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Sample records for biological invasion molecular

  1. The mathematics behind biological invasions

    CERN Document Server

    Lewis, Mark A; Potts, Jonathan R

    2016-01-01

    This book investigates the mathematical analysis of biological invasions. Unlike purely qualitative treatments of ecology, it draws on mathematical theory and methods, equipping the reader with sharp tools and rigorous methodology. Subjects include invasion dynamics, species interactions, population spread, long-distance dispersal, stochastic effects, risk analysis, and optimal responses to invaders. While based on the theory of dynamical systems, including partial differential equations and integrodifference equations, the book also draws on information theory, machine learning, Monte Carlo methods, optimal control, statistics, and stochastic processes. Applications to real biological invasions are included throughout. Ultimately, the book imparts a powerful principle: that by bringing ecology and mathematics together, researchers can uncover new understanding of, and effective response strategies to, biological invasions. It is suitable for graduate students and established researchers in mathematical ecolo...

  2. Microbial ecology of biological invasions

    NARCIS (Netherlands)

    Van der Putten, W.H.; Klironomos, J.N.; Wardle, D.A.

    2007-01-01

    Invasive microbes, plants and animals are a major threat to the composition and functioning of ecosystems; however, the mechanistic basis of why exotic species can be so abundant and disruptive is not well understood. Most studies have focused on invasive plants and animals, although few have consid

  3. Glycobiology Current Molecular Biology

    OpenAIRE

    Sabire KARAÇALI

    2003-01-01

    Carbohydrate chemistry evolved into carbohydrate biochemistry and gradually into the biology of carbohydrates, or glycobiology, at the end of the last century. Glycobiology is the new research area of modern molecular biology, and it investigates the structure, biosynthesis and biological functions of glycans. The numbers, linkage types (a or b), positions, binding points and functional group differences of monosaccharides create microheterogeneity. Thus, numerous glycoforms with precise stru...

  4. The Correlation Between Candida Colonization of Distinct Body Sites and Invasive Candidiasis in Emergency Intensive Care Units: Statistical and Molecular Biological Analysis.

    Science.gov (United States)

    Li, Zhen; Jiang, Cen; Dong, Danfeng; Zhang, Lihua; Tian, Yuan; Ni, Qi; Mao, Enqiang; Peng, Yibing

    2016-08-01

    Both statistical and molecular biological methods were used to evaluate the association between Candida colonization of different body sites and invasive candidiasis (IC) and analyse the potential infection sources of IC. Candida surveillance cultures from the urine, sputum, rectum and skin were performed on patients admitted to an emergency intensive care units (EICU) of a tertiary care hospital in Shanghai, China, from February 2014 to January 2015. Specimens were collected once a week at admission and thereafter. The patients' clinical data were collected, and Candida isolates were genotyped using polymorphic microsatellite markers. A total of 111 patients were enrolled. Patients with positive urine (23.3 vs. 2.5 %, p = 0.001) and rectal swab (13.6 vs. 0 %, p = 0.010) cultures were more likely to develop IC. However, the risk for IC was not significantly different among patients with and without respiratory (10.0 vs. 5.8 %, p = 0.503) and skin (33.3 vs. 6.5 %, p = 0.056) colonization. Gene microevolution frequently occurred at rectal swab and urine sites, and IC with possible source of infection was caused by rectal isolates (2/7), urine isolates (4/7) and sputum isolate (1/7).The colonization of gut and urinary tract maybe more relevant indicators of IC, which should be taken into consideration when selecting practical body sites for Candida surveillance cultures. PMID:26886444

  5. A Molecular Biology Database Digest

    OpenAIRE

    Bry, François; Kröger, Peer

    2000-01-01

    Computational Biology or Bioinformatics has been defined as the application of mathematical and Computer Science methods to solving problems in Molecular Biology that require large scale data, computation, and analysis [18]. As expected, Molecular Biology databases play an essential role in Computational Biology research and development. This paper introduces into current Molecular Biology databases, stressing data modeling, data acquisition, data retrieval, and the integration...

  6. Facing the broader dimensions of biological invasions

    OpenAIRE

    Tassin J.; Kull Ch. A.

    2015-01-01

    Invasive species are an excellent opportunity to think about the nature society desires, particularly in the face of global changes. Nature and human views of nature are rapidly evolving; our approach to bio- logical invasions through biosecurity institutions and land management policies must evolve in tandem with these changes. We review three dimensions that are insufficiently addressed. First, biological inva- sions are culturally shaped and interpreted. Humans play a major role in the mov...

  7. A molecular diagnostic tool for the preliminary assessment of host-parasitoid associations in biological control programmes for a new invasive pest.

    Science.gov (United States)

    Gariepy, T D; Haye, T; Zhang, J

    2014-08-01

    Evaluation of host-parasitoid associations can be tenuous using conventional methods. Molecular techniques are well placed to identify trophic links and resolve host-parasitoid associations. Establishment of the highly invasive brown marmorated stink bug, Halyomorpha halys (Hemiptera: Pentatomidae), outside Asia has prompted interest in the use of egg parasitoids (Hymenoptera: Scelionidae) as biological control agents. However, little is known regarding their host ranges. To address this, a DNA barcoding approach was taken wherein general PCR primers for Scelionidae and Pentatomidae were developed to amplify and sequence >500-bp products within the DNA barcoding region of the cytochrome oxidase I (COI) gene that would permit the identification of key players in this association. Amplification of DNA from Pentatomidae and Scelionidae was consistent across a broad range of taxa within these families, and permitted the detection of Scelionidae eggs within H. halys 1 h following oviposition. In laboratory assays, amplification and sequencing of DNA from empty, parasitized eggs was successful for both host (100% success) and parasitoid (50% success). When applied to field-collected, empty egg masses, the primers permitted host identification in 50-100% of the eggs analysed, and yielded species-level identifications. Parasitoid identification success ranged from 33 to 67% among field-collected eggs, with genus-level identification for most specimens. The inability to obtain species-level identities for these individuals is due to the lack of coverage of this taxonomic group in public DNA sequence databases; this situation is likely to improve as more species are sequenced and recorded in these databases. These primers were able to detect and identify both pentatomid host and scelionid parasitoid in a hyperparasitized egg mass, thereby clarifying trophic links otherwise unresolved by conventional methodology.

  8. Topology in Molecular Biology

    CERN Document Server

    Monastyrsky, Michail Ilych

    2007-01-01

    The book presents a class of new results in molecular biology for which topological methods and ideas are important. These include: the large-scale conformation properties of DNA; computational methods (Monte Carlo) allowing the simulation of large-scale properties of DNA; the tangle model of DNA recombination and other applications of Knot theory; dynamics of supercoiled DNA and biocatalitic properties of DNA; the structure of proteins; and other very recent problems in molecular biology. The text also provides a short course of modern topology intended for the broad audience of biologists and physicists. The authors are renowned specialists in their fields and some of the new results presented here are documented for the first time in monographic form.

  9. Bilingual teaching of molecular biology

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Recently bilingual teaching in China's universities has been widely carried out and become a popular subject for study. In this paper, the reasons for bilingual teaching of molecular biology are pointed out, the textbook of molecular biology and teaching method in bilingual teaching classes are determined after investigation and the practice of bilingually teaching molecular biology use both English and Chinese in a class. The effect has proved good. The bilingual teaching methods, the problem of bilingual teaching, the importance of understanding its significance and the possibilities of improving such teaching of the subject are also discussed.

  10. Molecular Biology of Medulloblastoma

    OpenAIRE

    J Gordon Millichap

    2007-01-01

    Current methods of diagnosis and treatment of medulloblastoma, and the influence of new biological advances in the development of more effective and less toxic therapies are reviewed by researchers at Children’s National Medical Center, The George Washington University, Washington, DC.

  11. Molecular biology of hearing [

    Directory of Open Access Journals (Sweden)

    Diensthuber, Marc

    2012-04-01

    Full Text Available [english] 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.

  12. Biology of cancer invasion and metastasis.

    Science.gov (United States)

    Mareel, M M; Crombez, R

    1992-01-01

    Current concepts of invasion eventually leading to metastasis are discussed and exemplified by cancers of the head and neck mucosa. Invasion occurs at a number of steps, each step making an ecosystem comprising not only the neoplastic cells but also their normal counterparts, a variety of host cells and the extracellular matrix. The ecosystem concept may explain aspects of metastasis such as site-dependence and organ-specificity of cancer metastasis as well as invasiveness of normal leucocytes. Genes implicated in invasion and metastasis are actively searched for. Recently, the epithelial cell-cell adhesion molecule E-cadherin has been identified as an i- (invasion suppressor) gene product, i.e. a molecule the expression of which counterbalances i+ (invasion promotor) gene activity. Downregulation of E-cadherin in human head and neck cancers may account for their invasive and metastatic behaviour.

  13. [Knowledgebases in postgenomic molecular biology].

    Science.gov (United States)

    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

  14. Biological markers of invasive breast cancer.

    Science.gov (United States)

    Matsumoto, Akiko; Jinno, Hiromitsu; Ando, Tomofumi; Fujii, Taku; Nakamura, Tetsuya; Saito, Junichi; Takahashi, Maiko; Hayashida, Tetsu; Kitagawa, Yuko

    2016-02-01

    Biological markers for breast cancer are biomolecules that result from cancer-related processes and are associated with particular clinical outcomes; they thus help predict responses to therapy. In recent years, gene expression profiling has made the molecular classification of breast cancer possible. Classification of breast cancer by immunohistochemical expression of estrogen receptor, progesterone receptor, human epidermal growth factor receptor 2 and Ki-67 is standard practice for clinical decision-making. Assessments of hormone receptor expression and human epidermal growth factor receptor 2 overexpression help estimate benefits from targeted therapies and have greatly improved prognoses for women with these breast cancer types. Although Ki-67 positivity is associated with an adverse outcome, its clear identification is an aid to optimal disease management. Standardization of testing methodology to minimize inter-laboratory measurement variations is a remaining issue. Multi-gene assays provide prognostic information and identify those most likely to benefit from systemic chemotherapy. Incorporating molecular profiles with conventional pathological classification would be more precise, and could enhance the clinical development of personalized therapy in breast cancer. PMID:26486826

  15. Dispersal Polymorphism and the Speed of Biological Invasions

    OpenAIRE

    Elizabeth C. Elliott; Cornell, Stephen J.

    2012-01-01

    The speed at which biological range expansions occur has important consequences for the conservation management of species experiencing climate change and for invasion by exotic organisms. Rates of dispersal and population growth are known to affect the speed of invasion, but little is known about the effect of having a community of dispersal phenotypes on the rate of range expansion. We use reaction-diffusion equations to model the invasion of a species with two dispersal phenotypes into a p...

  16. Evolution in invasive plants: implications for biological control

    OpenAIRE

    Müller-Schärer, Heinz; Schaffner, Urs; Steinger, Thomas

    2005-01-01

    Evidence is increasing that invasive plants can undergo rapid adaptive evolution during the process of range expansion. Here, we argue that evolutionary change during invasions will also affect plant–antagonist inter-actions and, thus, will have important implications for biological control programmes targeted at invasive plants. We explore how altered selection in the new range might influence the evolution of plant defence (resistance and tolerance) and life history. The degree to which suc...

  17. Molecular Processes in Biological Thermosensation

    Directory of Open Access Journals (Sweden)

    I. Digel

    2008-01-01

    Full Text Available 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”.

  18. Molecular biology of the cell

    CERN Document Server

    Alberts, Bruce; Lewis, Julian

    2000-01-01

    Molecular Biology of the Cell is the classic in-dept text reference in cell biology. By extracting the fundamental concepts from this enormous and ever-growing field, the authors tell the story of cell biology, and create a coherent framework through which non-expert readers may approach the subject. Written in clear and concise language, and beautifully illustrated, the book is enjoyable to read, and it provides a clear sense of the excitement of modern biology. Molecular Biology of the Cell sets forth the current understanding of cell biology (completely updated as of Autumn 2001), and it explores the intriguing implications and possibilities of the great deal that remains unknown. The hallmark features of previous editions continue in the Fourth Edition. The book is designed with a clean and open, single-column layout. The art program maintains a completely consistent format and style, and includes over 1,600 photographs, electron micrographs, and original drawings by the authors. Clear and concise concept...

  19. Measurement Frontiers in Molecular Biology

    Science.gov (United States)

    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.

  20. Marine molecular biology: An emerging field of biological sciences

    Digital Repository Service at National Institute of Oceanography (India)

    Thakur, N.L.; Jain, R.; Natalio, F.; Hamer, B.; Thakur, A.N.; Muller, W.E.G.

    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...

  1. Parasites and biological invasions: parallels, interactions, and control.

    Science.gov (United States)

    Dunn, Alison M; Hatcher, Melanie J

    2015-05-01

    Species distributions are changing at an unprecedented rate owing to human activity. We examine how two key processes of redistribution - biological invasion and disease emergence - are interlinked. There are many parallels between invasion and emergence processes, and invasions can drive the spread of new diseases to wildlife. We examine the potential impacts of invasion and disease emergence, and discuss how these threats can be countered, focusing on biosecurity. In contrast with international policy on emerging diseases of humans and managed species, policy on invasive species and parasites of wildlife is fragmented, and the lack of international cooperation encourages individual parties to minimize their input into control. We call for international policy that acknowledges the strong links between emerging diseases and invasion risk.

  2. Biological Invasion Risks and the Public Good: an Economic Perspective

    Directory of Open Access Journals (Sweden)

    Jason Shogren

    2002-06-01

    Full Text Available We postulate that the causes of the problem of invasive alien species are primarily economic and, as such, require economic solutions. Invasive alien species are of increasing concern for four reasons. First, introductions are increasing sharply, while mechanisms for excluding or eradicating alien species have been either withdrawn or progressively weakened. Both trends are due to the liberalization of and increase in international travel and trade, an economic phenomenon. Second, the costs of invasions are rising rapidly due partly to increasing human population density, and partly to increasing intensity of production in genetically impoverished agricultural systems. Third, biological invasions are associated with a high degree of uncertainty both because they involve novel interactions, and because invasion risks are endogenous. Actual risks depend on how people react to the possibility of invasions. Fourth, the exclusion and control of invasive species is a "weakest-link" public good. This places the well-being of society in the hands of the least effective provider. We argue that an economic solution to the problem of invasive species has two components. One is to use incentives to change human behavior so as to enhance protection against the introduction, establishment, and spread of invasive behavior. The other is to develop institutions that support the weakest members of global society, converting a "weakest-link" to a "best-shot" public good.

  3. Evolutionary increases in defense during a biological invasion.

    Science.gov (United States)

    Liao, Zhi-Yong; Zheng, Yu-Long; Lei, Yan-Bao; Feng, Yu-Long

    2014-04-01

    Invasive plants generally escape from specialist herbivores of their native ranges but may experience serious damage from generalists. As a result, invasive plants may evolve increased resistance to generalists and tolerance to damage. To test these hypotheses, we carried out a common garden experiment comparing 15 invasive populations with 13 native populations of Chromolaena odorata, including putative source populations identified with molecular methods and binary choice feeding experiments using three generalist herbivores. Plants from invasive populations of C. odorata had both higher resistance to three generalists and higher tolerance to simulated herbivory (shoot removal) than plants from native populations. The higher resistance of plants from invasive populations was associated with higher leaf C content and densities of leaf trichomes and glandular scales, and lower leaf N and water contents. Growth costs were detected for tolerance but not for resistance, and plants from invasive populations of C. odorata showed lower growth costs of tolerance. Our results suggest that invasive plants may evolve to increase both resistance to generalists and tolerance to damage in introduced ranges, especially when the defense traits have low or no fitness costs. Greater defenses in invasive populations may facilitate invasion by C. odorata by reducing generalist impacts and increasing compensatory growth after damage has occurred. PMID:24326694

  4. Biological invasions in agricultural settings: insights from evolutionary biology and population genetics.

    Science.gov (United States)

    Guillemaud, Thomas; Ciosi, Marc; Lombaert, Eric; Estoup, Arnaud

    2011-03-01

    Invasion biology and agriculture are intimately related for several reasons and in particular because many agricultural pest species are recent invaders. In this article we suggest that the reconstruction of invasion routes with population genetics-based methods can address fundamental questions in ecology and practical aspects of the management of biological invasions in agricultural settings. We provide a brief description of the methods used to reconstruct invasion routes and describe their main characteristics. In particular, we focus on a scenario--the bridgehead invasion scenario --which had been overlooked until recently. We show that this scenario, in which an invasive population is the source of other invasive populations, is evolutionarily parsimonious and may have played a crucial role in shaping the distribution of many recent agricultural pests.

  5. Molecular markers of tumor invasiveness in ameloblastoma: An update

    OpenAIRE

    Zhong, Yi; Guo, Wei; Wang, Li; CHEN, XINMING

    2011-01-01

    The aim of the present article was to review the current new knowledge on the molecular markers of tumor invasion in ameloblastoma. In this review, tumor molecular markers were identified and allocated to the following six groups according to their functions: (I) Markers involved in extracellular matrix degradation, (II) Molecular markers involved in cell adhesion lost, (III) Molecular markers involved in bone remodeling, (IV) Cytokines involved in angiogenesis, (V) Molecular markers related ...

  6. The molecular biology of ilarviruses.

    Science.gov (United States)

    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

  7. The molecular biology of cancer.

    Science.gov (United States)

    Bertram, J S

    2000-12-01

    identifies key genes directly involved in carcinogenesis and demonstrates how mutations in these genes allow cells to circumvent cellular controls. This detailed understanding of the process of carcinogenesis at the molecular level has only been possible because of the advent of modern molecular biology. This new discipline, by precisely identifying the molecular basis of the differences between normal and malignant cells, has created novel opportunities and provided the means to specifically target these modified genes. Whenever possible this review highlights these opportunities and the attempts being made to generate novel, molecular based therapies against cancer. Successful use of these new therapies will rely upon a detailed knowledge of the genetic defects in individual tumors. The review concludes with a discussion of how the use of high throughput molecular arrays will allow the molecular pathologist/therapist to identify these defects and direct specific therapies to specific mutations.

  8. Research Status of Molecular Biology in Flax

    Institute of Scientific and Technical Information of China (English)

    Wu Jian-zhong

    2016-01-01

    Flax is a kind of worldwide fiber and oil crops, and it has a very important role in economic crop production in the world. With the development of molecular biology techniques, the research of flax molecular level has a very big breakthrough. But, flax molecular biology researches are less reported due to the later starting. This paper summarized the latest research progress of molecular biology of flax, including molecular marker technology, construction of genetic map, gene engineering and omics researches, in order to provide the reference to understand the development and research status for flax molecular breeding researchers.

  9. Phenological response of a key ecosystem function to biological invasion.

    Science.gov (United States)

    Alp, Maria; Cucherousset, Julien; Buoro, Mathieu; Lecerf, Antoine

    2016-05-01

    Although climate warming has been widely demonstrated to induce shifts in the timing of many biological events, the phenological consequences of other prominent global change drivers remain largely unknown. Here, we investigated the effects of biological invasions on the seasonality of leaf litter decomposition, a crucial freshwater ecosystem function. Decomposition rates were quantified in 18 temperate shallow lakes distributed along a gradient of crayfish invasion and a temperature-based model was constructed to predict yearly patterns of decomposition. We found that, through direct detritus consumption, omnivorous invasive crayfish accelerated decomposition rates up to fivefold in spring, enhancing temperature dependence of the process and shortening the period of major detritus availability in the ecosystem by up to 39 days (95% CI: 15-61). The fact that our estimates are an order of magnitude higher than any previously reported climate-driven phenological shifts indicates that some powerful drivers of phenological change have been largely overlooked. PMID:26931804

  10. Molecular characteristics versus biological activity

    Science.gov (United States)

    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.

  11. REPRODUCTIVE BIOLOGY OF INVASIVE LIONFISH (PTEROIS SPP.

    Directory of Open Access Journals (Sweden)

    Patrick G Gardner

    2015-02-01

    Full Text Available Indo-Pacific lionfishes, Pterois volitans (Linnaeus, 1758 and Pterois miles (Bennett, 1828, native to the Pacific and Indian Oceans, respectively, were first observed in the western Atlantic off Florida in 1985. They have since spread and are established throughout the broader Caribbean region. Despite potentially devastating ecological and economic effects, information on key life history characteristics for lionfish in the invaded range is sparse. Objectives of this study were to quantify 1 periodicity in gonad development and spawning, 2 spawning frequency, 3 batch fecundity and 4 female size at maturity for fish from Little Cayman. Calculation of gonadosomatic indices, histological and macroscopic staging of gonads, and counts of hydrated oocytes were applied to determine reproductive characteristics. Higher gonadosomatic indices were recorded for females during periods of stable warm or cool water temperatures indicating that extreme temperatures did not constrain reproduction. Histological and macroscopic staging suggested that male and female lionfish were capable of reproducing year-round. However, higher gonadosomatic indices in females, as expected before spawning, were most pronounced in March/April and August. Based on the proportion of females containing hydrated oocytes, mature lionfish had the potential to spawn every 2–3 d. Ovaries of mature females contained 1800–41945 oocytes that were hydrated in preparation for spawning, with greater numbers of oocytes in larger females. Female lionfish matured at 189–190 mm total length. Parameters estimated in this study can improve outputs from population dynamic models, which will help resource managers design removals and other efforts to control invasive lionfish.

  12. “...those left behind.” Biology and Oncology of Invasive Glioma Cells

    Directory of Open Access Journals (Sweden)

    Michael E Berens

    1999-08-01

    Full Text Available Although significant technical advances in surgical and radiation treatment for brain tumors have emerged in recent years, their impact on clinical outcome for patients has been disappointing. A fundamental source of the management challenge presented by glioma patients is the insidious propensity of the malignant cells to invade into adjacent normal brain. Invasive tumor cells escape surgical removal and geographically dodge lethal radiation exposure. Recent improved understanding of the biochemistry and molecular determinants of glioma cell invasion provide valuable insight to the underlying biological features of the disease, as well as illuminating possible new therapeutic targets. Heightened commitment to migrate and invade is accompanied by a glioma cell's reduced proliferative activity. The microenvironmental manipulations coincident to invasion and migration may also impact the glioma cell's response to cytotoxic treatments. These collateral aspects of the glioma cell invasive phenotype should be further explored and exploited as novel antiglioma therapies.

  13. Laboratory of Cell and Molecular Biology

    Data.gov (United States)

    Federal Laboratory Consortium — The Laboratory of Cell and Molecular Biology investigates the organization, compartmentalization, and biochemistry of eukaryotic cells and the pathology associated...

  14. Molecular Biology of Esophageal Cancer

    Institute of Scientific and Technical Information of China (English)

    HuanXi; JanBrabender; RalfMetzger; PaulM.Schneider

    2004-01-01

    There have been many new developments in our understanding of esophageal carcinoma biology over the past several years. Information regarding both of the major forms of this disease, adenocarcinoma and squamous cell carcinoma, has accumulated in conjunction with data on precursor conditions such as Barrett's esophagus. Interesting and promising findings have included overexpression of proto-oncogenes,loss of heterozygosity at multiple chromosomal loci, tumor suppressor gene inactivation, epigenetic silencing by DNA methylation, and mutations and deletions involving the tumor suppressor gene p53. Important cancer pathways, the cyclin kinase inhibitor cascade and the DNA mismatch repair process, implicated in the genesis of multiple tumor types have also been inculpated in esophageal carcinogenesis. Alterations in the p16 and p15 cyclin kinase inhibitors including point mutations and homozygous deletions have been reported in primary esophageal tumors. Further developments in the field of molecular carcinogenesis of esophageal malignancies promise to yield improvements in prevention, early detection, prognostic categorization, and perhaps gene-based therapy of this deadly disease.

  15. Molecular ferroelectrics: where electronics meet biology.

    Science.gov (United States)

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

    2013-12-28

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

  16. Biochemistry and Molecular Biology Education (BAMBED

    Directory of Open Access Journals (Sweden)

    Voet Donald

    2004-05-01

    Full Text Available Biochemistry and Molecular Biology Education (BAMBED is a journal that is a publication of the In-ternational Union of Biochemistry and Molecular Biology (IUBMB and is published by the AmericanSociety of Biochemistry and Molecular Biology (ASBMB. BAMBED, as its name indicates, publishesarticles of interest to educators in biochemistry and molecular biology. These include invited reviewson subjects not yet in textbooks, discussions of curricular development, new laboratory exercises,and articles on educational research. BAMBED also publishes Features on Problem-Based Learning(PBL, Biotechnology Education, and Multimedia in Biochemistry and Molecular Biology Educati-on. An important aspect of these articles is that their educational eectiveness must be assessed. Ishall discuss in greater detail the types of articles that BAMBED publishes and the criteria used foraccepting them for publication. Conference attendees are encouraged to submit articles to BAMBED.

  17. Molecular biology: Self-sustaining chemistry

    OpenAIRE

    Wrede Paul

    2007-01-01

    Abstract Molecular biology is an established interdisciplinary field within biology that deals fundamentally with the function of any nucleic acid in the cellular context. The molecular biology section in Chemistry Central Journal focusses on the genetically determined chemistry and biochemistry occuring in the cell. How can thousands of chemical reactions interact smoothly to maintain the life of cells, even in a variable environment? How is this self-sustaining system achieved? These are qu...

  18. Molecular biology of microbial ureases.

    Science.gov (United States)

    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

  19. Origins of molecular biology in Japan.

    Science.gov (United States)

    Obayashi, M

    1986-06-01

    The purpose of this paper is to discuss the origins of molecular biology in Japan. Japanese molecular biology does not have a long history since it started only after World War II. Especially, molecular genetics which uses "bacteriophage" had hardly been studied before the war and only a few scientists were interested in it immediately after the war. This is one of the origins of molecular biology in Japan. But there are other origins, one of which is the group formed by biologists, biochemists and physicists interested in nucleic acids. This group also started just after the war. Still another origin is the group of enzymologists. Enzymology was one of the main subjects of biochemistry from before the war. In Japan, biochemistry developed in conjunction with the medical and agricultural sciences from the pre-war era. These played an important role in introducing molecular biology from Europe and the United States after the war. A historical study of the development of molecular biology in Japan, comparing it with the history of molecular biology in Europe and the United States, should contribute to the elucidation of the features of the history of molecular biology in Japan.

  20. Applications of next-generation sequencing to the study of biological invasions

    Institute of Scientific and Technical Information of China (English)

    Marc RIUS; Steve BOURNE; Harry Guy HORNSBY; Mark A CHAPMAN

    2015-01-01

    Through the widespread implementation of next-generation sequencing (NGS), analyses of the whole genome (the entire DNA content) and the whole transcriptome (the genes being expressed) are becoming commonplace. NGS enables the analysis of a vast amount of previously unattainable genetic information. Despite this potential, NGS has yet to be widely imple-mented in genetic studies of biological invasions. The study of the genomic causes and consequences of biological invasions al-lows a deeper understanding of the molecular mechanisms underpinning the invasion process. In this review, we present a brief introduction to NGS followed by a synthesis of current research in the genomics and transcriptomics of adaptation and coloniza-tion. We then highlight research opportunities in the field, including: (1) assembling genomes and transcriptomes of non-model organisms, (2) identifying genomic regions and candidate genes underlying evolutionary processes, and (3) studying the adaptive role of gene expression variation. In particular, because introduced species face a broad range of physiological and biotic chal-lenges when colonizing novel and variable environments, transcriptomics will enable the study of gene regulatory pathways that may be responsible for acclimation or adaptation. To conclude, we identify a number of research approaches that will aid our fu-ture understanding of biological invasions [Current Zoology 61 (3): 488–504, 2015].

  1. Molecular biology: Self-sustaining chemistry

    Directory of Open Access Journals (Sweden)

    Wrede Paul

    2007-10-01

    Full Text Available Abstract Molecular biology is an established interdisciplinary field within biology that deals fundamentally with the function of any nucleic acid in the cellular context. The molecular biology section in Chemistry Central Journal focusses on the genetically determined chemistry and biochemistry occuring in the cell. How can thousands of chemical reactions interact smoothly to maintain the life of cells, even in a variable environment? How is this self-sustaining system achieved? These are questions that should be answered in the light of molecular biology and evolution, but with the application of biophysical, physico-chemical, analytical and preparative technologies. As the Section Editor for the molecular biology section in Chemistry Central Journal, I hope to receive manuscripts that present new approaches aimed at better answering and shedding light upon these fascinating questions related to the chemistry of livings cells.

  2. Confronting the wicked problem of managing biological invasions

    Directory of Open Access Journals (Sweden)

    Darragh J. Woodford

    2016-09-01

    Full Text Available The Anthropocene Epoch is characterized by novel and increasingly complex dependencies between the environment and human civilization, with many challenges of biodiversity management emerging as wicked problems. Problems arising from the management of biological invasions can be either tame (with simple or obvious solutions or wicked, where difficulty in appropriately defining the problem can make complete solutions impossible to find. We review four case studies that reflect the main goals in the management of biological invasions – prevention, eradication, and impact reduction – assessing the drivers and extent of wickedness in each. We find that a disconnect between the perception and reality of how wicked a problem is can profoundly influence the likelihood of successful management. For example, managing species introductions can be wicked, but shifting from species-focused to vector-focused risk management can greatly reduce the complexity, making it a tame problem. The scope and scale of the overall management goal will also dictate the wickedness of the problem and the achievability of management solutions (cf. eradication and ecosystem restoration. Finally, managing species that have both positive and negative impacts requires engagement with all stakeholders and scenario-based planning. Effective management of invasions requires either recognizing unavoidable wickedness, or circumventing it by seeking alternative management perspectives.

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

    Science.gov (United States)

    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…

  4. European Conference on Molecular Biology EMBO

    CERN Multimedia

    1967-01-01

    European Conference on Molecular Biology, which eventually led to the setting up of EMBO, was held at CERN in April. Olivier Reverdin is adressing the delegates. Bernard Gregory is on the left and Willy Spuhler in the centre.

  5. Application of molecular biology in exercise physiology.

    Science.gov (United States)

    Booth, F W

    1989-01-01

    Past progress in exercise biochemical research has often depended on the use of knowledge and techniques which were originally reported from other disciplines. With the advent of newer methodologies in molecular biology, the purpose of this review has been to document the status of information gained from the application of molecular biological techniques to questions in exercise physiology. Furthermore, this review has speculated how new methods in molecular biology might be employed to answer classic questions in exercise physiology. A powerful revolution in science, that is, molecular biology, will provide new information about exercise mechanisms, which ideally will improve the training programs for elite athletes as well as continue to be associated with the public's interest in exercise training.

  6. Genetics and molecular biology of breast cancer

    Energy Technology Data Exchange (ETDEWEB)

    King, M.C. [California Univ., Berkeley, CA (United States); Lippman, M. [Georgetown Univ. Medical Center, Washington, DC (United States)] [comps.

    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.

  7. The Molecular Era of Surfactant Biology

    OpenAIRE

    Jeffrey A Whitsett

    2014-01-01

    Advances in the physiology, biochemistry, molecular and cell biology of the pulmonary surfactant system transformed the clinical care and outcome of preterm infants with respiratory distress syndrome. The molecular era of surfactant biology provided genetic insights into the pathogenesis of pulmonary disorders, previously termed “idiopathic” that affect newborn infants, children and adults. Knowledge related to the structure and function of the surfactant proteins and their roles in alveolar ...

  8. Molecular ferroelectrics: where electronics meet biology

    OpenAIRE

    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 ferroele...

  9. Synthetic Tools for Molecular Biology

    OpenAIRE

    Dervan, Peter B.

    1988-01-01

    Chemistry has made tremendous advances over the past four decades in the broad fields of synthesis and understanding chemical reactivity. In that same time span, a series of revolutionary events occurred in biology. First came the discovery of the double helical structure of DNA in the 1950s by Watson and Crick. This discovery allowed the elucidation of the mechanisms of DNA replication -- how DNA makes copies of itself -- and DNA transcription and translation -- the processes that allow the ...

  10. Molecular biology of pancreatic cancer

    Institute of Scientific and Technical Information of China (English)

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

    2011-01-01

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

  11. Progress of biological invasions research in China over the last decade

    OpenAIRE

    Chengjen Shih; Bo Li; Hui Li; Ruiting Ju

    2012-01-01

    As one of the five major global environmental problems, invasive species have posed serious threats to native ecosystems, public health, and regional economies. Although much progress has been madein the field of biological invasions research in China over the last decade, there are still large knowledge gaps. This paper reviews progress in the field of biological invasions research since 2000 as it relates to China, covering the diversity, colonization and immigration patterns of invasive sp...

  12. Molecular biological research on Foraminifera

    Institute of Scientific and Technical Information of China (English)

    LI Baohua; Kemal Topac ERTAN; Christoph HEMLEBEN

    2005-01-01

    As one of the most important groups in micropaleontology, Foraminifera is traditionally described to have a membranous, agglutinated or carbonate shell according to its morphology, which resembles the marine granuloreticuloseans. However, recent molecular analyses on its ribosomal RNA gene have disclosed the existence of the naked, and also freshwater and terrestrial species.Foraminiferal SSU rDNA sequence suggests that this group is positioned at the base of the Eukaryotes phylogenetic trees, between Euglenoida and Diplomonadida. Existence of a large amount of genetic types in planktonic foraminifera suggests an underestimation of the biodiversity for the nearly 50 species in world oceans and their close relationship with the ocean environment, such as bio-geographic distribution and water currents. This provides a more reliable proxy for future paleoenvironmental study.

  13. The Human Release Hypothesis for biological invasions: human activity as a determinant of the abundance of invasive plant species.

    Science.gov (United States)

    Zimmermann, Heike; Brandt, Patric; Fischer, Joern; Welk, Erik; von Wehrden, Henrik

    2014-01-01

    Research on biological invasions has increased rapidly over the past 30 years, generating numerous explanations of how species become invasive. While the mechanisms of invasive species establishment are well studied, the mechanisms driving abundance patterns (i.e. patterns of population density and population size) remain poorly understood. It is assumed that invasive species typically have higher abundances in their new environments than in their native ranges, and patterns of invasive species abundance differ between invaded regions. To explain differences in invasive species abundance, we propose the Human Release Hypothesis. In parallel to the established Enemy Release Hypothesis, this hypothesis states that the differences in abundance of invasive species are found between regions because population expansion is reduced in some regions through continuous land management and associated cutting of the invasive species. The Human Release Hypothesis does not negate other important drivers of species invasions, but rather should be considered as a potentially important complementary mechanism. We illustrate the hypothesis via a case study on an invasive rose species, and hypothesize which locations globally may be most likely to support high abundances of invasive species. We propose that more extensive empirical work on the Human Release Hypothesis could be useful to test its general applicability. PMID:25352979

  14. Insights into invasion and restoration ecology: Time to collaborate towards a holistic approach to tackle biological invasions

    Directory of Open Access Journals (Sweden)

    Mirijam Gaertner

    2012-02-01

    Full Text Available The aim of our study is to provide an integrated framework for the management of alien plant invasions, combining insights and experiences from the fields of invasion and restoration ecology to enable more effective management of invasive species. To determine linkages between the scientific outputs of the two disciplines we used an existing data base on restoration studies between 2000 and 2008 and did a bibliometric analysis. We identified the type of restoration applied, determined by the aim of the study, and conducted a content analysis on 208 selected studies with a link to biological invasions (invasion-restoration studies. We found a total of 1075 articles on ecosystem restoration, with only eight percent of the studiesthe main objective to control alien invasions. The content analysis of 208 invasion-restoration studies showed that the majority of the studies focused on causes of degradation other than alien invasions. If invaders were referred to as the main driver of degradation, the prevalent cause for degradation was invaders outcompeting and replacing native species. Mechanical control of alien plant invasions was by far the most common control method used. Measures that went beyond the removal of alien plants were implemented in sixty-five percent of the studies.Although invasion control was not as common as other types of restoration, a closer look at the sub-group of invasion-restoration studies shows a clear link between restoration and invasion ecology. Concerns, as identified in the literature review, are firstly that restoration activities mostly focus on controlling the invader while other underlying causes for degradation are neglected, and secondly that the current approach of dealing with alien invasions lacks a combination of theoretical and practical aspects. We suggest that closer collaboration between invasion and restoration ecologists can help to improve the management of alien plant invasions. We conclude with a

  15. Frontiers of NMR in Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    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.

  16. Archaea: Evolution, Physiology, and Molecular Biology

    DEFF Research Database (Denmark)

    to honor the archaea pioneers Wolfram Zillig and Karl O. Stetter, the book provides a thorough survey of the field from its controversial beginnings to its ongoing expansion to include aspects of eukaryotic biology. The editors have assembled articles from the premier researchers in this rapidly burgeoning...... and technological context, and include accounts of cutting-edge research developments. The book spans archaeal evolution, physiology, and molecular and cellular biology and will be an essential reference for both graduate students and researchers....

  17. Molecular Mechanism of Biological Proton Transport

    Energy Technology Data Exchange (ETDEWEB)

    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.

  18. Arterivirus molecular biology and pathogenesis.

    Science.gov (United States)

    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. Dictyostelium discoideum: Molecular approaches to cell biology

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. Modelling biological invasions: Individual to population scales at interfaces

    KAUST Repository

    Belmonte-Beitia, J.

    2013-10-01

    Extracting the population level behaviour of biological systems from that of the individual is critical in understanding dynamics across multiple scales and thus has been the subject of numerous investigations. Here, the influence of spatial heterogeneity in such contexts is explored for interfaces with a separation of the length scales characterising the individual and the interface, a situation that can arise in applications involving cellular modelling. As an illustrative example, we consider cell movement between white and grey matter in the brain which may be relevant in considering the invasive dynamics of glioma. We show that while one can safely neglect intrinsic noise, at least when considering glioma cell invasion, profound differences in population behaviours emerge in the presence of interfaces with only subtle alterations in the dynamics at the individual level. Transport driven by local cell sensing generates predictions of cell accumulations along interfaces where cell motility changes. This behaviour is not predicted with the commonly used Fickian diffusion transport model, but can be extracted from preliminary observations of specific cell lines in recent, novel, cryo-imaging. Consequently, these findings suggest a need to consider the impact of individual behaviour, spatial heterogeneity and especially interfaces in experimental and modelling frameworks of cellular dynamics, for instance in the characterisation of glioma cell motility. © 2013 Elsevier Ltd.

  1. Biological control of alien and invasive species in agriculture

    International Nuclear Information System (INIS)

    Agricultural production in Europe faces many challenges including limited availability of water, nitrogen input and fossil fuels. It is necessary, therefore, to identify methods of production and new technologies to increase the efficiency of the primary systems, guaranteeing amount of food, quality, safety and eco-sustainability . One of the most important aspects, though often undervalued in relation to the food chain, is the adversity of biological management of agricultural crops due to pests, pathogens or fitomizi with potential invasive already present in the territory or of recent origin alien. In this context, two main objectives should be implemented at the same time reduce production losses and protect the agro-ecosystem. To meet these expectations, as of January 1, 2015 all farms in the European Union countries are bound to the application of the Integrated Defense principles, as indicated by the Directive on the sustainable use of plant protection products (128/09 / EC) .In response to this and other new entomological emergencies plant health and medical-veterinary entomologist researchers of the Laboratory sustainable management of Agro-Ecosystems in ENEA, have directed their research towards the development of innovative systems for the sustainable control of invasive species of insects is in the agricultural sector that health.

  2. Molecular biology of the Chlamydia pneumoniae surface

    DEFF Research Database (Denmark)

    Christiansen, Gunna; Østergaard, Lars; Birkelund, Svend

    1997-01-01

    Chlamydia pneumoniaeis a fastidious microorganism with a characteristic biphasic lifecycle causing a variety of human respiratory tract infections. There is limited knowledge about the molecular biology of C. pneumoniae, and only a few genes have been sequenced. The structure of the chlamydial...

  3. Book review: Baculovirus Molecular Biology, Second Edition

    Science.gov (United States)

    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...

  4. Text Mining applied to Molecular Biology

    NARCIS (Netherlands)

    R. Jelier (Rob)

    2008-01-01

    textabstractThis thesis describes the development of text-mining algorithms for molecular biology, in particular for DNA microarray data analysis. Concept profiles were introduced, which characterize the context in which a gene is mentioned in literature, to retrieve functional associations

  5. Molecular biology applications to infectious diseases diagnostic

    International Nuclear Information System (INIS)

    This project goes directed to the applications of the techniques of molecular biology in hepatitis virus.A great advance of these techniques it allows its application to the diagnose molecular and it becomes indispensable to have these fundamental tools in the field of the Health Public for the detection precocious, pursuit of the treatment, the one predicts and the evolution of the patient hepatitis bearing virus technical.Use of molecular biology to increase the handling and the control of the patients with hepatitis B and C and to detect an adult numbers of positive cases by means of the training and integration of all the countries participating.Implement the technique of PCR to identify the virus of the hepatitis B and C,implement quantification methods and genotipification for these virus

  6. Guiding Classical Biological Control of an Invasive Mealybug Using Integrative Taxonomy.

    Directory of Open Access Journals (Sweden)

    Aleixandre Beltrà

    Full Text Available Delottococcus aberiae De Lotto (Hemiptera: Pseudococcidae is a mealybug of Southern African origin that has recently been introduced into Eastern Spain. It causes severe distortions on young citrus fruits and represents a growing threat to Mediterranean citrus production. So far, biological control has proven unsatisfactory due to the absence of efficient natural enemies in Spain. Hence, the management of this pest currently relies only on chemical control. The introduction of natural enemies of D. aberiae from the native area of the pest represents a sustainable and economically viable alternative to reduce the risks linked to pesticide applications. Since biological control of mealybugs has been traditionally challenged by taxonomic misidentification, an intensive survey of Delottococcus spp. and their associated parasitoids in South Africa was required as a first step towards a classical biological control programme. Combining morphological and molecular characterization (integrative taxonomy a total of nine mealybug species were identified in this study, including three species of Delottococcus. Different populations of D. aberiae were found on wild olive trees, in citrus orchards and on plants of Chrysanthemoides monilifera, showing intra-specific divergences according to their host plants. Interestingly, the invasive mealybug populations from Spanish orchards clustered together with the population on citrus from Limpopo Province (South Africa, sharing COI haplotypes. This result pointed to an optimum location to collect natural enemies against the invasive mealybug. A total of 14 parasitoid species were recovered from Delottococcus spp. and identified to genus and species level, by integrating morphological and molecular data. A parasitoid belonging to the genus Anagyrus, collected from D. aberiae in citrus orchards in Limpopo, is proposed here as a good biological control agent to be introduced into Spain.

  7. Guiding Classical Biological Control of an Invasive Mealybug Using Integrative Taxonomy

    Science.gov (United States)

    Beltrà, Aleixandre; Addison, Pia; Ávalos, Juan Antonio; Crochard, Didier; Garcia-Marí, Ferran; Guerrieri, Emilio; Giliomee, Jan H.; Malausa, Thibaut; Navarro-Campos, Cristina; Palero, Ferran; Soto, Antonia

    2015-01-01

    Delottococcus aberiae De Lotto (Hemiptera: Pseudococcidae) is a mealybug of Southern African origin that has recently been introduced into Eastern Spain. It causes severe distortions on young citrus fruits and represents a growing threat to Mediterranean citrus production. So far, biological control has proven unsatisfactory due to the absence of efficient natural enemies in Spain. Hence, the management of this pest currently relies only on chemical control. The introduction of natural enemies of D. aberiae from the native area of the pest represents a sustainable and economically viable alternative to reduce the risks linked to pesticide applications. Since biological control of mealybugs has been traditionally challenged by taxonomic misidentification, an intensive survey of Delottococcus spp. and their associated parasitoids in South Africa was required as a first step towards a classical biological control programme. Combining morphological and molecular characterization (integrative taxonomy) a total of nine mealybug species were identified in this study, including three species of Delottococcus. Different populations of D. aberiae were found on wild olive trees, in citrus orchards and on plants of Chrysanthemoides monilifera, showing intra-specific divergences according to their host plants. Interestingly, the invasive mealybug populations from Spanish orchards clustered together with the population on citrus from Limpopo Province (South Africa), sharing COI haplotypes. This result pointed to an optimum location to collect natural enemies against the invasive mealybug. A total of 14 parasitoid species were recovered from Delottococcus spp. and identified to genus and species level, by integrating morphological and molecular data. A parasitoid belonging to the genus Anagyrus, collected from D. aberiae in citrus orchards in Limpopo, is proposed here as a good biological control agent to be introduced into Spain. PMID:26047349

  8. Guiding Classical Biological Control of an Invasive Mealybug Using Integrative Taxonomy.

    Science.gov (United States)

    Beltrà, Aleixandre; Addison, Pia; Ávalos, Juan Antonio; Crochard, Didier; Garcia-Marí, Ferran; Guerrieri, Emilio; Giliomee, Jan H; Malausa, Thibaut; Navarro-Campos, Cristina; Palero, Ferran; Soto, Antonia

    2015-01-01

    Delottococcus aberiae De Lotto (Hemiptera: Pseudococcidae) is a mealybug of Southern African origin that has recently been introduced into Eastern Spain. It causes severe distortions on young citrus fruits and represents a growing threat to Mediterranean citrus production. So far, biological control has proven unsatisfactory due to the absence of efficient natural enemies in Spain. Hence, the management of this pest currently relies only on chemical control. The introduction of natural enemies of D. aberiae from the native area of the pest represents a sustainable and economically viable alternative to reduce the risks linked to pesticide applications. Since biological control of mealybugs has been traditionally challenged by taxonomic misidentification, an intensive survey of Delottococcus spp. and their associated parasitoids in South Africa was required as a first step towards a classical biological control programme. Combining morphological and molecular characterization (integrative taxonomy) a total of nine mealybug species were identified in this study, including three species of Delottococcus. Different populations of D. aberiae were found on wild olive trees, in citrus orchards and on plants of Chrysanthemoides monilifera, showing intra-specific divergences according to their host plants. Interestingly, the invasive mealybug populations from Spanish orchards clustered together with the population on citrus from Limpopo Province (South Africa), sharing COI haplotypes. This result pointed to an optimum location to collect natural enemies against the invasive mealybug. A total of 14 parasitoid species were recovered from Delottococcus spp. and identified to genus and species level, by integrating morphological and molecular data. A parasitoid belonging to the genus Anagyrus, collected from D. aberiae in citrus orchards in Limpopo, is proposed here as a good biological control agent to be introduced into Spain. PMID:26047349

  9. Understanding biological functions through molecular networks

    Institute of Scientific and Technical Information of China (English)

    Jing-Dong Jackie Han

    2008-01-01

    The completion of genome sequences and subsequent high-throughput mapping of molecular networks have allowed us to study biology from the network perspective. Experimental, statistical and mathematical modeling approaches have been employed to study the structure, function and dynamics of molecular networks, and begin to reveal important links of various network properties to the functions of the biological systems. In agreement with these functional links, evolutionary selection of a network is apparently based on the function, rather than directly on the structure of the network. Dynamic modularity is one of the prominent features of molecular networks. Taking advantage of such a feature may simplify network-based biological studies through construction of process-specific modular networks and provide functional and mechanistic insights linking genotypic variations to complex traits or diseases, which is likely to be a key approach in the next wave of understanding complex human diseases. With the development of ready-to-use network analysis and modeling tools the networks approaches will be infused into everyday biological research in the near future.

  10. Molecular knots in biology and chemistry.

    Science.gov (United States)

    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

  11. Molecular knots in biology and chemistry

    International Nuclear Information System (INIS)

    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. (paper)

  12. Bioenergetics molecular biology, biochemistry, and pathology

    CERN Document Server

    Ozawa, Takayuki

    1990-01-01

    The emergence of the Biochemical Sciences is underlined by the FAOB symposium in Seoul and highlighted by this Satellite meeting on the "New Bioenergetics. " Classical mitochondrial electron transfer and energy coupling is now complemented by the emerging molecular biology of the respiratory chain which is studied hand in hand with the recognition of mitochondrial disease as a major and emerging study in the basic and clinical medical sciences. Thus, this symposium has achieved an important balance of the fundamental and applied aspects of bioenergetics in the modern setting of molecular biology and mitochondrial disease. At the same time, the symposium takes note not only of the emerging excellence of Biochemical Studies in the Orient and indeed in Korea itself, but also retrospectively enjoys the history of electron transport and energy conservation as represented by the triumvirate ofYagi, King and Slater. Many thanks are due Drs. Kim and Ozawa for their elegant organization of this meeting and its juxtapo...

  13. Imaging cellular and molecular biological functions

    Energy Technology Data Exchange (ETDEWEB)

    Shorte, S.L. [Institut Pasteur, 75 - Paris (France). Plateforme d' Imagerie Dynamique PFID-Imagopole; Frischknecht, F. (eds.) [Heidelberg Univ. Medical School (Germany). Dept. of Parasitology

    2007-07-01

    'Imaging cellular and molecular biological function' provides a unique selection of essays by leading experts, aiming at scientist and student alike who are interested in all aspects of modern imaging, from its application and up-scaling to its development. Indeed the philosophy of this volume is to provide student, researcher, PI, professional or provost the means to enter this applications field with confidence, and to construct the means to answer their own specific questions. (orig.)

  14. 2004 Reversible Associations in Structure & Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)

    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.

  15. Discovering the intelligence in molecular biology.

    Science.gov (United States)

    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.

  16. Can molecular cell biology explain chromosome motions?

    Directory of Open Access Journals (Sweden)

    Gagliardi L

    2011-05-01

    Full Text Available Abstract Background Mitotic chromosome motions have recently been correlated with electrostatic forces, but a lingering "molecular cell biology" paradigm persists, proposing binding and release proteins or molecular geometries for force generation. Results Pole-facing kinetochore plates manifest positive charges and interact with negatively charged microtubule ends providing the motive force for poleward chromosome motions by classical electrostatics. This conceptual scheme explains dynamic tracking/coupling of kinetochores to microtubules and the simultaneous depolymerization of kinetochore microtubules as poleward force is generated. Conclusion We question here why cells would prefer complex molecular mechanisms to move chromosomes when direct electrostatic interactions between known bound charge distributions can accomplish the same task much more simply.

