    2016-01-01

    Biological systems exploit self-assembly to create complex structures whose arrangements are finely controlled from the molecular to mesoscopic level. We report an example of using fully synthetic systems that mimic two levels of self-assembly. We show the formation of vesicles using amphiphilic copolymers whose chemical nature is chosen to control both membrane formation and membrane-confined interactions. We report polymersomes with patterns that emerge by engineering interfacial tension within the polymersome surface. This allows the formation of domains whose topology is tailored by chemical synthesis, paving the avenue to complex supramolecular designs functionally similar to those found in viruses and trafficking vesicles. PMID:27152331

  18. Arterivirus molecular biology and pathogenesis.

    PubMed

    Snijder, Eric J; Kikkert, Marjolein; Fang, Ying

    2013-10-01

    Arteriviruses are positive-stranded RNA viruses that infect mammals. They can cause persistent or asymptomatic infections, but also acute disease associated with a respiratory syndrome, abortion or lethal haemorrhagic fever. During the past two decades, porcine reproductive and respiratory syndrome virus (PRRSV) and, to a lesser extent, equine arteritis virus (EAV) have attracted attention as veterinary pathogens with significant economic impact. Particularly noteworthy were the 'porcine high fever disease' outbreaks in South-East Asia and the emergence of new virulent PRRSV strains in the USA. Recently, the family was expanded with several previously unknown arteriviruses isolated from different African monkey species. At the molecular level, arteriviruses share an intriguing but distant evolutionary relationship with coronaviruses and other members of the order Nidovirales. Nevertheless, several of their characteristics are unique, including virion composition and structure, and the conservation of only a subset of the replicase domains encountered in nidoviruses with larger genomes. During the past 15 years, the advent of reverse genetics systems for EAV and PRRSV has changed and accelerated the structure-function analysis of arterivirus RNA and protein sequences. These systems now also facilitate studies into host immune responses and arterivirus immune evasion and pathogenesis. In this review, we have summarized recent advances in the areas of arterivirus genome expression, RNA and protein functions, virion architecture, virus-host interactions, immunity, and pathogenesis. We have also briefly reviewed the impact of these advances on disease management, the engineering of novel candidate live vaccines and the diagnosis of arterivirus infection. PMID:23939974

  19. 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

  20. Engineering life through Synthetic Biology.

    PubMed

    Chopra, Paras; Kamma, Akhil

    2006-01-01

    Synthetic Biology is a field involving synthesis of novel biological systems which are not generally found in nature. It has brought a new paradigm in science as it has enabled scientists to create life from the scratch, hence helping better understand the principles of biology. The viability of living organisms that use unnatural molecules is also being explored. Unconventional projects such as DNA playing tic-tac-toe, bacterial photographic film, etc. are taking biology to its extremes. The field holds a promise for mass production of cheap drugs and programming bacteria to seek-and-destroy tumors in the body. However, the complexity of biological systems make the field a challenging one. In addition to this, there are other major technical and ethical challenges which need to be addressed before the field realizes its true potential. PMID:17274769

  1. Engineering reduced evolutionary potential for synthetic biology

    PubMed Central

    Renda, Brian A.; Hammerling, Michael J.

    2014-01-01

    The field of synthetic biology seeks to engineer reliable and predictable behaviors in organisms from collections of standardized genetic parts. However, unlike other types of machines, genetically encoded biological systems are prone to changes in their designed sequences due to mutations in their DNA sequences after these devices are constructed and deployed. Thus, biological engineering efforts can be confounded by undesired evolution that rapidly breaks the functions of parts and systems, particularly when they are costly to the host cell to maintain. Here, we explain the fundamental properties that determine the evolvability of biological systems. Then, we use this framework to review current efforts to engineer the DNA sequences that encode synthetic biology devices and the genomes of their microbial hosts to reduce their ability to evolve and therefore increase their genetic reliability so that they maintain their intended functions over longer timescales. PMID:24556867

  2. 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

  3. Molecular biology of microbial ureases.

    PubMed

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

    1995-09-01

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

  4. ENGINEERING BULLETIN: ROTATING BIOLOGICAL CONTACTORS

    EPA Science Inventory

    Rotating biological contactors employ aerobic fixed-film treatment to degrade either organic and/or nitrogenous (ammonia-nitrogen) constituents present in aqueous waste streams. ixed-film systems provide a surface to which the biomass can adhere. Treatment is achieved as the wast...

  5. Generating new blood flow: integrating developmental biology and tissue engineering.

    PubMed

    Krenning, Guido; Moonen, Jan-Renier A J; van Luyn, Marja J A; Harmsen, Martin C

    2008-11-01

    Vascular tissue engineering aims to restore blood flow by seeding artificial tubular scaffolds with endothelial and smooth muscle cells, thus creating bioartificial blood vessels. Herein, the progenitors of smooth muscle and endothelial cells hold great promise because they efficiently differentiate and harbor longevity. In this review, we describe a novel tissue engineering approach that uses current insights from developmental biology, that is, progenitor cell plasticity, and the latest advances in biomaterial design. We focus specifically on developmental processes that regulate progenitor cell (trans)differentiation and offer a platform for the integration of these molecular clues into biomaterial design. We propose a novel engineering paradigm for the creation of a small-diameter blood vessel wherein progenitor cell differentiation and tissue organization are instructed by the biomaterial solely. With this review, we emphasize the power of integrating developmental biology and material science for vascular tissue engineering. PMID:19345319

  6. 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…

  7. 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.

  8. Network-Based Models in Molecular Biology

    NASA Astrophysics Data System (ADS)

    Beyer, Andreas

    Biological systems are characterized by a large number of diverse interactions. Interaction maps have been used to abstract those interactions at all biological scales ranging from food webs at the ecosystem level down to protein interaction networks at the molecular scale.

  9. An engineering viewpoint on biological robustness.

    PubMed

    Khammash, Mustafa

    2016-01-01

    In his splendid article "Can a biologist fix a radio?--or, what I learned while studying apoptosis," Y. Lazebnik argues that when one uses the right tools, similarity between a biological system, like a signal transduction pathway, and an engineered system, like a radio, may not seem so superficial. Here I advance this idea by focusing on the notion of robustness as a unifying lens through which to view complexity in biological and engineered systems. I show that electronic amplifiers and gene expression circuits share remarkable similarities in their dynamics and robustness properties. I explore robustness features and limitations in biology and engineering and highlight the role of negative feedback in shaping both. PMID:27007299

  10. 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…

  11. Engineering colloidal assembly via biological adhesion

    NASA Astrophysics Data System (ADS)

    Hiddessen, Amy Lynn

    Due to highly specialized recognition properties, biological receptor-ligand interactions offer valuable tools for engineering the assembly of novel colloidal materials. A unique sub-class of these macromolecules, called selectins, was exploited to develop binary suspensions where particles are programmed to associate reversibly or irreversibly via specific biomolecular cross-linking. Flow cytometry and videomicroscopy were used to examine factors controlling suspension assembly and structure, including biomolecular affinity and density, and individual and total particle volume fractions. By functionalizing small (RA = 0.47 mum) and larger (RB = 2.75 mum) particles with high surface densities of complementary E-selectin/sialyl Lewis X (sLeX) carbohydrate chemistry, a series of structures, from colloidal micelles (large particle coated with smaller particles) and clusters, to rings and elongated chains, was synthesized by decreasing the number ratio, NA/NB, of small (A) to large (B) particles (2 ≤ NA/NB ≤ 200) at low total volume fraction (10-4 ≤ φT ≤ 10-3 ). Using significantly lower surface densities, the low affinity binding between E-selectin and sLeX was exploited to create particles that interact reversibly, and average particle interaction lifetimes were tuned from minutes down to single selectin-carbohydrate bond lifetimes (≈1 s) by reducing sLeX density, a significant step toward assembling ordered microstructures. Particle binding lifetimes were analyzed with a receptor-ligand binding model, yielding estimates for molecular parameters, including on rate, 10-2 s-1 < kon < 10-1 s-1, and unstressed off rate, 0.25 s-1 ≤ kor ≤ 1.0 s-1, that characterize the docking dynamics of particles. Finally, at significantly higher volume fraction (φ T ≥ 10-1) and low number ratio, the rheology of space-filling networks crosslinked by high affinity streptavidin-biotin chemistry was probed to acquire knowledge on bulk properties of biocolloidal suspensions

  12. Engineering and Assembly of Protein Modules into Functional Molecular Systems.

    PubMed

    Hirschi, Stephan; Stauffer, Mirko; Harder, Daniel; Müller, Daniel J; Meier, Wolfgang; Fotiadis, Dimitrios

    2016-01-01

    Synthetic biology approaches range from the introduction of unique features into organisms to the assembly of isolated biomacromolecules or synthetic building blocks into artificial biological systems with biomimetic or completely novel functionalities. Simple molecular systems can be based on containers on the nanoscale that are equipped with tailored functional modules for various applications in healthcare, industry or biological and medical research. The concept, or vision, of assembling native or engineered proteins and/or synthetic components as functional modules into molecular systems is discussed. The main focus is laid on the engineering of energizing modules generating chemical energy, transport modules using this energy to translocate molecules between compartments of a molecular system, and catalytic modules (bio-)chemically processing the molecules. Further key aspects of this discourse are possible approaches for the assembly of simple nanofactories and their applications in biotechnology and medical health. PMID:27363367

  13. 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.

  14. Can biological complexity be reverse engineered?

    PubMed

    Green, Sara

    2015-10-01

    Concerns with the use of engineering approaches in biology have recently been raised. I examine two related challenges to biological research that I call the synchronic and diachronic underdetermination problem. The former refers to challenges associated with the inference of design principles underlying system capacities when the synchronic relations between lower-level processes and higher-level systems capacities are degenerate (many-to-many). The diachronic underdetermination problem regards the problem of reverse engineering a system where the non-linear relations between system capacities and lower-level mechanisms are changing over time. Braun and Marom argue that recent insights to biological complexity leave the aim of reverse engineering hopeless - in principle as well as in practice. While I support their call for systemic approaches to capture the dynamic nature of living systems, I take issue with the conflation of reverse engineering with naïve reductionism. I clarify how the notion of design principles can be more broadly conceived and argue that reverse engineering is compatible with a dynamic view of organisms. It may even help to facilitate an integrated account that bridges the gap between mechanistic and systems approaches. PMID:25903121

  15. [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). PMID:23587623

  16. From Gene to Protein: A 3-Week Intensive Course in Molecular Biology for Physical Scientists

    ERIC Educational Resources Information Center

    Nadeau, Jay L.

    2009-01-01

    This article describes a 3-week intensive molecular biology methods course based upon fluorescent proteins, which is successfully taught at the McGill University to advanced undergraduates and graduates in physics, chemical engineering, biomedical engineering, and medicine. No previous knowledge of biological terminology or methods is expected, so…

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. Glycan Engineering for Cell and Developmental Biology

    PubMed Central

    Griffin, Matthew E.; Hsieh-Wilson, Linda C.

    2016-01-01

    Cell-surface glycans are a diverse class of macromolecules that participate in many key biological processes, including cell-cell communication, development, and disease progression. Thus, the ability to modulate the structures of glycans on cell surfaces provides a powerful means not only to understand fundamental processes but also to direct activity and elicit desired cellular responses. Here, we describe methods to sculpt glycans on cell surfaces and highlight recent successes in which artificially engineered glycans have been employed to control biological outcomes such as the immune response and stem cell fate. PMID:26933739

  2. Engineering biological systems with synthetic RNA molecules

    PubMed Central

    Liang, Joe C.; Bloom, Ryan J.; Smolke, Christina D.

    2011-01-01

    RNA molecules play diverse functional roles in natural biological systems. There has been growing interest in designing synthetic RNA counterparts for programming biological function. The design of synthetic RNA molecules that exhibit diverse activities, including sensing, regulatory, information processing, and scaffolding activities, has highlighted the advantages of RNA as a programmable design substrate. Recent advances in implementing these engineered RNA molecules as key control elements in synthetic genetic networks are highlighting the functional relevance of this class of synthetic elements in programming cellular behaviors. PMID:21925380

  3. Mapping the moral boundaries of biological engineering

    PubMed Central

    Russ, Zachary N

    2009-01-01

    The following essay was written by a sophomore undergraduate student majoring in Bioengineering at the University of Maryland, Mr. Zachary Russ. Mr. Russ was one of 174 students who submitted a 1000–1200 word essay to the 4th Annual Bioethics Contest sponsored by the Institute of Biological Engineering (IBE). A group of professionals in Biological Engineering assessed and ranked the essays in a blinded process. Five semi-finalists were invited to present their essays at a session at the annual meeting of IBE in Santa Clara, CA on March 21, 2009. Five judges scored all the presentation at the annual meeting and selected Mr. Russ's contribution as the overall winner (1st Place). PMID:19422721

  4. Book review: Baculovirus Molecular Biology, Second Edition

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  5. 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.

