Independence and Interdependence in Diverse Cultural Contexts.

Science.gov (United States)

Killen, Melanie; Wainryb, Cecilia

2000-01-01

Argues that the individualistic-collectivistic dichotomy results in mislabeling both cultures and individuals. Discusses ways in which individualistic concerns with independence and collectivistic concerns with interdependence coexist in Western and non-Western cultures. Outlines a theoretical framework explaining the coexistence of diverse social…

Bacterial community structure associated with white band disease in the elkhorn coral Acropora palmata determined using culture-independent 16S rRNA techniques.

Science.gov (United States)

Pantos, Olga; Bythell, John C

2006-03-23

Culture-independent molecular (16S ribosomal RNA) techniques showed distinct differences in bacterial communities associated with white band disease (WBD) Type I and healthy elkhorn coral Acropora palmata. Differences were apparent at all levels, with a greater diversity present in tissues of diseased colonies. The bacterial community associated with remote, non-diseased coral was distinct from the apparently healthy tissues of infected corals several cm from the disease lesion. This demonstrates a whole-organism effect from what appears to be a localised disease lesion, an effect that has also been recently demonstrated in white plague-like disease in star coral Montastraea annularis. The pattern of bacterial community structure changes was similar to that recently demonstrated for white plague-like disease and black band disease. Some of the changes are likely to be explained by the colonisation of dead and degrading tissues by a micro-heterotroph community adapted to the decomposition of coral tissues. However, specific ribosomal types that are absent from healthy tissues appear consistently in all samples of each of the diseases. These ribotypes are closely related members of a group of alpha-proteobacteria that cause disease, notably juvenile oyster disease, in other marine organisms. It is clearly important that members of this group are isolated for challenge experiments to determine their role in the diseases.

Microbial diversity and dynamics throughout manufacturing and ripening of surface ripened semi-hard Danish Danbo cheeses investigated by culture-independent techniques

DEFF Research Database (Denmark)

Ryssel, Mia; Johansen, Pernille; Abu Al-Soud, Waleed

2015-01-01

) and pyrosequencing, using amplicons of 16S and 26S rRNA genes for prokaryotes and eukaryotes, respectively. With minor exceptions, the results from the culture-independent analyses correlated to the culture-dependent plating results. Even though the predominant microorganisms detected with the two culture...

OSART Independent Safety Culture Assessment (ISCA) Guidelines

International Nuclear Information System (INIS)

2016-01-01

Safety culture is understood as an important part of nuclear safety performance. This has been demonstrated by the analysis of significant events such as Chernobyl, Davis Besse, Vandellos II, Asco, Paks, Mihamma and Forsmark, among others. In order to enhance safety culture, one essential activity is to perform assessments. IAEA Safety Standard Series No. GS-R-3, The Management System for Facilitites and Activities, states requirements for continuous improvement of safety culture, of which self, peer and independent safety culture assessments constitute an essential part. In line with this requirement, the Independent Safety Culture Assessment (ISCA) module is offered as an add-on module to the IAEA Operational Safety Review Team (OSART) programme. The OSART programme provides advice and assistance to Member States to enhance the safety of nuclear power plants during commissioning and operation. By including the ISCA module in an OSART mission, the receiving organization benefits from the synergy between the technical and the safety culture aspects of the safety review. The joint operational safety and safety culture assessment provides the organization with the opportunity to better understand the interactions between technical, human, organizational and cultural aspects, helping the organization to take a systemic approach to safety through identifying actions that fully address the root causes of any identified issue. Safety culture assessments provide insight into the fundamental drivers that shape organizational patterns of behaviour, safety consciousness and safety performance. The complex nature of safety culture means that the analysis of the results of such assessments is not as straightforward as for other types of assessment. The benefits of the results of nuclear safety culture assessments are maximized only if appropriate tools and guidance for these assessments is used; hence, this comprehensive guideline has been developed. The methodology explained

Molecular profiling of fungal communities in moisture damaged buildings before and after remediation--a comparison of culture-dependent and culture-independent methods.

Science.gov (United States)

Pitkäranta, Miia; Meklin, Teija; Hyvärinen, Anne; Nevalainen, Aino; Paulin, Lars; Auvinen, Petri; Lignell, Ulla; Rintala, Helena

2011-10-21

Indoor microbial contamination due to excess moisture is an important contributor to human illness in both residential and occupational settings. However, the census of microorganisms in the indoor environment is limited by the use of selective, culture-based detection techniques. By using clone library sequencing of full-length internal transcribed spacer region combined with quantitative polymerase chain reaction (qPCR) for 69 fungal species or assay groups and cultivation, we have been able to generate a more comprehensive description of the total indoor mycoflora. Using this suite of methods, we assessed the impact of moisture damage on the fungal community composition of settled dust and building material samples (n = 8 and 16, correspondingly). Water-damaged buildings (n = 2) were examined pre- and post- remediation, and compared with undamaged reference buildings (n = 2). Culture-dependent and independent methods were consistent in the dominant fungal taxa in dust, but sequencing revealed a five to ten times higher diversity at the genus level than culture or qPCR. Previously unknown, verified fungal phylotypes were detected in dust, accounting for 12% of all diversity. Fungal diversity, especially within classes Dothideomycetes and Agaricomycetes tended to be higher in the water damaged buildings. Fungal phylotypes detected in building materials were present in dust samples, but their proportion of total fungi was similar for damaged and reference buildings. The quantitative correlation between clone library phylotype frequencies and qPCR counts was moderate (r = 0.59, p environments. However, making conclusions concerning the effect of building conditions on building mycobiota using this methodology was complicated by the wide natural diversity in the dust samples, the incomplete knowledge of material-associated fungi fungi and the semiquantitative nature of sequencing based methods.

Recent advances in molecular techniques to study microbial communities in food-associated matrices and processes

NARCIS (Netherlands)

Justé, A.; Thomma, B.P.H.J.; Lievens, B.

2008-01-01

In the last two decades major changes have occurred in how microbial ecologists study microbial communities. Limitations associated with traditional culture-based methods have pushed for the development of culture-independent techniques, which are primarily based on the analysis of nucleic acids.

ADSA Foundation Scholar Award: Trends in culture-independent methods for assessing dairy food quality and safety: emerging metagenomic tools.

Science.gov (United States)

Yeung, Marie

2012-12-01

Enhancing the quality and safety of dairy food is critical to maintaining the competitiveness of dairy products in the food and beverage market and in reinforcing consumer confidence in the dairy industry. Raw milk quality has a significant effect on finished product quality. Several microbial groups found in raw milk have been shown to adversely affect the shelf life of pasteurized milk. Current microbiological criteria used to define milk quality are based primarily on culture-dependent methods, some of which are perceived to lack the desired sensitivity and specificity. To supplement traditional methods, culture-independent methods are increasingly being used to identify specific species or microbial groups, and to detect indicator genes or proteins in raw milk or dairy products. Some molecular subtyping techniques have been developed to track the transmission of microbes in dairy environments. The burgeoning "-omics" technologies offer new and exciting opportunities to enhance our understanding of food quality and safety in relation to microbes. Metagenomics has the potential to characterize microbial diversity, detect nonculturable microbes, and identify unique sequences or other factors associated with dairy product quality and safety. In this review, fluid milk will be used as the primary example to examine the adequacy and validity of conventional methods, the current trend of culture-independent methods, and the potential applications of metagenomics in dairy food research. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables.

Science.gov (United States)

Jackson, Colin R; Randolph, Kevin C; Osborn, Shelly L; Tyler, Heather L

2013-12-01

Plants harbor a diverse bacterial community, both as epiphytes on the plant surface and as endophytes within plant tissue. While some plant-associated bacteria act as plant pathogens or promote plant growth, others may be human pathogens. The aim of the current study was to determine the bacterial community composition of organic and conventionally grown leafy salad vegetables at the point of consumption using both culture-dependent and culture-independent methods. Total culturable bacteria on salad vegetables ranged from 8.0 × 10(3) to 5.5 × 10(8) CFU g(-1). The number of culturable endophytic bacteria from surface sterilized plants was significantly lower, ranging from 2.2 × 10(3) to 5.8 × 10(5) CFU g(-1). Cultured isolates belonged to six major bacterial phyla, and included representatives of Pseudomonas, Pantoea, Chryseobacterium, and Flavobacterium. Eleven different phyla and subphyla were identified by culture-independent pyrosequencing, with Gammaproteobacteria, Betaproteobacteria, and Bacteroidetes being the most dominant lineages. Other bacterial lineages identified (e.g. Firmicutes, Alphaproteobacteria, Acidobacteria, and Actinobacteria) typically represented less than 1% of sequences obtained. At the genus level, sequences classified as Pseudomonas were identified in all samples and this was often the most prevalent genus. Ralstonia sequences made up a greater portion of the community in surface sterilized than non-surface sterilized samples, indicating that it was largely endophytic, while Acinetobacter sequences appeared to be primarily associated with the leaf surface. Analysis of molecular variance indicated there were no significant differences in bacterial community composition between organic versus conventionally grown, or surface-sterilized versus non-sterilized leaf vegetables. While culture-independent pyrosequencing identified significantly more bacterial taxa, the dominant taxa from pyrosequence data were also detected by traditional

Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables

Science.gov (United States)

2013-01-01

Background Plants harbor a diverse bacterial community, both as epiphytes on the plant surface and as endophytes within plant tissue. While some plant-associated bacteria act as plant pathogens or promote plant growth, others may be human pathogens. The aim of the current study was to determine the bacterial community composition of organic and conventionally grown leafy salad vegetables at the point of consumption using both culture-dependent and culture-independent methods. Results Total culturable bacteria on salad vegetables ranged from 8.0 × 103 to 5.5 × 108 CFU g-1. The number of culturable endophytic bacteria from surface sterilized plants was significantly lower, ranging from 2.2 × 103 to 5.8 × 105 CFU g-1. Cultured isolates belonged to six major bacterial phyla, and included representatives of Pseudomonas, Pantoea, Chryseobacterium, and Flavobacterium. Eleven different phyla and subphyla were identified by culture-independent pyrosequencing, with Gammaproteobacteria, Betaproteobacteria, and Bacteroidetes being the most dominant lineages. Other bacterial lineages identified (e.g. Firmicutes, Alphaproteobacteria, Acidobacteria, and Actinobacteria) typically represented less than 1% of sequences obtained. At the genus level, sequences classified as Pseudomonas were identified in all samples and this was often the most prevalent genus. Ralstonia sequences made up a greater portion of the community in surface sterilized than non-surface sterilized samples, indicating that it was largely endophytic, while Acinetobacter sequences appeared to be primarily associated with the leaf surface. Analysis of molecular variance indicated there were no significant differences in bacterial community composition between organic versus conventionally grown, or surface-sterilized versus non-sterilized leaf vegetables. While culture-independent pyrosequencing identified significantly more bacterial taxa, the dominant taxa from pyrosequence data were also detected by

Characterisation of prototype Nurmi cultures using culture-based microbiological techniques and PCR-DGGE.

Science.gov (United States)

Waters, Sinéad M; Murphy, Richard A; Power, Ronan F G

2006-08-01

Undefined Nurmi-type cultures (NTCs) have been used successfully to prevent salmonella colonisation in poultry for decades. Such cultures are derived from the caecal contents of specific-pathogen-free birds and are administered via drinking water or spray application onto eggs in the hatchery. These cultures consist of many non-culturable and obligately anaerobic bacteria. Due to their undefined nature it is difficult to obtain approval from regulatory agencies to use these preparations as direct fed microbials for poultry. In this study, 10 batches of prototype NTCs were produced using an identical protocol over a period of 2 years. Traditional microbiological techniques and a molecular culture-independent methodology, polymerase chain reaction combined with denaturing gradient gel electrophoresis (PCR-DGGE), were applied to characterise these cultures and also to examine if the constituents of the NTCs were identical. Culture-dependent analysis of these cultures included plating on a variety of selective and semi-selective agars, examination of colony morphology, Gram-staining and a series of biochemical tests (API, BioMerieux, France). Two sets of PCR-DGGE studies were performed. These involved the amplification of universal and subsequently lactic acid bacteria (LAB)-specific hypervariable regions of a 16S rRNA gene by PCR. Resultant amplicons were subjected to DGGE. Sequence analysis was performed on subsequent bands present in resultant DGGE profiles using the Basic Local Alignment Search Tool (BLAST). Microbiological culturing techniques tended to isolate common probiotic bacterial species from the genera Lactobacillus, Lactococcus, Bifidobacterium, Enterococcus, Clostridium, Escherichia, Pediococcus and Enterobacterium as well as members of the genera, Actinomyces, Bacteroides, Propionibacterium, Capnocytophaga, Proteus, and Klebsiella. Bacteroides, Enterococcus, Escherichia, Brevibacterium, Klebsiella, Lactobacillus, Clostridium, Bacillus, Eubacterium

The independent molecular interaction sites model. Pt. 1

International Nuclear Information System (INIS)

Naumann, K.H.; Lippert, E.

1981-01-01

A new reference system for the treatment of molecular fluids within the framework of thermodynamic perturbation theory is presented. The basic ingredient of our approach is a potential transformation which allows us to view molecular liquids and gases as mixtures of formally independent molecular interaction sites (IMIS model). Some relations between out method and the RAM theory are discussed. (orig.)

Independent Learning Crossing Cultures: Learning Cultures and Shifting Meanings

Science.gov (United States)

Spiro, Jane; Henderson, Juliet; Clifford, Valerie

2012-01-01

This paper contrasts the notion of "independent learning" as perceived by two informant groups at a UK institution of higher education: (1) teachers, educators and providers of education and (2) their students or "consumers" of education. Both informant groups are staff and students studying in a culture different to that of…

[Molecular techniques in mycology].

Science.gov (United States)

Rodríguez-Tudela, Juan Luis; Cuesta, Isabel; Gómez-López, Alicia; Alastruey-Izquierdo, Ana; Bernal-Martínez, Leticia; Cuenca-Estrella, Manuel

2008-11-01

An increasing number of molecular techniques for the diagnosis of fungal infections have been developed in the last few years, due to the growing prevalence of mycoses and the length of time required for diagnosis when classical microbiological methods are used. These methods are designed to resolve the following aspects of mycological diagnosis: a) Identification of fungi to species level by means of sequencing relevant taxonomic targets; b) early clinical diagnosis of invasive fungal infections; c) detection of molecular mechanisms of resistance to antifungal agents; and d) molecular typing of fungi. Currently, these methods are restricted to highly developed laboratories. However, some of these techniques will probably be available in daily clinical practice in the near future.

Novel co-culture plate enables growth dynamic-based assessment of contact-independent microbial interactions.

Directory of Open Access Journals (Sweden)

Thomas J Moutinho

Full Text Available Interactions between microbes are central to the dynamics of microbial communities. Understanding these interactions is essential for the characterization of communities, yet challenging to accomplish in practice. There are limited available tools for characterizing diffusion-mediated, contact-independent microbial interactions. A practical and widely implemented technique in such characterization involves the simultaneous co-culture of distinct bacterial species and subsequent analysis of relative abundance in the total population. However, distinguishing between species can be logistically challenging. In this paper, we present a low-cost, vertical membrane, co-culture plate to quantify contact-independent interactions between distinct bacterial populations in co-culture via real-time optical density measurements. These measurements can be used to facilitate the analysis of the interaction between microbes that are physically separated by a semipermeable membrane yet able to exchange diffusible molecules. We show that diffusion across the membrane occurs at a sufficient rate to enable effective interaction between physically separate cultures. Two bacterial species commonly found in the cystic fibrotic lung, Pseudomonas aeruginosa and Burkholderia cenocepacia, were co-cultured to demonstrate how this plate may be implemented to study microbial interactions. We have demonstrated that this novel co-culture device is able to reliably generate real-time measurements of optical density data that can be used to characterize interactions between microbial species.

Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils.

Directory of Open Access Journals (Sweden)

Franck O P Stefani

Full Text Available Bioremediation is a cost-effective and sustainable approach for treating polluted soils, but our ability to improve on current bioremediation strategies depends on our ability to isolate microorganisms from these soils. Although culturing is widely used in bioremediation research and applications, it is unknown whether the composition of cultured isolates closely mirrors the indigenous microbial community from contaminated soils. To assess this, we paired culture-independent (454-pyrosequencing of total soil DNA with culture-dependent (isolation using seven different growth media techniques to analyse the bacterial and fungal communities from hydrocarbon-contaminated soils. Although bacterial and fungal rarefaction curves were saturated for both methods, only 2.4% and 8.2% of the bacterial and fungal OTUs, respectively, were shared between datasets. Isolated taxa increased the total recovered species richness by only 2% for bacteria and 5% for fungi. Interestingly, none of the bacteria that we isolated were representative of the major bacterial OTUs recovered by 454-pyrosequencing. Isolation of fungi was moderately more effective at capturing the dominant OTUs observed by culture-independent analysis, as 3 of 31 cultured fungal strains ranked among the 20 most abundant fungal OTUs in the 454-pyrosequencing dataset. This study is one of the most comprehensive comparisons of microbial communities from hydrocarbon-contaminated soils using both isolation and high-throughput sequencing methods.

Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils.

Science.gov (United States)

Stefani, Franck O P; Bell, Terrence H; Marchand, Charlotte; de la Providencia, Ivan E; El Yassimi, Abdel; St-Arnaud, Marc; Hijri, Mohamed

2015-01-01

Bioremediation is a cost-effective and sustainable approach for treating polluted soils, but our ability to improve on current bioremediation strategies depends on our ability to isolate microorganisms from these soils. Although culturing is widely used in bioremediation research and applications, it is unknown whether the composition of cultured isolates closely mirrors the indigenous microbial community from contaminated soils. To assess this, we paired culture-independent (454-pyrosequencing of total soil DNA) with culture-dependent (isolation using seven different growth media) techniques to analyse the bacterial and fungal communities from hydrocarbon-contaminated soils. Although bacterial and fungal rarefaction curves were saturated for both methods, only 2.4% and 8.2% of the bacterial and fungal OTUs, respectively, were shared between datasets. Isolated taxa increased the total recovered species richness by only 2% for bacteria and 5% for fungi. Interestingly, none of the bacteria that we isolated were representative of the major bacterial OTUs recovered by 454-pyrosequencing. Isolation of fungi was moderately more effective at capturing the dominant OTUs observed by culture-independent analysis, as 3 of 31 cultured fungal strains ranked among the 20 most abundant fungal OTUs in the 454-pyrosequencing dataset. This study is one of the most comprehensive comparisons of microbial communities from hydrocarbon-contaminated soils using both isolation and high-throughput sequencing methods.

Plant tissue culture techniques

Directory of Open Access Journals (Sweden)

Rolf Dieter Illg

1991-01-01

Full Text Available Plant cell and tissue culture in a simple fashion refers to techniques which utilize either single plant cells, groups of unorganized cells (callus or organized tissues or organs put in culture, under controlled sterile conditions.

Introduction to basic molecular biologic techniques for molecular imaging researches

International Nuclear Information System (INIS)

Kang, Joo Hyun

2004-01-01

Molecular imaging is a rapidly growing field due to the advances in molecular biology and imaging technologies. With the introduction of imaging reporter genes into the cell, diverse cellular processes can be monitored, quantified and imaged non-invasively in vivo. These processes include the gene expression, protein-protein interactions, signal transduction pathways, and monitoring of cells such as cancer cells, immune cells, and stem cells. In the near future, molecular imaging analysis will allow us to observe the incipience and progression of the disease. These will make us easier to give a diagnosis in the early stage of intractable diseases such as cancer, neuro-degenerative disease, and immunological disorders. Additionally, molecular imaging method will be a valuable tool for the real-time evaluation of cells in molecular biology and the basic biological studies. As newer and more powerful molecular imaging tools become available, it will be necessary to corporate clinicians, molecular biologists and biochemists for the planning, interpretation, and application of these techniques to their fullest potential. In order for such a multidisciplinary team to be effective, it is essential that a common understanding of basic biochemical and molecular biologic techniques is achieved. Basic molecular techniques for molecular imaging methods are presented in this paper

Characterization of microbial communities in pest colonized books by molecular biology tools

Directory of Open Access Journals (Sweden)

Franco Palla

2011-08-01

Full Text Available This work presents the identification of bacteria and fungi colonies in insect infesting books, by cultural-independent methodologies based on molecular biology techniques. Microbial genomic DNA extraction, in vitro amplification of specific target sequences by polymerase chain reactions (PCR, sequencing and sequence analysis were performed. These procedures minimized the samples amount, optimized the diagnostic studies on bacteria and fungi colonization and allowed the identification of many species also in complex microbial consortia. The molecular techniques for sure accomplish and integrate the microbiological standard methods (in vitro culture and morphological analyses (OM, SEM, CLSM, in order to understand the role of microorganisms in bio-deterioration of cultural assets. This monitoring is also indispensable to shed light on the risk for visitors and/or professionals to contract potential illnesses within indoor environments.

Culture-independent molecular approaches reveal a mostly unknown high diversity of active nitrogen-fixing bacteria associated with Pennisetum purpureum—a bioenergy crop

NARCIS (Netherlands)

Videira, Sandy Sampaio; de Cássia Pereira e Silva, Michele; Galisa, Pericles de Souza; Franco Dias, Armando Cavalcante; Nissinen, Riitta; Baldani Divan, Vera Lucia; van Elsas, Jan Dirk; Baldani, Jose Ivo; Salles, Joana Falcao

2013-01-01

Previous studies have shown that elephant grass is colonized by nitrogen-fixing bacterial species; however, these results were based on culture-dependent methods, an approach that introduces bias due to an incomplete assessment of the microbial community. In this study, we used culture-independent

Molecular profiling of fungal communities in moisture damaged buildings before and after remediation - a comparison of culture-dependent and culture-independent methods

Directory of Open Access Journals (Sweden)

Auvinen Petri

2011-10-01

Full Text Available Abstract Background Indoor microbial contamination due to excess moisture is an important contributor to human illness in both residential and occupational settings. However, the census of microorganisms in the indoor environment is limited by the use of selective, culture-based detection techniques. By using clone library sequencing of full-length internal transcribed spacer region combined with quantitative polymerase chain reaction (qPCR for 69 fungal species or assay groups and cultivation, we have been able to generate a more comprehensive description of the total indoor mycoflora. Using this suite of methods, we assessed the impact of moisture damage on the fungal community composition of settled dust and building material samples (n = 8 and 16, correspondingly. Water-damaged buildings (n = 2 were examined pre- and post- remediation, and compared with undamaged reference buildings (n = 2. Results Culture-dependent and independent methods were consistent in the dominant fungal taxa in dust, but sequencing revealed a five to ten times higher diversity at the genus level than culture or qPCR. Previously unknown, verified fungal phylotypes were detected in dust, accounting for 12% of all diversity. Fungal diversity, especially within classes Dothideomycetes and Agaricomycetes tended to be higher in the water damaged buildings. Fungal phylotypes detected in building materials were present in dust samples, but their proportion of total fungi was similar for damaged and reference buildings. The quantitative correlation between clone library phylotype frequencies and qPCR counts was moderate (r = 0.59, p Conclusions We examined a small number of target buildings and found indications of elevated fungal diversity associated with water damage. Some of the fungi in dust were attributable to building growth, but more information on the material-associated communities is needed in order to understand the dynamics of microbial communities between

Interactions between contemporary American independent cinema and popular music culture

OpenAIRE

Nicholls, Matthew

2011-01-01

In recent years, many American independent films have become increasingly engaged with popular music culture and have used various forms of pop music in their soundtracks to various effects. Disparate films from a variety of genres use different forms of popular music in different ways, however these negotiations with pop music and its cultural surroundings have one true implication: that the 'independentness' (or 'indieness') of these movies is informed, anchored and embellished by their rel...

Morphological, cultural, pathogenic and molecular variability ...

African Journals Online (AJOL)

Alternaria blight (Alternaria brassicae) causes severe foliar damage to Indian mustard in Uttarakhand. Ten (10) isolates of A. brassicae were collected from different hosts and characterized for cultural, morphological, pathogenic and molecular variations. A. brassicae colonies varied in their cultural behaviour ranging from ...

Cultural, morphological, pathogenic and molecular characterization ...

African Journals Online (AJOL)

Alternaria blotch (Alternaria mali) causes severe foliar damage to apple trees in Kashmir. Twenty one (21) isolates of A. mali were collected from different locations and characterized for cultural, morphological, pathogenic and molecular variations. A. mali colonies varied in their cultural behaviour ranging from velvety to ...

INDICATORS AND DIAGNOSTICS OF INDEPENDENT WORK CULTURE FORMATION IN FUTURE MATHEMATICS TEACHERS

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Олена Соя

2015-09-01

Full Text Available The article highlights the results of research of formation the culture of independent work of future mathematics teachers, indicating the effectiveness of selected theoretically grounded and practically implemented pedagogical conditions of its formation. Its semantic components that are interconnected and interdependent unity of cognitive, procedural, technological and motivational components were singled out on the basis of definition of independent work culture of future mathematics teachers. The system of indicators, which assessed the degree of mastering by students the culture of independent work by value-orientation, content-effective, reflective, constructive and operationally-activity criteria is reviewed.

Characterization of the Bacterial Community Naturally Present on Commercially Grown Basil Leaves: Evaluation of Sample Preparation Prior to Culture-Independent Techniques

Directory of Open Access Journals (Sweden)

Siele Ceuppens

2015-08-01

Full Text Available Fresh herbs such as basil constitute an important food commodity worldwide. Basil provides considerable culinary and health benefits, but has also been implicated in foodborne illnesses. The naturally occurring bacterial community on basil leaves is currently unknown, so the epiphytic bacterial community was investigated using the culture-independent techniques denaturing gradient gel electrophoresis (DGGE and next-generation sequencing (NGS. Sample preparation had a major influence on the results from DGGE and NGS: Novosphingobium was the dominant genus for three different basil batches obtained by maceration of basil leaves, while washing of the leaves yielded lower numbers but more variable dominant bacterial genera including Klebsiella, Pantoea, Flavobacterium, Sphingobacterium and Pseudomonas. During storage of basil, bacterial growth and shifts in the bacterial community were observed with DGGE and NGS. Spoilage was not associated with specific bacterial groups and presumably caused by physiological tissue deterioration and visual defects, rather than by bacterial growth.