  17. Non-invasive Optical Molecular Imaging for Cancer Detection

    Science.gov (United States)

    Luo, Zhen

    Cancer is a leading cause of death worldwide. It remains the second most common cause of death in the US, accounting for nearly 1 out of every 4 deaths. Improved fundamental understanding of molecular processes and pathways resulting in cancer development has catalyzed a shift towards molecular analysis of cancer using imaging technologies. It is expected that the non-invasive or minimally invasive molecular imaging analysis of cancer can significantly aid in improving the early detection of cancer and will result in reduced mortality and morbidity associated with the disease. The central hypothesis of the proposed research is that non-invasive imaging of changes in metabolic activity of individual cells, and extracellular pH within a tissue will improve early stage detection of cancer. The specific goals of this research project were to: (a) develop novel optical imaging probes to image changes in choline metabolism and tissue pH as a function of progression of cancer using clinically isolated tissue biopsies; (b) correlate changes in tissue extracellular pH and metabolic activity of tissues as a function of disease state using clinically isolated tissue biopsies; (c) provide fundamental understanding of relationship between tumor hypoxia, acidification of the extracellular space and altered cellular metabolism with progression of cancer. Three novel molecular imaging probes were developed to detect changes in choline and glucose metabolism and extracellular pH in model systems and clinically isolated cells and biopsies. Glucose uptake and metabolism was measured using a fluorescence analog of glucose, 2-NBDG (2-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino]-2-deoxy-D-glucose), while choline metabolism was measured using a click chemistry analog of choline, propargyl choline, which can be in-situ labeled with a fluorophore Alexa-488 azide via a click chemistry reaction. Extracellular pH in tissue were measured by Alexa-647 labeled pHLIP (pH low insertion peptide

  18. Orchid-pollinator interactions and potential vulnerability to biological invasion.

    Science.gov (United States)

    Chupp, Adam D; Battaglia, Loretta L; Schauber, Eric M; Sipes, Sedonia D

    2015-01-01

    Mutualistic relationships between plants and their pollinators have played a major role in the evolution of biodiversity. While the vulnerability of these relationships to environmental change is a major concern, studies often lack a framework for predicting impacts from emerging threats (e.g. biological invasions). The objective of this study was to determine the reliance of Platanthera ciliaris (orange-fringed orchid) on Papilio palamedes (Palamedes swallowtail butterfly) for pollination and the relative availability of alternative pollinators. Recent declines of P. palamedes larval host plants due to laurel wilt disease (LWD) could endanger P. ciliaris populations that rely heavily on this butterfly for pollination. We monitored pollinator visitation and fruit set and measured nectar spur lengths of P. ciliaris flowers and proboscis lengths of its floral visitors in Jackson County, MS, USA. Papilio palamedes was the primary visitor with minimal visitation by Phoebis sennae (cloudless sulfur butterfly). Lengths of P. ciliaris nectar spurs were similar to proboscis lengths of both pollinator species. Fruit set was moderate with access to pollinators (55 ± 10.8 %), yet failed (0 %) when pollinators were excluded. Visitation increased with inflorescence size, but there was no such pattern in fruit set, indicating that fruit set was not limited by pollinator visitation within the range of visitation rates we observed. Our results are supported by historical data that suggest P. palamedes and P. sennae are important pollinators of P. ciliaris. Although P. sennae may provide supplemental pollination service, this is likely constrained by habitat preferences that do not always overlap with those of P. cilaris. Observed declines of P. palamedes due to LWD could severely limit the reproductive success and persistence of P. ciliaris and similar orchid species populations. This empirical-based prediction is among the first to document exotic forest pests and pathogens as

  19. The molecular biology of vertebrate olfaction.

    Science.gov (United States)

    Hayden, Sara; Teeling, Emma C

    2014-11-01

    The importance of chemosensation for vertebrates is reflected in the vast and variable nature of their chemosensory tissues, neurons, and genes, which we explore in this review. Immense progress has been made in elucidating the molecular biology of olfaction since the discovery of the olfactory receptor genes by Buck and Axel, which eventually won the authors the Nobel Prize. In particular, research linking odor ligands to olfactory receptors (ORs) is truly revolutionizing our understanding of how a large but limited number of chemosensory receptors can allow us to perceive the massive diversity of odors in our habitat. This research is providing insight into the evolution of genomes and providing the raw data needed to explore links between genotype and phenotype, still a grand challenge in biology. Research into olfaction is still developing and will no doubt continue until we have a clear understanding of how all odors are detected and the evolutionary forces that have molded the chemosensory subgenome in vertebrates. This knowledge will not only be a huge step in elucidating olfactory function, advancing scientific knowledge and techniques, but there are also commercial applications for this research. This review focuses on the molecular basis of chemosensation, particularly olfaction, its evolution across vertebrates and the recent molecular advances linking odors to their cognate receptors.

  20. The molecular biology of vertebrate olfaction.

    Science.gov (United States)

    Hayden, Sara; Teeling, Emma C

    2014-11-01

    The importance of chemosensation for vertebrates is reflected in the vast and variable nature of their chemosensory tissues, neurons, and genes, which we explore in this review. Immense progress has been made in elucidating the molecular biology of olfaction since the discovery of the olfactory receptor genes by Buck and Axel, which eventually won the authors the Nobel Prize. In particular, research linking odor ligands to olfactory receptors (ORs) is truly revolutionizing our understanding of how a large but limited number of chemosensory receptors can allow us to perceive the massive diversity of odors in our habitat. This research is providing insight into the evolution of genomes and providing the raw data needed to explore links between genotype and phenotype, still a grand challenge in biology. Research into olfaction is still developing and will no doubt continue until we have a clear understanding of how all odors are detected and the evolutionary forces that have molded the chemosensory subgenome in vertebrates. This knowledge will not only be a huge step in elucidating olfactory function, advancing scientific knowledge and techniques, but there are also commercial applications for this research. This review focuses on the molecular basis of chemosensation, particularly olfaction, its evolution across vertebrates and the recent molecular advances linking odors to their cognate receptors. PMID:25312375

  1. Immunophenotyping invasive breast cancer: paving the road for molecular imaging

    Directory of Open Access Journals (Sweden)

    Vermeulen Jeroen F

    2012-06-01

    Full Text Available Abstract Background Mammographic population screening in The Netherlands has increased the number of breast cancer patients with small and non-palpable breast tumors. Nevertheless, mammography is not ultimately sensitive and specific for distinct subtypes. Molecular imaging with targeted tracers might increase specificity and sensitivity of detection. Because development of new tracers is labor-intensive and costly, we searched for the smallest panel of tumor membrane markers that would allow detection of the wide spectrum of invasive breast cancers. Methods Tissue microarrays containing 483 invasive breast cancers were stained by immunohistochemistry for a selected set of membrane proteins known to be expressed in breast cancer. Results The combination of highly tumor-specific markers glucose transporter 1 (GLUT1, epidermal growth factor receptor (EGFR, insulin-like growth factor-1 receptor (IGF1-R, human epidermal growth factor receptor 2 (HER2, hepatocyte growth factor receptor (MET, and carbonic anhydrase 9 (CAIX 'detected' 45.5% of tumors, especially basal/triple negative and HER2-driven ductal cancers. Addition of markers with a 2-fold tumor-to-normal ratio increased the detection rate to 98%. Including only markers with >3 fold tumor-to-normal ratio (CD44v6 resulted in an 80% detection rate. The detection rate of the panel containing both tumor-specific and less tumor-specific markers was not dependent on age, tumor grade, tumor size, or lymph node status. Conclusions In search of the minimal panel of targeted probes needed for the highest possible detection rate, we showed that 80% of all breast cancers express at least one of a panel of membrane markers (CD44v6, GLUT1, EGFR, HER2, and IGF1-R that may therefore be suitable for molecular imaging strategies. This study thereby serves as a starting point for further development of a set of antibody-based optical tracers with a high breast cancer detection rate.

  2. Immunophenotyping invasive breast cancer: paving the road for molecular imaging

    International Nuclear Information System (INIS)

    Mammographic population screening in The Netherlands has increased the number of breast cancer patients with small and non-palpable breast tumors. Nevertheless, mammography is not ultimately sensitive and specific for distinct subtypes. Molecular imaging with targeted tracers might increase specificity and sensitivity of detection. Because development of new tracers is labor-intensive and costly, we searched for the smallest panel of tumor membrane markers that would allow detection of the wide spectrum of invasive breast cancers. Tissue microarrays containing 483 invasive breast cancers were stained by immunohistochemistry for a selected set of membrane proteins known to be expressed in breast cancer. The combination of highly tumor-specific markers glucose transporter 1 (GLUT1), epidermal growth factor receptor (EGFR), insulin-like growth factor-1 receptor (IGF1-R), human epidermal growth factor receptor 2 (HER2), hepatocyte growth factor receptor (MET), and carbonic anhydrase 9 (CAIX) 'detected' 45.5% of tumors, especially basal/triple negative and HER2-driven ductal cancers. Addition of markers with a 2-fold tumor-to-normal ratio increased the detection rate to 98%. Including only markers with >3 fold tumor-to-normal ratio (CD44v6) resulted in an 80% detection rate. The detection rate of the panel containing both tumor-specific and less tumor-specific markers was not dependent on age, tumor grade, tumor size, or lymph node status. In search of the minimal panel of targeted probes needed for the highest possible detection rate, we showed that 80% of all breast cancers express at least one of a panel of membrane markers (CD44v6, GLUT1, EGFR, HER2, and IGF1-R) that may therefore be suitable for molecular imaging strategies. This study thereby serves as a starting point for further development of a set of antibody-based optical tracers with a high breast cancer detection rate

  3. 2009 Archaea: Ecology, Metabolism & Molecular Biology GRC

    Energy Technology Data Exchange (ETDEWEB)

    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.

  4. 2011 Archaea: Ecology, Metabolism, & Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)

    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.

  5. Biological invasions in the aquatic ecosystems of Europe as a threat to biodiversity

    OpenAIRE

    Wołczuk, Katarzyna; Mięsikowski, Michał; Jarzynka, Karolina; Wilczyńska, Bogdana

    2011-01-01

    In recent years biological invasions have become a serious ecological and socio-economic problem for many countries. Invasions are promoted by anthropogenic activity which is broadly understood as well as the instability of ecosystems. It carries a number of threats, often difficult to predict. The effects of invasion are long-term and occur on many levels of life. They can very often contribute to the extinction of native species, thus reducing biodiversity. According to the concept of susta...

  6. Molecular Biological Methods in Environmental Engineering.

    Science.gov (United States)

    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

  7. The impact of new trends in POCTs for companion diagnostics, non-invasive testing and molecular diagnostics.

    Science.gov (United States)

    Huckle, David

    2015-06-01

    Point-of-care diagnostics have been slowly developing over several decades and have taken on a new importance in current healthcare delivery for both diagnostics and development of new drugs. Molecular diagnostics have become a key driver of technology change and opened up new areas in companion diagnostics for use alongside pharmaceuticals and in new clinical approaches such as non-invasive testing. Future areas involving smartphone and other information technology advances, together with new developments in molecular biology, microfluidics and surface chemistry are adding to advances in the market. The focus for point-of-care tests with molecular diagnostic technologies is focused on advancing effective applications. PMID:25990929

  8. 2007 Archaea: Ecology, Metabolism and Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)

    Imke Schroeder

    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.

  9. Biological invasions and the study of vertebrate dispersal of plants: Opportunities and integration

    Science.gov (United States)

    Westcott, David A.; Fletcher, Cameron S.

    2011-11-01

    Biological invasions are a key threat to natural ecosystems and consequently a major focus of ecological research. Even though it is dispersal processes that result in the movement of invasive populations through landscapes, dispersal ecology has played a relatively minor role in invasion ecology research. This is particularly true for vertebrate-dispersed plants. To encourage thinking around these issues and a greater involvement of dispersal ecologists in invasion research, we review contributions made to invasion ecology by dispersal ecology and highlight opportunities that the study of biological invasions offers for improving our understanding of dispersal processes. We suggest that by working in the context of invasions dispersal ecologists are not only able to contribute to the development of process-based management but also gain new opportunities for developing and testing predictions in their field. Because biological invasions are perturbations of natural systems they provide excellent opportunities for both natural and manipulative experimentation with potential for a range of forms of replication. Significantly, the need to develop a predictive understanding of population-level patterns of spread in order to manage invasives demands a shift away from studying individual vectors to developing predictions that integrate across all vectors and processes in the dispersal loop. This is a significant development for dispersal ecology and is a major opportunity for dispersal ecologists to contribute to a current environmental issue.

  10. Evidence of climatic niche shift during biological invasion.

    Science.gov (United States)

    Broennimann, O; Treier, U A; Müller-Schärer, H; Thuiller, W; Peterson, A T; Guisan, A

    2007-08-01

    Niche-based models calibrated in the native range by relating species observations to climatic variables are commonly used to predict the potential spatial extent of species' invasion. This climate matching approach relies on the assumption that invasive species conserve their climatic niche in the invaded ranges. We test this assumption by analysing the climatic niche spaces of Spotted Knapweed in western North America and Europe. We show with robust cross-continental data that a shift of the observed climatic niche occurred between native and non-native ranges, providing the first empirical evidence that an invasive species can occupy climatically distinct niche spaces following its introduction into a new area. The models fail to predict the current invaded distribution, but correctly predict areas of introduction. Climate matching is thus a useful approach to identify areas at risk of introduction and establishment of newly or not-yet-introduced neophytes, but may not predict the full extent of invasions. PMID:17594425

  11. Evidence of climatic niche shift during biological invasion

    OpenAIRE

    Broennimann, Olivier; Urs A Treier; Müller-Schärer, Heinz; Thuiller, W.; Peterson, A. T.; Guisan, Antoine

    2007-01-01

    Niche-based models calibrated in the native range by relating species observations to climatic variables are commonly used to predict the potential spatial extent of species’ invasion. This climate matching approach relies on the assumption that invasive species conserve their climatic niche in the invaded ranges. We test this assumption by analysing the climatic niche spaces of Spotted Knapweed in western North America and Europe. We show with robust cross-continental data that a shift of th...

  12. Progress of biological invasions research in China over the last decade

    Directory of Open Access Journals (Sweden)

    Chengjen Shih

    2012-09-01

    Full Text Available As one of the five major global environmental problems, invasive species have posed serious threats to native ecosystems, public health, and regional economies. Although much progress has been madein the field of biological invasions research in China over the last decade, there are still large knowledge gaps. This paper reviews progress in the field of biological invasions research since 2000 as it relates to China, covering the diversity, colonization and immigration patterns of invasive species, mechanisms and ecological effects of biological invasions, and management and control of invasive species. In China, 529 invasive alien species have been identified, which originated primarily from South and North America, and the major taxa included terrestrial plants, terrestrial invertebrates, and microorganisms. We found a higher prevalence of invasive species in the eastern and southern provinces, compared to the western and northern provinces in China. This pattern is likely due to the differences in the level of economic development and environmental suitability between the two regions. Moreover, with further economic development, China may face more serious biological invasions in the future. These invasions of alien species are largely the combined results of the interactions between the intrinsic traits of these species along with resource opportunities and disturbances by human beings. Many mechanisms are responsible for successful invasionsof alien species, but phenotypic plasticity, adaptive evolution, enemy release, interspecific mutualism or commensalism, and new allelochemicals may be primary causative factors. Biological invasions in China have caused serious impacts on native ecosystems, including biodiversity and ecosystem services, alteration of biogeochemical cycles, threats to agricultural and forestry production, traffic and shipping, environmental safety, and public facilities. China has also made progress in the detection and

  13. Molecular biology approaches in bioadhesion research

    Directory of Open Access Journals (Sweden)

    Marcelo Rodrigues

    2014-07-01

    Full Text Available The use of molecular biology tools in the field of bioadhesion is still in its infancy. For new research groups who are considering taking a molecular approach, the techniques presented here are essential to unravelling the sequence of a gene, its expression and its biological function. Here we provide an outline for addressing adhesion-related genes in diverse organisms. We show how to gradually narrow down the number of candidate transcripts that are involved in adhesion by (1 generating a transcriptome and a differentially expressed cDNA list enriched for adhesion-related transcripts, (2 setting up a BLAST search facility, (3 perform an in situ hybridization screen, and (4 functional analyses of selected genes by using RNA interference knock-down. Furthermore, latest developments in genome-editing are presented as new tools to study gene function. By using this iterative multi-technologies approach, the identification, isolation, expression and function of adhesion-related genes can be studied in most organisms. These tools will improve our understanding of the diversity of molecules used for adhesion in different organisms and these findings will help to develop innovative bio-inspired adhesives.

  14. Rhabdomyosarcoma: Advances in Molecular and Cellular Biology

    Directory of Open Access Journals (Sweden)

    Xin Sun

    2015-01-01

    Full Text Available 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.

  15. Molecular biology of the lung cancer

    International Nuclear Information System (INIS)

    Background. Lung cancer is one of the most common malignant diseases and leading cause of cancer death worldwide. The advances in molecular biology and genetics, including the modern microarray technology and rapid sequencing techniques, have enabled a remarkable progress into elucidating the lung cancer ethiopathogenesis. Numerous studies suggest that more than 20 different genetic and epigenetic alterations are accumulating during the pathogenesis of clinically evident pulmonary cancers as a clonal, multistep process. Thus far, the most investigated alterations are the inactivational mutations and losses of tumour suppressor genes and the overexpression of growth-promoting oncogenes. More recently, the acquired epigenetic inactivation of tumour suppressor genes by promoter hypermethylation has been recognized. The early clonal genetic abnormalities that occur in preneoplastic bronchial epithelium damaged by smoking or other carcinogenes are being identified. The molecular distinctions between small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC), as well as between tumors with different clinical outcomes have been described. These investigations lead to the hallmarks of lung cancer. Conclusions. It is realistic to expect that the molecular and cell culture-based investigations will lead to discoveries of new clinical applications with the potential to provide new avenues for early diagnosis, risk assessment, prevention, and most important, new more effective treatment approaches for the lung cancer patients. (author)

  16. Reproductive biology and early establishment of Pinus elliottii var. elliottii in Brazilian sandy coastal plain vegetation: implications for biological invasion

    Directory of Open Access Journals (Sweden)

    Fernando Campanhã Bechara

    2013-04-01

    Full Text Available Pinus is the most invasive woody taxon, exceeded only by herbaceous plants. This study reports the reproductive biology and early establishment of Pinus elliottii Engelm. var. elliottii, describing its invasive properties in a protected natural area of the Brazilian coastal sandy plains. We evaluated the seed germination and rain, longevity of seed viability and the initial dynamics of the seedlings of Pinus elliottii var elliottii through field and laboratory experiments. We recorded a continuous seed rain of about 204.0 viable seeds m- 2 per year, with a 90 % germination rate. The seeds exhibited a low longevity of viability in the soil and a dense, permanent seedling bank that may explain the high levels of pine invasion. The environmental impact caused by the pine's biological invasion suggests the recommendation for its immediate eradication, together with a restoration plan to restitute the native biodiversity gradually.

  17. [Molecular biological predictors for kidney cancer].

    Science.gov (United States)

    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

  18. Evidence of climatic niche shift during biological invasion

    DEFF Research Database (Denmark)

    Broennimann, O.; Treier, Urs; Müller-Schärer, H.;

    2007-01-01

    Niche-based models calibrated in the native range by relating species observations to climatic variables are commonly used to predict the potential spatial extent of species' invasion. This climate matching approach relies on the assumption that invasive species conserve their climatic niche...... evidence that an invasive species can occupy climatically distinct niche spaces following its introduction into a new area. The models fail to predict the current invaded distribution, but correctly predict areas of introduction. Climate matching is thus a useful approach to identify areas at risk...... in the invaded ranges. We test this assumption by analysing the climatic niche spaces of Spotted Knapweed in western North America and Europe. We show with robust cross-continental data that a shift of the observed climatic niche occurred between native and non-native ranges, providing the first empirical...

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

    Science.gov (United States)

    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,…

  20. Synthetic biology: A foundation for multi-scale molecular biology

    OpenAIRE

    Bower, Adam G; McClintock, Maria K; Stephen S. Fong

    2010-01-01

    The field of synthetic biology has made rapid progress in a number of areas including method development, novel applications and community building. In seeking to make biology “engineerable,” synthetic biology is increasing the accessibility of biological research to researchers of all experience levels and backgrounds. One of the underlying strengths of synthetic biology is that it may establish the framework for a rigorous bottom-up approach to studying biology starting at the DNA level. Bu...

  1. The cytoskeleton significantly impacts invasive behavior of biological cells

    Science.gov (United States)

    Fritsch, Anatol; Käs, Josef; Seltman, Kristin; Magin, Thomas

    2014-03-01

    Cell migration is a key determinant of cancer metastasis and nerve regeneration. The role of the cytoskeleton for the epithelial-meschenymal transition (EMT), i.e, for invasive behavior of cells, is only partially understood. Here, we address this issue in cells lacking all keratins upon genome engineering. In contrast to prediction, keratin-free cells show a 60% higher deformability compared to less pronounced softening effects for actin depolymerization. To relate these findings with functional consequences, we use invasion and three-dimensional growth assays. These reveal higher invasiveness of keratin-free cells. This study supports the view that downregulation of keratins observed during EMT directly contributes to the migratory and invasive behavior of tumor cells. Cancer cells that effectively move through tissues are softer and more contractile than cells that stay local in tissues. Soft and contractile avoids jamming. Naturally, softness has to have its limits. So neuronal growth cones are too soft to carry large loads to move efficiently through scar tissue, which is required for nerve regeneration. In synopsis, the physical bounds that the functional modules of a moving cell experience in tissues may provide an overarching motif for novel approaches in diagnosis and therapy.

  2. 2010 Plant Molecular Biology Gordon Research Conference

    Energy Technology Data Exchange (ETDEWEB)

    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.

  3. Biological (molecular and cellular) markers of toxicity

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Hallick, R.B. [ed.

    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.

  5. Molecular Insights on the Transition of Non-invasive DCIS to Invasive ductal Carcinoma

    Institute of Scientific and Technical Information of China (English)

    Dihua YU

    2009-01-01

    @@ More than 90% of breast cancer-related deaths are caused by metastasis not primary tumor. To effectively reduce cancer mortality, it is extremely im-portant to predict the risk of, and to intervene in, the critical transition from non-invasive ductal carcinoma in situ (DCIS) to life-threatening invasive ductal carcinoma (IDC).

  6. Linking climate change and biological invasions: Ocean warming facilitates nonindigenous species invasions

    OpenAIRE

    Stachowicz, John J.; Terwin, Jeffrey R.; Whitlatch, Robert B.; Osman, Richard W.

    2002-01-01

    The spread of exotic species and climate change are among the most serious global environmental threats. Each independently causes considerable ecological damage, yet few data are available to assess whether changing climate might facilitate invasions by favoring introduced over native species. Here, we compare our long-term record of weekly sessile marine invertebrate recruitment with interannual variation in water temperature to assess the likely effect of climate change on the success and ...

  7. 2003 Archaea: Ecology, Metabolism and Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

    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…

  9. A Diagnostic Assessment for Introductory Molecular and Cell Biology

    Science.gov (United States)

    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…

  10. Biological invasions: deriving the regions at risk from partial measurements

    CERN Document Server

    Cristofol, Michel

    2009-01-01

    We consider the problem of forecasting the regions at higher risk for newly introduced invasive species. Favourable and unfavourable regions may indeed not be known a priori, especially for exotic species whose hosts in native range and newly-colonised areas can be different. Assuming that the species is modelled by a logistic-like reaction-diffusion equation, we prove that the spatial arrangement of the favourable and unfavourable regions can theoretically be determined using only partial measurements of the population density: 1) a local "spatio-temporal" measurement, during a short time period and, 2) a "spatial" measurement in the whole region susceptible to colonisation. We then present a stochastic algorithm which is proved analytically, and then on several numerical examples, to be effective in deriving these regions.

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

    OpenAIRE

    Gunn, Peter; Walsh, Simon; Roux, Claude

    2014-01-01

    Molecular biology has evolved far beyond that which could have been predicted at the time DNA identity testing was established. Indeed we should now perhaps be referring to “forensic molecular biology.” Aside from DNA’s established role in identifying the “who” in crime investigations, other developments in medical and developmental molecular biology are now ripe for application to forensic challenges. The impact of DNA methylation and other post-fertilization DNA modifications, plus the emer...

  12. Biological invasion by Myrica faya alters ecosystem development in Hawaii

    Science.gov (United States)

    Vitousek, Peter M.; Walker, Lawrence R.; Whiteaker, Louis D.; Mueller-Dombois, Dieter; Matson, Pamela A.

    1987-01-01

    The exotic nitrogen-fixing tree Myrica faya invades young volcanic sites where the growth of native plants is limited by a lack of nitrogen. Myrica quadruples the amount of nitrogen entering certain sites and increases the overall biological availability of nitrogen, thereby altering the nature of ecosystem development after volcanic eruptions.

  13. Hsp70 May Be a Molecular Regulator of Schistosome Host Invasion.

    Science.gov (United States)

    Ishida, Kenji; Jolly, Emmitt R

    2016-09-01

    Schistosomiasis is a debilitating disease that affects over 240 million people worldwide and is considered the most important neglected tropical disease following malaria. Free-swimming freshwater cercariae, one of the six morphologically distinct schistosome life stages, infect humans by directly penetrating through the skin. Cercariae identify and seek the host by sensing chemicals released from human skin. When they reach the host, they burrow into the skin with the help of proteases and other contents released from their acetabular glands and transform into schistosomula, the subsequent larval worm stage upon skin infection. Relative to host invasion, studies have primarily focused on the nature of the acetabular gland secretions, immune response of the host upon exposure to cercariae, and cercaria-schistosomulum transformation methods. However, the molecular signaling pathways involved from host-seeking through the decision to penetrate skin are not well understood. We recently observed that heat shock factor 1 (Hsf1) is localized to the acetabular glands of infectious schistosome cercariae, prompting us to investigate a potential role for heat shock proteins (HSPs) in cercarial invasion. In this study, we report that cercarial invasion behavior, similar to the behavior of cercariae exposed to human skin lipid, is regulated through an Hsp70-dependent process, which we show by using chemical agents that target Hsp70. The observation that biologically active protein activity modulators can elicit a direct and clear behavioral change in parasitic schistosome larvae is itself interesting and has not been previously observed. This finding suggests a novel role for Hsp70 to act as a switch in the cercaria-schistosomulum transformation, and it allows us to begin elucidating the pathways associated with cercarial host invasion. In addition, because the Hsp70 protein and its structure/function is highly conserved, the model that Hsp70 acts as a behavior transitional

  14. Interactive analysis of systems biology molecular expression data

    OpenAIRE

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

    2008-01-01

    Abstract 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 preferr...

  15. Molecular biological enhancement of coal biodesulfurization

    Energy Technology Data Exchange (ETDEWEB)

    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. (Battelle, Columbus, OH (United States)); Chakravarty, L.; Tuovinen, O.H. (Ohio State Univ., Columbus, OH (United States))

    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.

  16. Investigating Biological Control Agents for Controlling Invasive Populations of the Mealybug Pseudococcus comstocki in France.

    Directory of Open Access Journals (Sweden)

    Thibaut Malausa

    Full Text Available Pseudococcus comstocki (Hemiptera: Pseudococcidae is a mealybug species native to Eastern Asia and present as an invasive pest in northern Italy and southern France since the start of the century. It infests apple and pear trees, grapevines and some ornamental trees. Biocontrol programmes against this pest proved successful in central Asia and North America in the second half of the 20th century. In this study, we investigated possible biocontrol agents against P. comstocki, with the aim of developing a biocontrol programme in France. We carried out systematic DNA-barcoding at each step in the search for a specialist parasitoid. First we characterised the French target populations of P. comstocki. We then identified the parasitoids attacking P. comstocki in France. Finally, we searched for foreign mealybug populations identified a priori as P. comstocki and surveyed their hymenopteran parasitoids. Three mealybug species (P. comstocki, P. viburni and P. cryptus were identified during the survey, together with at least 16 different parasitoid taxa. We selected candidate biological control agent populations for use against P. comstocki in France, from the species Allotropa burrelli (Hymenoptera: Platygastridae and Acerophagus malinus (Hymenoptera: Encyrtidae. The coupling of molecular and morphological characterisation for both pests and natural enemies facilitated the programme development and the rejection of unsuitable or generalist parasitoids.

  17. Investigating Biological Control Agents for Controlling Invasive Populations of the Mealybug Pseudococcus comstocki in France

    Science.gov (United States)

    Malausa, Thibaut; Delaunay, Mathilde; Fleisch, Alexandre; Groussier-Bout, Géraldine; Warot, Sylvie; Crochard, Didier; Guerrieri, Emilio; Delvare, Gérard; Pellizzari, Giuseppina; Kaydan, M. Bora; Al-Khateeb, Nadia; Germain, Jean-François; Brancaccio, Lisa; Le Goff, Isabelle; Bessac, Melissa; Ris, Nicolas; Kreiter, Philippe

    2016-01-01

    Pseudococcus comstocki (Hemiptera: Pseudococcidae) is a mealybug species native to Eastern Asia and present as an invasive pest in northern Italy and southern France since the start of the century. It infests apple and pear trees, grapevines and some ornamental trees. Biocontrol programmes against this pest proved successful in central Asia and North America in the second half of the 20th century. In this study, we investigated possible biocontrol agents against P. comstocki, with the aim of developing a biocontrol programme in France. We carried out systematic DNA-barcoding at each step in the search for a specialist parasitoid. First we characterised the French target populations of P. comstocki. We then identified the parasitoids attacking P. comstocki in France. Finally, we searched for foreign mealybug populations identified a priori as P. comstocki and surveyed their hymenopteran parasitoids. Three mealybug species (P. comstocki, P. viburni and P. cryptus) were identified during the survey, together with at least 16 different parasitoid taxa. We selected candidate biological control agent populations for use against P. comstocki in France, from the species Allotropa burrelli (Hymenoptera: Platygastridae) and Acerophagus malinus (Hymenoptera: Encyrtidae). The coupling of molecular and morphological characterisation for both pests and natural enemies facilitated the programme development and the rejection of unsuitable or generalist parasitoids. PMID:27362639

  18. Molecular biology techniques and applications for ocean sensing

    Directory of Open Access Journals (Sweden)

    J. P. Zehr

    2008-11-01

    Full Text Available 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.

  19. Host range of the inadvertent biological control agent Caloptilia triadicae: an invasive herbivore of Chinese tallowtree

    Science.gov (United States)

    An inadvertent biological control agent of the invasive weed Chinese tallowtree (Triadica sebifera) first appeared in North America in 2004. Identified as a Caloptilia triadicae, this leaf miner was found damaging T. sebifera saplings. In Gainesville, FL we exposed naturalized populations of C. tria...

  20. Status of biological control projects on terrestrial invasive alien weeds in California

    Science.gov (United States)

    In cooperation with foreign scientists, we are currently developing new classical biological control agents for five species of invasive alien terrestrial weeds. Cape-Ivy. A gall-forming fly, Parafreutreta regalis, and a stem-boring moth, Digitivalva delaireae, have been favorably reviewed by TAG...

  1. Molecular biology of liver disorders: the hepatitis C virus and molecular targets for drug development

    Institute of Scientific and Technical Information of China (English)

    Howard J. Worman; Feng Lin

    2000-01-01

    Molecular biology has made a tremendous impact on the diagnosis and treatment of liver diseases[1,2]. In particular, advances in molecular biology made possible the discovery of the virus that causes hepatitis C. In this review, we use hepatitis C as an example of the impact that molecular biology has made in the area of liver disorders. We emphasize how our growing understanding of the hepatitis C virus (HCV) has lead to the identification of targets for development of new treatments.

  2. CSMB | Center For Structural Molecular Biology

    Data.gov (United States)

    Federal Laboratory Consortium — The Center for Structural Molecular Biologyat ORNL is dedicated to developing instrumentation and methods for determining the 3-dimensional structures of proteins,...

  3. Recent advances in high-throughput molecular marker identification for superficial and invasive bladder cancers

    DEFF Research Database (Denmark)

    Andersen, Lars Dyrskjøt; Zieger, Karsten; Ørntoft, Torben Falck

    2007-01-01

    individually contributed to the management of the disease. However, the development of high-throughput techniques for simultaneous assessment of a large number of markers has allowed classification of tumors into clinically relevant molecular subgroups beyond those possible by pathological classification. Here......, we review the recent advances in high-throughput molecular marker identification for superficial and invasive bladder cancers....

  4. Reproductive biology in an invasive plant Solidago canadensis

    Institute of Scientific and Technical Information of China (English)

    HUANG Hua; GUO Shuiliang; CHEN Guoqi

    2007-01-01

    Solidago canadensis,a perennial Compositae plant originating from North America,was introduced into China as a horticultural plant in 1935.Under natural conditions,S.canadensis allocates large amounts of energy to sexual reproduction and produces many seeds,which reflects an r-strategy with high seed number and small seed size.In addition,naturalized populations have a great capacity to grow clonally with underground stems.S.canadensis has become an invasive weed in eastern China,and has caused serious damages to agricultural production and ecosystems in several provinces in China.In order to understand the reproductive characteristics of S.canadensis and effectively control its spread,we examined soil conditions,seed characteristics,seed germination and the capacity for asexual reproduction in different plant parts.We investigated the population dispersion of S.canadensis in fixed sites for three years,and analyzed the seasonal dynamics of the morphological parameters of the underground parts and the caloric values of different organs of S.canadensis.We also compared differences in the root systems of S.canadensis and composite exotic weeds.The following results were obtained:1)Under natural conditions,the germination season of S.canadensis lasts from March to October,with a peak from April to May.Vegetative growth and asexual reproduction are especially vigorous during summer due to high temperatures and soil drought stress.On the other hand,the rainy season proves suitable for seed germination.Most S.canadensis flower between September and January,and fruit in late October.A mature plant can produce about 20000 seeds.The mean weight of 1000 seeds ranges from 0.045 g to 0.050 g,and the mean seed moisture content ranges from 60% to 80%.The light-winged seeds disperse readily by air,water,vehicles,human activity or through livestock.2)S.canadensis seeds have a wide tolerance for different values of pH,salinity and soil moisture.The mean percent germination of seeds

  5. Using counterfactuals to evaluate the cost-effectiveness of controlling biological invasions.

    Science.gov (United States)

    McConnachie, Matthew M; van Wilgen, Brian W; Ferraro, Paul J; Forsyth, Aurelia T; Richardson, David M; Gaertner, Mirijam; Cowling, Richard M

    2016-03-01

    Prioritizing limited conservation funds for controlling biological invasions requires accurate estimates of the effectiveness of interventions to remove invasive species and their cost-effectiveness (cost per unit area or individual). Despite billions of dollars spent controlling biological invasions worldwide, it is unclear whether those efforts are effective, and cost-effective. The paucity of evidence results from the difficulty in measuring the effect of invasive species removal: a researcher must estimate the difference in outcomes (e.g. invasive species cover) between where the removal program intervened and what might have been observed if the program had not intervened. In the program evaluation literature, this is called a counterfactual analysis, which formally compares what actually happened and what would have happened in the absence of an intervention. When program implementation is not randomized, estimating counterfactual outcomes is especially difficult. We show how a thorough understanding of program implementation, combined with a matching empirical design can improve the way counterfactual outcomes are estimated in nonexperimental contexts. As a practical demonstration, we estimated the cost-effectiveness of South Africa's Working for Water program, arguably the world's most ambitious invasive species control program, in removing invasive alien trees from different land use types, across a large area in the Cape Floristic Region. We estimated that the proportion of the treatment area covered by invasive trees would have been 49% higher (5.5% instead of 2.7% of the grid cells occupied) had the program not intervened. Our estimates of cost per hectare to remove invasive species, however, are three to five times higher than the predictions made when the program was initiated. Had there been no control (counter-factual), invasive trees would have spread on untransformed land, but not on land parcels containing plantations or land transformed by

  6. Biology, ecology and management of the invasive parthenium weed (Parthenium hysterophorus L.).

    Science.gov (United States)

    Adkins, Steve; Shabbir, Asad

    2014-07-01

    Parthenium weed (Parthenium hysterophorus L.) is one of the most aggressive invasive weeds, threatening natural ecosystems and agroecosystems in over 30 countries worldwide. Parthenium weed causes losses of crops and pastures, degrading the biodiversity of natural plant communities, causing human and animal health hazards and resulting in serious economic losses to people and their interests in many countries around the globe. Several of its biological and ecological attributes contribute towards its invasiveness. Various management approaches (namely cultural, mechanical, chemical and biological control) have been used to minimise losses caused by this weed, but most of these approaches are ineffective and uneconomical and/or have limitations. Although chemical control using herbicides and biological control utilising exotic insects and pathogens have been found to contribute to the management of the weed, the weed nevertheless remains a significant problem. An integrated management approach is proposed here for the effective management of parthenium weed on a sustainable basis.

  7. Structural Biology and Molecular Applications Research

    Science.gov (United States)

    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.

  8. Molecular biology techniques and applications for ocean sensing

    Directory of Open Access Journals (Sweden)

    J. P. Zehr

    2009-05-01

    Full Text Available 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.

  9. Risk assessment, eradication, and biological control: global efforts to limit Australian acacia invasions

    Science.gov (United States)

    Wilson, John R.U.; Gairifo, Carla; Gibson, Michelle R.; Arianoutsou, Margarita; Bakar, Baki B.; Baret, Stephane; Celesti-Grapow, Laura; DiTomaso, Joseph M.; Dufour-Dror, Jean-Marc; Kueffer, Christoph; Kull, Christian A.; Hoffman, John H.; Impson, Fiona A.C.; Loope, Lloyd L.; Marchante, Elizabete; Harchante, Helia; Moore, Joslin L.; Murphy, Daniel J.; Tassin, Jacques; Witt, Arne; Zenni, Rafael D.; Richardson, David M.

    2011-01-01

    Aim Many Australian Acacia species have been planted around the world, some are highly valued, some are invasive, and some are both highly valued and invasive. We review global efforts to minimize the risk and limit the impact of invasions in this widely used plant group. Location Global. Methods Using information from literature sources, knowledge and experience of the authors, and the responses from a questionnaire sent to experts around the world, we reviewed: (1) a generalized life cycle of Australian acacias and how to control each life stage, (2) different management approaches and (3) what is required to help limit or prevent invasions. Results Relatively few Australian acacias have been introduced in large numbers, but all species with a long and extensive history of planting have become invasive somewhere. Australian acacias, as a group, have a high risk of becoming invasive and causing significant impacts as determined by existing assessment schemes. Moreover, in most situations, long-lived seed banks mean it is very difficult to control established infestations. Control has focused almost exclusively on widespread invaders, and eradication has rarely been attempted. Classical biological control is being used in South Africa with increasing success. Main conclusions A greater emphasis on pro-active rather than reactive management is required given the difficulties managing established invasions of Australian acacias. Adverse effects of proposed new introductions can be minimized by conducting detailed risk assessments in advance, planning for on-going monitoring and management, and ensuring resources are in place for long-term mitigation. Benign alternatives (e.g. sterile hybrids) could be developed to replace existing utilized taxa. Eradication should be set as a management goal more often to reduce the invasion debt. Introducing classical biological control agents that have a successful track-record in South Africa to other regions and identifying new

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    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.

  11. Biological control of invasive plant species: a reassessment for the Anthropocene.

    Science.gov (United States)

    Seastedt, Timothy R

    2015-01-01

    The science of finding, testing and releasing herbivores and pathogens to control invasive plant species has achieved a level of maturity and success that argues for continued and expanded use of this program. The practice, however, remains unpopular with some conservationists, invasion biologists, and stakeholders. The ecological and economic benefits of controlling densities of problematic plant species using biological control agents can be quantified, but the risks and net benefits of biological control programs are often derived from social or cultural rather than scientific criteria. Management of invasive plants is a 'wicked problem', and local outcomes to wicked problems have both positive and negative consequences differentially affecting various groups of stakeholders. The program has inherent uncertainties; inserting species into communities that are experiencing directional or even transformational changes can produce multiple outcomes due to context-specific factors that are further confounded by environmental change drivers. Despite these uncertainties, biological control could play a larger role in mitigation and adaptation strategies used to maintain biological diversity as well as contribute to human well-being by protecting food and fiber resources. PMID:25303317

  12. Biological control of invasive plant species: a reassessment for the Anthropocene.

    Science.gov (United States)

    Seastedt, Timothy R

    2015-01-01

    The science of finding, testing and releasing herbivores and pathogens to control invasive plant species has achieved a level of maturity and success that argues for continued and expanded use of this program. The practice, however, remains unpopular with some conservationists, invasion biologists, and stakeholders. The ecological and economic benefits of controlling densities of problematic plant species using biological control agents can be quantified, but the risks and net benefits of biological control programs are often derived from social or cultural rather than scientific criteria. Management of invasive plants is a 'wicked problem', and local outcomes to wicked problems have both positive and negative consequences differentially affecting various groups of stakeholders. The program has inherent uncertainties; inserting species into communities that are experiencing directional or even transformational changes can produce multiple outcomes due to context-specific factors that are further confounded by environmental change drivers. Despite these uncertainties, biological control could play a larger role in mitigation and adaptation strategies used to maintain biological diversity as well as contribute to human well-being by protecting food and fiber resources.

  13. Bacteriophages: The viruses for all seasons of molecular biology

    Directory of Open Access Journals (Sweden)

    Karam Jim D

    2005-03-01

    Full Text Available Abstract Bacteriophage research continues to break new ground in our understanding of the basic molecular mechanisms of gene action and biological structure. The abundance of bacteriophages in nature and the diversity of their genomes are two reasons why phage research brims with excitement. The pages of Virology Journal will reflect the excitement of the "New Phage Biology."

  14. Proceedings of the symposium on molecular biology and radiation protection

    International Nuclear Information System (INIS)

    The symposium on molecular biology and radiation protection was organized in sessions with the following titles: Radiation protection and the human genome; Molecular changes in DNA induced by radiation; Incidence of genetic changes - pre-existing, spontaneous and radiation-induced; Research directions and ethical implications. The ten papers in the symposium have been abstracted individually

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

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

    2008-01-01

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

  17. Molecular biology of human muscle disease

    Energy Technology Data Exchange (ETDEWEB)

    Dunne, P.W.; Epstein, H.F. (Baylor Coll. of Medicine, Houston, TX (United States))

    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.

  18. 09091 Executive Summary -- Formal Methods in Molecular Biology

    OpenAIRE

    Breitling, Rainer; Gilbert, David Roger; Heiner, Monika; Priami, Corrado

    2009-01-01

    Formal logical models play an increasing role in the newly emerging field of Systems Biology. Compared to the classical, well-established approach of modeling biological processes using continuous and stochastic differential equations, formal logical models offer a number of important advantages. Many different formal modeling paradigms have been applied to molecular biology, each with its own community, formalisms and tools. In this seminar we brought together modelers from variou...

  19. The cellular and molecular biology of medulloblastoma

    NARCIS (Netherlands)

    Peringa, A; Fung, KM; Muragaki, Y; Trojanowski, JQ

    1995-01-01

    Medulloblastomas are prototypical of primitive neuroectodermal tumors which are some of the most frequent malignant brain tumors of childhood. The cell biology of medulloblastomas is still poorly understood, but recent studies of the expression of trophic factors and their receptors in medulloblasto

  20. Methods in molecular biology: plant cytogenetics

    Science.gov (United States)

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

  1. Molecular biological enhancement of coal biodesulfurization

    Energy Technology Data Exchange (ETDEWEB)

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

    1991-12-01

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

  2. Interactive analysis of systems biology molecular expression data

    Directory of Open Access Journals (Sweden)

    Prabhakar Sunil

    2008-02-01

    Full Text Available Abstract 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.

  3. The role of adaptive trans-generational plasticity in biological invasions of plants.

    Science.gov (United States)

    Dyer, Andrew R; Brown, Cynthia S; Espeland, Erin K; McKay, John K; Meimberg, Harald; Rice, Kevin J

    2010-03-01

    High-impact biological invasions often involve establishment and spread in disturbed, high-resource patches followed by establishment and spread in biotically or abiotically stressful areas. Evolutionary change may be required for the second phase of invasion (establishment and spread in stressful areas) to occur. When species have low genetic diversity and short selection history, within-generation phenotypic plasticity is often cited as the mechanism through which spread across multiple habitat types can occur. We show that trans-generational plasticity (TGP) can result in pre-adapted progeny that exhibit traits associated with increased fitness both in high-resource patches and in stressful conditions. In the invasive sedge, Cyperus esculentus, maternal plants growing in nutrient-poor patches can place disproportional number of propagules into nutrient-rich patches. Using the invasive annual grass, Aegilops triuncialis, we show that maternal response to soil conditions can confer greater stress tolerance in seedlings in the form of greater photosynthetic efficiency. We also show TGP for a phenological shift in a low resource environment that results in greater stress tolerance in progeny. These lines of evidence suggest that the maternal environment can have profound effects on offspring success and that TGP may play a significant role in some plant invasions. PMID:25567918

  4. Comment on "Invasive harlequin ladybird carries biological weapons against native competitors".

    Science.gov (United States)

    de Jong, Peter W; van Lenteren, Joop C; Raak-van den Berg, C Lidwien

    2013-09-20

    We comment on the implications that Vilcinskas et al. (Reports, 17 May 2013, p. 862) attach to the finding that the exotic, invasive ladybird Harmonia axyridis carries microsporidia to which this species is insensitive but that is lethal to species that are native to the invaded areas. The authors suggest that these microsporidia might serve as "biological weapons" against the native competitors, but we cast doubt on the importance of this suggestion in the field.

  5. Biological invasions in terrestrial Antarctica: what is the current status and can we respond?

    OpenAIRE

    Hughes, Kevin A; Pertierra, Luis R.; Marco A Molina-Montenegro; Convey, Peter

    2015-01-01

    Until recently the Antarctic continent and Peninsula have been little impacted by non-native species, compared to other regions of the Earth. However, reports of species introductions are increasing as awareness of biological invasions as a major conservation threat, within the context of increased human activities and climate change scenarios, has grown within the Antarctic community. Given the recent increase in documented reports, here we provide an up-to-date inventory of known terrestria...

  6. The biology and ecology of the invasive Indo-Pacific lionfish

    OpenAIRE

    James A. Morris Jr.

    2009-01-01

    The Indo-Pacific lionfishes, Pterois miles and P. volitans, are now established along the Southeast U.S. and Caribbean and are expected to expand into the Gulf of Mexico and Central and South America. Prior to this invasion little was known regarding the biology and ecology of these lionfishes. I provide a synopsis of chronology, taxonomy, local abundance, reproduction, early life history and dispersal, venomology, feeding ecology, parasitology, potential impacts, and possible control and man...

  7. Invasion by P. falciparum merozoites suggests a hierarchy of molecular interactions.

    Directory of Open Access Journals (Sweden)

    Jake Baum

    2005-12-01

    Full Text Available Central to the pathology of malaria disease are the repeated cycles of parasite invasion and destruction of human erythrocytes. In Plasmodium falciparum, the most virulent species causing malaria, erythrocyte invasion involves several specific receptor-ligand interactions that direct the pathway used to invade the host cell, with parasites varying in their dependency on these different pathways. Gene disruption of a key invasion ligand in the 3D7 parasite strain, the P. falciparum reticulocyte binding-like homolog 2b (PfRh2b, resulted in the parasite invading via a novel pathway. Here, we show results that suggest the molecular basis for this novel pathway is not due to a molecular switch but is instead mediated by the redeployment of machinery already present in the parent parasite but masked by the dominant role of PfRh2b. This would suggest that interactions directing invasion are organized hierarchically, where silencing of dominant invasion ligands reveal underlying alternative pathways. This provides wild parasites with the ability to adapt to immune-mediated selection or polymorphism in erythrocyte receptors and has implications for the use of invasion-related molecules in candidate vaccines.

  8. Immunophenotyping invasive breast cancer: paving the road for molecular imaging.

    NARCIS (Netherlands)

    Vermeulen, J.F.; Brussel, A.S. van; Groep, P. van der; Morsink, F.H.; Bult, P.; Wall, E. van der; Diest, P.J. van

    2012-01-01

    ABSTRACT: BACKGROUND: Mammographic population screening in The Netherlands has increased the number of breast cancer patients with small and non-palpable breast tumors. Nevertheless, mammography is not ultimately sensitive and specific for distinct subtypes. Molecular imaging with targeted tracers m

  9. Classical Biological Control of Invasive Legacy Crop Pests: New Technologies Offer Opportunities to Revisit Old Pest Problems in Perennial Tree Crops.

    Science.gov (United States)

    Hoddle, Mark S; Warner, Keith; Steggall, John; Jetter, Karen M

    2014-12-23

    Advances in scientific disciplines that support classical biological control have provided "new tools" that could have important applications for biocontrol programs for some long-established invasive arthropod pests. We suggest that these previously unavailable tools should be used in biological control programs targeting "legacy pests", even if they have been targets of previously unsuccessful biocontrol projects. Examples of "new tools" include molecular analyses to verify species identities and likely geographic area of origin, climate matching and ecological niche modeling, preservation of natural enemy genetic diversity in quarantine, the use of theory from invasion biology to maximize establishment likelihoods for natural enemies, and improved understanding of the interactions between natural enemy and target pest microbiomes. This review suggests that opportunities exist for revisiting old pest problems and funding research programs using "new tools" for developing biological control programs for "legacy pests" could provide permanent suppression of some seemingly intractable pest problems. As a case study, we use citricola scale, Coccus pseudomagnoliarum, an invasive legacy pest of California citrus, to demonstrate the potential of new tools to support a new classical biological control program targeting this insect.

  10. Classical Biological Control of Invasive Legacy Crop Pests: New Technologies Offer Opportunities to Revisit Old Pest Problems in Perennial Tree Crops

    Directory of Open Access Journals (Sweden)

    Mark S. Hoddle

    2014-12-01

    Full Text Available Advances in scientific disciplines that support classical biological control have provided “new tools” that could have important applications for biocontrol programs for some long-established invasive arthropod pests. We suggest that these previously unavailable tools should be used in biological control programs targeting “legacy pests”, even if they have been targets of previously unsuccessful biocontrol projects. Examples of “new tools” include molecular analyses to verify species identities and likely geographic area of origin, climate matching and ecological niche modeling, preservation of natural enemy genetic diversity in quarantine, the use of theory from invasion biology to maximize establishment likelihoods for natural enemies, and improved understanding of the interactions between natural enemy and target pest microbiomes. This review suggests that opportunities exist for revisiting old pest problems and funding research programs using “new tools” for developing biological control programs for “legacy pests” could provide permanent suppression of some seemingly intractable pest problems. As a case study, we use citricola scale, Coccus pseudomagnoliarum, an invasive legacy pest of California citrus, to demonstrate the potential of new tools to support a new classical biological control program targeting this insect.

  11. Morphological and molecular characterisation of Mycosphaerellaceae associated with the invasive weed, Chromolaena odorata

    NARCIS (Netherlands)

    Breeijen, A. van den; Groenewald, J.Z.; Verkley, G.J.M.; Crous, P.W.

    2006-01-01

    Chromolaena odorata, originating from South and Central America, is a bushy shrub invasive in many tropical and subtropical regions of the world. Several species of Mycosphaerellaceae have been reported on C. odorata in recent years as potential biological control agents. As a result, several explor

  12. Morphological and molecular characterisation of Mycosphaerellaceae associated with the invasive weed, Chromolaena odorata

    NARCIS (Netherlands)

    Breeÿen, den A.; Groenewald, J.Z.; Verkley, G.J.M.; Crous, P.W.

    2006-01-01

    Chromolaena odorata, originating from South and Central America, is a bushy shrub invasive in many tropical and Subtropical regions of the world. Several species of Mycosphaerellaceae have been reported on C. odorata in recent years as potential biological control agents. As a result, several explor

  13. Asymmetry at the molecular level in biology

    Science.gov (United States)

    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.

  14. Development of New Molecular EZH2 on Lung Cancer Invasion and Metastasis

    Directory of Open Access Journals (Sweden)

    Hui XIA

    2016-02-01

    Full Text Available Lung cancer is a serious threat to human health malignancies upward trend in morbidity and mortality. It is hot topic to investigate the molecular mechanisms of lung cancer development and explore the new therapeutic targets. The underlying mechanism of EZH2 on lung cancer development will demonstrate the new pathway of lung cancer development, invasion and metastasis. The exploration and application of new targeted molecular will improve the survival rate and living quality of lung cancer patients in future.