  6. Molecular Engineering of DNA: Molecular Beacons

    PubMed Central

    Tang, Zhiwen; Yang, Chaoyong James; Kim, Youngmi; Fang, Xiaohong; Li, Wei; Wu, Yanrong; Medley, Colin D.; Cao, Zehui; Li, Jun; Colon, Patrick; Lin, Hui

    2009-01-01

    Molecular beacons (MBs) are specifically designed DNA hairpin structures that are widely used as fluorescent probes. Applications of MBs range from genetic screening, biosensor development, biochip construction, and the detection of single-nucleotide polymorphisms to mRNA monitoring in living cells. The inherent signal-transduction mechanism of MBs enables the analysis of target oligonucleotides without the separation of unbound probes. The MB stem–loop structure holds the fluorescence-donor and fluorescence-acceptor moieties in close proximity to one another, which results in resonant energy transfer. A spontaneous conformation change occurs upon hybridization to separate the two moieties and restore the fluorescence of the donor. Recent research has focused on the improvement of probe composition, intracellular gene quantitation, protein–DNA interaction studies, and protein recognition. PMID:19065690

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

    PubMed

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

    2016-01-01

    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. PMID:27311441

  8. New journal: Algorithms for Molecular Biology.

    PubMed

    Morgenstern, Burkhard; Stadler, Peter F

    2006-01-01

    This editorial announces Algorithms for Molecular Biology, a new online open access journal published by BioMed Central. By launching the first open access journal on algorithmic bioinformatics, we provide a forum for fast publication of high-quality research articles in this rapidly evolving field. Our journal will publish thoroughly peer-reviewed papers without length limitations covering all aspects of algorithmic data analysis in computational biology. Publications in Algorithms for Molecular Biology are easy to find, highly visible and tracked by organisations such as PubMed. An established online submission system makes a fast reviewing procedure possible and enables us to publish accepted papers without delay. All articles published in our journal are permanently archived by PubMed Central and other scientific archives. We are looking forward to receiving your contributions. PMID:16722576

  9. New faster CHARMM molecular dynamics engine

    PubMed Central

    Hynninen, Antti-Pekka; Crowley, Michael F

    2014-01-01

    We introduce a new faster molecular dynamics (MD) engine into the CHARMM software package. The new MD engine is faster both in serial (i.e., single CPU core) and parallel execution. Serial performance is approximately two times higher than in the previous version of CHARMM. The newly programmed parallelization method allows the MD engine to parallelize up to hundreds of CPU cores. PMID:24302199

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

    PubMed

    Phair, Robert D

    2014-11-01

    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. PMID:25368428

  11. Ship diesel emission aerosols: A comprehensive study on the chemical composition, the physical properties and the molecular biological and toxicological effects on human lung cells of aerosols from a ship diesel engine operated with heavy or light diesel fuel oil

    NASA Astrophysics Data System (ADS)

    Zimmermann, R.; Buters, J.; Öder, S.; Dietmar, G.; Kanashova, T.; Paur, H.; Dilger, M.; Mülhopt, S.; Harndorf, H.; Stengel, B.; Rabe, R.; Hirvonen, M.; Jokiniemi, J.; Hiller, K.; Sapcariu, S.; Berube, K.; Sippula, O.; Streibel, T.; Karg, E.; Schnelle-Kreis, J.; Lintelmann, J.; Sklorz, M.; Arteaga Salas, M.; Orasche, J.; Müller, L.; Reda, A.; Passig, J.; Radischat, C.; Gröger, T.; Weiss, C.

    2013-12-01

    The Virtual Helmholtz Institute-HICE (www.hice-vi.eu) addresses chemical & physical properties, transformation processes and health effects of anthropogenic combustion emissions. This is performed by thorough comprehensive chemical and physical characterization of combustion aerosols (including application of advantageous on-line methods) and studying of biological effects on human lung cell-cultures. A new ALI air-liquid-interface (ALI) exposition system and a mobile S2-biological laboratory were developed for the HICE-measurements. Human alveolar basal epithelial cells (A549 etc.) are ALI-exposed to fresh, diluted (1:40-1:100) combustion aerosols and subsequently were toxicologically and molecular-biologically characterized (e.g. proteomics). By using stable isotope labeling technologies (13C-Glucose/metabolomics; 2H-Lysine/SILAC-proteomics), high sensitivity and accuracy for detection of molecular-biological effects is achievable even at sub-toxic effect dose levels. Aerosols from wood combustion and ship diesel engine (heavy/light fuel oil) have been investigated. The effect of wood combustion and ship diesel PM e.g. on the protein expression of ALI-exposed A549 cells was compared. Filtered aerosol is used as gas-reference for the isotope labeling based method (SILAC). Therefore the effects of wood combustion- and shipping diesel-PM can be directly compared. Ship diesel aerosol causes a broader distribution in the observed fold changes (log2), i.e. more proteins are significantly up-/down-regulated in case of shipping diesel PM-exposure. This corresponds to a stronger biological reaction if compared to wood combustion-PM exposure. The chemical analysis results on wood combustion- and ship diesel-PM depict more polycyclic aromatic hydrocarbons (PAH)/oxidized-PAH but less of some transition metals (V, Fe) in the wood combustion case. Interestingly, alkylated PAH are considerably more abundant in shipping PM, suggesting that PAH/Oxy-PAH may be less relevant for

  12. 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.

  13. Molecular knots in biology and chemistry.

    PubMed

    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. PMID:26291690

  14. 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.

  15. Synthesis of biological molecules on molecular sieves.

    PubMed

    Poncelet, G; Van Assche, A T; Fripiat, J J

    1975-07-01

    Catalytic properties of aluminosilicates may play a role in the synthesis of biological molecules from simple gaseous molecules commonly found in planetary atmospheres. Urea, amino acids and UV absorbing substances have been obtained by heating CO and NH3 with Linde molecular sieves saturated with Ca+2, NH4+ or Fe+3. The yields of amino acids produced have been determined by an amino acid analyzer. The quantity of urea produced largely depends on the nature of the saturating cation. Experiments using 14CO confirm that the amino acids are not due to contaminants adsorbed on the surface of the molecular sieves. PMID:171609

  16. Molecular neurodegeneration: basic biology and disease pathways.

    PubMed

    Vassar, Robert; Zheng, Hui

    2014-01-01

    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. PMID:25248568

  17. 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.

  18. Engineering supported membranes for cell biology

    PubMed Central

    Yu, Cheng-han

    2010-01-01

    Cell membranes exhibit multiple layers of complexity, ranging from their specific molecular content to their emergent mechanical properties and dynamic spatial organization. Both compositional and geometrical organizations of membrane components are known to play important roles in life processes, including signal transduction. Supported membranes, comprised of a bilayer assembly of phospholipids on the solid substrate, have been productively served as model systems to study wide range problems in cell biology. Because lateral mobility of membrane components is readily preserved, supported lipid membranes with signaling molecules can be utilized to effectively trigger various intercellular reactions. The spatial organization and mechanical deformation of supported membranes can also be manipulated by patterning underlying substrates with modern micro- and nano-fabrication techniques. This article focuses on various applications and methods to spatially patterned biomembranes by means of curvature modulations and spatial reorganizations, and utilizing them to interface with live cells. The integration of biological components into synthetic devices provides a unique approach to investigate molecular mechanisms in cell biology. PMID:20559751

  19. Engineering biological systems toward a sustainable bioeconomy.

    PubMed

    Lopes, Mateus Schreiner Garcez

    2015-06-01

    The nature of our major global risks calls for sustainable innovations to decouple economic growth from greenhouse gases emission. The development of sustainable technologies has been negatively impacted by several factors including sugar production costs, production scale, economic crises, hydraulic fracking development and the market inability to capture externality costs. However, advances in engineering of biological systems allow bridging the gap between exponential growth of knowledge about biology and the creation of sustainable value chains for a broad range of economic sectors. Additionally, industrial symbiosis of different biobased technologies can increase competitiveness and sustainability, leading to the development of eco-industrial parks. Reliable policies for carbon pricing and revenue reinvestments in disruptive technologies and in the deployment of eco-industrial parks could boost the welfare while addressing our major global risks toward the transition from a fossil to a biobased economy. PMID:25845304

  20. 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. PMID:21836667

  1. Recent Advances in Engineering Polyvalent Biological Interactions

    PubMed Central

    2015-01-01

    Polyvalent interactions, where multiple ligands and receptors interact simultaneously, are ubiquitous in nature. Synthetic polyvalent molecules, therefore, have the ability to affect biological processes ranging from protein–ligand binding to cellular signaling. In this review, we discuss recent advances in polyvalent scaffold design and applications. First, we will describe recent developments in the engineering of polyvalent scaffolds based on biomolecules and novel materials. Then, we will illustrate how polyvalent molecules are finding applications as toxin and pathogen inhibitors, targeting molecules, immune response modulators, and cellular effectors. PMID:25426695

  2. 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. PMID:8595133

  3. Systems Biology: The Role of Engineering in the Reverse Engineering of Biological Signaling

    PubMed Central

    Iglesias, Pablo A.

    2013-01-01

    One of the principle tasks of systems biology has been the reverse engineering of signaling networks. Because of the striking similarities to engineering systems, a number of analysis and design tools from engineering disciplines have been used in this process. This review looks at several examples including the analysis of homeostasis using control theory, the attenuation of noise using signal processing, statistical inference and the use of information theory to understand both binary decision systems and the response of eukaryotic chemotactic cells. PMID:24709707

  4. [The molecular biology of epithelial ovarian cancer].

    PubMed

    Leary, Alexandra; Pautier, Patricia; Tazi, Youssef; Morice, Philippe; Duvillard, Pierre; Gouy, Sébastien; Uzan, Catherine; Gauthier, Hélène; Balleyguier, Corinne; Lhommé, Catherine

    2012-12-01

    Epithelial ovarian cancer frequently presents at an advanced stage where the cornerstone of management remains surgery and platinum-based chemotherapy. Unfortunately, despite sometimes dramatic initial responses, advanced ovarian cancer almost invariably relapses. Little progress has been made in the identification of effective targeted-therapies for ovarian cancer. The majority of clinical trials investigating novel agents have been negative and the only approved targeted-therapy is bevacizumab, for which reliable predictive biomarkers still elude us. Ovarian cancer is treated as a uniform disease. Yet, biological studies have highlighted the heterogeneity of this malignancy with marked differences in histology, oncogenesis, prognosis, chemo-responsiveness, and molecular profile. Recent high throughput molecular analyses have identified a huge number of genomic/phenotypic alterations. Broadly speaking, high grade serous carcinomas (type II) display significant genomic instability and numerous amplifications and losses; low grade (type I) tumors are genomically stable but display frequent mutations. Importantly, many of these genomic alterations relate to known oncogenes for which targeted-therapies are available or in development. There is today a real potential for personalized medicine in ovarian cancer. We will review the current literature regarding the molecular characterization of epithelial ovarian cancer and discuss the biological rationale for a number of targeted strategies. In order to translate these biological advances into meaningful clinical improvements for our patients, it is imperative to incorporate translational research in ovarian cancer trials, a number of strategies will be proposed such as the acquisition of quality tumor samples, including sequential pre- and post-treatment biopsies, the potential of liquid biopsies, and novel trial designs more adapted to the molecular era of ovarian cancer research. PMID:23238064

  5. The Molecular Biology Database Collection: 2004 update

    PubMed Central

    Galperin, Michael Y.

    2004-01-01

    The Molecular Biology Database Collection is a public resource listing key databases of value to the biologist, including those featured in this issue of Nucleic Acids Research, and other high-quality databases. All databases included in this Collection are freely available to the public. This listing aims to serve as a convenient starting point for searching the web for reliable information on various aspects of molecular biology, biochemistry and genetics. This year’s update includes 548 databases, 162 more than the previous one. The databases are organized in a hierarchical classification that should simplify finding the right database for each given task. Each database in the list comes with a recently updated brief description. The database list and the database descriptions can be accessed online at the Nucleic Acids Research web site http://nar.oupjournals.org/. The great challenge in biological research today is how to turn data into knowledge. I have met people who think data is knowledge but these people are then striving for a means of turning knowledge into understanding.Sydney Brenner. The Scientist 16[6]:12, March 18, 2002 PMID:14681349

  6. Parts plus pipes: synthetic biology approaches to metabolic engineering

    PubMed Central

    Boyle, Patrick M.; Silver, Pamela A.

    2011-01-01

    Synthetic biologists combine modular biological “parts” to create higher-order devices. Metabolic engineers construct biological “pipes” by optimizing the microbial conversion of basic substrates to desired compounds. Many scientists work at the intersection of these two philosophies, employing synthetic devices to enhance metabolic engineering efforts. These integrated approaches promise to do more than simply improve product yields; they can expand the array of products that are tractable to produce biologically. In this review, we explore the application of synthetic biology techniques to next-generation metabolic engineering challenges, as well as the emerging engineering principles for biological design. PMID:22037345

  7. 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.

  8. Interfacial Engineering of Molecular Photovoltaics

    NASA Astrophysics Data System (ADS)

    Shelton, Steven Wade

    One of the most worthy pursuits in the field of organic solar cells is that of discovering ways to more effectively harvest charge generated by light absorption. The measure of the efficacy of this process is the external quantum efficiency (EQE). It is determined by the efficiency of incident light absorption, exciton diffusion, exciton splitting and charge transfer, and charge collection. Enhanced EQE can be realized by engineering interfaces between materials in the device to allow for smoother charge transfer throughout the extent of the device, which is usually between 10 and 200 nanometers. Improvements in charge transport are vitally important because the photogenerated excitons in electron donating polymers and small molecules typically only diffuse between 5 and 10 nanometers. These excitons must reach the interface between the electron donor and electron acceptor in order to be split so that the resulting electron and hole can be harvested at the cathode and anode, respectively. The aim of much of this dissertation is to describe a method by which the donor-acceptor interfacial area can be augmented using nanoimprint lithography, first with a single donor and then with multiple donors. Nanoimprint lithography is introduced as a simple embossing technique that can create features in a single component donor with dimensions as small as 20 nm. Solution-processable small molecules are of interest for their ease of synthesis and fabrication. I continue the discussion of nanoimprint lithography by offering candidates for a two-component donor combination. A two-component donor can extend the absorption range across a broader portion of the solar spectrum than just one donor to improve energy harvesting. After considering ways of optimizing the donor-acceptor interface, I describe the use of a charge selective layer for better charge transport and collection. When incorporated into a bilayer solar cell and an inverted solar cell, these two molecules markedly

  9. Molecular recognition in chemical and biological systems.

    PubMed

    Persch, Elke; Dumele, Oliver; Diederich, François

    2015-03-01

    Structure-based ligand design in medicinal chemistry and crop protection relies on the identification and quantification of weak noncovalent interactions and understanding the role of water. Small-molecule and protein structural database searches are important tools to retrieve existing knowledge. Thermodynamic profiling, combined with X-ray structural and computational studies, is the key to elucidate the energetics of the replacement of water by ligands. Biological receptor sites vary greatly in shape, conformational dynamics, and polarity, and require different ligand-design strategies, as shown for various case studies. Interactions between dipoles have become a central theme of molecular recognition. Orthogonal interactions, halogen bonding, and amide⋅⋅⋅π stacking provide new tools for innovative lead optimization. The combination of synthetic models and biological complexation studies is required to gather reliable information on weak noncovalent interactions and the role of water. PMID:25630692

  10. 2009 Archaea: Ecology, Metabolism & Molecular Biology GRC

    SciTech Connect

    Dr. Julie Maupin- Furlow

    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.

  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. Molecular Engineering of Acoustic Protein Nanostructures.

    PubMed

    Lakshmanan, Anupama; Farhadi, Arash; Nety, Suchita P; Lee-Gosselin, Audrey; Bourdeau, Raymond W; Maresca, David; Shapiro, Mikhail G

    2016-08-23

    Ultrasound is among the most widely used biomedical imaging modalities, but has limited ability to image specific molecular targets due to the lack of suitable nanoscale contrast agents. Gas vesicles-genetically encoded protein nanostructures isolated from buoyant photosynthetic microbes-have recently been identified as nanoscale reporters for ultrasound. Their unique physical properties give gas vesicles significant advantages over conventional microbubble contrast agents, including nanoscale dimensions and inherent physical stability. Furthermore, as a genetically encoded material, gas vesicles present the possibility that the nanoscale mechanical, acoustic, and targeting properties of an imaging agent can be engineered at the level of its constituent proteins. Here, we demonstrate that genetic engineering of gas vesicles results in nanostructures with new mechanical, acoustic, surface, and functional properties to enable harmonic, multiplexed, and multimodal ultrasound imaging as well as cell-specific molecular targeting. These results establish a biomolecular platform for the engineering of acoustic nanomaterials. PMID:27351374

  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. 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.