Status of biotechnology with emphasis on molecular techniques for mutation breeding in the Philippines

Energy Technology Data Exchange (ETDEWEB)

Lapade, A.G.; Nazarea, T.Y.; Veluz, A.M.S.; Marbella, L.J.; Nato, A.Q.; Coloma, C.B. Jr.; Asencion, A.B. [Philippine Nuclear Research Institute, Commonwealth Avenue, Quezon (Philippines)

2002-02-01

This paper summarizes the status of biotechnology with emphasis on molecular techniques for plant breeding in the Philippines. Several molecular and in-vitro culture techniques are integrated in plant breeding for crop improvement at PNRI, UPLB, IRRI and PhilRice. At IRRI, PCR techniques, RFLP and RAPD, PCR techniques, RFLP and RAPD were developed to establish high density molecular maps, determine breadth and diversity of germplasm and characterize alien introgression. The molecular maps have identified DNA sequence of resistance genes of HYVs and NPTs to abiotic and biotic stresses, the major achievement is the development of high density molecular maps in rice with at least 2000 markers. The biotechnology program at PhilRice for varietal improvement includes: (1) utilization of molecular marker technology such gene mapping of desired traits in rice, analysis of genetic relationships of germplasm materials and breeding lines through DNA fingerprinting and genetic diversity studies and development and application of marker aided selection for disease resistance (RTD and BLB); (2) application of in-vitro techniques in the development of lines with tolerance to adverse conditions; (3) molecular cloning of important genes for RTD resistance; (4) genetic transformation for male sterility and resistance to sheath blight and stem borers; and (5) transfer of disease resistance from wild species to cultivated varieties. In IPB, molecular markers:microsatellites or SSR, AFLP and RGA are being used for mapping and diversity studies in coconut, mango, banana, mungbean, corn and tomato. Mutation breeding at PNRI using gamma radiation has resulted in the development of crop varieties with desirable traits. The use of AFLP coupled to PCR is being used to study polymorphism in plant variants of radiation-induced mutants of rice, pineapple and ornamentals. (author)

Single Spore Isolation as a Simple and Efficient Technique to obtain fungal pure culture

Science.gov (United States)

Noman, E.; Al-Gheethi, AA; Rahman, N. K.; Talip, B.; Mohamed, R.; H, N.; Kadir, O. A.

2018-04-01

The successful identification of fungi by phenotypic methods or molecular technique depends mainly on the using an advanced technique for purifying the isolates. The most efficient is the single spore technique due to the simple requirements and the efficiency in preventing the contamination by yeast, mites or bacteria. The method described in the present work is depends on the using of a light microscope to transfer one spore into a new culture medium. The present work describes a simple and efficient procedure for single spore isolation to purify of fungi recovered from the clinical wastes.

Microbiological study of lactic acid bacteria in kefir grains by culture-dependent and culture-independent methods.

Science.gov (United States)

Chen, Hsi-Chia; Wang, Sheng-Yao; Chen, Ming-Ju

2008-05-01

Lactic acid bacteria (LAB) in different original kefir grains were first assessed using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) by a culture-dependent way, and were further confirmed by DNA sequencing techniques. Results indicated that a combined method of cultivation with PCR-DGGE and subsequent DNA sequencing could successfully identify four LAB strains from three kefir grains from Taiwan (named Hsinchu, Mongolia and Ilan). Lactobacillus kefiri accounted, in the three kefir grains, for at least half of the isolated colonies while Lb. kefiranofaciens was the second most frequently isolated species. Leuconostoc mesenteroides was less frequently found but still in the three kefir grains conversely to Lactococcus lactis which based on culture-dependent isolation was only found in two of the kefir grains. It was interesting to find that all three kefir grains contain similar LAB species. Furthermore, the DGGE as a culture-independent method was also applied to detect the LAB strains. Results indicated that Lb. kefiranofaciens was found in all three kefir grains, whereas Lb. kefiri was only observed in Hsinchu kefir grain and Lc. lactis was found in both Mongolia and Ilan samples. Two additional strains, Pseudomonas spp. and E. coli, were also detected in kefir grains.

Diversity of endophytic bacteria of Dendrobium officinale based on culture-dependent and culture-independent methods

Directory of Open Access Journals (Sweden)

Cong Pei

2017-01-01

Full Text Available Culture-dependent and culture-independent methods were compared and evaluated in the study of the endophytic diversity of Dendrobium officinale. Culture-independent methods consisted of polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE and metagenome methods. According to the results, differences were found between the three methods. Three phyla, namely Firmicutes, Proteobacteria, and Actinobacteria, were detected using the culture-dependent method, and two phyla, Firmicutes and Proteobacteria, were detected by the DGGE method. Using the metagenome method, four major phyla were determined, including Proteobacteria (76.54%, Actinobacteria (18.56%, Firmicutes (2.27%, and Bacteroidetes (1.56%. A distinct trend was obtained at the genus level in terms of the method and the corresponding number of genera determined. There were 449 genera and 16 genera obtained from the metagenome and DGGE methods, respectively, and only 7 genera were obtained through the culture-dependent method. By comparison, all the genera from the culture-dependent and DGGE methods were contained in the members determined using the metagenome method. Overall, culture-dependent methods are limited to ‘finding’ endophytic bacteria in plants. DGGE is an alternative to investigating primary diversity patterns; however, the metagenome method is still the best choice for determining the endophytic profile in plants. It is essential to use multiphasic approaches to study cultured and uncultured microbes.

The isolated Leptospira Spp. Identification by molecular biological techniques

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Duangjai Suwancharoen

2017-01-01

Full Text Available Leptospirosis is a zoonotic disease caused by the bacteria of Leptospira spp. Identification of this bacterium relies on serotyping and genotyping. Data base for animal causative serovars in Thailand is limited. As the unknown serovars are found in the laboratory, they need to be sent overseas for referent identification. To reduce the cost, this research intended to develop a leptospiral identification method which is user–friendly and able to classify efficiently. Ten Leptospira isolations were cultured from urine samples. They were identified by three molecular biological techniques, including Pulsed-Field Gel Electrophoresis (PFGE, Variable Number Tandem Repeat (VNTR and Multilocus Sequence Typing (MLST. These methods were developed and compared to find the most suitable one for leptospiral identification. VNTR was found to be inappropriate since it could not identify the agents and it did not show the PCR product. PFGE and MLST gave the same results of the unknown 1 and 2 which were L.weilii sv Samin st Samin. Unknown 4 showed different results by each technique. Unknown 5 to 10 were likely to be L.meyeri sv Ranarum st ICF and Leptonema illini sv Illini st 3055 by PFGE but MLST could not identify the serovar. However, molecular biological technique for Leptospira identification should be done by several methods in order to confirm the result of each other.

Cultural orientations, parental beliefs and practices, and latino adolescents' autonomy and independence.

Science.gov (United States)

Roche, Kathleen M; Caughy, Margaret O; Schuster, Mark A; Bogart, Laura M; Dittus, Patricia J; Franzini, Luisa

2014-08-01

Despite the salience of behavioral autonomy and independence to parent-child interactions during middle adolescence, little is known about parenting processes pertinent to youth autonomy development for Latino families. Among a diverse sample of 684 Latino-origin parent-adolescent dyads in Houston, Texas, this study examines how parents' cultural orientations are associated directly and indirectly, through parental beliefs, with parenting practices giving youth behavioral autonomy and independence. Informed by social domain theory, the study's parenting constructs pertain to youth behaviors in an "ambiguously personal" domain-activities that adolescents believe are up to youth to decide, but which parents might argue require parents' supervision, knowledge, and/or decision-making. Results for latent profile analyses of parents' cultural identity across various facets of acculturation indicate considerable cultural heterogeneity among Latino parents. Although 43% of parents have a Latino cultural orientation, others represent Spanish-speaking/bicultural (21%), bilingual/bicultural (15%), English-speaking/bicultural (15%), or US (6%) cultural orientations. Structural equation modeling results indicate that bilingual/bicultural, English-speaking/bicultural, and US-oriented parents report less emphasis on the legitimacy of parental authority and younger age expectations for youth to engage in independent behaviors than do Latino-oriented parents. Parental beliefs endorsing youth's behavioral independence and autonomy, in turn, are associated with less stringent parental rules (parental report), less parental supervision (parental and youth report), and more youth autonomy in decision-making (parental and youth report). Evidence thus supports the idea that the diverse cultural orientations of Latino parents in the US may result in considerable variations in parenting processes pertinent to Latino adolescents' development.

Culture -independent Pathogenic Bacterial Communities in Bottled Mineral Water

Directory of Open Access Journals (Sweden)

Hamdy A. Hassan

2015-08-01

Full Text Available Bottled mineral water (BMW is an alternative to mains water and consider it to be better and safer. Access to safe BMW from the bacteria involving potential health hazard is essential to health. Cultivation-independent technique PCR-based single-strand conformation polymorphism (SSCP for genetic profiling of PCR-amplified 16S rRNA genes was performed using Com primer set targeting the 16S rRNA genes for detection of pathogenic bacteria in bottled mineral water from the final product of six factories for bottled mineral drinking water in Wadi El-natron region- Egypt. These factories use often ozone technology to treat large quantities of water because of its effectiveness in purifying and conditioning water. A total of 27 single products were isolated from the profiles by PCR re-amplification and cloning. Sequence analysis of 27 SSCP bands revealed that the 16S rRNA sequences were clustered into seven operational taxonomic units (OTUs and the compositions of the communities of the six samples were all common. The results showed that most communities from phyla Alphaproteobacteria and certainly in the Sphingomonas sp. Culture-independent approaches produced complementary information, thus generating a more accurate view for the bacterial community in the BMW, particularly in the disinfection step, as it constitutes the final barrier before BMW distribution to the consumer

Use of a culture independent method to analyze the diversity of soil fungi surrounding Chroogomphus rutilus in the Beijing region of China

DEFF Research Database (Denmark)

Liu, Yu; Wang, Shouxian; Yin, Yonggang

2012-01-01

habitat to facilitate its large-scale cultivation. A culture-independent molecular approach—a powerful technology for microbiological ecology studies—was used to investigate the diversity of soil fungal communities in samples surrounding C. rutilus from the Beijing region of China. Metagenomic DNA...... was isolated from soil samples collected around C. rutilus, and an internal transcribed spacer (ITS) gene library was constructed. Subsequently, polymerase chain reaction products were digested with HinfI, HaeIII, MspI, TaqI, or MboI. Clones were selected and sequenced based on their restriction fragment...... length polymorphisms. The diversity of the fungi represented by their ITS sequences was analyzed. Our results indicate the presence of numerous fungi in the C. rutilus habitat. This study is the first demonstration of the fungal ecology surrounding C. rutilus using a culture independent method...

Molecular detection of pathogens in water--the pros and cons of molecular techniques.

Science.gov (United States)

Girones, Rosina; Ferrús, Maria Antonia; Alonso, José Luis; Rodriguez-Manzano, Jesus; Calgua, Byron; Corrêa, Adriana de Abreu; Hundesa, Ayalkibet; Carratala, Anna; Bofill-Mas, Sílvia

2010-08-01

Pollution of water by sewage and run-off from farms produces a serious public health problem in many countries. Viruses, along with bacteria and protozoa in the intestine or in urine are shed and transported through the sewer system. Even in highly industrialized countries, pathogens, including viruses, are prevalent throughout the environment. Molecular methods are used to monitor viral, bacterial, and protozoan pathogens, and to track pathogen- and source-specific markers in the environment. Molecular techniques, specifically polymerase chain reaction-based methods, provide sensitive, rapid, and quantitative analytical tools with which to study such pathogens, including new or emerging strains. These techniques are used to evaluate the microbiological quality of food and water, and to assess the efficiency of virus removal in drinking and wastewater treatment plants. The range of methods available for the application of molecular techniques has increased, and the costs involved have fallen. These developments have allowed the potential standardization and automation of certain techniques. In some cases they facilitate the identification, genotyping, enumeration, viability assessment, and source-tracking of human and animal contamination. Additionally, recent improvements in detection technologies have allowed the simultaneous detection of multiple targets in a single assay. However, the molecular techniques available today and those under development require further refinement in order to be standardized and applicable to a diversity of matrices. Water disinfection treatments may have an effect on the viability of pathogens and the numbers obtained by molecular techniques may overestimate the quantification of infectious microorganisms. The pros and cons of molecular techniques for the detection and quantification of pathogens in water are discussed. (c) 2010 Elsevier Ltd. All rights reserved.

Culture-independent discovery of natural products from soil metagenomes.

Science.gov (United States)

Katz, Micah; Hover, Bradley M; Brady, Sean F

2016-03-01

Bacterial natural products have proven to be invaluable starting points in the development of many currently used therapeutic agents. Unfortunately, traditional culture-based methods for natural product discovery have been deemphasized by pharmaceutical companies due in large part to high rediscovery rates. Culture-independent, or "metagenomic," methods, which rely on the heterologous expression of DNA extracted directly from environmental samples (eDNA), have the potential to provide access to metabolites encoded by a large fraction of the earth's microbial biosynthetic diversity. As soil is both ubiquitous and rich in bacterial diversity, it is an appealing starting point for culture-independent natural product discovery efforts. This review provides an overview of the history of soil metagenome-driven natural product discovery studies and elaborates on the recent development of new tools for sequence-based, high-throughput profiling of environmental samples used in discovering novel natural product biosynthetic gene clusters. We conclude with several examples of these new tools being employed to facilitate the recovery of novel secondary metabolite encoding gene clusters from soil metagenomes and the subsequent heterologous expression of these clusters to produce bioactive small molecules.

Human nasal turbinates as a viable source of respiratory epithelial cells using co-culture system versus dispase-dissociation technique.

Science.gov (United States)

Noruddin, Nur Adelina Ahmad; Saim, Aminuddin B; Chua, Kien Hui; Idrus, Ruszymah

2007-12-01

To compare a co-culture system with a conventional dispase-dissociation method for obtaining functional human respiratory epithelial cells from the nasal turbinates for tissue engineering application. Human respiratory epithelial cells were serially passaged using a co-culture system and a conventional dispase-dissociation technique. The growth kinetics and gene expression levels of the cultured respiratory epithelial cells were compared. Four genes were investigated, namely cytokeratin-18, a marker for ciliated and secretory epithelial cells; cytokeratin-14, a marker for basal epithelial cells; MKI67, a proliferation marker; and MUC5B, a marker for mucin secretion. Immunocytochemical analysis was performed using monoclonal antibodies against the high molecular-weight cytokeratin 34 beta E12, cytokeratin 18, and MUC5A to investigate the protein expression from cultured respiratory epithelial cells. Respiratory epithelial cells cultured using both methods maintained polygonal morphology throughout the passages. At passage 1, co-cultured respiratory epithelial showed a 2.6-times higher growth rate compared to conventional dispase dissociation technique, and 7.8 times higher at passage 2. Better basal gene expression was observed by co-cultured respiratory epithelial cells compared to dispase dissociated cells. Immunocytochemical analyses were positive for the respiratory epithelial cells cultured using both techniques. Co-culture system produced superior quality of cultured human respiratory epithelial cells from the nasal turbinates as compared to dispase dissociation technique.

Metagenomics: The Next Culture-Independent Game Changer

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Jessica D. Forbes

2017-07-01

Full Text Available A trend towards the abandonment of obtaining pure culture isolates in frontline laboratories is at a crossroads with the ability of public health agencies to perform their basic mandate of foodborne disease surveillance and response. The implementation of culture-independent diagnostic tests (CIDTs including nucleic acid and antigen-based assays for acute gastroenteritis is leaving public health agencies without laboratory evidence to link clinical cases to each other and to food or environmental substances. This limits the efficacy of public health epidemiology and surveillance as well as outbreak detection and investigation. Foodborne outbreaks have the potential to remain undetected or have insufficient evidence to support source attribution and may inadvertently increase the incidence of foodborne diseases. Next-generation sequencing of pure culture isolates in clinical microbiology laboratories has the potential to revolutionize the fields of food safety and public health. Metagenomics and other ‘omics’ disciplines could provide the solution to a cultureless future in clinical microbiology, food safety and public health. Data mining of information obtained from metagenomics assays can be particularly useful for the identification of clinical causative agents or foodborne contamination, detection of AMR and/or virulence factors, in addition to providing high-resolution subtyping data. Thus, metagenomics assays may provide a universal test for clinical diagnostics, foodborne pathogen detection, subtyping and investigation. This information has the potential to reform the field of enteric disease diagnostics and surveillance and also infectious diseases as a whole. The aim of this review will be to present the current state of CIDTs in diagnostic and public health laboratories as they relate to foodborne illness and food safety. Moreover, we will also discuss the diagnostic and subtyping utility and concomitant bias limitations of

Characterization of microbial communities in pest colonized books by molecular biology tools

OpenAIRE

Franco Palla

2011-01-01

This work presents the identification of bacteria and fungi colonies in insect infesting books, by cultural-independent methodologies based on molecular biology techniques. Microbial genomic DNA extraction, in vitro amplification of specific target sequences by polymerase chain reactions (PCR), sequencing and sequence analysis were performed. These procedures minimized the samples amount, optimized the diagnostic studies on bacteria and fungi colonization and allowed the identification of man...

Detection of microbial diversity in endocarditis using cultivation-independent molecular techniques

DEFF Research Database (Denmark)

Wolff, Tine Y; Moser, Claus Ernst; Bundgaard, Henning

2011-01-01

Background: The aim of this study was to investigate whether the diagnosis of infective endocarditis (IE) could be improved using molecular tools in addition to standard microscopy and cultivation methods. Methods: Cultivation was performed on blood or tissue samples as recommended in the modified...

Exploration of the speleotherapeutic potential through the cellular and molecular biology techniques

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Munteanu Constantin

2011-02-01

Full Text Available Objective: Exploring the speleotherapy effects on morphology and physiology of dermal and pulmonary fibroblast obtained from Wistar rats tissue in normal conditions and after induction of experimental “astma” awareness with ovalbumin. Materials and methods: Before initiation of dermal and pulmonary fibroblast cultures, 60 of Wistar rats 75-100 g were divided into two groups: control and sensitized with ovalalbumin. 10 animals of each group were sent to Cacica and Dej salt mines and maintained in a speleotherapy regime. Another 10 animals in each group were monitored separately in INRMFB Biobase . Dermal and pulmonary fibroblast cultures were initiated by enzymatic techniques from appropriate tissue taken of each group Wistar rats. Morphological monitoring was done by phase contast microscopy; biochemical and molecular changes of cultures obtained from animals treated speleothropic compared to control, was experimental establised by electrophoresis and Western Blotting techniques.Results: Experimental data revealed the expression of several proteins after the speleotherapeutic treatment. These data were analysed compared with control, using a specific software.Conclusions: Speleotherapeutic treatment of Wistar rats caused significant differences in morphology and protein expression of dermal and pulmonary fibroblatst grown in the laboratory. These differences support the protective effects of speleotherapy compared with data obtained from animals untreated and sensitized with ovalbumin, having induced experimental asthma status.

Analysis of hairy root culture of Rauvolfia serpentina using direct analysis in real time mass spectrometric technique.

Science.gov (United States)

Madhusudanan, K P; Banerjee, Suchitra; Khanuja, Suman P S; Chattopadhyay, Sunil K

2008-06-01

The applicability of a new mass spectrometric technique, DART (direct analysis in real time) has been studied in the analysis of the hairy root culture of Rauvolfia serpentina. The intact hairy roots were analyzed by holding them in the gap between the DART source and the mass spectrometer for measurements. Two nitrogen-containing compounds, vomilenine and reserpine, were characterized from the analysis of the hairy roots almost instantaneously. The confirmation of the structures of the identified compounds was made through their accurate molecular formula determinations. This is the first report of the application of DART technique for the characterization of compounds that are expressed in the hairy root cultures of Rauvolfia serpentina. Moreover, this also constitutes the first report of expression of reserpine in the hairy root culture of Rauvolfia serpentina. Copyright (c) 2008 John Wiley & Sons, Ltd.

Techniques for Investigating Molecular Toxicology of Nanomaterials.

Science.gov (United States)

Wang, Yanli; Li, Chenchen; Yao, Chenjie; Ding, Lin; Lei, Zhendong; Wu, Minghong

2016-06-01

Nanotechnology has been a rapidly developing field in the past few decades, resulting in the more and more exposure of nanomaterials to human. The increased applications of nanomaterials for industrial, commercial and life purposes, such as fillers, catalysts, semiconductors, paints, cosmetic additives and drug carriers, have caused both obvious and potential impacts on human health and environment. Nanotoxicology is used to study the safety of nanomaterials and has grown at the historic moment. Molecular toxicology is a new subdiscipline to study the interactions and impacts of materials at the molecular level. To better understand the relationship between the molecular toxicology and nanomaterials, this review summarizes the typical techniques and methods in molecular toxicology which are applied when investigating the toxicology of nanomaterials and include six categories: namely; genetic mutation detection, gene expression analysis, DNA damage detection, chromosomal aberration analysis, proteomics, and metabolomics. Each category involves several experimental techniques and methods.

Withania somnifera: Advances and Implementation of Molecular and Tissue Culture Techniques to Enhance Its Application

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Vibha Pandey

2017-08-01

Full Text Available Withania somnifera, commonly known as Ashwagandha an important medicinal plant largely used in Ayurvedic and indigenous medicine for over 3,000 years. Being a medicinal plant, dried powder, crude extract as well as purified metabolies of the plant has shown promising therapeutic properties. Withanolides are the principal metabolites, responsible for the medicinal properties of the plant. Availability and amount of particular withanolides differ with tissue type and chemotype and its importance leads to identification characterization of several genes/ enzymes related to withanolide biosynthetic pathway. The modulation in withanolides can be achieved by controlling the environmental conditions like, different tissue culture techniques, altered media compositions, use of elicitors, etc. Among all the in vitro techniques, hairy root culture proved its importance at industrial scale, which also gets benefits due to more accumulation (amount and number of withanolides in roots tissues of W. somnifera. Use of media compostion and elicitors further enhances the amount of withanolides in hairy roots. Another important modern day technique used for accumulation of desired secondary metabolites is modulating the gene expression by altering environmental conditions (use of different media composition, elicitors, etc. or through genetic enginnering. Knowing the significance of the gene and the key enzymatic step of the pathway, modulation in withanolide contents can be achieved upto required amount in therapeutic industry. To accomplish maximum productivity through genetic enginnering different means of Withania transformation methods have been developed to obtain maximum transformation efficiency. These standardized transformation procedues have been used to overexpress/silence desired gene in W. somnifera to understand the outcome and succeed with enhanced metabolic production for the ultimate benefit of human race.

Culture-dependent and -independent investigations of microbial diversity on urinary catheters

DEFF Research Database (Denmark)

Xu, Yijuan; Moser, Claus Ernst; Abu Al-Soud, Waleed

2012-01-01

Catheter-associated urinary tract infection is caused by bacteria, which ascend the catheter along its external or internal surface to the bladder and subsequently develop into biofilms on the catheter and uroepithelium. Antibiotic-treated bacteria and bacteria residing in biofilm can be difficult...... to culture. In this study we used culture-based and 16S rRNA gene-based culture-independent methods (fingerprinting, cloning, and pyrosequencing) to determine the microbial diversity of biofilms on 24 urinary catheters. Most of the patients were catheterized for...

Evidence for a Cultural Influence on Field-Independence in Autism Spectrum Disorder

Science.gov (United States)

Koh, Hwan Cui; Milne, Elizabeth

2012-01-01

Field-independence, or weak central coherence, is a recognised phenotype of autism spectrum disorder (ASD). There is also evidence of cultural variation in this perceptual style, as neurotypical individuals from Western nations are more field-independent than neurotypical individuals from East-Asian nations. The majority of research on perceptual…

Techniques to extract physical modes in model-independent analysis of rings

International Nuclear Information System (INIS)

Wang, C.-X.

2004-01-01

A basic goal of Model-Independent Analysis is to extract the physical modes underlying the beam histories collected at a large number of beam position monitors so that beam dynamics and machine properties can be deduced independent of specific machine models. Here we discuss techniques to achieve this goal, especially the Principal Component Analysis and the Independent Component Analysis.

Molecular techniques as complementary tools in orchid mutagenesis

Energy Technology Data Exchange (ETDEWEB)

Mohd Nazir Basiran; Sakinah Ariffin [Malaysian Institute for Nuclear Technology Research (MINT), Bangi (Malaysia)

2002-02-01

Orchid breeders have always been dependent on hybridization technology to produce new orchid hybrids and varieties. The technology has proven very reliable and easy to use and has produced wide range of successful cultivars with attractive combinations of spray length, bud number, flower colour and form, vase life, fragrance, seasonality, and compactness. By introducing mutagenesis however, wide variations of flower colours, form and size can still be obtained in addition to overcoming the problem of sexual incompatibility and sterility. In addition, complementary use of molecular techniques will allow breeders to target more specific characteristic changes and cut short breeding time. PCR-based techniques used to analyse the DNA of mutagenic clones found polymorphic fragments that can be developed as molecular markers. This paper describes how mutagenesis and molecular techniques can be used to enhance orchid breeding efforts. (author)

Cell culture techniques in honey bee research

Science.gov (United States)

Cell culture techniques are indispensable in most if not all life science disciplines to date. Wherever cell culture models are lacking scientific development is hampered. Unfortunately this has been and still is the case in honey bee research because permanent honey bee cell lines have not yet been...

Development of the KINS Safety Culture Maturity Model for Self and Independent Assessment

International Nuclear Information System (INIS)

Sheen, C.; Choi, Y.S.

2016-01-01

Safety culture of an organization is cultivated and affected not only by societal and regulatory environment of the organization, but by its philosophies, policies, events and activities experienced in the process of accomplishing its mission. The safety culture would be continuously changed by the interactions between its members along with time as an organic entity. In order to perform a systematic self- or independent assessment of safety culture, a safety culture assessment model (SCAM) properly reflecting cultural characteristics should be necessary. In addition, a SCAM should be helpful not only to establish correct directions, goals, and strategies for safety culture development, but should anticipating obstacles against safety culture development in the implementation process derived from the assessment. In practical terms, a SCAM should be useful for deriving effective guidelines and implementing of corrective action programs for the evaluated organization. Korea Institute of Nuclear Safety (KINS) performed a research project for six years to develop a SCAM satisfying the above prerequisites for self- and independent assessment. The KINS SCAM was developed based on the five stage safety culture maturity model proposed by Professor Patrick Hudson and was modified into four stages to reflect existing safety culture assessment experiences at Korean nuclear power plants. In order to define the change mechanism of safety culture for development and reversion, the change model proposed by Prochaska and DiClemente was introduced into KINS SCAM and developed into the Spiral Change Model.

Revisiting bovine pyometra-New insights into the disease using a culture-independent deep sequencing approach

DEFF Research Database (Denmark)

Knudsen, Lif Rødtness Vesterby; Karstrup, Cecilia Christensen; Pedersen, Hanne Gervi

2015-01-01

-independent studies have demonstrated that the bacterial diversity in most environments is underestimated in culture-based studies. Consequently, fastidious pyometra-associated pathogens may have been overlooked. Therefore, the primary purpose of this study was to investigate the diversity of bacteria in the uterus......The bacteria present in the uterus during pyometra have previously been studied using bacteriological culturing. These studies identified Fusobacterium necrophorum and Trueperella pyogenes as the major contributors to the pathogenesis of pyometra. However, an increasing number of culture...... of cows with pyometra by using culture-independent 16S rRNA PCR combined with next generation sequencing. We investigated the microbial composition in the uterus of 21 cows with pyometra, which were obtained from a Danish slaughterhouse. Similar to the observations from the culture studies...

Identity and quantity of microorganisms in necrotising fasciitis determined by culture and molecular methods

DEFF Research Database (Denmark)

Rudkjøbing, Vibeke Børsholt; Thomsen, Trine Rolighed; Nielsen, Per Halkjær

communities were more common by molecular methods than culture. Correspondence between findings by culture and molecular methods indicates that the latter may be an appropriate method. The advantages of using molecular methods are: 1) identification of the pathogen(s) even when antibiotics have been...... involved in the disease may add to the knowledge of NF pathogenesis and influence the administration of antibiotics, thereby potentially improving the outcome for the patients. In this study the aim was to investigate the applicability of different molecular methods as compared to standard culture......-based methods. We investigated the microbial communities in 21 samples obtained during debridement of NF patients (n=8). Samples were examined by standard bacteriological examination (culture and microscopy) at Rigshospitalet (Copenhagen, Denmark) and a range of molecular methods. The best DNA extraction...