  15. Molecular characterization of an early invasive Staphylococcus epidermidis prosthetic joint infection.

    Science.gov (United States)

    Rosenthal, Marnie E; Dever, Lisa L; Moucha, Calin S; Chavda, Kalyan D; Otto, Michael; Kreiswirth, Barry N

    2011-09-01

    Historically regarded as a skin commensal, Staphylococcus epidermidis has been increasingly implicated in invasive foreign body infections such as catheter-related bloodstream infections, indwelling device infections, and prosthetic joint infections. We report a case of an aggressive, difficult-to-eradicate, invasive prosthetic hip infection occurring early after hardware implant and associated with a high-grade bacteremia and assess its salient molecular characteristics. The clinical and molecular characteristics of this isolate mirror the pathogenesis and persistence commonly seen with invasive methicillin-resistant S. aureus and may be attributed to the combination of resistance genes (SCCmec type IV), putative virulence factors (arcA and opp3a), cytolytic peptide production (α-type phenol-soluble modulins), and biofilm adhesion, interaction, and maturation (bhp, aap, and β-type phenol-soluble modulins).

  16. Molecular classification of non-invasive breast lesions for personalised therapy and chemoprevention.

    Science.gov (United States)

    Buckley, Niamh; Boyle, David; McArt, Darragh; Irwin, Gareth; Harkin, D Paul; Lioe, Tong; McQuaid, Stephen; James, Jacqueline A; Maxwell, Perry; Hamilton, Peter; Mullan, Paul B; Salto-Tellez, Manuel

    2015-12-22

    Breast cancer screening has led to a dramatic increase in the detection of pre-invasive breast lesions. While mastectomy is almost guaranteed to treat the disease, more conservative approaches could be as effective if patients can be stratified based on risk of co-existing or recurrent invasive disease.Here we use a range of biomarkers to interrogate and classify purely non-invasive lesions (PNL) and those with co-existing invasive breast cancer (CEIN). Apart from Ductal Carcinoma In Situ (DCIS), relative homogeneity is observed. DCIS contained a greater spread of molecular subtypes. Interestingly, high expression of p-mTOR was observed in all PNL with lower expression in DCIS and invasive carcinoma while the opposite expression pattern was observed for TOP2A.Comparing PNL with CEIN, we have identified p53 and Ki67 as predictors of CEIN with a combined PPV and NPV of 90.48% and 43.3% respectively. Furthermore, HER2 expression showed the best concordance between DCIS and its invasive counterpart.We propose that these biomarkers can be used to improve the management of patients with pre-invasive breast lesions following further validation and clinical trials. p53 and Ki67 could be used to stratify patients into low and high-risk groups for co-existing disease. Knowledge of expression of more actionable targets such as HER2 or TOP2A can be used to design chemoprevention or neo-adjuvant strategies. Increased knowledge of the molecular profile of pre-invasive lesions can only serve to enhance our understanding of the disease and, in the era of personalised medicine, bring us closer to improving breast cancer care. PMID:26657114

  17. Xenon preconditioning: molecular mechanisms and biological effects

    Directory of Open Access Journals (Sweden)

    Liu Wenwu

    2013-01-01

    Full Text Available Abstract Xenon is one of noble gases and has been recognized as an anesthetic for more than 50 years. Xenon possesses many of the characteristics of an ideal anesthetic, but it is not widely applied in clinical practice mainly because of its high cost. In recent years, numerous studies have demonstrated that xenon as an anesthetic can exert neuroprotective and cardioprotective effects in different models. Moreover, xenon has been applied in the preconditioning, and the neuroprotective and cardioprotective effects of xenon preconditioning have been investigated in a lot of studies in which some mechanisms related to these protections are proposed. In this review, we summarized these mechanisms and the biological effects of xenon preconditioning.

  18. Overview of selected molecular biological databases

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

    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…

  20. Cold Spring Harbor symposia on quantitative biology: Volume 51, Molecular biology of /ital Homo sapiens/

    International Nuclear Information System (INIS)

    This volume is the second part of a collection of papers submitted by the participants to the 1986 Cold Spring Harbor Symposium on Quantitative Biology entitled Molecular Biology of /ital Homo sapiens/. The 49 papers included in this volume are grouped by subject into receptors, human cancer genes, and gene therapy. (DT)

  1. Biological (molecular and cellular) markers of toxicity

    Energy Technology Data Exchange (ETDEWEB)

    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.

  2. Comparative molecular modelling of biologically active sterols

    Science.gov (United States)

    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.

  3. Biological (molecular and cellular) markers of toxicity

    International Nuclear Information System (INIS)

    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). NO6-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 O6-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

  4. Using non-invasive molecular spectroscopic techniques to detect unique aspects of protein Amide functional groups and chemical properties of modeled forage from different sourced-origins

    Science.gov (United States)

    Ji, Cuiying; Zhang, Xuewei; Yu, Peiqiang

    2016-03-01

    The non-invasive molecular spectroscopic technique-FT/IR is capable to detect the molecular structure spectral features that are associated with biological, nutritional and biodegradation functions. However, to date, few researches have been conducted to use these non-invasive molecular spectroscopic techniques to study forage internal protein structures associated with biodegradation and biological functions. The objectives of this study were to detect unique aspects and association of protein Amide functional groups in terms of protein Amide I and II spectral profiles and chemical properties in the alfalfa forage (Medicago sativa L.) from different sourced-origins. In this study, alfalfa hay with two different origins was used as modeled forage for molecular structure and chemical property study. In each forage origin, five to seven sources were analyzed. The molecular spectral profiles were determined using FT/IR non-invasive molecular spectroscopy. The parameters of protein spectral profiles included functional groups of Amide I, Amide II and Amide I to II ratio. The results show that the modeled forage Amide I and Amide II were centered at 1653 cm- 1 and 1545 cm- 1, respectively. The Amide I spectral height and area intensities were from 0.02 to 0.03 and 2.67 to 3.36 AI, respectively. The Amide II spectral height and area intensities were from 0.01 to 0.02 and 0.71 to 0.93 AI, respectively. The Amide I to II spectral peak height and area ratios were from 1.86 to 1.88 and 3.68 to 3.79, respectively. Our results show that the non-invasive molecular spectroscopic techniques are capable to detect forage internal protein structure features which are associated with forage chemical properties.

  5. Progress in Modeling Biological Invasion%生物入侵模型研究进展

    Institute of Scientific and Technical Information of China (English)

    王勤龙; 李百炼

    2011-01-01

    Biological invasion is now one of the six hot research topics in modern ecology.Modeling the invasion processes,the diffusions and the spreading mechanisms of invasive species including diseases is important not only for theoretical puposes,but also for practical purposes,such as in ecological risk assessments,and optimal control and management of those invasive species.In this paper the widely adopted models of biological invasion are systematically reviewed such as diffusion-reaction equations,integral-difference models,space-discrete models,and stochastic models.The fundamental issues of modeling biological invasions are discussed,and the characteristics and analytic conditions of various models are analyzed with typical exampies and recent research results.Various modeling techniques are compared,and some commonly used methods in solving biological invasion models are outlined,including numerical computing and simulating,exact solutions,methods for functional differential equation and qualitative analysis of differential equations Some key and unsolved problems in building mathematical models of biological invasion,and future research directions are also Hiscussed.%生物入侵的机制与控制已经成为生态学关注的重点和研究的热点问题.建立数学模型是解释生物入侵机制的主要手段,对外来生物包括疾病的入侵扩散过程进行模型分析不仅具有重要的理论意义,还有助于风险评估,特别对入侵进行早期预测、控制、科学管理与防治.然而,目前有关生物入侵的数理模型方法还远不能满足实际的需要,本文系统地介绍和分析了生物入侵模型的研究现状.首先分析了对于生物入侵过程建模所要考虑的基本问题;然后讨论了几类典型的入侵数学模型,分析了各自的特点及条件,同时给出了有代表性的实例和最近的研究成果;其次比较列出了入侵模型分析的各类方法:最后探讨了生物入侵建模与求

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

    Science.gov (United States)

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

    2011-09-23

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

  7. Molecular circuits, biological switches, and nonlinear dose-response relationships.

    OpenAIRE

    Andersen, Melvin E.; Yang, Raymond S.H.; French, C. Tenley; Chubb, Laura S; Dennison, James E

    2002-01-01

    Signaling motifs (nuclear transcriptional receptors, kinase/phosphatase cascades, G-coupled protein receptors, etc.) have composite dose-response behaviors in relation to concentrations of protein receptors and endogenous signaling molecules. "Molecular circuits" include the biological components and their interactions that comprise the workings of these signaling motifs. Many of these molecular circuits have nonlinear dose-response behaviors for endogenous ligands and for exogenous toxicants...

  8. Biology of Leipothrix dipsacivagus (Acari: Eriophyidae), a candidate for biological control of invasive teasels (Dipsacus spp.)

    Science.gov (United States)

    The present study describes key aspects of the biology of Leipothrix dipsacivagus, an eriophyid mite that was recently described as a new species from Dipsacus fullonum and D. laciniatus (Dipsacaceae). Preliminary host-specificity tests have shown that it can develop and reproduce only on Dipsacus s...

  9. Molecular evidence for multiple phylogenetic groups within two species of invasive spiny whiteflies and their parasitoid wasp.

    Science.gov (United States)

    Uesugi, R; Sato, Y; Han, B-Y; Huang, Z-D; Yara, K; Furuhashi, K

    2016-06-01

    The invasive orange spiny whitefly (OSW) Aleurocanthus spiniferus has extended its distribution to non-native areas since the early 20th century. In a similar manner, the invasive tea spiny whitefly (TSW) A. camelliae has been expanding over East Asia in recent decades. In this study, the genetic diversity of OSW and TSW and of their important parasitoid wasp Encarsia smithi was investigated in China and Japan to enable more efficient biological control policies. We detected two phylogenetic groups (haplogroups A1 and A2) in OSW and three phylogenetic groups (haplotypes B1 and B2, and haplogroup B3) in TSW in China; however, only a single haplotype was detected in each whitefly species in Japan. Based on historical records and molecular data, OSW was considered to be native to China whereas TSW has probably expanded to China from a more southern location in the last 50 years; China appears to be the source region for OSW and TSW invading Japan. In E. smithi, two phylogenetic groups were detected in Japan: haplotype I, associated with OSW, and haplogroup II mostly associated with TSW, except in two locations. These data support the hypothesis that E. smithi parasitizing TSW in Japan did not originate from the existent population parasitizing OSW but was newly imported into Japan following the invasion of its host. PMID:26782948

  10. A possible molecular metric for biological evolvability

    Indian Academy of Sciences (India)

    Aditya Mittal; B Jayaram

    2012-07-01

    Proteins manifest themselves as phenotypic traits, retained or lost in living systems via evolutionary pressures. Simply put, survival is essentially the ability of a living system to synthesize a functional protein that allows for a response to environmental perturbations (adaptation). Loss of functional proteins leads to extinction. Currently there are no universally applicable quantitative metrics at the molecular level for either measuring ‘evolvability’ of life or for assessing the conditions under which a living system would go extinct and why. In this work, we show emergence of the first such metric by utilizing the recently discovered stoichiometric margin of life for all known naturally occurring (and functional) proteins. The constraint of having well-defined stoichiometries of the 20 amino acids in naturally occurring protein sequences requires utilization of the full scope of degeneracy in the genetic code, i.e. usage of all codons coding for an amino acid, by only 11 of the 20 amino acids. This shows that the non-availability of individual codons for these 11 amino acids would disturb the fine stoichiometric balance resulting in non-functional proteins and hence extinction. Remarkably, these amino acids are found in close proximity of any given amino acid in the backbones of thousands of known crystal structures of folded proteins. On the other hand, stoichiometry of the remaining 9 amino acids, found to be farther/distal from any given amino acid in backbones of folded proteins, is maintained independent of the number of codons available to synthesize them, thereby providing some robustness and hence survivability.

  11. Bivalve Forensics: Sclerochronological Constraints on the Timing of a Biological Invasion in San Francisco Bay

    Science.gov (United States)

    Goodwin, D. H.; Cohen, A. N.; Roopnarine, P. D.

    2007-12-01

    Clams are biological chart recorders: their shells contain a record of environmental conditions in the form of periodic growth increments and geochemical variation. In most species, this archive begins with the deposition of the dissoconch following metamorphosis and ultimately ends with the death of the individual. In fossil specimens, the exact date of the beginning or end of the archive cannot be determined. Therefore, sclerochronologic and geochemical records from fossils represent short intervals of time that cannot be directly tied to absolute time--so called "floating chronologies." In contrast, the date of the end of the archive from live- collected specimens can be precisely resolved--in many cases to the day collection. Using this date as a pinning point, one can establish the timing of events throughout the remainder of the chronology relatively precisely. Here, we use this approach to constrain the timing of a biological invasion event in San Francisco Bay. The basic idea is simple. The timing of an invasion event (i.e., successful recruitment), can be resolved if the date of the initiation of shell deposition is established from the first specimens to appear in a new area. To absolutely establish the timing of an invasion, one must assume that specimens represent the initial cohort of invaders. If this assumption cannot be met, then this method provides minimum estimates for the timing of invasion events. This technique is best suited for regions where species composition is closely monitored and the likelihood of collecting the initial cohort is high. To demonstrate this technique, we examined specimens thought to represent the initial cohort of the oyster Crassostrea gigas to establish a population in South San Francisco Bay. All individuals were collected live in July or August of 2006. Sclerochronological examination suggested that the specimens were at least four years old. These age estimates were confirmed using stable oxygen isotope (δ18O) and

  12. Breast cancer. From molecular biology to personified therapy

    Directory of Open Access Journals (Sweden)

    Bondarenko I.N.

    2016-03-01

    Full Text Available Advances in molecular biology had changed approaches to systemic treatment of breast cancer. Clinical decisions on the choice of optimal treatment regimens are performing on the basis of immunohistochemical and molecular genetic classifications. Their increasing uses have contributed changes of paradigm for cancer treatment - from the empirical to the individualized and personalized. The basis for such approaches is knowledge of molecular epidemiology, heterogeneity of expression of molecular subtypes, prognostic and predictive biomarkers of breast cancer. Breast cancer is a widely heterogeneous disease with 20 histological types, 8, molecular-genetic, 6 genomic subtypes, which are characterized by specific molecular and biochemical properties, different clinical course and different outcomes. Molecular genetic classification, created not on the basis of clinical, anatomical and morphological heterogeneity of tumor cells, and on the basis of their molecular-genetic heterogeneity is widely used in clinical practice. This allowed to separate the patients with breast cancer to molecular 4 subtypes - luminal A, luminal B, HER / 2 positive and triple-negative. The significant role of immunohistochemical tissue tumor markers, estrogen and progesterone receptors, HER / 2-neu, Ki-67, p53 for selection the optimal treatment strategy is analyzing in this review. To increase the effectiveness of breast cancer treatment is possible, using a differentiated and personalized approach based on new molecular genetic classification of breast cancer (gene profiling or to its analogue - expression classification of breast cancer, based on the principle of diversity of immunohistochemical tumor tissue. Personification of cancer treatment involves a therapy based on the study of individual characteristics of tissue is not only the primary tumor but also its metastases. Citation: Bondarenko IN, Elhajj Mohammad H, Prokhach AV, Zavizion VF, Chebanov KO. [Breast cancer

  13. Hybridization of an invasive shrub affects tolerance and resistance to defoliation by a biological control agent

    Science.gov (United States)

    Williams, Wyatt I.; Friedman, Jonathan M.; Gaskin, John F.; Norton, Andrew P.

    2014-01-01

    Evolution has contributed to the successful invasion of exotic plant species in their introduced ranges, but how evolution affects particular control strategies is still under evaluation. For instance, classical biological control, a common strategy involving the utilization of highly specific natural enemies to control exotic pests, may be negatively affected by host hybridization because of shifts in plant traits, such as root allocation or chemical constituents. We investigated introgression between two parent species of the invasive shrub tamarisk (Tamarix spp.) in the western United States, and how differences in plant traits affect interactions with a biological control agent. Introgression varied strongly with latitude of origin and was highly correlated with plant performance. Increased levels of T. ramosissima introgression resulted in both higher investment in roots and tolerance to defoliation and less resistance to insect attack. Because tamarisk hybridization occurs predictably on the western U.S. landscape, managers may be able to exploit this information to maximize control efforts. Genetic differentiation in plant traits in this system underpins the importance of plant hybridization and may explain why some biological control releases are more successful than others.

  14. The sensitivity of real-time PCR amplification targeting invasive Salmonella serovars in biological specimens

    Directory of Open Access Journals (Sweden)

    Chau Tran

    2010-05-01

    Full Text Available Abstract Background PCR amplification for the detection of pathogens in biological material is generally considered a rapid and informative diagnostic technique. Invasive Salmonella serovars, which cause enteric fever, can be commonly cultured from the blood of infected patients. Yet, the isolation of invasive Salmonella serovars from blood is protracted and potentially insensitive. Methods We developed and optimised a novel multiplex three colour real-time PCR assay to detect specific target sequences in the genomes of Salmonella serovars Typhi and Paratyphi A. We performed the assay on DNA extracted from blood and bone marrow samples from culture positive and negative enteric fever patients. Results The assay was validated and demonstrated a high level of specificity and reproducibility under experimental conditions. All bone marrow samples tested positive for Salmonella, however, the sensitivity on blood samples was limited. The assay demonstrated an overall specificity of 100% (75/75 and sensitivity of 53.9% (69/128 on all biological samples. We then tested the PCR detection limit by performing bacterial counts after inoculation into blood culture bottles. Conclusions Our findings corroborate previous clinical findings, whereby the bacterial load of S. Typhi in peripheral blood is low, often below detection by culture and, consequently, below detection by PCR. Whilst the assay may be utilised for environmental sampling or on differing biological samples, our data suggest that PCR performed directly on blood samples may be an unsuitable methodology and a potentially unachievable target for the routine diagnosis of enteric fever.

  15. The Human Release Hypothesis for biological invasions: human activity as a determinant of the abundance of invasive plant species [v2; ref status: indexed, http://f1000r.es/4wp

    OpenAIRE

    Heike Zimmermann; Patric Brandt; Joern Fischer; Erik Welk; Henrik von Wehrden

    2014-01-01

    Research on biological invasions has increased rapidly over the past 30 years, generating numerous explanations of how species become invasive. While the mechanisms of invasive species establishment are well studied, the mechanisms driving abundance patterns (i.e. patterns of population density and population size) remain poorly understood. It is assumed that invasive species typically have higher abundances in their new environments than in their native ranges, and patterns of invasive speci...

  16. From Molecular Biology to Biomedicine; De la Biologia Molecular a la Biomedicina

    Energy Technology Data Exchange (ETDEWEB)

    Salas, M.

    2009-07-01

    From Molecular Biology to Biomedicine. The well known molecular biologist Margarita S alas offered an informative conference at the CSN on progress in these areas since the discovery, more than half a century ago, of the structure of the molecule carrying genetic information, DNA, work that is having an enormous impact in areas such as biomedicine and foodstuff production. (Author)

  17. T-cell acute lymphoblastic leukaemia : recent molecular biology findings

    NARCIS (Netherlands)

    Kraszewska, Monika D.; Dawidowska, Malgorzata; Szczepanski, Tomasz; Witt, Michal

    2012-01-01

    For many years, T-cell acute lymphoblastic leukaemia (T-ALL) has been considered and treated as a single malignancy, but divergent outcomes in T-ALL patients receiving uniform treatment protocols encouraged intensive research on the molecular biology of this disease. Recent findings in the field dem

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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…

  20. Assessing Practical Laboratory Skills in Undergraduate Molecular Biology Courses

    Science.gov (United States)

    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…

  1. A Streamlined Molecular Biology Module for Undergraduate Biochemistry Labs

    Science.gov (United States)

    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,…

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

    Science.gov (United States)

    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…

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    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.

  4. Pollination biology of an invasive weed Ipomoea cairica (Convolvulaceae) in Guangdong Province, China

    OpenAIRE

    Xiaocheng Jia; Xinliang Li; Yang Dan; Guohui Lu; Yingqiang Wang

    2007-01-01

    During May to July, 2006 and April to May, 2007, we studied pollination biology in Ipomoea cairica, an invasive weed in Guangdong Province, China. Ipomoea cairica is a perennial creeping or climbing herbaceous vine, blooming all year round in Guangdong. The flowers gathered in cymes, with a purple or bluish purple bell-formed corolla. The petals unfolded at about 4:30–5:20 and closed at 17:40, lasting for about 12 hours. The proximity of the stigma and anthers during flowering period facilita...

  5. Cellular and Molecular Biological Approaches to Interpreting Ancient Biomarkers

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  7. Morphological and molecular characterisation of Mycosphaerellaceae associated with the invasive weed, Chromolaena odorata

    OpenAIRE

    Breeijen, A. van den; Groenewald, J.Z.; Verkley, G.J.M.; Crous, P.W.

    2006-01-01

    Chromolaena odorata, originating from South and Central America, is a bushy shrub invasive in many tropical and subtropical regions of the world. Several species of Mycosphaerellaceae have been reported on C. odorata in recent years as potential biological control agents. As a result, several exploratory trips were undertaken to south, north and Central America from 1988 until 1997 to survey for pathogens on C. odorata. Three new species of Passalora, and one species of Septoria and Pseudocer...

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

    Science.gov (United States)

    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.

  9. Mathematical modeling of cancer cell invasion of tissue: biological insight from mathematical analysis and computational simulation.

    Science.gov (United States)

    Andasari, Vivi; Gerisch, Alf; Lolas, Georgios; South, Andrew P; Chaplain, Mark A J

    2011-07-01

    The ability of cancer cells to break out of tissue compartments and invade locally gives solid tumours a defining deadly characteristic. One of the first steps of invasion is the remodelling of the surrounding tissue or extracellular matrix (ECM) and a major part of this process is the over-expression of proteolytic enzymes, such as the urokinase-type plasminogen activator (uPA) and matrix metalloproteinases (MMPs), by the cancer cells to break down ECM proteins. Degradation of the matrix enables the cancer cells to migrate through the tissue and subsequently to spread to secondary sites in the body, a process known as metastasis. In this paper we undertake an analysis of a mathematical model of cancer cell invasion of tissue, or ECM, which focuses on the role of the urokinase plasminogen activation system. The model consists of a system of five reaction-diffusion-taxis partial differential equations describing the interactions between cancer cells, uPA, uPA inhibitors, plasmin and the host tissue. Cancer cells react chemotactically and haptotactically to the spatio-temporal effects of the uPA system. The results obtained from computational simulations carried out on the model equations produce dynamic heterogeneous spatio-temporal solutions and using linear stability analysis we show that this is caused by a taxis-driven instability of a spatially homogeneous steady-state. Finally we consider the biological implications of the model results, draw parallels with clinical samples and laboratory based models of cancer cell invasion using three-dimensional invasion assay, and go on to discuss future development of the model.

  10. The Biological Effect of Hepsin on the Proliferation and Invasion of PC-3 Prostate Cancer Cells

    Institute of Scientific and Technical Information of China (English)

    Yong Xu; Zhiqiang Fan; Jantao Sun; Ranlu Liu; Weiming Zhao; Chunyu Wang; Ju Zhang

    2006-01-01

    OBJECTIVE Recent studies have shown that hepsin, a type of transmembrane serine protease, is highly upregulated in prostate cancer, but, little is known about its role in progression and invasion of this cancer. We constructed a hepsin-expressing plasmid and transfected it into PC-3 cells to investigate the effect of the hepsin gene on the biological behavior of the PC-3 cells.METHODS Plasmid pHepsin-IRES2 was transfected into prostate cancer PC-3 cells using Fugene6, and the cells with stable hepsin expression were screened and selected with Zeocin (600 mg/L). The hepsin mRNA level was measured by real-time PCR and the growth curve of the PC-3-transfected cells assessed using MTT and BrdU assays. A Boyden chamber was used to examine the difference in invasion and metastases between transfected and non-transfected cells.RESULTS The hepsin mRNA level in pHepsin-IRES2 transfected -PC-3 cells was significantly higher than that found in the control PC-3 cells. While the growth curve of the hepsin gene transfected PC-3 cells showed that there was no significant effect on proliferation, the invasive ability of the pHepsin-IRES2 transfected PC-3 cells, as compared with control cells, was significantly increased (P<0.05).CONCLUSION The results suggest that even though hepsin has no effect on the proliferation of prostate cancer PC-3 cells, it does promote cellular invasion and metastasis.Therefore hepsin may have a role in the development of prostate cancer.

  11. PathSys: integrating molecular interaction graphs for systems biology

    Directory of Open Access Journals (Sweden)

    Raval Alpan

    2006-02-01

    Full Text Available Abstract Background The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. Results Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping. Conclusion Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  13. Time scale of diffusion in molecular and cellular biology

    Science.gov (United States)

    Holcman, D.; Schuss, Z.

    2014-05-01

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

  14. Molecular biology of gliomas: present and future challenges.

    Science.gov (United States)

    Altieri, R; Agnoletti, A; Quattrucci, F; Garbossa, D; Calamo Specchia, F M; Bozzaro, M; Fornaro, R; Mencarani, C; Lanotte, M; Spaziante, R; Ducati, A

    2014-09-01

    Malignant brain tumours are one of the most relevant causes of morbidity and mortality across a wide range of individuals. Malignant glioma is the most common intra axial tumor in the adult. Many researches on this theme brought advances in the knowledge of gliomas biology and pathogenesis and to the development of new agents for targeted molecular therapy. Recent studies focused on either tumor metabolism analysis or epigenetic regulation in the pathogenesis or maintenance of brain tumors. This Review summarizes these developments analyzing molecular pathology and possible further developments for targeted therapies.

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

    Science.gov (United States)

    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

  16. Molecular biology of the renin-angiotensin system

    Energy Technology Data Exchange (ETDEWEB)

    Dzau, V.J.; Burt, D.W.; Pratt, R.E. (Harvard Medical School, Boston, MA (USA))

    1988-10-01

    This paper reviews the molecular biology of the renin-angiotensin system. The renin gene structure is analyzed in detail, including an examination of the putative regulatory regions. The combined action of these regulatory sequences would result in the complex, tissue-specific expression and regulation observed in vivo. The expression of the tissue renin-angiotensin systems, which may have important physiological functions, is also described. In addition, the pathway of renin biosynthesis and secretion is reviewed. This includes speculation on the fate of circulating prorenin and the physiological role of multiple renin forms and secretory pathways. The molecular approaches described in this paper have greatly advanced our knowledge of the biology of the renin-angiotensin system. Future studies using these and other approaches should provide further insight into this complex system.

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

    Science.gov (United States)

    Citi, Sandra; Berg, Douglas E

    2016-01-01

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

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

    Science.gov (United States)

    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

  19. Molecular biological factors in the diagnosis of cervical intraepithelial neoplasias

    Directory of Open Access Journals (Sweden)

    Yu. N. Ponomareva

    2010-01-01

    Full Text Available The authors have made a complex analysis of the molecular biological factors associated with cervical intraepithelial neoplasia. They have revealed that infection by oncogenic human papillomavirus types is associated with suppressed apoptosis and enhanced cellular proliferative activity, which can be effectively used in the diagnosis and prediction of cervical neoplasias to optimize management tac- tics and to improve the results of treatment.

  20. Towards an Upper-Level Ontology for Molecular Biology

    OpenAIRE

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

    2006-01-01

    There is a growing need for the general-purpose description of the basic ontological entities in the life sciences domain. Up until now, upper-level models are mainly 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, as an ontologically more conscious re-design of the GENIA ontology.

  1. Application of Mitochondrial DNA Polymorphism to Meloidogyne Molecular Population Biology

    OpenAIRE

    Hyman, B. C.; Whipple, L.E.

    1996-01-01

    Recent advances in molecular biology have enabled the genotyping of individual nematodes, facilitating the analysis of genetic variability within and among plant-pathogenic nematode isolates. This review first describes representative examples of how RFLP, RAPD, AFLP, and DNA sequence analysis have been employed to describe populations of several phytonematodes, including the pinewood, burrowing, root-knot, and cyst nematodes. The second portion of this paper evaluates the utility of a size-v...

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

    Science.gov (United States)

    Yao, Xuebiao; Li, Dangsheng; Pei, Gang

    2013-09-01

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

  3. Twenty years of invasion: a review of round goby Neogobius melanostomus biology, spread and ecological implications.

    Science.gov (United States)

    Kornis, M S; Mercado-Silva, N; Vander Zanden, M J

    2012-02-01

    are presented; most pressing are evaluating the economic effects of N. melanostomus invasion, determining long-term population level effects of egg predation on game-fish recruitment and comparing several variables (density, ecological effects morphology and life history) among invaded ecosystems. This review provides a central reference as researchers continue studying N. melanostomus, often as examples for advancing basic ecology and invasion biology. PMID:22268429

  4. Molecular biology in studies of oceanic primary production

    International Nuclear Information System (INIS)

    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

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

    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

  7. Hydrogen Isotopes as a Sentinel of Biological Invasion by the Japanese Beetle, Popillia japonica (Newman.

    Directory of Open Access Journals (Sweden)

    Bruce A Hungate

    Full Text Available Invasive species alter ecosystems, threaten native and endangered species, and have negative economic impacts. Knowing where invading individuals are from and when they arrive to a new site can guide management. Here, we evaluated how well the stable hydrogen isotope composition (δ2H records the recent origin and time since arrival of specimens of the invasive Japanese beetle (Popillia japonica Newman captured near the Portland International Airport (Oregon, U.S.A.. The δ2H of Japanese beetle specimens collected from sites across the contiguous U.S.A. reflected the δ2H of local precipitation, a relationship similar to that documented for other organisms, and one confirming the utility of δ2H as a geographic fingerprint. Within weeks after experimental relocation to a new isotopic environment, the δ2H of beetles changed linearly with time, demonstrating the potential for δ2H to also mark the timing of arrival to a new location. We used a hierarchical Bayesian model to estimate the recent geographical origin and timing of arrival of each specimen based on its δ2H value. The geographic resolution was broad, with values consistent with multiple regions of origin in the eastern U.S.A., slightly favoring the southeastern U.S.A. as the more likely source. Beetles trapped from 2007-2010 had arrived 30 or more days prior to trapping, whereas the median time since arrival declined to 3-7 days for beetles trapped from 2012-2014. This reduction in the time between arrival and trapping at the Portland International Airport supports the efficacy of trapping and spraying to prevent establishment. More generally, our analysis shows how stable isotopes can serve as sentinels of biological invasions, verifying the efficacy of control measures, or, alternatively, indicating when those measures show signs of failure.

  8. Hydrogen Isotopes as a Sentinel of Biological Invasion by the Japanese Beetle, Popillia japonica (Newman).

    Science.gov (United States)

    Hungate, Bruce A; Kearns, Diana N; Ogle, Kiona; Caron, Melanie; Marks, Jane C; Rogg, Helmuth W

    2016-01-01

    Invasive species alter ecosystems, threaten native and endangered species, and have negative economic impacts. Knowing where invading individuals are from and when they arrive to a new site can guide management. Here, we evaluated how well the stable hydrogen isotope composition (δ2H) records the recent origin and time since arrival of specimens of the invasive Japanese beetle (Popillia japonica Newman) captured near the Portland International Airport (Oregon, U.S.A.). The δ2H of Japanese beetle specimens collected from sites across the contiguous U.S.A. reflected the δ2H of local precipitation, a relationship similar to that documented for other organisms, and one confirming the utility of δ2H as a geographic fingerprint. Within weeks after experimental relocation to a new isotopic environment, the δ2H of beetles changed linearly with time, demonstrating the potential for δ2H to also mark the timing of arrival to a new location. We used a hierarchical Bayesian model to estimate the recent geographical origin and timing of arrival of each specimen based on its δ2H value. The geographic resolution was broad, with values consistent with multiple regions of origin in the eastern U.S.A., slightly favoring the southeastern U.S.A. as the more likely source. Beetles trapped from 2007-2010 had arrived 30 or more days prior to trapping, whereas the median time since arrival declined to 3-7 days for beetles trapped from 2012-2014. This reduction in the time between arrival and trapping at the Portland International Airport supports the efficacy of trapping and spraying to prevent establishment. More generally, our analysis shows how stable isotopes can serve as sentinels of biological invasions, verifying the efficacy of control measures, or, alternatively, indicating when those measures show signs of failure. PMID:26959686

  9. Hydrogen Isotopes as a Sentinel of Biological Invasion by the Japanese Beetle, Popillia japonica (Newman)

    Science.gov (United States)

    Ogle, Kiona; Caron, Melanie; Marks, Jane C.; Rogg, Helmuth W.

    2016-01-01

    Invasive species alter ecosystems, threaten native and endangered species, and have negative economic impacts. Knowing where invading individuals are from and when they arrive to a new site can guide management. Here, we evaluated how well the stable hydrogen isotope composition (δ2H) records the recent origin and time since arrival of specimens of the invasive Japanese beetle (Popillia japonica Newman) captured near the Portland International Airport (Oregon, U.S.A.). The δ2H of Japanese beetle specimens collected from sites across the contiguous U.S.A. reflected the δ2H of local precipitation, a relationship similar to that documented for other organisms, and one confirming the utility of δ2H as a geographic fingerprint. Within weeks after experimental relocation to a new isotopic environment, the δ2H of beetles changed linearly with time, demonstrating the potential for δ2H to also mark the timing of arrival to a new location. We used a hierarchical Bayesian model to estimate the recent geographical origin and timing of arrival of each specimen based on its δ2H value. The geographic resolution was broad, with values consistent with multiple regions of origin in the eastern U.S.A., slightly favoring the southeastern U.S.A. as the more likely source. Beetles trapped from 2007–2010 had arrived 30 or more days prior to trapping, whereas the median time since arrival declined to 3–7 days for beetles trapped from 2012–2014. This reduction in the time between arrival and trapping at the Portland International Airport supports the efficacy of trapping and spraying to prevent establishment. More generally, our analysis shows how stable isotopes can serve as sentinels of biological invasions, verifying the efficacy of control measures, or, alternatively, indicating when those measures show signs of failure. PMID:26959686

  10. Biologia molecular do câncer cervical Molecular biology of cervical cancer

    Directory of Open Access Journals (Sweden)

    Waldemar Augusto Rivoire

    2006-01-01

    . How HPV immortalizes cervical cells is not fully understood. Advances have been made in the application of molecular biology techniques in the understanding of this mechanism. Once established, these techniques will lead to a better assessment of cervical neoplasias and help the development of new therapies, hopefully less invasive and more effective.

  11. The biological basis of non-invasive strategies for selection of human oocytes and embryos.

    Science.gov (United States)

    Scott, Lynette

    2003-01-01

    There is a need for more accurate embryo selection in human assisted reproduction, if the goal of reducing the number of embryos used in embryo transfer is to be realized. Furthermore, any selection strategy should be non-invasive if the embryos are to be used in embryo transfer. Currently, the strategy is selection by one to three parameters in the cleaving- and blastocyst-stage embryo, sometimes with additional pronuclear selection. It is clear that no one system is ideal, as the vast majority of transferred embryos do not implant. As the health of the embryo is largely dictated by the originating gametes, the very early events in oocyte development should be considered. This review will point to the early biological events in the unfertilized and fertilized oocyte that can be scored non-invasively and which can have a profound effect on the later developmental stages. Using a sequential scoring system, with emphasis on the oocyte, a system for selecting the most viable single embryo for transfer may hopefully be achieved.

  12. Biological control through intraguild predation: case studies in pest control, invasive species and range expansion.

    Science.gov (United States)

    Bampfylde, C J; Lewis, M A

    2007-04-01

    Intraguild predation (IGP), the interaction between species that eat each other and compete for shared resources, is ubiquitous in nature. We document its occurrence across a wide range of taxonomic groups and ecosystems with particular reference to non-indigenous species and agricultural pests. The consequences of IGP are complex and difficult to interpret. The purpose of this paper is to provide a modelling framework for the analysis of IGP in a spatial context. We start by considering a spatially homogeneous system and find the conditions for predator and prey to exclude each other, to coexist and for alternative stable states. Management alternatives for the control of invasive or pest species through IGP are presented for the spatially homogeneous system. We extend the model to include movement of predator and prey. In this spatial context, it is possible to switch between alternative stable steady states through local perturbations that give rise to travelling waves of extinction or control. The direction of the travelling wave depends on the details of the nonlinear intraguild interactions, but can be calculated explicitly. This spatial phenomenon suggests means by which invasions succeed or fail, and yields new methods for spatial biological control. Freshwater case studies are used to illustrate the outcomes.

  13. Open minded and open access : introducing NeoBiota,a new peer-reviewed journal of biological invasions

    OpenAIRE

    Ingolf Kühn; Ingo Kowarik; Johannes Kollmann; Uwe Starfinger; Sven Bacher; Tim Blackburn; Ramiro Bustamante; Laura Celesti-Grapow; Milan Chytrý; Robert Colautti; Franz Essl; Llewellyn Foxcroft; Stephan Gollasch; Emili García-Berthou; José Hierro

    2011-01-01

    The Editorial presents the focus, scope, policies, and the inaugural issue of NeoBiota, a new open access peer-reviewed journal of biological invasions. The new journal NeoBiota is a continuation of the former NEOBIOTA publication series. The journal will deal with all aspects of invasion biology and impose no restrictions on manuscript size neither on use of color. NeoBiota implies an XML-based editorial workflow and several cutting-edge innovations in publishing and dissemination, such as s...

  14. Rate of biological invasions is lower in coastal marine protected areas.

    Science.gov (United States)

    Ardura, A; Juanes, F; Planes, S; Garcia-Vazquez, E

    2016-01-01

    Marine biological invasions threaten biodiversity worldwide. Here we explore how Marine Protected areas, by reducing human use of the coast, confer resilience against the introduction of non-indigenous species (NIS), using two very different Pacific islands as case studies for developing and testing mathematical models. We quantified NIS vectors and promoters on Vancouver (Canada) and Moorea (French Polynesia) islands, sampled and barcoded NIS, and tested models at different spatial scales with different types of interaction among vectors and between marine protection and NIS frequency. In our results NIS were negatively correlated with the dimension of the protected areas and the intensity of the protection. Small to medium geographical scale protection seemed to be efficient against NIS introductions. The likely benefit of MPAs was by exclusion of aquaculture, principally in Canada. These results emphasize the importance of marine protected areas for biodiversity conservation, and suggest that small or medium protected zones would confer efficient protection against NIS introduction. PMID:27609423

  15. Rate of biological invasions is lower in coastal marine protected areas

    Science.gov (United States)

    Ardura, A.; Juanes, F.; Planes, S.; Garcia-Vazquez, E.

    2016-01-01

    Marine biological invasions threaten biodiversity worldwide. Here we explore how Marine Protected areas, by reducing human use of the coast, confer resilience against the introduction of non-indigenous species (NIS), using two very different Pacific islands as case studies for developing and testing mathematical models. We quantified NIS vectors and promoters on Vancouver (Canada) and Moorea (French Polynesia) islands, sampled and barcoded NIS, and tested models at different spatial scales with different types of interaction among vectors and between marine protection and NIS frequency. In our results NIS were negatively correlated with the dimension of the protected areas and the intensity of the protection. Small to medium geographical scale protection seemed to be efficient against NIS introductions. The likely benefit of MPAs was by exclusion of aquaculture, principally in Canada. These results emphasize the importance of marine protected areas for biodiversity conservation, and suggest that small or medium protected zones would confer efficient protection against NIS introduction. PMID:27609423

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  17. Towards molecular computers that operate in a biological environment

    Science.gov (United States)

    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.

  18. Biological Applications of Hybrid Quantum Mechanics/Molecular Mechanics Calculation

    Directory of Open Access Journals (Sweden)

    Jiyoung Kang

    2012-01-01

    Full Text Available Since in most cases biological macromolecular systems including solvent water molecules are remarkably large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Accordingly, QM calculations that are jointed with MM calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. A UNIX-shell-based interface program connecting the quantum mechanics (QMs and molecular mechanics (MMs calculation engines, GAMESS and AMBER, was developed in our lab. The system was applied to a metalloenzyme, azurin, and PU.1-DNA complex; thereby, the significance of the environmental effects on the electronic structures of the site of interest was elucidated. Subsequently, hybrid QM/MM molecular dynamics (MD simulation using the calculation system was employed for investigation of mechanisms of hydrolysis (editing reaction in leucyl-tRNA synthetase complexed with the misaminoacylated tRNALeu, and a novel mechanism of the enzymatic reaction was revealed. Thus, our interface program can play a critical role as a powerful tool for state-of-the-art sophisticated hybrid ab initio QM/MM MD simulations of large systems, such as biological macromolecules.

  19. Using Molecular Biology to Develop Drugs for Renal Cell Carcinoma

    Science.gov (United States)

    Cowey, C. Lance; Rathmell, W. Kimryn

    2010-01-01

    Background Renal cell carcinoma is a disease marked by a unique biology which has governed it’s long history of poor response to conventional cancer treatments. The discovery of the signaling pathway activated as a result of inappropriate constitutive activation of the hypoxia inducible factors (HIF), transcription factors physiologically and transiently stabilized in response to low oxygen, has provided a primary opportunity to devise treatment strategies to target this oncogenic pathway. Objective A review of the molecular pathogenesis of renal cell cancer as well as molecularly targeted therapies, both those currently available and those in development, will be provided. In addition, trials involving combination or sequential targeted therapy are discussed. Methods A detailed review of the literature describing the molecular biology of renal cell cancer and novel therapies was performed and summarized. Results/Conclusion Therapeutics targeting angiogenesis have provided the first class of agents which provide clinical benefit in a large majority of patients and heralded renal cell carcinoma as a solid tumor paradigm for the development of novel therapeutics. Multiple strategies targeting this pathway and now other identified pathways in renal cell carcinoma provide numerous potential opportunities to make major improvements in treating this historically devastating cancer. PMID:20648240

  20. Biodiversity: molecular biological domains, symbiosis and kingdom origins

    Science.gov (United States)

    Margulis, L.

    1992-01-01

    The number of extant species of organisms is estimated to be from fewer than 3 to more than 30 x 10(6) (May, 1992). Molecular biology, comparative genetics and ultrastructural analyses provide new insights into evolutionary relationships between these species, including increasingly precise ideas of how species and higher taxa have evolved from common ancestors. Accumulation of random mutations and large macromolecular sequence change in all organisms since the Proterozoic Eon has been importantly supplemented by acquisition of inherited genomes ('symbiogenesis'). Karyotypic alterations (polyploidization and karyotypic fissioning) have been added to these other mechanisms of species origin in plants and animals during the Phanerozoic Eon. The new evolution concepts (coupled with current rapid rates of species extinction and ignorance of the extent of biodiversity) prompted this analysis of the field of systematic biology and its role in the reorganization of extant species into higher taxa. Two superkingdoms (= Domains: Prokaryotae and Eukaryotae) and five kingdoms (Monera = Procaryotae or Bacteria; Protoctista: algae, amoebae, ciliates, foraminifera, oomycetes, slime molds, etc.; Mychota: 'true' fungi; Plantae: one phylum (division) of bryophytes and nine phyla of tracheophytes; and Animalia) are recognized. Two subkingdoms comprise the monera: the great diverse lineages are Archaebacteria and Eubacteria. The criteria for classification using molecular, ultrastructural and genetic data for this scheme are mentioned. For the first time since the nineteenth century, logical, technical definitions for each group are given with their time of appearance as inferred from the fossil record in the primary scientific literature. This classification scheme, which most closely reflects the evolutionary history, molecular biology, genetics and ultrastructure of extant life, requires changes in social organization of biologists, many of whom as botanists and zoologists, still

  1. Organization of a radioisotope based molecular biology laboratory

    International Nuclear Information System (INIS)

    Polymerase chain reaction (PCR) has revolutionized the application of molecular techniques to medicine. Together with other molecular biology techniques it is being increasingly applied to human health for identifying prognostic markers and drug resistant profiles, developing diagnostic tests and genotyping systems and for treatment follow-up of certain diseases in developed countries. Developing Member States have expressed their need to also benefit from the dissemination of molecular advances. The use of radioisotopes, as a step in the detection process or for increased sensitivity and specificity is well established, making it ideally suitable for technology transfer. Many molecular based projects using isotopes for detecting and studying micro organisms, hereditary and neoplastic diseases are received for approval every year. In keeping with the IAEA's programme, several training activities and seminars have been organized to enhance the capabilities of developing Member States to employ in vitro nuclear medicine technologies for managing their important health problems and for undertaking related basic and clinical research. The background material for this publication was collected at training activities and from feedback received from participants at research and coordination meetings. In addition, a consultants' meeting was held in June 2004 to compile the first draft of this report. Previous IAEA TECDOCS, namely IAEA-TECDOC-748 and IAEA-TECDOC-1001, focused on molecular techniques and their application to medicine while the present publication provides information on organization of the laboratory, quality assurance and radio-safety. The technology has specific requirements of the way the laboratory is organized (e.g. for avoiding contamination and false positives in PCR) and of quality assurance in order to provide accurate information to decision makers. In addition while users of the technology accept the scientific rationale of using radio

  2. Research Applications of Proteolytic Enzymes in Molecular Biology

    Directory of Open Access Journals (Sweden)

    József Tőzsér

    2013-11-01

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

  3. Diagnosis of Whipple's disease using molecular biology techniques.

    Science.gov (United States)

    Cosme, Ángel; Ojeda, Evelia; Muñagorri, Ana I; Gaminde, Eduardo; Bujanda, Luis; Larzabal, Mikel; Gil, Inés

    2011-04-01

    The diagnosis of Whipple's disease (WD) is based on the existence of clinical signs and symptoms compatible with the disease and in the presence of PAS-positive diastase-resistant granules in the macrophages of the small intestine. If there is suspicion of the disease but no histological findings or only isolated extraintestinal manifestations, species-specific PCR using different sequences of the T. whippleii genome from different tissue types and biological fluids is recommended.This study reports two cases: the first patient had diarrhea and the disease was suspected after an endoscopic examination of the ileum, while the second patient had multi-systemic manifestations,particularly abdominal, thoracic, and peripheral lymphadenopathies. In both cases, the diagnosis was confirmed using molecular biology techniques to samples from the small intestine or from a retroperineal lymph node, respectively. PMID:21526877

  4. The molecular biology and diagnostics of Chlamydia trachomatis

    DEFF Research Database (Denmark)

    Birkelund, Svend

    1992-01-01

    The rapid development of biotechnological methods provides the potential of dissecting the molecular structure of microorganisms. In this review the molecular biology of chlamydia is described. The genus Chlamydia contains three species C. trachomatis, C. psittaci, and C. pneumonia which all...... negative bacteria since incubation of EB with antibodies against LPS will liberate it from the chlamydial surface. Therefore the surface localized LPS may be important for chlamydial survival. OMP1 varies between the different serovar of C. trachomatis. Several very conserved regions are separated....... Patient serum samples will recognize the chlamydial DnaK-like protein. From the determined DNA sequence the amino acid sequence was determined. It was 57% homologous to the Eschrichia coli DnaK protein. Also the GroEL-like protein is antigenic and very conserved. Factors of importance for pathogenicity...

  5. International Symposium on Insect Physiology, Biochemistry and Molecular Biology

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    @@ We are building on the success of the Sixth Chinese Insect Physiology, Biochemistry and Molecular Biology Symposium, Beijing, held in 2005. The 2005 symposium saw many Chinese and international authorities share their expertise in a broad range of insect science, including analyses of insect genomes and proteomes, functional gene expression and regulation during development, insect immunity, insect neurobiology, insect-host interactions and insect chemical communication. The coming symposium, which will be held in Shandong University,Jinan, Shandong province, September 19-22, 2007, will offer material along similar lines.

  6. A complex systems approach to computational molecular biology

    Energy Technology Data Exchange (ETDEWEB)

    Lapedes, A. [Los Alamos National Lab., NM (United States)]|[Santa Fe Inst., NM (United States)

    1993-09-01

    We report on the containing research program at Santa Fe Institute that applies complex systems methodology to computational molecular biology. Two aspects are stressed here are the use of co-evolving adaptive neutral networks for determining predictable protein structure classifications, and the use of information theory to elucidate protein structure and function. A ``snapshot`` of the current state of research in these two topics is presented, representing the present state of two major research thrusts in the program of Genetic Data and Sequence Analysis at the Santa Fe Institute.

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

    Science.gov (United States)

    Yamasaki, Mami; Kanemura, Yonehiro

    2015-01-01

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

  8. Egg Parasitoids from Pakistan as possible classical biological control agents of the invasive pest, Bagrada hilaris (Heteroptera: Pentatomidae)

    Science.gov (United States)

    The newly invasive pest stink bug, Bagrada hilaris, threatens the cole crop industry and certain ornamentals in the U.S. Without its co-evolved natural enemies, it is likely to spread from the Southwest U.S. to the east coast, requiring millions more dollars to control it. If key biological control ...

  9. Biology of the invasive ascidian Ascidiella aspersa in its native habitat: Reproductive patterns and parasite load

    Science.gov (United States)

    Lynch, Sharon A.; Darmody, Grainne; O'Dwyer, Katie; Gallagher, Mary Catherine; Nolan, Sinead; McAllen, Rob; Culloty, Sarah C.

    2016-11-01

    The European sea squirt Ascidiella aspersa is a solitary tunicate native to the northeastern Atlantic, commonly found in shallow and sheltered marine ecosystems where it is capable of forming large clumps and outcompeting other invertebrate fauna at settlement. To date, there have been relatively few studies looking at the reproductive biology and health status of this invasive species. Between 2006 and 2010 sampling of a native population took place to investigate gametogenesis and reproductive cycle and to determine the impact of settlement depth on reproduction. In addition, parasite diversity and impact was assessed. A staging system to assess reproductive development was determined. The study highlighted that from year to year the tunicate could change its reproductive strategy from single sex to hermaphrodite, with spawning possible throughout the year. Depth did not impact on sex determination, however, gonad maturation and spawning occurred earlier in individuals in deeper waters compared to shallow depth and it also occurred later in A. aspersa at sites further away from the open sea. Four significant parasite groups including eugregarines, ciliates, trematodes and turbellarians were detected and prevalence of parasite infections increased in A. aspersa at sites with a reduced water flow rate. This study demonstrates the high biotic potential of this ascidian bioinvader to have a negative impact on native fauna in an introduced ecosystem, due to its highly efficient reproductive and resource allocation strategies. Artificial structures such as mooring lines can harbour large aggregations of A. aspersa, however, these manmade habitats may facilitate the colonisation and establishment of this invasive species in the benthos. Additionally, the parasite communities that A. aspersa harbour may also exacerbate its negative impact, both ecologically and economically, in an introduced area by possibly leading to the emergence of new disease in native species i

  10. Errant life, molecular biology, and biopower: Canguilhem, Jacob, and Foucault.

    Science.gov (United States)

    Talcott, Samuel

    2014-01-01

    This paper considers the theoretical circumstances that urged Michel Foucault to analyse modern societies in terms of biopower. Georges Canguilhem's account of the relations between science and the living forms an essential starting point for Foucault's own later explorations, though the challenges posed by the molecular revolution in biology and François Jacob's history of it allowed Foucault to extend and transform Canguilhem's philosophy of error. Using archival research into his 1955-1956 course on "Science and Error," I show that, for Canguilhem, it is inauthentic to treat a living being as an error, even if living things are capable of making errors in the domain of knowledge. The emergent molecular biology in the 1960s posed a grave challenge, however, since it suggested that individuals could indeed be errors of genetic reproduction. The paper discusses how Canguilhem and Foucault each responded to this by examining, among other texts, their respective reviews of Jacob's The Logic of the Living. For Canguilhem this was an opportunity to reaffirm the creativity of life in the living individual, which is not a thing to be evaluated, but the source of values. For Foucault, drawing on Jacob's work, this was the opportunity to develop a transformed account of valuation by posing biopower as the DNA of society. Despite their disagreements, the paper examines these three authors as different iterations of a historical epistemology attuned to errancy, error, and experimentation.