  15. Biologically inspired highly efficient buoyancy engine

    NASA Astrophysics Data System (ADS)

    Akle, Barbar; Habchi, Wassim; Abdelnour, Rita; Blottman, John, III; Leo, Donald

    2012-04-01

    Undersea distributed networked sensor systems require a miniaturization of platforms and a means of both spatial and temporal persistence. One aspect of this system is the necessity to modulate sensor depth for optimal positioning and station-keeping. Current approaches involve pneumatic bladders or electrolysis; both require mechanical subsystems and consume significant power. These are not suitable for the miniaturization of sensor platforms. Presented in this study is a novel biologically inspired method that relies on ionic motion and osmotic pressures to displace a volume of water from the ocean into and out of the proposed buoyancy engine. At a constant device volume, the displaced water will alter buoyancy leading to either sinking or floating. The engine is composed of an enclosure sided on the ocean's end by a Nafion ionomer and by a flexible membrane separating the water from a gas enclosure. Two electrodes are placed one inside the enclosure and the other attached to the engine on the outside. The semi-permeable membrane Nafion allows water motion in and out of the enclosure while blocking anions from being transferred. The two electrodes generate local concentration changes of ions upon the application of an electrical field; these changes lead to osmotic pressures and hence the transfer of water through the semi-permeable membrane. Some aquatic organisms such as pelagic crustacean perform this buoyancy control using an exchange of ions through their tissue to modulate its density relative to the ambient sea water. In this paper, the authors provide an experimental proof of concept of this buoyancy engine. The efficiency of changing the engine's buoyancy is calculated and optimized as a function of electrode surface area. For example electrodes made of a 3mm diameter Ag/AgCl proved to transfer approximately 4mm3 of water consuming 4 Joules of electrical energy. The speed of displacement is optimized as a function of the surface area of the Nafion

  16. Rhabdomyosarcoma: Advances in Molecular and Cellular Biology

    PubMed Central

    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. PMID:26420980

  17. From Cellular Mechanotransduction to Biologically Inspired Engineering

    PubMed Central

    Ingber, Donald E.

    2010-01-01

    This article is based on a lecture I presented as the recipient of the 2009 Pritzker Distinguished Lecturer Award at the Biomedical Engineering Society annual meeting in October 2009. Here, I review more than thirty years of research from my laboratory, beginning with studies designed to test the theory that cells use tensegrity (tensional integrity) architecture to stabilize their shape and sense mechanical signals, which I believed to be critical for control of cell function and tissue development. Although I was trained as a cell biologist, I found that the tools I had at my disposal were insufficient to experimentally test these theories, and thus I ventured into engineering to find critical solutions. This path has been extremely fruitful as it has led to confirmation of the critical role that physical forces play in developmental control, as well as how cells sense and respond to mechanical signals at the molecular level through a process known as cellular mechanotransduction. Many of the predictions of the cellular tensegrity model relating to cell mechanical behaviors have been shown to be valid, and this vision of cell structure led to discovery of the central role that transmembrane adhesion receptors, such as integrins, and the cytoskeleton play in mechanosensing and mechanochemical conversion. In addition, these fundamental studies have led to significant unexpected technology fallout, including development of micromagnetic actuators for non-invasive control of cellular signaling, microfluidic systems as therapeutic extracorporeal devices for sepsis therapy, and new DNA-based nanobiotechnology approaches that permit construction of artificial tensegrities that mimic properties of living materials for applications in tissue engineering and regenerative medicine. PMID:20140519

  18. Reverse engineering chemical structures from molecular descriptors : how many solutions?

    SciTech Connect

    Brown, William Michael; Martin, Shawn Bryan; Faulon, Jean-Loup Michel

    2005-06-01

    Physical, chemical and biological properties are the ultimate information of interest for chemical compounds. Molecular descriptors that map structural information to activities and properties are obvious candidates for information sharing. In this paper, we consider the feasibility of using molecular descriptors to safely exchange chemical information in such a way that the original chemical structures cannot be reverse engineered. To investigate the safety of sharing such descriptors, we compute the degeneracy (the number of structure matching a descriptor value) of several 2D descriptors, and use various methods to search for and reverse engineer structures. We examine degeneracy in the entire chemical space taking descriptors values from the alkane isomer series and the PubChem database. We further use a stochastic search to retrieve structures matching specific topological index values. Finally, we investigate the safety of exchanging of fragmental descriptors using deterministic enumeration.

  19. Open computing grid for molecular science and engineering.

    PubMed

    Sild, Sulev; Maran, Uko; Lomaka, Andre; Karelson, Mati

    2006-01-01

    Grid is an emerging infrastructure for distributed computing that provides secure and scalable mechanisms for discovering and accessing remote software and data resources. Applications built on this infrastructure have great potential for addressing and solving large scale chemical, pharmaceutical, and material science problems. The article describes the concept behind grid computing and will present the OpenMolGRID system that is an open computing grid for molecular science and engineering. This system provides grid enabled components, such as a data warehouse for chemical data, software for building QSPR/QSAR models, and molecular engineering tools for generating compounds with predefined chemical properties or biological activities. The article also provides an overview about the availability of chemical applications in the grid. PMID:16711713

  20. 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

  1. 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…

  2. 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,…

  3. 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. PMID:17249499

  4. PREFACE: Nanobiology: from physics and engineering to biology

    NASA Astrophysics Data System (ADS)

    Nussinov, Ruth; Alemán, Carlos

    2006-03-01

    Biological systems are inherently nano in scale. Unlike nanotechnology, nanobiology is characterized by the interplay between physics, materials science, synthetic organic chemistry, engineering and biology. Nanobiology is a new discipline, with the potential of revolutionizing medicine: it combines the tools, ideas and materials of nanoscience and biology; it addresses biological problems that can be studied and solved by nanotechnology; it devises ways to construct molecular devices using biomacromolecules; and it attempts to build molecular machines utilizing concepts seen in nature. Its ultimate aim is to be able to predictably manipulate these, tailoring them to specified needs. Nanobiology targets biological systems and uses biomacromolecules. Hence, on the one hand, nanobiology is seemingly constrained in its scope as compared to general nanotechnology. Yet the amazing intricacy of biological systems, their complexity, and the richness of the shapes and properties provided by the biological polymers, enrich nanobiology. Targeting biological systems entails comprehension of how they work and the ability to use their components in design. From the physical standpoint, ultimately, if we are to understand biology we need to learn how to apply physical principles to figure out how these systems actually work. The goal of nanobiology is to assist in probing these systems at the appropriate length scale, heralding a new era in the biological, physical and chemical sciences. Biology is increasingly asking quantitative questions. Quantitation is essential if we are to understand how the cell works, and the details of its regulation. The physical sciences provide tools and strategies to obtain accurate measurements and simulate the information to allow comprehension of the processes. Nanobiology is at the interface of the physical and the biological sciences. Biology offers to the physical sciences fascinating problems, sophisticated systems and a rich repertoire of

  5. Software agents in molecular computational biology.

    PubMed

    Keele, John W; Wray, James E

    2005-12-01

    Progress made in applying agent systems to molecular computational biology is reviewed and strategies by which to exploit agent technology to greater advantage are investigated. Communities of software agents could play an important role in helping genome scientists design reagents for future research. The advent of genome sequencing in cattle and swine increases the complexity of data analysis required to conduct research in livestock genomics. Databases are always expanding and semantic differences among data are common. Agent platforms have been developed to deal with generic issues such as agent communication, life cycle management and advertisement of services (white and yellow pages). This frees computational biologists from the drudgery of having to re-invent the wheel on these common chores, giving them more time to focus on biology and bioinformatics. Agent platforms that comply with the Foundation for Intelligent Physical Agents (FIPA) standards are able to interoperate. In other words, agents developed on different platforms can communicate and cooperate with one another if domain-specific higher-level communication protocol details are agreed upon between different agent developers. Many software agent platforms are peer-to-peer, which means that even if some of the agents and data repositories are temporarily unavailable, a subset of the goals of the system can still be met. Past use of software agents in bioinformatics indicates that an agent approach should prove fruitful. Examination of current problems in bioinformatics indicates that existing agent platforms should be adaptable to novel situations. PMID:16420735

  6. 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.

  7. 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.

  8. Systematic technology transfer from biology to engineering.

    PubMed

    Vincent, Julian F V; Mann, Darrell L

    2002-02-15

    Solutions to problems move only very slowly between different disciplines. Transfer can be greatly speeded up with suitable abstraction and classification of problems. Russian researchers working on the TRIZ (Teoriya Resheniya Izobretatelskikh Zadatch) method for inventive problem solving have identified systematic means of transferring knowledge between different scientific and engineering disciplines. With over 1500 person years of effort behind it, TRIZ represents the biggest study of human creativity ever conducted, whose aim has been to establish a system into which all known solutions can be placed, classified in terms of function. At present, the functional classification structure covers nearly 3 000 000 of the world's successful patents and large proportions of the known physical, chemical and mathematical knowledge-base. Additional tools are the identification of factors which prevent the attainment of new technology, leading directly to a system of inventive principles which will resolve the impasse, a series of evolutionary trends of development, and to a system of methods for effecting change in a system (Su-fields). As yet, the database contains little biological knowledge despite early recognition by the instigator of TRIZ (Genrich Altshuller) that one day it should. This is illustrated by natural systems evolved for thermal stability and the maintenance of cleanliness. PMID:16210175

  9. Biological hydroperoxides and singlet molecular oxygen generation.

    PubMed

    Miyamoto, Sayuri; Ronsein, Graziella E; Prado, Fernanda M; Uemi, Miriam; Corrêa, Thais C; Toma, Izaura N; Bertolucci, Agda; Oliveira, Mauricio C B; Motta, Flávia D; Medeiros, Marisa H G; Mascio, Paolo Di

    2007-01-01

    The decomposition of lipid hydroperoxides (LOOH) into peroxyl radicals is a potential source of singlet molecular oxygen ((1)O(2)) in biological systems. Recently, we have clearly demonstrated the generation of (1)O(2) in the reaction of lipid hydroperoxides with biologically important oxidants such as metal ions, peroxynitrite and hypochlorous acid. The approach used to unequivocally demonstrate the generation of (1)O(2) in these reactions was the use of an isotopic labeled hydroperoxide, the (18)O-labeled linoleic acid hydroperoxide, the detection of labeled compounds by HPLC coupled to tandem mass spectrometry (HPLC-MS/MS) and the direct spectroscopic detection and characterization of (1)O(2) light emission. Using this approach we have observed the formation of (18)O-labeled (1)O(2) by chemical trapping of (1)O(2) with anthracene derivatives and detection of the corresponding labeled endoperoxide by HPLC-MS/MS. The generation of (1)O(2) was also demonstrated by direct spectral characterization of (1)O(2) monomol light emission in the near-infrared region (lambda = 1270 nm). In summary, our studies demonstrated that LOOH can originate (1)O(2). The experimental evidences indicate that (1)O(2) is generated at a yield close to 10% by the Russell mechanism, where a linear tetraoxide intermediate is formed in the combination of two peroxyl radicals. In addition to LOOH, other biological hydroperoxides, including hydroperoxides formed in proteins and nucleic acids, may also participate in reactions leading to the generation (1)O(2). This hypothesis is currently being investigated in our laboratory. PMID:17505972

  10. 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. PMID:26697989

  11. 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.

  12. Challenges and opportunities in synthetic biology for chemical engineers

    PubMed Central

    Luo, Yunzi; Lee, Jung-Kul; Zhao, Huimin

    2012-01-01

    Synthetic biology provides numerous great opportunities for chemical engineers in the development of new processes for large-scale production of biofuels, value-added chemicals, and protein therapeutics. However, challenges across all scales abound. In particular, the modularization and standardization of the components in a biological system, so-called biological parts, remain the biggest obstacle in synthetic biology. In this perspective, we will discuss the main challenges and opportunities in the rapidly growing synthetic biology field and the important roles that chemical engineers can play in its advancement. PMID:24222925

  13. Challenges and opportunities in synthetic biology for chemical engineers

    SciTech Connect

    Luo, YZ; Lee, JK; Zhao, HM

    2013-11-15

    Synthetic biology provides numerous great opportunities for chemical engineers in the development of new processes for large-scale production of biofuels, value-added chemicals, and protein therapeutics. However, challenges across all scales abound. In particular, the modularization and standardization of the components in a biological system, so-called biological parts, remain the biggest obstacle in synthetic biology. In this perspective, we will discuss the main challenges and opportunities in the rapidly growing synthetic biology field and the important roles that chemical engineers can play in its advancement. (C) 2012 Elsevier Ltd. All rights reserved.

  14. Systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

    PubMed

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-01-01

    Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875

  15. Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

    PubMed Central

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-01-01

    Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875

  16. IntegromeDB: an integrated system and biological search engine

    PubMed Central

    2012-01-01

    Background With the growth of biological data in volume and heterogeneity, web search engines become key tools for researchers. However, general-purpose search engines are not specialized for the search of biological data. Description Here, we present an approach at developing a biological web search engine based on the Semantic Web technologies and demonstrate its implementation for retrieving gene- and protein-centered knowledge. The engine is available at http://www.integromedb.org. Conclusions The IntegromeDB search engine allows scanning data on gene regulation, gene expression, protein-protein interactions, pathways, metagenomics, mutations, diseases, and other gene- and protein-related data that are automatically retrieved from publicly available databases and web pages using biological ontologies. To perfect the resource design and usability, we welcome and encourage community feedback. PMID:22260095

  17. 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.

  18. Molecular biology of breast tumors and prognosis

    PubMed Central

    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. PMID:27134741

  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. 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…

  1. 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…

  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. Unconventional biological threats and the molecular biological response to biological threats.