Bacterial diversity associated with the rotifer Brachionus plicatilis sp. complex determined by culture-dependent and -independent methods.

Science.gov (United States)

Ishino, Ryota; Iehata, Shunpei; Nakano, Miyo; Tanaka, Reiji; Yoshimatsu, Takao; Maeda, Hiroto

2012-03-01

The bacterial communities associated with rotifers (Brachionus plicatilis sp. complex) and their culture water were determined using culture-dependent and -independent methods (16S rRNA gene clone library). The bacterial communities determined by the culture-independent method were more diverse than those determined by the culture-dependent method. Although the culture-dependent method indicated the bacterial community of rotifers was relatively similar to that of the culture water, 16S rRNA gene clone library analyses revealed a great difference between the two microbiotas. Our results suggest that most bacteria associated with rotifers are not easily cultured using conventional methods, and that the microbiota of rotifers do not correspond with that of the culture water completely.

Nuclear techniques and in vitro culture for plant improvement

International Nuclear Information System (INIS)

1986-01-01

The continuous series of food shortages in many parts of the world have led scientists to consider the possibilities of using the new techniques to develop better varieties of plants. The basis for plant breeding is suitable genetic variability and mutation induction as the means to create additional variation. In vitro techniques are a relatively new tool in practical plant breeding. These Proceedings contain 62 papers and posters presented at the symposium, as well as excerpts from the discussions. The Symposium presentations are divided into the following sessions: Genetic variation from in vitro culture; Genetic stability of in vitro cultures; In vitro culture with application of mutagens; Haploids; In vitro mutant selection; Use of genetic variation derived by in vitro culture; In vitro techniques as aids in mutation breeding and Genetic engineering. A separate abstract is prepared for each of these papers and posters

A Brief Review of Molecular Techniques to Assess Plant Diversity

Directory of Open Access Journals (Sweden)

Ibrahim A. Arif

2010-05-01

Full Text Available Massive loss of valuable plant species in the past centuries and its adverse impact on environmental and socioeconomic values has triggered the conservation of plant resources. Appropriate identification and characterization of plant materials is essential for the successful conservation of plant resources and to ensure their sustainable use. Molecular tools developed in the past few years provide easy, less laborious means for assigning known and unknown plant taxa. These techniques answer many new evolutionary and taxonomic questions, which were not previously possible with only phenotypic methods. Molecular techniques such as DNA barcoding, random amplified polymorphic DNA (RAPD, amplified fragment length polymorphism (AFLP, microsatellites and single nucleotide polymorphisms (SNP have recently been used for plant diversity studies. Each technique has its own advantages and limitations. These techniques differ in their resolving power to detect genetic differences, type of data they generate and their applicability to particular taxonomic levels. This review presents a basic description of different molecular techniques that can be utilized for DNA fingerprinting and molecular diversity analysis of plant species.

A Brief Review of Molecular Techniques to Assess Plant Diversity

Science.gov (United States)

Arif, Ibrahim A.; Bakir, Mohammad A.; Khan, Haseeb A.; Al Farhan, Ahmad H.; Al Homaidan, Ali A.; Bahkali, Ali H.; Sadoon, Mohammad Al; Shobrak, Mohammad

2010-01-01

Massive loss of valuable plant species in the past centuries and its adverse impact on environmental and socioeconomic values has triggered the conservation of plant resources. Appropriate identification and characterization of plant materials is essential for the successful conservation of plant resources and to ensure their sustainable use. Molecular tools developed in the past few years provide easy, less laborious means for assigning known and unknown plant taxa. These techniques answer many new evolutionary and taxonomic questions, which were not previously possible with only phenotypic methods. Molecular techniques such as DNA barcoding, random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), microsatellites and single nucleotide polymorphisms (SNP) have recently been used for plant diversity studies. Each technique has its own advantages and limitations. These techniques differ in their resolving power to detect genetic differences, type of data they generate and their applicability to particular taxonomic levels. This review presents a basic description of different molecular techniques that can be utilized for DNA fingerprinting and molecular diversity analysis of plant species. PMID:20559503

Comparison of Standard Culture-Based Method to Culture-Independent Method for Evaluation of Hygiene Effects on the Hand Microbiome.

Science.gov (United States)

Zapka, C; Leff, J; Henley, J; Tittl, J; De Nardo, E; Butler, M; Griggs, R; Fierer, N; Edmonds-Wilson, S

2017-03-28

Hands play a critical role in the transmission of microbiota on one's own body, between individuals, and on environmental surfaces. Effectively measuring the composition of the hand microbiome is important to hand hygiene science, which has implications for human health. Hand hygiene products are evaluated using standard culture-based methods, but standard test methods for culture-independent microbiome characterization are lacking. We sampled the hands of 50 participants using swab-based and glove-based methods prior to and following four hand hygiene treatments (using a nonantimicrobial hand wash, alcohol-based hand sanitizer [ABHS], a 70% ethanol solution, or tap water). We compared results among culture plate counts, 16S rRNA gene sequencing of DNA extracted directly from hands, and sequencing of DNA extracted from culture plates. Glove-based sampling yielded higher numbers of unique operational taxonomic units (OTUs) but had less diversity in bacterial community composition than swab-based sampling. We detected treatment-induced changes in diversity only by using swab-based samples ( P hand hygiene industry methods and for future hand microbiome studies. On the basis of our results and previously published studies, we propose recommendations for best practices in hand microbiome research. IMPORTANCE The hand microbiome is a critical area of research for diverse fields, such as public health and forensics. The suitability of culture-independent methods for assessing effects of hygiene products on microbiota has not been demonstrated. This is the first controlled laboratory clinical hand study to have compared traditional hand hygiene test methods with newer culture-independent characterization methods typically used by skin microbiologists. This study resulted in recommendations for hand hygiene product testing, development of methods, and future hand skin microbiome research. It also demonstrated the importance of inclusion of skin physiological metadata in

Method to Increase Undergraduate Laboratory Student Confidence in Performing Independent Research

Directory of Open Access Journals (Sweden)

Colton E. Kempton

2017-05-01

Full Text Available The goal of an undergraduate laboratory course should be not only to introduce the students to biology methodologies and techniques, but also to teach them independent analytical thinking skills and proper experiment design.  This is especially true for advanced biology laboratory courses that undergraduate students typically take as a junior or senior in college.  Many courses achieve the goal of teaching techniques, but fail to approach the larger goal of teaching critical thinking, experimental design, and student independence.  Here we describe a study examining the application of the scaffolding instructional philosophy in which students are taught molecular techniques with decreasing guidance to force the development of analytical thinking skills and prepare undergraduate students for independent laboratory research. This method was applied to our advanced molecular biology laboratory class and resulted in an increase of confidence among the undergraduate students in their abilities to perform independent research.

Multiparticle 3D imaging technique to study the structure of molecular ions

International Nuclear Information System (INIS)

Koenig, W.; Faibis, A.; Kanter, E.P.; Vager, Z.; Zabransky, B.J.

1984-01-01

When energetic molecular ions (E/sub ion/ = 0.1 to 0.5 MeV/amu) pass through thin solid targets a Coulomb explosion ensues due to the rapid (approx. 10 -17 s) stripping of the valence electrons. This process has been successfully used to derive stereochemical information on diatomic and on selected triatomic ions. In order to investigate more complex molecular ions as well as to obtain more accurate and detailed structure information, a large area, multiparticle, position- and time-sensitive detector has been developed to detect all atomic fragments in coincidence. The requirement of multiparticle detection independent of the relative particle positions leads to a rather complex data-readout and -reduction system containing approx. 650 analog-to-digital conversions per event. The system relies heavily on techniques developed for high energy physics experiments during recent years. The single event resolution of the apparatus with respect to bond-lengths and -angles has been studied by Monte Carlo simulations and is typically a few percent

The dopamine D4 receptor gene (DRD4) moderates cultural difference in independent versus interdependent social orientation.

Science.gov (United States)

Kitayama, Shinobu; King, Anthony; Yoon, Carolyn; Tompson, Steve; Huff, Sarah; Liberzon, Israel

2014-06-01

Prior research suggests that cultural groups vary on an overarching dimension of independent versus interdependent social orientation, with European Americans being more independent, or less interdependent, than Asians. Drawing on recent evidence suggesting that the dopamine D4 receptor gene (DRD4) plays a role in modulating cultural learning, we predicted that carriers of DRD4 polymorphisms linked to increased dopamine signaling (7- or 2-repeat alleles) would show higher levels of culturally dominant social orientations, compared with noncarriers. European Americans and Asian-born Asians (total N = 398) reported their social orientation on multiple scales. They were also genotyped for DRD4. As in earlier work, European Americans were more independent, and Asian-born Asians more interdependent. This cultural difference was significantly more pronounced for carriers of the 7- or 2-repeat alleles than for noncarriers. Indeed, no cultural difference was apparent among the noncarriers. Implications for potential coevolution of genes and culture are discussed. © The Author(s) 2014.

Molecular Imprinting Techniques Used for the Preparation of Biosensors

Directory of Open Access Journals (Sweden)

Gizem Ertürk

2017-02-01

Full Text Available Molecular imprinting is the technology of creating artificial recognition sites in polymeric matrices which are complementary to the template in their size, shape and spatial arrangement of the functional groups. Molecularly imprinted polymers (MIPs and their incorporation with various transducer platforms are among the most promising approaches for detection of several analytes. There are a variety of molecular imprinting techniques used for the preparation of biomimetic sensors including bulk imprinting, surface imprinting (soft lithography, template immobilization, grafting, emulsion polymerization and epitope imprinting. This chapter presents an overview of all of these techniques with examples from particular publications.

Towards a culturally independent participatory design method: Fusing game elements into the design process

DEFF Research Database (Denmark)

Jensen, Mika Yasuoka; Nakatani, Momoko; Ohno, Takehiko

2013-01-01

Historically, Participatory Design (PD) was introduced and applied in the Scandinavian and American context as a practical design method for collective creativity and stakeholder involvement. In this paper, by fusing game elements into PD, we suggest a first step towards a culturally independent ...... imply that the introduction of game elements allows PD to be effectively utilized in culturally diverse settings.......Historically, Participatory Design (PD) was introduced and applied in the Scandinavian and American context as a practical design method for collective creativity and stakeholder involvement. In this paper, by fusing game elements into PD, we suggest a first step towards a culturally independent PD...... method called the ICT Service Design Game to ease the prevailing concern that PD has limited applicability in other cultural settings. We conduct four experiments on ICT Service Design Game in Scandinavia and Asia to evaluate its feasibility. The experiments identify some differences in the PD process...

Beyond Blood Culture and Gram Stain Analysis: A Review of Molecular Techniques for the Early Detection of Bacteremia in Surgical Patients.

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Scerbo, Michelle H; Kaplan, Heidi B; Dua, Anahita; Litwin, Douglas B; Ambrose, Catherine G; Moore, Laura J; Murray, Col Clinton K; Wade, Charles E; Holcomb, John B

2016-06-01

Sepsis from bacteremia occurs in 250,000 cases annually in the United States, has a mortality rate as high as 60%, and is associated with a poorer prognosis than localized infection. Because of these high figures, empiric antibiotic administration for patients with systemic inflammatory response syndrome (SIRS) and suspected infection is the second most common indication for antibiotic administration in intensive care units (ICU)s. However, overuse of empiric antibiotics contributes to the development of opportunistic infections, antibiotic resistance, and the increase in multi-drug-resistant bacterial strains. The current method of diagnosing and ruling out bacteremia is via blood culture (BC) and Gram stain (GS) analysis. Conventional and molecular methods for diagnosing bacteremia were reviewed and compared. The clinical implications, use, and current clinical trials of polymerase chain reaction (PCR)-based methods to detect bacterial pathogens in the blood stream were detailed. BC/GS has several disadvantages. These include: some bacteria do not grow in culture media; others do not GS appropriately; and cultures can require up to 5 d to guide or discontinue antibiotic treatment. PCR-based methods can be potentially applied to detect rapidly, accurately, and directly microbes in human blood samples. Compared with the conventional BC/GS, particular advantages to molecular methods (specifically, PCR-based methods) include faster results, leading to possible improved antibiotic stewardship when bacteremia is not present.

Healing in Herero culture and Namibian African independent churches

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Selaelo T. Kgatla

2015-09-01

Full Text Available The current phenomenon of Namibian African Independent Churches (NAICs draws attention from various people in civil society in Namibia. Although the ministries of NAICs are engaged with activities which are unusual for Christian churches, such as healing the people, fighting against evil spirits and power, performing certain rituals, prophesying and leading the worship services with African Traditional Religion (ATR as a frame of reference in 21st century, they do have a very big influence on various aspects of society in Namibia, which cannot be ignored. This is because those activities are familiar to the everyday lives of Africans and in touch with their culture. With regards to this, this article focuses on the causes of integration or harmony between the Herero culture and the NAICs.

Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils

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Stefani, Franck O. P.; Bell, Terrence H.; Marchand, Charlotte; de la Providencia, Ivan E.; El Yassimi, Abdel; St-Arnaud, Marc; Hijri, Mohamed

2015-01-01

Bioremediation is a cost-effective and sustainable approach for treating polluted soils, but our ability to improve on current bioremediation strategies depends on our ability to isolate microorganisms from these soils. Although culturing is widely used in bioremediation research and applications, it is unknown whether the composition of cultured isolates closely mirrors the indigenous microbial community from contaminated soils. To assess this, we paired culture-independent (454-pyrosequenci...

The effects of culture independent diagnostic testing on the diagnosis and reporting of enteric bacterial pathogens in Queensland, 2010 to 2014.

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May, Fiona J; Stafford, Russell J; Carroll, Heidi; Robson, Jennifer Mb; Vohra, Renu; Nimmo, Graeme R; Bates, John; Kirk, Martyn D; Fearnley, Emily J; Polkinghorne, Benjamin G

2017-09-01

Changes in diagnostic laboratory testing procedures can impact on the number of cases notified and the public health surveillance of enteric pathogens. Culture independent diagnostic testing using a multiplex polymerase chain reaction (PCR) test was introduced for the rapid detection of bacterial enteric pathogens in pathology laboratories in Queensland, Australia, from late 2013 onwards. We conducted a retrospective descriptive study using laboratory data to assess the impact of the introduction of PCR testing on four common enteric pathogens, Salmonella, Campylobacter, Shigella and Yersinia, in Queensland between 2010 and 2014. The number of stool specimens tested and the proportion positive for each of the four pathogens increased in 2014 after the introduction of culture independent diagnostic testing. Among the specimens tested by both PCR and culture, 12% of Salmonella positive stools, 36% of Campylobacter positive stools, 74% of Shigella / enteroinvasive Escherichia coli positive stools and 65% of Yersinia positive stools were PCR positive only. Including those where culture was not performed, 19% of Salmonella positive stools, 44% of Campylobacter positive stools, 83% of Shigella positive stools and 79% of Yersinia positive stools had no cultured isolate available for further characterisation. The detection and tracking of foodborne and non-foodborne gastrointestinal outbreaks will become more difficult as culture independent diagnostic testing becomes more widespread. Until new techniques for characterisation of pathogens directly from clinical specimens have been developed, we recommend laboratories continue to culture specimens concurrently or reflexively with culture independent diagnostic tests. This work is copyright. You may download, display, print and reproduce the whole or part of this work in unaltered form for your own personal use or, if you are part of an organisation, for internal use within your organisation, but only if you or your

Application of Hanging Drop Technique for Kidney Tissue Culture.

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Wang, Shaohui; Wang, Ximing; Boone, Jasmine; Wie, Jin; Yip, Kay-Pong; Zhang, Jie; Wang, Lei; Liu, Ruisheng

2017-01-01

The hanging drop technique is a well-established method used in culture of animal tissues. However, this method has not been used in adult kidney tissue culture yet. This study was to explore the feasibility of using this technique for culturing adult kidney cortex to study the time course of RNA viability in the tubules and vasculature, as well as the tissue structural integrity. In each Petri dish with the plate covered with sterile buffer, a section of mouse renal cortex was cultured within a drop of DMEM culture medium on the inner surface of the lip facing downward. The tissue were then harvested at each specific time points for Real-time PCR analysis and histological studies. The results showed that the mRNA level of most Na+ related transporters and cotransporters were stably maintained within 6 hours in culture, and that the mRNA level of most receptors found in the vasculature and glomeruli were stably maintained for up to 9 days in culture. Paraffin sections of the cultured renal cortex indicated that the tubules began to lose tubular integrity after 6 hours, but the glomeruli and vasculatures were still recognizable up to 9 days in culture. We concluded that adult kidney tissue culture by hanging drop method can be used to study gene expressions in vasculature and glomeruli. © 2017 The Author(s). Published by S. Karger AG, Basel.

Application of Hanging Drop Technique for Kidney Tissue Culture

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Shaohui Wang

2017-05-01

Full Text Available Background/Aims: The hanging drop technique is a well-established method used in culture of animal tissues. However, this method has not been used in adult kidney tissue culture yet. This study was to explore the feasibility of using this technique for culturing adult kidney cortex to study the time course of RNA viability in the tubules and vasculature, as well as the tissue structural integrity. Methods: In each Petri dish with the plate covered with sterile buffer, a section of mouse renal cortex was cultured within a drop of DMEM culture medium on the inner surface of the lip facing downward. The tissue were then harvested at each specific time points for Real-time PCR analysis and histological studies. Results: The results showed that the mRNA level of most Na+ related transporters and cotransporters were stably maintained within 6 hours in culture, and that the mRNA level of most receptors found in the vasculature and glomeruli were stably maintained for up to 9 days in culture. Paraffin sections of the cultured renal cortex indicated that the tubules began to lose tubular integrity after 6 hours, but the glomeruli and vasculatures were still recognizable up to 9 days in culture. Conclusions: We concluded that adult kidney tissue culture by hanging drop method can be used to study gene expressions in vasculature and glomeruli.

Hlaallele Detection Using Molecular Techniques

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Philip A. Dyer

1993-01-01

Full Text Available There are now many molecular biological techniques available to define HLA class I and class II alleles. Some of these are also applicable to other human polymorphic genes, in particular to those non-HLA genes encoded within the Mhc. The range of techniques available allows laboratories to choose those most suited to their purpose. The routine laboratory supporting solid organ transplants will need to type large numbers of potential recipients over a period of time, probably using PCR-SSOP while donors will be typed singly and rapidly using PCR-SSP with HLA allele compatibility determined by heteroduplex analysis. Laboratories supporting bone marrow transplantation, where time is less pressing, can choose from the whole range of techniques to determine accurately donor recipient Mhc compatibility. For disease studies, techniques defining precise HLA allele sequence polymorphisms are needed and high sample numbers have to be accommodated. When an association is established allele sequencing has to be used. In the near future, the precise role of HLA alleles in transplantation and disease susceptibility is likely to be established unambiguously.

Ethos of independence across regions in the United States: the production-adoption model of cultural change.

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Kitayama, Shinobu; Conway, Lucian Gideon; Pietromonaco, Paula R; Park, Hyekyung; Plaut, Victoria C

2010-09-01

Contemporary U.S. culture has a highly individualistic ethos. Nevertheless, exactly how this ethos was historically fostered remains unanalyzed. A new model of dynamic cultural change maintains that sparsely populated, novel environments that impose major threats to survival, such as the Western frontier in the United States during the 18th and 19th centuries, breed strong values of independence, which in turn guide the production of new practices that encourage self-promotion and focused, competitive work. Faced with few significant threats to survival, residents in traditional areas are likely to seek social prestige by adopting existing practices of other, higher status groups. Because of both the massive economic success of the frontier and the official endorsement of the frontier by the federal government, eastern residents of the United States in the 18th and 19th centuries may have actively adopted the frontier practices of independence, thus incorporating the frontier ethos of independence to form the contemporary U.S. national culture. Available evidence is reviewed, and implications for further research on cultural change are suggested. Copyright 2010 APA, all rights reserved.

Molecular dynamics in porous media studied by nuclear magnetic resonance techniques

International Nuclear Information System (INIS)

Mattea, C.

2006-01-01

Field cycling NMR relaxometry was used to study dynamics of fluids under confinement in different scenarios: fluids flowing through porous media, fluids partially filling porous media and polymer melts in nanoscopic pores. Diffusion in partially filled porous media was also studied with the aid of an NMR diffusometry technique. It is shown that hydrodynamic flow influences the spin-lattice relaxation rate of water confined in mesoscopic porous media under certain conditions. The effect is predicted by an analytical theory and Monte Carlo simulations, and confirmed experimentally by field-cycling NMR relaxometry. Field-cycling NMR relaxometry has been applied to polar and non polar adsorbates in partially filled silica porous glasses. The dependence of the spin-lattice relaxation rate on the filling degree shows that limits for slow and fast exchange between different phases can be distinguished and identified depending on the pore size and polarity of the solvents. Diffusion in the same unsaturated systems was studied with the aid of NMR diffusometry technique. The effective diffusion coefficient of solvents with different polarities displays opposite tendencies as a function of the liquid content. A two-phase fast exchange model including Knudsen and ordinary diffusion and different effective tortuosities is presented accounting for these phenomena. In the case of polymer melts confined in narrow artificial tubes of a porous solid matrix with variable diameter (9 to 57 nm), the characteristics of reptation were experimentally verified using proton field cycling NMR relaxometry technique. This observation is independent of the molecular mass and pore size. In bulk, the same polymer melts show either Rouse or renormalized Rouse dynamics, depending on the molecular mass. The polymers under confinement show features specific for reptation even with a pore diameter 15 times larger than the Flory radius while bulk melts of the same polymers do not. (orig.)

Propagation of Aquilaria malaccensis seedlings through tissue culture techniques

International Nuclear Information System (INIS)

Salahbiah Abdul Majid; Zaiton Ahmad; Mohd Rafaie Abdul Salam; Nurhayati Irwan; Affrida Abu Hassan; Rusli Ibrahim

2010-01-01

Aquilaria malaccensis or karas is the principal source of gaharu resin, which is used in many cultures for incense, perfumes and traditional medicines. The species is mainly propagated conventionally through seeds, cuttings and graftings. Propagation by seeds is usually a reliable method for other forest species, but for karas, this technique is inadequate to meet the current demand of seedling supplies. This is principally due to its low seed viability, low germination rate, delayed rooting of seedlings, long life-cycle and rare seed production. Tissue culture has several advantages over conventional propagation, especially for obtaining large number of uniform and high-yielding plantlets or clones. This paper presents the current progress on mass-propagation of Aquilaria malaccensis seedlings through tissue culture technique at Nuclear Malaysia. (author)

Improvement of Leukemia diagnose with molecular techniques

International Nuclear Information System (INIS)

Campos Rudin, M.E.

1997-01-01

The objective of this study was to contribute with new techniques to the clinical diagnosis and to the monitoring of mycloid chronic leukemias in Costa Rica. The same one achieved to determine that is viable to apply radioactive and non reactive methodologies, for the molecular detection of the Philadelphia chromosome.It also found that the application of techniques of cellular biology, helps to classify better the mycloide leukemias and the chronic mycloproliferatives and miclodisplaced disorders. (S. Grainger) [es

[Comparative characterization of cultured methane-oxidizing bacteria by serological and molecular methods].

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Slobodova, N V; Kolganova, T V; Bulygina, E S; Kuznetsov, B B; Turova, T P; Kravchenko, I K

2006-01-01

Three stable methane-oxidizing enrichment cultures, SB26, SB31, and SB31A were analyzed by transmission electron microscopy and by serological and molecular techniques. Electron microscopy revealed the presence of both type I and type II methanotrophs in SB31 and SB31A enrichments; only type II methanotrophs were found in SB26 enrichment. Methylosinus trichosporium was detected in all three enrichments by the application of species-specific antibodies. Additionally, Methylocystis echinoides was found in SB26 culture; Methylococcus capsulatus, in SB31 and SB31A; and Methylomonas methanica, in SB31. The analysis with pmoA and nifH gene sequences as phylogenetic markers revealed the presence of Methylosinus/Methylocystis group in all communities. Moreover, the analysis of pmoA sequences revealed the presence of Methylomonas in SB31. Methylocella was detected in SB31 and SB31A enrichments only by nifH analysis. It was concluded that the simultaneous application of different approaches reveals more reliable information on the diversity of methanotrophs.

The role and future of in-vitro isotopic techniques in molecular biology

International Nuclear Information System (INIS)

Dar, L.; Khan, B.K.

2004-01-01

In this review we discuss isotopic in-vitro molecular biology techniques, and their advantages and applications. Isotopic methods have helped to shape molecular biology since its early days. Despite the availability of non-isotopic alternatives, isotopic methods continue to be used in molecular biology due to certain advantages, especially related to sensitivity and cost-effectiveness. Numerous techniques involving the use of isotopes help in the characterization of genes, including the detection of single nucleotide polymorphisms (SNPs) or mutations. Other isotopic molecular methods are utilized to study the phenotypic expression of gene sequences and their mutation. Emerging branches of molecular biology like functional genomics and proteomics are extremely important for exploiting the rapidly growing data derived from whole genomic sequencing of human and microbial genomes. Recent molecular biology applications like the high-throughput array techniques are relevant in the context of both structural and functional genomics. In proteomics, stable isotope based technology has found applications in the analysis of protein structure and interactions. (author)

Use of cultivation-dependent and -independent techniques to assess contamination of central venous catheters: a pilot study

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Høiby Niels

2008-10-01

Full Text Available Abstract Background Catheters are the most common cause of nosocomial infections and are associated with increased risk of mortality, length of hospital stay and cost. Prevention of infections and fast and correct diagnosis is highly important. Methods In this study traditional semiquantitative culture-dependent methods for diagnosis of bacteria involved in central venous catheter-related infections as described by Maki were compared with the following culture-independent molecular biological methods: Clone libraries, denaturant gradient gel electrophoresis, phylogeny and fluorescence in situ hybridization. Results In accordance with previous studies, the cultivation of central venous catheters from 18 patients revealed that S. epidermidis and other coagulase-negative staphylococci were most abundant and that a few other microorganisms such as P. aeruginosa and K. pneumoniae occasionally were found on the catheters. The molecular analysis using clone libraries and sequencing, denaturant gradient gel electrophoresis and sequencing provided several important results. The species found by cultivation were confirmed by molecular methods. However, many other bacteria belonging to the phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes were also found, stressing that only a minor portion of the species present were found by cultivation. Some of these bacteria are known to be pathogens, some have not before been described in relation to human health, and some were not closely related to known pathogens and may represent new pathogenic species. Furthermore, there was a clear difference between the bacterial species found in biofilm on the external (exluminal and internal (luminal side of the central venous catheter, which can not be detected by Maki's method. Polymicrobial biofilms were observed on most of the catheters and were much more common than the cultivation-dependent methods indicated. Conclusion The results show that diagnosis

Microbiological studies to select compatible rhizobia for application in wastelands using molecular and nuclear techniques

International Nuclear Information System (INIS)

Abdel Raouf, A.M.N

2010-01-01

The present work aimed at utilization of wastelands and improving their fertility status through the following topics:1- Isolation and identification of rhizobia from wastelands, then selecting the most resistant isolate to saline conditions.2- Studying the effect of radiation on the most salt tolerant rhizobia and marketing rhizobia using molecular and microbiological techniques.3- Identification and culturing of selected compatible rhizobia to be used in application experiments as a bio fertilizer to inoculate the leguminous crops in order to improve the efficiency of the Rhizobium-legume symbiosis and reclamation of wastelands.4- Application of molecular and nuclear techniques such 16S ribosomal RNA and studying the sequence for these strains for comparison between the most potent rhizobia.5- Determination of protein profile for the most potent rhizobia to throw light about similarities between these strains.6- Attempts to apply polymerase chain reaction (PCR) and use primers for differentiation between the most potent rhizobia.7- Experimental fields for growing some leguminous plants inoculated with irradiated and non-irradiated rhizobia and irrigated with different concentrations of sea water and their effects on growth and total N content of plants.