  11. How phenotypic plasticity made its way into molecular biology

    Indian Academy of Sciences (India)

    Michel Morange

    2009-10-01

    Phenotypic plasticity has been fashionable in recent years. It has never been absent from the studies of evolutionary biologists, although the availability of stable animal models has limited its role. Although opposed by the reductionist and deterministic approach of molecular biology, phenotypic plasticity has nevertheless recently made its way into this discipline, in particular through the limits of the molecular description. Its resurrection has been triggered by a small group of theoreticians, the rise of epigenetic descriptions and the publicized discovery of stem cell plasticity. The notion of phenotypic plasticity remains vague. History shows that too strong a belief in plasticity can be an obstacle to the development of biology. Two important questions are still pending: the link between the different forms of plasticity present at different levels of organization, and the relation, if any, between the modular organization of organisms and phenotypic plasticity. Future research will help to discriminate between possible and actual mechanisms of phenotypic plasticity, and to give phenotypic plasticity its real place in the living world.

  12. Obstructive renal injury: from fluid mechanics to molecular cell biology

    Directory of Open Access Journals (Sweden)

    Alvaro C Ucero

    2010-04-01

    Full Text Available Alvaro C Ucero1,*, Sara Gonçalves2,*, Alberto Benito-Martin1, Beatriz Santamaría1, Adrian M Ramos1, Sergio Berzal1, Marta Ruiz-Ortega1, Jesus Egido1, Alberto Ortiz11Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Fundación Renal Iñigo Alvarez de Toledo, Madrid, Spain; 2Nefrologia e Transplantação Renal, Hospital de Santa Maria EPE, Lisbon, Portugal *Both authors contributed equally to the manuscriptAbstract: Urinary tract obstruction is a frequent cause of renal impairment. The physiopathology of obstructive nephropathy has long been viewed as a mere mechanical problem. However, recent advances in cell and systems biology have disclosed a complex physiopathology involving a high number of molecular mediators of injury that lead to cellular processes of apoptotic cell death, cell injury leading to inflammation and resultant fibrosis. Functional studies in animal models of ureteral obstruction using a variety of techniques that include genetically modified animals have disclosed an important role for the renin-angiotensin system, transforming growth factor-β1 (TGF-β1 and other mediators of inflammation in this process. In addition, high throughput techniques such as proteomics and transcriptomics have identified potential biomarkers that may guide clinical decision-making.Keywords: urinary tract obstruction, renal injury, fluid mechanics, molecular cell biology

  13. Developing protein documentaries and other multimedia presentations for molecular biology.

    Science.gov (United States)

    Quinn, G; Wang, H P; Martinez, D; Bourne, P E

    1999-01-01

    Computer-based multimedia technology for distance learning and research has come of age--the price point is acceptable, domain experts using off-the-shelf software can prepare compelling materials, and the material can be efficiently delivered via the Internet to a large audience. While not presenting any new scientific results, this paper outlines experiences with a variety of commercial and free software tools and the associated protocols we have used to prepare protein documentaries and other multimedia presentations relevant to molecular biology. A protein documentary is defined here as a description of the relationship between structure and function in a single protein or in a related family of proteins. A description using text and images which is further enhanced by the use of sound and interactive graphics. Examples of documentaries prepared to describe cAMP dependent protein kinase, the founding structural member of the protein kinase family for which there is now over 40 structures can be found at http://franklin.burnham-inst.org/rcsb. A variety of other prototype multimedia presentations for molecular biology described in this paper can be found at http://fraklin.burnham-inst.org. PMID:10380212

  14. On the shoulders of giants: Molecular Biology in Public Health

    Directory of Open Access Journals (Sweden)

    Carmine Melino

    2005-03-01

    Full Text Available

    We accepted with great pleasure the invitation by professor Walter Ricciardi,our friend and colleague, to write an editorial in order to introduce this special issue dedicated to Molecular Biology in Hygiene. We are delighted for two connected reasons.

    First, Carmine,as a former professor of Hygiene,has passed his concepts of Hygiene on to his family and, despite significant difficulties, keeps working on the problems of preventive medicine in the work environment and in geriatrics. Second, Gerry, raised in an environment of hygienists, has dedicated all his professional efforts to Molecular Biology. As these two distinct experiences have constantly mixed within our family over time, we appreciate the promiscuous intermingling of these two disciplines in this thematic issue.

    The result is a useful common effort aiming at understanding the problems of diseases in the work environment and in the human environment in general.

    These problems have a profound social meaning, for which it is necessary to create an essential collaboration with scientific research.

    This is the only way to benefit human society.

  15. Different Responses of an Invasive Clonal Plant Wedelia trilobata and its Native Congener to Gibberellin: Implications for Biological Invasion.

    Science.gov (United States)

    Dai, Zhi-Cong; Fu, Wei; Qi, Shan-Shan; Zhai, De-Li; Chen, Si-Chong; Wan, Ling-Yun; Huang, Ping; Du, Dao-Lin

    2016-02-01

    The invasive clonal plant Wedelia trilobata contains higher levels of ent-kaurane diterpenes, which are precursors of gibberellins (GAs), and higher rates of clonal growth than its native congener W. chinensis in invaded habitats. We hypothesized that the higher levels of endogenous GAs facilitate greater ramet growth in W. trilobata compared with W. chinensis. We quantified endogenous levels of GA1+3 in the two species and compared their growth responses to the changes of endogenous and exogenous GA3 by using short-term and long-term hydroponics experiments. After a period of homogeneous cultivation, levels of endogenous GA1+3 were higher in W. trilobata than in W. chinensis. The reduction of endogenous GAs repressed the emergence of adventitious roots and the growth of W. trilobata in the initial cultivation stage, and inhibited its shoot elongation and biomass. Levels of endogenous GA1+3 were positively correlated with the length of shoots and adventitious roots of W. trilobata. Adventitious roots of W. trilobata also emerged earlier and grew faster when treated with exogenous GA3. In contrast, exogenous GA3 treatment inhibited the length of adventitious roots in W. chinensis, and levels of endogenous GA1+3 did not correlate with shoot or adventitious root length. Our study suggests that GAs accelerate the rapid clonal growth of W. trilobata, more than that of its native congener W. chinensis, illustrating the relationship between plant hormones and the clonal growth of invasive plants. These findings are important for understanding the mechanisms associated with the invasiveness of clonal plants and their potential management. PMID:26879680

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

    Directory of Open Access Journals (Sweden)

    Rietman Edward A

    2011-06-01

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

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

    Science.gov (United States)

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

    2011-01-01

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

  18. The Impact of Collective Molecular Dynamics on Physiological and Biological Functionalities of Artificial and Biological Membranes

    Science.gov (United States)

    Rheinstadter, Maikel

    2008-03-01

    We use neutron, X-ray and light scattering techniques to determine dynamical and structural properties of artificial and biological membranes. The combination of various techniques enlarges the window to length scales from the nearest-neighbor distances of lipid molecules to more than 10-6m, covering time scales from about 0.1 ps to 1 s. The main research objective is to quantify collective molecular fluctuations in these systems and to establish relationships to physiological and biological functions of the bilayers, such as transmembrane transport. The motivation for this project is twofold: 1) By understanding fundamental properties of bilayers at the microscopic and mesoscopic level, we aim to tailor membranes with specific properties such as permeability and elasticity. 2) By relating dynamical fluctuations to physiological and biological functions, we can gain a deeper understanding of the bilayers on a molecular scale that may help optimizing the transmembrane transport of certain drugs. We show how bilayer permeability, elasticity and inter protein excitations can be determined from the experiments. M.C. Rheinstädter et al., Phys. Rev. Lett. 93, 108107 (2004); Phys. Rev. Lett. 97, 048103 (2006); Phys. Rev. E 75, 011907 (2007);J. Vac. Soc. Technol. A 24, 1191 (2006).

  19. Exploiting Molecular Biology by Time-Resolved Fluorescence Imaging

    Science.gov (United States)

    Müller, Francis; Fattinger, Christof

    Many contemporary biological investigations rely on highly sensitive in vitro assays for the analysis of specific molecules in biological specimens, and the main part of these assays depends on high-sensitivity fluorescence detection techniques for the final readout. The analyzed molecules and molecular interactions in the specimen need to be detected in the presence of other highly abundant biomolecules, while the analyzed molecules themselves are only present at nano-, pico-, or even femtomolar concentration.A short scientific rationale of fluorescence is presented. It emphasizes the use of fluorescent labels for sensitive assays in life sciences and specifies the main properties of an ideal fluorophore. With fluorescence lifetimes in the microsecond range and fluorescence quantum yield of 0.4 some water soluble complexes of Ruthenium like modified Ru(sulfobathophenanthroline) complexes fulfill these properties. They are outstanding fluorescent labels for ultrasensitive assays as illustrated in two examples, in drug discovery and in point of care testing.We discuss the fundamentals and the state-of-the-art of the most sensitive time-gated fluorescence assays. We reflect on how the imaging devices currently employed for readout of these assays might evolve in the future. Many contemporary biological investigations rely on highly sensitive in vitro assays for the analysis of specific molecules in biological specimens, and the main part of these assays depends on high-sensitivity fluorescence detection techniques for the final readout. The analyzed molecules and molecular interactions in the specimen need to be detected in the presence of other highly abundant biomolecules, while the analyzed molecules themselves are only present at nano-, pico-, or even femtomolar concentration.A short scientific rationale of fluorescence is presented. It emphasizes the use of fluorescent labels for sensitive assays in life sciences and specifies the main properties of an ideal

  20. Implementation and Assessment of a Molecular Biology and Bioinformatics Undergraduate Degree Program

    Science.gov (United States)

    Pham, Daphne Q. -D.; Higgs, David C.; Statham, Anne; Schleiter, Mary Kay

    2008-01-01

    The Department of Biological Sciences at the University of Wisconsin-Parkside has developed and implemented an innovative, multidisciplinary undergraduate curriculum in Molecular Biology and Bioinformatics (MBB). The objective of the MBB program is to give students a hands-on facility with molecular biology theories and laboratory techniques, an…

  1. Traffic phenomena in biology: from molecular motors to organisms

    CERN Document Server

    Chowdhury, D; Nishinari, K; Chowdhury, Debashish; Schadschneider, Andreas; Nishinari, Katsuhiro

    2007-01-01

    Traffic-like collective movements are observed at almost all levels of biological systems. Molecular motor proteins like, for example, kinesin and dynein, which are the vehicles of almost all intra-cellular transport in eukayotic cells, sometimes encounter traffic jam that manifests as a disease of the organism. Similarly, traffic jam of collagenase MMP-1, which moves on the collagen fibrils of the extracellular matrix of vertebrates, has also been observed in recent experiments. Traffic-like movements of social insects like ants and termites on trails are, perhaps, more familiar in our everyday life. Experimental, theoretical and computational investigations in the last few years have led to a deeper understanding of the generic or common physical principles involved in these phenomena. In particular, some of the methods of non-equilibrium statistical mechanics, pioneered almost a hundred years ago by Einstein, Langevin and others, turned out to be powerful theoretical tools for quantitative analysis of mode...

  2. 2. Molecular Biology as a Tool in Cancer Epidemiology

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@There can be little doubt that we are entering a new era in our understanding of the origins of human cancer. Unfortunately from the point of view of the cancer epidemiology community, some of the more recent advances in the molecular biology of cancer (once fully assimilated) will tend to make the talk of the up-to-date cancer epidemiologist a great deal less straightforward than many of us had previously envisaged it to be, There may still be a few cancers that will prove to result from only a few distinctive types of mutation in a relatively small number of genes, but I strongly suspect that the great majority of human cancers that we wish to study will prove to have their origins in a complex set of DNA changes whose precise

  3. Above-belowground interactions govern the course and impact of biological invasions

    DEFF Research Database (Denmark)

    Vestergård, Mette; Rønn, Regin; Ekelund, Flemming

    2015-01-01

    in an evolutionary and ecological context; in the case of invasive plants, we must have a major focus on above-belowground interactions. Thus, we discuss different theories that have been proposed to explain the course of invasions through interactions between plants and soil organisms. Further, a thorough analysis......Introduction of exotic organisms that subsequently become invasive is considered a serious threat to global biodiversity, and both scientists and nature-conservationists attempt to find explanations and means to meet this challenge. This requires a thorough analysis of the invasion phenomenon...... of invasion must include a temporal context. Invasions will typically include an initial acute phase, where the invader expands its territory and a later chronic phase where equilibrium is re-established. Many studies fail to make this distinction, which is unfortunate as it makes it impossible to thoroughly...

  4. Escherichia coli and the French School of Molecular Biology.

    Science.gov (United States)

    Ullmann, Agnes

    2010-09-01

    André Lwoff, Jacques Monod, and François Jacob, the leaders of the French school of molecular biology, greatly contributed between 1937 and 1965 to its development and triumph. The main discovery of Lwoff was the elucidation of the mechanism of bacteriophage induction, the phenomenon of lysogeny, that led to the model of genetic regulation uncovered later by Jacob and Monod. Working on bacterial growth, Monod discovered in 1941 the phenomenon of diauxy and uncovered the nature of enzyme induction. By combining genetic and biochemical approaches, Monod brought to light the structure and functions of the Escherichia coli lactose system, comprising the genes necessary for lactose metabolism, i.e., β-galactosidase and lactose permease, a pump responsible for accumulation of galactosides into the cells. An additional genetic factor (the i gene) determines the inducibility and constitutivity of enzyme synthesis. Around the same time, François Jacob and Elie Wollman dissected the main events of bacterial conjugation that enabled them to construct a map of the E. coli chromosome and to demonstrate its circularity. The genetic analysis of the lactose system led Monod and Jacob to elucidate the mechanism of the regulation of gene expression and to propose the operon model: a unit of coordinate transcription. One of the new concepts that emerged from the operon model was messenger RNA. In 1963, Monod developed one of the most elegant concepts of molecular biology, the theory of allostery. In 1965, Lwoff, Monod and Jacob were awarded the Nobel Prize in Physiology or Medicine.

  5. Above-belowground interactions govern the course and impact of biological invasions.

    Science.gov (United States)

    Vestergård, Mette; Rønn, Regin; Ekelund, Flemming

    2015-01-01

    Introduction of exotic organisms that subsequently become invasive is considered a serious threat to global biodiversity, and both scientists and nature-conservationists attempt to find explanations and means to meet this challenge. This requires a thorough analysis of the invasion phenomenon in an evolutionary and ecological context; in the case of invasive plants, we must have a major focus on above-belowground interactions. Thus, we discuss different theories that have been proposed to explain the course of invasions through interactions between plants and soil organisms. Further, a thorough analysis of invasion must include a temporal context. Invasions will typically include an initial acute phase, where the invader expands its territory and a later chronic phase where equilibrium is re-established. Many studies fail to make this distinction, which is unfortunate as it makes it impossible to thoroughly understand the invasion of focus. Thus, we claim that invasions fall into two broad categories. Some invasions irreversibly change pools and pathways of matter and energy in the invaded system; even if the abundance of the invader is reduced or it is completely removed, the system will not return to its former state. We use earthworm invasion in North America as a particular conspicuous example of invasive species that irreversibly change ecosystems. However, invasions may also be reversible, where the exotic organism dominates the system for a period, but in the longer term it either disappears, declines or its negative impact decreases. If the fundamental ecosystem structure and flows of energy and matter have not been changed, the system will return to a state not principally different from the original. PMID:25854693

  6. Molecular Biology and Infection of Hepatitis E Virus

    Science.gov (United States)

    Nan, Yuchen; Zhang, Yan-Jin

    2016-01-01

    Hepatitis E virus (HEV) is a viral pathogen transmitted primarily via fecal-oral route. In humans, HEV mainly causes acute hepatitis and is responsible for large outbreaks of hepatitis across the world. The case fatality rate of HEV-induced hepatitis ranges from 0.5 to 3% in young adults and up to 30% in infected pregnant women. HEV strains infecting humans are classified into four genotypes. HEV strains from genotypes 3 and 4 are zoonotic, whereas those from genotypes 1 and 2 have no known animal reservoirs. Recently, notable progress has been accomplished for better understanding of HEV biology and infection, such as chronic HEV infection, in vitro cell culture system, quasi-enveloped HEV virions, functions of the HEV proteins, mechanism of HEV antagonizing host innate immunity, HEV pathogenesis and vaccine development. However, further investigation on the cross-species HEV infection, host tropism, vaccine efficacy, and HEV-specific antiviral strategy is still needed. This review mainly focuses on molecular biology and infection of HEV and offers perspective new insight of this enigmatic virus. PMID:27656178

  7. Low angle neutron data acquisition system for molecular biology

    International Nuclear Information System (INIS)

    The low angle spectrometer system utilizing a 2-dimensional position sensitive counter was designed to accommodate a variety of experiments in molecular biology requiring good low angle resolution. Biological structures requiring low angle analysis techniques fall into two groups: non-ordered systems (proteins or protein complexes in solution) and ordered systems with large spacings like muscle, collagen, and membranes. For structural investigations into such systems, data are ideally needed to a low scattering angle of 0.20 at 4.5 A or a minimum Q of 0.005 A-1 (Q = theta . 2π/lambda). Depending on the type of structure, data often extend to the high angle region, say 300. Apart from the low angle requirements, the spectrometer has to have good resolution to resolve diffraction peaks from samples with crystal spacings up to 1000 A or even larger. While it is desirable to build a spectrometer to such scattering conditions, given reactor conditions might not permit this and compromises have to be made between flux, resolution and lowest angle. The low angle spectrometer described here was designed to be used at the HFBR neutron beam pipe working at approximately 4.2 A or at the H4 satellite station working at 2.4 A

  8. Molecular Sociology: Further Insights from Biological and Environmental Aspects

    Directory of Open Access Journals (Sweden)

    Ahed Jumah Mahmoud Al-Khatib

    2015-11-01

    Full Text Available The present study expanded our previous study in which features of molecular sociology were mentioned. In this study, we added the microbial dimensions in which it is thought that religiosity may be impacted by microbes that manipulate brains to create better conditions for their existence. This hypothesis is called “biomeme hypothesis”. We talked about other environmental impacts on human behaviors through three studies in which exposure to lead caused violent behaviors ending with arresting in prisons. By conclusion, the present study has expanded our horizon about interferences on various levels including biological and environmental impacts with our behaviors. Although we are convinced that behavior is a very diverse and complex phenomenon and cannot be understood within certain frame as either biologically or environmentally, but further new insights are possible to participate in better understanding of human behaviors. Many behaviors have their roots in religion, and we showed how religious rituals may be affected by some microbes that make to form a microenvironment within the host for microbial benefits.

  9. Systems biology analysis of Brucella infected Peyer's patch reveals rapid invasion with modest transient perturbations of the host transcriptome.

    Directory of Open Access Journals (Sweden)

    Carlos A Rossetti

    Full Text Available Brucella melitensis causes the most severe and acute symptoms of all Brucella species in human beings and infects hosts primarily through the oral route. The epithelium covering domed villi of jejunal-ileal Peyer's patches is an important site of entry for several pathogens, including Brucella. Here, we use the calf ligated ileal loop model to study temporal in vivo Brucella-infected host molecular and morphological responses. Our results document Brucella bacteremia occurring within 30 min after intraluminal inoculation of the ileum without histopathologic traces of lesions. Based on a system biology Dynamic Bayesian Network modeling approach (DBN of microarray data, a very early transient perturbation of the host enteric transcriptome was associated with the initial host response to Brucella contact that is rapidly averted allowing invasion and dissemination. A detailed analysis revealed active expression of Syndecan 2, Integrin alpha L and Integrin beta 2 genes, which may favor initial Brucella adhesion. Also, two intestinal barrier-related pathways (Tight Junction and Trefoil Factors Initiated Mucosal Healing were significantly repressed in the early stage of infection, suggesting subversion of mucosal epithelial barrier function to facilitate Brucella transepithelial migration. Simultaneously, the strong activation of the innate immune response pathways would suggest that the host mounts an appropriate protective immune response; however, the expression of the two key genes that encode innate immunity anti-Brucella cytokines such as TNF-α and IL12p40 were not significantly changed throughout the study. Furthermore, the defective expression of Toll-Like Receptor Signaling pathways may partially explain the lack of proinflammatory cytokine production and consequently the absence of morphologically detectable inflammation at the site of infection. Cumulatively, our results indicate that the in vivo pathogenesis of the early infectious process

  10. Molecular codes in biological and chemical reaction networks.

    Directory of Open Access Journals (Sweden)

    Dennis Görlich

    Full Text Available Shannon's theory of communication has been very successfully applied for the analysis of biological information. However, the theory neglects semantic and pragmatic aspects and thus cannot directly be applied to distinguish between (bio- chemical systems able to process "meaningful" information from those that do not. Here, we present a formal method to assess a system's semantic capacity by analyzing a reaction network's capability to implement molecular codes. We analyzed models of chemical systems (martian atmosphere chemistry and various combustion chemistries, biochemical systems (gene expression, gene translation, and phosphorylation signaling cascades, an artificial chemistry, and random reaction networks. Our study suggests that different chemical systems possess different semantic capacities. No semantic capacity was found in the model of the martian atmosphere chemistry, the studied combustion chemistries, and highly connected random networks, i.e. with these chemistries molecular codes cannot be implemented. High semantic capacity was found in the studied biochemical systems and in random reaction networks where the number of second order reactions is twice the number of species. We conclude that our approach can be applied to evaluate the information processing capabilities of a chemical system and may thus be a useful tool to understand the origin and evolution of meaningful information, e.g. in the context of the origin of life.

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

    Institute of Scientific and Technical Information of China (English)

    REN Yi-jin

    2005-01-01

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

  12. Protocols for assessing radiofrequency interactions with gold nanoparticles and biological systems for non-invasive hyperthermia cancer therapy.

    Science.gov (United States)

    Corr, Stuart J; Cisneros, Brandon T; Green, Leila; Raoof, Mustafa; Curley, Steven A

    2013-08-28

    Cancer therapies which are less toxic and invasive than their existing counterparts are highly desirable. The use of RF electric-fields that penetrate deep into the body, causing minimal toxicity, are currently being studied as a viable means of non-invasive cancer therapy. It is envisioned that the interactions of RF energy with internalized nanoparticles (NPs) can liberate heat which can then cause overheating (hyperthermia) of the cell, ultimately ending in cell necrosis. In the case of non-biological systems, we present detailed protocols relating to quantifying the heat liberated by highly-concentrated NP colloids. For biological systems, in the case of in vitro experiments, we describe the techniques and conditions which must be adhered to in order to effectively expose cancer cells to RF energy without bulk media heating artifacts significantly obscuring the data. Finally, we give a detailed methodology for in vivo mouse models with ectopic hepatic cancer tumors.

  13. The molecular biology of ear development - “Twenty years are nothing”#

    OpenAIRE

    Giraldez, Fernando; FRITZSCH, BERND

    2007-01-01

    Views of classical biological problems changed dramatically with the rise of molecular biology as a common framework. It was indeed the new language of life sciences. Molecular biology increasingly moved us towards a unified view of developmental genetics as ideas and techniques were imported to vertebrates from other biological systems where genetics was in a more advanced state. The ultimate advance has been the ability to actually perform genetic manipulations in vertebrate organisms that ...

  14. STRUCTURAL BIOLOGY AND MOLECULAR MEDICINE RESEARCH PROGRAM (LSBMM)

    International Nuclear Information System (INIS)

    The UCLA-DOE Institute of Genomics and Proteomics is an organized research unit of the University of California, sponsored by the Department of Energy through the mechanism of a Cooperative Agreement. Today the Institute consists of 10 Principal Investigators and 7 Associate Members, developing and applying technologies to promote the biological and environmental missions of the Department of Energy, and 5 Core Technology Centers to sustain this work. The focus is on understanding genomes, pathways and molecular machines in organisms of interest to DOE, with special emphasis on developing enabling technologies. Since it was founded in 1947, the UCLA-DOE Institute has adapted its mission to the research needs of DOE and its progenitor agencies as these research needs have changed. The Institute started as the AEC Laboratory of Nuclear Medicine, directed by Stafford Warren, who later became the founding Dean of the UCLA School of Medicine. In this sense, the entire UCLA medical center grew out of the precursor of our Institute. In 1963, the mission of the Institute was expanded into environmental studies by Director Ray Lunt. I became the third director in 1993, and in close consultation with David Galas and John Wooley of DOE, shifted the mission of the Institute towards genomics and proteomics. Since 1993, the Principal Investigators and Core Technology Centers are entirely new, and the Institute has separated from its former division concerned with PET imaging. The UCLA-DOE Institute shares the space of Boyer Hall with the Molecular Biology Institute, and assumes responsibility for the operation of the main core facilities. Fig. 1 gives the organizational chart of the Institute. Some of the benefits to the public of research carried out at the UCLA-DOE Institute include the following: The development of publicly accessible, web-based databases, including the Database of Protein Interactions, and the ProLinks database of genomicly inferred protein function linkages

  15. STRUCTURAL BIOLOGY AND MOLECULAR MEDICINE RESEARCH PROGRAM (LSBMM)

    Energy Technology Data Exchange (ETDEWEB)

    Eisenberg, David S.

    2008-07-15

    The UCLA-DOE Institute of Genomics and Proteomics is an organized research unit of the University of California, sponsored by the Department of Energy through the mechanism of a Cooperative Agreement. Today the Institute consists of 10 Principal Investigators and 7 Associate Members, developing and applying technologies to promote the biological and environmental missions of the Department of Energy, and 5 Core Technology Centers to sustain this work. The focus is on understanding genomes, pathways and molecular machines in organisms of interest to DOE, with special emphasis on developing enabling technologies. Since it was founded in 1947, the UCLA-DOE Institute has adapted its mission to the research needs of DOE and its progenitor agencies as these research needs have changed. The Institute started as the AEC Laboratory of Nuclear Medicine, directed by Stafford Warren, who later became the founding Dean of the UCLA School of Medicine. In this sense, the entire UCLA medical center grew out of the precursor of our Institute. In 1963, the mission of the Institute was expanded into environmental studies by Director Ray Lunt. I became the third director in 1993, and in close consultation with David Galas and John Wooley of DOE, shifted the mission of the Institute towards genomics and proteomics. Since 1993, the Principal Investigators and Core Technology Centers are entirely new, and the Institute has separated from its former division concerned with PET imaging. The UCLA-DOE Institute shares the space of Boyer Hall with the Molecular Biology Institute, and assumes responsibility for the operation of the main core facilities. Fig. 1 gives the organizational chart of the Institute. Some of the benefits to the public of research carried out at the UCLA-DOE Institute include the following: The development of publicly accessible, web-based databases, including the Database of Protein Interactions, and the ProLinks database of genomicly inferred protein function linkages

  16. MODEL ORGANISMS USED IN MOLECULAR BIOLOGY OR MEDICAL RESEARCH

    Directory of Open Access Journals (Sweden)

    Pandey Govind

    2011-11-01

    Full Text Available A model organism is a non-human species that is studied to understand specific biological phenomena with the expectation that investigations made in the organism model will provide insight into the workings of other organisms. The model organisms are widely used to explore potential causes and treatments for human as well as animal diseases when experiments on animals or humans would be unfeasible or considered less ethical. Studying model organisms may be informative, but care must be taken when generalizing from one organism to another. Often, model organisms are chosen on the basis that they are amenable to experimental manipulation. When researchers look for an organism to use in their studies, they look for several traits. Among these are size, generation time, accessibility, manipulation, genetics, conservation of mechanisms and potential economic benefit. As comparative molecular biology has become more common, some researchers have sought model organisms from a wider assortment of lineages on the tree of life. There are many model organisms, such as viruses (e.g., Phage lambda virus, Tobacco mosaic virus, etc., bacteria (e.g., Bacillus subtilis, Escherichia coli, Pseudomonas fluorescens, Vibrio fischeri, etc., algae (e.g., Chlamydomonas reinhardtii, Emiliania huxleyi, etc., molds (e.g., Aspergillus nidulans, Neurospora crassa, etc., yeasts (e.g., Saccharomyces cerevisiae, Ustilago maydis, etc., higher plants (e.g., Arabidopsis thaliana, Lemna gibba, Lotus japonicus, Nicotiana tabaccum, Oryza sativa, Physcomitrella patens, Zea mays, etc. and animals (e.g., Caenorhabditis elegans, guinea pig, hamster, mouse, rat, cat, chicken, dog, frog, Hydra, Drosophila melanogaster fruit fly, fish, etc..

  17. Molecular biology of Homo sapiens: Abstracts of papers presented at the 51st Cold Spring Harbor symposium on quantitative biology

    International Nuclear Information System (INIS)

    This volume contains abstracts of papers presented at the 51st Cold Springs Harbor Symposium on Quantitative Biology. The topic for this meeting was the ''Molecular Biology of Homo sapiens.'' Sessions were entitled Human Gene Map, Human Cancer Genes, Genetic Diagnosis, Human Evolution, Drugs Made Off Human Genes, Receptors, and Gene Therapy. (DT)

  18. Molecular biology of Homo sapiens: Abstracts of papers presented at the 51st Cold Spring Harbor symposium on quantitative biology

    Energy Technology Data Exchange (ETDEWEB)

    Watson, J.D.; Siniscalco, M.

    1986-01-01

    This volume contains abstracts of papers presented at the 51st Cold Springs Harbor Symposium on Quantitative Biology. The topic for this meeting was the ''Molecular Biology of Homo sapiens.'' Sessions were entitled Human Gene Map, Human Cancer Genes, Genetic Diagnosis, Human Evolution, Drugs Made Off Human Genes, Receptors, and Gene Therapy. (DT)

  19. Biological control of sentinel egg masses of the exotic invasive stink bug halyomorpha halys (Stål) in Mid-Atlantic USA ornamental landscapes

    Science.gov (United States)

    Biological invasions have far reaching effects on native plant and arthropod communities. This study evaluated the effect of natural enemies on eggs of the exotic invasive stink bug Halyomorpha halys (Stål) in experimental plots comprising species pairs of 16 ornamental trees and shrub genera from e...

  20. The Human Release Hypothesis for biological invasions: human activity as a determinant of the abundance of invasive plant species [v1; ref status: indexed, http://f1000r.es/33c

    Directory of Open Access Journals (Sweden)

    Heike Zimmermann

    2014-05-01

    Full Text Available Research on biological invasions has increased rapidly over the past 30 years, generating numerous explanations of how species become invasive. While the mechanisms of invasive species establishment are well studied, the mechanisms driving abundance patterns (i.e. patterns of population density remain poorly understood. Invasive species typically have higher abundances in their new environments than in their native ranges, and patterns of invasive species abundance differ between invaded regions. To explain differences in invasive species abundance, we propose the Human Release Hypothesis. In parallel to the established Enemy Release Hypothesis, this hypothesis states that the abundance of invasive species may be partly explained by the level of human activity or landscape maintenance, with intermediate levels of human activity providing optimal conditions for high abundance. The Human Release Hypothesis does not negate other important drivers of species invasions, but rather should be considered as a potentially important additional or complementary mechanism. We illustrate the hypothesis via a case study on an invasive rose species, and hypothesize which locations globally may be most likely to support high abundances of invasive species. We propose that more extensive empirical work on the Human Release Hypothesis could be useful to test its general applicability.

  1. The roles of integration in molecular systems biology.

    Science.gov (United States)

    O'Malley, Maureen A; Soyer, Orkun S

    2012-03-01

    A common way to think about scientific practice involves classifying it as hypothesis- or data-driven. We argue that although such distinctions might illuminate scientific practice very generally, they are not sufficient to understand the day-to-day dynamics of scientific activity and the development of programmes of research. One aspect of everyday scientific practice that is beginning to gain more attention is integration. This paper outlines what is meant by this term and how it has been discussed from scientific and philosophical points of view. We focus on methodological, data and explanatory integration, and show how they are connected. Then, using some examples from molecular systems biology, we will show how integration works in a range of inquiries to generate surprising insights and even new fields of research. From these examples we try to gain a broader perspective on integration in relation to the contexts of inquiry in which it is implemented. In today's environment of data-intensive large-scale science, integration has become both a practical and normative requirement with corresponding implications for meta-methodological accounts of scientific practice. We conclude with a discussion of why an understanding of integration and its dynamics is useful for philosophy of science and scientific practice in general.

  2. Do biological molecular machines act as Maxwell's demons?

    CERN Document Server

    Kurzynski, Michal

    2014-01-01

    In the intention of its creator, Maxwell's demon was thought to be an intelligent being able to perform work at the expense of the entropy reduction of a closed operating system. The perplexing notion of the demon's intelligence was formalized in terms of the memory and information processing by Szilard and followers. A non-informational formulation of the problem was proposed by Smoluchowski and popularized by Feynman as the ratchet and pawl machine. A. F. Huxley and followers adopted this way of thinking to propose numerous ratchet mechanisms of the protein molecular machines action, but no entropy reduction takes place for these models. More general models of protein dynamics have been proposed with a number of intramolecular states organized in a network of stochastic transitions. Here, a computer realization of such a network is investigated, displaying, like networks of the systems biology, a transition from the fractal organization on a small length-scale to the small-world organization on the large le...

  3. Diagnosis of Mycobacterium tuberculosis using molecular biology technology

    Institute of Scientific and Technical Information of China (English)

    Juan Garberi; Jorge Labrador; Federico Garberi; Juan Ezequiel Garberi; Julian Peneipil; Miguel Garberi; Luis Scigliano; Alcides Troncoso

    2011-01-01

    Objective:To present an integrated molecular biology dedicated system for tuberculosis diagnosis.Methods:One hundred and five sputum specimens from patients strongly suspected by clinical parameters of tuberculosis were studied by Ziehl-Neelsen staining, by cultivation on solid medium and by a balanced heminested fluorometricPCR system (OrangeG3TB) that could preserve worker safety and produce a rather pure material free of potential inhibitors. DNA amplification was performed in a low cost tuberculosis termocycler-fluorometer. Produced double stranded DNA was flurometrically detected. The whole reaction was conducted in one single tube which would not be opened after adding the processed sample in order to minimize the risk of cross contamination with amplicons.Results: The assay was able to detect30 bacillus per sample mL with99.8% interassay variation coefficient.PCR was positive in23 (21.9%) tested samples (21 of them were smear negative). In our study it showed a preliminary sensitivity of 94.5% for sputum and an overall specificity of98.7%.Conclusions:Total run time of the test is4 h with2.5 real working time. AllPCR positive samples are also positive by microbiological culture and clinical criteria. Results show that it could be a very useful tool to increase detection efficiency of tuberculosis disease in low bacilus load samples. Furthermore, its low cost and friendly using make it feasible to run in poor regions.

  4. The Molecular Biology of Feline Immunodeficiency Virus (FIV

    Directory of Open Access Journals (Sweden)

    Andrew M. L. Lever

    2011-11-01

    Full Text Available Feline immunodeficiency virus (FIV is widespread in feline populations and causes an AIDS-like illness in domestic cats. It is highly prevalent in several endangered feline species. In domestic cats FIV infection is a valuable small animal model for HIV infection. In recent years there has been a significant increase in interest in FIV, in part to exploit this, but also because of the potential it has as a human gene therapy vector. Though much less studied than HIV there are many parallels in the replication of the two viruses, but also important differences and, despite their likely common origin, the viruses have in some cases used alternative strategies to overcome similar problems. Recent advances in understanding the structure and function of FIV RNA and proteins and their interactions has enhanced our knowledge of FIV replication significantly, however, there are still many gaps. This review summarizes our current knowledge of FIV molecular biology and its similarities with, and differences from, other lentiviruses.

  5. RT-PCR Protocols - Methods in Molecular Biology

    Directory of Open Access Journals (Sweden)

    Manuela Monti

    2011-03-01

    Full Text Available “The first record I have of it, is when I made a computer file which I usually did whenever I had an idea, that would have been on the Monday when I got back, and I called it Chain Reaction.POL, meaning polymerase. That was the identifier for it and later I called the thing the Polymerase Chain Reaction, which a lot of people thought was a dumb name for it, but it stuck, and it became PCR”. With these words the Nobel prize winner, Kary Mullis, explains how he named the PCR: one of the most important techniques ever invented and currently used in molecular biology. This book “RT-PCR Protocols” covers a wide range of aspects important for the setting of a PCR experiment for both beginners and advanced users. In my opinion the book is very well structured in three different sections. The first one describes the different technologies now available, like competitive RT-PCR, nested RT-PCR or RT-PCR for cloning. An important part regards the usage of PCR in single cell mouse embryos, stressing how important...........

  6. Abstracts of the 26. Annual meeting of the Brazilian Society on Biochemistry and Molecular Biology; Resumos da 26. reuniao anual da Sociedade Brasileira de Bioquimica e Biologia Molecular

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-07-01

    This meeting was about biochemistry and molecular biology. It was discussed topics related to bio energetic, channels, transports, biotechnology, metabolism, cellular biology, immunology, toxicology, photobiology and pharmacology.

  7. Abstracts of the 27. Annual meeting of the Brazilian Society on Biochemistry and Molecular Biology; Resumos da 27. reuniao anual da Sociedade Brasileira de Bioquimica e Biologia Molecular

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-07-01

    This meeting was about biochemistry and molecular biology. It was discussed topics related to bio energetic, channels, transports, biotechnology, metabolism, cellular biology, immunology, toxicology, photobiology and pharmacology.

  8. Polyphenol-rich strawberry extract (PRSE) shows in vitro and in vivo biological activity against invasive breast cancer cells.

    Science.gov (United States)

    Amatori, Stefano; Mazzoni, Luca; Alvarez-Suarez, Josè Miguel; Giampieri, Francesca; Gasparrini, Massimiliano; Forbes-Hernandez, Tamara Yuliett; Afrin, Sadia; Errico Provenzano, Alfredo; Persico, Giuseppe; Mezzetti, Bruno; Amici, Augusto; Fanelli, Mirco; Battino, Maurizio

    2016-01-01

    We describe the biological effects of a polyphenol-rich strawberry extract (PRSE), obtained from the "Alba" variety, on the highly aggressive and invasive basal-like breast cancer cell line A17. Dose-response and time-course experiments showed that PRSE is able to decrease the cellular viability of A17 cells in a time- and dose-dependent manner. PRSE effect on cell survival was investigated in other tumor and normal cell lines of both mouse and human origin, demonstrating that PRSE is more active against breast cancer cells. Cytofluorimetric analysis of A17 cells demonstrated that sub-lethal doses of PRSE reduce the number of cells in S phase, inducing the accumulation of cells in G1 phase of cell cycle. In addition, the migration of A17 cells was studied monitoring the ability of PRSE to inhibit cellular mobility. Gene expression analysis revealed the modulation of 12 genes playing different roles in the cellular migration, adhesion and invasion processes. Finally, in vivo experiments showed the growth inhibition of A17 cells orthotopically transplanted into FVB syngeneic mice fed with PRSE. Overall, we demonstrated that PRSE exerts important biological activities against a highly invasive breast cancer cell line both in vitro and in vivo suggesting the strawberry extracts as preventive/curative food strategy. PMID:27498973

  9. Digital learning material for experimental design and model building in molecular biology

    NARCIS (Netherlands)

    Aegerter-Wilmsen, T.

    2005-01-01

    Designing experimental approaches is a major cognitive skill in molecular biology research, and building models, including quantitative ones, is a cognitive skill which is rapidly gaining importance. Since molecular biology education at university level is aimed at educating future researchers, we c

  10. The stable isotopic signature of biologically produced molecular hydrogen (H2)

    NARCIS (Netherlands)

    Walter, S.; Laukenmann, S.; Stams, A.J.M.; Vollmer, M.K.; Gleixner, G.; Roeckmann, T.

    2011-01-01

    Biologically produced molecular hydrogen (H2) is characterized by a very strong depletion in deuterium. Although the biological source to the atmosphere is small compared to photochemical or combustion sources, it makes an important contribution to the global isotope budget of molecular hydrogen (H2

  11. Just Working with the Cellular Machine: A High School Game for Teaching Molecular Biology

    Science.gov (United States)

    Cardoso, Fernanda Serpa; Dumpel, Renata; Gomes da Silva, Luisa B.; Rodrigues, Carlos R.; Santos, Dilvani O.; Cabral, Lucio Mendes; Castro, Helena C.

    2008-01-01

    Molecular biology is a difficult comprehension subject due to its high complexity, thus requiring new teaching approaches. Herein, we developed an interdisciplinary board game involving the human immune system response against a bacterial infection for teaching molecular biology at high school. Initially, we created a database with several…

  12. Book Review of "The Molecular Biology of Cancer" by Stella Pelengaris, Michael Khan (Editors

    Directory of Open Access Journals (Sweden)

    Schmidt Christian

    2007-11-01

    Full Text Available Abstract Here, a review of "The Molecular Biology of Cancer" (Stella Pelengaris and Michael Khan [Editors] is given. The detailed description of the book is provided here: Pelengaris S, Khan M (Eds: The Molecular Biology of Cancer; Blackwell Publishing, Oxford (U.K.; 2006. 531 pages, 214 illustrations, ISBN 9-78140-511-814-9, £31.99.

  13. Monitoring molecular, functional and morphologic aspects of bone metastases using non-invasive imaging.

    Science.gov (United States)

    Bauerle, Tobias; Komljenovic, Dorde; Semmler, Wolfhard

    2012-03-01

    Bone is among the most common locations of metastasis and therefore represents an important clinical target for diagnostic follow-up in cancer patients. In the pathogenesis of bone metastases, disseminated tumor cells proliferating in bone interact with the local microenvironment stimulating or inhibiting osteoclast and osteoblast activity. Non-invasive imaging methods monitor molecular, functional and morphologic changes in both compartments of these skeletal lesions - the bone and the soft tissue tumor compartment. In the bone compartment, morphologic information on skeletal destruction is assessed by computed tomography (CT) and radiography. Pathogenic processes of osteoclast and osteoblast activity, however, can be imaged using optical imaging, positron emission tomography (PET), single photon emission CT (SPECT) and skeletal scintigraphy. Accordingly, conventional magnetic resonance imaging (MRI) and CT as well as diffusion- weighted MRI and optical imaging are used to assess morphologic aspects on the macroscopic and cellular level of the soft tissue tumor compartment. Imaging methods such as PET, MR spectroscopy, dynamic contrast-enhanced techniques and vessel size imaging further elucidate on pathogenic processes in this compartment including information on metabolism and vascularization. By monitoring these aspects in bone lesions, new insights in the pathogenesis of skeletal metastases can be gained. In translation to the clinical situation, these novel methods for the monitoring of bone metastases might be applied in patients to improve follow-up of these lesions, in particular after therapeutic intervention. This review summarizes established and experimental imaging techniques for the monitoring of tumor and bone cell activity including molecular, functional and morphological aspects in bone metastases. PMID:22214500

  14. Molecular Biology of Pancreatic Cancer: How Useful Is It in Clinical Practice?

    OpenAIRE

    Sakorafas, George H; Vasileios Smyrniotis

    2012-01-01

    Context During the recent two decades dramatic advances of molecular biology allowed an in-depth understanding of pancreatic carcinogenesis. It is currently accepted that pancreatic cancer has a genetic component. The real challenge is now how these impressive advances could be used in clinical practice. Objective To critically present currently available data regarding clinical application of molecular biology in pancreatic cancer. Methods Reports about clinical implications of molecular bio...

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

    Energy Technology Data Exchange (ETDEWEB)

    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. [Battelle, Columbus, OH (United States); Chakravarty, L.; Tuovinen, O.H. [Ohio State Univ., Columbus, OH (United States)

    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.

  16. Molecular Biology of Pancreatic Cancer: How Useful Is It in Clinical Practice?

    Directory of Open Access Journals (Sweden)

    George H Sakorafas

    2012-07-01

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

  17. Molecular imaging of prostate cancer: translating molecular biology approaches into the clinical realm

    Energy Technology Data Exchange (ETDEWEB)

    Vargas, Hebert Alberto; Sala, Evis; Hricak, Hedvig [Memorial Sloan Kettering Cancer Center, Department of Radiology, New York, NY (United States); Grimm, Jan [Memorial Sloan Kettering Cancer Center, Department of Radiology, New York, NY (United States); Program in Molecular Pharmacology and Chemistry, Memorial Sloan Kettering Cancer Center, New York (United States); Donati, Olivio F. [Memorial Sloan Kettering Cancer Center, Department of Radiology, New York, NY (United States); University Hospital Zurich, Institute of Diagnostic and Interventional Radiology, Zurich (Switzerland)

    2015-05-01

    The epidemiology of prostate cancer has dramatically changed since the introduction of prostate-specific antigen (PSA) screening in the 1980's. Most prostate cancers today are detected at early stages of the disease and are considered 'indolent'; however, some patients' prostate cancers demonstrate a more aggressive behaviour which leads to rapid progression and death. Increasing understanding of the biology underlying the heterogeneity that characterises this disease has led to a continuously evolving role of imaging in the management of prostate cancer. Functional and metabolic imaging techniques are gaining importance as the impact on the therapeutic paradigm has shifted from structural tumour detection alone to distinguishing patients with indolent tumours that can be managed conservatively (e.g., by active surveillance) from patients with more aggressive tumours that may require definitive treatment with surgery or radiation. In this review, we discuss advanced imaging techniques that allow direct visualisation of molecular interactions relevant to prostate cancer and their potential for translation to the clinical setting in the near future. The potential use of imaging to follow molecular events during drug therapy as well as the use of imaging agents for therapeutic purposes will also be discussed. (orig.)

  18. Comment on "Invasive Harlequin Ladybird Carries Biological Weapons Against Native Competitors"

    NARCIS (Netherlands)

    Jong, de P.W.; Lenteren, van J.C.; Raak-van den Berg, C.L.

    2013-01-01

    We comment on the implications that Vilcinskas et al. (Reports, 17 May 2013, p. 862) attach to the finding that the exotic, invasive ladybird Harmonia axyridis carries microsporidia to which this species is insensitive but that is lethal to species that are native to the invaded areas. The authors s

  19. 2012 PLANT MOLECULAR BIOLOGY GORDON RESEARCH CONFERENCE, JULY 15-20, 2012

    Energy Technology Data Exchange (ETDEWEB)

    Sussman, Michael

    2013-07-20

    The 2012 Gordon Conference on Plant Molecular Biology will present cutting-edge research on molecular aspects of plant growth and development, with particular emphasis on recent discoveries in molecular mechanisms involved with plant signaling systems. The Conference will feature a wide range of topics in plant molecular biology including hormone receptors and early events in hormone signaling, plant perception of and response to plant pathogen and symbionts, as well as technological and biological aspects of epigenomics particularly as it relates to signaling systems that regulate plant growth and development. Genomic approaches to plant signaling will be emphasized, including genomic profiling technologies for quantifying various biological subsystems, such as the epigenome, transcriptome, phosphorylome, and metabolome. The meeting will include an important session devoted to answering the question, "What are the biological and technological limits of plant breeding/genetics, and how can they be solved"?

  20. Molecular eco-systems biology: towards an understanding of community function

    OpenAIRE

    Raes, J.; Bork, P.

    2008-01-01

    Systems-biology approaches, which are driven by genome sequencing and high-throughput functional genomics data, are revolutionizing single-cell-organism biology. With the advent of various high-throughput techniques that aim to characterize complete microbial ecosystems (metagenomics, meta-transcriptomics and meta-metabolomics), we propose that the time is ripe to consider molecular systems biology at the ecosystem level (eco-systems biology). Here, we discuss the necessary data types that ar...

  1. Procathepsin D and cancer: From molecular biology to clinical applications

    OpenAIRE

    Vetvicka, Vaclav; Vashishta, Aruna; Saraswat-Ohri, Sujata; Vetvickova, Jana

    2010-01-01

    Procathepsin D (pCD) is overexpressed and secreted by cells of various tumor types including breast and lung carcinomas. pCD affects multiple features of tumor cells including proliferation, invasion, metastases and apoptosis. Several laboratories have previously shown that the mitogenic effect of pCD on cancer cells is mediated via its propeptide part (APpCD). However, the exact mechanism of how pCD affects cancer cells has not been identified. Recent observations have also revealed the poss...

  2. Biology and ecology of the invasive lionfishes, Pterois miles and Pterois volitans

    OpenAIRE

    Morris, Jr., J. Glenn; Akins, J. L.; Barse, A.; Cerino, D.; Freshwater, D W; Green, S J; R. C. Muñoz; Paris, C.; Whitfield, P. E.

    2009-01-01

    The Indo-Pacific lionfishes, Pterois miles and P. volitans, are now established along the U.S. southeast coast, Bermuda, Bahamas, and are becoming established in the Caribbean. While these lionfish are popular in the aquarium trade, their biology and ecology are poorly understood in their native range. Given the rapid establishment and potential adverse impacts of these invaders, comprehensive studies of their biology and ecology are warranted. Here we provide a synopsis of lionfish biology a...

  3. Biology and impacts of Pacific island invasive species 9. Capra hircus, the feral goat, (Mammalia: Bovidae)

    Science.gov (United States)

    Chynoweth, Mark W.; Litton, Creighton M.; Lepczyk, Christopher A.; Hess, Steve A.; Cordell, Susan

    2013-01-01

    Domestic goats, Capra hircus, were intentionally introduced to numerous oceanic islands beginning in the sixteenth century. The remarkable ability of C. hircus to survive in a variety of conditions has enabled this animal to become feral and impact native ecosystems on islands throughout the world. Direct ecological impacts include consumption and trampling of native plants, leading to plant community modification and transformation of ecosystem structure. While the negative impacts of feral goats are well-known and effective management strategies have been developed to control this invasive species, large populations persist on many islands. This review summarizes the impacts of feral goats on Pacific island ecosystems, and the management strategies available to control this invasive species.

  4. The shape of the spatial kernel and its implications for biological invasions in patchy environments

    OpenAIRE

    Lindström, Tom; Håkansson, Nina; Wennergren, Uno

    2010-01-01

    Ecological and epidemiological invasions occur in a spatial context. We investigated how these processes correlate to the distance dependence of spread or dispersal between spatial entities such as habitat patches or epidemiological units. Distance dependence is described by a spatial kernel, characterized by its shape (kurtosis) and width (variance). We also developed a novel method to analyse and generate point-pattern landscapes based on spectral representation. This involves two measures:...