    PubMed

    Greenfield, Ronald A; Lutz, Brock D; Huycke, Mark M; Gilmore, Michael S

    2002-06-01

    This article concludes this symposium on potential agents of warfare and terrorism with discussion of 3 topics. First, influenza A virus is discussed as a potential biological weapon. Although it does not receive much attention in this role, the potential for mass casualties and public panic certainly exist if an epidemic of a virulent influenza A virus were initiated. Second, agroterrorism, terrorism directed at livestock or poultry or crops, is briefly discussed. Finally, the potential role of techniques of modern molecular biology to create new agents for bioterrorism or enhance the terrorist potential of available agents, and the known roles of these techniques in defense against biological warfare or terrorism are discussed. PMID:12074489

  4. At the birth of molecular radiation biology.

    PubMed

    Devoret, R

    2001-01-01

    Rational thinking builds on feelings, too. This article starts with a tribute to Richard Setlow, an eminent scientist; it retraces as well some studies in molecular genetics that helped to understand basic questions of radiation biology. In the mid-1950s, the induction of a dormant virus (prophage) by irradiation of its host was an intriguing phenomenon. Soon, it was found that prophage induction results from the inactivation of the prophage repressor. Similarly, a score of induced cellular SOS functions were found to be induced when the LexA repressor is inactivated. Repressor inactivation involves the formation of a newly formed distinctive structure: a RecA-polymer wrapped around single-stranded DNA left by the arrest of replication at damaged sites. By touching this RecA nucleofilament, the LexA repressor is inactivated, triggering the sequential expression of SOS functions. The RecA nucleofilament acts as a chaperone, allowing recombinational repair to occur after nucleotide excision repair is over. The UmuD'C complex, synthesized slowly and parsimoniously, peaks at the end of recombinational repair, ready to be positioned at the tip of a RecA nucleofilament, placing the UmuD'C complex right at a lesion. At this location, UmuD'C prevents recombinational repair, and now acts as an error-prone paucimerase that fills the discontinuity opposite the damaged DNA. Finally, the elimination of lesions from the path of DNA polymerase, allows the resumption of DNA replication, and the SOS repair cycle switches to a normal cell cycle. PMID:11746747

  5. Advancing metabolic engineering through systems biology of industrial microorganisms.

    PubMed

    Dai, Zongjie; Nielsen, Jens

    2015-12-01

    Development of sustainable processes to produce bio-based compounds is necessary due to the severe environmental problems caused by the use of fossil resources. Metabolic engineering can facilitate the development of highly efficient cell factories to produce these compounds from renewable resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further. PMID:26318074

  6. Accessing Nature's diversity through metabolic engineering and synthetic biology.

    PubMed

    King, Jason R; Edgar, Steven; Qiao, Kangjian; Stephanopoulos, Gregory

    2016-01-01

    In this perspective, we highlight recent examples and trends in metabolic engineering and synthetic biology that demonstrate the synthetic potential of enzyme and pathway engineering for natural product discovery. In doing so, we introduce natural paradigms of secondary metabolism whereby simple carbon substrates are combined into complex molecules through "scaffold diversification", and subsequent "derivatization" of these scaffolds is used to synthesize distinct complex natural products. We provide examples in which modern pathway engineering efforts including combinatorial biosynthesis and biological retrosynthesis can be coupled to directed enzyme evolution and rational enzyme engineering to allow access to the "privileged" chemical space of natural products in industry-proven microbes. Finally, we forecast the potential to produce natural product-like discovery platforms in biological systems that are amenable to single-step discovery, validation, and synthesis for streamlined discovery and production of biologically active agents. PMID:27081481

  7. Acellular assessments of engineered-manufactured nanoparticle biological surface reactivity

    EPA Science Inventory

    It is critical to assess the surface properties and reactivity of engineered-manufactured nanoparticles (NPs) as these will influence their interactions with biological systems, biokinetics and toxicity. We examined the physicochemical properties and surface reactivity of metal o...

  8. The molecular biology of pulmonary metastasis.

    PubMed

    Krishnan, Kartik; Khanna, Chand; Helman, Lee J

    2006-05-01

    Curing cancer requires the treatment of metastatic disease. Whether this is a patient with advanced disease and clinically apparent metastases, or if the patient with localized disease is at risk for development of dissemination, failure to control metastasis will result in a poor outcome. Here, we have presented a molecular guide to our current understanding of the processes underlying metastasis. Experimental clinical trials designed to further the understanding of metastasis are often limited by selection of patients with advanced disease. Therefore, our understanding of the processes involved in the metastatic cascade is limited by the availability of comprehensive experimental model systems. The study of metastasis relies most heavily on xenografts, tumors using human cell lines, or tumor tissue that can grow in mice. These models present a limited recapitulation of the patients. Xenograft models require some degree of immunosuppression on the part of the host, because mice with native immune systems will reject transplanted human tumors, preventing their growth. As a result, mice with immune defects ranging from depleted T cells (nude mice) to absent T, B, and NK cells (SCID-Beige) are used as hosts. As the evasion of the immune system is a key function demonstrated by the metastatic cancer cell, xenograft models, by necessity, subvert this step. Furthermore, recent studies have established that angiogenesis in transplanted tumors is different than in native tumors, further highlighting the limitations of these models. With these limitations, studies of metastasis may require development of models of autochthonous tumors, that is, tumors originating in the study animals. A number of cell lines of autochthonous murine tumors have been established that generate metastatic disease after implantation into mice. Moreover, some transgenic animals spontaneously develop metastatic tumors that, although occurring in genetically engineered animals, may represent the

  9. Infusing Bioinformatics and Research-Like Experience into a Molecular Biology Laboratory Course

    ERIC Educational Resources Information Center

    Nogaj, Luiza A.

    2014-01-01

    A nine-week laboratory project designed for a sophomore level molecular biology course is described. Small groups of students (3-4 per group) choose a tumor suppressor gene (TSG) or an oncogene for this project. Each group researches the role of their TSG/oncogene from primary literature articles and uses bioinformatics engines to find the gene…

  10. Introduction to bioengineering: melding of engineering and biological sciences.

    PubMed

    Shoureshi, Rahmat A

    2005-04-01

    Engineering has traditionally focused on the external extensions of organisms, such as transportation systems, high-rise buildings, and entertainment systems. In contrast, bioengineering is concerned with inward processes of biologic organisms. Utilization of engineering principles and techniques in the analysis and solution of problems in medicine and biology is the basis for bioengineering. This article discusses subspecialties in bioengineering and presents examples of projects in this discipline. PMID:15823588

  11. Synthetic biology: new engineering rules for an emerging discipline

    PubMed Central

    Andrianantoandro, Ernesto; Basu, Subhayu; Karig, David K; Weiss, Ron

    2006-01-01

    Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development. PMID:16738572

  12. Biological Engineering: A New Discipline for the Next Century.

    ERIC Educational Resources Information Center

    Tao, Bernard Y.

    1993-01-01

    Reviews the issues driving the need for a biological engineering discipline and summarizes current curricula at several universities. The Purdue Biochemical and Food Processing Engineering program is presented as a model for the implementation of curriculum objectives. (23 references) (Author/MCO)

  13. Molecular biology techniques and applications for ocean sensing

    NASA Astrophysics Data System (ADS)

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

    2008-11-01

    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. Here we review some of the most commonly used molecular biological techniques. Molecular biological techniques permit study of the abundance, distribution, diversity, and physiology of microorganisms in situ. 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.

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

    PubMed Central

    Bartlett, Rebecca; Jetté, 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 DNA, RNA and protein assays and their relevance in the field of communication sciences and disorders (CSD). Methods Over the past two 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 CSD 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. PMID:22232415

  15. [The biologic functional surfaces and their applications in tissue engineering].

    PubMed

    Yao, Fanglian; Chen, Man; Zhang, Hong; Zhang, Haiyue; An, Xiaoyan; Yao, Kangde

    2007-10-01

    The construction of biologic functional surfaces of materials, from the visual angle of material science, is aimed to make the biomaterials adapted by tissues, and to endow them with dynamic conformity; moreover, from the view-point of clinical applications, it is the functional surface to join the environmental tissues with the implanted material, playing the role of artificial extracellular matrix (ECM). The architecture of biologic functional surface is very important in tissue engineering science. Here the primary concepts of biological surface science and the construction and application of biofunctional surfaces in tissue engineering are reviewed. PMID:18027721

  16. Industrial waste treatment process engineering. Volume 2: Biological processes

    SciTech Connect

    Celenza, G.J.

    1999-11-01

    Industrial Waste Treatment Process Engineering is a step-by-step implementation manual in three volumes, detailing the selection and design of industrial liquid and solid waste treatment systems. It consolidates all the process engineering principles required to evaluate a wide range of industrial facilities, starting with pollution prevention and source control and ending with end-of-pipe treatment technologies. This three-volume set is a practical guide for environmental engineers with process implementation responsibilities; a one-stop resource for process engineering requirements--from plant planning to implementing specific treatment technologies for unit operations; a comprehensive reference for industrial waste treatment technologies; and includes calculations and worked problems based on industry cases. The contents of Volume 2 include: aeration; aerobic biological oxidation; activated sludge system; biological oxidation: lagoons; biological oxidation: fixed film processes; aerobic digesters; anaerobic waste treatment, anaerobic sludge treatment; and sedimentation.

  17. 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.

  18. 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)

  19. 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)

  20. 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.

  1. 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.

  2. Resilin-Like Polypeptide Hydrogels Engineered for Versatile Biological Functions.

    PubMed

    Li, Linqing; Tong, Zhixiang; Jia, Xinqiao; Kiick, Kristi L

    2013-01-01

    Natural resilin, the rubber-like protein that exists in specialized compartments of most arthropods, possesses excellent mechanical properties such as low stiffness, high resilience and effective energy storage. Recombinantly-engineered resilin-like polypeptides (RLPs) that possess the favorable attributes of native resilin would be attractive candidates for the modular design of biomaterials for engineering mechanically active tissues. Based on our previous success in creating a novel RLP-based hydrogel and demonstrating useful mechanical and cell-adhesive properties, we have produced a suite of new RLP-based constructs, each equipped with 12 repeats of the putative resilin consensus sequence and a single, distinct biologically active domain. This approach allows independent control over the concentrations of cell-binding, MMP-sensitive, and polysaccharide-sequestration domains in hydrogels comprising mixtures of the various RLPs. The high purity, molecular weight and correct compositions of each new polypeptide have been confirmed via high performance liquid chromatography (HPLC), sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), and amino acid analysis. These RLP-based polypeptides exhibit largely random-coil conformation, both in solution and in the cross-linked hydrogels, as indicated by circular dichroic and infrared spectroscopic analyses. Hydrogels of various compositions, with a range of elastic moduli (1kPa to 25kPa) can be produced from these polypeptides, and the activity of the cell-binding and matrix metalloproteinase (MMP) sensitive domains was confirmed. Tris(hydroxymethyl phosphine) cross-linked RLP hydrogels were able to maintain their mechanical integrity as well as the viability of encapsulated primary human mesenchymal stem cells (MSCs). These results validate the promising properties of these RLP-based elastomeric biomaterials. PMID:23505396

  3. 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…

  4. 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.…

  5. 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…

  6. 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…

  7. 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…

  8. 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.

  9. Microenvironmental Regulation of Tumor Angiogenesis: Biological and Engineering Considerations

    NASA Astrophysics Data System (ADS)

    Infanger, David W.; Pathi, Siddharth P.; Fischbach, Claudia

    Tumor angiogenesis is fundamental to tumor growth and metastasis, and antiangiogenic therapies have been developed to target this process. However, the clinical success of these treatments has been limited, which may be due, in part, to an incomplete understanding of cell-microenvironment interactions and their role in tumor angiogenesis. Traditionally, two-dimensional (2D) culture approaches have been used to study tumor progression in vitro, but these systems fail to faithfully recreate tumor microenvironmental conditions contributing to tumor angiogenesis in vivo. By integrating cancer biology with tissue engineering and drug delivery approaches, the development of biologically inspired tumor models has emerged. Such 3D model systems allow studying the specific role of soluble factor signaling, cell-extracellular matrix (ECM) interactions, cell-cell interactions, mechanical cues, and metabolic stress. This chapter discusses specific biological and engineering design considerations for tissue-engineered tumor models and highlights their application for defining the underpinnings of tumor angiogenesis.

  10. Tissue Engineering Organs for Space Biology Research

    NASA Technical Reports Server (NTRS)

    Vandenburgh, H. H.; Shansky, J.; DelTatto, M.; Lee, P.; Meir, J.

    1999-01-01

    Long-term manned space flight requires a better understanding of skeletal muscle atrophy resulting from microgravity. Atrophy most likely results from changes at both the systemic level (e.g. decreased circulating growth hormone, increased circulating glucocorticoids) and locally (e.g. decreased myofiber resting tension). Differentiated skeletal myofibers in tissue culture have provided a model system over the last decade for gaining a better understanding of the interactions of exogenous growth factors, endogenous growth factors, and muscle fiber tension in regulating protein turnover rates and muscle cell growth. Tissue engineering these cells into three dimensional bioartificial muscle (BAM) constructs has allowed us to extend their use to Space flight studies for the potential future development of countermeasures.

  11. Molecular biology and spinal disorders. A survey for the clinician.

    PubMed

    Altman, D A; Titus, L; Hair, G A; Boden, S D

    1999-04-01

    Over the past 10 years, advances in molecular biology techniques have extended the potential for understanding spinal disorders from the microscopic (histologic) level down to the molecular level of gene expression within individual cells. These advances are initiating new avenues of research and, ultimately, novel clinical treatments. The intent of this update is to provide the spine clinician with a basic understanding of molecular biology, the type of information that may be learned from its application, and the potential for gene therapy in spine disorders. PMID:10209806

  12. 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)

  13. 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.

  14. Interactive analysis of systems biology molecular expression data

    PubMed Central

    Zhang, Mingwu; Ouyang, Qi; Stephenson, Alan; Kane, Michael D; Salt, David E; Prabhakar, Sunil; Burgner, John; Buck, Charles; Zhang, Xiang

    2008-01-01

    Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe) in growth media (an ionomics dataset). This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology. PMID:18312669

  15. Computational approaches to metabolic engineering utilizing systems biology and synthetic biology

    PubMed Central

    Fong, Stephen S.

    2014-01-01

    Metabolic engineering modifies cellular function to address various biochemical applications. Underlying metabolic engineering efforts are a host of tools and knowledge that are integrated to enable successful outcomes. Concurrent development of computational and experimental tools has enabled different approaches to metabolic engineering. One approach is to leverage knowledge and computational tools to prospectively predict designs to achieve the desired outcome. An alternative approach is to utilize combinatorial experimental tools to empirically explore the range of cellular function and to screen for desired traits. This mini-review focuses on computational systems biology and synthetic biology tools that can be used in combination for prospective in silico strain design. PMID:25379141

  16. From Biology to Mathematical Models and Back: Teaching Modeling to Biology Students, and Biology to Math and Engineering Students

    ERIC Educational Resources Information Center

    Chiel, Hillel J.; McManus, Jeffrey M.; Shaw, Kendrick M.