A review of gastrointestinal microbiology with special emphasis on molecular microbial ecology approaches

International Nuclear Information System (INIS)

Mackie, R.I.; Cann, I.K.O.

2005-01-01

All animals, including humans, are adapted to life in a microbial world. Large populations of micro-organisms inhabit the gastrointestinal tract of all animals and form a closely integrated ecological unit with the host. This complex, mixed, microbial culture can be considered the most metabolically adaptable and rapidly renewable organ of the body, which plays a vital role in the normal nutritional, physiological, immunological and protective functions of the host animal. Bacteria have traditionally been classified mainly on the basis of phenotypic properties. Despite the vast amount of knowledge generated for ruminal and other intestinal ecosystems using traditional techniques, the basic requisites for ecological studies, namely, enumeration and identification of all community members, have limitations. The two major problems faced by microbial ecologists are bias introduced by culture-based enumeration and characterization techniques, and the lack of a phylogenetically-based classification scheme. Modem molecular ecology techniques based on sequence comparisons of nucleic acids (DNA or RNA) can be used to provide molecular characterization while at the same time providing a classification scheme that predicts natural evolutionary relationships. These molecular methods provide results that are independent of growth conditions and media used. Also, using these techniques, bacteria can be classified and identified before they can be grown in pure culture. These nucleic acid-based techniques will enable gut microbiologists to answer the most difficult question in microbial ecology: namely, describing the exact role or function a specific bacterium plays in its natural environment and its quantitative contribution to the whole. However, rather than replacing the classical culture-based system, the new molecular-based techniques can be used in combination with the classical approach to improve cultivation, speciation and evaluation of diversity. The study of microbial

The comparison of pyrosequencing molecular Gram stain, culture, and conventional Gram stain for diagnosing orthopaedic infections.

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Kobayashi, Naomi; Bauer, Thomas W; Tuohy, Marion J; Lieberman, Isador H; Krebs, Viktor; Togawa, Daisuke; Fujishiro, Takaaki; Procop, Gary W

2006-08-01

We have developed a combined real-time PCR and pyrosequencing assay that successfully differentiated the vast majority of gram-positive and gram-negative bacteria when bacterial isolates were tested. The purpose of this study was to evaluate this assay on clinical specimens obtained from orthopedic surgeries, and to prospectively compare the results of "molecular Gram stain" with culture and conventional direct Gram stain. Forty-five surgical specimens were obtained from patients who underwent orthopedic surgery procedures. The DNA was extracted and a set of broad-range PCR primers that targeted a part of the 16S rDNA gene was used for pan-bacterial PCR. The amplicons were submitted for pyrosequencing and the resulting molecular Gram stain characteristics were recorded. Culture and direct Gram staining were performed using standard methods for all cases. Surgical specimens were reviewed histologically for all cases that had a discrepancy between culture and molecular results. There was an 86.7% (39/45) agreement between the traditional and molecular methods. In 12/14 (85.7%) culture-proven cases of bacterial infection, molecular Gram stain characteristics were in agreement with the culture results, while the conventional Gram stain result was in agreement only for five cases (35.7%). In the 31 culture negative cases, 27 cases were also PCR negative, whereas 4 were PCR positive. Three of these were characterized as gram negative and one as gram positive by this molecular method. Molecular determination of the Gram stain characteristics of bacteria that cause orthopedic infections may be achieved, in most instances, by this method. Further studies are necessary to understand the clinical importance of PCR-positive/culture-negative results.

Culture-Independent Techniques for Rapid Detection of Bacteria Associated with Loss of Chloramine Residual in a Drinking Water System

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Hoefel, Daniel; Monis, Paul T.; Grooby, Warwick L.; Andrews, Stuart; Saint, Christopher P.

2005-01-01

Chloramination is often the disinfection regimen of choice for extended drinking water systems. However, this process is prone to instability due to the growth of nitrifying bacteria. This is the first study to use alternative approaches for rapid investigation of chloraminated drinking water system instability in which flow cytometric cell sorting of bacteria with intact membranes (membrane-intact fraction) (BacLight kit) or with active esterases (esterase-active fraction) (carboxyfluorescein diacetate) was combined with 16S rRNA gene-directed PCR and denaturing gradient gel electrophoresis (DGGE). No active bacteria were detected when water left the water treatment plant (WTP), but 12 km downstream the chloramine residual had diminished and the level of active bacteria in the bulk water had increased to more than 1 × 105 bacteria ml−1. The bacterial diversity in the system was represented by six major DGGE bands for the membrane-intact fraction and 10 major DGGE bands for the esterase-active fraction. PCR targeting of the 16S rRNA gene of chemolithotrophic ammonia-oxidizing bacteria (AOB) and subsequent DGGE and DNA sequence analysis revealed the presence of an active Nitrosospira-related species and Nitrosomonas cryotolerans in the system, but no AOB were detected in the associated WTP. The abundance of active AOB was then determined by quantitative real-time PCR (qPCR) targeting the amoA gene; 3.43 × 103 active AOB ml−1 were detected in the membrane-intact fraction, and 1.40 × 104 active AOB ml−1 were detected in the esterase-active fraction. These values were several orders of magnitude greater than the 2.5 AOB ml−1 detected using a routine liquid most-probable-number assay. Culture-independent techniques described here, in combination with existing chemical indicators, should allow the water industry to obtain more comprehensive data with which to make informed decisions regarding remedial action that may be required either prior to or during an

Proceedings of the FNCA workshop on plant mutation breeding 2001. Molecular biological techniques

International Nuclear Information System (INIS)

Kume, Tamikazu; Watanabe, Kazuo; Tano, Shigemitsu

2002-02-01

The FNCA (Forum for Nuclear Cooperation in Asia) Workshop on Plant Mutation Breeding was held on 20-24 August 2001 in Bangkok, Thailand. The Workshop was sponsored by the Ministry of Education, Culture, Sports, Science and Technology (MEXT). The Kasetsart University (KU), the Office of Atomic Energy for Peace (OAEP) and Department of Agriculture (DOA) acted as local host and the organizer with the cooperation of the Ministry of Agriculture, Forestry and Fisheries (MAFF) of Japan, the Japan Atomic Industrial Forum (JAIF) and Japan Atomic Energy Research Institute (JAERI). The Workshop was attended by two participants, a Project Leader and an expert on molecular biological techniques for plant mutation breeding, from each of the participating countries, i.e. China, Indonesia, Malaysia, the Philippines and Vietnam. One participant from the Republic of Korea, nine participants from Japan and thirteen participants from Thailand including three invited speakers attended the Workshop. Eleven papers including three invited papers on the current status of molecular biological techniques for plant mutation breeding were presented. Discussions were focused to further regional cooperation, to review and discuss results of past activities. The Medium-Term Plan of the project on the application of radiation and radioisotopes for agriculture in participating countries of Regional Nuclear Cooperation Activities (RNCA) was formulated and agreed. This proceeding compiles the invited and contributed papers that were submitted from the speakers. (author)

[Advances of Molecular Diagnostic Techniques Application in Clinical Diagnosis.

Science.gov (United States)

Ying, Bin-Wu

2016-11-01

Over the past 20 years,clinical molecular diagnostic technology has made rapid development,and became the most promising field in clinical laboratory medicine.In particular,with the development of genomics,clinical molecular diagnostic methods will reveal the nature of clinical diseases in a deeper level,thus guiding the clinical diagnosis and treatments.Many molecular diagnostic projects have been routinely applied in clinical works.This paper reviews the advances on application of clinical diagnostic techniques in infectious disease,tumor and genetic disorders,including nucleic acid amplification,biochip,next-generation sequencing,and automation molecular system,and so on.

On the number of independent cultural traits carried by individuals and populations.

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Lehmann, Laurent; Aoki, Kenichi; Feldman, Marcus W

2011-02-12

In species subject to individual and social learning, each individual is likely to express a certain number of different cultural traits acquired during its lifetime. If the process of trait innovation and transmission reaches a steady state in the population, the number of different cultural traits carried by an individual converges to some stationary distribution. We call this the trait-number distribution. In this paper, we derive the trait-number distributions for both individuals and populations when cultural traits are independent of each other. Our results suggest that as the number of cultural traits becomes large, the trait-number distributions approach Poisson distributions so that their means characterize cultural diversity in the population. We then analyse how the mean trait number varies at both the individual and population levels as a function of various demographic features, such as population size and subdivision, and social learning rules, such as conformism and anti-conformism. Diversity at the individual and population levels, as well as at the level of cultural homogeneity within groups, depends critically on the details of population demography and the individual and social learning rules.

A fermionic molecular dynamics technique to model nuclear matter

International Nuclear Information System (INIS)

Vantournhout, K.; Jachowicz, N.; Ryckebusch, J.

2009-01-01

Full text: At sub-nuclear densities of about 10 14 g/cm 3 , nuclear matter arranges itself in a variety of complex shapes. This can be the case in the crust of neutron stars and in core-collapse supernovae. These slab like and rod like structures, designated as nuclear pasta, have been modelled with classical molecular dynamics techniques. We present a technique, based on fermionic molecular dynamics, to model nuclear matter at sub-nuclear densities in a semi classical framework. The dynamical evolution of an antisymmetric ground state is described making the assumption of periodic boundary conditions. Adding the concepts of antisymmetry, spin and probability distributions to classical molecular dynamics, brings the dynamical description of nuclear matter to a quantum mechanical level. Applications of this model vary from investigation of macroscopic observables and the equation of state to the study of fundamental interactions on the microscopic structure of the matter. (author)

Determining the stereochemical structures of molecular ions by ''Coulomb-explosion'' techniques with fast (MeV) molecular ion beams

International Nuclear Information System (INIS)

Gemmell, D.S.

1980-01-01

Recent studies on the dissociation of fast (MeV) molecular ion beams in thin foils suggest a novel alternative approach to the determination of molecular ion structures. In this article we review some recent high-resolution studies on the interactions of fast molecular ion beams with solid and gaseous targets and indicate how such studies may be applied to the problem of determining molecular ion structures. The main features of the Coulomb explosion of fast-moving molecular ion projectiles and the manner in which Coulomb-explosion techniques may be applied to the problem (difficult to attack by more conventional means) of determining the stereochemical structures of molecular ions has been described in this paper. Examples have been given of early experiments designed to elicit structure information. The techniques are still in their infancy, and it is to be expected that as both the technology and the analysis are refined, the method will make valuable contributions to the determination of molecular ion structures

Culture and Healthy Eating: The Role of Independence and Interdependence in the U.S. and Japan

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Levine, Cynthia S.; Miyamoto, Yuri; Markus, Hazel Rose; Rigotti, Attilio; Boylan, Jennifer Morozink; Park, Jiyoung; Kitayama, Shinobu; Karasawa, Mayumi; Kawakami, Norito; Coe, Christopher L.; Love, Gayle D.; Ryff, Carol D.

2016-01-01

Healthy eating is important for physical health. Using large probability samples of middle-aged adults in the U.S. and Japan, we show that fitting with the culturally normative way of being predicts healthy eating. In the U.S, a culture that prioritizes and emphasizes independence, being independent predicts eating a healthy diet (an index of fish, protein, fruit, vegetables, reverse-coded sugared beverages, and reverse-coded high fat meat consumption; Study 1) and not using food as a way to cope with stress (Study 2a). In Japan, a culture that prioritizes and emphasizes interdependence, being interdependent predicts eating a healthy diet (Studies 1 and 2b). Further, reflecting the types of agency that are prevalent in each context, these relationships are mediated by autonomy in the U.S. and positive relations with others in Japan. These findings highlight the importance of understanding cultural differences in shaping healthy behavior and have implications for designing health-promoting interventions. PMID:27516421

Molecular characterization of some lignicolous species from fungal culture collection

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Stević Nevena

2014-01-01

Full Text Available Culture collections of microorganisms, including fungi, are strain deposits recognised as Biological Resource Centers (BRCs with a great importance in science, industry and education. Their objective is to preserve the purity, viability and genomic integrity of every single strain as a member of such collection. Since improvement of molecular methods nowadays brought many novel approaches in manipulation with strains of microorganisms, they can also be useful for characterization of existing stored strains. ITS1 region in nuclear DNA is preferred barcoding marker for taxon identification, which can be explained by its great inter-species variability. This paper presents results from analysing ITS1 region sequences (17 obtained from fungal DNA of culture collection of autochthonous, lignicolous genera Piptoporus, Pleurotus, Ganoderma and Schizophyllum cultured on malt agar plates for 14 days at 25°C. BLAST (Basic Local Alignment Search Tool was used for comparison with online databases, while alignment of sequences was made with MEGA 5.10 software. Morphological determination of species or genus was confirmed for 13 cultures, while the others were disproved. The resulting alignment indicated small intra-species variability of ITS1 region and pointed to it as an ideal marker for verification of fungal culture collections' authenticity. [Projekat Ministarstva nauke Republike Srbije, br. III43002 and by the Provincial Secretariat for Science and Technological Development, Vojvodina, Serbia APV 114-4513592/2013-03: Molecular and phenotypic diversity of taxa of economical and epidemiological importance, and endangered and endemic species in Europe

Diagnostic accuracy of semi-quantitative and quantitative culture techniques for the diagnosis of catheter-related infections in newborns and molecular typing of isolated microorganisms.

Science.gov (United States)

Riboli, Danilo Flávio Moraes; Lyra, João César; Silva, Eliane Pessoa; Valadão, Luisa Leite; Bentlin, Maria Regina; Corrente, José Eduardo; Rugolo, Ligia Maria Suppo de Souza; da Cunha, Maria de Lourdes Ribeiro de Souza

2014-05-22

Catheter-related bloodstream infections (CR-BSIs) have become the most common cause of healthcare-associated bloodstream infections in neonatal intensive care units (ICUs). Microbiological evidence implicating catheters as the source of bloodstream infection is necessary to establish the diagnosis of CR-BSIs. Semi-quantitative culture is used to determine the presence of microorganisms on the external catheter surface, whereas quantitative culture also isolates microorganisms present inside the catheter. The main objective of this study was to determine the sensitivity and specificity of these two techniques for the diagnosis of CR-BSIs in newborns from a neonatal ICU. In addition, PFGE was used for similarity analysis of the microorganisms isolated from catheters and blood cultures. Semi-quantitative and quantitative methods were used for the culture of catheter tips obtained from newborns. Strains isolated from catheter tips and blood cultures which exhibited the same antimicrobial susceptibility profile were included in the study as positive cases of CR-BSI. PFGE of the microorganisms isolated from catheters and blood cultures was performed for similarity analysis and detection of clones in the ICU. A total of 584 catheter tips from 399 patients seen between November 2005 and June 2012 were analyzed. Twenty-nine cases of CR-BSI were confirmed. Coagulase-negative staphylococci (CoNS) were the most frequently isolated microorganisms, including S. epidermidis as the most prevalent species (65.5%), followed by S. haemolyticus (10.3%), yeasts (10.3%), K. pneumoniae (6.9%), S. aureus (3.4%), and E. coli (3.4%). The sensitivity of the semi-quantitative and quantitative techniques was 72.7% and 59.3%, respectively, and specificity was 95.7% and 94.4%. The diagnosis of CR-BSIs based on PFGE analysis of similarity between strains isolated from catheter tips and blood cultures showed 82.6% sensitivity and 100% specificity. The semi-quantitative culture method showed higher

Can we trust intraoperative culture results in nonunions?

Science.gov (United States)

Palmer, Michael P; Altman, Daniel T; Altman, Gregory T; Sewecke, Jeffrey J; Ehrlich, Garth D; Hu, Fen Z; Nistico, Laura; Melton-Kreft, Rachel; Gause, Trent M; Costerton, John W

2014-07-01

To identify the presence of bacterial biofilms in nonunions comparing molecular techniques (multiplex polymerase chain reaction and mass spectrometry, fluorescent in situ hybridization) with routine intraoperative cultures. Thirty-four patients with nonunions were scheduled for surgery and enrolled in this ongoing prospective study. Intraoperative specimens were collected from removed implants, surrounding tissue membrane, and local soft tissue followed by standard culture analysis, Ibis's second generation molecular diagnostics (Ibis Biosystems), and bacterial 16S rRNA-based fluorescence in situ hybridization (FISH). Confocal microscopy was used to visualize the tissue specimens reacted with the FISH probes, which were chosen based on the Ibis analysis. Thirty-four patient encounters were analyzed. Eight were diagnosed as infected nonunions by positive intraoperative culture results. Ibis confirmed the presence of bacteria in all 8 samples. Ibis identified bacteria in a total of 30 of 34 encounters, and these data were confirmed by FISH. Twenty-two of 30 Ibis-positive samples were culture-negative. Four samples were negative by all methods of analysis. No samples were positive by culture, but negative by molecular techniques. Our preliminary data indicate that molecular diagnostics are more sensitive for identifying bacteria than cultures in cases of bony nonunion. This is likely because of the inability of cultures to detect biofilms and bacteria previously exposed to antibiotic therapy. Diagnostic Level I. See Instructions for Authors for a complete description of levels of evidence.

Independent technique of verifying high-dose rate (HDR) brachytherapy treatment plans

International Nuclear Information System (INIS)

Saw, Cheng B.; Korb, Leroy J.; Darnell, Brenda; Krishna, K. V.; Ulewicz, Dennis

1998-01-01

Purpose: An independent technique for verifying high-dose rate (HDR) brachytherapy treatment plans has been formulated and validated clinically. Methods and Materials: In HDR brachytherapy, dwell times at respective dwell positions are computed, using an optimization algorithm in a HDR treatment-planning system to deliver a specified dose to many target points simultaneously. Because of the variability of dwell times, concerns have been expressed regarding the ability of the algorithm to compute the correct dose. To address this concern, a commercially available low-dose rate (LDR) algorithm was used to compute the doses at defined distances, based on the dwell times obtained from the HDR treatment plans. The percent deviation between doses computed using the HDR and LDR algorithms were reviewed for HDR procedures performed over the last year. Results: In this retrospective study, the difference between computed doses using the HDR and LDR algorithms was found to be within 5% for about 80% of the HDR procedures. All of the reviewed procedures have dose differences of less than 10%. Conclusion: An independent technique for verifying HDR brachytherapy treatment plans has been validated based on clinical data. Provided both systems are available, this technique is universal in its applications and not limited to either a particular implant applicator, implant site, or implant type

Effects of transfer of embryos independently cultured in essential and sequential culture media on pregnancy rates in assisted reproduction cycles.

Science.gov (United States)

Geber, Selmo; Bossi, Renata; Guimarães, Fernando; Valle, Marcello; Sampaio, Marcos

2012-10-01

Several culture media are available to be used in ART. However it is uncertain whether embryos would preferably benefit from one type of medium or the association of different media. We performed this study to evaluate the impact of simultaneous transfer of embryos independently cultured in two distinct culture media, on pregnancy outcome. A total of 722 couples who underwent infertility treatment were sequentially allocated into three groups: those who had half of the embryos individually cultured in MEM and the other half cultured in sequential media (MEM + Seq Group) (n = 243); those who had all embryos cultured only in sequential medium (Seq Group) (n = 239); and those who had all embryos cultured only in MEM (MEM Group) (n = 240). The pregnancy rate was higher in the MEM + Seq group (51.8 %) than the Seq group (36.7 %) (p < 0.001). However the pregnancy rate observed in the MEM group was similar to the others (44.2 %). When a logistic regression test was applied it demonstrated that the number of transferred embryos did not interfere in the pregnancy rates. Our results suggests that offering different culture conditions for sibling embryos with subsequent transfer of embryos that were kept in distinct culture media, might increase pregnancy rates in assisted reproduction cycles.

Analytical techniques applied to study cultural heritage objects

Energy Technology Data Exchange (ETDEWEB)

Rizzutto, M.A.; Curado, J.F.; Bernardes, S.; Campos, P.H.O.V.; Kajiya, E.A.M.; Silva, T.F.; Rodrigues, C.L.; Moro, M.; Tabacniks, M.; Added, N., E-mail: rizzutto@if.usp.br [Universidade de Sao Paulo (USP), SP (Brazil). Instituto de Fisica

2015-07-01

The scientific study of artistic and cultural heritage objects have been routinely performed in Europe and the United States for decades. In Brazil this research area is growing, mainly through the use of physical and chemical characterization methods. Since 2003 the Group of Applied Physics with Particle Accelerators of the Physics Institute of the University of Sao Paulo (GFAA-IF) has been working with various methodologies for material characterization and analysis of cultural objects. Initially using ion beam analysis performed with Particle Induced X-Ray Emission (PIXE), Rutherford Backscattering (RBS) and recently Ion Beam Induced Luminescence (IBIL), for the determination of the elements and chemical compounds in the surface layers. These techniques are widely used in the Laboratory of Materials Analysis with Ion Beams (LAMFI-USP). Recently, the GFAA expanded the studies to other possibilities of analysis enabled by imaging techniques that coupled with elemental and compositional characterization provide a better understanding on the materials and techniques used in the creative process in the manufacture of objects. The imaging analysis, mainly used to examine and document artistic and cultural heritage objects, are performed through images with visible light, infrared reflectography (IR), fluorescence with ultraviolet radiation (UV), tangential light and digital radiography. Expanding more the possibilities of analysis, new capabilities were added using portable equipment such as Energy Dispersive X-Ray Fluorescence (ED-XRF) and Raman Spectroscopy that can be used for analysis 'in situ' at the museums. The results of these analyzes are providing valuable information on the manufacturing process and have provided new information on objects of different University of Sao Paulo museums. Improving the arsenal of cultural heritage analysis it was recently constructed an 3D robotic stage for the precise positioning of samples in the external beam setup

Analytical techniques applied to study cultural heritage objects

International Nuclear Information System (INIS)

Rizzutto, M.A.; Curado, J.F.; Bernardes, S.; Campos, P.H.O.V.; Kajiya, E.A.M.; Silva, T.F.; Rodrigues, C.L.; Moro, M.; Tabacniks, M.; Added, N.

2015-01-01

The scientific study of artistic and cultural heritage objects have been routinely performed in Europe and the United States for decades. In Brazil this research area is growing, mainly through the use of physical and chemical characterization methods. Since 2003 the Group of Applied Physics with Particle Accelerators of the Physics Institute of the University of Sao Paulo (GFAA-IF) has been working with various methodologies for material characterization and analysis of cultural objects. Initially using ion beam analysis performed with Particle Induced X-Ray Emission (PIXE), Rutherford Backscattering (RBS) and recently Ion Beam Induced Luminescence (IBIL), for the determination of the elements and chemical compounds in the surface layers. These techniques are widely used in the Laboratory of Materials Analysis with Ion Beams (LAMFI-USP). Recently, the GFAA expanded the studies to other possibilities of analysis enabled by imaging techniques that coupled with elemental and compositional characterization provide a better understanding on the materials and techniques used in the creative process in the manufacture of objects. The imaging analysis, mainly used to examine and document artistic and cultural heritage objects, are performed through images with visible light, infrared reflectography (IR), fluorescence with ultraviolet radiation (UV), tangential light and digital radiography. Expanding more the possibilities of analysis, new capabilities were added using portable equipment such as Energy Dispersive X-Ray Fluorescence (ED-XRF) and Raman Spectroscopy that can be used for analysis 'in situ' at the museums. The results of these analyzes are providing valuable information on the manufacturing process and have provided new information on objects of different University of Sao Paulo museums. Improving the arsenal of cultural heritage analysis it was recently constructed an 3D robotic stage for the precise positioning of samples in the external beam setup

Culture and Healthy Eating: The Role of Independence and Interdependence in the United States and Japan.

Science.gov (United States)

Levine, Cynthia S; Miyamoto, Yuri; Markus, Hazel Rose; Rigotti, Attilio; Boylan, Jennifer Morozink; Park, Jiyoung; Kitayama, Shinobu; Karasawa, Mayumi; Kawakami, Norito; Coe, Christopher L; Love, Gayle D; Ryff, Carol D

2016-10-01

Healthy eating is important for physical health. Using large probability samples of middle-aged adults in the United States and Japan, we show that fitting with the culturally normative way of being predicts healthy eating. In the United States, a culture that prioritizes and emphasizes independence, being independent predicts eating a healthy diet (an index of fish, protein, fruit, vegetables, reverse-coded sugared beverages, and reverse-coded high fat meat consumption; Study 1) and not using nonmeat food as a way to cope with stress (Study 2a). In Japan, a culture that prioritizes and emphasizes interdependence, being interdependent predicts eating a healthy diet (Studies 1 and 2b). Furthermore, reflecting the types of agency that are prevalent in each context, these relationships are mediated by autonomy in the United States and positive relations with others in Japan. These findings highlight the importance of understanding cultural differences in shaping healthy behavior and have implications for designing health-promoting interventions. © 2016 by the Society for Personality and Social Psychology, Inc.

CATEGORICAL IMAGE COMPONENTS IN THE FORMING SYSTEM OF A MARKETING TECHNIQUES MANAGER’S IMAGE CULTURE

Directory of Open Access Journals (Sweden)

Anna Borisovna Cherednyakova

2015-08-01

Full Text Available Based on the understanding of the image culture formation of managers of marketing techniques, as a representative of the social and communication interaction of public structures, categorical apparatus of image culture with an emphasis on the etymology of the image, as an integral component of image culture was analyzed. Categorical components of the image are presented from the standpoint of image culture, as personal new formation, an integral part of the professional activity of the marketing techniques manager: object-communicative categorical component, subject-activity categorical component of image, personality-oriented categorical component, value-acmeological categorical component of image.The aim is to identify and justify the image categorical components as a component of image culture of the marketing techniques manager.Method and methodology of work – a general scientific research approach reflecting scientific apparatus of research.Results. Categorical components of the image, as an image culture component of manager of marketing techniques were defined.Practical implication of the results. The theoretical part of «Imageology» course, special course «Image culture of manager of marketing techniques», the theoretical and methodological study and the formation of image culture.

Combined neutron imaging techniques for cultural heritage purpose

International Nuclear Information System (INIS)

Materna, T.

2009-01-01

This article presents the different new neutron techniques developed by the Ancient Charm collaboration to image objects of cultural heritage importance: Prompt-gamma-ray activation imaging (PGAI) coupled to cold/thermal neutron transmission tomography, Neutron Resonance Capture Imaging (NRCI) and Neutron Resonance Tomography.

The diagnosis of chronic endometritis in infertile asymptomatic women: a comparative study of histology, microbial cultures, hysteroscopy, and molecular microbiology.