  5. Systems biology for molecular life sciences and its impact in biomedicine.

    Science.gov (United States)

    Medina, Miguel Ángel

    2013-03-01

    Modern systems biology is already contributing to a radical transformation of molecular life sciences and biomedicine, and it is expected to have a real impact in the clinical setting in the next years. In this review, the emergence of systems biology is contextualized with a historic overview, and its present state is depicted. The present and expected future contribution of systems biology to the development of molecular medicine is underscored. Concerning the present situation, this review includes a reflection on the "inflation" of biological data and the urgent need for tools and procedures to make hidden information emerge. Descriptions of the impact of networks and models and the available resources and tools for applying them in systems biology approaches to molecular medicine are provided as well. The actual current impact of systems biology in molecular medicine is illustrated, reviewing two cases, namely, those of systems pharmacology and cancer systems biology. Finally, some of the expected contributions of systems biology to the immediate future of molecular medicine are commented.

  6. Molecular biology of cancer-associated fibroblasts: can these cells be targeted in anti-cancer therapy?

    Science.gov (United States)

    Gonda, Tamas A; Varro, Andrea; Wang, Timothy C; Tycko, Benjamin

    2010-02-01

    It is increasingly recognized that the non-neoplastic stromal compartment in most solid cancers plays an active role in tumor proliferation, invasion and metastasis. Cancer-associated fibroblasts (CAFs) are one of the most abundant cell types in the tumor stroma, and these cells are pro-tumorigenic. Evidence that CAFs are epigenetically and possibly also genetically distinct from normal fibroblasts is beginning to define these cells as potential targets of anti-cancer therapy. Here, we review the cell-of-origin and molecular biology of CAFs, arguing that such knowledge provides a rational basis for designing therapeutic strategies to coordinately and synergistically target both the stromal and malignant epithelial component of human cancers.

  7. STUDIES OF RELATIONSHIPS BETWEEN MOLECULAR STRUCTURE AND BIOLOGICAL ACTIVITY BY PATTERN RECOGNITION METHODS

    Science.gov (United States)

    The attempt to rationalize the connections between the molecular structures of organic compounds and their biological activities comprises the field of structure-activity relations (SAR) studies. Correlations between structure and activity are important for the understanding and ...

  8. Mechanistic modeling confronts the complexity of molecular cell biology

    OpenAIRE

    Phair, Robert D.

    2014-01-01

    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 fu...

  9. Non-Invasive Early Detection and Molecular Analysis of Low X-ray Dose Effects in the Lens

    Energy Technology Data Exchange (ETDEWEB)

    Goldstein, Lee [Boston University

    2014-07-02

    This is the Final Progress Report for DOE-funded research project DE-PS02-08ER08-01 titled “Non-Invasive Early Detection and Molecular Analysis of Low X-ray Dose Effects in the Lens”. The project focuses on the effects of low-linear energy transfer (LET) radiation on the ocular lens. The lens is an exquisitely radiosensitive tissue with a highly-ordered molecular structure that is amenable to non-invasive optical study from the periphery. These merits point to the lens as an ideal target for laser-based molecular biodosimetry (MBD). Following exposure to different types of ionizing radiations, the lens demonstrates molecular changes (e.g., oxidation, racemization, crosslinkage, truncation, aggregation, etc.) that impact the structure and function of the long-lived proteins in the cytosol of lens fiber cells. The vast majority of proteins in the lens comprise the highly-ordered crystallins. These highly conserved lens proteins are amongst the most concentrated and stable in the body. Once synthesized, the crystallins are retained in the fiber cell cytoplasm for life. Taken together, these properties point to the lens as an ideal system for quantitative in vivo MBD assessment using quasi-elastic light scattering (QLS) analysis. In this project, we deploy a purpose-designed non-invasive infrared laser QLS instrument as a quantitative tool for longitudinal assessment of pre-cataractous molecular changes in the lenses of living mice exposed to low-dose low-LET radiation compared to non-irradiated sham controls. We hypothesize that radiation exposure will induce dose-dependent changes in the molecular structure of matrix proteins in the lens. Mechanistic assays to ascertain radiation-induced molecular changes in the lens focus on protein aggregation and gene/protein expression patterns. We anticipate that this study will contribute to our understanding of early molecular changes associated with radiation-induced tissue pathology. This study also affords potential for

  10. 2012 CELLULAR & MOLECULAR FUNGAL BIOLOGY GORDON RESEARCH CONFERENCE, JUNE 17 - 22, 2012

    Energy Technology Data Exchange (ETDEWEB)

    Judith Berman

    2012-06-22

    The Gordon Research Conference on CELLULAR & MOLECULAR FUNGAL BIOLOGY was held at Holderness School, Holderness New Hampshire, June 17 - 22, 2012. The 2012 Gordon Conference on Cellular and Molecular Fungal Biology (CMFB) will present the latest, cutting-edge research on the exciting and growing field of molecular and cellular aspects of fungal biology. Topics will range from yeast to filamentous fungi, from model systems to economically important organisms, and from saprophytes and commensals to pathogens of plants and animals. The CMFB conference will feature a wide range of topics including systems biology, cell biology and morphogenesis, organismal interactions, genome organisation and regulation, pathogenesis, energy metabolism, biomass production and population genomics. The Conference was well-attended with 136 participants. Gordon Research Conferences does not permit publication of meeting proceedings.

  11. Progress in nucleic acid research and molecular biology

    Energy Technology Data Exchange (ETDEWEB)

    Cohn, W.E. (Biology Div., Oak Ridge National Lab., Oak Ridge, TN (US)); Moldave, K. (Univ. of California, Santa Cruz, CA (US))

    1989-01-01

    This book is organized under the following headings: Transposable elements in Drosophilia; Regulation of gene expression; Structure and function of repetitive and unusual sequences; Retroviruses; Molecular analysis of chromosomal translocation and gene insertion.

  12. Workshop in computational molecular biology, April 15, 1991--April 14, 1994

    Energy Technology Data Exchange (ETDEWEB)

    Tavare, S.

    1995-04-12

    Funds from this award were used to the Workshop in Computational Molecular Biology, `91 Symposium entitled Interface: Computing Science and Statistics, Seattle, Washington, April 21, 1991; the Workshop in Statistical Issues in Molecular Biology held at Stanford, California, August 8, 1993; and the Session on Population Genetics a part of the 56th Annual Meeting, Institute of Mathematical Statistics, San Francisco, California, August 9, 1993.

  13. Phosphorus-32 in the Phage Group: radioisotopes as historical tracers of molecular biology

    OpenAIRE

    Creager, Angela N. H.

    2009-01-01

    The recent historiography of molecular biology features key technologies, instruments and materials, which offer a different view of the field and its turning points than preceding intellectual and institutional histories. Radioisotopes, in this vein, became essential tools in postwar life science research, including molecular biology, and are here analyzed through their use in experiments on bacteriophage. Isotopes were especially well suited for studying the dynamics of chemical transformat...

  14. Biological Control of the Invasive Dryocosmus kuriphilus (Hymenoptera: Cynipidae - an Overview and the First Trials in Croatia

    Directory of Open Access Journals (Sweden)

    Dinka Matošević

    2014-06-01

    Full Text Available Background and Purpose: Dryocosmus kuriphilus is a globally invasive insect pest, spreading very quickly in new habitats and making serious damage to sweet chestnut forests in Croatia and in several other European countries. Indigenous parasitoid species trophically associated with oak gallwasps have adapted to this new host but cannot effectively regulate its population density. Classical biological control using parasitoid Torymus sinensis has been proven to be the only effective method of controlling the populations of D. kuriphilus and has been successfully applied in Japan, South Korea, the USA and Italy. The aim of this review paper is to provide overview and up-to date knowledge about biological control of D. kurphilus and to describe first steps of introduction of T. sinensis to sweet chestnut forests in Croatia. Conclusions and Future Prospects: Results presented in this paper show adapted biology and behavioural traits of T. sinensis to its host D. kuriphilus. The history and results of introductions of T. sinensis to Japan, the USA, Italy, France and Hungary are shown. The first report of release of T. sinensis to sweet chestnut forests in Croatia is given with discussion on native parasitoids attacking D. kuriphilus. Possible negative effects of T. sinensis on native parasitoid fauna and risks that could influence the successful establishment of T. sinensis in Croatia are discussed. Previous experiences have shown that T. sinensis can successfully control the population density of D. kuriphilus, slowing down the spread and mitigating negative impact of this invasive chestnut pest and keeping the damage of D. kuriphilus at acceptable level. High specificity of T. sinensis suggests that it has limited potential of exploiting native hosts but further detailed monitoring of native parasitoid and possible interactions with introduced T. sinensis is strongly suggested.

  15. Predicting potential global distributions of two Miscanthus grasses: implications for horticulture, biofuel production, and biological invasions.

    Directory of Open Access Journals (Sweden)

    Heather A Hager

    Full Text Available In many regions, large proportions of the naturalized and invasive non-native floras were originally introduced deliberately by humans. Pest risk assessments are now used in many jurisdictions to regulate the importation of species and usually include an estimation of the potential distribution in the import area. Two species of Asian grass (Miscanthus sacchariflorus and M. sinensis that were originally introduced to North America as ornamental plants have since escaped cultivation. These species and their hybrid offspring are now receiving attention for large-scale production as biofuel crops in North America and elsewhere. We evaluated their potential global climate suitability for cultivation and potential invasion using the niche model CLIMEX and evaluated the models' sensitivity to the parameter values. We then compared the sensitivity of projections of future climatically suitable area under two climate models and two emissions scenarios. The models indicate that the species have been introduced to most of the potential global climatically suitable areas in the northern but not the southern hemisphere. The more narrowly distributed species (M. sacchariflorus is more sensitive to changes in model parameters, which could have implications for modelling species of conservation concern. Climate projections indicate likely contractions in potential range in the south, but expansions in the north, particularly in introduced areas where biomass production trials are under way. Climate sensitivity analysis shows that projections differ more between the selected climate change models than between the selected emissions scenarios. Local-scale assessments are required to overlay suitable habitat with climate projections to estimate areas of cultivation potential and invasion risk.

  16. A Biochemistry and Molecular Biology Experiment and Evaluation System for Biotechnology Specialty Students: An Effective Evaluation System to Improve the Biochemistry and Molecular Biology Experiment Teaching

    Science.gov (United States)

    Li, Suxia; Wu, Haizhen; Zhao, Jian; Ou, Ling; Zhang, Yuanxing

    2010-01-01

    In an effort to achieve high success in knowledge and technique acquisition as a whole, a biochemistry and molecular biology experiment was established for high-grade biotechnology specialty students after they had studied essential theory and received proper technique training. The experiment was based on cloning and expression of alkaline…

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

    NARCIS (Netherlands)

    Ren, Yjin

    2005-01-01

    : Molecular biology is an exciting, rapidly expanding field, which has enabled enormously greater understanding of the biology of diseases and malfunctions in many fields. It chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interrelatio

  18. The stable isotopic signature of biologically produced molecular hydrogen (H-2)

    NARCIS (Netherlands)

    Walter, S.; Laukenmann, S.; Stams, A.J.M.; Vollmer, M.K.; Gleixner, G.; Rockmann, T.

    2012-01-01

    Biologically produced molecular hydrogen (H-2) is characterised by a very strong depletion in deuterium. Although the biological source to the atmosphere is small compared to photochemical or combustion sources, it makes an important contribution to the global isotope budget of H-2. Large uncertaint

  19. Size Matters: Molecular Weight Specificity of Hyaluronan Effects in Cell Biology

    OpenAIRE

    Jaime M. Cyphert; Trempus, Carol S.; Stavros Garantziotis

    2015-01-01

    Hyaluronan signaling properties are unique among other biologically active molecules, that they are apparently not influenced by postsynthetic molecular modification, but by hyaluronan fragment size. This review summarizes the current knowledge about the generation of hyaluronan fragments of different size and size-dependent differences in hyaluronan signaling as well as their downstream biological effects.

  20. The stable isotopic signature of biologically produced molecular hydrogen (H2)

    NARCIS (Netherlands)

    Walter, S.; Laukenmann, S.; Stams, A.J.M.; Vollmer, M.K.; Gleixner, G.; Roeckmann, T.

    2012-01-01

    Biologically produced molecular hydrogen (H2) is characterised by a very strong depletion in deuterium. Although the biological source to the atmosphere is small compared to photochemical or combustion sources, it makes an important contribution to the global isotope budget of H2. Large uncertaintie

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

    Science.gov (United States)

    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…

  2. Cloning Yeast Actin cDNA Leads to an Investigative Approach for the Molecular Biology Laboratory

    Science.gov (United States)

    Black, Michael W.; Tuan, Alice; Jonasson, Erin

    2008-01-01

    The emergence of molecular tools in multiple disciplines has elevated the importance of undergraduate laboratory courses that train students in molecular biology techniques. Although it would also be desirable to provide students with opportunities to apply these techniques in an investigative manner, this is generally not possible in the…

  3. Design, synthesis, and biological evaluation of potent discodermolide fluorescent and photoaffinity molecular probes.

    Science.gov (United States)

    Smith, Amos B; Rucker, Paul V; Brouard, Ignacio; Freeze, B Scott; Xia, Shujun; Horwitz, Susan Band

    2005-11-10

    [structure: see text] The design, synthesis, and biological evaluation of a series of (+)-discodermolide molecular probes possessing photoaffinity and fluorescent appendages has been achieved. Stereoselective olefin cross-metathesis comprised a key tactic for construction of two of the molecular probes. Three photoaffinity probes were radiolabeled with tritium.

  4. The challenges for molecular nutrition research 4: the "nutritional systems biology level"

    NARCIS (Netherlands)

    Ommen, B. van; Cavallieri, D.; Roche, H.M.; Klein, U.I.; Daniel, H.

    2008-01-01

    Nutritional systems biology may be defined as the ultimate goal of molecular nutrition research, where all relevant aspects of regulation of metabolism in health and disease states at all levels of its complexity are taken into account to describe the molecular physiology of nutritional processes. T

  5. Molecular characterization of invasive Neisseria meningitidis strains isolated in Chile during 2010-2011.

    Directory of Open Access Journals (Sweden)

    Gisselle N Barra

    Full Text Available BACKGROUND: With the upcoming licensure of Outer Membrane Protein-based vaccines against meningococcal disease, data on disease incidence and molecular characteristic of circulating N. meningitidis strains in Latin American countries is needed. Chile is, to date, one of the few countries in the region that has performed this type of work in a comprehensive collection of disease-associated strains from two consecutive years, 2010-2011. METHODS: A total of 119 N. meningitidis strains isolated from patients with invasive disease in Chile in 2010-2011 were characterized by the National Reference Laboratory. Serogroup determination, MLST and porA typing were performed. RESULTS: Serogroup B was predominant in both study years, but W135 experienced a noticeable increase in 2011 compared to 2010. ST-11 complex, ST-41/44 complex ST-32 complex were the most prevalent among the isolates, and were strongly associated with serogroups W135 (ST-11 Complex and B (ST-41/44 and ST-32 complexes. Likewise, the major porA types detected were strongly associated with these three clonal complexes: P1.5,2 was found exclusively among W135:ST-11 isolates, whereas P1.7, 2-3 was only detected in C:ST-11. ST-41/44 isolates mainly had P1.10-8, and ST-32 complex were associated with a P1.18-8 porA. CONCLUSIONS: Our data show disease-associated N. meningitidis circulating in Chile are similar to those found in other parts of the world. The increase on W135:ST-11 isolates observed in 2011 foretold the unusual epidemiological situation experienced in the country in 2012, and MLST data show that this strain is indistinguishable from the one linked to the global Hajj 2000-related outbreak that occurred in 2001. Finally, this work demonstrates the importance of maintaining a strong national surveillance program integrating clinical, epidemiological and laboratory data and incorporating gold standard diagnostic and characterization techniques that allow the data to be compared all

  6. A general concept for molecular biology of cancer.

    Science.gov (United States)

    Busch, H

    1976-11-01

    The demonstrations that "fetal" isozymes and other fetal or "oncodevelopmental" antigens are present in tumor cells has led to the general concept that genes normally silent in adult tissues are activated during the neoplastic process. Recent evidence that some chromatin proteins of tumor cells are fetal antigens has suggested that some of the "switches" involved in gene activation for tumor growth may also be fetal or oncodevelopmental. These results have led to current theoretical concept that fetal gene derepressors interact with the genome to produce messenger RNA for the protein products involved for growth, invasiveness, and metastasis. These processes may not be controllable in adult cells because of the lack of inhibitors, which were present during embryonic development but are not produced in adult tissues.

  7. Effects of pollutant accumulation by the invasive weed saltcedar (Tamarix ramosissima) on the biological control agent Diorhabda elongata (Coleoptera: Chrysomelidae)

    Energy Technology Data Exchange (ETDEWEB)

    Sorensen, Mary A. [Department of Entomology, University of California, Riverside, CA 92521 (United States)], E-mail: mary.sorensen@ucr.edu; Parker, David R. [Department of Environmental Science, University of California, Riverside, CA 92521 (United States); Trumble, John T. [Department of Entomology, University of California, Riverside, CA 92521 (United States)

    2009-02-15

    Hydroponic greenhouse studies were used to investigate the effect of four anthropogenic pollutants (perchlorate (ClO{sub 4}{sup -}), selenium (Se), manganese (Mn), and hexavalent chromium (Cr (VI))) on the biological control agent Diorhabda elongata Brulle. Contaminant concentrations were quantified for experimental Tamarix ramosissima Ledab. plants and D. elongata beetles. Growth of larvae was significantly reduced by Se contamination, but was not affected by the presence of perchlorate, Mn, or Cr (VI). All of the contaminants were transferred from plants to D. elongata beetles. Only Cr (VI) was accumulated at greater levels in beetles than in their food. Because T. ramosissima grows in disturbed areas, acquires salts readily, and utilizes groundwater, this plant is likely to accumulate anthropogenic pollutants in contaminated areas. This study is one of the first to investigate the potential of an anthropogenic pollutant to influence a weed biological control system. - The presence of Se, but not perchlorate, Mn, or Cr (VI), in foliage of the invasive weed saltcedar was shown to reduce growth of the biological control agent Diorhabda elongata.

  8. Systems biology of cancer: entropy, disorder, and selection-driven evolution to independence, invasion and "swarm intelligence".

    Science.gov (United States)

    Tarabichi, M; Antoniou, A; Saiselet, M; Pita, J M; Andry, G; Dumont, J E; Detours, V; Maenhaut, C

    2013-12-01

    Our knowledge of the biology of solid cancer has greatly progressed during the last few years, and many excellent reviews dealing with the various aspects of this biology have appeared. In the present review, we attempt to bring together these subjects in a general systems biology narrative. It starts from the roles of what we term entropy of signaling and noise in the initial oncogenic events, to the first major transition of tumorigenesis: the independence of the tumor cell and the switch in its physiology, i.e., from subservience to the organism to its own independent Darwinian evolution. The development after independence involves a constant dynamic reprogramming of the cells and the emergence of a sort of collective intelligence leading to invasion and metastasis and seldom to the ultimate acquisition of immortality through inter-individual infection. At each step, the probability of success is minimal to infinitesimal, but the number of cells possibly involved and the time scale account for the relatively high occurrence of tumorigenesis and metastasis in multicellular organisms.

  9. HMM Search for Apoptotic Domains (MOLECULAR BIOLOGY AND INFORMATION-Biological Information Science)

    OpenAIRE

    Hattori, Masahiro; Kanehisa, Minoru

    2000-01-01

    For the purpose of analyzing apoptotic molecular interactions, we have developed a knowledge base, which consists of apoptotic molecular interactions, together with the WWW interface for it. This database and the user interface enabled us to find out entries containing various information about cell death. This information tells us that the apoptotic molecular interactions are likely to be controlled under a series of specific conserved domains. Thus, the viewpoint of domain seems to be more ...

  10. Teaching Cell and Molecular Biology for Gender Equity

    Science.gov (United States)

    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…

  11. Molecular probes for nonlinear optical imaging of biological membranes

    Science.gov (United States)

    Blanchard-Desce, Mireille H.; Ventelon, Lionel; Charier, Sandrine; Moreaux, Laurent; Mertz, Jerome

    2001-12-01

    Second-harmonic generation (SHG) and two-photon excited fluorescence (TPEF) are nonlinear optical (NLO) phenomena that scale with excitation intensity squared, and hence give rise to an intrinsic 3-dimensional resolution when used in microscopic imaging. TPEF microscopy has gained widespread popularity in the biology community whereas SHG microscopy promises to be a powerful tool because of its sensitivity to local asymmetry. We have implemented an approach toward the design of NLO-probes specifically adapted for SHG and/or TPEF imaging of biological membranes. Our strategy is based on the design of nanoscale amphiphilic NLO-phores. We have prepared symmetrical bolaamphiphilic fluorophores combining very high two-photon absorption (TPA) cross-sections in the visible red region and affinity for cellular membranes. Their incorporation and orientation in lipid membranes can be monitored via TPEF anisotropy. We have also prepared amphiphilic push-pull chromophores exhibiting both large TPA cross-sections and very large first hyperpolarizabilities in the near-IR region. These NLO-probes have proved to be particularly useful for imaging of biological membranes by simultaneous SHG and TPEF microscopy and offer attractive prospects for real-time imaging of fundamental biological processes such as adhesion, fusion or reporting of membrane potentials.

  12. How was teleology eliminated in early molecular biology?

    Science.gov (United States)

    Sloan, Phillip R

    2012-03-01

    This paper approaches the issue of the status of teleological reasoning in contemporary biology through a historical examination of events of the 1930s that surrounded Niels Bohr's efforts to introduce 'complementarity' into biological discussions. The paper examines responses of three theoretical physicists who engaged boundary questions between the biological and physical sciences in this period in response to Bohr-Ernst Pascual Jordan (1902-80), Erwin Schrödinger (1887-1961), and Max Delbrück (1906-81). It is claimed that none of these physicists sufficiently understood Bohr's 'critical' teleological arguments, which are traced to the lineage of Kant and Harald Høffding and their respective resolutions of the Antinomy of Teleological Judgment. The positions of these four historical actors are discussed in terms of Ernst Mayr's distinction of 'teleological,' 'teleomatic,' and 'teleonomic' explanations. A return to some of the views articulated by Bohr, and behind him, to Høffding and Kant, is claimed to provide a framework for reintroducing a 'critical' teleology into biological discussions. PMID:22326083

  13. A conundrum in molecular toxicology: molecular and biological changes during neoplastic transformation of human cells.

    Science.gov (United States)

    Milo, G E; Shuler, C F; Lee, H; Casto, B C

    1995-12-01

    The process of multistage carcinogenesis lends itself to the concept that the effects of carcinogens are mediated through dose-related, multi-hit, linear changes. Multiple in vitro model systems have been developed that are designed to examine the cellular changes associated with the progression of cells through the different stages in the process; however, these systems may have inherent limitations due to the cell lines used for these studies, the manner of assessing the effects of the carcinogens, and the subsequent growth and differentiation of the exposed cells. Each of these variables results in increasing levels of uncertainty relative to the correlation of the events with the actual process of human tumor development. Therefore, the prediction of the ultimate effect of any carcinogen is difficult. Moreover, relationships between individual biological endpoints resulting from carcinogen treatment appear at best to be approximations. The presence of an activated carcinogen inside the cell can give rise to multiple outcomes, only some of which may be critical events. For example, site-specific modification of the 12th and 13th codons of H-ras is different than that in the adjacent 14th and 15th codons. It is interesting to speculate what effect these differences might have on a biological outcome, e.g., transformation to anchorage-independent growth. The use of different model systems to examine the effects of activated carcinogens also creates additional problems. Comparisons of in vitro transformed cells with similar cells isolated from human tumors indicate that the culture environment appears to influence the expression of a particular phenotype, in that human tumor cells in culture express many of the same parameters as those found in cells transformed with carcinogens in vitro. If the process of transformation is linear, then less aggressive phenotypes should progress to a more aggressive transformed stage. However, in carcinogen-transformed human cells

  14. Defining invasiveness and invasibility in ecological networks

    OpenAIRE

    C. Hui; Richardson, D. M.; Landi, P; H.O. Minoarivelo; Garnas, J.; Roy, H.E.

    2016-01-01

    The success of a biological invasion is context dependent, and yet two key concepts—the invasiveness of species and the invasibility of recipient ecosystems—are often defined and considered separately. We propose a framework that can elucidate the complex relationship between invasibility and invasiveness. It is based on trait-mediated interactions between species and depicts the response of an ecological network to the intrusion of an alien species, drawing on the concept of community satura...

  15. Recent advances in yeast molecular biology: recombinant DNA. [Lead abstract

    Energy Technology Data Exchange (ETDEWEB)

    1982-09-01

    Separate abstracts were prepared for the 25 papers presented at a workshop focusing on chromosomal structure, gene regulation, recombination, DNA repair, and cell type control, that have been obtained by experimental approaches incorporating the new technologies of yeast DNA transformation, molecular cloning, and DNA sequence analysis. (KRM)

  16. Molecular biology of Plasmodiophora brassicae

    DEFF Research Database (Denmark)

    Siemens, Johannes; Bulman, Simon; Rehn, Frank;

    2009-01-01

    Initially, molecular techniques were used to detect and distinguish Plasmodiophora pathotypes in soil. Meanwhile, chromosomes from 2.2 Mb to 680 kb are characterized and the total genome size is estimated to be approximately 20 Mb. Furthermore, the genomic gene structure and the cDNA structure of...

  17. Recent advances in yeast molecular biology: recombinant DNA

    International Nuclear Information System (INIS)

    Separate abstracts were prepared for the 25 papers presented at a workshop focusing on chromosomal structure, gene regulation, recombination, DNA repair, and cell type control, that have been obtained by experimental approaches incorporating the new technologies of yeast DNA transformation, molecular cloning, and DNA sequence analysis

  18. Molecular dynamics simulation of a charged biological membrane

    NARCIS (Netherlands)

    López Cascales, J.J.; García de la Torre, J.; Marrink, S.J.; Berendsen, H.J.C.

    1996-01-01

    A molecular dynamics simulation of a membrane with net charge in its liquid-crystalline state was carried out. It was modeled by dipalmitoylphosphatidylserine lipids with net charge, sodium ions as counterions and water molecules. The behavior of this membrane differs from that was shown by other me

  19. Eco-evolutionary responses of Bromus tectorum to climate change: implications for biological invasions

    Science.gov (United States)

    Zelikova, Tamara J.; Hufbauer, Ruth A.; Reed, Sasha C.; Wertin, Timothy M.; Fettig, Christa; Belnap, Jayne

    2013-01-01

    How plant populations, communities, and ecosystems respond to climate change is a critical focus in ecology today. The responses of introduced species may be especially rapid. Current models that incorporate temperature and precipitation suggest that future Bromus tectorum invasion risk is low for the Colorado Plateau. With a field warming experiment at two sites in southeastern Utah, we tested this prediction over 4 years, measuring B. tectorum phenology, biomass, and reproduction. In a complimentary greenhouse study, we assessed whether changes in field B. tectorum biomass and reproductive output influence offspring performance. We found that following a wet winter and early spring, the timing of spring growth initiation, flowering, and summer senescence all advanced in warmed plots at both field sites and the shift in phenology was progressively larger with greater warming. Earlier green-up and development was associated with increases in B. tectorum biomass and reproductive output, likely due early spring growth, when soil moisture was not limiting, and a lengthened growing season. Seeds collected from plants grown in warmed plots had higher biomass and germination rates and lower mortality than seeds from ambient plots. However, in the following two dry years, we observed no differences in phenology between warmed and ambient plots. In addition, warming had a generally negative effect on B. tectorum biomass and reproduction in dry years and this negative effect was significant in the plots that received the highest warming treatment. In contrast to models that predict negative responses of B. tectorum to warmer climate on the Colorado Plateau, the effects of warming were more nuanced, relied on background climate, and differed between the two field sites. Our results highlight the importance of considering the interacting effects of temperature, precipitation, and site-specific characteristics such as soil texture, on plant demography and have direct

  20. Runge-Kutta and Hermite Collocation for a biological invasion problem modeled by a generalized Fisher equation

    International Nuclear Information System (INIS)

    Fisher's equation has been widely used to model the biological invasion of single-species communities in homogeneous one dimensional habitats. In this study we develop high order numerical methods to accurately capture the spatiotemporal dynamics of the generalized Fisher equation, a nonlinear reaction-diffusion equation characterized by density dependent non-linear diffusion. Working towards this direction we consider strong stability preserving Runge-Kutta (RK) temporal discretization schemes coupled with the Hermite cubic Collocation (HC) spatial discretization method. We investigate their convergence and stability properties to reveal efficient HC-RK pairs for the numerical treatment of the generalized Fisher equation. The Hadamard product is used to characterize the collocation discretized non linear equation terms as a first step for the treatment of generalized systems of relevant equations. Numerical experimentation is included to demonstrate the performance of the methods

  1. Invasion biology meets parasitology: a case study of parasite spill-back with Egyptian Fasciola gigantica in the invasive snail Pseudosuccinea columella.

    Directory of Open Access Journals (Sweden)

    Daniel S Grabner

    Full Text Available The liver fluke Fasciola gigantica is a trematode parasite of ruminants and humans that occurs naturally in Africa and Asia. Cases of human fascioliasis, attributable at least in part to F. gigantica, are significantly increasing in the last decades. The introduced snail species Galba truncatula was already identified to be an important intermediate host for this parasite and the efficient invader Pseudosuccinea columella is another suspect in this case. Therefore, we investigated snails collected in irrigation canals in Fayoum governorate in Egypt for prevalence of trematodes with focus on P. columella and its role for the transmission of F. gigantica. Species were identified morphologically and by partial sequencing of the cytochrome oxidase subunit I gene (COI. Among all 689 snails found at the 21 sampling sites, P. columella was the most abundant snail with 296 individuals (42.96% and it was also the most dominant species at 10 sites. It was not found at 8 sites. Molecular detection by PCR and sequencing of the ITS1-5.8S-ITS2 region of the ribosomal DNA (rDNA revealed infections with F. gigantica (3.38%, Echinostoma caproni (2.36% and another echinostome (7.09% that could not be identified further according to its sequence. No dependency of snail size and trematode infection was found. Both high abundance of P. columella in the Fayoum irrigation system and common infection with F. gigantica might be a case of parasite spill-back (increased prevalence in local final hosts due to highly susceptible introduced intermediate host species from the introduced P. columella to the human population, explaining at least partly the observed increase of reported fascioliasis-cases in Egypt. Eichhornia crassipes, the invasive water hyacinth, which covers huge areas of the irrigation canals, offers safe refuges for the amphibious P. columella during molluscicide application. As a consequence, this snail dominates snail communities and efficiently transmits

  2. Invasion Biology Meets Parasitology: A Case Study of Parasite Spill-Back with Egyptian Fasciola gigantica in the Invasive Snail Pseudosuccinea columella

    Science.gov (United States)

    Grabner, Daniel S.; Mohamed, Faten A. M. M.; Nachev, Milen; Méabed, Eman M. H.; Sabry, Abdel Hameed A.; Sures, Bernd

    2014-01-01

    The liver fluke Fasciola gigantica is a trematode parasite of ruminants and humans that occurs naturally in Africa and Asia. Cases of human fascioliasis, attributable at least in part to F. gigantica, are significantly increasing in the last decades. The introduced snail species Galba truncatula was already identified to be an important intermediate host for this parasite and the efficient invader Pseudosuccinea columella is another suspect in this case. Therefore, we investigated snails collected in irrigation canals in Fayoum governorate in Egypt for prevalence of trematodes with focus on P. columella and its role for the transmission of F. gigantica. Species were identified morphologically and by partial sequencing of the cytochrome oxidase subunit I gene (COI). Among all 689 snails found at the 21 sampling sites, P. columella was the most abundant snail with 296 individuals (42.96%) and it was also the most dominant species at 10 sites. It was not found at 8 sites. Molecular detection by PCR and sequencing of the ITS1-5.8S-ITS2 region of the ribosomal DNA (rDNA) revealed infections with F. gigantica (3.38%), Echinostoma caproni (2.36%) and another echinostome (7.09%) that could not be identified further according to its sequence. No dependency of snail size and trematode infection was found. Both high abundance of P. columella in the Fayoum irrigation system and common infection with F. gigantica might be a case of parasite spill-back (increased prevalence in local final hosts due to highly susceptible introduced intermediate host species) from the introduced P. columella to the human population, explaining at least partly the observed increase of reported fascioliasis-cases in Egypt. Eichhornia crassipes, the invasive water hyacinth, which covers huge areas of the irrigation canals, offers safe refuges for the amphibious P. columella during molluscicide application. As a consequence, this snail dominates snail communities and efficiently transmits F. gigantica

  3. Competition between honeydew producers in an ant-hemipteran interaction may enhance biological control of an invasive pest.

    Science.gov (United States)

    Tena, A; Hoddle, C D; Hoddle, M S

    2013-12-01

    Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Liviidae), is an invasive citrus pest in southern California, which secretes honeydew and has the potential to spread a lethal bacterial disease, huanglongbing, of citrus. In urban citrus, Argentine ant, Linepithema humile (Mayr) (Hymenoptera: Formicidae), also an invasive pest, tends honeydew-producing hemipterans. We used field data to determine whether the mutualistic relationship between L. humile and six established species of honeydew producers may hinder or favor the establishment of D. citri and its biological control with Tamarixia radiata (Waterston) (Hymenoptera: Eulophidae) in citrus via competition or mutualism for ants, respectively. In the field, L. humile and D. citri are engaged in a mutualistic relationship. Ants harvest solid honeydew secreted by psyllid nymphs and tended more than 55% of observed D. citri colonies. Linepithema humile displayed a preference hierarchy when tending honeydew producers infesting citrus. It responded equally or less intensively to D. citri than to other honeydew-producing species. Consequently, the mutualism between L. humile and D. citri was affected by the presence of other honeydew-producing species, and the percentage of D. citri colonies tended by L. humile. The number of ants per D. citri colony also decreased as the number of other honeydew producers increased. Diaphorina citri density was also affected by the presence of other honeydew producers. Both colony size and the number of D. citri nymphs counted per tree decreased as the number of other honeydew producers increased. Our results indicate that competition between honeydew producers for the mutualist ant L. humile may hinder the establishment of D. citri by possibly facilitating increased biological control.

  4. Competition between honeydew producers in an ant-hemipteran interaction may enhance biological control of an invasive pest.

    Science.gov (United States)

    Tena, A; Hoddle, C D; Hoddle, M S

    2013-12-01

    Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Liviidae), is an invasive citrus pest in southern California, which secretes honeydew and has the potential to spread a lethal bacterial disease, huanglongbing, of citrus. In urban citrus, Argentine ant, Linepithema humile (Mayr) (Hymenoptera: Formicidae), also an invasive pest, tends honeydew-producing hemipterans. We used field data to determine whether the mutualistic relationship between L. humile and six established species of honeydew producers may hinder or favor the establishment of D. citri and its biological control with Tamarixia radiata (Waterston) (Hymenoptera: Eulophidae) in citrus via competition or mutualism for ants, respectively. In the field, L. humile and D. citri are engaged in a mutualistic relationship. Ants harvest solid honeydew secreted by psyllid nymphs and tended more than 55% of observed D. citri colonies. Linepithema humile displayed a preference hierarchy when tending honeydew producers infesting citrus. It responded equally or less intensively to D. citri than to other honeydew-producing species. Consequently, the mutualism between L. humile and D. citri was affected by the presence of other honeydew-producing species, and the percentage of D. citri colonies tended by L. humile. The number of ants per D. citri colony also decreased as the number of other honeydew producers increased. Diaphorina citri density was also affected by the presence of other honeydew producers. Both colony size and the number of D. citri nymphs counted per tree decreased as the number of other honeydew producers increased. Our results indicate that competition between honeydew producers for the mutualist ant L. humile may hinder the establishment of D. citri by possibly facilitating increased biological control. PMID:23941659

  5. The physiology and molecular biology of sponge tissues.

    Science.gov (United States)

    Leys, Sally P; Hill, April

    2012-01-01

    Sponges have become the focus of studies on molecular evolution and the evolution of animal body plans due to their ancient branching point in the metazoan lineage. Whereas our former understanding of sponge function was largely based on a morphological perspective, the recent availability of the first full genome of a sponge (Amphimedon queenslandica), and of the transcriptomes of other sponges, provides a new way of understanding sponges by their molecular components. This wealth of genetic information not only confirms some long-held ideas about sponge form and function but also poses new puzzles. For example, the Amphimedon sponge genome tells us that sponges possess a repertoire of genes involved in control of cell proliferation and in regulation of development. In vitro expression studies with genes involved in stem cell maintenance confirm that archaeocytes are the main stem cell population and are able to differentiate into many cell types in the sponge including pinacocytes and choanocytes. Therefore, the diverse roles of archaeocytes imply differential gene expression within a single cell ontogenetically, and gene expression is likely also different in different species; but what triggers cells to enter one pathway and not another and how each archaeocyte cell type can be identified based on this gene knowledge are new challenges. Whereas molecular data provide a powerful new tool for interpreting sponge form and function, because sponges are suspension feeders, their body plan and physiology are very much dependent on their physical environment, and in particular on flow. Therefore, in order to integrate new knowledge of molecular data into a better understanding the sponge body plan, it is important to use an organismal approach. In this chapter, we give an account of sponge body organization as it relates to the physiology of the sponge in light of new molecular data. We focus, in particular, on the structure of sponge tissues and review descriptive as

  6. Pathogens penetrating the central nervous system: infection pathways and the cellular and molecular mechanisms of invasion.

    Science.gov (United States)

    Dando, Samantha J; Mackay-Sim, Alan; Norton, Robert; Currie, Bart J; St John, James A; Ekberg, Jenny A K; Batzloff, Michael; Ulett, Glen C; Beacham, Ifor R

    2014-10-01

    The brain is well protected against microbial invasion by cellular barriers, such as the blood-brain barrier (BBB) and the blood-cerebrospinal fluid barrier (BCSFB). In addition, cells within the central nervous system (CNS) are capable of producing an immune response against invading pathogens. Nonetheless, a range of pathogenic microbes make their way to the CNS, and the resulting infections can cause significant morbidity and mortality. Bacteria, amoebae, fungi, and viruses are capable of CNS invasion, with the latter using axonal transport as a common route of infection. In this review, we compare the mechanisms by which bacterial pathogens reach the CNS and infect the brain. In particular, we focus on recent data regarding mechanisms of bacterial translocation from the nasal mucosa to the brain, which represents a little explored pathway of bacterial invasion but has been proposed as being particularly important in explaining how infection with Burkholderia pseudomallei can result in melioidosis encephalomyelitis.

  7. Nutritional systems biology modeling: from molecular mechanisms to physiology.

    OpenAIRE

    de Graaf, Albert A.; Freidig, Andreas P.; Baukje De Roos; Neema Jamshidi; Matthias Heinemann; Rullmann, Johan A.C.; Hall, Kevin D.; Martin Adiels; Ben van Ommen

    2009-01-01

    The use of computational modeling and simulation has increased in many biological fields, but despite their potential these techniques are only marginally applied in nutritional sciences. Nevertheless, recent applications of modeling have been instrumental in answering important nutritional questions from the cellular up to the physiological levels. Capturing the complexity of today's important nutritional research questions poses a challenge for modeling to become truly integrative in the co...

  8. Nutritional Systems Biology Modeling: From Molecular Mechanisms to Physiology

    OpenAIRE

    de Graaf, A A; Freidig, A.P.; Roos, B.; Jamshidi, N.; M. Heinemann; Rullmann, J.A.C.; Hall, K. D.; Adiels, M.; Ommen, B. van

    2009-01-01

    The use of computational modeling and simulation has increased in many biological fields, but despite their potential these techniques are only marginally applied in nutritional sciences. Nevertheless, recent applications of modeling have been instrumental in answering important nutritional questions from the cellular up to the physiological levels. Capturing the complexity of today's important nutritional research questions poses a challenge for modeling to become truly integrative in the co...

  9. Nutritional Systems Biology Modeling: From Molecular Mechanisms to Physiology

    OpenAIRE

    de Graaf, Albert A.; Freidig, Andreas P.; de Roos, Baukje; Jamshidi, Neema; Heinemann, Matthias; Rullmann, Johan A.C.; Hall, Kevin D.; Adiels, Martin; van Ommen, Ben; Bourne, Philip E.

    2009-01-01

    The use of computational modeling and simulation has increased in many biological fields, but despite their potential these techniques are only marginally applied in nutritional sciences. Nevertheless, recent applications of modeling have been instrumental in answering important nutritional questions from the cellular up to the physiological levels. Capturing the complexity of today’s important nutritional research questions poses a challenge for modeling to become truly integrative in the co...

  10. Optimal Information Retrieval Model for Molecular Biology Information

    OpenAIRE

    Paulsen, Jon Rune

    2007-01-01

    Search engines for biological information are not a new technology. Since the 1960s computers have emerged as an important tool for biologists. Online Mendelian Inheritance in Man (OMIM) is a comprehensive catalogue containing approximately 14 000 records with information about human genes and genetic disorders. An approach called Latent Semantic Indexing (LSI) was introduced in 1990 that is based on Singular Value Decomposition (SVD). This approach improved the information retrieval and red...

  11. Biomarkers of Aging: From Function to Molecular Biology

    OpenAIRE

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

    2016-01-01

    Aging is a major risk factor for most chronic diseases and functional impairments. Within a homogeneous age sample there is a considerable variation in the extent of disease and functional impairment risk, revealing a need for valid biomarkers to aid in characterizing the complex aging processes. The identification of biomarkers is further complicated by the diversity of biological living situations, lifestyle activities and medical treatments. Thus, there has been no identification of a sing...

  12. MODEL ORGANISMS USED IN MOLECULAR BIOLOGY OR MEDICAL RESEARCH

    OpenAIRE

    Pandey Govind

    2011-01-01

    A model organism is a non-human species that is studied to understand specific biological phenomena with the expectation that investigations made in the organism model will provide insight into the workings of other organisms. The model organisms are widely used to explore potential causes and treatments for human as well as animal diseases when experiments on animals or humans would be unfeasible or considered less ethical. Studying model organisms may be informative, but care must be taken ...

  13. Recent advances in molecular biology of gastric carcinogenesis

    Institute of Scientific and Technical Information of China (English)

    萧树东; 冉志华

    2003-01-01

    Gastric cancer is a major health care problem and the second most common fatal cancer worldwide. In the last decade, better insight has been gained into the molecular basis underlying the neoplasitc transformation of stomach. The dramatic variation in the incidence of gastric cancer in different geographical areas and from one generation to the next have led to the hypothesis that the incidence of gastric cancer is determined largely by environmental rather than genetic factors.

  14. Molecular biology of Philadelphia-negative myeloproliferative neoplasms

    Directory of Open Access Journals (Sweden)

    Paulo Vidal Campregher

    2012-01-01

    Full Text Available Myeloproliferative neoplasms are clonal diseases of hematopoietic stem cells characterized by myeloid hyperplasia and increased risk of developing acute myeloid leukemia. Myeloproliferative neoplasms are caused, as any other malignancy, by genetic defects that culminate in the neoplastic phenotype. In the past six years, since the identification of JAK2V617F, we have experienced a substantial increase in our knowledge about the genetic mechanisms involved in the genesis of myeloproliferative neoplasms. Mutations described in several genes have revealed a considerable degree of molecular homogeneity between different subtypes of myeloproliferative neoplasms. At the same time, the molecular differences between each subtype have become clearer. While mutations in several genes, such as JAK2, myeloproliferative leukemia (MPL and LNK have been validated in functional assays or animal models as causative mutations, the roles of other recurring mutations in the development of disease, such as TET2 and ASXL1 remain to be elucidated. In this review we will examine the most prevalent recurring gene mutations found in myeloproliferative neoplasms and their molecular consequences.

  15. Molecular biology on the ICU. From understanding to treating sepsis.

    Science.gov (United States)

    Winning, J; Claus, R A; Huse, K; Bauer, M

    2006-05-01

    Mounting evidence suggests that beside well established factors, such as virulence of pathogens or site of infection, individual differences in disease manifestation are a result of the genetic predisposition of the patient on an Intensive Care Unit (ICU). Specific genetic factors might not only predict the risk to acquire severe infections but also to develop organ dysfunction or ultimately to die. Thus, the advent of molecular techniques allowing screening for a wide variety of genetic factors, such as single nucleotide polymorphisms in genes controlling expression of important mediator systems in patients as well as their purposeful targeting in animal models of sepsis, are revolutionizing understanding of pathophysiology in the critically ill. Molecular tools are about to challenge ''state-of-the-art'' diagnostic tests such as blood culture as they not only increase sensitivity but dramatically reduce time requirements to identify pathogens and their resistance patterns. Similarly, knowledge of genetic factors might in the near future help to identify ''patients at risk'', i.e. those with a high likelihood to develop organ dysfunction or to guide therapeutic interventions in particular regarding resource-consuming and/or expensive therapies (''theragnostics''). While therapeutic options in molecular intensive care medicine, such as stem cells in the treatment of organ failure or therapeutic gene transfer are possible along the road and might become an option in the future, recombinant DNA technology has already a well defined role in the production of recombinant human proteins from insulin to activated protein C. PMID:16675935

  16. Invasion Success by Plant Breeding Evolutionary Changes as a Critical Factor for the Invasion of the Ornamental Plant Mahonia aquifolium

    CERN Document Server

    Ross, Christel Anne

    2009-01-01

    Invasive species are a major threat to global biodiversity and cause significant economic costs. Studying biological invasions is both essential for preventing future invasions and is also useful in order to understand basic ecological processes. Christel Ross investigates whether evolutionary changes by plant breeding are a relevant factor for the invasion success of Mahonia aquifolium in Germany. Her findings show that invasive populations differ from native populations in quantitative-genetic traits and molecular markers, whereas their genetic diversity is similar. She postulates that these evolutionary changes are rather a result of plant breeding, which includes interspecific hybridisation, than the result of a genetic bottleneck or the releases from specialist herbivores.

  17. Developing Molecular Interaction Database and Searching for Similar Pathways (MOLECULAR BIOLOGY AND INFORMATION-Biological Information Science)

    OpenAIRE

    Kawashima, Shuichi; Katayama, Toshiaki; Kanehisa, Minoru

    1998-01-01

    We have developed a database named BRITE, which contains knowledge of interacting molecules and/or genes concering cell cycle and early development. Here, we report an overview of the database and the method of automatic search for functionally common sub-pathways between two biological pathways in BRITE.

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

    OpenAIRE

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

    2010-01-01

    We describe an ongoing collaborative curriculum materials development project between Sweet Briar College and Western Michigan University, with support from the National Science Foundation. We present a collection of modules under development that can be used in existing mathematics and biology courses, and we address a critical national need to introduce students to mathematical methods beyond the interface of biology with calculus. Based on ongoing research, and designed to use the project-...

  19. Machine learning in systems biology at different scales : from molecular biology to ecology

    OpenAIRE

    Aderhold, Andrej

    2015-01-01

    Machine learning has been a source for continuous methodological advances in the field of computational learning from data. Systems biology has profited in various ways from machine learning techniques but in particular from network inference, i.e. the learning of interactions given observed quantities of the involved components or data that stem from interventional experiments. Originally this domain of system biology was confined to the inference of gene regulation networks but ...

  20. Modeling human risk: Cell ampersand molecular biology in context

    International Nuclear Information System (INIS)

    It is anticipated that early in the next century manned missions into outer space will occur, with a mission to Mars scheduled between 2015 and 2020. However, before such missions can be undertaken, a realistic estimation of the potential risks to the flight crews is required. One of the uncertainties remaining in this risk estimation is that posed by the effects of exposure to the radiation environment of outer space. Although the composition of this environment is fairly well understood, the biological effects arising from exposure to it are not. The reasons for this are three-fold: (1) A small but highly significant component of the radiation spectrum in outer space consists of highly charged, high energy (HZE) particles which are not routinely experienced on earth, and for which there are insufficient data on biological effects; (2) Most studies on the biological effects of radiation to date have been high-dose, high dose-rate, whereas in space, with the exception of solar particle events, radiation exposures will be low-dose, low dose-rate; (3) Although it has been established that the virtual absence of gravity in space has a profound effect on human physiology, it is not clear whether these effects will act synergistically with those of radiation exposure. A select panel will evaluate the utilizing experiments and models to accurately predict the risks associated with exposure to HZE particles. Topics of research include cellular and tissue response, health effects associated with radiation damage, model animal systems, and critical markers of Radiation response

  1. Modeling human risk: Cell & molecular biology in context

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-06-01

    It is anticipated that early in the next century manned missions into outer space will occur, with a mission to Mars scheduled between 2015 and 2020. However, before such missions can be undertaken, a realistic estimation of the potential risks to the flight crews is required. One of the uncertainties remaining in this risk estimation is that posed by the effects of exposure to the radiation environment of outer space. Although the composition of this environment is fairly well understood, the biological effects arising from exposure to it are not. The reasons for this are three-fold: (1) A small but highly significant component of the radiation spectrum in outer space consists of highly charged, high energy (HZE) particles which are not routinely experienced on earth, and for which there are insufficient data on biological effects; (2) Most studies on the biological effects of radiation to date have been high-dose, high dose-rate, whereas in space, with the exception of solar particle events, radiation exposures will be low-dose, low dose-rate; (3) Although it has been established that the virtual absence of gravity in space has a profound effect on human physiology, it is not clear whether these effects will act synergistically with those of radiation exposure. A select panel will evaluate the utilizing experiments and models to accurately predict the risks associated with exposure to HZE particles. Topics of research include cellular and tissue response, health effects associated with radiation damage, model animal systems, and critical markers of Radiation response.

  2. Phylogeography and population structure of the biologically invasive phytopathogen Erwinia amylovora inferred using minisatellites.

    Science.gov (United States)

    Bühlmann, Andreas; Dreo, Tanja; Rezzonico, Fabio; Pothier, Joël F; Smits, Theo H M; Ravnikar, Maja; Frey, Jürg E; Duffy, Brion

    2014-07-01

    Erwinia amylovora causes a major disease of pome fruit trees worldwide, and is regulated as a quarantine organism in many countries. While some diversity of isolates has been observed, molecular epidemiology of this bacterium is hindered by a lack of simple molecular typing techniques with sufficiently high resolution. We report a molecular typing system of E. amylovora based on variable number of tandem repeats (VNTR) analysis. Repeats in the E. amylovora genome were identified with comparative genomic tools, and VNTR markers were developed and validated. A Multiple-Locus VNTR Analysis (MLVA) was applied to E. amylovora isolates from bacterial collections representing global and regional distribution of the pathogen. Based on six repeats, MLVA allowed the distinction of 227 haplotypes among a collection of 833 isolates of worldwide origin. Three geographically separated groups were recognized among global isolates using Bayesian clustering methods. Analysis of regional outbreaks confirmed presence of diverse haplotypes but also high representation of certain haplotypes during outbreaks. MLVA analysis is a practical method for epidemiological studies of E. amylovora, identifying previously unresolved population structure within outbreaks. Knowledge of such structure can increase our understanding on how plant diseases emerge and spread over a given geographical region.

  3. Gradual versus punctuated equilibrium evolution in the Turkana Basin molluscs: evolutionary events or biological invasions?