    2010-01-01

    We describe the development of a course to teach modeling and mathematical analysis skills to students of biology and to teach biology to students with strong backgrounds in mathematics, physics, or engineering. The two groups of students have different ways of learning material and often have strong negative feelings toward the area of knowledge…

  17. 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

  18. Molecular biology of retinal ganglion cells.

    PubMed Central

    Xiang, M; Zhou, H; Nathans, J

    1996-01-01

    Retinal ganglion cells are the output neurons that encode and transmit information from the eye to the brain. Their diverse physiologic and anatomic properties have been intensively studied and appear to account well for a number of psychophysical phenomena such as lateral inhibition and chromatic opponency. In this paper, we summarize our current view of retinal ganglion cell properties and pose a number of questions regarding underlying molecular mechanisms. As an example of one approach to understanding molecular mechanisms, we describe recent work on several POU domain transcription factors that are expressed in subsets of retinal ganglion cells and that appear to be involved in ganglion cell development. Images Fig. 1 Fig. 2 Fig. 4 Fig. 5 Fig. 6 PMID:8570601

  19. Molecular biological enhancement of coal biodesulfurization. Final technical report

    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.

  20. Engineering Titanium for Improved Biological Response

    SciTech Connect

    Orme, C; Bearinger, J; Dimasi, E; Gilbert, J

    2002-01-23

    The human body and its aggressive environment challenge the survival of implanted foreign materials. Formidable biocompatibility issues arise from biological, chemical, electrical, and tribological origins. The body's electrolytic solution provides the first point of contact with any kind of implant, and is responsible for transport, healing, integration, or attack. Therefore, determining how to successfully control the integration of a biomaterial should begin with an analysis of the early interfacial dynamics involved. setting, a complicated feedback system of solution chemistry, pH, ions, and solubility exists. The introduction of a fixation device instantly confounds this system. The body is exposed to a range of voltages, and wear can bring about significant shifts in potentials across an implant. In the environment of a new implant the solution pH becomes acidic, ionic concentrations shift, cathodic currents can lead to corrosion, and oxygen levels can be depleted; all of these impact the ability of the implant to retain its protective oxide layer and to present a stable interface for the formation of a biolayer. Titanium has been used in orthopedic and maxilofacial surgery for many years due to its reputation as being biocompatible and its ability to osseointegrate. Osseointegration is defined as direct structural and functional connection between ordered, living bone, and the surface of a load carrying implant. Branemark discovered this phenomenon in the 60's while examining titanium juxtaposed to bone. The mechanism by which titanium and its passivating oxide encourage osseosynthetic activity remains unknown. However in general terms the oxide film serves two purposes: first to provide a kinetic barrier that prevents titanium from corroding and second to provide a substrate that allows the constituents of bone (calcium phosphate crystals, cells, proteins, and collagen) to bond to it. We believe that the electrochemical environment dictates the titanium

  1. CellNet: Network Biology Applied to Stem Cell Engineering

    PubMed Central

    Cahan, Patrick; Li, Hu; Morris, Samantha A.; da Rocha, Edroaldo Lummertz; Daley, George Q.; Collins, James J.

    2014-01-01

    SUMMARY Somatic cell reprogramming, directed differentiation of pluripotent stem cells, and direct conversions between differentiated cell lineages represent powerful approaches to engineer cells for research and regenerative medicine. We have developed CellNet, a network biology platform that more accurately assesses the fidelity of cellular engineering than existing methodologies and generates hypotheses for improving cell derivations. Analyzing expression data from 56 published reports, we found that cells derived via directed differentiation more closely resemble their in vivo counterparts than products of direct conversion, as reflected by the establishment of target cell-type gene regulatory networks (GRNs). Furthermore, we discovered that directly converted cells fail to adequately silence expression programs of the starting population, and that the establishment of unintended GRNs is common to virtually every cellular engineering paradigm. CellNet provides a platform for quantifying how closely engineered cell populations resemble their target cell type and a rational strategy to guide enhanced cellular engineering. PMID:25126793

  2. Towards Engineering Biological Systems in a Broader Context.

    PubMed

    Venturelli, Ophelia S; Egbert, Robert G; Arkin, Adam P

    2016-02-27

    Significant advances have been made in synthetic biology to program information processing capabilities in cells. While these designs can function predictably in controlled laboratory environments, the reliability of these devices in complex, temporally changing environments has not yet been characterized. As human society faces global challenges in agriculture, human health and energy, synthetic biology should develop predictive design principles for biological systems operating in complex environments. Natural biological systems have evolved mechanisms to overcome innumerable and diverse environmental challenges. Evolutionary design rules should be extracted and adapted to engineer stable and predictable ecological function. We highlight examples of natural biological responses spanning the cellular, population and microbial community levels that show promise in synthetic biology contexts. We argue that synthetic circuits embedded in host organisms or designed ecologies informed by suitable measurement of biotic and abiotic environmental parameters could be used as engineering substrates to achieve target functions in complex environments. Successful implementation of these methods will broaden the context in which synthetic biological systems can be applied to solve important problems. PMID:26546279

  3. Using molecular biology to maximize concurrent training.

    PubMed

    Baar, Keith

    2014-11-01

    Very few sports use only endurance or strength. Outside of running long distances on a flat surface and power-lifting, practically all sports require some combination of endurance and strength. Endurance and strength can be developed simultaneously to some degree. However, the development of a high level of endurance seems to prohibit the development or maintenance of muscle mass and strength. This interaction between endurance and strength is called the concurrent training effect. This review specifically defines the concurrent training effect, discusses the potential molecular mechanisms underlying this effect, and proposes strategies to maximize strength and endurance in the high-level athlete. PMID:25355186

  4. Molecular model for hydrated biological tissues.

    PubMed

    Sato, Erika Tiemi; Rocha, Alexandre Reily; de Carvalho, Luis Felipe das Chagas e Silva; Almeida, Janete Dias; Martinho, Herculano

    2015-06-01

    A density-functional microscopic model for soft tissues (STmod) is presented. The model was based on a prototype molecular structure from experimentally resolved type I collagen peptide residues and water clusters treated in periodic boundary conditions. We obtained the optimized geometry, binding and coupling energies, dipole moments, and vibrational frequencies. The results concerning the stability of the confined water clusters, the water-water, and water-collagen interactions were successfully correlated to some important experimental trends of normal and inflammatory tissues. PMID:26172825

  5. 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.

  6. Molecular biology approaches to control of intractable weeds: New strategies and complements to existing biological practices

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular genetic tools and concepts are in relentless and continuous development, affecting every field of biology. Biological control of weeds, an applied science with over a century of history, is no exception. This field has been dominated from the beginning by its foundation concept, classical ...

  7. 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…

  8. Molecular Response of Crop Plants to Engineered Nanomaterials.

    PubMed

    Pagano, Luca; Servin, Alia D; De La Torre-Roche, Roberto; Mukherjee, Arnab; Majumdar, Sanghamitra; Hawthorne, Joseph; Marmiroli, Marta; Maestri, Elena; Marra, Robert E; Isch, Susan M; Dhankher, Om Parkash; White, Jason C; Marmiroli, Nelson

    2016-07-01

    Functional toxicology has enabled the identification of genes involved in conferring tolerance and sensitivity to engineered nanomaterial (ENM) exposure in the model plant Arabidopsis thaliana (L.) Heynh. Several genes were found to be involved in metabolic functions, stress response, transport, protein synthesis, and DNA repair. Consequently, analysis of physiological parameters, metal content (through ICP-MS quantification), and gene expression (by RT-qPCR) of A. thaliana orthologue genes were performed across different plant species of agronomic interest to highlight putative biomarkers of exposure and effect related to ENMs. This approach led to the identification of molecular markers in Solanum lycopersicum L. and Cucurbita pepo L. (tomato and zucchini) that might not only indicate exposure to ENMs (CuO, CeO2, and La2O3) but also provide mechanistic insight into response to these materials. Through Gene Ontology (GO) analysis, the target genes were mapped in complex interatomic networks representing molecular pathways, cellular components, and biological processes involved in ENM response. The transcriptional response of 38 (out of 204) candidate genes studied varied according to particle type, size, and plant species. Importantly, some of the genes studied showed potential as biomarkers of ENM exposure and effect and may be useful for risk assessment in foods and in the environment. PMID:27301997

  9. 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.

  10. Biological (molecular and cellular) markers of toxicity

    SciTech Connect

    Shugart, L.R.; D'Surney, S.J.; Gettys-Hull, C.; Greeley, M.S. Jr.

    1991-12-15

    Several molecular and cellular markers of genotoxicity were adapted for measurement in the Medaka (Oryzias latipes), and were used to describe the effects of treatment of the organism with diethylnitrosamine (DEN). NO{sup 6}-ethyl guanine adducts were detected, and a slight statistically significant, increase in DNA strand breaks was observed. These results are consistent with the hypothesis that prolonged exposure to high levels of DEN induced alkyltransferase activity which enzymatically removes any O{sup 6}-ethyl guanine adducts but does not result in strand breaks or hypomethylation of the DNA such as might be expected from excision repair of chemically modified DNA. Following a five week continuous DEN exposure with 100 percent renewal of DEN-water every third day, the F values (DNA double strandedness) increased considerably and to similar extent in fish exposed to 25, 50, and 100 ppM DEN. This has been observed also in medaka exposed to BaP.

  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. PMID:26482724

  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. A decade of molecular cell biology: achievements and challenges

    PubMed Central

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

    2012-01-01

    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. PMID:21941276

  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. 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. PMID:23385529

  16. Molecular biology of coal bio-desulfurization

    SciTech Connect

    Young, K.D.; Gallagher, J.R.

    1991-07-18

    The aim of this project is to use the techniques of molecular genetics to identify, clone, sequence, and enhance the expression of proteins which remove sulfur covalently bound to coal. The cloned dox genes from strain C18 were more fully characterized. Another gene, doxG, is almost identical with the nahC gene, also involved in the naphthalene pathway. These results lead us to believe that dibenzothiophene (DBT) is degraded by the oxidative route along the naphthalene degradative pathway. At least one other gene, doxI, is implicated in the formation of the unidentified fluorescent product from DBT. The Rhodococcus rhodochrous isolate IGTS8 was mutated to produce a variant (strain UV1) that was negative for DBT utilization. This mutant was exposed to further rounds of UV mutagenesis and was used as the host for attempts to introduce various plasmid DNAs. Two plasmids could be introduced into UV1: pRF29 and pLAFR5. A cosmid library of IGTS8 DNA was constructed in pLAFR5 and was electroporated into UV1. Of over 2000 colonies tested three bulk batches, one flask of about 600 clones produced a fluorescent product from DBT. These are being screened to determine if one of these represents a clone that complements the DBT negative phenotype of the UV1 mutant. We obtained chloramphenicol resistant Thiobacillus ferrooxidans after electroporation but these transformants contained no plasmid or transposon sequences, so that insertion of DNA into T. ferrooxidans had not occurred.

  17. [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. PMID:18268896

  18. [Molecular biological predictors for kidney cancer].

    PubMed

    Vtorushin, S V; Tarakanova, V O; Zavyalova, M V

    2016-01-01

    The paper considers the data available in the modern literature on studies of potential molecular predictors for renal cell carcinoma (RCC). Investigations of cell death markers, namely; Bcl-2 as an inhibitor of apoptosis, are of interest. Its high expression correlates with a more favorable prognosis. Inactivation of Berclin 1 that is an authophagy indicator in intact tissues gives rise to t high risk for tumorigenesis. At the same time, high Beclin 1 expression in the tissue of the tumor itself results in the lower efficiency of performed chemotherapy. Excess annexin A2 in the tumor promotes the growth and invasion of cancer cells. Patients with tumor over-expression of SAM68 protein involved in cell proliferation have a lower overall survival rate. The lifespan of patients without distinct metastases survive significantly longer in the overexpression of epithelial cell adhesion molecule (EpCAM). High PD-L1 protein expression on the cell membrane is considered to be a potential marker of effective immunotherapy for RCC. PMID:27077146

  19. Advances and Computational Tools towards Predictable Design in Biological Engineering

    PubMed Central

    2014-01-01

    The design process of complex systems in all the fields of engineering requires a set of quantitatively characterized components and a method to predict the output of systems composed by such elements. This strategy relies on the modularity of the used components or the prediction of their context-dependent behaviour, when parts functioning depends on the specific context. Mathematical models usually support the whole process by guiding the selection of parts and by predicting the output of interconnected systems. Such bottom-up design process cannot be trivially adopted for biological systems engineering, since parts function is hard to predict when components are reused in different contexts. This issue and the intrinsic complexity of living systems limit the capability of synthetic biologists to predict the quantitative behaviour of biological systems. The high potential of synthetic biology strongly depends on the capability of mastering this issue. This review discusses the predictability issues of basic biological parts (promoters, ribosome binding sites, coding sequences, transcriptional terminators, and plasmids) when used to engineer simple and complex gene expression systems in Escherichia coli. A comparison between bottom-up and trial-and-error approaches is performed for all the discussed elements and mathematical models supporting the prediction of parts behaviour are illustrated. PMID:25161694

  20. Teaching Cell and Molecular Biology for Gender Equity

    ERIC Educational Resources Information Center

    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…

  1. Biological magnetic cellular spheroids as building blocks for tissue engineering

    PubMed Central

    Mattix, Brandon; Olsen, Timothy R.; Gu, Yu; Casco, Megan; Herbst, Austin; Simionescu, Dan T.; Visconti, Richard P.; Kornev, Konstantin G.; Alexis, Frank

    2016-01-01

    Magnetic nanoparticles (MNPs), primarily iron oxide nanoparticles, have been incorporated into cellular spheroids to allow for magnetic manipulation into desired shapes, patterns and 3-D tissue constructs using magnetic forces. However, the direct and long-term interaction of iron oxide nanoparticles with cells and biological systems can induce adverse effects on cell viability, phenotype and function, and remain a critical concern. Here we report the preparation of biological magnetic cellular spheroids containing magnetoferritin, a biological MNP, capable of serving as a biological alternative to iron oxide magnetic cellular spheroids as tissue engineered building blocks. Magnetoferritin NPs were incorporated into 3-D cellular spheroids with no adverse effects on cell viability up to 1 week. Additionally, cellular spheroids containing magnetoferritin NPs were magnetically patterned and fused into a tissue ring to demonstrate its potential for tissue engineering applications. These results present a biological approach that can serve as an alternative to the commonly used iron oxide magnetic cellular spheroids, which often require complex surface modifications of iron oxide NPs to reduce the adverse effects on cells. PMID:24176725