Science.gov (United States)

Moreno, Inmaculada; Cicinelli, Ettore; Garcia-Grau, Iolanda; Gonzalez-Monfort, Marta; Bau, Davide; Vilella, Felipe; De Ziegler, Dominique; Resta, Leonardo; Valbuena, Diana; Simon, Carlos

2018-06-01

Chronic endometritis is a persistent inflammation of the endometrial mucosa caused by bacterial pathogens such as Enterobacteriaceae, Enterococcus, Streptococcus, Staphylococcus, Mycoplasma, and Ureaplasma. Although chronic endometritis can be asymptomatic, it is found in up to 40% of infertile patients and is responsible for repeated implantation failure and recurrent miscarriage. Diagnosis of chronic endometritis is based on hysteroscopy of the uterine cavity, endometrial biopsy with plasma cells being identified histologically, while specific treatment is determined based on microbial culture. However, not all microorganisms implicated are easily or readily culturable needing a turnaround time of up to 1 week. We sought to develop a molecular diagnostic tool for chronic endometritis based on real-time polymerase chain reaction equivalent to using the 3 classic methods together, overcoming the bias of using any of them alone. Endometrial samples from patients assessed for chronic endometritis (n = 113) using at least 1 or several conventional diagnostic methods namely histology, hysteroscopy, and/or microbial culture, were blindly evaluated by real-time polymerase chain reaction for the presence of 9 chronic endometritis pathogens: Chlamydia trachomatis, Enterococcus, Escherichia coli, Gardnerella vaginalis, Klebsiella pneumoniae, Mycoplasma hominis, Neisseria gonorrhoeae, Staphylococcus, and Streptococcus. The sensitivity and specificity of the molecular analysis vs the classic diagnostic techniques were compared in the 65 patients assessed by all 3 recognized classic methods. The molecular method showed concordant results with histological diagnosis in 30 samples (14 double positive and 16 double negative) with a matching accuracy of 46.15%. Concordance of molecular and hysteroscopic diagnosis was observed in 38 samples (37 double positive and 1 double negative), with an accuracy of 58.46%. When the molecular method was compared to microbial culture

Efficacy of the FilmArray blood culture identification panel for direct molecular diagnosis of infectious diseases from samples other than blood.

Science.gov (United States)

Micó, Miquel; Navarro, Ferran; de Miniac, Daniela; González, Yésica; Brell, Albert; López, Cristina; Sánchez-Reus, Ferran; Mirelis, Beatriz; Coll, Pere

2015-12-01

Molecular-based techniques reduce the delay in diagnosing infectious diseases and therefore contribute to better patient outcomes. We assessed the FilmArray blood culture identification (BCID) panel (Biofire Diagnostics/bioMérieux) directly on clinical specimens other than blood: cerebrospinal, joint, pleural and ascitic fluids, bronchoscopy samples and abscesses. We compared the results from 88 samples obtained by culture-based techniques. The percentage of agreement between the two methods was 75 % with a Cohen κ value of 0.51. Global sensitivity and specificity using the FilmArray BCID panel were 71 and 97 %, respectively. Sensitivity was poorer in samples with a low bacterial load, such as ascitic and pleural fluids (25 %), whereas the sensitivity for abscess samples was high (89 %). These findings suggest that the FilmArray BCID panel could be useful to perform microbiological diagnosis directly from samples other than positive blood cultures, as it offers acceptable sensitivity and moderate agreement with conventional microbiological methods. Nevertheless, cost-benefit studies should be performed before introducing this method into algorithms for microbiological diagnostics.

The influence of organizational culture on the use of quality techniques and its impact on performance

DEFF Research Database (Denmark)

Gambi, Lillian; Jørgensen, Frances; Boer, Harry

2013-01-01

This report presents the results of a study about the influence of organizational culture on quality techniques and the impact of matching culture and technique to enhance performance. Data were drawn from 250 manufacturing companies in Brazil and Denmark. Profiles were identified according....... 2- Quality techniques contribute to improve performance, provided they are supported by appropriate cultural characteristics. For instance, the use of goal setting, continuous improvement, and failure prevention and control techniques supported by group and developmental cultures contribute...

Microbial ecology of the skin in the era of metagenomics and molecular microbiology.

Science.gov (United States)

Hannigan, Geoffrey D; Grice, Elizabeth A

2013-12-01

The skin is the primary physical barrier between the body and the external environment and is also a substrate for the colonization of numerous microbes. Previously, dermatological microbiology research was dominated by culture-based techniques, but significant advances in genomic technologies have enabled the development of less-biased, culture-independent approaches to characterize skin microbial communities. These molecular microbiology approaches illustrate the great diversity of microbiota colonizing the skin and highlight unique features such as site specificity, temporal dynamics, and interpersonal variation. Disruptions in skin commensal microbiota are associated with the progression of many dermatological diseases. A greater understanding of how skin microbes interact with each other and with their host, and how we can therapeutically manipulate those interactions, will provide powerful tools for treating and preventing dermatological disease.

Definition and dynamic control of a continuous chromatography process independent of cell culture titer and impurities.

Science.gov (United States)

Chmielowski, Rebecca A; Mathiasson, Linda; Blom, Hans; Go, Daniel; Ehring, Hanno; Khan, Heera; Li, Hong; Cutler, Collette; Lacki, Karol; Tugcu, Nihal; Roush, David

2017-12-01

Advances in cell culture technology have enabled the production of antibody titers upwards of 30g/L. These highly productive cell culture systems can potentially lead to productivity bottlenecks in downstream purification due to lower column loadings, especially in the primary capture chromatography step. Alternative chromatography solutions to help remedy this bottleneck include the utilization of continuous processing systems such as periodic counter-current chromatography (PCC). Recent studies have provided methods to optimize and improve the design of PCC for cell culture titers up to about 3g/L. This paper defines a continuous loading strategy for PCC that is independent of cell culture background and encompasses cell culture titers up to about 31g/L. Initial experimentation showed a challenge with determining a difference in change in UV280nm signal (ie. ΔUV) between cell culture feed and monoclonal antibody (mAb) concentration. Further investigation revealed UV280nm absorbance of the cell culture feedstock without antibody was outside of the linear range of detection for a given cell pathlength. Additional experimentation showed the difference in ΔUV for various cell culture feeds can be either theoretically predicted by Beer's Law given a known absorbance of the media background and impurities or experimentally determined using various UV280nm cell pathlengths. Based on these results, a 0.35mm pathlength at UV280nm was chosen for dynamic control to overcome the background signal. The pore diffusion model showed good agreement with the experimental frontal analysis data, which resulted in definition of a ΔUV setpoint range between 20 and 70% for 3C-PCC experiments. Product quality of the elution pools was acceptable between various cell culture feeds and titers up to about 41g/L. Results indicated the following ΔUV setpoints to achieve robust dynamic control and maintain 3C-PCC yield: ∼20-45% for titers greater than 10g/L depending on UV absorbance of

Serotonin regulates C. elegans fat and feeding through independent molecular mechanisms

DEFF Research Database (Denmark)

Srinivasan, Supriya; Sadegh, Leila; Elle, Ida C

2008-01-01

We investigated serotonin signaling in C. elegans as a paradigm for neural regulation of energy balance and found that serotonergic regulation of fat is molecularly distinct from feeding regulation. Serotonergic feeding regulation is mediated by receptors whose functions are not required for fat...... feeding behavior. These findings suggest that, as in mammals, C. elegans feeding behavior is regulated by extrinsic and intrinsic cues. Moreover, obesity and thinness are not solely determined by feeding behavior. Rather, feeding behavior and fat metabolism are coordinated but independent responses...

Sponge cell culture? A molecular identification method for sponge cells

NARCIS (Netherlands)

Sipkema, D.; Heilig, G.H.J.; Akkermans, A.D.L.; Osinga, R.; Tramper, J.; Wijffels, R.H.

2003-01-01

Dissociated sponge cells are easily confused with unicellular organisms. This has been an obstacle in the development of sponge-cell lines. We developed a molecular detection method to identify cells of the sponge Dysidea avara in dissociated cell cultures. The 18S ribosomal RNA gene from a Dysidea

Introducing Mammalian Cell Culture and Cell Viability Techniques in the Undergraduate Biology Laboratory.

Science.gov (United States)

Bowey-Dellinger, Kristen; Dixon, Luke; Ackerman, Kristin; Vigueira, Cynthia; Suh, Yewseok K; Lyda, Todd; Sapp, Kelli; Grider, Michael; Crater, Dinene; Russell, Travis; Elias, Michael; Coffield, V McNeil; Segarra, Verónica A

2017-01-01

Undergraduate students learn about mammalian cell culture applications in introductory biology courses. However, laboratory modules are rarely designed to provide hands-on experience with mammalian cells or teach cell culture techniques, such as trypsinization and cell counting. Students are more likely to learn about cell culture using bacteria or yeast, as they are typically easier to grow, culture, and manipulate given the equipment, tools, and environment of most undergraduate biology laboratories. In contrast, the utilization of mammalian cells requires a dedicated biological safety cabinet and rigorous antiseptic techniques. For this reason, we have devised a laboratory module and method herein that familiarizes students with common cell culture procedures, without the use of a sterile hood or large cell culture facility. Students design and perform a time-efficient inquiry-based cell viability experiment using HeLa cells and tools that are readily available in an undergraduate biology laboratory. Students will become familiar with common techniques such as trypsinizing cells, cell counting with a hemocytometer, performing serial dilutions, and determining cell viability using trypan blue dye. Additionally, students will work with graphing software to analyze their data and think critically about the mechanism of death on a cellular level. Two different adaptations of this inquiry-based lab are presented-one for non-biology majors and one for biology majors. Overall, these laboratories aim to expose students to mammalian cell culture and basic techniques and help them to conceptualize their application in scientific research.

Mixed-culture transcriptome analysis reveals the molecular basis of mixed-culture growth in Streptococcus thermophilus and Lactobacillus bulgaricus.

Science.gov (United States)

Sieuwerts, Sander; Molenaar, Douwe; van Hijum, Sacha A F T; Beerthuyzen, Marke; Stevens, Marc J A; Janssen, Patrick W M; Ingham, Colin J; de Bok, Frank A M; de Vos, Willem M; van Hylckama Vlieg, Johan E T

2010-12-01

Many food fermentations are performed using mixed cultures of lactic acid bacteria. Interactions between strains are of key importance for the performance of these fermentations. Yogurt fermentation by Streptococcus thermophilus and Lactobacillus bulgaricus (basonym, Lactobacillus delbrueckii subsp. bulgaricus) is one of the best-described mixed-culture fermentations. These species are believed to stimulate each other's growth by the exchange of metabolites such as folic acid and carbon dioxide. Recently, postgenomic studies revealed that an upregulation of biosynthesis pathways for nucleotides and sulfur-containing amino acids is part of the global physiological response to mixed-culture growth in S. thermophilus, but an in-depth molecular analysis of mixed-culture growth of both strains remains to be established. We report here the application of mixed-culture transcriptome profiling and a systematic analysis of the effect of interaction-related compounds on growth, which allowed us to unravel the molecular responses associated with batch mixed-culture growth in milk of S. thermophilus CNRZ1066 and L. bulgaricus ATCC BAA-365. The results indicate that interactions between these bacteria are primarily related to purine, amino acid, and long-chain fatty acid metabolism. The results support a model in which formic acid, folic acid, and fatty acids are provided by S. thermophilus. Proteolysis by L. bulgaricus supplies both strains with amino acids but is insufficient to meet the biosynthetic demands for sulfur and branched-chain amino acids, as becomes clear from the upregulation of genes associated with these amino acids in mixed culture. Moreover, genes involved in iron uptake in S. thermophilus are affected by mixed-culture growth, and genes coding for exopolysaccharide production were upregulated in both organisms in mixed culture compared to monocultures. The confirmation of previously identified responses in S. thermophilus using a different strain combination

Improvement of Leukemia diagnose with molecular techniques; Mejoran diagnostico de leucemias con tecnicas moleculares

Energy Technology Data Exchange (ETDEWEB)

Campos Rudin, M E

1997-07-01

The objective of this study was to contribute with new techniques to the clinical diagnosis and to the monitoring of mycloid chronic leukemias in Costa Rica. The same one achieved to determine that is viable to apply radioactive and non reactive methodologies, for the molecular detection of the Philadelphia chromosome.It also found that the application of techniques of cellular biology, helps to classify better the mycloide leukemias and the chronic mycloproliferatives and miclodisplaced disorders. (S. Grainger) [Spanish] El objetivode este estudio fue el de aportar nuevas tecnicas al diagnostico clinico y monitoreo de las leucemias micloides cronicas en Costa Rica. El mismo logro determinar que es viable aplicar metodologias radioactivas y no radioactivas, para la deteccion molecular del cromosoma Filadelfia. Tambien encontro que la aplicacion de tecnicas de biologia celular, ayudan a clasificar mejor las leucemias mieloides y los desordenes cronicos micloproliferativos y myclodisplacicos. (S. Grainger)

Culture- and molecular-based detection of swine-adapted Salmonella shed by avian scavengers.

Science.gov (United States)

Blanco, Guillermo; Díaz de Tuesta, Juan A

2018-04-13

Salmonella can play an important role as a disease agent in wildlife, which can then act as carriers and reservoirs of sanitary importance at the livestock-human interface. Transmission from livestock to avian scavengers can occur when these species consume contaminated carcasses and meat remains in supplementary feeding stations and rubbish dumps. We compared the performance of PCR-based detection with conventional culture-based methods to detect Salmonella in the faeces of red kites (Milvus milvus) and griffon vultures (Gyps fulvus) in central Spain. The occurrence of culturable Salmonella was intermediate in red kites (1.9%, n=52) and high in griffon vultures (26.3%, n=99). These proportions were clearly higher with PCR-based detection (13.5% and 40.4%, respectively). Confirmation cultures failed to grow Salmonella in all faecal samples positive by the molecular assay but negative by the initial conventional culture in both scavenger species, indicating the occurrence of false (non-culturable) positives by PCR-based detection. This suggests that the molecular assay is highly sensitive to detecting viable Salmonella in cultures, but also partial genomes and dead or unviable bacteria from past infections or contamination. Thus, the actual occurrence of Salmonella in a particular sampling time period can be underestimated when using only culture detection. The serovars found in the scavenger faeces were among the most frequently isolated in pigs from Spain and other EU countries, especially those generally recognized as swine-adapted monophasic variants of S. Typhimurium. Because the studied species obtain much of their food from pig carcasses, this livestock may be the primary source of Salmonella via direct ingestion of infected carcasses and indirectly via contamination due to the unsanitary conditions found in supplementary feeding stations established for scavenger conservation. Combining culture- and molecular-based detection is encouraged to understand the

[Etiologic diagnosis in meningitis and encephalitis molecular biology techniques].

Science.gov (United States)

Conca, Natalia; Santolaya, María Elena; Farfan, Mauricio J; Cofré, Fernanda; Vergara, Alejandra; Salazar, Liliana; Torres, Juan Pablo

2016-01-01

The aetiological study of infections of the central nervous system has traditionally been performed using bacterial cultures and, more recently, using polymerase chain reaction (PCR) for herpes simplex virus (HSV). Bacterial cultures may not have good performance, especially in the context of patients who have received antibiotics prior to sampling, and a request for HSV only by PCR reduces the information to only one aetiological agent. The aim of this study is to determine the infectious causes of meningitis and encephalitis, using traditional microbiology and molecular biology to improve the aetiological diagnosis of these diseases. A prospective study was conducted on 19 patients with suspected meningitis, admitted to the Luis Calvo Mackenna Hospital in Santiago, Chile, from March 1, 2011 to March 30, 2012. After obtaining informed consent, the CSF samples underwent cytochemical study, conventional culture, multiplex PCR for the major producing bacterial meningitis (N. meningitidis, S. pneumoniae, H. influenzae), real-time single PCR for HSV-1 and 2, VZV, EBV, CMV, HHV-6 and enterovirus. Clinical and epidemiological data were also collected from the clinical records. Of the 19 patients analysed, 2 were diagnosed by conventional methods and 7 by adding molecular biology (increase to 37%). Three patients had meningitis due to S. pneumoniae, one due to Enterobacter cloacae, 2 patients meningoencephalitis HSV-1, and one VZV meningitis. The addition of PCR to conventional diagnostic methods in CNS infections increases the probability of finding the causal agent. This allows a more adequate, timely and rational management of the disease. Copyright © 2014. Publicado por Elsevier España, S.L.U.

Microbial community composition of the ileum and cecum of broiler chickens as revealed by molecular and culture-based techniques

DEFF Research Database (Denmark)

Friis-Holm, Lotte Bjerrum; Engberg, R.M.; Leser, T.D.

2006-01-01

The microbial communities of the ileum and cecum of broiler chickens from a conventional and an organic farm were investigated using conventional culture techniques as well as cloning and sequencing of 16S rRNA genes. Eighty-five percent of the 557 cloned sequences were ...% of the cecal clones belonged to this cluster in conventional and organic broiler chickens, respectively. We were, however, able to recover a number of these phylotypes by cultivation, and the isolates were shown to be butyric acid producers. The investigation was a descriptive rather than a comparative study...

Effect of postmortem sampling technique on the clinical significance of autopsy blood cultures.

Science.gov (United States)

Hove, M; Pencil, S D

1998-02-01

Our objective was to investigate the value of postmortem autopsy blood cultures performed with an iodine-subclavian technique relative to the classical method of atrial heat searing and antemortem blood cultures. The study consisted of a prospective autopsy series with each case serving as its own control relative to subsequent testing, and a retrospective survey of patients coming to autopsy who had both autopsy blood cultures and premortem blood cultures. A busy academic autopsy service (600 cases per year) at University of Texas Medical Branch Hospitals, Galveston, Texas, served as the setting for this work. The incidence of non-clinically relevant (false-positive) culture results were compared using different methods for collecting blood samples in a prospective series of 38 adult autopsy specimens. One hundred eleven adult autopsy specimens in which both postmortem and antemortem blood cultures were obtained were studied retrospectively. For both studies, positive culture results were scored as either clinically relevant or false positives based on analysis of the autopsy findings and the clinical summary. The rate of false-positive culture results obtained by an iodine-subclavian technique from blood drawn soon after death were statistically significantly lower (13%) than using the classical method of obtaining blood through the atrium after heat searing at the time of the autopsy (34%) in the same set of autopsy subjects. When autopsy results were compared with subjects' antemortem blood culture results, there was no significant difference in the rate of non-clinically relevant culture results in a paired retrospective series of antemortem blood cultures and postmortem blood cultures using the iodine-subclavian postmortem method (11.7% v 13.5%). The results indicate that autopsy blood cultures obtained using the iodine-subclavian technique have reliability equivalent to that of antemortem blood cultures.

Identifying the bacterial community on the surface of Intralox belting in a meat boning room by culture-dependent and culture-independent 16S rDNA sequence analysis.

Science.gov (United States)

Brightwell, Gale; Boerema, Jackie; Mills, John; Mowat, Eilidh; Pulford, David

2006-05-25

We examined the bacterial community present on an Intralox conveyor belt system in an operating lamb boning room by sequencing the 16S ribosomal DNA (rDNA) of bacteria extracted in the presence or absence of cultivation. RFLP patterns for 16S rDNA clone library and cultures were generated using HaeIII and MspI restriction endonucleases. 16S rDNA amplicons produced 8 distinct RFLP pattern groups. RFLP groups I-IV were represented in the clone library and RFLP groups I and V-VIII were represented amongst the cultured isolates. Partial DNA sequences from each RFLP group revealed that all group I, II and VIII representatives were Pseudomonas spp., group III were Sphingomonas spp., group IV clones were most similar to an uncultured alpha proteobacterium, group V was similar to a Serratia spp., group VI with an Alcaligenes spp., and group VII with Microbacterium spp. Sphingomonads were numerically dominant in the culture-independent clone library and along with the group IV alpha proteobacterium were not represented amongst the cultured isolates. Serratia, Alcaligenes and Microbacterium spp. were only represented with cultured isolates. Pseudomonads were detected by both culture-dependent (84% of isolates) and culture-independent (12.5% of clones) methods and their presence at high frequency does pose the risk of product spoilage if transferred onto meat stored under aerobic conditions. The detection of sphingomonads in large numbers by the culture-independent method demands further analysis because sphingomonads may represent a new source of meat spoilage that has not been previously recognised in the meat processing environment. The 16S rDNA collections generated by both methods were important at representing the diversity of the bacterial population associated with an Intralox conveyor belt system.

Molecular biology - Part I: Techniques, terminology, and concepts

International Nuclear Information System (INIS)

Brown, J. Martin

1996-01-01

Purpose/Objective: One of the barriers to understanding modern molecular biology is the lack of a clear understanding of the relevant terminology, techniques, and concepts. This refresher course is intended to address these deficiencies starting from a basic level. The lecture will cover many of the common uses of recombinant DNA, including gene cloning and manipulation. The goal is to enable the nonspecialist to increase his or her understanding of molecular biology in order to more fully enjoy reading current publications and/or listening seminars. Radiation biologists trying to understand a little more molecular biology should also benefit. The following concepts will be among those explained and illustrated: restriction endonucleases, gel electrophoresis, gene cloning, use of vectors such as plasmids, bacteriophage, cosmids and viruses, cDNA and genomic libraries, Southern, Northern, and Western blotting, fluorescent in situ hybridization, polymerase chain reaction (PCR), gel retardation, and reporter gene assays

Molecular techniques for MRSA typing: current issues and perspectives

Directory of Open Access Journals (Sweden)

P. A. Trindade

Full Text Available Staphylococcus aureus has long been recognised as an important pathogen in human disease. Serious staphylococcal infections can frequently occur in inpatients and may lead to dire consequences, especially as to therapy with antimicrobial agents. The increase in the frequency of Methicillin-Resistant Staphylococcus aureus (MRSA as the causal agent of nosocomial infection and the possibility of emergence of resistance to vancomycin demands a quick and trustworthy characterization of isolates and identification of clonal spread within hospitals. Enough information must be generated to permit the implementation of appropriate measures for control of infection, so that outbreaks can be contained. Molecular typing techniques reviewed in this manuscript include: plasmid profile analysis, analysis of chromosomal DNA after enzymatic restriction, Southern blotting, pulsed field gel electrophoresis (PFGE, techniques involving polymerase chain reaction and multilocus sequence typing (MLST. Repetitive DNA Sequence PCR (rep-PCR may be used for screening due to its practicality, low cost and reproducibility. Because of its high discriminatory power Pulsed-Field Gel Electrophoresis (PFGE still remains the gold standard for MRSA typing. New techniques with higher reproducibility and discriminatory power, such as Multi-Locus Sequence Typing (MLST, are appearing. These are mostly useful for global epidemiology studies. Molecular typing techniques are invaluable tools for the assessment of putative MRSA outbreaks and so should be extensively used for this purpose.

Molecular techniques for MRSA typing: current issues and perspectives

Directory of Open Access Journals (Sweden)

Trindade P. A.

2003-01-01

Full Text Available Staphylococcus aureus has long been recognised as an important pathogen in human disease. Serious staphylococcal infections can frequently occur in inpatients and may lead to dire consequences, especially as to therapy with antimicrobial agents. The increase in the frequency of Methicillin-Resistant Staphylococcus aureus (MRSA as the causal agent of nosocomial infection and the possibility of emergence of resistance to vancomycin demands a quick and trustworthy characterization of isolates and identification of clonal spread within hospitals. Enough information must be generated to permit the implementation of appropriate measures for control of infection, so that outbreaks can be contained. Molecular typing techniques reviewed in this manuscript include: plasmid profile analysis, analysis of chromosomal DNA after enzymatic restriction, Southern blotting, pulsed field gel electrophoresis (PFGE, techniques involving polymerase chain reaction and multilocus sequence typing (MLST. Repetitive DNA Sequence PCR (rep-PCR may be used for screening due to its practicality, low cost and reproducibility. Because of its high discriminatory power Pulsed-Field Gel Electrophoresis (PFGE still remains the gold standard for MRSA typing. New techniques with higher reproducibility and discriminatory power, such as Multi-Locus Sequence Typing (MLST, are appearing. These are mostly useful for global epidemiology studies. Molecular typing techniques are invaluable tools for the assessment of putative MRSA outbreaks and so should be extensively used for this purpose.

Salesperson Self-Regulation of Pride: Effects on Adaptability, Effort, and Citizenship Behaviors between Independent-Based and Interdependent-Based Cultures

NARCIS (Netherlands)

Bagozzi, R.P.; Belschak, F.; Verbeke, W.; Gavino, J.R.

2016-01-01

We investigate and compare how salespersons within an independent-based culture (the Netherlands) and an interdependent-based culture (the Philippines) experience and self-regulate pride that is evoked through praise and recognition by their managers. This self-regulation differentially influences

Comparison of Standard Culture-Based Method to Culture-Independent Method for Evaluation of Hygiene Effects on the Hand Microbiome

Science.gov (United States)

Leff, J.; Henley, J.; Tittl, J.; De Nardo, E.; Butler, M.; Griggs, R.; Fierer, N.

2017-01-01

ABSTRACT Hands play a critical role in the transmission of microbiota on one’s own body, between individuals, and on environmental surfaces. Effectively measuring the composition of the hand microbiome is important to hand hygiene science, which has implications for human health. Hand hygiene products are evaluated using standard culture-based methods, but standard test methods for culture-independent microbiome characterization are lacking. We sampled the hands of 50 participants using swab-based and glove-based methods prior to and following four hand hygiene treatments (using a nonantimicrobial hand wash, alcohol-based hand sanitizer [ABHS], a 70% ethanol solution, or tap water). We compared results among culture plate counts, 16S rRNA gene sequencing of DNA extracted directly from hands, and sequencing of DNA extracted from culture plates. Glove-based sampling yielded higher numbers of unique operational taxonomic units (OTUs) but had less diversity in bacterial community composition than swab-based sampling. We detected treatment-induced changes in diversity only by using swab-based samples (P hand hygiene industry methods and for future hand microbiome studies. On the basis of our results and previously published studies, we propose recommendations for best practices in hand microbiome research. PMID:28351915

Are Independent Probes Truly Independent?

Science.gov (United States)

Camp, Gino; Pecher, Diane; Schmidt, Henk G.; Zeelenberg, Rene

2009-01-01

The independent cue technique has been developed to test traditional interference theories against inhibition theories of forgetting. In the present study, the authors tested the critical criterion for the independence of independent cues: Studied cues not presented during test (and unrelated to test cues) should not contribute to the retrieval…

Direct Detection and Identification of Enteroviruses from Faeces of Healthy Nigerian Children Using a Cell-Culture Independent RT-Seminested PCR Assay

Directory of Open Access Journals (Sweden)

Temitope Oluwasegun Cephas Faleye

2016-01-01

Full Text Available Recently, a cell-culture independent protocol for detection of enteroviruses from clinical specimen was recommended by the WHO for surveillance alongside the previously established protocols. Here, we investigated whether this new protocol will show the same enterovirus diversity landscape as the established cell-culture dependent protocols. Faecal samples were collected from sixty apparently healthy children in Ibadan, Nigeria. Samples were resuspended in phosphate buffered saline, RNA was extracted, and the VP1 gene was amplified using WHO recommended RT-snPCR protocol. Amplicons were sequenced and sequences subjected to phylogenetic analysis. Fifteen (25% of the 60 samples yielded the expected band size. Of the 15 amplicons sequenced, 12 were exploitable. The remaining 3 had electropherograms with multiple peaks and were unexploitable. Eleven of the 12 exploitable sequences were identified as Coxsackievirus A1 (CVA1, CVA3, CVA4, CVA8, CVA20, echovirus 32 (E32, enterovirus 71 (EV71, EVB80, and EVC99. Subsequently, the last exploitable sequence was identified as enterobacteriophage baseplate gene by nucleotide BLAST. The results of this study document the first description of molecular sequence data on CVA1, CVA8, and E32 strains present in Nigeria. The result further showed that species A enteroviruses were more commonly detected in the region when cell-culture bias is bypassed.