    Science.gov (United States)

    Van Bocxlaer, Bert; Damme, Dirk Van; Feibel, Craig S

    2008-03-01

    A running controversy in evolutionary thought was Eldredge and Gould's punctuated equilibrium model, which proposes long periods of morphological stasis interspersed with rapid bursts of dramatic evolutionary change. One of the earliest and most iconic pieces of research in support of punctuated equilibrium is the work of Williamson on the Plio-Pleistocene molluscs of the Turkana Basin. Williamson claimed to have found firm evidence for three episodes of rapid evolutionary change separated by long periods of stasis in a high-resolution sequence. Most of the discussions following this report centered on the topics of (eco)phenotype versus genotype and the possible presence of preservational and temporal artifacts. The debate proved inconclusive, leaving Williamson's reports as one of the empirical foundations of the paradigm of punctuated equilibrium. Here we conclusively show Williamson's original interpretations to be highly flawed. The supposed rapid bursts of punctuated evolutionary change represent artifacts resulting from the invasion of extrabasinal faunal elements in the Turkana palaeolakes during wet phases well known from elsewhere in Africa. PMID:17999724

  4. Effects of genotypic and phenotypic variation on establishment are important for conservation, invasion, and infection biology.

    Science.gov (United States)

    Forsman, Anders

    2014-01-01

    There is abundant evidence that the probability of successful establishment in novel environments increases with number of individuals in founder groups and with number of repeated introductions. Theory posits that the genotypic and phenotypic variation among individuals should also be important, but few studies have examined whether founder diversity influences establishment independent of propagule pressure, nor whether the effect is model or context dependent. I summarize the results of 18 experimental studies and report on a metaanalysis that provides strong evidence that higher levels of genotypic and phenotypic diversity in founder groups increase establishment success in plants and animals. The effect of diversity is stronger in experiments carried out under natural conditions in the wild than under seminatural or standardized laboratory conditions. The realization that genetic and phenotypic variation is key to successful establishment may improve the outcome of reintroduction and translocation programs used to vitalize or restore declining and extinct populations. Founder diversity may also improve the ability of invasive species to establish and subsequently spread in environments outside of their native community, and enhance the ability of pathogens and parasites to colonize and invade the environment constituted by their hosts. It is argued that exchange of ideas, methodological approaches, and insights of the role of diversity for establishment in different contexts may further our knowledge, vitalize future research, and improve management plans in different disciplines. PMID:24367109

  5. [Biological factors influencing infectious diseases transmitted by invasive species of mosquitoes].

    Science.gov (United States)

    Boštíková, Vanda; Pasdiorová, Markéta; Marek, Jan; Prášil, Petr; Salavec, Miloslav; Sleha, Radek; Střtítecká, Hana; Blažek, Pavel; Hanovcová, Irena; Šošovičková, Renáta; Špliňo, Milan; Smetana, Jan; Chlíbek, Roman; Hytych, Václav; Kuča, Kamil; Boštík, Pavel

    2016-06-01

    Studies focused on arbovirus diseases transmitted by invasive species of mosquitoes have become increasingly significant in recent years, due to the fact that these vectors have successfully migrated to Europe and become established in the region. Mosquitoes, represented by more than 3 200 species, occur naturally worldwide, except in Antarctica. They feed on the blood of warm-blooded animals and by this route, they are capable of transmitting dangerous diseases. Some species can travel a distance of 10 km per night and can fly continuously for up to 4 hours at a speed of 1-2 km/h. Most species are active at night, in the evening or morning. It usually takes a mosquito female about 50 seconds to penetrate the skin of mammals and the subsequent blood meal usually takes about 2.5 minutes. Mosquitoes live for several weeks or months, depending on the environmental conditions. The VectorNet project is a European network of information exchange and sharing of data relating to the geographical distribution of arthropod vectors and transmission of infectious agents between human populations and animals. It aims at the development of strategic plans and vaccination policies which are the main tasks of this time, as well as the development and application of new disinfectants to control vector populations.

  6. [Biological factors influencing infectious diseases transmitted by invasive species of mosquitoes].

    Science.gov (United States)

    Boštíková, Vanda; Pasdiorová, Markéta; Marek, Jan; Prášil, Petr; Salavec, Miloslav; Sleha, Radek; Střtítecká, Hana; Blažek, Pavel; Hanovcová, Irena; Šošovičková, Renáta; Špliňo, Milan; Smetana, Jan; Chlíbek, Roman; Hytych, Václav; Kuča, Kamil; Boštík, Pavel

    2016-06-01

    Studies focused on arbovirus diseases transmitted by invasive species of mosquitoes have become increasingly significant in recent years, due to the fact that these vectors have successfully migrated to Europe and become established in the region. Mosquitoes, represented by more than 3 200 species, occur naturally worldwide, except in Antarctica. They feed on the blood of warm-blooded animals and by this route, they are capable of transmitting dangerous diseases. Some species can travel a distance of 10 km per night and can fly continuously for up to 4 hours at a speed of 1-2 km/h. Most species are active at night, in the evening or morning. It usually takes a mosquito female about 50 seconds to penetrate the skin of mammals and the subsequent blood meal usually takes about 2.5 minutes. Mosquitoes live for several weeks or months, depending on the environmental conditions. The VectorNet project is a European network of information exchange and sharing of data relating to the geographical distribution of arthropod vectors and transmission of infectious agents between human populations and animals. It aims at the development of strategic plans and vaccination policies which are the main tasks of this time, as well as the development and application of new disinfectants to control vector populations. PMID:27450526

  7. Two-dimensional engineering of molecular nanoparticles for biological applications

    OpenAIRE

    Tatkiewicz, Witold Ireneusz; Palet, Cristina

    2015-01-01

    El trabajo realizado en esta tesis se ha centrado en dos sistemas de nanopartículas moleculares que tienen un uso potencial en el campo de la nanomedicina: i) vesículas lipídicas – entidades supramoleculares que se proponen como sistemas de liberación de fármacos y ii) cuerpos de inclusión (Inclusion Bodies, IBs) – nanopartículas formadas por agregados proteicos. La primiera parte del trabajo se ha centrado en el estudio comparativo de sistemas vesiculares preparados por i) diferentes metodol...

  8. Two-dimensional engineering of molecular nanoparticles for biological applications

    OpenAIRE

    Tatkiewicz, Witold Ireneusz

    2015-01-01

    El trabajo realizado en esta tesis se ha centrado en dos sistemas de nanopartículas moleculares que tienen un uso potencial en el campo de la nanomedicina: i) vesículas lipídicas – entidades supramoleculares que se proponen como sistemas de liberación de fármacos y ii) cuerpos de inclusión (Inclusion Bodies, IBs) – nanopartículas formadas por agregados proteicos. La primiera parte del trabajo se ha centrado en el estudio comparativo de sistemas vesiculares preparados por i) diferentes meto...

  9. Biological and molecular characterizations of Toxoplasma gondii strains

    Science.gov (United States)

    Cole, R.A.; Lindsay, D.S.; Howe, D.K.; Roderick, Constance L.; Dubey, J.P.; Thomas, N.J.; Baeten, L.A.

    2000-01-01

    Toxoplasma gondii was isolated from brain or heart tissue from 15 southern sea otters (Enhydra lutris nereis) in cell cultures. These strains were used to infect mice that developed antibodies to T. gondii as detected in the modified direct agglutination test and had T. gondii tissue cysts in their brains at necropsy. Mouse brains containing tissue cysts from 4 of the strains were fed to 4 cats. Two of the cats excreted T. gondii oocysts in their feces that were infectious for mice. Molecular analyses of 13 strains indicated that they were all type II strains, but that they were genetically distinct from one another.

  10. The structural biology of molecular recognition by vancomycin.

    Science.gov (United States)

    Loll, P J; Axelsen, P H

    2000-01-01

    Vancomycin is the archetype among naturally occurring compounds known as glycopeptide antibiotics. Because it is a vital therapeutic agent used world-wide for the treatment of infections with gram-positive bacteria, emerging bacterial resistance to vancomycin is a major public health threat. Recent investigations into the mechanisms of action of glycopeptide antibiotics are driven by a need to understand their detailed mechanism of action so that new agents can be developed to overcome resistance. These investigations have revealed that glycopeptide antibiotics exhibit a rich array of complex cooperative phenomena when they bind target ligands, making them valuable model systems for the study of molecular recognition. PMID:10940250

  11. Nutritional Systems Biology Modeling: From Molecular Mechanisms to Physiology

    Science.gov (United States)

    de Graaf, Albert A.; Freidig, Andreas P.; De Roos, Baukje; Jamshidi, Neema; Heinemann, Matthias; Rullmann, Johan A.C.; Hall, Kevin D.; Adiels, Martin; van Ommen, Ben

    2009-01-01

    The use of computational modeling and simulation has increased in many biological fields, but despite their potential these techniques are only marginally applied in nutritional sciences. Nevertheless, recent applications of modeling have been instrumental in answering important nutritional questions from the cellular up to the physiological levels. Capturing the complexity of today's important nutritional research questions poses a challenge for modeling to become truly integrative in the consideration and interpretation of experimental data at widely differing scales of space and time. In this review, we discuss a selection of available modeling approaches and applications relevant for nutrition. We then put these models into perspective by categorizing them according to their space and time domain. Through this categorization process, we identified a dearth of models that consider processes occurring between the microscopic and macroscopic scale. We propose a “middle-out” strategy to develop the required full-scale, multilevel computational models. Exhaustive and accurate phenotyping, the use of the virtual patient concept, and the development of biomarkers from “-omics” signatures are identified as key elements of a successful systems biology modeling approach in nutrition research—one that integrates physiological mechanisms and data at multiple space and time scales. PMID:19956660

  12. Nutritional systems biology modeling: from molecular mechanisms to physiology.

    Directory of Open Access Journals (Sweden)

    Albert A de Graaf

    2009-11-01

    Full Text Available The use of computational modeling and simulation has increased in many biological fields, but despite their potential these techniques are only marginally applied in nutritional sciences. Nevertheless, recent applications of modeling have been instrumental in answering important nutritional questions from the cellular up to the physiological levels. Capturing the complexity of today's important nutritional research questions poses a challenge for modeling to become truly integrative in the consideration and interpretation of experimental data at widely differing scales of space and time. In this review, we discuss a selection of available modeling approaches and applications relevant for nutrition. We then put these models into perspective by categorizing them according to their space and time domain. Through this categorization process, we identified a dearth of models that consider processes occurring between the microscopic and macroscopic scale. We propose a "middle-out" strategy to develop the required full-scale, multilevel computational models. Exhaustive and accurate phenotyping, the use of the virtual patient concept, and the development of biomarkers from "-omics" signatures are identified as key elements of a successful systems biology modeling approach in nutrition research--one that integrates physiological mechanisms and data at multiple space and time scales.

  13. Chemical Biology Studies on Molecular Diversity of Annonaceous Acetogenins

    Institute of Scientific and Technical Information of China (English)

    Yao Zhu-Jun

    2004-01-01

    Annonaceous acetogenins, isolated from the Annonaceae plants, have been attracting worldwide attention in recent years due to their biological activities, especially as growth inhibitors of certain tumor ceils [ 1 ]. They have been shown to function by blocking complex I in mitochondria [2] as well as ubiquinone-linked NADPH oxidase in the cells of specific tumor cell lines, including some multidrug-resistant ones [3]. These features make these acetogenins excellent leads for the new antitumor agents. In our previous work, the compounds 1a to 1d (Figure 1), which relies on structure simplification while maintaining all essential functionalities of the acetogenins, was in vitro tested against several human solid tumor cell lines and showed interesting cell selectivity [4]. All four analogues show remarkable activity against the HCT-8 and HT-29 cell lines, while compound 1c was found the best [4bi. In order to further investigate the effects of key structural features, a convergent parallel fragments assembly strategy was developed [4e]. In addition, the biological relevancies of typical annonaceous acetogenin mimetics were also studied [4f].

  14. Lepidopterans as potential agents for the biological control of the invasive plant, Miconia calvescens.

    Science.gov (United States)

    Morais, Elisangela G F; Picanço, Marcelo C; Semeão, Altair A; Barreto, Robert W; Rosado, Jander F; Martins, Julio C

    2012-01-01

    This work investigated eight species of Lepidoptera associated with Miconia calvescens DC. (Myrtales: Melastomataceae) in Brazil, including six defoliators, Salbia lotanalis Druce (Lepidoptera: Pyralidae), Druentia inscita Schaus (Mimallonidae), Antiblemma leucocyma Hampson (Noctuidae), three Limacodidae species, a fruit borer Carposina cardinata Meyrick (Carposinidae), and a damager of flowers Pleuroprucha rudimentaria Guenée (Geometridae). Based on host specificity and the damage caused to plants, S. lotanalis and D. inscita are the most promising species for biological control of M. calvescens. Furthermore, if C. cardinata and P. rudimentaria have host specificity in future tests, these caterpillars could also be considered as appropriate biocontrol agents. PMID:22938203

  15. Molecular characterization, biological forms and sporozoite rate of Anopheles stephensi in southern Iran

    Institute of Scientific and Technical Information of China (English)

    Ali Reza Chavshin; Mohammad Ali Oshaghi; Hasan Vatandoost; Ahmad Ali Hanafi-Bojd; Ahmad Raeisi; Fatemeh Nikpoor

    2014-01-01

    Objective: To identify the biological forms, sporozoite rate and molecular characterization of the Anopheles stephensi (An. stephensi) in Hormozgan and Sistan-Baluchistan provinces, the most important malarious areas in Iran. Methods: Wild live An. stephensi samples were collected from different malarious areas in southern Iran. The biological forms were identified based on number of egg-ridges. Molecular characterization of biological forms was verified by analysis of the mitochondrial cytochrome oxidase subunit I and II (mtDNA-COI/COII). The Plasmodium infection was examined in the wild female specimens by species-specific nested–PCR method. Results: Results showed that all three biological forms including mysorensis, intermediate and type are present in the study areas. Molecular investigations revealed no genetic variation between mtDNA COI/COII sequences of the biological forms and no Plasmodium parasites was detected in the collected mosquito samples. Conclusions:Presence of three biological forms with identical sequences showed that the known biological forms belong to a single taxon and the various vectorial capacities reported for these forms are more likely corresponded to other epidemiological factors than to the morphotype of the populations. Lack of malaria parasite infection in An. stephensi, the most important vector of malaria, may be partly due to the success and achievement of ongoing active malaria control program in the region.

  16. Molecular tests to detect human papillomavirus infection in patients with cervical dysplasia and invasive cervical cancer in Saudi Arabia

    Directory of Open Access Journals (Sweden)

    Sait KH

    2011-07-01

    Full Text Available Khalid H Sait1, Faten S Gazzaz21Obstetrics and Gynecology Department, 2Medical Virology Department, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi ArabiaPurpose: The aim of this study was to determine the actual human papillomavirus (HPV subtype that presents in cervical dysplasia and invasive carcinoma in the Saudi population, and the feasibility of using Hybrid Capture 2 technique (HC2 on biopsy specimens to detect certain HPV subtypes.Patients and methods: A prospective study was conducted from March 2007 to December 2008. The subjects studied were women with a mean age of 48.18 years, who attended the hospital for cervical biopsy due to the suspected diagnosis of cervical dysplasia or an invasive disease, based on previous suspicious Pap smear. HPV DNA hybridization by HC2 was performed on the cervical biopsies of these patients, to detect HPV infection.Results: During the period of this study, 45 patients had cervical biopsies taken for HPV testing. Seven patients had a negative HC2 result and were found to have no cervical dysplasia on the final pathology review. Seventeen cases with cervical dysplasia and 21 patients with invasive disease were presented; the mean age was 48 years. HC2 testing for HPV were found to be positive in patients with cervical dysplasia, invasive carcinoma, and all in 5 (29.4%, 13 (61.9% and 18 (47.4%, respectively. The sensitivity of the test is 47% and specificity is 100%.Conclusion: The use of molecular detection of HPV DNA by HC2 in biopsy is feasible and effective. These results confirm the finding that HPV contributes to the etiology of cervical cancer in Muslim society.Keywords: HPV, subtyping, cervical neoplasia

  17. Molecular biology of maize Ac/Ds elements: an overview.

    Science.gov (United States)

    Lazarow, Katina; Doll, My-Linh; Kunze, Reinhard

    2013-01-01

    Maize Activator (Ac) is one of the prototype transposable elements of the hAT transposon superfamily, members of which were identified in plants, fungi, and animals. The autonomous Ac and nonautonomous Dissociation (Ds) elements are mobilized by the single transposase protein encoded by Ac. To date Ac/Ds transposons were shown to be functional in approximately 20 plant species and have become the most widely used transposable elements for gene tagging and functional genomics approaches in plants. In this chapter we review the biology, regulation, and transposition mechanism of Ac/Ds elements in maize and heterologous plants. We discuss the parameters that are known to influence the functionality and transposition efficiency of Ac/Ds transposons and need to be considered when designing Ac transposase expression constructs and Ds elements for application in heterologous plant species.

  18. Cell and molecular biology for diagnostic and therapeutic technology

    Science.gov (United States)

    Tan, M. I.

    2016-03-01

    Our body contains 100 trillion cells. However, each cell has certain function and structure. For maintaining their integrity, cells will be collaborating with each other and with extracellular matrix surround them to form a tissue. These interactions effect internally on many networks or pathway such as signalling pathway, metabolic pathway and transport network in the cell. These networks interact with each other to maintain cell survival, cell structure and function and moreover the tissue as well as the organ which the cells built. Therefore, as part of a tissue, genetic and epigenetic abnormality of a cell can also alter these networks, and moreover disturb the function of the tissue itself. Hence, condition of genetic and epigenetic of the cell may affect other conditions in omics level such as transcriptomic, proteomic, metabolomics characteristics which can be differentiated by a particular unique molecular profile from each level, which can be used for diagnostic as well as for targeted therapy.

  19. Molecular biology and pathogenesis of hepatitis E virus

    Indian Academy of Sciences (India)

    Vivek Chandra; Shikha Taneja; Manjula Kalia; Shahid Jameel

    2008-11-01

    The hepatitis E virus (HEV) is a small RNA virus and the etiological agent for hepatitis E, a form of acute viral hepatitis. The virus has a feco-oral transmission cycle and is transmitted through environmental contamination, mainly through drinking water. Recent studies on the isolation of HEV-like viruses from animal species also suggest zoonotic transfer of the virus. The absence of small animal models of infection and efficient cell culture systems has precluded virological studies on the replication cycle and pathogenesis of HEV. A vaccine against HEV has undergone successful clinical testing and diagnostic tests are available. This review describes HEV epidemiology, clinical presentation, pathogenesis, molecular virology and the host response to HEV infection. The focus is on published literature in the past decade.

  20. Biotechnology of microbial xylanases: enzymology, molecular biology, and application.

    Science.gov (United States)

    Subramaniyan, S; Prema, P

    2002-01-01

    Xylanases are hydrolases depolymerizing the plant cell wall component xylan, the second most abundant polysaccharide. The molecular structure and hydrolytic pattern of xylanases have been reported extensively and the mechanism of hydrolysis has also been proposed. There are several models for the gene regulation of which this article could add to the wealth of knowledge. Future work on the application of these enzymes in the paper and pulp, food industry, in environmental science, that is, bio-fueling, effluent treatment, and agro-waste treatment, etc. require a complete understanding of the functional and genetic significance of the xylanases. However, the thrust area has been identified as the paper and pulp industry. The major problem in the field of paper bleaching is the removal of lignin and its derivatives, which are linked to cellulose and xylan. Xylanases are more suitable in the paper and pulp industry than lignin-degrading systems. PMID:11958335

  1. Molecular biological enhancement of coal biodesulfurization. [Rhodococcus rhodochrous

    Energy Technology Data Exchange (ETDEWEB)

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

    1990-07-01

    The overall objective of this project is to sue 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. The work planned for the current quarter (May 1990 to July 1990) includes the following activities: (1) Construct a cloning vector that can be used in Rhodococcus rhodochrous IGTS8 from the small cryptic plasmid found in Rhodococcus rhodochrous ATCC 190607; (2) Develop techniques for the genetic analysis of IGTS8; (3) Continue biochemical experiments, particularly those that may allow the identification of desulfurization-related enzymes; (4) Continue experiments with coal to determine the kinetics of organic sulfur removal.

  2. Molecular biology and genetics of embryonic eyelid development.

    Science.gov (United States)

    Rubinstein, Tal J; Weber, Adam C; Traboulsi, Elias I

    2016-09-01

    The embryology of the eyelid is a complex process that includes interactions between the surface ectoderm and mesenchymal tissues. In the mouse and human, the eyelids form and fuse before birth; they open prenatally in the human and postnatally in the mouse. In the mouse, cell migration is stimulated by different growth factors such as FGF10, TGF-α, Activin B, and HB-EGF. These growth factors modulate downstream BMP4 signaling, the ERK cascade, and JNK/c-JUN. Several mechanisms, such as the Wnt/β-catenin signaling pathway, may inhibit and regulate eyelid fusion. Eyelid opening, on the other hand, is driven by the BMP/Smad signaling system. Several human genetic disorders result from dysregulation of the above molecular pathways. PMID:26863902

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

    Science.gov (United States)

    Proctor, Elizabeth A; Dokholyan, Nikolay V

    2016-04-01

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

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

    Science.gov (United States)

    Proctor, Elizabeth A; Dokholyan, Nikolay V

    2016-04-01

    Discrete Molecular Dynamics (DMD) is a physics-based simulation method using discrete energetic potentials rather than traditional continuous potentials, allowing microsecond time scale simulations of biomolecular systems to be performed on personal computers rather than supercomputers or specialized hardware. With the ongoing explosion in processing power even in personal computers, applications of DMD have similarly multiplied. In the past two years, researchers have used DMD to model structures of disease-implicated protein folding intermediates, study assembly of protein complexes, predict protein-protein binding conformations, engineer rescue mutations in disease-causative protein mutants, design a protein conformational switch to control cell signaling, and describe the behavior of polymeric dispersants for environmental cleanup of oil spills, among other innovative applications. PMID:26638022

  5. The Physics of Proteins An Introduction to Biological Physics and Molecular Biophysics

    CERN Document Server

    Frauenfelder, Hans; Chan, Winnie S

    2010-01-01

    Physics and the life sciences have established new connections within the past few decades, resulting in biological physics as an established subfield with strong groups working in many physics departments. These interactions between physics and biology form a two-way street with physics providing new tools and concepts for understanding life, while biological systems can yield new insights into the physics of complex systems. To address the challenges of this interdisciplinary area, The Physics of Proteins: An Introduction to Biological Physics and Molecular Biophysics is divided into three interconnected sections. In Parts I and II, early chapters introduce the terminology and describe the main biological systems that physicists will encounter. Similarities between biomolecules, glasses, and solids are stressed with an emphasis on the fundamental concepts of living systems. The central section (Parts III and IV) delves into the dynamics of complex systems. A main theme is the realization that biological sys...

  6. Molecular characterization of MHC class II in the Australian invasive cane toad reveals multiple splice variants.

    Science.gov (United States)

    Lillie, Mette; Cui, Jian; Shine, Richard; Belov, Katherine

    2016-07-01

    The cane toad has gained notoriety for its invasion across the Australian landscape, with significant impacts on the native Australian fauna. The invasion has accelerated over time, with invading cane toads adapted for highly dispersive traits. This, however, has come at the cost of the immune system, with lower investment in some immune functions. To investigate the cane toad's immunogenetics, we characterized four major histocompatibility complex (MHC) class IIA and three MHC class IIB loci. Preliminary observations suggest very low allelic diversity at all loci. We also observed various splice isoforms. One isoform seen at one class IIA and two class IIB loci was missing exon 2, which is essential to peptide binding and presentation. The other isoform, observed at a class IIA locus, is likely to be a soluble MHC product. These results may suggest a significant role of alternative splicing of MHC loci in the Australian cane toad. PMID:27233954

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

    Science.gov (United States)

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

    2010-01-01

    We describe an ongoing collaborative curriculum materials development project between Sweet Briar College and Western Michigan University, with support from the National Science Foundation. We present a collection of modules under development that can be used in existing mathematics and biology courses, and we address a critical national need to…

  8. Essential concepts and underlying theories from physics, chemistry, and mathematics for "biochemistry and molecular biology" majors.

    Science.gov (United States)

    Wright, Ann; Provost, Joseph; Roecklein-Canfield, Jennifer A; Bell, Ellis

    2013-01-01

    Over the past two years, through an NSF RCN UBE grant, the ASBMB has held regional workshops for faculty members from around the country. The workshops have focused on developing lists of Core Principles or Foundational Concepts in Biochemistry and Molecular Biology, a list of foundational skills, and foundational concepts from Physics, Chemistry, and Mathematics that all Biochemistry or Molecular Biology majors must understand to complete their major coursework. The allied fields working group created a survey to validate foundational concepts from Physics, Chemistry, and Mathematics identified from participant feedback at various workshops. One-hundred twenty participants responded to the survey and 68% of the respondents answered yes to the question: "We have identified the following as the core concepts and underlying theories from Physics, Chemistry, and Mathematics that Biochemistry majors or Molecular Biology majors need to understand after they complete their major courses: 1) mechanical concepts from Physics, 2) energy and thermodynamic concepts from Physics, 3) critical concepts of structure from chemistry, 4) critical concepts of reactions from Chemistry, and 5) essential Mathematics. In your opinion, is the above list complete?" Respondents also delineated subcategories they felt should be included in these broad categories. From the results of the survey and this analysis the allied fields working group constructed a consensus list of allied fields concepts, which will help inform Biochemistry and Molecular Biology educators when considering the ASBMB recommended curriculum for Biochemistry or Molecular Biology majors and in the development of appropriate assessment tools to gauge student understanding of how these concepts relate to biochemistry and molecular biology.

  9. Disease Burden of Invasive Listeriosis and Molecular Characterization of Clinical Isolates in Taiwan, 2000-2013.

    Directory of Open Access Journals (Sweden)

    Yu-Tsung Huang

    Full Text Available The information about disease burden and epidemiology of invasive listeriosis in Asia is scarce. From 2000 to 2013, a total of 338 patients with invasive listeriosis (bacteremia, meningitis, and peritonitis were treated at four medical centers in Taiwan. The incidence (per 10,000 admissions of invasive listeriosis increased significantly during the 14-year period among the four centers (0.15 in 2000 and >1.25 during 2010-2012 and at each of the four medical centers. Among these patients, 45.9% were elderly (>65 years old and 3.3% were less than one year of age. More than one-third (36.7% of the patients acquired invasive listeriosis in the spring (April to June. Among the 132 preserved Listeria monocytogenes isolates analyzed, the most frequently isolated PCR serogroup-sequence type (ST was IIb-ST87 (23.5%, followed by IIa-ST378 (19.7% and IIa-ST155 (12.1%. Isolation of PCR serogroups IIb and IVb increased significantly with year, with a predominance of IIb-ST87 isolates (23.5% and IIb-ST 228 isolates emerging in 2013. A total of 12 different randomly amplified polymorphic DNA (RAPD patterns (Patterns I to XII were identified among the 112 L. monocytogenes isolates belonging to eight main PCR serogroup-STs. Identical RAPD patterns were found among the isolates exhibiting the same PCR serogroup-ST. In conclusion, our study revealed that during 2000-2013, listeriosis at four medical centers in Taiwan was caused by heterogeneous strains and that the upsurge in incidence beginning in 2005 was caused by at least two predominant clones.

  10. Tissue Diagnosis of Invasive Fungal Infections: Current Limitations and the Emerging Use of Molecular Techniques

    OpenAIRE

    Rickerts, Volker; Fredricks, David N.

    2012-01-01

    Invasive fungal diseases (IFD) due to opportunistic fungi are commonly treated using empirical antifungal therapy. Therefore, a comprehensive study of organisms associated with IFD is essential to define successful empiric therapies in each setting. Current diagnostic tests, such as culture, histology and serology are suboptimal, leading to delays in the initiation of antifungal therapies and resulting in high mortality rates despite the availability of several new antifungal agents. Using mo...

  11. Polyhydroyalkanoates: from Basic Research and Molecular Biology to Application

    Directory of Open Access Journals (Sweden)

    Amro Abd alFattah Amara

    2010-09-01

    Full Text Available This review describes the Polyhydroxyalkanoate (PHA, an intracellular biodegradable microbial polymer. PHAs is formed from different types of three hydroxyalkanoic acids monomers, each unit forms an ester bond with the hydroxyl group of the other one and the hydroxyl substituted carbon has R configuration. The C-3 atom in β position is branched with at least one carbon atom in the form of methyl group (C1 to thirteen carbons in the form of tridecyl (C13. This alkyl side chain is not necessarily saturated. PHAs are biosynthesized through regulated pathways by specific enzymes. PHAs are accumulated in bacterial cells from soluble to insoluble form as storage materials inside the inclusion bodies during unbalanced nutrition or to save organisms from reducing equivalents. PHAs are converted again to soluble components by PHAs depolymerases and the degraded materials enter various metabolic pathways. Until now, four classes of enzymes responsible for PHAs polymerization are known. PHAs were well studied regarding their promising applications, physical, chemical and biological properties. PHAs are biodegradable, biocompatible, have good material properties, renewable and can be used in many applications. The most limiting factor in PHAs commercialization is their high cost compared to the petroleum plastics. This review highlights the new knowledge and that established by the pioneers in this field as well as the factors, which affect PHAs commercialization.

  12. Chromatic alteration on marble surfaces analysed by molecular biology tools

    Directory of Open Access Journals (Sweden)

    Franco Palla

    2007-07-01

    Full Text Available The patina represents a superficial natural alteration of the constituting matter of the work of art. It emerges from the natural and usual stabilization process that the materials of the surface undergo because of the interaction with outdoor agents characterizing the surrounding environment. Besides, it is not linked to an obvious phenomenon of degradation that can be noticed through the change in the original colour of the matter. This is what we intend when we talk about biological patina usually generated by macro and/or micro-organic colonization (fungi, bacteria, alga which contributes to surface bio-deterioration and thus lead to the formation of orange, red or even brown and dark pigmented areas. The presence of chromatic alterations (rose-coloured areas, as a consequence of bacterial colonization, was most particularly pointed out in different sites, such as in the marble slabs on the facades of both the Cathedral of Siena (Duomo di Siena and the Certosa of Pavia. The present study shows an example of chromatic alteration of the surface of marble works due to bacterial colonization.

  13. Recent advances in biological effect and molecular mechanism of arabidopsis thaliana irradiated by ion beams

    International Nuclear Information System (INIS)

    Newly research progresses were summarized in effect of ion beams on seed surface, biological effect, growth, development, gravitropism and so on. Furthermore, mutation molecular mechanism of Arabidopsis thaliana was discussed, for example, alteration of DNA bases, DNA damage, chromosomal recombination, characteristics of mutant transmissibility, etc. Meanwhile, the achievements of transfer- ring extraneous gene to Arabidopsis thaliana by ion beams were reviewed in the paper. At last, the future prospective are also discussed here in mutation molecular mechanism and the potential application of biological effect of heavy ion beams. (authors)

  14. Molecular Imaging Approaches to Understanding the Roles of Hydrogen Peroxide Biology in Stress and Development

    OpenAIRE

    Dickinson, Bryan Craig

    2010-01-01

    The production of hydrogen peroxide (H2O2) in biological systems is associated with a variety of pathologies including neurodegenerative diseases, cancer, and the general process of aging. However, a growing body of evidence suggests that the reactivity of this particular reactive oxygen species (ROS) is also harnessed for physiological processes. Molecular imaging using fluorescence microscopy offers a valuable approach for deciphering the multifaceted roles of H2O2 in biological processes. ...

  15. Molecular motor traffic: From biological nanomachines to macroscopic transport

    Science.gov (United States)

    Lipowsky, Reinhard; Chai, Yan; Klumpp, Stefan; Liepelt, Steffen; Müller, Melanie J. I.

    2006-12-01

    All cells of animals and plants contain complex transport systems based on molecular motors which walk along cytoskeletal filaments. These motors are rather small and have a size of 20-100 nm but are able to pull vesicles, organelles and other types of cargo over large distances, from micrometers up to meters. There are several families of motors: kinesins, dyneins, and myosins. Most of these motors have two heads which are used as legs and perform discrete steps along the filaments. Several aspects of the motor behavior will be discussed: motor cycles of two-headed motors; walks of single motors or cargo particles which consist of directed movements interrupted by random, diffusive motion; cargo transport through tube-like compartments; active diffusion of cargo particles in slab-like compartments; cooperative transport of cargo by several motors which may be uni- or bi-directional; and systems with many interacting motors that exhibit traffic jams, self-organized density and flux patterns, and traffic phase transitions far from equilibrium. It is necessary to understand these traffic phenomena in a quantitative manner in order to construct and optimize biomimetic transport systems based on motors and filaments with many possible applications in bioengineering, pharmacology, and medicine.

  16. A systems biology approach identifies Molecular networks defining skeletal muscle abnormalities in chronic obstructive pulmonary disease.

    OpenAIRE

    Nil Turan; Susana Kalko; Anna Stincone; Kim Clarke; Ayesha Sabah; Katherine Howlett; S John Curnow; Rodriguez, Diego A.; Marta Cascante; Laura O'Neill; Stuart Egginton; Josep Roca; Francesco Falciani

    2011-01-01

    Chronic Obstructive Pulmonary Disease (COPD) is an inflammatory process of the lung inducing persistent airflow limitation. Extensive systemic effects, such as skeletal muscle dysfunction, often characterize these patients and severely limit life expectancy. Despite considerable research efforts, the molecular basis of muscle degeneration in COPD is still a matter of intense debate. In this study, we have applied a network biology approach to model the relationship between muscle molecular an...

  17. Targeting paraprotein biosynthesis for non-invasive characterization of myeloma biology.

    Directory of Open Access Journals (Sweden)

    Katharina Lückerath

    Full Text Available PURPOSE: Multiple myeloma is a hematologic malignancy originating from clonal plasma cells. Despite effective therapies, outcomes are highly variable suggesting marked disease heterogeneity. The role of functional imaging for therapeutic management of myeloma, such as positron emission tomography with 2-deoxy-2-[¹⁸F]fluoro-D-glucose (¹⁸F-FDG-PET, remains to be determined. Although some studies already suggested a prognostic value of ¹⁸F-FDG-PET, more specific tracers addressing hallmarks of myeloma biology, e.g. paraprotein biosynthesis, are needed. This study evaluated the amino acid tracers L-methyl-[¹¹C]-methionine (¹¹C-MET and [¹⁸F]-fluoroethyl-L-tyrosine ((¹⁸F-Fet for their potential to image myeloma and to characterize tumor heterogeneity. EXPERIMENTAL DESIGN: To study the utility of ¹¹C-MET, ¹⁸F-Fet and ¹⁸F-FDG for myeloma imaging, time activity curves were compared in various human myeloma cell lines (INA-6, MM1.S, OPM-2 and correlated to cell-biological characteristics, such as marker gene expression and immunoglobulin levels. Likewise, patient-derived CD138⁺ plasma cells were characterized regarding uptake and biomedical features. RESULTS: Using myeloma cell lines and patient-derived CD138⁺ plasma cells, we found that the relative uptake of ¹¹C-MET exceeds that of ¹⁸F-FDG 1.5- to 5-fold and that of ¹⁸F-Fet 7- to 20-fold. Importantly, ¹¹C-MET uptake significantly differed between cell types associated with worse prognosis (e.g. t(4;14 in OPM-2 cells and indolent ones and correlated with intracellular immunoglobulin light chain and cell surface CD138 and CXCR4 levels. Direct comparison of radiotracer uptake in primary samples further validated the superiority of ¹¹C-MET. CONCLUSION: These data suggest that ¹¹C-MET might be a versatile biomarker for myeloma superior to routine functional imaging with ¹⁸F-FDG regarding diagnosis, risk stratification, prognosis and discrimination of tumor

  18. Progresses of Molecular Markers Application in Invasive Plant Research%分子标记在入侵植物研究中的应用

    Institute of Scientific and Technical Information of China (English)

    王从彦; 刘雪艳; 杜道林

    2013-01-01

    入侵植物给入侵地的生态系统造成了多重影响,而入侵生态学研究对探析入侵植物成功入侵的机制及其可持续控制具有重要的理论和实际意义.分子标记作为一种基于DNA水平的遗传分析技术,为解决入侵生态学研究的许多基本问题提供了很好的手段与平台.基于此,简要综述了分子标记技术在入侵植物遗传多样性分析、入侵机制及入侵模式探究等方面的应用研究进展.%Invasive species can cause multiple effects on national ecosystems. The research of invasion ecology is of significance in understanding the invasion mechanisms of invasive species and in developing corresponding sustainable control methods. Molecular marker has been used to approach some essential issues in the research of invasion ecology as a useful tool base at DNA level. In this paper,the research progresses of molecular marker application in genetic diversities, invasion mechanisms,and spread pattern of invasive plants were reviewed to provide the relevant theoretical base for the further study.

  19. Biochemical and molecular biological aspects of silverfish allergens.

    Science.gov (United States)

    Barletta, Bianca; Di Felice, Gabriella; Pini, Carlo

    2007-01-01

    Insects and insect-derived materials have been implicated as a risk factor for sensitization and subsequent elicitation of allergic rhinitis and allergic bronchial asthma. During the last decades, insects other than those known as allergenic, were investigated for their potential role in inducing and triggering an IgE immune response. Among these, the silverfish, an insect belonging to the Thysanura order, appeared to be of particular interest. Silverfish (Lepisma saccharina) is the most primitive living insect, and represents a descendent of the ancestral wingless insects. They are 3-12 mm long, have three tail feelers and are covered with shiny scales. They shun light and need a humid environment and their diet consists of carbohydrate materials such as paper and book-binding glue, crumbs of bread and flour. Because of these features, silverfish finds an optimal habitat both in dwellings and workplaces and in spite of its antiquity, silverfish has succeeded in exploiting the new opportunity created by man. Although its importance significantly increased when it has been demonstrated that house dust contains significant silverfish levels even in houses where the inhabitants were unaware of its presence, no silverfish extract for diagnosis of allergic diseases is commercially available yet. Identification of optimal extraction conditions and characterization of allergenic extracts are the first steps to obtain an effective allergen preparation suitable for diagnosis and therapy, and will be useful as a reference preparation for assessing silverfish exposure in different indoor environments. It has been cloned and characterized a silverfish tropomyosin, named Lep s 1, which represents the first allergen identified in silverfish extract and can be regarded as a molecule cross-reactive among inhalant and edible invertebrates allergenic sources. rLep s 1 displayed biological activity, suggesting that it could be regarded as a useful tool to study the role of silverfish

  20. Chapter 27 -- Breast Cancer Genomics, Section VI, Pathology and Biological Markers of Invasive Breast Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Spellman, Paul T.; Heiser, Laura; Gray, Joe W.

    2009-06-18

    reveal the molecular differences between cancer and normal that may be exploited to therapeutic benefit or that provide targets for molecular assays that may enable early cancer detection, and predict individual disease progression or response to treatment. This chapter reviews current and future directions in genome analysis and summarizes studies that provide insights into breast cancer pathophysiology or that suggest strategies to improve breast cancer management.

  1. Nanoparticle-Templated Molecular Recognition Platforms for Detection of Biological Analytes.

    Science.gov (United States)

    Beyene, Abraham G; Demirer, Gozde S; Landry, Markita P

    2016-01-01

    Molecular recognition of biological analytes with optical nanosensors provides both spatial and temporal biochemical information. A recently developed sensing platform exploits near-infrared fluorescent single-wall carbon nanotubes combined with electrostatically pinned heteropolymers to yield a synthetic molecular recognition technique that is maximally transparent through biological matter. This molecular recognition technique is known as corona phase molecular recognition (CoPhMoRe). In CoPhMoRe, the specificity of a folded polymer toward an analyte does not arise from a pre-existing polymer-analyte chemical affinity. Rather, specificity is conferred through conformational changes undergone by a polymer that is pinned to the surface of a nanoparticle in the presence of an analyte and the subsequent modifications in fluorescence readout of the nanoparticles. The protocols in this article describe a novel single-molecule microscopy tool (near-infrared fluorescence and total internal reflection fluorescence [nIRF TIRF] hybrid microscope) to visualize the CoPhMoRe recognition process, enabling a better understanding of synthetic molecular recognition. We describe this requisite microscope for simultaneous single-molecule visualization of optical molecular recognition and signal transduction. We elaborate on the general procedures for synthesizing and identifying single-walled carbon nanotube-based sensors that employ CoPhMoRe via two biologically relevant examples of single-molecule recognition for the hormone estradiol and the neurotransmitter dopamine. © 2016 by John Wiley & Sons, Inc. PMID:27622569

  2. Biochemistry and molecular biology of the Caenorhabditis elegans dauer larva

    Energy Technology Data Exchange (ETDEWEB)

    Wadsworth, W.G.

    1989-01-01

    Biochemical and molecular techniques have been used to study the formation and recovery of the developmentally arrested, non-feeding dauer stage of the nematode Caenorhabditis elegans. While investigating developmental transitions in energy metabolism, a major metabolite isolated from perchloric acid extracts has been identified as a modified uridine nucleotide. The compound was isolated by gel filtration and ion-exchange chromatography and its structure was determined by {sup 1}H NMR and {sup 13}C NMR spectroscopy. This compound is the most abundant metabolite detected in {sup 31}PMR spectra of perchloric acid extracts from growing larvae. In the absence of phosphoarginine or phosphocreatine, this modified nucleotide may have an important function in the nematode's energy metabolism, and it may also be found in several other invertebrates. During recovery from the dauer stage, metabolic activation is accompanied by a decrease in intracellular pH (pH{sub i}). Although metabolic activation has been associated with an alkaline pH{sub i} shift in other organisms, in vivo {sup 31}P NMR analysis of recovering dauer larvae shows a pH{sub i} decrease from {approximately}7.3 to {approximately}6.3 within 3 hr after the animals encounter food. This shift occurs before feeding begins, and coincides with, or soon follows, the development commitment to recover from the dauer stage, suggesting that control of pH{sub i} may be important in the regulation of larval development in nematodes. A library enriched for sequences expressed specifically during the L2d (predauer) stage was made by selecting plaques from a genomic lambda library that hybridized to subtracted L2d cDNA probes. Ultimately, three clones that were shown to hybridize only to L2d RNA were selected.

  3. Hepatitis C virus: molecular biology & current therapeutic options.

    Science.gov (United States)

    Sharma, Suresh D

    2010-01-01

    Hepatitis C virus (HCV) is a small (approximately 55 to 65 nm), spherical, enveloped, hepatotropic RNA virus that causes acute and chronic hepatitis in humans. Persistent virus infection with HCV often leads to cirrhosis and hepatocellular carcinoma (HCC). At present there is neither a selective antiviral therapy nor a preventive vaccine. The only available treatment option is a long-acting pegylated-interferon-alpha, given in combination with nucleoside analog ribavirin, which is not very effective. Molecular studies of HCV began with the successful cloning of its genome in 1989. For many years, research to develop therapeutics was stalled by the inability to grow virus in tissue culture. A major milestone was achieved with the recent development of a robust cell culture system for HCV propagation. HCV proteins assemble and form replication complexes on modified host membranes, called as membranous webs. Even though HCV is detected and targeted by host immune mechanisms, it establishes and maintains a life-long persistent infection. HCV has evolved multiple strategies to survive and persist in hostile cellular environments; and the viral population is known to rapidly change during the course of a natural infection thereby escaping immune surveillance. Rapid mutations also help virus to survive by selecting for the variants which are resistant to antiviral drugs. Although precise mechanisms regulating HCV entry into hepatic cells via receptors remain unknown, HCV also has the capability of direct cell-to-cell transmission. The extremely complex and incompletely understood nature of the HCV lifecycle has complicated the discovery of new therapies. A complete understanding of the functional roles played by the HCV proteins during HCV lifecycle is vital for developing a successful cure. This review deals with current status of efforts in addressing these daunting tasks and challenges in developing therapeutics against chronic and rapidly changing hepatitis C virus

  4. Molecular biology of Lea genes of higher plants

    Energy Technology Data Exchange (ETDEWEB)

    1991-07-01

    This report contains our progress to date in determining the function of the D-7 Lea proteins in cotton embryos. We have completely sequenced the D-7 gene and established {ital E. coli} transformants which synthesize reasonable amounts of the D-7 protein. Two-dimensional electrophoresis was required to assay fractions for D-7 protein during purification to homogeneity, since D-7 has no known enzymatic activity, contains no Trp, and little Phe or Tyr, and {ital E. coli} has several proteins of similar molecular weight to D-7. Purified D-7 was used to generate monospecific antibodies which are being used for determination of the cellular distribution of D-7, and also for exact quantitation of D-7 in late-stage cotton embryos. Computerized modelling of D-7 has shown similarities to proteins with a coiled-coil structure, but fitting D-7 to this structure resulted in a violation of the handedness rule. If the pitch of the helix is changed from 3.6 to 3.667, however, a three dimensional structure (not a coiled coil) is generated which has overall energetics of formation nearly as favorable as the traditional {alpha} helix. The driving force for the change in pitch is proposed to result from favorable energetics of dimerization. Preliminary evidence indicates that D-7 does indeed dimerize in solution. Future experiments will determine the exact 3D structure of D-7 and the related protein D-29, as well as test the hypothesis that D-7 and D-29 are involved in mitigating dehydration of embryos and plants through sequestering phosphate or other ions in sufficient quantity to prevent ion precipitation or crystallization. 13 refs., 3 figs. (MHB)

  5. Description of a new species of Anagyrus Howard (Hymenoptera: Chalcidoidea: Encyrtidae), a promising biological control agent of the invasive Madeira mealybug, Phenacoccus madeirensis Green (Hemiptera: Sternorrhyncha: Pseudococcidae).

    Science.gov (United States)

    Rameshkumar, A; Noyes, J S; Poorani, J; Chong, J H

    2013-01-01

    Anagyrus amnestos sp. n. (Hymenoptera: Encyrtidae), a promising parasitoid of the invasive Madeira mealybug, Phenacoccus madeirensis Green (Hemiptera: Pseudococcidae), is described based on material collected from India. This parasitoid was identified as Anagyrus sp. nov. nr. sinope Noyes & Menezes in recent literature, and was initially collected in Georgia, USA. It was found to be a specific parasitoid of the Madeira mealybug and its biological attributes and potential as a biological control agent of this pest were studied. In what appears to be a case of fortuitous introduction, we detected this parasitoid in large numbers on Madeira mealybugs from the southern Indian state of Karnataka, where the mealybug is a recently introduced invasive pest. In view of its economic importance as a potential biological control agent of the Madeira mealybug, it is formally described and illustrated here. Comparative accounts of the new species vis-a-vis its close relatives in India and the Americas are provided.

  6. Description of a new species of Anagyrus Howard (Hymenoptera: Chalcidoidea: Encyrtidae), a promising biological control agent of the invasive Madeira mealybug, Phenacoccus madeirensis Green (Hemiptera: Sternorrhyncha: Pseudococcidae).

    Science.gov (United States)

    Rameshkumar, A; Noyes, J S; Poorani, J; Chong, J H

    2013-01-01

    Anagyrus amnestos sp. n. (Hymenoptera: Encyrtidae), a promising parasitoid of the invasive Madeira mealybug, Phenacoccus madeirensis Green (Hemiptera: Pseudococcidae), is described based on material collected from India. This parasitoid was identified as Anagyrus sp. nov. nr. sinope Noyes & Menezes in recent literature, and was initially collected in Georgia, USA. It was found to be a specific parasitoid of the Madeira mealybug and its biological attributes and potential as a biological control agent of this pest were studied. In what appears to be a case of fortuitous introduction, we detected this parasitoid in large numbers on Madeira mealybugs from the southern Indian state of Karnataka, where the mealybug is a recently introduced invasive pest. In view of its economic importance as a potential biological control agent of the Madeira mealybug, it is formally described and illustrated here. Comparative accounts of the new species vis-a-vis its close relatives in India and the Americas are provided. PMID:26176096

  7. 杂草管理的分子生物学途径%Molecular Biology Approaches to Weed Management

    Institute of Scientific and Technical Information of China (English)

    Wun S. CHAO

    2012-01-01

    全球气候变化有利于外来杂草的入侵与传播,因为外来种通常可以快速适应环境.除草剂和抗除草剂作物的滥用使抗性杂草严重威胁现代农业的发展,这就需要新技术有效缓解当前的和未来的杂草问题.分子生物学是研究DNA、RNA以及蛋白质分子之间相互作用的科学,该技术已在杂草科学中广泛应用,如决定杂草抗药性机制、抗性杂草的起源、杂草基因型和基因流动的传播、杂草特征的生态适应与进化发展等.这些信息有利于建立可持续发展的杂草管理方案.分子生物技术也具有可直接用于防除杂草的潜力,如可用于开发新的除草措施的技术,包括宏基因组学、病毒诱导基因沉默、转基因雌性不育性等.%Global climate change appears to be favorable for invasive weed development and spread because invasive species in general are proficient at succeeding in new environments.To worsen matters,herbicide - resistant weeds have become a severe threat in modern agricultural systems due to the extensive use of herbicides and the widespread use of herbicide resistant crops.Therefore,novel techniques are needed to effectively alleviate current and future weed problems.Molecular biology is the study of molecular interactions between DNA,RNA,and proteins.Molecular tools have been used in weed science to determine mechanisms of how weeds become resistant,origins of resistance,spread of weed genotypes and gene flow,ecological and evolutionary development of weedy characteristics,etc.Information obtained from these studies will contribute in proactive planning and applying environmentally sustainable solutions to weed management.Molecular tools also have the potential to be applied directly for weed control.Several technologies such as metagenomics,virus- induced gene silencing,and transgenic female -sterility are some.good examples of how these techniques may be used to develop novel control measures.

  8. Review on Invasive Tree of Heaven ( Ailanthus altissima (Mill.) Swingle) Conflicting Values: Assessment of Its Ecosystem Services and Potential Biological Threat

    Science.gov (United States)

    Sladonja, Barbara; Sušek, Marta; Guillermic, Julia

    2015-10-01

    Globally, invasions by alien plants are rapidly increasing in extent and severity, leading to large-scale ecosystem degradation. One of the most widespread invasive alien plant species in Europe and North America, Tree of Heaven ( Ailanthus altissima (Mill.) Swingle) was introduced intentionally for use as an ornamental plant in the 18th century. Since then, it has spread and is now frequently found in a number of countries. Today, Tree of Heaven is considered one of the worst invasive plant species in Europe and is also listed as invasive in North America and many other countries. Millennium Ecosystem Assessment is one of many systems trying to list and categorize biological services to humans and to provide a tool for identifying services delivered by natural ecosystems. Invasive species have generally caused degradation of the services, have a major impact on the environment, and are threatening biodiversity and reducing overall species abundance and diversity. On the other hand, some invasive species can provide services useful to human well-being. In the present review A. altissima impacts on ecosystems are identified and positive influences on some ecosystem services are weighed against the negative effects on the environment and human health. The aim of the present review is to resume the general knowledge of A. altissima, group available references on distribution and ecology according to countries, compare ecosystem services provided or enhanced by A. altissima presence and the negative effects it causes, identify gaps in current knowledge, and give recommendations for future lines of research.

  9. Review on Invasive Tree of Heaven (Ailanthus altissima (Mill.) Swingle) Conflicting Values: Assessment of Its Ecosystem Services and Potential Biological Threat.