  2. Biological magnetic cellular spheroids as building blocks for tissue engineering.

    PubMed

    Mattix, Brandon; Olsen, Timothy R; Gu, Yu; Casco, Megan; Herbst, Austin; Simionescu, Dan T; Visconti, Richard P; Kornev, Konstantin G; Alexis, Frank

    2014-02-01

    Magnetic nanoparticles (MNPs), primarily iron oxide nanoparticles, have been incorporated into cellular spheroids to allow for magnetic manipulation into desired shapes, patterns and 3-D tissue constructs using magnetic forces. However, the direct and long-term interaction of iron oxide nanoparticles with cells and biological systems can induce adverse effects on cell viability, phenotype and function, and remain a critical concern. Here we report the preparation of biological magnetic cellular spheroids containing magnetoferritin, a biological MNP, capable of serving as a biological alternative to iron oxide magnetic cellular spheroids as tissue engineered building blocks. Magnetoferritin NPs were incorporated into 3-D cellular spheroids with no adverse effects on cell viability up to 1 week. Additionally, cellular spheroids containing magnetoferritin NPs were magnetically patterned and fused into a tissue ring to demonstrate its potential for tissue engineering applications. These results present a biological approach that can serve as an alternative to the commonly used iron oxide magnetic cellular spheroids, which often require complex surface modifications of iron oxide NPs to reduce the adverse effects on cells. PMID:24176725

  3. Professor Joseph Warren Horton (1889-1967): biological engineer.

    PubMed

    Zeitlin, Gerald L

    2005-02-01

    Joseph Warren Horton graduated with a degree in electrical engineering from the Massachusetts Institute of Technology (MIT) in 1914. He became involved in the early development of electrical measurement devices, televised image transmission, and the detection of underwater sound transmission. In the mid-1930s he was appointed the first leader of the newly created Department of Biological Engineering at MIT and in this position he made major contributions to the application of physics to human physiology, in particular by increasing the safety of explosive inhalational anaesthetic agents. PMID:15682231

  4. Marek's disease virus molecular biology, oncogenesis and immunoprophylaxis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Significant advances in MD research in the field of molecular biology of MDV have occurred since 2000. The complete DNA sequence of representatives of all three MDV serotypes and the development of new techniques to mutate the MDV genome have resulted in a wealth of information on the function of MD...

  5. 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,…

  6. Cooperative Learning in Introductory Cell and Molecular Biology.

    ERIC Educational Resources Information Center

    Posner, Herbert B.; Markstein, James A.

    1994-01-01

    Discusses a pilot study conducted to determine whether cooperative learning had a beneficial effect on the academic performance of minority students and subsequent enrollments in the elective courses in biochemistry and molecular biology. Minority students average GPA increased from 2.13 (n=39) to 2.96 (n=17). Enrollment in aforementioned courses…

  7. The molecular biology of the positive strand RNA viruses

    SciTech Connect

    Rowlands, D.J.; Mayo, M.A.; Mahy, B.W.J.

    1987-01-01

    This book pulls together recent research findings on the molecular biology of the major families of positive strand RNA viruses infecting plants and animals. The topics covered include protein translation, processing and function, RNA replication, virus structure and antigenicity, mechanisms of infection and evolutionary relationships between the virus families.

  8. 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…

  9. 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.

  10. 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…

  11. Micropipetting: An Important Laboratory Skill for Molecular Biology

    ERIC Educational Resources Information Center

    Sass, Michell E.; Wong, Susan J.; Miller, Jon S.; Nienhuis, James

    2004-01-01

    Micropipetting is an important skill that plays a very active and critical role in the molecular biology laboratory. It is imperative for a person handling micropipettor to know the correct way of using it so that accurate and precise results are achieved.

  12. 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…

  13. 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)

  14. 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 genes, mRNA…

  15. 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. PMID:26549858

  16. Molecular engineering and characterization of self-assembled biorecognition surfaces

    NASA Astrophysics Data System (ADS)

    Pan, Sheng

    The development of molecular engineering techniques for the fabrication of biomaterial surfaces is of importance in the field of biomaterials. It offers opportunities for better understanding of biological processes on material surfaces and rational design of contemporary biomaterials. Our work in this area aims to develop novel engineering strategies to design biorecognition surfaces via self-assembly and surface derivatization. Fundamental issues regarding self-assembled monolayer (SAM) structure, formation kinetics, and chemical derivatization were investigated systematically using electron spectroscopy for chemical analysis (ESCA), time-of-flight secondary ion mass spectrometry (TOF-SIMS), infrared reflection absorption spectroscopy (IRAS), atomic force microscopy (AFM), and contact angle measurements. Novel engineering concepts based on multifunctionality and statistical pattern matching were introduced and applied to develop biomimetic surfaces. Our study illustrated that molecules underwent structural transition and orientation development during self-assembly formation, from a disordered, low-density, more liquid-like structure to a highly ordered, closed-packed crystalline-like structure. Surface properties, such as wettability and the reactivity of outermost functional groups can be related to film structure, packing density, as well as molecular orientation. Given the order and organization of SAMs, the accessibility and reactivity of the outermost functional groups, reaction kinetics, stoichiometry, and SAMs stability were studied systematically by surface derivatization of trifluoroacetic anhydride (TFAA). The TFAA derivatization reactions exhibited rapid kinetics on the hydroxyl-terminated SAMs. The data from complementary surface analytical techniques consistently indicated a nearly complete surface reaction. Biomimetic surfaces were made by random immobilization of amino acid of arginine (R), glycine (G), and aspartic acid (D) on well-defined SAMs

  17. 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.

  18. 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. PMID:27528656

  19. Synthetic Biology: Engineering, Evolution and Design (SEED) Conference 2014

    SciTech Connect

    Voigt, Christopher

    2014-07-01

    SEED2014 focused on advances in the science and technology emerging from the field of synthetic biology. We broadly define this as technologies that accelerate the process of genetic engineering. It highlighted new tool development, as well as the application of these tools to diverse problems in biotechnology, including therapeutics, industrial chemicals and fuels, natural products, and agriculture. Systems spanned from in vitro experiments and viruses, through diverse bacteria, to eukaryotes (yeast, mammalian cells, plants).

  20. Engineering C4 photosynthesis into C3 chassis in the synthetic biology age.

    PubMed

    Schuler, Mara L; Mantegazza, Otho; Weber, Andreas P M

    2016-07-01

    C4 photosynthetic plants outperform C3 plants in hot and arid climates. By concentrating carbon dioxide around Rubisco C4 plants drastically reduce photorespiration. The frequency with which plants evolved C4 photosynthesis independently challenges researchers to unravel the genetic mechanisms underlying this convergent evolutionary switch. The conversion of C3 crops, such as rice, towards C4 photosynthesis is a long-standing goal. Nevertheless, at the present time, in the age of synthetic biology, this still remains a monumental task, partially because the C4 carbon-concentrating biochemical cycle spans two cell types and thus requires specialized anatomy. Here we review the advances in understanding the molecular basis and the evolution of the C4 trait, advances in the last decades that were driven by systems biology methods. In this review we emphasise essential genetic engineering tools needed to translate our theoretical knowledge into engineering approaches. With our current molecular understanding of the biochemical C4 pathway, we propose a simplified rational engineering model exclusively built with known C4 metabolic components. Moreover, we discuss an alternative approach to the progressing international engineering attempts that would combine targeted mutagenesis and directed evolution. PMID:26945781

  1. Cell stretching devices as research tools: engineering and biological considerations.

    PubMed

    Kamble, Harshad; Barton, Matthew J; Jun, Myeongjun; Park, Sungsu; Nguyen, Nam-Trung

    2016-08-16

    Cells within the human body are subjected to continuous, cyclic mechanical strain caused by various organ functions, movement, and growth. Cells are well known to have the ability to sense and respond to mechanical stimuli. This process is referred to as mechanotransduction. A better understanding of mechanotransduction is of great interest to clinicians and scientists alike to improve clinical diagnosis and understanding of medical pathology. However, the complexity involved in in vivo biological systems creates a need for better in vitro technologies, which can closely mimic the cells' microenvironment using induced mechanical strain. This technology gap motivates the development of cell stretching devices for better understanding of the cell response to mechanical stimuli. This review focuses on the engineering and biological considerations for the development of such cell stretching devices. The paper discusses different types of stretching concepts, major design consideration and biological aspects of cell stretching and provides a perspective for future development in this research area. PMID:27440436

  2. The role of neutron scattering in molecular and cellular biology

    NASA Astrophysics Data System (ADS)

    Worcester, D. L.

    1982-09-01

    Neutron scattering measurements of biological macromolecules and materials have provided answers to numerous questions about molecular assemblies and arrangements. Studies of ribosomes, viruses, membranes, and other biological structures are reviewed, with emphasis on the importance of both deuterium labelling and contrast variation with H2O/D2O exchange. Although many studies of biological molecules have been made using contrast variation alone, it is the deuterium labelling experiments that have provided the most precise information and answers to major biological questions. This is largely the result of the low resolution of scattering data and the consequent rapid increase of information content that specific deuterium labelling provides. Procedures for specific deuterium labelling `in vivo' are described for recent work on myelin membranes together with basic aspects of such labelling useful for future research.

  3. 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

  4. [Value of molecular biology methods for diagnosis in bacteriology].

    PubMed

    Piémont, Y; Jaulhac, B

    1995-01-01

    Progress in molecular biology has led to the development of new tools for bacteriological diagnosis. Sporadic genes coding for virulence factors can be detected with highly specific genetic probes applied to cultured bacteria. Such genetic probes can also be used to specifically identified cultured bacteria whose general taxonomic classification is known. Another advantage of molecular genetics is the possibility that the cell culture step may not be needed, bacteria being identified directly in the sample specimen. Such techniques are particularly interesting to identify bacteria which are difficult to culture (for example: Borrelia burgdorferi, Chlamydia trachomatis) or which grow slowly (mycobacteria). The bacterial DNA must be isolated and amplified with an enzyme reaction. This is a critical step in the method: several positive and negative controls are required. When performed under optimal conditions, amplification techniques are excellent methods which can offer results similar to culture methods in culturable bacteria. Finally, molecular biology can be used to identify previously cultured bacteria for which there is no taxonomic orientation. Here the ribosome 165 DNA must be amplified and sequenced. The sequence is then compared with a data bank allowing classification. One could image future techniques applied to certain pathology samples for the detection and identification of bacteria without need for a culture step. However, direct microscope examination and bacterial culture remain the basic methods for bacteriologic diagnosis, the advantages and disadvantages of molecular biology leading to its use a complementary method for improving the quality of the diagnosis. PMID:8526414

  5. Teaching Molecular Biology to Undergraduate Biology Students: An Illustration of Protein Expression and Purification

    ERIC Educational Resources Information Center

    Sommer, Cesar Adolfo; Silva, Flavio Henrique; Novo, Maria Teresa Marques

    2004-01-01

    Practical classes on protein expression and purification were given to undergraduate biology students enrolled in the elective course "Introduction to Genetic Engineering." The heterologous expression of the green fluorescent protein (GFP)* of "Aequorea victoria" is an interesting system for didactic purposes because it can be viewed easily during…

  6. INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY (ISMB)

    SciTech Connect

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

    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.

  7. From biology to mathematical models and back: teaching modeling to biology students, and biology to math and engineering students.

    PubMed

    Chiel, Hillel J; McManus, Jeffrey M; Shaw, Kendrick M

    2010-01-01

    We describe the development of a course to teach modeling and mathematical analysis skills to students of biology and to teach biology to students with strong backgrounds in mathematics, physics, or engineering. The two groups of students have different ways of learning material and often have strong negative feelings toward the area of knowledge that they find difficult. To give students a sense of mastery in each area, several complementary approaches are used in the course: 1) a "live" textbook that allows students to explore models and mathematical processes interactively; 2) benchmark problems providing key skills on which students make continuous progress; 3) assignment of students to teams of two throughout the semester; 4) regular one-on-one interactions with instructors throughout the semester; and 5) a term project in which students reconstruct, analyze, extend, and then write in detail about a recently published biological model. Based on student evaluations and comments, an attitude survey, and the quality of the students' term papers, the course has significantly increased the ability and willingness of biology students to use mathematical concepts and modeling tools to understand biological systems, and it has significantly enhanced engineering students' appreciation of biology. PMID:20810957

  8. From Biology to Mathematical Models and Back: Teaching Modeling to Biology Students, and Biology to Math and Engineering Students

    PubMed Central

    McManus, Jeffrey M.; Shaw, Kendrick M.

    2010-01-01

    We describe the development of a course to teach modeling and mathematical analysis skills to students of biology and to teach biology to students with strong backgrounds in mathematics, physics, or engineering. The two groups of students have different ways of learning material and often have strong negative feelings toward the area of knowledge that they find difficult. To give students a sense of mastery in each area, several complementary approaches are used in the course: 1) a “live” textbook that allows students to explore models and mathematical processes interactively; 2) benchmark problems providing key skills on which students make continuous progress; 3) assignment of students to teams of two throughout the semester; 4) regular one-on-one interactions with instructors throughout the semester; and 5) a term project in which students reconstruct, analyze, extend, and then write in detail about a recently published biological model. Based on student evaluations and comments, an attitude survey, and the quality of the students' term papers, the course has significantly increased the ability and willingness of biology students to use mathematical concepts and modeling tools to understand biological systems, and it has significantly enhanced engineering students' appreciation of biology. PMID:20810957

  9. 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.