Culture-independent analysis of aerosol microbiology in a metropolitan subway system.

Science.gov (United States)

Robertson, Charles E; Baumgartner, Laura K; Harris, J Kirk; Peterson, Kristen L; Stevens, Mark J; Frank, Daniel N; Pace, Norman R

2013-06-01

The goal of this study was to determine the composition and diversity of microorganisms associated with bioaerosols in a heavily trafficked metropolitan subway environment. We collected bioaerosols by fluid impingement on several New York City subway platforms and associated sites in three sampling sessions over a 1.5-year period. The types and quantities of aerosolized microorganisms were determined by culture-independent phylogenetic analysis of small-subunit rRNA gene sequences by using both Sanger (universal) and pyrosequencing (bacterial) technologies. Overall, the subway bacterial composition was relatively simple; only 26 taxonomic families made up ~75% of the sequences determined. The microbiology was more or less similar throughout the system and with time and was most similar to outdoor air, consistent with highly efficient air mixing in the system. Identifiable bacterial sequences indicated that the subway aerosol assemblage was composed of a mixture of genera and species characteristic of soil, environmental water, and human skin commensal bacteria. Eukaryotic diversity was mainly fungal, dominated by organisms of types associated with wood rot. Human skin bacterial species (at 99% rRNA sequence identity) included the Staphylococcus spp. Staphylococcus epidermidis (the most abundant and prevalent commensal of the human integument), S. hominis, S. cohnii, S. caprae, and S. haemolyticus, all well-documented human commensal bacteria. We encountered no organisms of public health concern. This study is the most extensive culture-independent survey of subway microbiota so far and puts in place pre-event information required for any bioterrorism surveillance activities or monitoring of the microbiological impact of recent subway flooding events.

Characterization of Unexplored Deadwood Mycobiome in Highly Diverse Subtropical Forests Using Culture-independent Molecular Technique.

Science.gov (United States)

Purahong, Witoon; Pietsch, Katherina A; Lentendu, Guillaume; Schöps, Ricardo; Bruelheide, Helge; Wirth, Christian; Buscot, François; Wubet, Tesfaye

2017-01-01

The deadwood mycobiome, also known as wood-inhabiting fungi (WIF), are among the key players in wood decomposition, having a large impact on nutrient cycling in forest soils. However, our knowledge of WIF richness and distribution patterns in different forest biomes is limited. Here, we used pyrotag sequencing of the fungal internal transcribed spacer (ITS2) region to characterize the deadwood mycobiome of two tree species with greatly different wood characteristics ( Schima superba and Pinus massoniana ) in a Chinese subtropical forest ecosystem. Specifically, we tested (i) the effects of tree species and wood quality properties on WIF OTU richness and community composition; (ii) the role of biotic and abiotic factors in shaping the WIF communities; and (iii) the relationship between WIF OTU richness, community composition and decomposition rates. Due to different wood chemical properties, we hypothesized that the WIF communities derived from the two tree species would be correlated differently with biotic and abiotic factors. Our results show that deadwood in subtropical forests harbors diverse fungal communities comprising six ecological functional groups. We found interesting colonization patterns for this subtropical biome, where Resinicium spp. were highly detected in both broadleaved and coniferous deadwood. In addition, the members of Xylariales were frequently found in Schima . The two deadwood species differed significantly in WIF OTU richness ( Pinus > Schima ) and community composition ( P < 0.001). Variations in WIF community composition of both tree species were significantly explained by wood pH and ecological factors (biotic: deadwood species, basal area and abiotic: soil pH), but the WIF communities derived from each tree species correlated differently with abiotic factors. Interestingly, we found that deadwood decomposition rate significantly correlated with WIF communities and negatively correlated with WIF OTU richness. We conclude that the pattern of WIF OTU richness and community composition are controlled by multiple interacting biotic and abiotic factors. Overall, our study provides an in-depth picture of the deadwood mycobiome in this subtropical forest. Furthermore, by comparing our results to results from temperate and boreal forests we contribute to a better understanding of patterns of WIF communities across different biomes and geographic locations.

Evaluation of conventional castaneda and lysis centrifugation blood culture techniques for diagnosis of human brucellosis.

Science.gov (United States)

Mantur, Basappa G; Mangalgi, Smita S

2004-09-01

We investigated the role of the lysis centrifugation blood culture technique over the conventional Castaneda technique for the diagnosis of human brucellosis. The lysis centrifugation technique has been found to be more sensitive in both acute (20% higher sensitivity; P centrifugation was in the mean detection time, which was only 2.4 days in acute and 2.7 days in chronic cases, with 103 out of 110 (93.6%) and 17 out of 20 (85%) cultures from acute and chronic brucellosis, respectively, detected before the conventional culture was positive. Our results confirmed the potential usefulness of the lysis technique in diagnosis and institution of appropriate antibiotic therapy.

DNA-based culture-independent analysis detects the presence of group a streptococcus in throat samples from healthy adults in Japan.

Science.gov (United States)

Kulkarni, Tejaswini; Aikawa, Chihiro; Nozawa, Takashi; Murase, Kazunori; Maruyama, Fumito; Nakagawa, Ichiro

2016-10-11

Group A Streptococcus (GAS; Streptococcus pyogenes) causes a range of mild to severe infections in humans. It can also colonize healthy persons asymptomatically. Therefore, it is important to study GAS carriage in healthy populations, as carriage of it might lead to subsequent disease manifestation, clonal spread in the community, and/or diversification of the organism. Throat swab culture is the gold standard method for GAS detection. Advanced culture-independent methods provide rapid and efficient detection of microorganisms directly from clinical samples. We investigated the presence of GAS in throat swab samples from healthy adults in Japan using culture-dependent and culture-independent methods. Two throat swab samples were collected from 148 healthy volunteers. One was cultured on selective medium, while total DNA extracted from the other was polymerase chain reaction (PCR) amplified with two GAS-specific primer pairs: one was a newly designed 16S rRNA-specific primer pair, the other a previously described V-Na + -ATPase primer pair. Although only 5 (3.4 %) of the 148 samples were GAS-positive by the culture-dependent method, 146 (98.6 %) were positive for the presence of GAS DNA by the culture-independent method. To obtain serotype information by emm typing, we performed nested PCR using newly designed emm primers. We detected the four different emm types in 25 (16.9 %) samples, and these differed from the common emm types associated with GAS associated diseases in Japan. The different emm types detected in the healthy volunteers indicate that the presence of unique emm types might be associated with GAS carriage. Our results suggest that culture-independent methods should be considered for profiling GAS in the healthy hosts, with a view to obtaining better understanding of these organisms. The GAS-specific primers (16S rRNA and V-Na + -ATPase) used in this study can be used to estimate the maximum potential GAS carriage in people.

Synchrotron-Based Microspectroscopic Analysis of Molecular and Biopolymer Structures Using Multivariate Techniques and Advanced Multi-Components Modeling

International Nuclear Information System (INIS)

Yu, P.

2008-01-01

More recently, advanced synchrotron radiation-based bioanalytical technique (SRFTIRM) has been applied as a novel non-invasive analysis tool to study molecular, functional group and biopolymer chemistry, nutrient make-up and structural conformation in biomaterials. This novel synchrotron technique, taking advantage of bright synchrotron light (which is million times brighter than sunlight), is capable of exploring the biomaterials at molecular and cellular levels. However, with the synchrotron RFTIRM technique, a large number of molecular spectral data are usually collected. The objective of this article was to illustrate how to use two multivariate statistical techniques: (1) agglomerative hierarchical cluster analysis (AHCA) and (2) principal component analysis (PCA) and two advanced multicomponent modeling methods: (1) Gaussian and (2) Lorentzian multi-component peak modeling for molecular spectrum analysis of bio-tissues. The studies indicated that the two multivariate analyses (AHCA, PCA) are able to create molecular spectral corrections by including not just one intensity or frequency point of a molecular spectrum, but by utilizing the entire spectral information. Gaussian and Lorentzian modeling techniques are able to quantify spectral omponent peaks of molecular structure, functional group and biopolymer. By application of these four statistical methods of the multivariate techniques and Gaussian and Lorentzian modeling, inherent molecular structures, functional group and biopolymer onformation between and among biological samples can be quantified, discriminated and classified with great efficiency.

A thin-layer liquid culture technique for the growth of Helicobacter pylori.

Science.gov (United States)

Joo, Jung-Soo; Park, Kyung-Chul; Song, Jae-Young; Kim, Dong-Hyun; Lee, Kyung-Ja; Kwon, Young-Cheol; Kim, Jung-Min; Kim, Kyung-Mi; Youn, Hee-Shang; Kang, Hyung-Lyun; Baik, Seung-Chul; Lee, Woo-Kon; Cho, Myung-Je; Rhee, Kwang-Ho

2010-08-01

Several attempts have been successful in liquid cultivation of Helicobaccter pylori. However, there is a need to improve the growth of H. pylori in liquid media in order to get affluent growth and a simple approach for examining bacterial properties. We introduce here a thin-layer liquid culture technique for the growth of H. pylori. A thin-layer liquid culture system was established by adding liquid media to a 90-mm diameter Petri dish. Optimal conditions for bacterial growth were investigated and then viability, growth curve, and released proteins were examined. Maximal growth of H. pylori was obtained by adding 3 mL of brucella broth supplemented with 10% horse to a Petri dish. H. pylori grew in both DMEM and RPMI-1640 supplemented with 10% fetal bovine serum and 0.5% yeast extract. Serum-free RPMI-1640 supported the growth of H. pylori when supplemented with dimethyl-beta-cyclodextrin (200 microg/mL) and 1% yeast extract. Under optimal growth, H. pylori grew exponentially for 28 hours, reaching a density of 3.4 OD(600) with a generation time of 3.3 hours. After 24 hours, cultures at a cell density of 1.0 OD(600) contained 1.3 +/- 0.1 x 10(9 )CFU/mL. gamma-Glutamyl transpeptidase, nuclease, superoxide dismutase, and urease were not detected in culture supernatants at 24 hours in thin-layer liquid culture, but were present at 48 hours, whereas alcohol dehydrogenase, alkylhydroperoxide reductase, catalase, and vacuolating cytotoxin were detected at 24 hours. Thin-layer liquid culture technique is feasible, and can serve as a versatile liquid culture technique for investigating bacterial properties of H. pylori.

Study on Production of Useful Metabolites by Development of Advanced Cell Culture Techniques Using Radiation

Energy Technology Data Exchange (ETDEWEB)

Chung, Byung Yeoup; Kim, J. H.; Lee, S. S.; Shyamkumar, B.; An, B. C.; Moon, Y. R.; Lee, E. M.; Lee, M. H.

2009-02-15

The purpose of this project is improvement of investigation, materialization and evaluation techniques on effectiveness for functional natural compounds throughout development of tissue/cell culture techniques for mass production of useful metabolites using radiation. Research scope includes 1) Development of a technique for radiation tissue and cell culture, 2) Database construction for radiation response in plants and radiation effects, 3) Construction of general-purpose national based techniques of cell culture technique using radiation. Main results are as follow: Establishment of a tissue culture system (Rubus sp., Lithospermum erythrorhizon, and Rhodiola rosea); characterization of radiation activated gene expression from cultivated bokbunja (Rubus sp.) and Synechocystis sp., identification of gamma-ray induced color change in plants; identification of sensitivity to gamma-ray from Omija (Schisandra chinensis) extract; identification of the response of thylakoid proteins to gamma-ray in spinach and Arabidopsis; identification of gamma-ray induced gene relating to pigment metabolism; characterization of different NPQ changes to gamma-irradiated plants; verification of the effects of rare earth element including anti-bacterial and anti-fungal properties and as a growth enhancer; identification of changes in the growth of gamma-irradiated Synechocystis; and investigation of liquid cell culture conditions from Rhodiola rosea

Study on Production of Useful Metabolites by Development of Advanced Cell Culture Techniques Using Radiation

International Nuclear Information System (INIS)

Chung, Byung Yeoup; Kim, J. H.; Lee, S. S.; Shyamkumar, B.; An, B. C.; Moon, Y. R.; Lee, E. M.; Lee, M. H.

2009-02-01

The purpose of this project is improvement of investigation, materialization and evaluation techniques on effectiveness for functional natural compounds throughout development of tissue/cell culture techniques for mass production of useful metabolites using radiation. Research scope includes 1) Development of a technique for radiation tissue and cell culture, 2) Database construction for radiation response in plants and radiation effects, 3) Construction of general-purpose national based techniques of cell culture technique using radiation. Main results are as follow: Establishment of a tissue culture system (Rubus sp., Lithospermum erythrorhizon, and Rhodiola rosea); characterization of radiation activated gene expression from cultivated bokbunja (Rubus sp.) and Synechocystis sp., identification of gamma-ray induced color change in plants; identification of sensitivity to gamma-ray from Omija (Schisandra chinensis) extract; identification of the response of thylakoid proteins to gamma-ray in spinach and Arabidopsis; identification of gamma-ray induced gene relating to pigment metabolism; characterization of different NPQ changes to gamma-irradiated plants; verification of the effects of rare earth element including anti-bacterial and anti-fungal properties and as a growth enhancer; identification of changes in the growth of gamma-irradiated Synechocystis; and investigation of liquid cell culture conditions from Rhodiola rosea

Molecular detection of drug resistance in microbes by isotopic techniques: The IAEA experience

International Nuclear Information System (INIS)

Dar, L.; Boussaha, A.; Padhy, A.K.; Khan, B.

2003-01-01

The International Atomic Energy Agency (IAEA) supports various programmes on the uses of radionuclide techniques in the management of human communicable diseases. An important issue, being addressed through several technology transfer projects, is the detection of drug resistance in microbes by radioisotope based molecular-biology diagnostic procedures. The techniques employed include dot blot hybridisation with P-32 labelled oligonucleotide probes to detect point mutations, associated with drug resistance, in microbial genes amplified by the polymerase chain reaction (PCR). Molecular methods have been used for the detection of drug resistance in the malarial parasite, Plasmodium falciparum, and in Mycobacterium tuberculosis. Radioisotope based molecular-biology methods have been demonstrated to have comparative advantages in being sensitive, specific, cost-effective, and suitable for application to large-scale molecular surveillance for drug resistance. (author)

Methods for plant molecular biology

National Research Council Canada - National Science Library

Weissbach, Arthur; Weissbach, Herbert

1988-01-01

.... Current techniques to carry out plant cell culture and protoplast formation are described as are methods for gene and organelle transfer. The detection of DNA and RNA viruses by molecular probes or ELISA assays and the cloning and transcription of viral RNA complete the volume.

Biodeterioration of epoxy resin: a microbial survey through culture-independent and culture-dependent approaches.

Science.gov (United States)

Pangallo, Domenico; Bučková, Maria; Kraková, Lucia; Puškárová, Andrea; Šaková, Nikoleta; Grivalský, Tomaš; Chovanová, Katarina; Zemánková, Milina

2015-02-01

During the 20th century, synthetic polymers were greatly used in the field of art. In particular, the epoxy resins were used for both conservation and for creating sculptures. The biodeterioration of these polymers has not been adequately studied. The aim of this investigation was to examine the microflora responsible for the deterioration of an epoxy statue exposed to outdoor conditions. Fungal and bacterial microflora were isolated from the art object, clustered by fluorescence-ITS (internal transcribed spacer), identified by ITS and 16S rRNA sequencing and tested for their lipolytic abilities by three agar assays. Different algal, bacterial, cyanobacterial and fungal clone libraries were constructed. The surrounding airborne microflora was analyzed using culture-dependent and culture-independent approaches. The results indicated the presence, on the statue surface, of an interesting and differentiate microbial community composed of rock-inhabiting members, algal photobionts (Trebouxia spp., Chloroidium ellipsoideum and Chlorella angustoellipsoidea), Cyanobacteria (Leptolyngbya sp., Phormidium sp., Cylindrospermum stagnale, Hassallia byssoidea and Geitlerinema sp.), black yeasts related to the species Friedmanniomyces endolithicus, Pseudotaeniolina globosa, Phaeococcomyces catenatus and Catenulostroma germanicum and several plant-associated fungi. This investigation provides new information on the potential microfloral inhabitants of epoxy resin discovering a new ecological niche, occupied mainly by several members of rock-colonizing microbial species. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Experience of molecular monitoring techniques in upstream oil and gas operations

Energy Technology Data Exchange (ETDEWEB)

Mitchell, Anthony F.; Anfindsen, Hilde; Liengen, Turid; Molid, Solfrid [Statoil ASA (Denmark)

2011-07-01

For a numbers of years, molecular monitoring tools have been used in upstream oil and gas operations but the results have given only limited added value. This paper discusses the various techniques available for upstream molecular monitoring which provides scope for identification of microbial influenced problems. The methodology, which consists of analyzing solid samples using traditional as well as molecular techniques, is detailed. Two cases were studied with the objective of determining if microbial contamination was contributing to the problem. The first case was a study of amorphous deposits in production wells and mainly iron sulphide was found. The second study was of amorphous deposits in water injection wells and the analysis showed typical components of drilling and completion fluids with some organic material. Two more cases, corrosion of tubing in a water injection well and flow line corrosion, are discussed and the results are given. From the study, it can be concluded that failure can be due to several factors, chemical and biological.

Human mixed lymphocyte cultures. Evaluation of microculture technique utilizing the multiple automated sample harvester (MASH)

Science.gov (United States)

Thurman, G. B.; Strong, D. M.; Ahmed, A.; Green, S. S.; Sell, K. W.; Hartzman, R. J.; Bach, F. H.

1973-01-01

Use of lymphocyte cultures for in vitro studies such as pretransplant histocompatibility testing has established the need for standardization of this technique. A microculture technique has been developed that has facilitated the culturing of lymphocytes and increased the quantity of cultures feasible, while lowering the variation between replicate samples. Cultures were prepared for determination of tritiated thymidine incorporation using a Multiple Automated Sample Harvester (MASH). Using this system, the parameters that influence the in vitro responsiveness of human lymphocytes to allogeneic lymphocytes have been investigated. PMID:4271568

Culture Media and Individual Hosts Affect the Recovery of Culturable Bacterial Diversity from Amphibian Skin.

Science.gov (United States)

Medina, Daniel; Walke, Jenifer B; Gajewski, Zachary; Becker, Matthew H; Swartwout, Meredith C; Belden, Lisa K

2017-01-01

One current challenge in microbial ecology is elucidating the functional roles of the large diversity of free-living and host-associated bacteria identified by culture-independent molecular methods. Importantly, the characterization of this immense bacterial diversity will likely require merging data from culture-independent approaches with work on bacterial isolates in culture. Amphibian skin bacterial communities have become a recent focus of work in host-associated microbial systems due to the potential role of these skin bacteria in host defense against the pathogenic fungus Batrachochytrium dendrobatidis (Bd), which is associated with global amphibian population declines and extinctions. As there is evidence that some skin bacteria may inhibit growth of Bd and prevent infection in some cases, there is interest in using these bacteria as probiotic therapy for conservation of at-risk amphibians. In this study, we used skin swabs from American toads ( Anaxyrus americanus ) to: (1) assess the diversity and community structure of culturable amphibian skin bacteria grown on high and low nutrient culture media, (2) determine which culture media recover the highest proportion of the total skin bacterial community of individual toads relative to culture-independent data, and (3) assess whether the plated communities from the distinct media types vary in their ability to inhibit Bd growth in in-vitro assays. Overall, we found that culture media with low nutrient concentrations facilitated the growth of more diverse bacterial taxa and grew distinct communities relative to media with higher nutrient concentrations. Use of low nutrient media also resulted in culturing proportionally more of the bacterial diversity on individual toads relative to the overall community defined using culture-independent methods. However, while there were differences in diversity among media types, the variation among individual hosts was greater than variation among media types, suggesting

The study of cultural objects by nuclear and conventional techniques

International Nuclear Information System (INIS)

Palacios, Tulio A.

2000-01-01

A survey is given of the techniques that are used at the National Atomic Energy Commission of Argentina for the characterization and study of cultural and archaeological specimens. A short history of these activities is also given. (author)

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)

Method-independent, Computationally Frugal Convergence Testing for Sensitivity Analysis Techniques

Science.gov (United States)

Mai, J.; Tolson, B.

2017-12-01

The increasing complexity and runtime of environmental models lead to the current situation that the calibration of all model parameters or the estimation of all of their uncertainty is often computationally infeasible. Hence, techniques to determine the sensitivity of model parameters are used to identify most important parameters. All subsequent model calibrations or uncertainty estimation procedures focus then only on these subsets of parameters and are hence less computational demanding. While the examination of the convergence of calibration and uncertainty methods is state-of-the-art, the convergence of the sensitivity methods is usually not checked. If any, bootstrapping of the sensitivity results is used to determine the reliability of the estimated indexes. Bootstrapping, however, might as well become computationally expensive in case of large model outputs and a high number of bootstraps. We, therefore, present a Model Variable Augmentation (MVA) approach to check the convergence of sensitivity indexes without performing any additional model run. This technique is method- and model-independent. It can be applied either during the sensitivity analysis (SA) or afterwards. The latter case enables the checking of already processed sensitivity indexes. To demonstrate the method's independency of the convergence testing method, we applied it to two widely used, global SA methods: the screening method known as Morris method or Elementary Effects (Morris 1991) and the variance-based Sobol' method (Solbol' 1993). The new convergence testing method is first scrutinized using 12 analytical benchmark functions (Cuntz & Mai et al. 2015) where the true indexes of aforementioned three methods are known. This proof of principle shows that the method reliably determines the uncertainty of the SA results when different budgets are used for the SA. The results show that the new frugal method is able to test the convergence and therefore the reliability of SA results in an

Culture and molecular identification of fungal contaminants in edible bird nests.

Science.gov (United States)

Chen, Jennifer Xiao Jing; Wong, Shew Fung; Lim, Patricia Kim Chooi; Mak, Joon Wah

2015-01-01

Widespread food poisoning due to microbial contamination has been a major concern for the food industry, consumers and governing authorities. This study is designed to determine the levels of fungal contamination in edible bird nests (EBNs) using culture and molecular techniques. Raw EBNs were collected from five house farms, and commercial EBNs were purchased from five Chinese traditional medicine shops (companies A-E) in Peninsular Malaysia. The fungal contents in the raw and commercial EBNs, and boiled and unboiled EBNs were determined. Culturable fungi were isolated and identified. In this study, the use of these methods revealed that all EBNs had fungal colony-forming units (CFUs) that exceeded the limit set by Standards and Industrial Research Institute of Malaysia (SIRIM) for yeast and moulds in EBNs. There was a significant difference (p 0.05). The types of fungi isolated from the unboiled raw EBNs were mainly soil, plant and environmental fungi, while the types of fungi isolated from the boiled raw EBNs, unboiled and boiled commercial EBNs were mainly environmental fungi. Aspergillus sp., Candida sp., Cladosporium sp., Neurospora sp. and Penicillum sp. were the most common fungi isolated from the unboiled and boiled raw and commercial EBNs. Some of these fungi are mycotoxin producers and cause opportunistic infections in humans. Further studies to determine the mycotoxin levels and methods to prevent or remove these contaminations from EBNs for safe consumption are necessary. The establishment and implementation of stringent regulations for the standards of EBNs should be regularly updated and monitored to improve the quality of the EBNs and consumer safety.

Cellular Molecular Changes in Nerium oleander (L.) Cell Culture Under Gamma Radiation Stress

International Nuclear Information System (INIS)

Salama, I.M.; Abd EL-Megid, M.H.M.

2017-01-01

This study was done to analyze the relationship between the various effects of five different doses of gamma ray treatments (control, 0, 100, 200, 300 and 400 rad) on cell suspension culture of Nerium oleander belonging to the family Apocynaceae, Plant samples were collected from Egyptian flora. The five treatments of the plants were characterized by analyzing variability in frozen biomass cell suspension culture of N. oleander through SDS PAGE and peroxidase is ozymes. The electrophorogram showed a total of 36 bands of proteins with molecular weight ranging from 10 to 225 KDa. The protein diversity analysis was done based on the presence or the absence of bands trhus interpreting their relevance. The his togram analysis clearly showed a high degree of diversity a long these five treatments of the plant. The results of electrophoretic patterns of peroxidase is ozymes that was extracted from frozen biomass cell suspension cultures after receiving the different gamma doses revealed remarkable molecular changes in all treatments. These changes in peroxidase isozymes and protein bands indicate the effect of the different irradiation treatments on the gene expiration

PEDAGIGOCAL TECHNIQUE OF BUILDING THE CULTURE OF INTERPERSONAL RELATIONS IN PRESCHOOL CHILDREN AT ART CLASSES

Directory of Open Access Journals (Sweden)

Svetlana Vyacheslavovna Kahnovich

2013-10-01

Full Text Available The article looks at the pedagogical technique of building the culture of interpersonal relations in preschool children at the local and modular level. Interpersonal relations are viewed as the module and art classes as the local level. The research is timely as it can assist in studying the problem of moral development of preschool children by building the culture of interpersonal relations by artistic education means. The study presents novelty concluding from the survey of scientific literature. The process of building the culture of interpersonal relations in children has not been properly studied by preschool pedagogy. The task of the present study is to elaborate a pedagogical technique to build the culture of interpersonal relations between children at art classes. The article discusses ‘technological’ criteria (term by G.K. Selevko and presents interactive principles of the pedagogical technique. Group activities alongside with individual ones were viewed as organizational forms of art classes. Building the culture of interpersonal relations in preschool children at art classes is closely connected with the development of their personality, a child’s  consciousness, their motivational and conceptual spheres during their gradual moral development at various levels - emotional (attitude, axiological level, psychic (intentional cognitive processes, activity (artistic and interpersonal literacy. Graphic (projective methods were used to analyze age dynamics of ethical and moral development. The conclusion describes a set of pedagogical conditions for efficient building of the culture of interpersonal relations in children at art classes.  Goal. To elaborate a pedagogical technique for building the culture of interpersonal relations in preschool children at art classes. The technique can be applied at local and modular level.Methods and Methodology. The pedagogical technique is aimed at building the culture of interpersonal relations

Measurement techniques and safety culture in radiation protection -reflections after 37 years of occupation with measuring instruments

International Nuclear Information System (INIS)

Maushart, R.