    Science.gov (United States)

    Sladonja, Barbara; Sušek, Marta; Guillermic, Julia

    2015-10-01

    Globally, invasions by alien plants are rapidly increasing in extent and severity, leading to large-scale ecosystem degradation. One of the most widespread invasive alien plant species in Europe and North America, Tree of Heaven (Ailanthus altissima (Mill.) Swingle) was introduced intentionally for use as an ornamental plant in the 18th century. Since then, it has spread and is now frequently found in a number of countries. Today, Tree of Heaven is considered one of the worst invasive plant species in Europe and is also listed as invasive in North America and many other countries. Millennium Ecosystem Assessment is one of many systems trying to list and categorize biological services to humans and to provide a tool for identifying services delivered by natural ecosystems. Invasive species have generally caused degradation of the services, have a major impact on the environment, and are threatening biodiversity and reducing overall species abundance and diversity. On the other hand, some invasive species can provide services useful to human well-being. In the present review A. altissima impacts on ecosystems are identified and positive influences on some ecosystem services are weighed against the negative effects on the environment and human health. The aim of the present review is to resume the general knowledge of A. altissima, group available references on distribution and ecology according to countries, compare ecosystem services provided or enhanced by A. altissima presence and the negative effects it causes, identify gaps in current knowledge, and give recommendations for future lines of research.

  10. Singlet molecular oxygen generated in dark biological process.

    Science.gov (United States)

    Di Mascio, Paolo; Medeiros, Marisa H G

    2014-10-01

    Ultraweak chemiluminescence arising from biomolecules oxidation has been attributed to the radiative deactivation of singlet molecular oxygen [(1)O2] and electronically excited triplet carbonyl products involving dioxetane intermediates. As examples, we will discuss the generation of (1)O2 from lipid hydroperoxides, which involves a cyclic mechanism from a linear tetraoxide intermediate. The generation of (1)O2 in aqueous solution via energy transfer from the excited triplet acetone arising from the thermodecomposition of dioxetane a chemical source, and horseradish peroxidase-catalyzed oxidation of 2-methylpropanal, as an enzymatic source, will also be discussed. The approach used to unequivocally demonstrate the generation of (1)O2 in these reactions is the use of (18)O-labeled hydroperoxide / triplet dioxygen ((18)[(3)O2]), the detection of labeled compounds by HPLC coupled to tandem mass spectrometry (HPLC-MS/MS) and the direct spectroscopic detection and characterization of (1)O2 light emission. Characteristic light emission at 1,270nm, corresponding to the singlet delta state monomolecular decay was observed. Using(18)[(3)O2], we observed the formation of (18)O-labeled (1)O2 ((18)[(1)O2]) by the chemical trapping of (18)[(1)O2]with the anthracene-9,10-diyldiethane-2,1-diyl disulfate disodium salt (EAS) and detected the corresponding (18)O-labeled EAS endoperoxide usingHPLC-MS/MS. The combined use of the thermolysis of a water-soluble naphthalene endoperoxide as a generator of (18)O labeled (1)O2 and the sensitivity of HPLC-MS/MS allowed the study of (1)O2reactivity toward biomolecules. Photoemission properties and chemical trapping clearly demonstrate that the production of hydroperoxide and excited carbonyls generates (18)[(1)O2], and points to the involvement of (1)O2 in physiological and pathophysiological mechanism. Supported by FAPESP (2012/12663-1), CAPES, INCT Redoxoma (FAPESP/CNPq/CAPES; 573530/2008-4), NAP Redoxoma (PRPUSP; 2011.1.9352.1.8), CEPID

  11. A multilocus molecular phylogeny of combtooth blennies (Percomorpha: Blennioidei: Blenniidae): Multiple invasions of intertidal habitats

    KAUST Repository

    Hundt, Peter J.

    2014-01-01

    The combtooth blennies (f. Blenniidae) is a diverse family of primarily marine fishes with approximately 387 species that inhabit subtidal, intertidal, supralittoral habitats in tropical and warm temperate regions throughout the world. The Blenniidae has typically been divided into six groups based on morphological characters: Blenniini, Nemophini, Omobranchini, Phenablenniini, Parablenniini, and Salariini. There is, however, considerable debate over the validity of these groups and their relationships. Since little is known about the relationships in this group, other aspects of their evolutionary history, such as habitat evolution and remain unexplored. Herein, we use Bayesian and maximum likelihood analyses of four nuclear loci (ENC1, myh6, ptr, and tbr1) from 102 species, representing 41 genera, to resolve the phylogeny of the Blenniidae, determine the validity of the previously recognized groupings, and explore the evolution of habitat association using ancestral state reconstruction. Bayesian and maximum likelihood analyses of the resulting 3100. bp of DNA sequence produced nearly identical topologies, and identified many well-supported clades. Of these clades, Nemophini was the only traditionally recognized group strongly supported as monophyletic. This highly resolved and thoroughly sampled blenniid phylogeny provides strong evidence that the traditional rank-based classification does not adequately delimit monophyletic groups with the Blenniidae. This phylogeny redefines the taxonomy of the group and supports the use of 13 unranked clades for the classification of blenniids. Ancestral state reconstructions identified four independent invasions of intertidal habitats within the Blenniidae, and subsequent invasions into supralittoral and freshwater habitats from these groups. The independent invasions of intertidal habitats are likely to have played an important role in the evolutionary history of blennies. © 2013 Elsevier Inc.

  12. Geographic distribution of Staphylococcus aureus causing invasive infections in Europe: a molecular-epidemiological analysis.

    Directory of Open Access Journals (Sweden)

    Hajo Grundmann

    2010-01-01

    Full Text Available BACKGROUND: Staphylococcus aureus is one of the most important human pathogens and methicillin-resistant variants (MRSAs are a major cause of hospital and community-acquired infection. We aimed to map the geographic distribution of the dominant clones that cause invasive infections in Europe. METHODS AND FINDINGS: In each country, staphylococcal reference laboratories secured the participation of a sufficient number of hospital laboratories to achieve national geo-demographic representation. Participating laboratories collected successive methicillin-susceptible (MSSA and MRSA isolates from patients with invasive S. aureus infection using an agreed protocol. All isolates were sent to the respective national reference laboratories and characterised by quality-controlled sequence typing of the variable region of the staphylococcal spa gene (spa typing, and data were uploaded to a central database. Relevant genetic and phenotypic information was assembled for interactive interrogation by a purpose-built Web-based mapping application. Between September 2006 and February 2007, 357 laboratories serving 450 hospitals in 26 countries collected 2,890 MSSA and MRSA isolates from patients with invasive S. aureus infection. A wide geographical distribution of spa types was found with some prevalent in all European countries. MSSA were more diverse than MRSA. Genetic diversity of MRSA differed considerably between countries with dominant MRSA spa types forming distinctive geographical clusters. We provide evidence that a network approach consisting of decentralised typing and visualisation of aggregated data using an interactive mapping tool can provide important information on the dynamics of MRSA populations such as early signalling of emerging strains, cross border spread, and importation by travel. CONCLUSIONS: In contrast to MSSA, MRSA spa types have a predominantly regional distribution in Europe. This finding is indicative of the selection and spread

  13. Global existence and asymptotic behavior of a model for biological control of invasive species via supermale introduction

    KAUST Repository

    Parshad, Rana

    2013-01-01

    The purpose of this manuscript is to propose a model for the biological control of invasive species, via introduction of phenotypically modified organisms into a target population. We are inspired by the earlier Trojan Y Chromosome model [J.B. Gutierrez, J.L. Teem, J. Theo. Bio., 241(22), 333-341, 2006]. However, in the current work, we remove the assumption of logisticgrowth rate, and do not consider the addition of sex-reversed supermales. Also the constant birth and death coefficients, considered earlier, are replaced by functionally dependent ones. In this case the nonlinearities present serious difficulties since they change sign, and the components of the solution are not a priori bounded, in some Lp-space for p large, to permit theapplication of the well known regularizing effect principle. Thus functional methods to deducethe global existence in time, for the system in question, are not applicable. Our techniques are based on the Lyapunov functional method. We prove global existence of solutions, as well asexistence of a finite dimensional global attractor, that supports states of extinction. Our analytical finding are in accordance with numerical simulations, which we also present. © 2013 International Press.

  14. An Off-the-Shelf, Authentic, and Versatile Undergraduate Molecular Biology Practical Course

    Science.gov (United States)

    Whitworth, David E.

    2015-01-01

    We provide a prepackaged molecular biology course, which has a broad context and is scalable to large numbers of students. It is provided complete with technical setup guidance, a reliable assessment regime, and can be readily implemented without any development necessary. Framed as a forensic examination of blue/white cloning plasmids, the course…

  15. Allelic polymorphism of glucocorticoid receptor NR3C1 (GR: from molecular biology to clinical implications

    Directory of Open Access Journals (Sweden)

    Orlovsky M. A.

    2012-09-01

    Full Text Available Polymorphism of stress-related genes is a key factor determining difference in the stress reactivity and resistance among humans. Glucocorticoid receptors are important actors of stress responses. This review is focused on the molecular biology and clinical implications of glucocorticoid receptor gene polymorphism.

  16. Essential Concepts and Underlying Theories from Physics, Chemistry, and Mathematics for "Biochemistry and Molecular Biology" Majors

    Science.gov (United States)

    Wright, Ann; Provost, Joseph; Roecklein-Canfield, Jennifer A.; Bell, Ellis

    2013-01-01

    Over the past two years, through an NSF RCN UBE grant, the ASBMB has held regional workshops for faculty members from around the country. The workshops have focused on developing lists of Core Principles or Foundational Concepts in Biochemistry and Molecular Biology, a list of foundational skills, and foundational concepts from Physics, Chemistry,…

  17. Web based learning support for experimental design in molecular biology: a top-down approach

    NARCIS (Netherlands)

    Aegerter-Wilmsen, T.; Hartog, R.; Bisseling, T.

    2003-01-01

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

  18. Genetics and Faith: Religious Enchantment through Creative Engagement with Molecular Biology

    Science.gov (United States)

    Jenkins, Kathleen E.

    2007-01-01

    In this article I develop heuristic types for understanding how the U.S. evangelical Christian subculture engages the newer science of molecular biology as it works to legitimate and enchant religious worldview: 1.) "symbolic engagement," employing genes and DNA as sacred icon; 2.) "disputatious engagement," debating genetic essentialism and…

  19. BioFrameNet: A FrameNet Extension to the Domain of Molecular Biology

    Science.gov (United States)

    Dolbey, Andrew Eric

    2009-01-01

    In this study I introduce BioFrameNet, an extension of the Berkeley FrameNet lexical database to the domain of molecular biology. I examine the syntactic and semantic combinatorial possibilities exhibited in the lexical items used in this domain in order to get a better understanding of the grammatical properties of the language used in scientific…

  20. Designing and Implementing a Hands-On, Inquiry-Based Molecular Biology Course

    Science.gov (United States)

    Regassa, Laura B.; Morrison-Shetlar, Alison I.

    2007-01-01

    Inquiry-based learning was used to enhance an undergraduate molecular biology course at Georgia Southern University, a primarily undergraduate institution in rural southeast Georgia. The goal was to use a long-term, in-class project to accelerate higher-order thinking, thereby enabling students to problem solve and apply their knowledge to novel…

  1. Using Restriction Mapping to Teach Basic Skills in the Molecular Biology Lab

    Science.gov (United States)

    Walsh, Lauren; Shaker, Elizabeth; De Stasio, Elizabeth A.

    2007-01-01

    Digestion of DNA with restriction enzymes, calculation of volumes and concentrations of reagents for reactions, and the separation of DNA fragments by agarose gel electrophoresis are common molecular biology techniques that are best taught through repetition. The following open-ended, investigative laboratory exercise in plasmid restriction…

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

    Science.gov (United States)

    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…

  3. Using Biocatalysis to Integrate Organic Chemistry into a Molecular Biology Laboratory Course

    Science.gov (United States)

    Beers, Mande; Archer, Crystal; Feske, Brent D.; Mateer, Scott C.

    2012-01-01

    Current cutting-edge biomedical investigation requires that the researcher have an operational understanding of several diverse disciplines. Biocatalysis is a field of science that operates at the crossroads of organic chemistry, biochemistry, microbiology, and molecular biology, and provides an excellent model for interdisciplinary research. We…

  4. What Skills Should Students of Undergraduate Biochemistry and Molecular Biology Programs Have upon Graduation?

    Science.gov (United States)

    White, Harold B.; Benore, Marilee A.; Sumter, Takita F.; Caldwell, Benjamin D.; Bell, Ellis

    2013-01-01

    Biochemistry and molecular biology (BMB) students should demonstrate proficiency in the foundational concepts of the discipline and possess the skills needed to practice as professionals. To ascertain the skills that should be required, groups of BMB educators met in several focused workshops to discuss the expectations with the ultimate goal of…

  5. Using Active Learning in a Studio Classroom to Teach Molecular Biology

    Science.gov (United States)

    Nogaj, Luiza A.

    2013-01-01

    This article describes the conversion of a lecture-based molecular biology course into an active learning environment in a studio classroom. Specific assignments and activities are provided as examples. The goal of these activities is to involve students in collaborative learning, teach them how to participate in the learning process, and give…

  6. Glycoprotein Biochemistry (Biosynthesis)--A Vehicle for Teaching Many Aspects of Biochemistry and Molecular Biology.

    Science.gov (United States)

    Cole, Clair R.; Smith, Christopher A.

    1990-01-01

    Information about the biosynthesis of the carbohydrate portions or glycans of glycoproteins is presented. The teaching of glycosylation can be used to develop and emphasize many general aspects of biosynthesis, in addition to explaining specific biochemical and molecular biological features associated with producing the oligosaccharide portions of…

  7. Foundational Concepts and Underlying Theories for Majors in "Biochemistry and Molecular Biology"

    Science.gov (United States)

    Tansey, John T.; Baird, Teaster, Jr.; Cox, Michael M.; Fox, Kristin M.; Knight, Jennifer; Sears, Duane; Bell, Ellis

    2013-01-01

    Over the past two years, through an NSF RCN UBE grant, the ASBMB has held regional workshops for faculty members and science educators from around the country that focused on identifying: 1) core principles of biochemistry and molecular biology, 2) essential concepts and underlying theories from physics, chemistry, and mathematics, and 3)…

  8. Text-mining and information-retrieval services for molecular biology

    OpenAIRE

    Krallinger, Martin; Valencia, Alfonso

    2005-01-01

    Text-mining in molecular biology - defined as the automatic extraction of information about genes, proteins and their functional relationships from text documents - has emerged as a hybrid discipline on the edges of the fields of information science, bioinformatics and computational linguistics. A range of text-mining applications have been developed recently that will improve access to knowledge for biologists and database annotators.

  9. An Inquiry-Infused Introductory Biology Laboratory That Integrates Mendel's Pea Phenotypes with Molecular Mechanisms

    Science.gov (United States)

    Kudish, Philip; Schlag, Erin; Kaplinsky, Nicholas J.

    2015-01-01

    We developed a multi-week laboratory in which college-level introductory biology students investigate Mendel's stem length phenotype in peas. Students collect, analyze and interpret convergent evidence from molecular and physiological techniques. In weeks 1 and 2, students treat control and experimental plants with Gibberellic Acid (GA) to…

  10. Sclerotinia sclerotiorum (Lib.) de Bary: biology and molecular traits of a cosmopolitan pathogen

    NARCIS (Netherlands)

    Bolton, M.D.; Thomma, B.P.H.J.; Nelson, B.D.

    2006-01-01

    Sclerotinia sclerotiorum (Lib.) de Bary is a necrotrophic fungal pathogen causing disease in a wide range of plants. This review summarizes current knowledge of mechanisms employed by the fungus to parasitize its host with emphasis on biology, physiology and molecular aspects of pathogenicity. In ad

  11. Conservation biological control of pests in the molecular era: new opportunities to address old constraints

    Directory of Open Access Journals (Sweden)

    Gurr eGeoff

    2016-01-01

    Full Text Available ABSTRACTBiological control has long been considered a potential alternative to pesticidal strategies for pest management but its impact and level of use globally remain modest and inconsistent. A rapidly expanding range of molecular – particularly DNA-related – techniques is currently revolutionizing many life sciences. This review identifies a series of constraints on the development and uptake of conservation biological control and considers the contemporary and likely future influence of molecular methods on these constraints. Molecular approaches are now often used to complement morphological taxonomic methods for the identification and study of biological control agents including microbes. A succession of molecular techniques has been applied to ‘who eats whom’ questions in food-web ecology. Polymerase chain reaction (PCR approaches have largely superseded immunological approaches such as enzyme-linked immunosorbent assay (ELISA and now – in turn – are being overtaken by next generation sequencing (NGS- based approaches that offer unparalleled power at a rapidly diminishing cost. There is scope also to use molecular techniques to manipulate biological control agents, which will be accelerated with the advent of gene editing tools, the CRISPR/Cas9 system in particular. Gene editing tools also offer unparalleled power to both elucidate and manipulate the plant defence mechanisms including those that involve natural enemy attraction to attacked plants. Rapid advances in technology will allow the development of still more novel pest management options for which uptake is likely to be limited chiefly by regulatory hurdles.

  12. Phosphorus-32 in the Phage Group: radioisotopes as historical tracers of molecular biology.

    Science.gov (United States)

    Creager, Angela N H

    2009-03-01

    The recent historiography of molecular biology features key technologies, instruments and materials, which offer a different view of the field and its turning points than preceding intellectual and institutional histories. Radioisotopes, in this vein, became essential tools in postwar life science research, including molecular biology, and are here analyzed through their use in experiments on bacteriophage. Isotopes were especially well suited for studying the dynamics of chemical transformation over time, through metabolic pathways or life cycles. Scientists labeled phage with phosphorus-32 in order to trace the transfer of genetic material between parent and progeny in virus reproduction. Initial studies of this type did not resolve the mechanism of generational transfer but unexpectedly gave rise to a new style of molecular radiobiology based on the inactivation of phage by the radioactive decay of incorporated phosphorus-32. These 'suicide experiments', a preoccupation of phage researchers in the mid-1950s, reveal how molecular biologists interacted with the traditions and practices of radiation geneticists as well as those of biochemists as they were seeking to demarcate a new field. The routine use of radiolabels to visualize nucleic acids emerged as an enduring feature of molecular biological experimentation. PMID:19268872

  13. Molecular bioengineering of biomaterials in the 1990s and beyond: a growing liaison of polymers with molecular biology.

    Science.gov (United States)

    Hoffman, A S

    1992-02-01

    An important trend in biomaterials research and development is the synthesis of polymers that combine capabilities of biologic recognition (biomimetic) with special physicochemical properties of the synthetic polymer system. Another important trend in such "molecular bioengineering" is to develop, perhaps via computer-aided molecular design, new artificial biomimetic systems by exact placement of functional groups on rigid polymer backbones, cross-linked structures, or macromolecular assemblies. In this way, biocatalytic functioning or biorecognition similar to enzymes and antibodies can be achieved without the inherent instability often encountered with the native biomolecules or assemblies. Perhaps the most exciting trend in biomaterials research and development is the availability of new biomolecules, e.g., via protein engineering and of hardy cells with specific biofunctions and bioresponses that can be tailored to specific medical or biotechnological needs. The wide variety of ways that such biomolecules and cells can be combined with polymeric biomaterials provides tremendously exciting opportunities for the biomaterials scientists and engineers. In addition to these synthetic approaches, new and exciting analytical tools, such as the scanning tunneling microscope and the atomic force microscope, are permitting study on a molecular scale of individual and small clusters of proteins and other biomolecular assemblies on surfaces. Cell attachments and spreading may also be visualized at various depths within the cell using the confocal laser microscope. Such analytical techniques can lead to important new knowledge about biologic interactions with biomaterials and, therefore, to development of even more biocompatible implants and devices. This paper overviews the present state of polymeric biomaterials and highlights the important and exciting opportunities generated by the liaison of these materials with molecular biology.

  14. Abstracts of the 30. Annual meeting of the Brazilian Society on Biochemistry and Molecular Biology; Resumos da 30. Reuniao anual da Sociedade Brasileira de Bioquimica e Biologia Molecular

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-07-01

    Several aspects concerning biochemistry and molecular biology of either animals, plants and microorganisms are studied. Topics such as cell membrane structures (including receptors), enzymatic assays, biological pathways, structural chemical analysis, metabolism, biological functions are focused. The use of radiolabelled compounds (radioassay, radioreceptor assay) and nuclear magnetic resonance are the most applied techniques.

  15. Abstracts of the 29. annual meeting of the Brazilian Society on Biochemistry and Molecular Biology; Resumos da 29. reuniao anual da Sociedade Brasileira de Bioquimica e Biologia Molecular

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-07-01

    Several aspects concerning biochemistry and molecular biology of either animals (including man), plants and microorganisms are studied. Topics such as cell membrane structures (including receptors), enzymatic assays, biological pathways, structural chemical analysis, metabolism, biological functions are focused. The use of radiolabelled compounds (radioassay, radioenzymatic assay, radioreceptor assay) and nuclear magnetic resonance are the most applied techniques.

  16. Abstracts of the 28. Annual meeting of the Brazilian Society on Biochemistry and Molecular Biology; Resumos da 28. Reuniao anual da Sociedade Brasileira de Bioquimica e Biologia Molecular

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-07-01

    Biochemistry, genetic and molecular biology aspects of either animals (including man), plants and microorganisms are studied. Topics such as cell membrane structures (including receptors), enzymatic assays, biological pathways, structural chemical analysis, metabolism, biological functions are focused. The use of radiolabelled compounds (radioassay, radioenzymatic assay, radioreceptor assay) and nuclear magnetic resonance are the most applied techniques.

  17. [Molecular biology and childhood leukemia: E2A-PBX1 and central nervous system relapse].

    Science.gov (United States)

    Núñez-Enríquez, Juan Carlos; Mejía-Aranguré, Juan Manuel

    2015-01-01

    Acute lymphoblastic leukemia (ALL) is the most common cancer in children. The inclusion of molecular biology techniques in the diagnosis and prognostic stratification of these patients has allowed major treatment achievements in developed countries. One of the best studied gene rearrangements is E2A-PBX1, which predicts isolated central nervous system relapse in patients with ALL. However, further research on the search for new molecular markers related to prognosis of patients with childhood leukemia is required. Such studies need the integration of different disciplines, including epidemiology. Epidemiological studies are needed not only to accelerate the discovery of new molecular markers and new biological signals as to the etiology and pathophysiology of cancer, but also to evaluate the clinical impact of these findings in well-defined populations. PMID:26509298

  18. Third international conference on intelligent systems for molecular biology (ISMB-95): Summary. Final report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-12-31

    The specific aims of the Third International Conference on Intelligent Systems for Molecular Biology (ISMB-95) were to: convene a critical mass of researchers applying advanced computational techniques to problems in molecular biology; promote interchange of problems and solutions between computer scientists and molecular biologists; create education opportunities in this cross-disciplinary field for students and senior researchers wishing to either apply or benefit from these techniques; produce an archival proceedings as a forum for rapid dissemination of new results in a peer-reviewed manner; produce a set of tutorial materials for education and training of researchers interested in this field; maintain the momentum generated by the highly successful previous conferences in the series, and establish a regular event that will help to solidify the field; and foster the involvement of women and minorities in the field.

  19. A comprehensive study into the molecular methodology and molecular biology of methanogenic Archaea

    DEFF Research Database (Denmark)

    Lange, M.; Ahring, Birgitte Kiær

    2001-01-01

    Methanogens belong to the kingdom of Euryarchaeota in the domain of Archaea. The Archaea differ from Bacteria in many aspects important to molecular work. Among these are cell wall composition, their sensitivity to antibiotics, their translation and transcription machinery, and their very strict ...

  20. Understanding the biological invasion risk posed by the global wildlife trade: propagule pressure drives the introduction and establishment of Nearctic turtles.

    Science.gov (United States)

    García-Díaz, Pablo; Ross, Joshua V; Ayres, César; Cassey, Phillip

    2015-03-01

    Biological invasions are a key component of human-induced global change. The continuing increase in global wildlife trade has raised concerns about the parallel increase in the number of new invasive species. However, the factors that link the wildlife trade to the biological invasion process are still poorly understood. Moreover, there are analytical challenges in researching the role of global wildlife trade in biological invasions, particularly issues related to the under-reporting of introduced and established populations in areas with reduced sampling effort. In this work, we use high-quality data on the international trade in Nearctic turtles (1999-2009) coupled with a statistical modelling framework, which explicitly accounts for detection, to investigate the factors that influence the introduction (release, or escape into the wild) of globally traded Nearctic turtles and the establishment success (self-sustaining exotic populations) of slider turtles (Trachemys scripta), the most frequently traded turtle species. We found that the introduction of a species was influenced by the total number of turtles exported to a jurisdiction and the age at maturity of the species, while the establishment success of slider turtles was best associated with the propagule number (number of release events), and the number of native turtles in the jurisdiction of introduction. These results indicate both a direct and indirect association between the wildlife trade and the introduction of turtles and establishment success of slider turtles, respectively. Our results highlight the existence of gaps in the number of globally recorded introduction events and established populations of slider turtles, although the expected bias is low. We emphasize the importance of researching independently the factors that affect the different stages of the invasion pathway. Critically, we observe that the number of traded individuals might not always be an adequate proxy for propagule pressure

  1. Molecular phylogeny of Enchytraeidae (Oligochaeta) indicates separate invasions of the terrestrial environment

    DEFF Research Database (Denmark)

    Christensen, Bent; Glenner, Henrik

    2010-01-01

    Enchytraeidae is a family of soil inhabiting small- to medium-sized oligochaete worms using degradable plant material as a food source and primarily adapted to terrestrial or semi-terrestrial environments. The molecular phylogeny based upon both mitochondrial and nuclear genes indicates early...

  2. Design of a Comprehensive Biochemistry and Molecular Biology Experiment: Phase Variation Caused by Recombinational Regulation of Bacterial Gene Expression

    Science.gov (United States)

    Sheng, Xiumei; Xu, Shungao; Lu, Renyun; Isaac, Dadzie; Zhang, Xueyi; Zhang, Haifang; Wang, Huifang; Qiao, Zheng; Huang, Xinxiang

    2014-01-01

    Scientific experiments are indispensable parts of Biochemistry and Molecular Biology. In this study, a comprehensive Biochemistry and Molecular Biology experiment about "Salmonella enterica" serovar Typhi Flagellar phase variation has been designed. It consisted of three parts, namely, inducement of bacterial Flagellar phase variation,…

  3. Stochastic narrow escape in molecular and cellular biology analysis and applications

    CERN Document Server

    Holcman, David

    2015-01-01

    This book covers recent developments in the non-standard asymptotics of the mathematical narrow escape problem in stochastic theory, as well as applications of the narrow escape problem in cell biology. The first part of the book concentrates on mathematical methods, including advanced asymptotic methods in partial equations, and is aimed primarily at applied mathematicians and theoretical physicists who are interested in biological applications. The second part of the book is intended for computational biologists, theoretical chemists, biochemists, biophysicists, and physiologists. It includes a summary of output formulas from the mathematical portion of the book and concentrates on their applications in modeling specific problems in theoretical molecular and cellular biology. Critical biological processes, such as synaptic plasticity and transmission, activation of genes by transcription factors, or double-strained DNA break repair, are controlled by diffusion in structures that have both large and small sp...

  4. Biological and molecular characterization of classical swine fever challenge virus from India

    Directory of Open Access Journals (Sweden)

    Parveen Kumar

    2015-03-01

    Full Text Available Aim: The aim of this study was biological and molecular characterization of classical swine fever (CSF challenge virus from India. Materials and Methods: CSF challenge virus maintained at Division of Biological standardization was experimentally infected to two seronegative piglets. The biological characterization was done by clinical sign and symptoms along with postmortem findings. For molecular characterization 5’-nontranslated region, E2 and NS5B regions were amplified by reverse transcription polymerase chain reaction and sequenced. The sequences were compared with that of reference strains and the local field isolates to establish a phylogenetic relation. Results: The virus produced symptoms of acute disease in the piglets with typical post-mortem lesions. Phylogenetic analysis of the three regions showed that the current Indian CSF Challenge virus is having maximum similarity with the BresciaX strain (USA and Madhya Pradesh isolate (India and is belonging to subgroup 1.2 under Group 1. Conclusion: Based on biological and molecular characterization of CSF challenge virus from India is described as a highly virulent virus belonging to subgroup 1.2 under Group 1 along with some field isolates from India and Brescia strain.

  5. Classical biological control of an invasive forest pest: a world perspective of the management of Sirex noctilio using the parasitoid Ibalia leucospoides (Hymenoptera: Ibaliidae).

    Science.gov (United States)

    Fischbein, D; Corley, J C

    2015-02-01

    Classical biological control is a key method for managing populations of pests in long-lived crops such as plantation forestry. The execution of biological control programmes in general, as the evaluation of potential natural enemies remains, to a large extent, an empirical endeavour. Thus, characterizing specific cases to determine patterns that may lead to more accurate predictions of success is an important goal of the much applied ecological research. We review the history of introduction, ecology and behaviour of the parasitoid Ibalia leucospoides. The species is a natural enemy of Sirex noctilio, one of the most important pests of pine afforestation worldwide. We use an invasion ecology perspective given the analogy between the main stages involved in classical biological control and the biological invasion processes. We conclude that success in the establishment, a common reason of failure in biocontrol, is not a limiting factor of success by I. leucospoides. A mismatch between the spread capacity of the parasitoid and that of its host could nevertheless affect control at a regional scale. In addition, we suggest that given its known life history traits, this natural enemy may be a better regulator than suppressor of the host population. Moreover, spatial and temporal refuges of the host population that may favour the local persistence of the interaction probably reduce the degree to which S. noctilio population is suppressed by the parasitoid. We emphasize the fact that some of the biological attributes that promote establishment may negatively affect suppression levels achieved. Studies on established non-native pest-parasitoid interactions may contribute to defining selection criteria for classical biological control which may prove especially useful in integrated pest management IPM programmes of invasive forest insects.

  6. The molecular physiology of increased egg desiccation resistance during diapause in the invasive mosquito, Aedes albopictus

    OpenAIRE

    Urbanski, Jennifer M.; BENOIT, JOSHUA B.; Michaud, M. Robert; Denlinger, David L.; Armbruster, Peter

    2010-01-01

    Photoperiodic diapause is a crucial adaptation to seasonal environmental variation in a wide range of arthropods, but relatively little is known regarding the molecular basis of this important trait. In temperate populations of the mosquito Aedes albopictus, exposure to short-day (SD) lengths causes the female to produce diapause eggs. Tropical populations do not undergo a photoperiodic diapause. We identified a fatty acyl coA elongase transcript that is more abundant under SD versus long-day...

  7. Massively Parallel, Molecular Analysis Platform Developed Using a CMOS Integrated Circuit With Biological Nanopores

    Science.gov (United States)

    Roever, Stefan

    2012-01-01

    A massively parallel, low cost molecular analysis platform will dramatically change the nature of protein, molecular and genomics research, DNA sequencing, and ultimately, molecular diagnostics. An integrated circuit (IC) with 264 sensors was fabricated using standard CMOS semiconductor processing technology. Each of these sensors is individually controlled with precision analog circuitry and is capable of single molecule measurements. Under electronic and software control, the IC was used to demonstrate the feasibility of creating and detecting lipid bilayers and biological nanopores using wild type α-hemolysin. The ability to dynamically create bilayers over each of the sensors will greatly accelerate pore development and pore mutation analysis. In addition, the noise performance of the IC was measured to be 30fA(rms). With this noise performance, single base detection of DNA was demonstrated using α-hemolysin. The data shows that a single molecule, electrical detection platform using biological nanopores can be operationalized and can ultimately scale to millions of sensors. Such a massively parallel platform will revolutionize molecular analysis and will completely change the field of molecular diagnostics in the future.

  8. Physics in cell biology: on the physics of biopolymers and molecular motors.

    Science.gov (United States)

    Frey, Erwin

    2002-03-12

    "What is Life?" is the title of a book by Erwin Schrödinger, first published in 1944. This book is a bold attempt to try to understand some of the wonders of life in terms of physics, in particular statistical mechanics. Since the publication of this visionary book, we have seen a revolution in molecular biology complemented by the development of new physical tools like single-molecule spectroscopy. The goal of this article is to highlight some examples where physics can contribute to questions in cell biology. One might hope that through interdisciplinary research one can get closer to answering Schrödinger's fundamental question.

  9. A Research Project-Based and Self-Determined Teaching System of Molecular Biology Techniques for Undergraduates

    Science.gov (United States)

    Zhang, Shuping

    2008-01-01

    Molecular biology techniques play a very important role in understanding the biological activity. Students who major in biology should know not only how to perform experiments, but also the reasons for performing them. Having the concept of conducting research by integrating various techniques is especially important. This paper introduces a…

  10. Humic substances biological activity at the plant-soil interface: from environmental aspects to molecular factors.

    Science.gov (United States)

    Trevisan, Sara; Francioso, Ornella; Quaggiotti, Silvia; Nardi, Serenella

    2010-06-01

    Humic substances (HS) represent the organic material mainly widespread in nature. HS have positive effects on plant physiology by improving soil structure and fertility and by influencing nutrient uptake and root architecture. The biochemical and molecular mechanisms underlying these events are only partially known. HS have been shown to contain auxin and an "auxin-like" activity of humic substances has been proposed, but support to this hypothesis is fragmentary. In this review article, we are giving an overview of available data concerning molecular structures and biological activities of humic substances, with special emphasis on their hormone-like activities. PMID:20495384

  11. The role of the molecular biology laboratory in the management of chronic hepatitis B and C

    Directory of Open Access Journals (Sweden)

    Peter Karayiannis

    2013-03-01

    Full Text Available Molecular biology techniques are routinely used nowadays to diagnose and evaluate antiviral treatment of patients with chronic hepatitis B (HBV and hepatitis C virus (HCV infections. Current tools at our disposal include tests that quantify the amount of circulating virus in the blood, techniques that can analyse genomic sequences to determine viral genotypes or subtypes, or determine amino-acid substitutions that may confer resistance to existing antiviral drugs. What is more, continuously evolving serological tests for the detection of viral antigens or their corresponding antibodies, have made diagnosis of disease as sensitive as possible. The present review will concentrate primarily on molecular diagnostics.

  12. 近十年中国生物入侵研究进展%Progress of biological invasions research in China over the last decade

    Institute of Scientific and Technical Information of China (English)

    鞠瑞亭; 李慧; 石正人; 李博

    2012-01-01

    the field of biological invasions research in China over the last decade, there are still large knowledge gaps. This paper reviews progress in the field of biological invasions research since 2000 as it relates to China, covering the diversity, colonization and immigration patterns of invasive species, mechanisms and ecological effects of biological invasions, and management and control of invasive species. In China, 529 invasive alien species have been identified, which originated primarily from South and North America, and the major taxa included terrestrial plants, terrestrial invertebrates, and microorganisms. We found a higher prevalence of invasive species in the eastern and southern provinces, compared to the western and northern provinces in China. This pattern is likely due to the differences in the level of economic development and environmental suitability between the two regions. Moreover, with further economic development, China may face more serious biological invasions in the future. These invasions of alien species are largely the combined results of the interactions between the intrinsic traits of these species along with resource opportunities and disturbances by human beings. Many mechanisms are responsible for successful invasions of alien species, but phenotypic plasticity, adaptive evolution, enemy release, interspecific mutualism or commensalism, and new allelochemicals may be primary causative factors. Biological invasions in China have caused serious impacts on native ecosystems, including biodiversity and ecosystem services, alteration of biogeochemical cycles, threats to agricultural and forestry production, traffic and shipping, environmental safety, and public facilities. China has also made progress in the detection and monitoring of invasive species, risk analysis, biological control, radical elimination, and ecological restoration of degraded ecosystems. We suggest several issues that need to be addressed in invasive species research in

  13. Molecular phylogeny of Enchytraeidae (Oligochaeta) indicates separate invasions of the terrestrial environment

    DEFF Research Database (Denmark)

    Christensen, Bent; Glenner, H.

    2010-01-01

    Enchytraeidae is a family of soil inhabiting small- to medium-sized oligochaete worms using degradable plant material as a food source and primarily adapted to terrestrial or semi-terrestrial environments. The molecular phylogeny based upon both mitochondrial and nuclear genes indicates early....... Inland soils probably had to await the emergence of land plants in order to provide a similar food resource and here the major branch of enchytraeid genera diversified into a high number of species in the numerous decomposer networks of this varied environment. A subdivision into the genera Enchytraeus...

  14. Molecular subtype profiling of invasive breast cancers weakly positive for estrogen receptor.

    Science.gov (United States)

    Sheffield, Brandon S; Kos, Zuzana; Asleh-Aburaya, Karama; Wang, Xiu Qing; Leung, Samuel; Gao, Dongxia; Won, Jennifer; Chow, Christine; Rachamadugu, Rakesh; Stijleman, Inge; Wolber, Robert; Gilks, C Blake; Myles, Nickolas; Thomson, Tom; Hayes, Malcolm M; Bernard, Philip S; Nielsen, Torsten O; Chia, Stephen K L

    2016-02-01

    The estrogen receptor (ER) is a key predictive biomarker in the treatment of breast cancer. There is uncertainty regarding the use of hormonal therapy in the setting of weakly positive ER by immunohistochemistry (IHC). We report intrinsic subtype classification on a cohort of ER weakly positive early-stage breast cancers. Consecutive cases of breast cancer treated by primary surgical resection were retrospectively identified from 4 centers that engage in routine external proficiency testing for breast biomarkers. ER-negative (Allred 0 and 2) and ER weakly positive (Allred 3-5) cases were included. Gene expression profiling was performed using qRT-PCR. Intrinsic subtype prediction was made based upon the PAM50 gene expression signature. 148 cases were included in the series: 60 cases originally diagnosed as ER weakly positive and 88 ER negative. Of the cases originally assessed as ER weakly positive, only 6 (10 %) were confirmed to be of luminal subtype by gene expression profiling; the remaining 90 % of cases were classified as basal-like or HER2-enriched subtypes. This was not significantly different than the fraction of luminal cases identified in the IHC ER-negative cohort (5 (5 %) luminal, 83(95 %) non-luminal). Recurrence-free, and overall, survival rates were similar in both groups (p = 0.4 and 0.5, respectively) despite adjuvant hormonal therapy prescribed in the majority (59 %) of weakly positive ER cases. Weak ER expression by IHC is a poor correlate of luminal subtype in invasive breast cancer. In the setting of highly sensitive and robust IHC methodology, cutoffs for ER status determination and subsequent systemic therapy should be revisited. PMID:26846986

  15. Molecular biology of breast cancer metastasis Molecular expression of vascular markers by aggressive breast cancer cells

    International Nuclear Information System (INIS)

    During embryogenesis, the formation of primary vascular networks occurs via the processes of vasculogenesis and angiogenesis. In uveal melanoma, vasculogenic mimicry describes the 'embryonic-like' ability of aggressive, but not nonaggressive, tumor cells to form networks surrounding spheroids of tumor cells in three-dimensional culture; these recapitulate the patterned networks seen in patients' aggressive tumors and correlates with poor prognosis. The molecular profile of these aggressive tumor cells suggests that they have a deregulated genotype, capable of expressing vascular phenotypes. Similarly, the embryonic-like phenotype expressed by the aggressive human breast cancer cells is associated with their ability to express a variety of vascular markers. These studies may offer new insights for consideration in breast cancer diagnosis and therapeutic intervention strategies

  16. Molecular biology in marine science: Scientific questions, technological approaches, and practical implications

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1994-12-31

    This report describes molecular techniques that could be invaluable in addressing process-oriented problems in the ocean sciences that have perplexed oceanographers for decades, such as understanding the basis for biogeochemical processes, recruitment processes, upper-ocean dynamics, biological impacts of global warming, and ecological impacts of human activities. The coupling of highly sophisticated methods, such as satellite remote sensing, which permits synoptic monitoring of chemical, physical, and biological parameters over large areas, with the power of modern molecular tools for ``ground truthing`` at small scales could allow scientists to address questions about marine organisms and the ocean in which they live that could not be answered previously. Clearly, the marine sciences are on the threshold of an exciting new frontier of scientific discovery and economic opportunity.

  17. Molecular biological analysis of genotyping and phylogeny of severe acute respiratory syndrome associated coronavirus

    Institute of Scientific and Technical Information of China (English)

    王志刚; 李兰娟; 罗芸; 张俊彦; 王敏雅; 程苏云; 张严峻; 王晓萌; 卢亦愚; 吴南屏; 梅玲玲; 王赞信

    2004-01-01

    Background SARS-CoV is the causative agent of severe acute respiratory syndrome (SARS) which has been associated with outbreaks of SARS in Guangdong, Hong Kong and Beijing of China, and other regions worldwide. SARS-CoV from human has shown some variations but its origin is still unknown. The genotyping and phylogeny of SARS-CoV were analyzed and reported in this paper. Methods Full or partial genomes of 44 SARS-CoV strains were collected from GenBank. The genotype, single nucleotide polymorphism and phylogeny of these SARS-CoV strains were analyzed by molecular biological, bioinformatic and epidemiological methods. Conclusion The results mentioned above suggest that SARS-CoV is responding to host immunological pressures and experiencing variation which provide clues, information and evidence of molecular biology for the clinical pathology, vaccine developing and epidemic investigation.

  18. Molecular biology of liver disorders: the hepatitis C virus and moleculartargets for drug development

    Institute of Scientific and Technical Information of China (English)

    Howard J. Worman; Feng Lin

    2000-01-01

    Advances in molecular biology made possible the discovery of the virus that causes hepatitis C. However,little is known about the fundamental aspects of hepatitis C virus (HCV) replication, primarily because arobust cell culture has not been established. As a result, the currently available drugs for the treatment ofhepatitis C are not specifically directed against HCV. Based on what is known about the molecular biology ofHCV, however, drugs can now be developed against specific viral and cellular targets. The next generationof drugs for the treatment of hepatitis C will likely be directed against non-structural HCV proteins withknown enzymatic activities, such as the proteases, RNA helicase and RNA polymerase. Others agentstargeted against the viral RNA, core protein that assembles into the virion capsid and putative cellular“receptors” that bind HCV envelope proteins are also being developed. These drugs should have fewer sideeffects than those currently available and be much more effective for the treatment of chronic hepatitis C.

  19. Numerical study of the electroporation pulse shape effect on molecular uptake of biological cells

    OpenAIRE

    Miklavčič, Damijan; Towhidi, Leila

    2010-01-01

    Background In order to reduce the side-effects of chemotherapy, combined chemotherapy-electroporation (electrochemotherapy) has been suggested. Electroporation, application of appropriate electric pulses to biological cells, can significantly enhance molecular uptake of cells due to formation of transient pores in the cell membrane. It was experimentally demonstrated that the efficiency of electroporation is under the control of electric pulse parameters. However, the theoretical basis for th...

  20. A cooperative framework for molecular biology database integration using image object selection.

    OpenAIRE

    Khan, Nawaz

    2004-01-01

    The theme and the concept of 'Molecular Biology Database Integration’ and the problems associated with this concept initiated the idea for this Ph.D research. The available technologies facilitate to analyse the data independently and discretely but it fails to integrate the data resources for more meaningful information. This along with the integration issues created the scope for this Ph.D research. The research has reviewed the 'database interoperability' problems and it has suggested a...

  1. The molecular biology revolution and the rise of bioscience megacentres in North America and Europe

    OpenAIRE

    Philip Cooke

    2004-01-01

    This paper focuses on 'triple helix' effects in biosciences. Scientific change can have profound socioeconomic effects. The molecular biology revolution tilted pharmaceuticals production away from its fine chemistry path dependence into microbiology and biotechnology. The key to any triple helix effects has thus shifted to universities and spinouts buttressed with burgeoning public funding, leaving 'big pharma' increasingly playing the role of licenser and marketer of bought-in therapeutic tr...

  2. Molecular biology and riddle of cancer: the ‘Tom & Jerry’ show

    Directory of Open Access Journals (Sweden)

    Md. Al Mamun

    2011-11-01

    Full Text Available From the conventional Bird’s eye, cancer initiation and metastasis are generally intended to be understood beneath the light of classical clonal genetic, epigenetic and cancer stem cell model. But inspite decades of investigation, molecular biology has shown hard success to give Eagle’s eye in unraveling the riddle of cancer. And it seems, tiring Tom runs in vague behind naughty Jerry.

  3. Deposition rates in growing tissue: Implications for physiology, molecular biology, and response to environmental variation

    OpenAIRE

    Silk, Wendy K.; Bogeat-Triboulot, Marie-Béatrice

    2014-01-01

    Net rates of biosynthesis and mineral deposition are needed to understand the physiology and molecular biology of growth and plant responses to environmental variation. Many popular models ignore cell expansion and displacement. In contrast, the continuity equation, used with empirical data on growth velocity and concentration, allows computation of biosynthesis and deposition rates in growing tissue. This article describes data and methods needed to calculate deposition rates and reviews som...

  4. Utility of the molecular biology techniques to the analytical control of the microbiological quality of waters

    International Nuclear Information System (INIS)

    The molecular biology techniques made accessible to the water industry the ability to detect and quantify, in a few hours, any organism known. given this scenario, it is important to realize the strengths and weaknesses of these techniques to get a better picture of the scope of its implementation and its most that probably usefulness. We must be familiar with these techniques to understand the results and properly evaluate its detection limit. (Author) 4 refs.

  5. Geometric combinatorics and computational molecular biology: branching polytopes for RNA sequences

    OpenAIRE

    Drellich, Elizabeth; Gainer-Dewar, Andrew; Harrington, Heather A.; He, Qijun; Heitsch, Christine; Poznanović, Svetlana

    2015-01-01

    Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction. However, the optimal solutions are fundamentally dependent on the parameters used in the objective functions. The goal of a parametric analysis is to elucidate such dependencies, especially as they pertain to the accuracy and robustness of the optimal solutions. Techniques from geometric combinatorics, including polytopes and thei...

  6. Pulsed-Field Gel Electrophoresis (PFGE) Technique and its use in Molecular Biology

    OpenAIRE

    BASIM, Esin (HACIOĞLU)

    2001-01-01

    In recent years, the use of pulsed-field gel electrophoresis (PFGE) in the molecular biology area has been subject to much research. PFGE is a powerful tool for characterizing various strains at the DNA level, obtaining relevant information on genome size and constructing the physical and genetic map of the chromosome of bacteria that are poorly understood at the genetic level as well as in separating chromosomes in microorganisms, and in the long-range mapping of mammalian genes. PFGE also h...

  7. PASBio: predicate-argument structures for event extraction in molecular biology

    OpenAIRE

    Shah Parantu K; Wattarujeekrit Tuangthong; Collier Nigel

    2004-01-01

    Abstract Background The exploitation of information extraction (IE), a technology aiming to provide instances of structured representations from free-form text, has been rapidly growing within the molecular biology (MB) research community to keep track of the latest results reported in literature. IE systems have traditionally used shallow syntactic patterns for matching facts in sentences but such approaches appear inadequate to achieve high accuracy in MB event extraction due to complex sen...

  8. Molecular Biology for the Environment: an EC-US hands-on Course in Environmental Biotechnology

    Energy Technology Data Exchange (ETDEWEB)

    Victor de Lorenzo; Juan Luis Ramos; Jerome Kukor; Gerben J. Zylstra

    2004-02-15

    One of the central goals of this activity is to bring together young scientists (at the late Ph.D. or early postdoctoral stages of their careers) in a forum that should result in future collaborations. The course is designed to give scientists hands-on experience in modern, up-to-date biotechnological methods at the interface between molecular biology and environmental biotechnology for the analysis of microorganisms and their activities with regard to the remediation of pollutants in the environment.

  9. A framework for molecular biology databases integration using context graph keying.

    OpenAIRE

    Khan, Nawaz; Stockman, A. G.; Rahman, Shahedur

    2004-01-01

    This paper proposed a novel framework for integrating public domain molecular biology databases with the aid of a context graph. A context graph is used to map data in order to establish an integration domain for the participating multi-resource database federation. Data are presented in a consolidated form upon retrieval from the multiple databases. The approach presented in this paper is novel in the sense that, it can be implemented within a component database and can initiate data consoli...

  10. Extraction from Natural Planktonic Microorganisms of DNA Suitable for Molecular Biological Studies

    OpenAIRE

    Jed A. Fuhrman; Comeau, Dorothy E.; Hagström, Åke; Chan, Amy M.

    1988-01-01

    We developed a simple technique for the high-yield extraction of purified DNA from mixed populations of natural planktonic marine microbes (primarily bacteria). This is a necessary step for several molecular biological approaches to the study of microbial communities in nature. The microorganisms from near-shore marine and brackish water samples, ranging in volume from 8 to 40 liters, were collected on 0.22-μm-pore-size fluorocarbon-based filters, after prefiltration through glass fiber filte...

  11. Making Sense of Taste : Psychophysical, molecular biological and neurophysiological studies of umami taste processing in humans

    OpenAIRE

    2011-01-01

    Monosodium glutamate elicits a specific umami taste and increases palatability of food. In order to comprehensively study the mechanisms of the taste perception of glutamate, this work compiles results from several research fields namely, psychophysics, molecular biology and neurophysiology. At the perception level, the aim of the study was to explore individual variation in the perception of glutamate in the healthy population. At the cellular level, the question referred to the role of s...

  12. Plant invasions in the landscape

    OpenAIRE

    Vilà, Montserrat; Ibáñez, Inés

    2011-01-01

    Biological invasions and changes in land- use are two components of global change affecting biodiversity worldwide. There is overriding evidence that invasions can dramatically change the landscape and that particular land-use types facilitate invasions. Still, these issues have not formally percolated into risk analysis of biological invasions, and only recently has the influence of the surrounding land- scape on invasive species spread started to be considered. In this paper we r...

  13. The Role of Molecular Biology in the Biomonitoring of Human Exposure to Chemicals

    Directory of Open Access Journals (Sweden)

    Balam Muñoz

    2010-11-01

    Full Text Available Exposure to different substances in an occupational environment is of utmost concern to global agencies such as the World Health Organization and the International Labour Organization. Interest in improving work health conditions, particularly of those employees exposed to noxious chemicals, has increased considerably and has stimulated the search for new, more specific and selective tests. Recently, the field of molecular biology has been indicated as an alternative technique for monitoring personnel while evaluating work-related pathologies. Originally, occupational exposure to environmental toxicants was assessed using biochemical techniques to determine the presence of higher concentrations of toxic compounds in blood, urine, or other fluids or tissues; results were used to evaluate potential health risk. However, this approach only estimates the presence of a noxious chemical and its effects, but does not prevent or diminish the risk. Molecular biology methods have become very useful in occupational medicine to provide more accurate and opportune diagnostics. In this review, we discuss the role of the following common techniques: (1 Use of cell cultures; (2 evaluation of gene expression; (3 the “omic” sciences (genomics, transcriptomics, proteomics and metabolomics and (4 bioinformatics. We suggest that molecular biology has many applications in occupational health where the data can be applied to general environmental conditions.