  10. Using argument notation to engineer biological simulations with increased confidence

    PubMed Central

    Alden, Kieran; Andrews, Paul S.; Polack, Fiona A. C.; Veiga-Fernandes, Henrique; Coles, Mark C.; Timmis, Jon

    2015-01-01

    The application of computational and mathematical modelling to explore the mechanics of biological systems is becoming prevalent. To significantly impact biological research, notably in developing novel therapeutics, it is critical that the model adequately represents the captured system. Confidence in adopting in silico approaches can be improved by applying a structured argumentation approach, alongside model development and results analysis. We propose an approach based on argumentation from safety-critical systems engineering, where a system is subjected to a stringent analysis of compliance against identified criteria. We show its use in examining the biological information upon which a model is based, identifying model strengths, highlighting areas requiring additional biological experimentation and providing documentation to support model publication. We demonstrate our use of structured argumentation in the development of a model of lymphoid tissue formation, specifically Peyer's Patches. The argumentation structure is captured using Artoo (www.york.ac.uk/ycil/software/artoo), our Web-based tool for constructing fitness-for-purpose arguments, using a notation based on the safety-critical goal structuring notation. We show how argumentation helps in making the design and structured analysis of a model transparent, capturing the reasoning behind the inclusion or exclusion of each biological feature and recording assumptions, as well as pointing to evidence supporting model-derived conclusions. PMID:25589574

  11. 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

  12. Supramolecular Polymerization Engineered with Molecular Recognition.

    PubMed

    Haino, Takeharu

    2015-10-01

    Supramolecular polymeric assemblies represent an emerging, promising class of molecular assemblies with enormous versatility compared with their covalent polymeric counterparts. Although a large number of host-guest motifs have been produced over the history of supramolecular chemistry, only a limited number of recognition motifs have been utilized as supramolecular connections in polymeric assemblies. This account describes the molecular recognition of host molecules based on calix[5]arene and bisporphyrin that demonstrate unique guest encapsulations; subsequently, these host-guest motifs are applied to the synthesis of supramolecular polymers that display polymer-like properties in solution and solid states. In addition, new bisresorcinarenes are developed to form supramolecular polymers that are connected via a rim-to-rim hydrogen-bonded dimeric structure, which is composed of two resorcinarene moieties. PMID:26178364

  13. [Therapeutic consequences of molecular biology advances in oncology].

    PubMed

    Bauvet, F; Awada, A; Gil, T; Hendlisz, A

    2009-01-01

    This review article presents the improvements made in the field of molecular biology in oncology and their diagnostic and therapeutic consequences. As an illustration, three types of tumors for which these projections strongly modified the management will be used as a basis in this article: breast cancer, kidney cancer and colorectal cancer. Indeed, the last years, new prognostic factors (natural evolution of a specific patient's tumor) and predictive factors (prediction of the responsiveness to anticancer therapies) have emerged for these tumors. In addition, a better comprehension of the mechanisms implied in the development of cancers allowed the advent of many molecular-targeted therapies, which constitute a true revolution in oncology. PMID:19211361

  14. BIO2010 and beyond: What undergraduate physics does the next generation of molecular biology researchers need?

    NASA Astrophysics Data System (ADS)

    Howard, Jonathon

    2004-03-01

    What fundamental skills in mathematics, chemistry, physics, computer science and engineering are required at the undergraduate level to prepare the next generation of biology majors who will become research scientists? To address this question, Bruce Alberts, President of the National Academy of Sciences, established BIO2010, a committee of the National Research Council (USA), chaired by Lubert Stryer. The report of the committee was published in 2003 as BIO2010: Transforming Undergraduate Education for Future Research Biologists (National Academies Press, Washington DC, www.national-academies.com). I will summarize the recommendations of the Physics and Engineering Panel that was chaired by John Hopfield and give my own views of what physics is essential for researchers in cell and molecular biology.

  15. Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

    PubMed Central

    He, Fei; Murabito, Ettore; Westerhoff, Hans V.

    2016-01-01

    Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo, not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased production flux, however, often compromises that robustness. In this contribution, we review and investigate how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed by systems and control engineering. While trade-offs between production optimality and cellular robustness have already been studied diagnostically and statically, the dynamics also matter. Integration of the dynamic design aspects of control engineering with the more diagnostic aspects of metabolic, hierarchical control and regulation analysis is leading to the new, conceptual and operational framework required for the design of robust and productive dynamic pathways. PMID:27075000

  16. Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering.

    PubMed

    He, Fei; Murabito, Ettore; Westerhoff, Hans V

    2016-04-01

    Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo, not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased production flux, however, often compromises that robustness. In this contribution, we review and investigate how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed by systems and control engineering. While trade-offs between production optimality and cellular robustness have already been studied diagnostically and statically, the dynamics also matter. Integration of the dynamic design aspects of control engineering with the more diagnostic aspects of metabolic, hierarchical control and regulation analysis is leading to the new, conceptual and operational framework required for the design of robust and productive dynamic pathways. PMID:27075000

  17. 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. PMID:26677427

  18. Cell Engineering and Molecular Pharming for Biopharmaceuticals

    PubMed Central

    Abdullah, M.A; Rahmah, Anisa ur; Sinskey, A.J; Rha, C.K

    2008-01-01

    Biopharmaceuticals are often produced by recombinant E. coli or mammalian cell lines. This is usually achieved by the introduction of a gene or cDNA coding for the protein of interest into a well-characterized strain of producer cells. Naturally, each recombinant production system has its own unique advantages and disadvantages. This paper examines the current practices, developments, and future trends in the production of biopharmaceuticals. Platform technologies for rapid screening and analyses of biosystems are reviewed. Strategies to improve productivity via metabolic and integrated engineering are also highlighted. PMID:19662143

  19. 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

  20. 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. PMID:27607140

  1. StrateGene: object-oriented programming in molecular biology.

    PubMed

    Carhart, R E; Cash, H D; Moore, J F

    1988-03-01

    This paper describes some of the ways that object-oriented programming methodologies have been used to represent and manipulate biological information in a working application. When running on a Xerox 1100 series computer, StrateGene functions as a genetic engineering workstation for the management of information about cloning experiments. It represents biological molecules, enzymes, fragments, and methods as classes, subclasses, and members in a hierarchy of objects. These objects may have various attributes, which themselves can be defined and classified. The attributes and their values can be passed from the classes of objects down to the subclasses and members. The user can modify the objects and their attributes while using them. New knowledge and changes to the system can be incorporated relatively easily. The operations on the biological objects are associated with the objects themselves. This makes it easier to invoke them correctly and allows generic operations to be customized for the particular object. PMID:3164229

  2. Towards an upper level ontology for molecular biology.

    PubMed

    Schulz, Stefan; Beisswanger, Elena; Wermter, Joachim; Hahn, Udo

    2006-01-01

    There is a growing need for the general-purpose description of the basic conceptual entities in the life sciences. Up until now, upper level models have mainly been purpose-driven, such as the GENIA ontology, originally devised as a vocabulary for corpus annotation. As an alternative,we here present BioTop, a description-logic-based top level ontology for molecular biology, which we consider as an ontologically conscious redesign of the GENIA ontology. PMID:17238430

  3. Recent advances in developing molecular tools for targeted genome engineering of mammalian cells.

    PubMed

    Lim, Kwang-il

    2015-01-01

    Various biological molecules naturally existing in diversified species including fungi, bacteria, and bacteriophage have functionalities for DNA binding and processing. The biological molecules have been recently actively engineered for use in customized genome editing of mammalian cells as the molecule-encoding DNA sequence information and the underlying mechanisms how the molecules work are unveiled. Excitingly, multiple novel methods based on the newly constructed artificial molecular tools have enabled modifications of specific endogenous genetic elements in the genome context at efficiencies that are much higher than that of the conventional homologous recombination based methods. This minireview introduces the most recently spotlighted molecular genome engineering tools with their key features and ongoing modifications for better performance. Such ongoing efforts have mainly focused on the removal of the inherent DNA sequence recognition rigidity from the original molecular platforms, the addition of newly tailored targeting functions into the engineered molecules, and the enhancement of their targeting specificity. Effective targeted genome engineering of mammalian cells will enable not only sophisticated genetic studies in the context of the genome, but also widely-applicable universal therapeutics based on the pinpointing and correction of the disease-causing genetic elements within the genome in the near future. PMID:25104401

  4. Gate engineered performance of single molecular transistor

    NASA Astrophysics Data System (ADS)

    Ray, S. J.

    2016-05-01

    The operation, performance and electrostatics of multigated Single Molecular Transistor (SMT) devices are investigated using first-principles based density functional theory calculations for planar (pentacene) and non-planar (sucrose) molecules as islands. It has been found that the incorporation of larger numbers of gates allows enhanced electrostatic control in the SMT operation which has been quantified from the energy calculations and estimation of the gate capacitances. The effect of multiple gates is more dominant for a non-planar molecule than a planar molecule within an SMT which indicates the usefulness of such multi-gate architectures for future nanoelectronic devices.

  5. 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. PMID:12171609

  6. Mesoscopic Fluorescence Molecular Tomography for Evaluating Engineered Tissues.

    PubMed

    Ozturk, Mehmet S; Chen, Chao-Wei; Ji, Robin; Zhao, Lingling; Nguyen, Bao-Ngoc B; Fisher, John P; Chen, Yu; Intes, Xavier

    2016-03-01

    Optimization of regenerative medicine strategies includes the design of biomaterials, development of cell-seeding methods, and control of cell-biomaterial interactions within the engineered tissues. Among these steps, one paramount challenge is to non-destructively image the engineered tissues in their entirety to assess structure, function, and molecular expression. It is especially important to be able to enable cell phenotyping and monitor the distribution and migration of cells throughout the bulk scaffold. Advanced fluorescence microscopic techniques are commonly employed to perform such tasks; however, they are limited to superficial examination of tissue constructs. Therefore, the field of tissue engineering and regenerative medicine would greatly benefit from the development of molecular imaging techniques which are capable of non-destructive imaging of three-dimensional cellular distribution and maturation within a tissue-engineered scaffold beyond the limited depth of current microscopic techniques. In this review, we focus on an emerging depth-resolved optical mesoscopic imaging technique, termed laminar optical tomography (LOT) or mesoscopic fluorescence molecular tomography (MFMT), which enables longitudinal imaging of cellular distribution in thick tissue engineering constructs at depths of a few millimeters and with relatively high resolution. The physical principle, image formation, and instrumentation of LOT/MFMT systems are introduced. Representative applications in tissue engineering include imaging the distribution of human mesenchymal stem cells embedded in hydrogels, imaging of bio-printed tissues, and in vivo applications. PMID:26645079

  7. Topology and static response of interaction networks in molecular biology.

    PubMed

    Radulescu, Ovidiu; Lagarrigue, Sandrine; Siegel, Anne; Veber, Philippe; Le Borgne, Michel

    2006-02-22

    We introduce a mathematical framework describing static response of networks occurring in molecular biology. This formalism has many similarities with the Laplace-Kirchhoff equations for electrical networks. We introduce the concept of graph boundary and we show how the response of the biological networks to external perturbations can be related to the Dirichlet or Neumann problems for the corresponding equations on the interaction graph. Solutions to these two problems are given in terms of path moduli (measuring path rigidity with respect to the propagation of interaction along the graph). Path moduli are related to loop products in the interaction graph via generalized Mason-Coates formulae. We apply our results to two specific biological examples: the lactose operon and the genetic regulation of lipogenesis. Our applications show consistency with experimental results and in the case of lipogenesis check some hypothesis on the behaviour of hepatic fatty acids on fasting. PMID:16849230

  8. 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.

  9. Topology and static response of interaction networks in molecular biology

    PubMed Central

    Radulescu, Ovidiu; Lagarrigue, Sandrine; Siegel, Anne; Veber, Philippe; Le Borgne, Michel

    2005-01-01

    We introduce a mathematical framework describing static response of networks occurring in molecular biology. This formalism has many similarities with the Laplace–Kirchhoff equations for electrical networks. We introduce the concept of graph boundary and we show how the response of the biological networks to external perturbations can be related to the Dirichlet or Neumann problems for the corresponding equations on the interaction graph. Solutions to these two problems are given in terms of path moduli (measuring path rigidity with respect to the propagation of interaction along the graph). Path moduli are related to loop products in the interaction graph via generalized Mason–Coates formulae. We apply our results to two specific biological examples: the lactose operon and the genetic regulation of lipogenesis. Our applications show consistency with experimental results and in the case of lipogenesis check some hypothesis on the behaviour of hepatic fatty acids on fasting. PMID:16849230

  10. Reverse engineering for biologically inspired cognitive architectures: a critical analysis.

    PubMed

    Schierwagen, Andreas

    2011-01-01

    Research initiatives on both sides of the Atlantic try to utilize the operational principles of organisms and brains to develop biologically inspired, artificial cognitive systems. This paper describes the standard way bio-inspiration is gained, i.e. decompositional analysis or reverse engineering. The indisputable complexity of brain and mind raise the issue of whether they can be understood by applying the standard method. Using Robert Rosen's modeling relation, the scientific analysis method itself is made a subject of discussion. It is concluded that the fundamental assumption of cognitive science, i.e. complex cognitive systems are decomposable, must be abandoned. Implications for investigations of organisms and behavior as well as for engineering artificial cognitive systems are discussed. PMID:21744214

  11. Clinical Applications of Molecular Biology for Infectious Diseases

    PubMed Central

    Speers, David J

    2006-01-01

    Molecular biological methods for the detection and characterisation of microorganisms have revolutionised diagnostic microbiology and are now part of routine specimen processing. Polymerase chain reaction (PCR) techniques have led the way into this new era by allowing rapid detection of microorganisms that were previously difficult or impossible to detect by traditional microbiological methods. In addition to detection of fastidious microorganisms, more rapid detection by molecular methods is now possible for pathogens of public health importance. Molecular methods have now progressed beyond identification to detect antimicrobial resistance genes and provide public health information such as strain characterisation by genotyping. Treatment of certain microorganisms has been improved by viral resistance detection and viral load testing for the monitoring of responses to antiviral therapies. With the advent of multiplex PCR, real-time PCR and improvements in efficiency through automation, the costs of molecular methods are decreasing such that the role of molecular methods will further increase. This review will focus on the clinical utility of molecular methods performed in the clinical microbiology laboratory, illustrated with the many examples of how they have changed laboratory diagnosis and therefore the management of infectious diseases. PMID:16886046

  12. 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.

  13. 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.