1994-01-01

Safety Culture in radiation use and radiation protection implies primarily knowledge and competence of the decision makers. As the measuring techniques are basic for practical radiation protection, only such person can be called competent who has sufficient expertise on measuring techniques, and is able to evaluate its application and results. Safety Culture also implies the readiness to expose errors, and to learn from them. ''Believing in infallibility'' excludes Safety Culture. Therefore, correctly applied measuring technique contributes to recognize weak points early. How far it is used consciously and actively to prevent undesirable developments and exceeding of limits, can be considered outright as a yardstick for a high-ranking safety culture. Safety Culture as a whole, however, needs more than more measuring techniques. It requires its own and adequate Measurement Culture, presupposing also motivation and determination to measure. Therefore, education, training, knowledge and consciousness of safety of the people who are responsible for measurements are decisive for successful radiation protection. (orig.) [de

Study on production of useful metabolites by development of advanced cell culture techniques using radiation

Energy Technology Data Exchange (ETDEWEB)

Chung, Byung Yeoup; Lee, Seung Sik; Bai, Hyounwoo; Singh, Sudhir; Lee, Eun Mi; Hong, Sung Hyun; Park, Chul Hong; Srilatha, B.; Kim, Mi Ja; Lee, Ohchul

2012-01-15

The purpose of this project is improvement of investigation, materialization and evaluation techniques on effectiveness for functional natural compounds throughout development of tissue/cell culture techniques for mass production of useful metabolites using radiation. Research scope includes Development of a technique for radiation tissue and cell culture, Database construction for radiation response in plants and radiation effects, Construction of general-purpose national based techniques of cell culture technique using radiation. Main results are as follow: Development of a technique for radiation tissue and cell culture for Erigeron breviscapus (Vant.) Hand. Mazz.; Identification and functional analysis of AtTDX (chaperone and peroxidase activities); Functional analysis of radiation(gamma ray, electron beam, and proton beam) induced chaperon protein activities (AtTDX); Determine the action mechanism of yPrx2; Development of transgenic plant with bas I gene from Arabidopsis; Development of transgenic plant with EoP gene from centipedegrass; Identification of radiation induced multi functional compounds from Aloe; Determination of the effects of radiation on removing undesirable color and physiological activities (Schizandra chinensis baillon, centipedegrass); Determine the action mechanism of transgenic plant with 2-Cys Prx for heat stress resistance; Determination of the effects of centipedegrass extracts on anti-cancer activities; Functional analysis of centipedegrass extracts (anti-virus effects)

Element selective detection of molecular species applying chromatographic techniques and diode laser atomic absorption spectrometry.

Science.gov (United States)

Kunze, K; Zybin, A; Koch, J; Franzke, J; Miclea, M; Niemax, K

2004-12-01

Tunable diode laser atomic absorption spectroscopy (DLAAS) combined with separation techniques and atomization in plasmas and flames is presented as a powerful method for analysis of molecular species. The analytical figures of merit of the technique are demonstrated by the measurement of Cr(VI) and Mn compounds, as well as molecular species including halogen atoms, hydrogen, carbon and sulfur.

Applications of radiations, radioisotopes and nuclear techniques in biotechnology

International Nuclear Information System (INIS)

Bhatia, C.R.

1994-01-01

Applications of radiations, radioisotopes and other nuclear techniques has contributed a great deal in our understanding of microbial plant and animal biochemistry and molecular biology. Electron microscopy has provided visual evidence for molecular events. Developments in cell tissue culture of both plants and animals and immunology have contributed to advances in what we now refer as biotechnology. This paper focuses on the applications in the high-tech end of biotechnology, limited to the use of recombinant-DNA techniques. Molecular identification of the genes, their cloning and horizontal transfer across the species of microbes, plants and animals and expression of the transferred genes is the major strength of modern biotechnology. The techniques described in this paper have played a significant role in the development of biotechnology. 6 refs

Microbial diversity of a Camembert-type cheese using freeze-dried Tibetan kefir coculture as starter culture by culture-dependent and culture-independent methods.

Directory of Open Access Journals (Sweden)

Jun Mei

Full Text Available The biochemical changes occurring during cheese ripening are directly and indirectly dependent on the microbial associations of starter cultures. Freeze-dried Tibetan kefir coculture was used as a starter culture in the Camembert-type cheese production for the first time. Therefore, it's necessary to elucidate the stability, organization and identification of the dominant microbiota presented in the cheese. Bacteria and yeasts were subjected to culture-dependent on selective media and culture-independent polymerase chain reaction (PCR-denaturing gradient gel electrophoresis (DGGE analysis and sequencing of dominant bands to assess the microbial structure and dynamics through ripening. In further studies, kefir grains were observed using scanning electron microscopy (SEM methods. A total of 147 bacteria and 129 yeasts were obtained from the cheese during ripening. Lactobacillus paracasei represents the most commonly identified lactic acid bacteria isolates, with 59 of a total of 147 isolates, followed by Lactococcus lactis (29 isolates. Meanwhile, Kazachstania servazzii (51 isolates represented the mainly identified yeast isolate, followed by Saccharomyces cerevisiae (40 isolates. However, some lactic acid bacteria detected by sequence analysis of DGGE bands were not recovered by plating. The yeast S. cerevisiae and K. servazzii are described for the first time with kefir starter culture. SEM showed that the microbiota were dominated by a variety of lactobacilli (long and curved cells growing in close association with a few yeasts in the inner portion of the grain and the short lactobacilli were observed along with yeast cells on the exterior portion. Results indicated that conventional culture method and PCR-DGGE should be combined to describe in maximal detail the microbiological composition in the cheese during ripening. The data could help in the selection of appropriate commercial starters for Camembert-type cheese.

Microbial Diversity of a Camembert-Type Cheese Using Freeze-Dried Tibetan Kefir Coculture as Starter Culture by Culture-Dependent and Culture-Independent Methods

Science.gov (United States)

Mei, Jun; Guo, Qizhen; Wu, Yan; Li, Yunfei

2014-01-01

The biochemical changes occurring during cheese ripening are directly and indirectly dependent on the microbial associations of starter cultures. Freeze-dried Tibetan kefir coculture was used as a starter culture in the Camembert-type cheese production for the first time. Therefore, it's necessary to elucidate the stability, organization and identification of the dominant microbiota presented in the cheese. Bacteria and yeasts were subjected to culture-dependent on selective media and culture-independent polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) analysis and sequencing of dominant bands to assess the microbial structure and dynamics through ripening. In further studies, kefir grains were observed using scanning electron microscopy (SEM) methods. A total of 147 bacteria and 129 yeasts were obtained from the cheese during ripening. Lactobacillus paracasei represents the most commonly identified lactic acid bacteria isolates, with 59 of a total of 147 isolates, followed by Lactococcus lactis (29 isolates). Meanwhile, Kazachstania servazzii (51 isolates) represented the mainly identified yeast isolate, followed by Saccharomyces cerevisiae (40 isolates). However, some lactic acid bacteria detected by sequence analysis of DGGE bands were not recovered by plating. The yeast S. cerevisiae and K. servazzii are described for the first time with kefir starter culture. SEM showed that the microbiota were dominated by a variety of lactobacilli (long and curved) cells growing in close association with a few yeasts in the inner portion of the grain and the short lactobacilli were observed along with yeast cells on the exterior portion. Results indicated that conventional culture method and PCR-DGGE should be combined to describe in maximal detail the microbiological composition in the cheese during ripening. The data could help in the selection of appropriate commercial starters for Camembert-type cheese. PMID:25360757

Microbial diversity of a Camembert-type cheese using freeze-dried Tibetan kefir coculture as starter culture by culture-dependent and culture-independent methods.

Science.gov (United States)

Mei, Jun; Guo, Qizhen; Wu, Yan; Li, Yunfei

2014-01-01

The biochemical changes occurring during cheese ripening are directly and indirectly dependent on the microbial associations of starter cultures. Freeze-dried Tibetan kefir coculture was used as a starter culture in the Camembert-type cheese production for the first time. Therefore, it's necessary to elucidate the stability, organization and identification of the dominant microbiota presented in the cheese. Bacteria and yeasts were subjected to culture-dependent on selective media and culture-independent polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) analysis and sequencing of dominant bands to assess the microbial structure and dynamics through ripening. In further studies, kefir grains were observed using scanning electron microscopy (SEM) methods. A total of 147 bacteria and 129 yeasts were obtained from the cheese during ripening. Lactobacillus paracasei represents the most commonly identified lactic acid bacteria isolates, with 59 of a total of 147 isolates, followed by Lactococcus lactis (29 isolates). Meanwhile, Kazachstania servazzii (51 isolates) represented the mainly identified yeast isolate, followed by Saccharomyces cerevisiae (40 isolates). However, some lactic acid bacteria detected by sequence analysis of DGGE bands were not recovered by plating. The yeast S. cerevisiae and K. servazzii are described for the first time with kefir starter culture. SEM showed that the microbiota were dominated by a variety of lactobacilli (long and curved) cells growing in close association with a few yeasts in the inner portion of the grain and the short lactobacilli were observed along with yeast cells on the exterior portion. Results indicated that conventional culture method and PCR-DGGE should be combined to describe in maximal detail the microbiological composition in the cheese during ripening. The data could help in the selection of appropriate commercial starters for Camembert-type cheese.

Nonculture molecular techniques for diagnosis of bacterial disease in animals: a diagnostic laboratory perspective.

Science.gov (United States)

Cai, H Y; Caswell, J L; Prescott, J F

2014-03-01

The past decade has seen remarkable technical advances in infectious disease diagnosis, and the pace of innovation is likely to continue. Many of these techniques are well suited to pathogen identification directly from pathologic or clinical samples, which is the focus of this review. Polymerase chain reaction (PCR) and gene sequencing are now routinely performed on frozen or fixed tissues for diagnosis of bacterial infections of animals. These assays are most useful for pathogens that are difficult to culture or identify phenotypically, when propagation poses a biosafety hazard, or when suitable fresh tissue is not available. Multiplex PCR assays, DNA microarrays, in situ hybridization, massive parallel DNA sequencing, microbiome profiling, molecular typing of pathogens, identification of antimicrobial resistance genes, and mass spectrometry are additional emerging technologies for the diagnosis of bacterial infections from pathologic and clinical samples in animals. These technical advances come, however, with 2 caveats. First, in the age of molecular diagnosis, quality control has become more important than ever to identify and control for the presence of inhibitors, cross-contamination, inadequate templates from diagnostic specimens, and other causes of erroneous microbial identifications. Second, the attraction of these technologic advances can obscure the reality that medical diagnoses cannot be made on the basis of molecular testing alone but instead through integrated consideration of clinical, pathologic, and laboratory findings. Proper validation of the method is required. It is critical that veterinary diagnosticians understand not only the value but also the limitations of these technical advances for routine diagnosis of infectious disease.

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

Science.gov (United States)

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

2017-07-08

The deployment of molecular biology techniques for diagnosis and research in Nigeria is faced with a number of challenges, including the cost of equipment and reagents coupled with the dearth of personnel skilled in the procedures and handling of equipment. Short molecular biology training workshops were conducted at the Nigerian Institute of Medical Research (NIMR), to improve the knowledge and skills of laboratory personnel and academics in health, research, and educational facilities. Five-day molecular biology workshops were conducted annually between 2011 and 2014, with participants drawn from health, research facilities, and the academia. The courses consisted of theoretical and practical sessions. The impact of the workshops on knowledge and skill acquisition was evaluated by pre- and post-tests which consisted of 25 multiple choice and other questions. Sixty-five participants took part in the workshops. The mean knowledge of molecular biology as evaluated by the pre- and post-test assessments were 8.4 (95% CI 7.6-9.1) and 13.0 (95 CI 11.9-14.1), respectively. The mean post-test score was significantly greater than the mean pre-test score (p biology workshop significantly increased the knowledge and skills of participants in molecular biology techniques. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):313-317, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

Why are price stability and statutory independence of central banks negatively correlated? : the role of culture

NARCIS (Netherlands)

Jong, Eelke de

2001-01-01

This paper investigates whether in OECD-countries the negative relation between central bank independence and inflation is related to culture, in the sense of common values and norms. It appears that inflation is lower in countries where people dislike uncertainty. The tolerance in a society with

Is perceived emotional support beneficial? Well-being and health in independent and interdependent cultures.

Science.gov (United States)

Uchida, Yukiko; Kitayama, Shinobu; Mesquita, Batja; Reyes, Jose Alberto S; Morling, Beth

2008-06-01

Previous studies show there is little or no association between perceived emotional support and well-being in European American culture. The authors hypothesized that this paradoxical absence of any benefit of perceived support is unique to cultural contexts that privilege independence rather than interdependence of the self. Study 1 tested college students and found, as predicted, that among Euro-Americans a positive effect of perceived emotional support on subjective well-being (positive affect) was weak and, moreover, it disappeared entirely once self-esteem was statistically controlled. In contrast, among Asians in Asia (Japanese and Filipinos) perceived emotional support positively predicted subjective well-being even after self-esteem was controlled. Study 2 extended Study 1 by testing both Japanese and American adults in midlife with respect to multiple indicators of well-being and physical health. Overall, the evidence underscores the central significance of culture as a moderator of the effectiveness of perceived emotional support.

Using "Pseudomonas Putida xylE" Gene to Teach Molecular Cloning Techniques for Undergraduates

Science.gov (United States)

Dong, Xu; Xin, Yi; Ye, Li; Ma, Yufang

2009-01-01

We have developed and implemented a serial experiment in molecular cloning laboratory course for undergraduate students majored in biotechnology. "Pseudomonas putida xylE" gene, encoding catechol 2, 3-dioxygenase, was manipulated to learn molecular biology techniques. The integration of cloning, expression, and enzyme assay gave students…

Molecular imaging in Libman-Sacks endocarditis

DEFF Research Database (Denmark)

Dahl, Anders; Schaadt, Bente K; Santoni-Rugiu, Eric

2015-01-01

cardiothoracic surgery and pathologic examinations showed characteristic morphology of Libman-Sacks vegetations. All microbiological examinations including blood cultures, microscopy, culture and 16s PCR of the valve were negative and the diagnosis of Libman-Sacks endocarditis was convincing. It is difficult...... to distinguish Libman-Sacks endocarditis from culture-negative infective endocarditis (IE). Molecular imaging techniques are being used increasingly in cases of suspected IE but no studies have previously reported the use in patients with Libman-Sacks endocarditis. In the present case, (18)F-FDG-PET-CT clearly...

Culture-dependent and culture-independent characterization of potentially functional biphenyl-degrading bacterial community in response to extracellular organic matter from Micrococcus luteus.

Science.gov (United States)

Su, Xiao-Mei; Liu, Yin-Dong; Hashmi, Muhammad Zaffar; Ding, Lin-Xian; Shen, Chao-Feng

2015-05-01

Biphenyl (BP)-degrading bacteria were identified to degrade various polychlorinated BP (PCB) congers in long-term PCB-contaminated sites. Exploring BP-degrading capability of potentially useful bacteria was performed for enhancing PCB bioremediation. In the present study, the bacterial composition of the PCB-contaminated sediment sample was first investigated. Then extracellular organic matter (EOM) from Micrococcus luteus was used to enhance BP biodegradation. The effect of the EOM on the composition of bacterial community was investigated by combining with culture-dependent and culture-independent methods. The obtained results indicate that Proteobacteria and Actinobacteria were predominant community in the PCB-contaminated sediment. EOM from M. luteus could stimulate the activity of some potentially difficult-to-culture BP degraders, which contribute to significant enhancement of BP biodegradation. The potentially difficult-to-culture bacteria in response to EOM addition were mainly Rhodococcus and Pseudomonas belonging to Gammaproteobacteria and Actinobacteria respectively. This study provides new insights into exploration of functional difficult-to-culture bacteria with EOM addition and points out broader BP/PCB degrading, which could be employed for enhancing PCB-bioremediation processes. © 2015 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Recent developments in pathogen detection arrays: implications for fungal plant pathogens and use in practica

NARCIS (Netherlands)

Lievens, B.; Thomma, B.P.H.J.

2005-01-01

The failure to adequately identify plant pathogens from culture-based morphological techniques has led to the development of culture-independent molecular approaches. Increasingly, diagnostic laboratories are pursuing fast routine methods that provide reliable identification, sensitive detection,

Detection and identification of microbes in prosthetic joint infections by culture and molecular methods

DEFF Research Database (Denmark)

Xu, Yijuan; Schønheyder, Henrik Carl; Ehrlich, Garth

, indicating biofilm formation. In conclusion, this study indicated that to improve the microbiological diagnosis of prosthetic joint infections molecular methods may be useful supplements to routine cultures, and the current intraoperative sampling strategy needs to be optimized.......Bacterial biofilms have been observed in many device-related infections including orthopedic implants. This mode of growth makes the infection difficult to treat and constitutes a challenge to current sampling procedures and culture practices to obtain a reliable diagnosis. The aim of the study...... uncovered many more species including known pathogens and species not previously reported in orthopedic infections, and polymicrobial communities were commonly observed. Additionally the molecular findings suggested the bacterial composition and yield varied depending on the position and type of samples...

Assessment of Knowledge of Participants on Basic Molecular Biology Techniques after 5-Day Intensive Molecular Biology Training Workshops in Nigeria

Science.gov (United States)

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

2017-01-01

The deployment of molecular biology techniques for diagnosis and research in Nigeria is faced with a number of challenges, including the cost of equipment and reagents coupled with the dearth of personnel skilled in the procedures and handling of equipment. Short molecular biology training workshops were conducted at the Nigerian Institute of…

Study on production of useful metabolites by development of advanced cell culture techniques using radiation

Energy Technology Data Exchange (ETDEWEB)

Chung, Byung Yeoup; Kim, Jin Hong; Lee, Seung Sik; Kim, Jae Sung; An, Byung Chull; Moon, Yu Ran; Lee, Eun Mi; Lee, Min Hee; Lee, Jae Tack [KAERI, Daejeon (Korea, Republic of)

2010-02-15

The purpose of this project is improvement of investigation, materialization and evaluation techniques on effectiveness for functional natural compounds throughout development of tissue/cell culture techniques for mass production of useful metabolites using radiation. Research scope includes 1) Development of a technique for radiation tissue and cell culture, 2) Database construction for radiation response in plants and radiation effects, 3) Construction of general-purpose national based techniques of cell culture technique using radiation. Main results are as follow: mass culture of the adventitious roots of mountain ginseng (Panax ginseng C. A. Meyer) roots using rare earth elements in bioreactor: characterization of a transcription factor EoP gene from centipedegrass and the transcription regulation of LexA from Synechocystis sp PCC6803 and E. coli: identification of gamma-ray induced hydrogenase synthesis in hox gene transformed E. coli: transformation and the selection of the EoP transgene from Arabidopsis, rice and lettuce: Identification of the maysin and maysin derivatives in centipedegrass: characterization of gamma-ray induced color change in Taxus cuspidata: verification of the expression of antioxidant proteins (POD, APX and CAT) to gamma-ray in Arabidopsis: comparison of the response of the expression level to gamma-ray or H{sub 2}O{sub 2} in Arabidopsis; verification of the responses and effects to gamma-ray from plants (analysis of NPQ and ROS levels): the development method for rapidly enhancing maysin content of centipede grass; establishment of mass culture system for red beet

Study on production of useful metabolites by development of advanced cell culture techniques using radiation

International Nuclear Information System (INIS)

Chung, Byung Yeoup; Kim, Jin Hong; Lee, Seung Sik; Kim, Jae Sung; An, Byung Chull; Moon, Yu Ran; Lee, Eun Mi; Lee, Min Hee; Lee, Jae Tack

2010-02-01

The purpose of this project is improvement of investigation, materialization and evaluation techniques on effectiveness for functional natural compounds throughout development of tissue/cell culture techniques for mass production of useful metabolites using radiation. Research scope includes 1) Development of a technique for radiation tissue and cell culture, 2) Database construction for radiation response in plants and radiation effects, 3) Construction of general-purpose national based techniques of cell culture technique using radiation. Main results are as follow: mass culture of the adventitious roots of mountain ginseng (Panax ginseng C. A. Meyer) roots using rare earth elements in bioreactor: characterization of a transcription factor EoP gene from centipedegrass and the transcription regulation of LexA from Synechocystis sp PCC6803 and E. coli: identification of gamma-ray induced hydrogenase synthesis in hox gene transformed E. coli: transformation and the selection of the EoP transgene from Arabidopsis, rice and lettuce: Identification of the maysin and maysin derivatives in centipedegrass: characterization of gamma-ray induced color change in Taxus cuspidata: verification of the expression of antioxidant proteins (POD, APX and CAT) to gamma-ray in Arabidopsis: comparison of the response of the expression level to gamma-ray or H 2 O 2 in Arabidopsis; verification of the responses and effects to gamma-ray from plants (analysis of NPQ and ROS levels): the development method for rapidly enhancing maysin content of centipede grass; establishment of mass culture system for red beet

Isotopic and molecular fractionation in combustion; three routes to molecular marker validation, including direct molecular 'dating' (GC/AMS)

Science.gov (United States)

Currie, L. A.; Klouda, G. A.; Benner, B. A.; Garrity, K.; Eglinton, T. I.

The identification of unique isotopic, elemental, and molecular markers for sources of combustion aerosol has growing practical importance because of the potential effects of fine particle aerosol on health, visibility and global climate. It is urgent, therefore, that substantial efforts be directed toward the validation of assumptions involving the use of such tracers for source apportionment. We describe here three independent routes toward carbonaceous aerosol molecular marker identification and validation: (1) tracer regression and multivariate statistical techniques applied to field measurements of mixed source, carbonaceous aerosols; (2) a new development in aerosol 14C metrology: direct, pure compound accelerator mass spectrometry (AMS) by off-line GC/AMS ('molecular dating'); and (3) direct observation of isotopic and molecular source emissions during controlled laboratory combustion of specific fuels. Findings from the combined studies include: independent support for benzo( ghi)perylene as a motor vehicle tracer from the first (statistical) and second (direct 'dating') studies; a new indication, from the third (controlled combustion) study, of a relation between 13C isotopic fractionation and PAH molecular fractionation, also linked with fuel and stage of combustion; and quantitative data showing the influence of both fuel type and combustion conditions on the yields of such species as elemental carbon and PAH, reinforcing the importance of exercising caution when applying presumed conservative elemental or organic tracers to fossil or biomass burning field data as in the first study.

Tissue culture as a plant production technique for horticultural crops

African Journals Online (AJOL)

STORAGESEVER

2009-08-18

Aug 18, 2009 ... Recovery of regenerants from transformed cells. - Cell culture .... methods. Micropropagation techniques. Micropropagation is a simple concept. The basic pro- tocols were well established by the 1960s and a whole research field and ... the environment are naturally contaminated on their sur- faces (and ...

Characterisation and preservation of cultural heritage artefacts using nuclear techniques

International Nuclear Information System (INIS)

2011-01-01

This report covers the studies performed for the identification and preservation of cultural heritage using nuclear analytical techniques (NAT). Within the context of the project financed by the IAEA, cultural articles from various excavation regions and from the Anatolian Civilizations Museum were analyzed and identified using the instruments at our Center and information was provided regarding their manufacturing techniques, past restoration history and socioeconomic indicators about the period within which these articles were used. The analysis of the articles which could not be removed from the museum were performed in-situ using portable instruments and support was provided to the experts for some articles from excavation regions for the evaluation of their originality. Within the framework the of this Project, five experts attended to the workshops and meetings organised by the IAEA and in the context of scientific visits and bilateral cooperation, one expert from Greece and three experts from Macedonia visited our Center and Anatolian Civilizations Museum and experimental studies were performed together

Studies of molecular dynamics with neutron scattering techniques. Part of a coordinated programme on neutron scattering techniques

International Nuclear Information System (INIS)

Vinhas, L.A.

1980-05-01

Molecular dynamics was studied in samples of tert-butanol, cyclohexanol and methanol, using neutron inelastic and quasi-elastic techniques. The frequency spectra of cyclohexanol in crystalline phase were interpreted by assigning individual energy peaks to hindered rotation of molecules, lattice vibration, hydrogen bond stretching and ring bending modes. Neutron quasi-elastic scattering measurements permitted the testing of models for molecular diffusion as a function of temperature. The interpretation of neutron incoherent inelastic scattering on methanol indicated the different modes of molecular dynamics in this material; individual inelastic peaks in the spectra could be assigned to vibrations of crystalline lattice, stretching of hydrogen bond and vibrational and torsional modes of CH 3 OH molecule. The results of the experimental work on tertbutanol indicate two distinct modes of motion in this material: individual molecular librations are superposed to a cooperative rotation diffusion which occurs both in solid and in liquid state

Culture-independent quantification of Salmonella enterica in carcass gauze swabs by flotation prior to real-time PCR

DEFF Research Database (Denmark)

Löfström, Charlotta; Schelin, Jenny; Norling, Börje

2011-01-01

To facilitate quantitative risk assessment in the meat production chain, there is a need for culture-independent quantification methods. The aim of this study was to evaluate the use of flotation, a non-destructive sample preparation method based on traditional buoyant density centrifugation...

Culturing of respiratory viruses in well-differentiated pseudostratified human airway epithelium as a tool to detect unknown viruses

NARCIS (Netherlands)

Farsani, Seyed Mohammad Jazaeri; Deijs, Martin; Dijkman, Ronald; Molenkamp, Richard; Jeeninga, Rienk E.; Ieven, Margareta; Goossens, Herman; van der Hoek, Lia

2015-01-01

Currently, virus discovery is mainly based on molecular techniques. Here, we propose a method that relies on virus culturing combined with state-of-the-art sequencing techniques. The most natural ex vivo culture system was used to enable replication of respiratory viruses. Three respiratory clinical

The use of tissue culture techniques to detect irradiated vegetables

International Nuclear Information System (INIS)

Al-Safadi, B.; Sharabi, N.E.; Nabulsi, I

2001-01-01

the ability of two tissue culture methods, callus and vegetable growth induction, to detect irradiated vegetables was evaluated. Potato tubers, carrot roots, garlic cloves and onion bulbs were subjected to various gamma radiation doses (0, 25, 100, 150, 250, 500, 750, and 1000 Gy). Irradiated vegetables were cultured in vitro and in vivo (pots). Gamma irradiation significantly reduced callus-forming ability especially in carrot and potato where no callus was observed in doses higher than 50 Gy. Length of shoots and roots growing from irradiated garlic and onion explants was considerably reduced starting from the 25 Gy dose. No roots were formed on garlic explants at any irradiation dose. Garlic leaves growing from irradiated explants were spotted with purple to brown spots. The intensity of these spots increased as gamma ray dosage increased. In the pot experiment, potato plant appeared in the control only. On the contrary, a complete sprouting of garlic and onion was seen in all irradiation treatments. It was not possible to distinguish between the various irradiation treatments and the control 3 days after planting in pots. The two in vitro techniques, tested in our study, may effectively be used to detect irradiated vegetables and estimate the range of doses used. The callus formation method is more useful for potato and carrot, since regeneration of shoots in vitro from these two plants takes along time, making this method unpractical. The other technique is very useful in the case of onion and garlic since it is rapid. The two techniques can be used with most of the vegetables that can be cultured in vitro. (Author)

Culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs.

Science.gov (United States)

Orphan, V J; Taylor, L T; Hafenbradl, D; Delong, E F

2000-02-01

Recent investigations of oil reservoirs in a variety of locales have indicated that these habitats may harbor active thermophilic prokaryotic assemblages. In this study, we used both molecular and culture-based methods to characterize prokaryotic consortia associated with high-temperature, sulfur-rich oil reservoirs in California. Enrichment cultures designed for anaerobic thermophiles, both autotrophic and heterotrophic, were successful at temperatures ranging from 60 to 90 degrees C. Heterotrophic enrichments from all sites yielded sheathed rods (Thermotogales), pleomorphic rods resembling Thermoanaerobacter, and Thermococcus-like isolates. The predominant autotrophic microorganisms recovered from inorganic enrichments using H(2), acetate, and CO(2) as energy and carbon sources were methanogens, including isolates closely related to Methanobacterium, Methanococcus, and Methanoculleus species. Two 16S rRNA gene (rDNA) libraries were generated from total community DNA collected from production wellheads, using either archaeal or universal oligonucleotide primer sets. Sequence analysis of the universal library indicated that a large percentage of clones were highly similar to known bacterial and archaeal isolates recovered from similar habitats. Represented genera in rDNA clone libraries included Thermoanaerobacter, Thermococcus, Desulfothiovibrio, Aminobacterium, Acidaminococcus, Pseudomonas, Halomonas, Acinetobacter, Sphingomonas, Methylobacterium, and Desulfomicrobium. The archaeal library was dominated by methanogen-like rDNAs, with a lower percentage of clones belonging to the Thermococcales. Our results strongly support the hypothesis that sulfur-utilizing and methane-producing thermophilic microorganisms have a widespread distribution in oil reservoirs and the potential to actively participate in the biogeochemical transformation of carbon, hydrogen, and sulfur in situ.