  14. Molecular subtype analysis determines the association of advanced breast cancer in Egypt with favorable biology

    Directory of Open Access Journals (Sweden)

    DuQuette Rachelle A

    2011-09-01

    Full Text Available Abstract Background Prognostic markers and molecular breast cancer subtypes reflect underlying biological tumor behavior and are important for patient management. Compared to Western countries, women in North Africa are less likely to be prognosticated and treated based on well-characterized markers such as the estrogen receptor (ER, progesterone receptor (PR and Her2. We conducted this study to determine the prevalence of breast cancer molecular subtypes in the North African country of Egypt as a measure of underlying biological characteristics driving tumor manifestations. Methods To determine molecular subtypes we characterized over 200 tumor specimens obtained from Egypt by performing ER, PR, Her2, CK5/6, EGFR and Ki67 immunohistochemistry. Results Our study demonstrated that the Luminal A subtype, associated with favorable prognosis, was found in nearly 45% of cases examined. However, the basal-like subtype, associated with poor prognosis, was found in 11% of cases. These findings are in sharp contrast to other parts of Africa in which the basal-like subtype is over-represented. Conclusions Egyptians appear to have favorable underlying biology, albeit having advanced disease at diagnosis. These data suggest that Egyptians would largely profit from early detection of their disease. Intervention at the public health level, including education on the benefits of early detection is necessary and would likely have tremendous impact on breast cancer outcome in Egypt.

  15. Experimental genomics: The application of DNA microarrays in cellular and molecular biology studies

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The genome sequence information in combination with DNA microarrays promises to revolutionize the way of cellular and molecular biological research by allowing complex mixtures of RNA and DNA to interrogated in a parallel and quant itative fashion. DNA microarrays can be used to measure levels of gene expressio n for tens of thousands of gene simultaneously and take advantage of all availab le sequence information for experimental design and data interpretation in pursu it of biological understanding. Recent progress in experimental genomics allows DNA microarrays not simply to provide a catalogue of all the genes and informati on about their function, but to understand how the components work together to comprise functioning cells and organisms. This brief review gives a survey of DNA microarrays technology and its applications in genome and gene function analysis, gene expression studies, biological signal and defense system, cell cyclereg ulation, mechanism of transcriptional regulation, proteomics, and the functional ity of food component.

  16. Molecular Biology at the Quantum Level: Can Modern Density Functional Theory Forge the Path?

    CERN Document Server

    Kolb, Brian; 10.1142/S1793984412300063

    2012-01-01

    Recent years have seen vast improvements in the ability of rigorous quantum-mechanical methods to treat systems of interest to molecular biology. In this review article, we survey common computational methods used to study such large, weakly bound systems, starting from classical simulations and reaching to quantum chemistry and density functional theory. We sketch their underlying frameworks and investigate their strengths and weaknesses when applied to potentially large biomolecules. In particular, density functional theory---a framework that can treat thousands of atoms on firm theoretical ground---can now accurately describe systems dominated by weak van der Waals interactions. This newfound ability has rekindled interest in using this tried-and-true approach to investigate biological systems of real importance. In this review, we focus on some new methods within density functional theory that allow for accurate inclusion of the weak interactions that dominate binding in biological macromolecules. Recent ...

  17. Molecular biology in a distributed world. A Kantian perspective on scientific practices and the human mind

    Directory of Open Access Journals (Sweden)

    Mariagrazia Portera

    2016-01-01

    Full Text Available In recent years the number of scholarly publications devoted to Kant's theory of biology has rapidly growing, with particular attention being given to Kant's thoughts about the concepts of teleology, function, organism, and their respective roles in scientific practice. Moving from these recent studies, and distancing itself from their mostly evolutionary background, the main aim of the present paper is to suggest an original "cognitive turn" in the interpretation of Kant's theory of biology. More specifically, the Authors will trace a connection between some Kantian theses about the “peculiar” or special nature of the human mind (intellectus ectypus, advanced in the Critique of the Power of Judgement (§ 76, 77, and some specific epistemological issues pertaining to the research practice of contemporary molecular biology.

  18. Molecular dynamics of wetting layer formation and forced water invasion in angular nanopores with mixed wettability

    International Nuclear Information System (INIS)

    The depletion of conventional hydrocarbon reservoirs has prompted the oil and gas industry to search for unconventional resources such as shale gas/oil reservoirs. In shale rocks, considerable amounts of hydrocarbon reside in nanoscale pore spaces. As a result, understanding the multiphase flow of wetting and non-wetting phases in nanopores is important to improve oil and gas recovery from these formations. This study was designed to investigate the threshold capillary pressure of oil and water displacements in a capillary dominated regime inside nanoscale pores using nonequilibrium molecular dynamics (NEMD) simulations. The pores have the same cross-sectional area and volume but different cross-sectional shapes. Oil and water particles were represented with a coarse grained model and the NEMD simulations were conducted by assigning external pressure on an impermeable piston. Threshold capillary pressures were determined for the drainage process (water replaced by oil) in different pores. The molecular dynamics results are in close agreements with calculations using the Mayer-Stowe-Princen (MS-P) method which has been developed on the premise of energy balance in thermodynamic equilibrium. After the drainage simulations, a change in wall particles’ wettability from water-wet to oil-wet was implemented based on the final configuration of oil and water inside the pore. Waterflooding simulations were then carried out at the threshold capillary pressure. The results show that the oil layer formed between water in the corner and in the center of the pore is not stable and collapses as the simulation continues. This is in line with the predictions from the MS-P method

  19. Molecular dynamics of wetting layer formation and forced water invasion in angular nanopores with mixed wettability

    Energy Technology Data Exchange (ETDEWEB)

    Sedghi, Mohammad, E-mail: msedghi@uwyo.edu; Piri, Mohammad; Goual, Lamia [Department of Chemical and Petroleum Engineering, University of Wyoming, 1000 East University Avenue, Laramie, Wyoming 82071 (United States)

    2014-11-21

    The depletion of conventional hydrocarbon reservoirs has prompted the oil and gas industry to search for unconventional resources such as shale gas/oil reservoirs. In shale rocks, considerable amounts of hydrocarbon reside in nanoscale pore spaces. As a result, understanding the multiphase flow of wetting and non-wetting phases in nanopores is important to improve oil and gas recovery from these formations. This study was designed to investigate the threshold capillary pressure of oil and water displacements in a capillary dominated regime inside nanoscale pores using nonequilibrium molecular dynamics (NEMD) simulations. The pores have the same cross-sectional area and volume but different cross-sectional shapes. Oil and water particles were represented with a coarse grained model and the NEMD simulations were conducted by assigning external pressure on an impermeable piston. Threshold capillary pressures were determined for the drainage process (water replaced by oil) in different pores. The molecular dynamics results are in close agreements with calculations using the Mayer-Stowe-Princen (MS-P) method which has been developed on the premise of energy balance in thermodynamic equilibrium. After the drainage simulations, a change in wall particles’ wettability from water-wet to oil-wet was implemented based on the final configuration of oil and water inside the pore. Waterflooding simulations were then carried out at the threshold capillary pressure. The results show that the oil layer formed between water in the corner and in the center of the pore is not stable and collapses as the simulation continues. This is in line with the predictions from the MS-P method.

  20. Molecular modeling studies, synthesis and biological evaluation of dabigatran analogues as thrombin inhibitors.

    Science.gov (United States)

    Dong, Ming-Hui; Chen, Hai-Feng; Ren, Yu-Jie; Shao, Fang-Ming

    2016-01-15

    In this work, 48 thrombin inhibitors based on the structural scaffold of dabigatran were analyzed using a combination of molecular modeling techniques. We generated three-dimensional quantitative structure-activity relationship (3D-QSAR) models based on three alignments for both comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) to highlight the structural requirements for thrombin protein inhibition. In addition to the 3D-QSAR study, Topomer CoMFA model also was established with a higher leave-one-out cross-validation q(2) and a non-cross-validation r(2), which suggest that the three models have good predictive ability. The results indicated that the steric, hydrophobic and electrostatic fields play key roles in QSAR model. Furthermore, we employed molecular docking and re-docking simulation explored the binding relationship of the ligand and the receptor protein in detail. Molecular docking simulations identified several key interactions that were also indicated through 3D-QSAR analysis. On the basis of the obtained results, two compounds were designed and predicted by three models, the biological evaluation in vitro (IC50) demonstrated that these molecular models were effective for the development of novel potent thrombin inhibitors.

  1. Virtual Transgenics: Using a Molecular Biology Simulation to Impact Student Academic Achievement and Attitudes

    Science.gov (United States)

    Shegog, Ross; Lazarus, Melanie M.; Murray, Nancy G.; Diamond, Pamela M.; Sessions, Nathalie; Zsigmond, Eva

    2012-10-01

    The transgenic mouse model is useful for studying the causes and potential cures for human genetic diseases. Exposing high school biology students to laboratory experience in developing transgenic animal models is logistically prohibitive. Computer-based simulation, however, offers this potential in addition to advantages of fidelity and reach. This study describes and evaluates a computer-based simulation to train advanced placement high school science students in laboratory protocols, a transgenic mouse model was produced. A simulation module on preparing a gene construct in the molecular biology lab was evaluated using a randomized clinical control design with advanced placement high school biology students in Mercedes, Texas ( n = 44). Pre-post tests assessed procedural and declarative knowledge, time on task, attitudes toward computers for learning and towards science careers. Students who used the simulation increased their procedural and declarative knowledge regarding molecular biology compared to those in the control condition (both p < 0.005). Significant increases continued to occur with additional use of the simulation ( p < 0.001). Students in the treatment group became more positive toward using computers for learning ( p < 0.001). The simulation did not significantly affect attitudes toward science in general. Computer simulation of complex transgenic protocols have potential to provide a "virtual" laboratory experience as an adjunct to conventional educational approaches.

  2. Current status of molecular biological techniques for plant breeding in the Republic of Korea

    International Nuclear Information System (INIS)

    Classical plant breeding has played an important role in developing new varieties in current agriculture. For decades, the technique of cross-pollination has been popular for breeding in cereal and horticultural crops to introduce special traits. However, recently the molecular techniques get widely accepted as an alternative tool in both introducing a useful trait for developing the new cultivars and investigating the characteristics of a trait in plant, like the identification of a gene. Using the advanced molecular technique, several genetically modified (GM) crops (e.g., Roundup Ready Soybean, YieldGard, LibertyLink etc.) became commercially cultivated and appeared in the global market since 1996. The GM crops, commercially available at the moment, could be regarded as successful achievements in history of crop breeding conferring the specific gene into economically valuable crops to make them better. Along with such achievements, on the other hand these new crops have also caused the controversial debate on the safety of GM crops as human consumption and environmental release as well. Nevertheless, molecular techniques are widespread and popular in both investigating the basic science of plant biology and breeding new varieties compared to their conventional counterparts. Thus, the Department of Bioresources at the National Institute of Agricultural Science and Technology (NIAST) has been using the molecular biological techniques as a complimentary tool for the improvement of crop varieties for almost two decades. (author)

  3. Current status of molecular biological techniques for plant breeding in the Republic of Korea

    Energy Technology Data Exchange (ETDEWEB)

    Sohn, Seong-Han; Lee, Si-Myung; Park, Bum-Seok; Yun, In-Sun; Goo, Doe-Hoe; Kim, Seok-Dong [Rural Development Administration, National Institute of Agricultural Science and Technology, Suwon (Korea)

    2002-02-01

    Classical plant breeding has played an important role in developing new varieties in current agriculture. For decades, the technique of cross-pollination has been popular for breeding in cereal and horticultural crops to introduce special traits. However, recently the molecular techniques get widely accepted as an alternative tool in both introducing a useful trait for developing the new cultivars and investigating the characteristics of a trait in plant, like the identification of a gene. Using the advanced molecular technique, several genetically modified (GM) crops (e.g., Roundup Ready Soybean, YieldGard, LibertyLink etc.) became commercially cultivated and appeared in the global market since 1996. The GM crops, commercially available at the moment, could be regarded as successful achievements in history of crop breeding conferring the specific gene into economically valuable crops to make them better. Along with such achievements, on the other hand these new crops have also caused the controversial debate on the safety of GM crops as human consumption and environmental release as well. Nevertheless, molecular techniques are widespread and popular in both investigating the basic science of plant biology and breeding new varieties compared to their conventional counterparts. Thus, the Department of Bioresources at the National Institute of Agricultural Science and Technology (NIAST) has been using the molecular biological techniques as a complimentary tool for the improvement of crop varieties for almost two decades. (author)

  4. Anticipatory dynamics of biological systems: from molecular quantum states to evolution

    Science.gov (United States)

    Igamberdiev, Abir U.

    2015-08-01

    Living systems possess anticipatory behaviour that is based on the flexibility of internal models generated by the system's embedded description. The idea was suggested by Aristotle and is explicitly introduced to theoretical biology by Rosen. The possibility of holding the embedded internal model is grounded in the principle of stable non-equilibrium (Bauer). From the quantum mechanical view, this principle aims to minimize energy dissipation in expense of long relaxation times. The ideas of stable non-equilibrium were developed by Liberman who viewed living systems as subdivided into the quantum regulator and the molecular computer supporting coherence of the regulator's internal quantum state. The computational power of the cell molecular computer is based on the possibility of molecular rearrangements according to molecular addresses. In evolution, the anticipatory strategies are realized both as a precession of phylogenesis by ontogenesis (Berg) and as the anticipatory search of genetic fixation of adaptive changes that incorporates them into the internal model of genetic system. We discuss how the fundamental ideas of anticipation can be introduced into the basic foundations of theoretical biology.

  5. [Molecular biology of renal cancer: bases for genetic directed therapy in advanced disease].

    Science.gov (United States)

    Maroto Rey, José Pablo; Cillán Narvaez, Elena

    2013-06-01

    There has been expansion of therapeutic options in the management of metastatic renal cell carcinoma due to a better knowledge of the molecular biology of kidney cancers. There are different tumors grouped under the term renal cell carcinoma, being clear cell cancer the most frequent and accounting for 80% of kidney tumors. Mutations in the Von Hippel-Lindau gene can be identified in up to 80% of sporadic clear cell cancer, linking a genetically inheritable disease where vascular tumors are frequent, with renal cell cancer. Other histologic types present specific alterations in molecular pathways, like c-MET in papillary type I tumors, and Fumarase Hydratase in papillary type II tumors. Identification of the molecular alteration for a specific tumor may offer an opportunity for treatment selection based on biomarkers, and, in the future, for developing an engineering designed genetic treatment.

  6. Molecular analysis of ex-vivo CD133+ GBM cells revealed a common invasive and angiogenic profile but different proliferative signatures among high grade gliomas

    Directory of Open Access Journals (Sweden)

    Garcia Juan L

    2010-08-01

    Full Text Available Abstract Background Gliomas are the most common type of primary brain tumours, and in this group glioblastomas (GBMs are the higher-grade gliomas with fast progression and unfortunate prognosis. Two major aspects of glioma biology that contributes to its awful prognosis are the formation of new blood vessels through the process of angiogenesis and the invasion of glioma cells. Despite of advances, two-year survival for GBM patients with optimal therapy is less than 30%. Even in those patients with low-grade gliomas, that imply a moderately good prognosis, treatment is almost never curative. Recent studies have demonstrated the existence of a small fraction of glioma cells with characteristics of neural stem cells which are able to grow in vitro forming neurospheres and that can be isolated in vivo using surface markers such as CD133. The aim of this study was to define the molecular signature of GBM cells expressing CD133 in comparison with non expressing CD133 cells. This molecular classification could lead to the finding of new potential therapeutic targets for the rationale treatment of high grade GBM. Methods Eight fresh, primary and non cultured GBMs were used in order to study the gene expression signatures from its CD133 positive and negative populations isolated by FACS-sorting. Dataset was generated with Affymetrix U133 Plus 2 arrays and analysed using the software of the Affymetrix Expression Console. In addition, genomic analysis of these tumours was carried out by CGH arrays, FISH studies and MLPA; Results Gene expression analysis of CD133+ vs. CD133- cell population from each tumour showed that CD133+ cells presented common characteristics in all glioblastoma samples (up-regulation of genes involved in angiogenesis, permeability and down-regulation of genes implicated in cell assembly, neural cell organization and neurological disorders. Furthermore, unsupervised clustering of gene expression led us to distinguish between two groups

  7. The molecular physiology of increased egg desiccation resistance during diapause in the invasive mosquito, Aedes albopictus

    Science.gov (United States)

    Urbanski, Jennifer M.; Benoit, Joshua B.; Michaud, M. Robert; Denlinger, David L.; Armbruster, Peter

    2010-01-01

    Photoperiodic diapause is a crucial adaptation to seasonal environmental variation in a wide range of arthropods, but relatively little is known regarding the molecular basis of this important trait. In temperate populations of the mosquito Aedes albopictus, exposure to short-day (SD) lengths causes the female to produce diapause eggs. Tropical populations do not undergo a photoperiodic diapause. We identified a fatty acyl coA elongase transcript that is more abundant under SD versus long-day (LD) photoperiods in mature oocyte tissue of replicate temperate, but not tropical, A. albopictus populations. Fatty acyl CoA elongases are involved in the synthesis of long chain fatty acids (hydrocarbon precursors). Diapause eggs from a temperate population had one-third more surface hydrocarbons and one-half the water loss rates of non-diapause eggs. Eggs from a tropical population reared under SD and LD photoperiods did not differ in surface hydrocarbon abundance or water loss rates. In both a temperate and tropical population, composition of hydrocarbon chain lengths did not differ between eggs from SD versus LD conditions. These results implicate the expression of fatty acyl coA elongase and changes in quantity, but not composition, of egg surface hydrocarbons as important components of increased desiccation resistance during diapause in A. albopictus. PMID:20410035

  8. Normal and disease-related biological functions of Twist1 and underlying molecular mechanisms

    Institute of Scientific and Technical Information of China (English)

    Qian Qin; Young Xu; Tao He; Chunlin Qin; Jianming Xu

    2012-01-01

    This article reviews the molecular structure,expression pattern,physiological function,pathological roles and molecular mechanisms of Twist1 in development,genetic disease and cancer.Twist1 is a basic helix-loop-helix domaincontaining transcription factor.It forms homo- or hetero-dimers in order to bind the Nde1 E-box element and activate or repress its target genes.During development,Twistl is essential for mesoderm specification and differentiation.Heterozygous loss-of-function mutations of the human Twist1 gene cause several diseases including the SaethreChotzen syndrome.The Twist1-null mouse embryos die with unclosed cranial neural tubes and defective head mesenchyme,somites and limb buds.Twist1 is expressed in breast,liver,prostate,gastric and other types of cancers,and its expression is usually associated with invasive and metastatic cancer phenotypes.In cancer cells,Twistl is upregulated by multiple factors including SRC-1,STAT3,MSX2,HIF-1α,integrin-linked kinase and NF-κB.Twist1 significantly enhances epithelial-mesenchymal transition (EMT) and cancer cell migration and invasion,hence promoting cancer metastasis.Twistl promotes EMT in part by directly repressing E-cadherin expression by recruiting the nucleosome remodeling and deacetylase complex for gene repression and by upregulating Bmil,AKT2,YB-1,etc.Emerging evidence also suggests that Twist1 plays a role in expansion and chemotherapeutic resistance of cancer stem cells.Further understanding of the mechanisms by which Twist1 promotes metastasis and identification of Twist1 functional modulators may hold promise for developing new strategies to inhibit EMT and cancer metastasis.

  9. Mapping molecular orientational distributions for biological sample in 3D (Conference Presentation)

    Science.gov (United States)

    HE, Wei; Ferrand, Patrick; Richter, Benjamin; Bastmeyer, Martin; Brasselet, Sophie

    2016-04-01

    Measuring molecular orientation properties is very appealing for scientists in molecular and cell biology, as well as biomedical research. Orientational organization at the molecular scale is indeed an important brick to cells and tissues morphology, mechanics, functions and pathologies. Recent work has shown that polarized fluorescence imaging, based on excitation polarization tuning in the sample plane, is able to probe molecular orientational order in biological samples; however this applies only to information in 2D, projected in the sample plane. To surpass this limitation, we extended this approach to excitation polarization tuning in 3D. The principle is based on the decomposition of any arbitrary 3D linear excitation in a polarization along the longitudinal z-axis, and a polarization in the transverse xy-sample plane. We designed an interferometer with one arm generating radial polarization light (thus producing longitudinal polarization under high numerical aperture focusing), the other arm controlling a linear polarization in the transverse plane. The amplitude ratio between the two arms can vary so as to get any linear polarized excitation in 3D at the focus of a high NA objective. This technique has been characterized by polarimetry imaging at the back focal plane of the focusing objective, and modeled theoretically. 3D polarized fluorescence microscopy is demonstrated on actin stress fibers in non-flat cells suspended on synthetic polymer structures forming supporting pillars, for which heterogeneous actin orientational order could be identified. This technique shows a great potential in structural investigations in 3D biological systems, such as cell spheroids and tissues.

  10. Non-invasive detection of colorectal tumours by the combined application of molecular diagnosis and the faecal occult blood test.

    Science.gov (United States)

    Kutzner, Nadine; Hoffmann, Ingrid; Linke, Christina; Thienel, Thomas; Grzegorczyk, Marco; Urfer, Wolfgang; Martin, Dirk; Winde, Günther; Traska, Thilo; Hohlbach, Gerd; Müller, Klaus-Michael; Kuhnen, Cornelius; Müller, Oliver

    2005-11-01

    The treatment of early-stage tumours decreases the overall mortality of colorectal tumour patients. In this retrospective study we determined the sensitivity and the specificity of the faecal occult blood test (FOBT) and the molecular diagnosis (MD). We analysed 57 stool samples from patients with colorectal carcinomas for the presence of occult blood using a standard FOBT and for alterations in the three different tumour relevant markers APC, BAT26 and L-DNA. Stool samples from 44 control donors were analysed to determine the specificity of the applied methods. Twenty-nine (51%; 95% confidence interval (CI): 38-63%) stool samples of the cancer patients gave positive FOBT results. Thirty-seven (65%; CI: 52-76%) samples showed alterations in at least one DNA marker. Sixteen (28%) samples were positive only in the FOBT, and 24 (42%) samples showed a positive result exclusively in MD. The combined application of both methods resulted in a sensitivity of 93% (CI: 83-97%) and an overall specificity of 89% (CI: 76-95%). The combined application of FOBT and MD resulted in an overall sensitivity, which could not be achieved by any of the methods alone and which is in the range of invasive diagnostic methods. PMID:16157216

  11. Molecular evidence for Lessepsian invasion of soritids (larger symbiont bearing benthic foraminifera.

    Directory of Open Access Journals (Sweden)

    Gily Merkado

    Full Text Available The Mediterranean Sea is considered as one of the hotspots of marine bioinvasions, largely due to the influx of tropical species migrating through the Suez Canal, so-called Lessepsian migrants. Several cases of Lessepsian migration have been documented recently, however, little is known about the ecological characteristics of the migrating species and their aptitude to colonize the new areas. This study focused on Red Sea soritids, larger symbiont-bearing benthic foraminifera (LBF that are indicative of tropical and subtropical environments and were recently found in the Israeli coast of the Eastern Mediterranean. We combined molecular phylogenetic analyses of soritids and their algal symbionts as well as network analysis of Sorites orbiculus Forskål to compare populations from the Gulf of Elat (northern Red Sea and from a known hotspot in Shikmona (northern Israel that consists of a single population of S. orbiculus. Our phylogenetic analyses show that all specimens found in Shikmona are genetically identical to a population of S. orbiculus living on a similar shallow water pebbles habitat in the Gulf of Elat. Our analyses also show that the symbionts found in Shikmona and Elat soritids belong to the Symbiodinium clade F5, which is common in the Red Sea and also present in the Indian Ocean and Caribbean Sea. Our study therefore provides the first genetic and ecological evidences that indicate that modern population of soritids found on the Mediterranean coast of Israel is probably Lessepsian, and is less likely the descendant of a native ancient Mediterranean species.

  12. Molecular evidence for the predation of Critically Endangered endemic Aphanius transgrediens from the stomach contents of world wide invasive Gambusia affinis.

    Science.gov (United States)

    Keskin, Emre

    2016-01-01

    Predation and competition among native and invasive species are difficult to study in aquatic environments. Identification of preys from semi-digested body parts sampled from stomach contents of the predator is very challenging. Recent studies were mainly based on use of DNA extracted from stomach content to identify the prey species. This study presents the molecular evidence that reveals the predation of critically endangered Aphanius transgrediens by world-wide invasive Gambusia affinis for a better understanding of the link between the invasion and the extinction of native species in freshwater ecosystems. DNA samples were extracted from semi-digested stomach contents of the invader and short fragments of mitochondrial NADH1 gene were amplified using species-specific primers designed in this study to make identification at species level. Existence of both the prey and the predator species were also confirmed using environmental DNA extracted from water samples.

  13. The emergence of molecular profiling and omics techniques in seagrass biology; furthering our understanding of seagrasses.

    Science.gov (United States)

    Davey, Peter A; Pernice, Mathieu; Sablok, Gaurav; Larkum, Anthony; Lee, Huey Tyng; Golicz, Agnieszka; Edwards, David; Dolferus, Rudy; Ralph, Peter

    2016-09-01

    Seagrass meadows are disappearing at alarming rates as a result of increasing coastal development and climate change. The emergence of omics and molecular profiling techniques in seagrass research is timely, providing a new opportunity to address such global issues. Whilst these applications have transformed terrestrial plant research, they have only emerged in seagrass research within the past decade; In this time frame we have observed a significant increase in the number of publications in this nascent field, and as of this year the first genome of a seagrass species has been sequenced. In this review, we focus on the development of omics and molecular profiling and the utilization of molecular markers in the field of seagrass biology. We highlight the advances, merits and pitfalls associated with such technology, and importantly we identify and address the knowledge gaps, which to this day prevent us from understanding seagrasses in a holistic manner. By utilizing the powers of omics and molecular profiling technologies in integrated strategies, we will gain a better understanding of how these unique plants function at the molecular level and how they respond to on-going disturbance and climate change events. PMID:27443314

  14. The Molecular Biology of Soft-Tissue Sarcomas and Current Trends in Therapy

    Directory of Open Access Journals (Sweden)

    Jorge Quesada

    2012-01-01

    Full Text Available Basic research in sarcoma models has been fundamental in the discovery of scientific milestones leading to a better understanding of the molecular biology of cancer. Yet, clinical research in sarcoma has lagged behind other cancers because of the multiple clinical and pathological entities that characterize sarcomas and their rarity. Sarcomas encompass a very heterogeneous group of tumors with diverse pathological and clinical overlapping characteristics. Molecular testing has been fundamental in the identification and better definition of more specific entities among this vast array of malignancies. A group of sarcomas are distinguished by specific molecular aberrations such as somatic mutations, intergene deletions, gene amplifications, reciprocal translocations, and complex karyotypes. These and other discoveries have led to a better understanding of the growth signals and the molecular pathways involved in the development of these tumors. These findings are leading to treatment strategies currently under intense investigation. Disruption of the growth signals is being targeted with antagonistic antibodies, tyrosine kinase inhibitors, and inhibitors of several downstream molecules in diverse molecular pathways. Preliminary clinical trials, supported by solid basic research and strong preclinical evidence, promises a new era in the clinical management of these broad spectrum of malignant tumors.

  15. THE EVALUATION OF A TOOL FOR DISSEMINATION OF BIOTECHNOLOGY AND MOLECULAR BIOLOGY CONCEPTS IN FORMAL EDUCATION

    Directory of Open Access Journals (Sweden)

    F.M. Escanhoela

    2007-05-01

    Full Text Available Since 2003, the CBME Scientific Dissemination Coordination hasdeveloped a project related to the production and distribution of a scientificdissemination newspaper, called CBME InFORMAÇÃO, directed to high-schoolstudents and teachers. It is a quarterly publication and shows the concepts andadvances of studies in molecular biology and biotechnology. In order to evaluatethe newspaper, a research was accomplished in 2005. It involved 177 studentsfrom six high schools of São Carlos and region. In addition, opinions of fivescience teachers that worked with the newspaper in their classrooms, as well aseight Biology undergraduates were collected. The teachers received somequestionnaires that had to be answered by them and their students after a specifyactivity with the periodical – basically, the activities consisted of three stages:individual reading of the newspaper; formulation of questions by the teacher and,finally, group discussion on the chosen theme. The research confirmed theimportance of the use of the periodical as a tool in the formation of critical readersof facts related to the biotechnology and molecular biology, what should contributewith the citizenship development in the students. Moreover, it provided a possibilityto reorganize the periodical.

  16. Correlative Study on MRI Morphologic Features,Pathology, and Molecular Biology of Breast Cancer

    Institute of Scientific and Technical Information of China (English)

    Rong Chen; Shuigen Gong; Weiguo Zhang; Jinhua Chen; Shuangwu He; Baohua Liu; Zengpeng Li

    2005-01-01

    OBJECTIVE To investigate the correlation among MRI morphologic features,pathology, and molecular biology of breast cancer.METHORDS MRI was used to analyze the morphologic features of breast cancers of 78 patients before operation. The mastectomy specimens of the breast neoplasms were immunohistochemically stained, and the expression of the estrogen (ER), progesterone receptor (PR), C-erbB-2, P53, and the distribution of microvessel density (MVD) measured. The pathologic results were compared with the MRI features.RESULTS Among the 80 breast cancers, ER positive expression was positively correlated with the spicular contour of breast cancers (P<0.01),while showing a significant inverse correlation with the T-stage (P<0.05). CerbB-2 and P53 positive expression were positively correlated with the necrotic center of the cancers (P<0.05). The expression of PR was not significantly correlated with the spicular contour, obscure margin, necrotic center, and T-stage of these cancers (P>0.05). Among 41 breast cancers examined with dynamic contrast enhanced MR, there was a positive correlation between the spatial distribution of the contrast agent and MVD(P<0.01).CONCLUSION To a certain extent there is some correlation among the MRI morphologic features, pathology, and molecular biological factors in breast cancer. The biological behavior and prognosis of breast cancer can be assessed based on MRI features.

  17. The Development and Implementation of an Instrument to Assess Students’ Data Analysis Skills in Molecular Biology

    Directory of Open Access Journals (Sweden)

    Brian J. Rybarczyk

    2014-03-01

    Full Text Available Developing visual literacy skills is an important component of scientific literacy in undergraduate science education.  Comprehension, analysis, and interpretation are parts of visual literacy that describe related data analysis skills important for learning in the biological sciences. The Molecular Biology Data Analysis Test (MBDAT was developed to measure students’ data analysis skills connected with scientific reasoning when analyzing and interpreting scientific data generated from experimental research.  The skills analyzed included basic skills such as identification of patterns and trends in data and connecting a method that generated the data and advanced skills such as distinguishing positive and negative controls, synthesizing conclusions, determining if data supports a hypothesis, and predicting alternative or next-step experiments.  Construct and content validity were established and calculated statistical parameters demonstrate that the MBDAT is valid and reliable for measuring students’ data analysis skills in molecular and cell biology contexts.  The instrument also measures students’ perceived confidence in their data interpretation abilities.  As scientific research continues to evolve in complexity, interpretation of scientific information in visual formats will continue to be an important component of scientific literacy.  Thus science education will need to support and assess students’ development of these skills as part of students’ scientific training.

  18. KRAS and BRAF Mutation Detection: Is Immunohistochemistry a Possible Alternative to Molecular Biology in Colorectal Cancer?

    Directory of Open Access Journals (Sweden)

    Nicolas Piton

    2015-01-01

    Full Text Available KRAS genotyping is mandatory in metastatic colorectal cancer treatment prior to undertaking antiepidermal growth factor receptor (EGFR monoclonal antibody therapy. BRAF V600E mutation is often present in colorectal carcinoma with CpG island methylator phenotype and microsatellite instability. Currently, KRAS and BRAF evaluation is based on molecular biology techniques such as SNaPshot or Sanger sequencing. As molecular testing is performed on formalin-fixed paraffin-embedded (FFPE samples, immunodetection would appear to be an attractive alternative for detecting mutations. Thus, our objective was to assess the validity of KRAS and BRAF immunodetection of mutations compared with the genotyping reference method in colorectal adenocarcinoma. KRAS and BRAF genotyping was assessed by SNaPshot. A rabbit anti-human KRAS polyclonal antibody was tested on 33 FFPE colorectal tumor samples with known KRAS status. Additionally, a mouse anti-human BRAF monoclonal antibody was tested on 30 FFPE tumor samples with known BRAF status. KRAS immunostaining demonstrated both poor sensitivity (27% and specificity (64% in detecting KRAS mutation. Conversely, BRAF immunohistochemistry showed perfect sensitivity (100% and specificity (100% in detecting V600E mutation. Although molecular biology remains the reference method for detecting KRAS mutation, immunohistochemistry could be an attractive method for detecting BRAF V600E mutation in colorectal cancer.

  19. KRAS and BRAF Mutation Detection: Is Immunohistochemistry a Possible Alternative to Molecular Biology in Colorectal Cancer?

    Science.gov (United States)

    Piton, Nicolas; Borrini, Francesco; Bolognese, Antonio; Lamy, Aude; Sabourin, Jean-Christophe

    2015-01-01

    KRAS genotyping is mandatory in metastatic colorectal cancer treatment prior to undertaking antiepidermal growth factor receptor (EGFR) monoclonal antibody therapy. BRAF V600E mutation is often present in colorectal carcinoma with CpG island methylator phenotype and microsatellite instability. Currently, KRAS and BRAF evaluation is based on molecular biology techniques such as SNaPshot or Sanger sequencing. As molecular testing is performed on formalin-fixed paraffin-embedded (FFPE) samples, immunodetection would appear to be an attractive alternative for detecting mutations. Thus, our objective was to assess the validity of KRAS and BRAF immunodetection of mutations compared with the genotyping reference method in colorectal adenocarcinoma. KRAS and BRAF genotyping was assessed by SNaPshot. A rabbit anti-human KRAS polyclonal antibody was tested on 33 FFPE colorectal tumor samples with known KRAS status. Additionally, a mouse anti-human BRAF monoclonal antibody was tested on 30 FFPE tumor samples with known BRAF status. KRAS immunostaining demonstrated both poor sensitivity (27%) and specificity (64%) in detecting KRAS mutation. Conversely, BRAF immunohistochemistry showed perfect sensitivity (100%) and specificity (100%) in detecting V600E mutation. Although molecular biology remains the reference method for detecting KRAS mutation, immunohistochemistry could be an attractive method for detecting BRAF V600E mutation in colorectal cancer.

  20. Features of Knowledge Building in Biology: Understanding Undergraduate Students’ Ideas about Molecular Mechanisms

    Science.gov (United States)

    Southard, Katelyn; Wince, Tyler; Meddleton, Shanice; Bolger, Molly S.

    2016-01-01

    Research has suggested that teaching and learning in molecular and cellular biology (MCB) is difficult. We used a new lens to understand undergraduate reasoning about molecular mechanisms: the knowledge-integration approach to conceptual change. Knowledge integration is the dynamic process by which learners acquire new ideas, develop connections between ideas, and reorganize and restructure prior knowledge. Semistructured, clinical think-aloud interviews were conducted with introductory and upper-division MCB students. Interviews included a written conceptual assessment, a concept-mapping activity, and an opportunity to explain the biomechanisms of DNA replication, transcription, and translation. Student reasoning patterns were explored through mixed-method analyses. Results suggested that students must sort mechanistic entities into appropriate mental categories that reflect the nature of MCB mechanisms and that conflation between these categories is common. We also showed how connections between molecular mechanisms and their biological roles are part of building an integrated knowledge network as students develop expertise. We observed differences in the nature of connections between ideas related to different forms of reasoning. Finally, we provide a tentative model for MCB knowledge integration and suggest its implications for undergraduate learning. PMID:26931398

  1. Structural parameters, molecular properties, and biological evaluation of some terpenes targeting Schistosoma mansoni parasite.

    Science.gov (United States)

    Mafud, Ana C; Silva, Marcos P N; Monteiro, Daniela C; Oliveira, Maria F; Resende, João G; Coelho, Mayara L; de Sousa, Damião P; Mendonça, Ronaldo Z; Pinto, Pedro L S; Freitas, Rivelilson M; Mascarenhas, Yvonne P; de Moraes, Josué

    2016-01-25

    The use of natural products has a long tradition in medicine, and they have proven to be an important source of lead compounds in the development of new drugs. Among the natural compounds, terpenoids present broad-spectrum activity against infective agents such as viruses, bacteria, fungi, protozoan and helminth parasites. In this study, we report a biological screening of 38 chemically characterized terpenes from different classes, which have a hydroxyl group connected by hydrophobic chain or an acceptor site, against the blood fluke Schistosoma mansoni, the parasite responsible for schistosomiasis mansoni. In vitro bioassays revealed that 3,7-dimethyl-1-octanol (dihydrocitronellol) (10) was the most active terpene (IC50 values of 13-52 μM) and, thus, we investigated its antischistosomal activity in greater detail. Confocal laser scanning microscopy revealed that compound 10 induced severe tegumental damage in adult schistosomes and a correlation between viability and tegumental changes was observed. Furthermore, we compared all the inactive compounds with dihydrocitronellol structurally by using shape and charge modeling. Lipophilicity (miLogP) and other molecular properties (e.g. molecular polar surface area, molecular electrostatic potential) were also calculated. From the 38 terpenes studied, compound 10 is the one with the greatest flexibility, with a sufficient apolar region by which it may interact in a hydrophobic active site. In conclusion, the integration of biological and chemical analysis indicates the potential of the terpene dihydrocitronellol as an antiparasitic agent. PMID:26697994

  2. Features of Knowledge Building in Biology: Understanding Undergraduate Students' Ideas about Molecular Mechanisms.

    Science.gov (United States)

    Southard, Katelyn; Wince, Tyler; Meddleton, Shanice; Bolger, Molly S

    2016-01-01

    Research has suggested that teaching and learning in molecular and cellular biology (MCB) is difficult. We used a new lens to understand undergraduate reasoning about molecular mechanisms: the knowledge-integration approach to conceptual change. Knowledge integration is the dynamic process by which learners acquire new ideas, develop connections between ideas, and reorganize and restructure prior knowledge. Semistructured, clinical think-aloud interviews were conducted with introductory and upper-division MCB students. Interviews included a written conceptual assessment, a concept-mapping activity, and an opportunity to explain the biomechanisms of DNA replication, transcription, and translation. Student reasoning patterns were explored through mixed-method analyses. Results suggested that students must sort mechanistic entities into appropriate mental categories that reflect the nature of MCB mechanisms and that conflation between these categories is common. We also showed how connections between molecular mechanisms and their biological roles are part of building an integrated knowledge network as students develop expertise. We observed differences in the nature of connections between ideas related to different forms of reasoning. Finally, we provide a tentative model for MCB knowledge integration and suggest its implications for undergraduate learning.

  3. The system-biological GLOBE 3D Genome Platform. : A new holistic genome viewer for molecular genetics

    NARCIS (Netherlands)

    M. Lesnussa (Michael); F.N. Kepper (Nick); H.J.F.M.M. Eussen (Bert); T.A. Knoch (Tobias)

    2009-01-01

    textabstractGenomes are tremendous co-evolutionary holistic systems for molecular storage, processing and fabrication of information. Their system-biological complexity remains, however, still largely mysterious, despite immense sequencing achievements and huge advances in the understanding of the

  4. Biology and host specificity of Coelocephalapion gandolfoi Kissinger (Brentidae) a promising candidate for the biological control of invasive Prosopis species (Leguminosae) in South Africa

    Science.gov (United States)

    Invasive Prosopis species (Leguminosae) (mesquite) pose a significant threat to biodiversity, pasture production, and water resources in South Africa. In an attempt to contain the spread of this noxious weed the South African authorities have supported the introduction of host-specific and damaging...

  5. Avian hepatitis B viruses: Molecular and cellular biology, phylogenesis, and host tropism

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The human hepatitis B virus (HBV) and the duck hepatitis B virus (DHBV) share several fundamental features.Both viruses have a partially double-stranded DNA genome that is replicated via a RNA intermediate and the coding open reading frames (ORFs) overlap extensively.In addition, the genomic and structural organization,as well as replication and biological characteristics, are very similar in both viruses. Most of the key features of hepadnaviral infection were first discovered in the DHBV model system and subsequently confirmed for HBV.There are, however, several differences between human HBV and DHBV. This review will focus on the molecular and cellular biology, evolution, and host adaptation of the avian hepatitis B viruses with particular emphasis on DHBV as a model system.

  6. Plant Molecular Biology 2008 Gordon Research Conference - July 13-18, 2008

    Energy Technology Data Exchange (ETDEWEB)

    Richard M. Amasino

    2009-08-28

    The Plant Molecular Biology Conference has traditionally covered a breadth of exciting topics and the 2008 conference will continue in that tradition. There will be sessions on metabolism; new methods to study genomes, proteomes and metabolomes; plant-microbe interactions; plant hormones; epigenetics. A new topic for the conference this year will be bioenergy. Thus this conference will bring together a range of disciplines to foster the exchange ideas and to permit the 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.

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

    Science.gov (United States)

    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.

  8. Molecular, biological, and morphometric comparisons between different geographical populations of Rhipicephalus sanguineus sensu lato (Acari: Ixodidae).

    Science.gov (United States)

    Sanches, Gustavo S; Évora, Patrícia M; Mangold, Atílio J; Jittapalapong, Sattaporn; Rodriguez-Mallon, Alina; Guzmán, Pedro E E; Bechara, Gervásio H; Camargo-Mathias, Maria I

    2016-01-15

    In this study, different geographical populations of Rhipicephalus sanguineus sensu lato were compared by molecular, biological, and morphometric methods. Phylogenetic trees were constructed using 12S and 16S rDNA sequences and showed two distinct clades: one composed of ticks from Brazil (Jaboticabal, SP), Cuba (Havana) Thailand (Bangkok) and the so-called "tropical strain" ticks. The second clade was composed of ticks from Spain (Zaragoza), Argentina (Rafaela, Santa Fe) and the so-called "temperate strain" ticks. Morphometric analysis showed good separation between females of the two clades and within the temperate clade. Males also exhibited separation between the two clades, but with some overlap. Multiple biological parameters revealed differences between the two clades, especially the weight of the engorged female. These results confirm the existence of at least two species under the name "R. sanguineus". PMID:26790741

  9. Synthesis, molecular modeling and biological evaluation of dithiocarbamates as novel antitubulin agents.

    Science.gov (United States)

    Qian, Yong; Ma, Gao-Yuan; Yang, Ying; Cheng, Kui; Zheng, Qing-Zhong; Mao, Wen-Jun; Shi, Lei; Zhao, Jing; Zhu, Hai-Liang

    2010-06-15

    A series of novel dithiocarbamate compounds with the chalcone scaffold have been designed and synthesized, and their biological activities were also evaluated as potential antiproliferation and antitubulin polymerization inhibitors. Compound 2n showed the most potent biological activity in vitro, which inhibited the growth of MCF-7 cells with IC(50) of 0.04+/-0.01 microM and the polymerization of tubulin with IC(50) of 6.8+/-0.6 microM. To understand the tubulin-inhibitor interaction and the selectivity of the most active compound towards tubulin, molecular modeling studies were performed to dock compound 2n into the colchicine binding site, which suggested probable inhibition mechanism. PMID:20493717

  10. Overview of significant challenges in molecular biology amenable to computational methods.

    Science.gov (United States)

    Glaeser, R M

    1994-01-01

    Many challenging but significant opportunities exist for the development of theoretical approaches in modern Cell and Molecular Biology. The creation of data bases which contain extremely large amounts of information has proven to be an unexpectedly important facto-tin gaining acceptance and respectability for theoretical work that builds on nothing more than what is in the data base itself, such as theoretical work involving the analysis of known protein structures, or the development of more powerful homology searches. Other opportunities, not yet accepted by a broad community, involve work on complex networks (metabolic, genetic, immunologic and neural networks) and work on the "physics of how things work." The DOE National Laboratory System represents the ideal institution that would be well suited to the role of being an "incubator" for the creation of a theoretical and computational discipline within modern biology. PMID:7755540

  11. Computer Simulation and Data Analysis in Molecular Biology and Biophysics An Introduction Using R

    CERN Document Server

    Bloomfield, Victor

    2009-01-01

    This book provides an introduction, suitable for advanced undergraduates and beginning graduate students, to two important aspects of molecular biology and biophysics: computer simulation and data analysis. It introduces tools to enable readers to learn and use fundamental methods for constructing quantitative models of biological mechanisms, both deterministic and with some elements of randomness, including complex reaction equilibria and kinetics, population models, and regulation of metabolism and development; to understand how concepts of probability can help in explaining important features of DNA sequences; and to apply a useful set of statistical methods to analysis of experimental data from spectroscopic, genomic, and proteomic sources. These quantitative tools are implemented using the free, open source software program R. R provides an excellent environment for general numerical and statistical computing and graphics, with capabilities similar to Matlab®. Since R is increasingly used in bioinformat...

  12. Particular aspects in the cytogenetics and molecular biology of salivary gland tumours - current review of reports.

    Science.gov (United States)

    Ochal-Choińska, Aleksandra J; Osuch-Wójcikiewicz, Ewa

    2016-01-01

    Salivary gland tumours are a group of lesions whose heterogeneity of biological and pathological features is widely reflected in the molecular aspect. This is demonstrated by an increasing number of studies in the field of genetics of these tumours. The aim of this study was to collect the most significant scientific reports on the cytogenetic and molecular data concerning these tumours, which might facilitate the identification of potential biomarkers and therapeutic targets. The analysis covered 71 papers included in the PubMed database. We focused on the most common tumours, such as pleomorphic adenoma, Warthin tumour, mucoepidermoid carcinoma, and others. The aim of this study is to present current knowledge about widely explored genotypic alterations (such as PLAG1 gene in pleomorphic adenoma or MECT1 gene in mucoepidermoid carcinoma), and also about rare markers, like Mena or SOX10 protein, which might also be associated with tumourigenesis and carcinogenesis of these tumours. PMID:27688723

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

    Science.gov (United States)

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

    2014-03-01

    Testicular germ cell tumors (TGCTs) are the most common solid tumors in young adult men characterized by distinct biologic features and clinical behavior. Both genetic predispositions and environmental factors probably play a substantial role in their etiology. TGTCs arise from a malignant transformation of primordial germ cells in a process that starts prenatally, is often associated with a certain degree of gonadal dysgenesis, and involves the acquirement of several specific aberrations, including activation of SCF-CKIT, amplification of 12p with up-regulation of stem cell genes, and subsequent genetic and epigenetic alterations. Their embryonic and germ origin determines the unique sensitivity of TGCTs to platinum-based chemotherapy. Contrary to the vast majority of other malignancies, no molecular prognostic/predictive factors nor targeted therapy is available for patients with these tumors. This review summarizes the principal molecular characteristics of TGCTs that could represent a potential basis for development of novel diagnostic and treatment approaches. PMID:24182421

  14. A systems biology approach identifies molecular networks defining skeletal muscle abnormalities in chronic obstructive pulmonary disease.

    Directory of Open Access Journals (Sweden)

    Nil Turan

    2011-09-01

    Full Text Available Chronic Obstructive Pulmonary Disease (COPD is an inflammatory process of the lung inducing persistent airflow limitation. Extensive systemic effects, such as skeletal muscle dysfunction, often characterize these patients and severely limit life expectancy. Despite considerable research efforts, the molecular basis of muscle degeneration in COPD is still a matter of intense debate. In this study, we have applied a network biology approach to model the relationship between muscle molecular and physiological response to training and systemic inflammatory mediators. Our model shows that failure to co-ordinately activate expression of several tissue remodelling and bioenergetics pathways is a specific landmark of COPD diseased muscles. Our findings also suggest that this phenomenon may be linked to an abnormal expression of a number of histone modifiers, which we discovered correlate with oxygen utilization. These observations raised the interesting possibility that cell hypoxia may be a key factor driving skeletal muscle degeneration in COPD patients.

  15. Biologically relevant molecular transducer with increased computing power and iterative abilities.

    Science.gov (United States)

    Ratner, Tamar; Piran, Ron; Jonoska, Natasha; Keinan, Ehud

    2013-05-23

    As computing devices, which process data and interconvert information, transducers can encode new information and use their output for subsequent computing, offering high computational power that may be equivalent to a universal Turing machine. We report on an experimental DNA-based molecular transducer that computes iteratively and produces biologically relevant outputs. As a proof of concept, the transducer accomplished division of numbers by 3. The iterative power was demonstrated by a recursive application on an obtained output. This device reads plasmids as input and processes the information according to a predetermined algorithm, which is represented by molecular software. The device writes new information on the plasmid using hardware that comprises DNA-manipulating enzymes. The computation produces dual output: a quotient, represented by newly encoded DNA, and a remainder, represented by E. coli phenotypes. This device algorithmically manipulates genetic codes. PMID:23706637

  16. Searching for microbial biological control candidates for invasive grasses: coupling expanded field research with strides in biotechnology and grassland restoration

    Science.gov (United States)

    Highly invasive grasses (e.g. Bromus spp., Pennisetum ciliare, Taeniatherum caput-medusae) are largely unabated in much of the arid Western U.S., despite more than 70 years of control attempts with a wide array of tools and management practices. The development and sustained integration of new appro...

  17. Using restriction mapping to teach basic skills in the molecular biology lab.

    Science.gov (United States)

    Walsh, Lauren; Shaker, Elizabeth; De Stasio, Elizabeth A

    2007-05-01

    Digestion of DNA with restriction enzymes, calculation of volumes and concentrations of reagents for reactions, and the separation of DNA fragments by agarose gel electrophoresis are common molecular biology techniques that are best taught through repetition. The following open-ended, investigative laboratory exercise in plasmid restriction mapping allows students to gain technical expertise while simultaneously exploring the utility of gel electrophoresis and restriction mapping. Because of its interpretive nature, this project also provides data suitable for a written report, and can thus be used to reinforce lessons on figure presentation and science writing skills. PMID:21591089

  18. Theoretical study of the molecular bases that control photochemical processes with biological and nanotechnological interest

    OpenAIRE

    Saurí Peris, Vicenta

    2013-01-01

    El trabajo desarrollado en la tesis doctoral que lleva por título "Theoretical study of the molecular bases that control photochemical processes with biological and nanotechnological interest" se enmarca en las líneas de investigación del grupo QCEXVAL (Quantum Chemistry of the Excited State University of Valencia), que nació en el seno del departamento de Química Física de la Universitat de València en 1993. Se han abordado temas de interés metodológico, biológico y nanotecnológico. La prime...

  19. Molecular advances in the cell biology of SARS-CoV and current disease prevention strategies

    OpenAIRE

    Atreya CD; Stark Caren J

    2005-01-01

    Abstract In the aftermath of the SARS epidemic, there has been significant progress in understanding the molecular and cell biology of SARS-CoV. Some of the milestones are the availability of viral genome sequence, identification of the viral receptor, development of an infectious cDNA clone, and the identification of viral antigens that elicit neutralizing antibodies. However, there is still a large gap in our understanding of how SARS-CoV interacts with the host cell and the rapidly changin...

  20. Principal manifolds and graphs in practice: from molecular biology to dynamical systems

    CERN Document Server

    Gorban, A N

    2010-01-01

    We present several applications of non-linear data modeling, using principal manifolds and principal graphs constructed using the metaphor of elasticity (elastic principal graph approach). These approaches are generalizations of the Kohonen's self-organizing maps, a class of artificial neural networks. On several examples we show advantages of using non-linear objects for data approximation in comparison to the linear ones. We propose four numerical criteria for comparing linear and non-linear mappings of datasets into the spaces of lower dimension. The examples are taken from comparative political science, from analysis of high-throughput data in molecular biology, from analysis of dynamical systems.