  14. Molecular biology of the skin introduction: approaches and principles.

    PubMed

    Slater, C; Goldsmith, L A

    1993-09-01

    This issue of Seminars in Dermatology describes our current understanding of the molecular nature of skin diseases. Some would say it is hubris to even contemplate this charge considering the rapid progress in molecular genetics. We implore the gods protecting the nucleotides to look kindly on our efforts. This introductory article discussed some general methodological considerations and techniques and provides a glossary of common terms used in molecular biology, useful for understanding this issue of Seminars in Dermatology. This article is aimed at neophytes to enhance their ability to enter the magical realm of the gene. The articles in this issue describe diseases with a defined defect at the DNA level or diseases in which there is a rapid closing in on the basic defect. PMID:8217556

  15. Recent Progress on Systems and Synthetic Biology Approaches to Engineer Fungi As Microbial Cell Factories.

    PubMed

    Amores, Gerardo Ruiz; Guazzaroni, María-Eugenia; Arruda, Letícia Magalhães; Silva-Rocha, Rafael

    2016-04-01

    Filamentous fungi are remarkable organisms naturally specialized in deconstructing plant biomass and this feature has a tremendous potential for biofuel production from renewable sources. The past decades have been marked by a remarkable progress in the genetic engineering of fungi to generate industry-compatible strains needed for some biotech applications. In this sense, progress in this field has been marked by the utilization of high-throughput techniques to gain deep understanding of the molecular machinery controlling the physiology of these organisms, starting thus the Systems Biology era of fungi. Additionally, genetic engineering has been extensively applied to modify wellcharacterized promoters in order to construct new expression systems with enhanced performance under the conditions of interest. In this review, we discuss some aspects related to significant progress in the understating and engineering of fungi for biotechnological applications, with special focus on the construction of synthetic promoters and circuits in organisms relevant for industry. Different engineering approaches are shown, and their potential and limitations for the construction of complex synthetic circuits in these organisms are examined. Finally, we discuss the impact of engineered promoter architecture in the single-cell behavior of the system, an often-neglected relationship with a tremendous impact in the final performance of the process of interest. We expect to provide here some new directions to drive future research directed to the construction of high-performance, engineered fungal strains working as microbial cell factories. PMID:27226765

  16. 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

  17. 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

  18. Biological Responses to Engineered Nanomaterials: Needs for the Next Decade

    PubMed Central

    2015-01-01

    The interaction of nanomaterials with biomolecules, cells, and organisms is an enormously vital area of current research, with applications in nanoenabled diagnostics, imaging agents, therapeutics, and contaminant removal technologies. Yet the potential for adverse biological and environmental impacts of nanomaterial exposure is considerable and needs to be addressed to ensure sustainable development of nanomaterials. In this Outlook four research needs for the next decade are outlined: (i) measurement of the chemical nature of nanomaterials in dynamic, complex aqueous environments; (ii) real-time measurements of nanomaterial–biological interactions with chemical specificity; (iii) delineation of molecular modes of action for nanomaterial effects on living systems as functions of nanomaterial properties; and (iv) an integrated systems approach that includes computation and simulation across orders of magnitude in time and space. PMID:27162961

  19. Biological Responses to Engineered Nanomaterials: Needs for the Next Decade.

    PubMed

    Murphy, Catherine J; Vartanian, Ariane M; Geiger, Franz M; Hamers, Robert J; Pedersen, Joel; Cui, Qiang; Haynes, Christy L; Carlson, Erin E; Hernandez, Rigoberto; Klaper, Rebecca D; Orr, Galya; Rosenzweig, Ze'ev

    2015-06-24

    The interaction of nanomaterials with biomolecules, cells, and organisms is an enormously vital area of current research, with applications in nanoenabled diagnostics, imaging agents, therapeutics, and contaminant removal technologies. Yet the potential for adverse biological and environmental impacts of nanomaterial exposure is considerable and needs to be addressed to ensure sustainable development of nanomaterials. In this Outlook four research needs for the next decade are outlined: (i) measurement of the chemical nature of nanomaterials in dynamic, complex aqueous environments; (ii) real-time measurements of nanomaterial-biological interactions with chemical specificity; (iii) delineation of molecular modes of action for nanomaterial effects on living systems as functions of nanomaterial properties; and (iv) an integrated systems approach that includes computation and simulation across orders of magnitude in time and space. PMID:27162961

  20. Biological responses to engineered nanomaterials: Needs for the next decade

    DOE PAGESBeta

    Murphy, Catherine J.; Vartanian, Ariane M.; Geiger, Franz M.; Hamers, Robert J.; Pedersen, Joel A.; Cui, Qiang; Haynes, Christy L.; Carlson, Erin E.; Hernandez, Rigoberto; Klaper, Rebecca D.; et al

    2015-06-09

    In this study, the interaction of nanomaterials with biomolecules, cells, and organisms is an enormously vital area of current research, with applications in nanoenabled diagnostics, imaging agents, therapeutics, and contaminant removal technologies. Yet the potential for adverse biological and environmental impacts of nanomaterial exposure is considerable and needs to be addressed to ensure sustainable development of nanomaterials. In this Outlook four research needs for the next decade are outlined: (i) measurement of the chemical nature of nanomaterials in dynamic, complex aqueous environments; (ii) real-time measurements of nanomaterial-biological interactions with chemical specificity; (iii) delineation of molecular modes of action for nanomaterialmore » effects on living systems as functions of nanomaterial properties; and (iv) an integrated systems approach that includes computation and simulation across orders of magnitude in time and space.« less

  1. Biological responses to engineered nanomaterials: Needs for the next decade

    SciTech Connect

    Murphy, Catherine J.; Vartanian, Ariane M.; Geiger, Franz M.; Hamers, Robert J.; Pedersen, Joel A.; Cui, Qiang; Haynes, Christy L.; Carlson, Erin E.; Hernandez, Rigoberto; Klaper, Rebecca D.; Orr, Galya; Rosenzweig, Ze'ev

    2015-06-09

    In this study, the interaction of nanomaterials with biomolecules, cells, and organisms is an enormously vital area of current research, with applications in nanoenabled diagnostics, imaging agents, therapeutics, and contaminant removal technologies. Yet the potential for adverse biological and environmental impacts of nanomaterial exposure is considerable and needs to be addressed to ensure sustainable development of nanomaterials. In this Outlook four research needs for the next decade are outlined: (i) measurement of the chemical nature of nanomaterials in dynamic, complex aqueous environments; (ii) real-time measurements of nanomaterial-biological interactions with chemical specificity; (iii) delineation of molecular modes of action for nanomaterial effects on living systems as functions of nanomaterial properties; and (iv) an integrated systems approach that includes computation and simulation across orders of magnitude in time and space.

  2. Substrate-assisted catalysis: molecular basis and biological significance.

    PubMed Central

    Dall'Acqua, W.; Carter, P.

    2000-01-01

    Substrate-assisted catalysis (SAC) is the process by which a functional group in a substrate contributes to catalysis by an enzyme. SAC has been demonstrated for representatives of three major enzyme classes: serine proteases, GTPases, and type II restriction endonucleases, as well as lysozyme and hexose-1-phosphate uridylyltransferase. Moreover, structure-based predictions of SAC have been made for many additional enzymes. Examples of SAC include both naturally occurring enzymes such as type II restriction endonucleases as well as engineered enzymes including serine proteases. In the latter case, a functional group from a substrate can substitute for a catalytic residue replaced by site-directed mutagenesis. From a protein engineering perspective, SAC provides a strategy for drastically changing enzyme substrate specificity or even the reaction catalyzed. From a biological viewpoint, SAC contributes significantly to the activity of some enzymes and may represent a functional intermediate in the evolution of catalysis. This review focuses on advances in engineering enzyme specificity and activity by SAC, together with the biological significance of this phenomenon. PMID:10739241

  3. Engineering Molecular Transformations for Sustainable Energy Conversion

    SciTech Connect

    Neurock, Matthew

    2010-12-03

    Future strategies for sustainable energy production will undoubtedly require processes and materials that can efficiently convert renewable resources into fuels. Nature’s enzymes can exquisitely integrate highly active catalytic centers within flexible environments that can adaptively guide reactants to products with very high activities and selectivities. They are limited, however, by their stability and ability to integrate into large scale production processes. The design of more robust heterogeneous catalytic materials that mimic the performance of enzymes, however, has been hindered by our limited understanding of how such transformations proceed. The tremendous advances in ab initio quantum mechanical methods, atomistic simulations, and high performance computing that have occurred over the past two decades, however, provide unprecedented ability to track molecular transformations and how they proceed at specific sites and within particular environments. This information together with the advances in in situ spectroscopic methods that follow such transformations can begin to enable the design of atomic surface ensembles and nanoscale reaction environments. This paper provides the author’s perspective on how theory and simulation can be used to move from current onedimensional design efforts based on catalytic descriptors to the design of two-dimensional surfaces, threedimensional reaction environments, and proton-coupled electron transfer systems that mimic enzymes in the transformation of molecules.

  4. Gene gymnastics: Synthetic biology for baculovirus expression vector system engineering.

    PubMed

    Vijayachandran, Lakshmi S; Thimiri Govinda Raj, Deepak B; Edelweiss, Evelina; Gupta, Kapil; Maier, Josef; Gordeliy, Valentin; Fitzgerald, Daniel J; Berger, Imre

    2013-01-01

    Most essential activities in eukaryotic cells are catalyzed by large multiprotein assemblies containing up to ten or more interlocking subunits. The vast majority of these protein complexes are not easily accessible for high resolution studies aimed at unlocking their mechanisms, due to their low cellular abundance and high heterogeneity. Recombinant overproduction can resolve this bottleneck and baculovirus expression vector systems (BEVS) have emerged as particularly powerful tools for the provision of eukaryotic multiprotein complexes in high quality and quantity. Recently, synthetic biology approaches have begun to make their mark in improving existing BEVS reagents by de novo design of streamlined transfer plasmids and by engineering the baculovirus genome. Here we present OmniBac, comprising new custom designed reagents that further facilitate the integration of heterologous genes into the baculovirus genome for multiprotein expression. Based on comparative genome analysis and data mining, we herein present a blueprint to custom design and engineer the entire baculovirus genome for optimized production properties using a bottom-up synthetic biology approach. PMID:23328086

  5. Fully Automated Molecular Biology Routines on a Plasmid-Based Functional Proteomic Workcell: Evaluation and Characterization of Yeast Strains Optimized for Growth on Xylose and Engineered to Express an Insecticidal Peptide

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Optimization of genes important to production of fuel ethanol from hemicellulosic biomass for use in engineering improved commercial yeast strains is necessary to meet the United States' rapidly expanding need for ethanol. United States Department of Agriculture, Agricultural Research Service, Nati...

  6. 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.

  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

    important consequences when performed in a proper context. We envision that molecular computers that operate in a biological environment can be the basis of “smart drugs”, which are potent drugs that activate only if certain environmental conditions hold. These conditions could include abnormalities in the molecular composition of the biological environment that are indicative of a particular disease. Here we review the research direction that set this vision and attempts to realize it.

  8. Proteomics in reproductive biology: beacon for unraveling the molecular complexities.

    PubMed

    Upadhyay, Rahul D; Balasinor, N H; Kumar, Anita V; Sachdeva, Geetanjali; Parte, Priyanka; Dumasia, Kushaan

    2013-01-01

    Proteomics, an interface of rapidly evolving advances in physics and biology, is rapidly developing and expanding its potential applications to molecular and cellular biology. Application of proteomics tools has contributed towards identification of relevant protein biomarkers that can potentially change the strategies for early diagnosis and treatment of several diseases. The emergence of powerful mass spectrometry-based proteomics technique has added a new dimension to the field of medical research in liver, heart diseases and certain forms of cancer. Most proteomics tools are also being used to study physiological and pathological events related to reproductive biology. There have been attempts to generate the proteomes of testes, sperm, seminal fluid, epididymis, oocyte, and endometrium from reproductive disease patients. Here, we have reviewed proteomics based investigations in humans over the last decade, which focus on delineating the mechanism underlying various reproductive events such as spermatogenesis, oogenesis, endometriosis, polycystic ovary syndrome, embryo development. The challenge is to harness new technologies like 2-DE, DIGE, MALDI-MS, SELDI-MS, MUDPIT, LC-MS etc., to a greater extent to develop widely applicable clinical tools in understanding molecular aspects of reproduction both in health and disease. PMID:23072795

  9. PGASO: A synthetic biology tool for engineering a cellulolytic yeast

    PubMed Central

    2012-01-01

    Background To achieve an economical cellulosic ethanol production, a host that can do both cellulosic saccharification and ethanol fermentation is desirable. However, to engineer a non-cellulolytic yeast to be such a host requires synthetic biology techniques to transform multiple enzyme genes into its genome. Results A technique, named Promoter-based Gene Assembly and Simultaneous Overexpression (PGASO), that employs overlapping oligonucleotides for recombinatorial assembly of gene cassettes with individual promoters, was developed. PGASO was applied to engineer Kluyveromycesmarxianus KY3, which is a thermo- and toxin-tolerant yeast. We obtained a recombinant strain, called KR5, that is capable of simultaneously expressing exoglucanase and endoglucanase (both of Trichodermareesei), a beta-glucosidase (from a cow rumen fungus), a neomycin phosphotransferase, and a green fluorescent protein. High transformation efficiency and accuracy were achieved as ~63% of the transformants was confirmed to be correct. KR5 can utilize beta-glycan, cellobiose or CMC as the sole carbon source for growth and can directly convert cellobiose and beta-glycan to ethanol. Conclusions This study provides the first example of multi-gene assembly in a single step in a yeast species other than Saccharomyces cerevisiae. We successfully engineered a yeast host with a five-gene cassette assembly and the new host is capable of co-expressing three types of cellulase genes. Our study shows that PGASO is an efficient tool for simultaneous expression of multiple enzymes in the kefir yeast KY3 and that KY3 can serve as a host for developing synthetic biology tools. PMID:22839502

  10. The mismeasure of machine: Synthetic biology and the trouble with engineering metaphors.

    PubMed

    Boudry, Maarten; Pigliucci, Massimo

    2013-12-01

    The scientific study of living organisms is permeated by machine and design metaphors. Genes are thought of as the "blueprint" of an organism, organisms are "reverse engineered" to discover their functionality, and living cells are compared to biochemical factories, complete with assembly lines, transport systems, messenger circuits, etc. Although the notion of design is indispensable to think about adaptations, and engineering analogies have considerable heuristic value (e.g., optimality assumptions), we argue they are limited in several important respects. In particular, the analogy with human-made machines falters when we move down to the level of molecular biology and genetics. Living organisms are far more messy and less transparent than human-made machines. Notoriously, evolution is an opportunistic tinkerer, blindly stumbling on "designs" that no sensible engineer would come up with. Despite impressive technological innovation, the prospect of artificially designing new life forms from scratch has proven more difficult than the superficial analogy with "programming" the right "software" would suggest. The idea of applying straightforward engineering approaches to living systems and their genomes-isolating functional components, designing new parts from scratch, recombining and assembling them into novel life forms-pushes the analogy with human artifacts beyond its limits. In the absence of a one-to-one correspondence between genotype and phenotype, there is no straightforward way to implement novel biological functions and design new life forms. Both the developmental complexity of gene expression and the multifarious interactions of genes and environments are serious obstacles for "engineering" a particular phenotype. The problem of reverse-engineering a desired phenotype to its genetic "instructions" is probably intractable for any but the most simple phenotypes. Recent developments in the field of bio-engineering and synthetic biology reflect these