Characterization-Based Molecular Design of Biofuel Additives Using Chemometric and Property Clustering Techniques

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Subin eHada

2014-06-01

Full Text Available In this work, multivariate characterization data such as infrared (IR spectroscopy was used as a source of descriptor data involving information on molecular architecture for designing structured molecules with tailored properties. Application of multivariate statistical techniques such as principal component analysis (PCA allowed capturing important features of the molecular architecture from complex data to build appropriate latent variable models. Combining the property clustering techniques and group contribution methods (GCM based on characterization data in a reverse problem formulation enabled identifying candidate components by combining or mixing molecular fragments until the resulting properties match the targets. The developed methodology is demonstrated using molecular design of biodiesel additive which when mixed with off-spec biodiesel produces biodiesel that meets the desired fuel specifications. The contribution of this work is that the complex structures and orientations of the molecule can be included in the design, thereby allowing enumeration of all feasible candidate molecules that matched the identified target but were not part of original training set of molecules.

Coulomb-explosion technique for determining geometrical structures of molecular ions

International Nuclear Information System (INIS)

Gemmell, D.S.

1981-01-01

Traditional experimental techniques (e.g. studies on photon absorption or emission) for determining the sterochemical structures of neutral molecules are extremeley difficult to apply to molecular ions because of problems in obtaining a sufficient spatial density of the ions to be studied. Recent high-resolution measurements on the energy and angle distributions of the fragments produced when fast (MeV) molecular-ion beams from an electrostatic accelerator dissociate (Coulomb explode) in thin foils and in gases, offer promising possibilities for deducing the sterochemical structures of the molecular ions constituting the incident beams. Bond lengths have been determined in this way for several diatomic projectiles (H 2+ , HeH + , CH + , NH + , OH + , N 2+ , O 2+ , etc.) with an accuracy of approx. 0.01 A. H 3+ has been demonstrated (for the first time) to be equilateral triangular and the interproton distance measured. Measurements on single fragments from CO 2+ , N 2 O + , C 3 H 3+ , and CH/sub n/ + have revealed the gross structures of the projectiles. An apparatus has recently been constructed at Argonne to permit precise measurements on fragments in coincidence. The apparatus has been tested on a known structure (OH 2+ ). The O-H bond length was found to be 1.0 +- 0.04 A and the H-O-H bond angle was measured as 110 --- 2 0 . These values are in excellent agreement with those found in optical experiments (0.999 A and 110.5 0 ). This Coulomb explosion technique can be expected to be refined in accuracy and to be extended to a wide range of molecular ions whose structures are inaccessible by other means

Aragonite precipitation by "proto-polyps" in coral cell cultures.

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Tali Mass

Full Text Available The mechanisms of coral calcification at the molecular, cellular and tissue levels are poorly understood. In this study, we examine calcium carbonate precipitation using novel coral tissue cultures that aggregate to form "proto-polyps". Our goal is to establish an experimental system in which calcification is facilitated at the cellular level, while simultaneously allowing in vitro manipulations of the calcifying fluid. This novel coral culturing technique enables us to study the mechanisms of biomineralization and their implications for geochemical proxies. Viable cell cultures of the hermatypic, zooxanthellate coral, Stylophora pistillata, have been maintained for 6 to 8 weeks. Using an enriched seawater medium with aragonite saturation state similar to open ocean surface waters (Ω(arag~4, the primary cell cultures assemble into "proto-polyps" which form an extracellular organic matrix (ECM and precipitate aragonite crystals. These extracellular aragonite crystals, about 10 µm in length, are formed on the external face of the proto-polyps and are identified by their distinctive elongated crystallography and X-ray diffraction pattern. The precipitation of aragonite is independent of photosynthesis by the zooxanthellae, and does not occur in control experiments lacking coral cells or when the coral cells are poisoned with sodium azide. Our results demonstrate that proto-polyps, aggregated from primary coral tissue culture, function (from a biomineralization perspective similarly to whole corals. This approach provides a novel tool for investigating the biophysical mechanism of calcification in these organisms.

The impact of culture collections on molecular identification, taxonomy, and solving real problems

Science.gov (United States)

Among the fungi, Fusarium has stood out as a major focus for culture collection resource development over the last century. This has facilitated unprecedented molecular taxonomic advancements, which in turn has led to problem solving in plant pathology, mycotoxicology, medical mycology, and basic re...

Intelligent Techniques Using Molecular Data Analysis in Leukaemia: An Opportunity for Personalized Medicine Support System.

Science.gov (United States)

Banjar, Haneen; Adelson, David; Brown, Fred; Chaudhri, Naeem

2017-01-01

The use of intelligent techniques in medicine has brought a ray of hope in terms of treating leukaemia patients. Personalized treatment uses patient's genetic profile to select a mode of treatment. This process makes use of molecular technology and machine learning, to determine the most suitable approach to treating a leukaemia patient. Until now, no reviews have been published from a computational perspective concerning the development of personalized medicine intelligent techniques for leukaemia patients using molecular data analysis. This review studies the published empirical research on personalized medicine in leukaemia and synthesizes findings across studies related to intelligence techniques in leukaemia, with specific attention to particular categories of these studies to help identify opportunities for further research into personalized medicine support systems in chronic myeloid leukaemia. A systematic search was carried out to identify studies using intelligence techniques in leukaemia and to categorize these studies based on leukaemia type and also the task, data source, and purpose of the studies. Most studies used molecular data analysis for personalized medicine, but future advancement for leukaemia patients requires molecular models that use advanced machine-learning methods to automate decision-making in treatment management to deliver supportive medical information to the patient in clinical practice.

Kinetic and Diagnostic Studies of Molecular Plasmas Using Laser Absorption Techniques

International Nuclear Information System (INIS)

Welzel, S; Rousseau, A; Davies, P B; Roepcke, J

2007-01-01

Within the last decade mid infrared absorption spectroscopy between 3 and 20 μm, known as Infrared Laser Absorption Spectroscopy (IRLAS) and based on tuneable semiconductor lasers, namely lead salt diode lasers, often called tuneable diode lasers (TDL), and quantum cascade lasers (QCL) has progressed considerably as a powerful diagnostic technique for in situ studies of the fundamental physics and chemistry of molecular plasmas. The increasing interest in processing plasmas containing hydrocarbons, fluorocarbons, organo-silicon and boron compounds has lead to further applications of IRLAS because most of these compounds and their decomposition products are infrared active. IRLAS provides a means of determining the absolute concentrations of the ground states of stable and transient molecular species, which is of particular importance for the investigation of reaction kinetics. Information about gas temperature and population densities can also be derived from IRLAS measurements. A variety of free radicals and molecular ions have been detected, especially using TDLs. Since plasmas with molecular feed gases are used in many applications such as thin film deposition, semiconductor processing, surface activation and cleaning, and materials and waste treatment, this has stimulated the adaptation of infrared spectroscopic techniques to industrial requirements. The recent development of QCLs offers an attractive new option for the monitoring and control of industrial plasma processes as well as for highly time-resolved studies on the kinetics of plasma processes. The aim of the present article is threefold: (i) to review recent achievements in our understanding of molecular phenomena in plasmas (ii) to report on selected studies of the spectroscopic properties and kinetic behaviour of radicals, and (iii) to describe the current status of advanced instrumentation for TDLAS in the mid infrared

Culture-Independent Identification of Mycobacterium avium Subspecies paratuberculosis in Ovine Tissues: Comparison with Bacterial Culture and Histopathological Lesions

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Kamal R. Acharya

2017-12-01

Full Text Available Johne’s disease is a chronic debilitating enteropathy of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP. Current abattoir surveillance programs detect disease via examination of gross lesions and confirmation by histopathological and/or tissue culture, which is time-consuming and has relatively low sensitivity. This study aimed to investigate whether a high-throughput quantitative PCR (qPCR test is a viable alternative for tissue testing. Intestine and mesenteric lymph nodes were sourced from sheep experimentally infected with MAP and the DNA extracted using a protocol developed for tissues, comprised enzymatic digestion of the tissue homogenate, chemical and mechanical lysis, and magnetic bead-based DNA purification. The extracted DNA was tested by adapting a previously validated qPCR for fecal samples, and the results were compared with culture and histopathology results of the corresponding tissues. The MAP tissue qPCR confirmed infection in the majority of sheep with gross lesions on postmortem (37/38. Likewise, almost all tissue culture (61/64 or histopathology (52/58 positives were detected with good to moderate agreement (Cohen’s kappa statistic and no significant difference to the reference tests (McNemar’s Chi-square test. Higher MAP DNA quantities corresponded to animals with more severe histopathology (odds ratio: 1.82; 95% confidence interval: 1.60, 2.07. Culture-independent strain typing on tissue DNA was successfully performed. This MAP tissue qPCR method had a sensitivity equivalent to the reference tests and is thus a viable replacement for gross- and histopathological examination of tissue samples in abattoirs. In addition, the test could be validated for testing tissue samples intended for human consumption.

Validation of the prognostic gene portfolio, ClinicoMolecular Triad Classification, using an independent prospective breast cancer cohort and external patient populations

Science.gov (United States)

2014-01-01

Introduction Using genome-wide expression profiles of a prospective training cohort of breast cancer patients, ClinicoMolecular Triad Classification (CMTC) was recently developed to classify breast cancers into three clinically relevant groups to aid treatment decisions. CMTC was found to be both prognostic and predictive in a large external breast cancer cohort in that study. This study serves to validate the reproducibility of CMTC and its prognostic value using independent patient cohorts. Methods An independent internal cohort (n = 284) and a new external cohort (n = 2,181) were used to validate the association of CMTC between clinicopathological factors, 12 known gene signatures, two molecular subtype classifiers, and 19 oncogenic signalling pathway activities, and to reproduce the abilities of CMTC to predict clinical outcomes of breast cancer. In addition, we also updated the outcome data of the original training cohort (n = 147). Results The original training cohort reached a statistically significant difference (p risk groups. Conclusions Both prospective internal cohorts and the independent external cohorts reproduced the triad classification of CMTC and its prognostic significance. CMTC is an independent prognostic predictor, and it outperformed 12 other known prognostic gene signatures, molecular subtype classifications, and all other standard prognostic clinicopathological factors. Our results support further development of CMTC portfolio into a guide for personalized breast cancer treatments. PMID:24996446

Induced mutations and molecular techniques for crop improvement. Proceedings of an international symposium

International Nuclear Information System (INIS)

1995-01-01

The symposium was aimed at reviewing current aspects of mutation and molecular biology techniques for use in crop improvement and to bridge the gap between practical plant breeding and molecular laboratory techniques. Over the past few years, many transgenic plants have been developed in important crops such as rice, wheat, maize, soybean, banana, cassava and cotton, as well as in many food, industrial and pharmaceutical plant species. More than 180 participants from 48 countries of which 31 were from developing countries, attended which provided a forum for the discussion of problems related to crop improvement world wide, and their possible solutions. Refs, figs and tabs

A review of the public health management of shigellosis in Australia in the era of culture-independent diagnostic testing.

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Tai, Alex Y C; Easton, Marion; Encena, Jess; Rotty, Jessica; Valcanis, Mary; Howden, Benjamin P; Slota-Kan, Simon; Gregory, Joy

2016-12-01

To review the national case definition for shigellosis following the introduction of culture independent diagnostic testing by clinical laboratories and provide evidence to reform jurisdictional public health practices for the management shigellosis., . A review of all Australian jurisdictional public health guidelines for shigellosis was conducted. Victorian 2014 shigellosis data were analysed: demographics and risk factors for cases identified by conventional culture or culture-independent diagnostic methods were described. There was considerable variation in reporting of cases to the National Notifiable Disease Surveillance System (NNDSS) by the eight Australian jurisdictions, with an array of classifications based on diagnostic testing methodologies. Analysis of Victorian 2014 shigellosis data found that culture positive cases were more likely to have reported men who have sex with men (MSM) as a risk factor than PCR positive only cases (p<0.0001) and less likely to have reported overseas travel during their incubation period (p<0.0001). Over a 10-year period (2005 to 2014), only two of 86 cases who were employed in high-risk occupations had ongoing positive faecal cultures after appropriate treatment. The national surveillance case definition for shigellosis should be reviewed to facilitate standardised reporting across Australia. All jurisdictions must consider the public health significance of PCR positive only results in their surveillance risk assessments to inform management of shigellosis cases. © 2016 Public Health Association of Australia.

Prevalence of periodontopathogenic bacteria in patients suffering from periodontitis using culture and PCR methods

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Amir Aliramezani

2012-01-01

Full Text Available Background and Aims: Periodontitis is one of the most common oral diseases with the various incidence rates in different populations. A number of bacteria are considered as the major etiologic agents of periodontitis. The aim of the present study was to determine the prevalence of periodontopathogen bacteria in patients using both PCR and culture techniques.Materials and Methods: In this study, one-hundred patients (including 62 females and 38 males with an average age of 49±11.5 years with adult periodontitis referred to periodontics department of School of Dentistry/Tehran University of Medical Sciences were investigated. The samples were taken and sent immediately to the laboratory for culture and molecular evaluation. The PCR was performed using specific primers and the statistical analysis of data was performed using SPSS statistic software and McNemar test.Results: The results demonstrated that the total detection rate in culture method was 64%. The rate of Aggregatibacter actinomycetemcomitans (Aa was 28% which was significantly higher than that of Porphyromonas gingivalis (Pg (6% and Prevotella intermedia (Pi (3%. 27% of cases showed mixed bacterial growth. 65% of patients were positive using molecular method. The rate of Aa (30% was significantly higher than that of Pg (7% and Pi (5%. The mixed PCR positive rate containing of Aa, Pg and Pi was (23%.Conclusion: In this study, it was found that most of the bacteria isolated using culture and molecular methods were Aa, Pg and Pi, respectively. Although the detection frequencies of both techniques were similar, the specificity, sensitivity and bacterial detection speed of the PCR technique is obviously higher. Therefore, the use of molecular techniques is strongly recommended. However, both techniques seem to be suitable for microbiological diagnostics.

Validation of the prognostic gene portfolio, ClinicoMolecular Triad Classification, using an independent prospective breast cancer cohort and external patient populations.

Science.gov (United States)

Wang, Dong-Yu; Done, Susan J; Mc Cready, David R; Leong, Wey L

2014-07-04

Using genome-wide expression profiles of a prospective training cohort of breast cancer patients, ClinicoMolecular Triad Classification (CMTC) was recently developed to classify breast cancers into three clinically relevant groups to aid treatment decisions. CMTC was found to be both prognostic and predictive in a large external breast cancer cohort in that study. This study serves to validate the reproducibility of CMTC and its prognostic value using independent patient cohorts. An independent internal cohort (n = 284) and a new external cohort (n = 2,181) were used to validate the association of CMTC between clinicopathological factors, 12 known gene signatures, two molecular subtype classifiers, and 19 oncogenic signalling pathway activities, and to reproduce the abilities of CMTC to predict clinical outcomes of breast cancer. In addition, we also updated the outcome data of the original training cohort (n = 147). The original training cohort reached a statistically significant difference (p value of the triad classification was reproduced in the second independent internal cohort and the new external validation cohort. CMTC achieved even higher prognostic significance when all available patients were analyzed (n = 4,851). Oncogenic pathways Myc, E2F1, Ras and β-catenin were again implicated in the high-risk groups. Both prospective internal cohorts and the independent external cohorts reproduced the triad classification of CMTC and its prognostic significance. CMTC is an independent prognostic predictor, and it outperformed 12 other known prognostic gene signatures, molecular subtype classifications, and all other standard prognostic clinicopathological factors. Our results support further development of CMTC portfolio into a guide for personalized breast cancer treatments.

Characterization-Based Molecular Design of Bio-Fuel Additives Using Chemometric and Property Clustering Techniques

International Nuclear Information System (INIS)

Hada, Subin; Solvason, Charles C.; Eden, Mario R.

2014-01-01

In this work, multivariate characterization data such as infrared spectroscopy was used as a source of descriptor data involving information on molecular architecture for designing structured molecules with tailored properties. Application of multivariate statistical techniques such as principal component analysis allowed capturing important features of the molecular architecture from enormous amount of complex data to build appropriate latent variable models. Combining the property clustering techniques and group contribution methods based on characterization (cGCM) data in a reverse problem formulation enabled identifying candidate components by combining or mixing molecular fragments until the resulting properties match the targets. The developed methodology is demonstrated using molecular design of biodiesel additive, which when mixed with off-spec biodiesel produces biodiesel that meets the desired fuel specifications. The contribution of this work is that the complex structures and orientations of the molecule can be included in the design, thereby allowing enumeration of all feasible candidate molecules that matched the identified target but were not part of original training set of molecules.

Characterization-Based Molecular Design of Bio-Fuel Additives Using Chemometric and Property Clustering Techniques

Energy Technology Data Exchange (ETDEWEB)

Hada, Subin; Solvason, Charles C.; Eden, Mario R., E-mail: edenmar@auburn.edu [Department of Chemical Engineering, Auburn University, Auburn, AL (United States)

2014-06-10

In this work, multivariate characterization data such as infrared spectroscopy was used as a source of descriptor data involving information on molecular architecture for designing structured molecules with tailored properties. Application of multivariate statistical techniques such as principal component analysis allowed capturing important features of the molecular architecture from enormous amount of complex data to build appropriate latent variable models. Combining the property clustering techniques and group contribution methods based on characterization (cGCM) data in a reverse problem formulation enabled identifying candidate components by combining or mixing molecular fragments until the resulting properties match the targets. The developed methodology is demonstrated using molecular design of biodiesel additive, which when mixed with off-spec biodiesel produces biodiesel that meets the desired fuel specifications. The contribution of this work is that the complex structures and orientations of the molecule can be included in the design, thereby allowing enumeration of all feasible candidate molecules that matched the identified target but were not part of original training set of molecules.

Ex Vivo Produced Oral Mucosa Equivalent by Using the Direct Explant Cell Culture Technique

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Kamile Öztürk

2012-09-01

Full Text Available Objective: The aim of this study is the histological and immunohistochemical evaluation of ex vivo produced oral mucosal equivalents using keratinocytes cultured by direct explant technique.Material and Methods: Oral mucosa tissue samples were obtained from the keratinized gingival tissues of 14 healthy human subjects. Human oral mucosa keratinocytes from an oral mucosa biopsy specimen were dissociated by the explant technique. Once a sufficient population of keratinocytes was reached, they were seeded onto the type IV collagen coated “AlloDerm” and taken for histological and immunohistochemical examinations at 11 days postseeding of the keratinocytes on the cadaveric human dermal matrix.Results: Histopathologically and immunohistochemically, 12 out of 14 successful ex vivo produced oral mucosa equivalents (EVPOME that consisted of a stratified epidermis on a dermal matrix have been developed with keratinocytes cultured by the explant technique.Conclusion: The technical handling involved in the direct explant method at the beginning of the process has fewer steps than the enzymatic method and use of the direct explant technique protocol for culturing of human oral mucosa keratinocyte may be more adequate for EVPOME production.

Improvement of molecular techniques: A multidisciplinar vision

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Bruno do Amaral Crispim

2016-08-01

Full Text Available The advances in molecular technologies since the discovery of the PCR (Polymerase Chain Reaction and their association with the use of molecular markers, allowed a rapid progress in the development of technologies and equipment able to generate and analyze data on a large scale, revolutionizing research that until recently was only based on single marker, like the analysis of Single Nucleotide Polymorphism (SNP, and nowadays with the genomic era is already possible in a few hours genotyping millions or even thousands of SNPs. This evolution has allowed improvements in research to the knowledge of genomes creating expectations and real possibilities of application of these techniques in various fields, from medicine to animal production. These new technologies of molecular analysis of DNA variability determining points of interest in chromosomes, which are technically called as molecular markers. These markers can be used in various applications, including paternity test, construction of genetic maps, mapping of quantitative inheritance of characteristics, isolation of genes, marker-assisted selection and characterization of the genetic diversity of different species. The improvement of sequencing and bioinformatics technologies were crucial to studies with characteristics of interest using high-density genetic information. The SNP genotyping panels stimulated researches in the human area, especially in studies of cancer and exoma, and also in agribusiness, aiming the search for superior genotypes for domestic plants and animals. The differential use of the panels is the possibility to seek complex characteristics, once the wide distribution of markers favors through the linkage disequilibrium, the identification of genomic regions associated with expression phenotypes in study. Therefore, this advance has become essential for greater accuracy and speed in molecular diagnostics, increasing the accuracy in the selection of individuals with

Study on production of useful metabolites by development of advanced cell culture techniques using radiation

Energy Technology Data Exchange (ETDEWEB)

Chung, Byung Yeoup; Kim, Jinhong; Lee, Seung Sik; Bai, Hyounwoo; An, Byung Chull; Lee, Eun Mi; Lee, Jae Taek; Kim, Mi Ja

2010-12-15

The purpose of this project is improvement of investigation, materialization and evaluation techniques on effectiveness for functional natural compounds throughout development of tissue/cell culture techniques for mass production of useful metabolites using radiation. Research scope includes Development of a technique for radiation tissue and cell culture, Database construction for radiation response in plants and radiation effects, Construction of general-purpose national based techniques of cell culture technique using radiation. Main results are as follow: Isolation and identification of radiation induced basI gene; Determination of stresses sensitivities by transformating basI gene into arabidopsis; Isolation and identification of radiation induced chaperon proteins (PaAhpC and yPrxII) from Pseudomonas and yeast, and structural and functional analysis of the proteins; Determination of oxidative and heat resistance by transformating PaAhpC; Isolation and identification of maysin and its derivatives from centipedgrass; Investigation of enhancement technique for improving maysin and its derivatives production using radiation; Investigation of removing undesirable color in maysin and its derivatives using radiation; Determination of the effect of radiation on physiological functions of centipedgrass extracts; Identification of H{sub 2}O{sub 2} removing enzyme in radiation irradiated plant (Spinach); Determination of the effects of centipedgrass extracts on anti-obesity and anti-cancer activities.

Study on production of useful metabolites by development of advanced cell culture techniques using radiation

International Nuclear Information System (INIS)

Chung, Byung Yeoup; Kim, Jinhong; Lee, Seung Sik; Bai, Hyounwoo; An, Byung Chull; Lee, Eun Mi; Lee, Jae Taek; Kim, Mi Ja

2010-12-01

The purpose of this project is improvement of investigation, materialization and evaluation techniques on effectiveness for functional natural compounds throughout development of tissue/cell culture techniques for mass production of useful metabolites using radiation. Research scope includes Development of a technique for radiation tissue and cell culture, Database construction for radiation response in plants and radiation effects, Construction of general-purpose national based techniques of cell culture technique using radiation. Main results are as follow: Isolation and identification of radiation induced basI gene; Determination of stresses sensitivities by transformating basI gene into arabidopsis; Isolation and identification of radiation induced chaperon proteins (PaAhpC and yPrxII) from Pseudomonas and yeast, and structural and functional analysis of the proteins; Determination of oxidative and heat resistance by transformating PaAhpC; Isolation and identification of maysin and its derivatives from centipedgrass; Investigation of enhancement technique for improving maysin and its derivatives production using radiation; Investigation of removing undesirable color in maysin and its derivatives using radiation; Determination of the effect of radiation on physiological functions of centipedgrass extracts; Identification of H 2 O 2 removing enzyme in radiation irradiated plant (Spinach); Determination of the effects of centipedgrass extracts on anti-obesity and anti-cancer activities

Ion beam analysis and spectrometry techniques for Cultural Heritage studies

International Nuclear Information System (INIS)

Beck, L.

2013-01-01

The implementation of experimental techniques for the characterisation of Cultural heritage materials has to take into account some requirements. The complexity of these past materials requires the development of new techniques of examination and analysis, or the transfer of technologies developed for the study of advanced materials. In addition, due to precious aspect of artwork it is also necessary to use the non-destructive methods, respecting the integrity of objects. It is for this reason that the methods using radiations and/or particles play a important role in the scientific study of art history and archaeology since their discovery. X-ray and γ-ray spectrometry as well as ion beam analysis (IBA) are analytical tools at the service of Cultural heritage. This report mainly presents experimental developments for IBA: PIXE, RBS/EBS and NRA. These developments were applied to the study of archaeological composite materials: layered materials or mixtures composed of organic and non-organic phases. Three examples are shown: evolution of silvering techniques for the production of counterfeit coinage during the Roman Empire and in the 16. century, the characterization of composites or mixed mineral/organic compounds such as bone and paint. In these last two cases, the combination of techniques gave original results on the proportion of both phases: apatite/collagen in bone, pigment/binder in paintings. Another part of this report is then dedicated to the non-invasive/non-destructive characterization of prehistoric pigments, in situ, for rock art studies in caves and in the laboratory. Finally, the perspectives of this work are presented. (author) [fr

Storm loads of culturable and molecular fecal indicators in an inland urban stream.

Science.gov (United States)

Liao, Hehuan; Krometis, Leigh-Anne H; Cully Hession, W; Benitez, Romina; Sawyer, Richard; Schaberg, Erin; von Wagoner, Emily; Badgley, Brian D

2015-10-15

Elevated concentrations of fecal indicator bacteria in receiving waters during wet-weather flows are a considerable public health concern that is likely to be exacerbated by future climate change and urbanization. Knowledge of factors driving the fate and transport of fecal indicator bacteria in stormwater is limited, and even less is known about molecular fecal indicators, which may eventually supplant traditional culturable indicators. In this study, concentrations and loading rates of both culturable and molecular fecal indicators were quantified throughout six storm events in an instrumented inland urban stream. While both concentrations and loading rates of each fecal indicator increased rapidly during the rising limb of the storm hydrographs, it is the loading rates rather than instantaneous concentrations that provide a better estimate of transport through the stream during the entire storm. Concentrations of general fecal indicators (both culturable and molecular) correlated most highly with each other during storm events but not with the human-associated HF183 Bacteroides marker. Event loads of general fecal indicators most strongly correlated with total runoff volume, maximum discharge, and maximum turbidity, while event loads of HF183 most strongly correlated with the time to peak flow in a hydrograph. These observations suggest that collection of multiple samples during a storm event is critical for accurate predictions of fecal indicator loading rates and total loads during wet-weather flows, which are required for effective watershed management. In addition, existing predictive models based on general fecal indicators may not be sufficient to predict source-specific genetic markers of fecal contamination. Copyright © 2015 Elsevier B.V. All rights reserved.

Comparison of Standard Culture-Based Method to Culture-Independent Method for Evaluation of Hygiene Effects on the Hand Microbiome

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C. Zapka

2017-03-01

Full Text Available Hands play a critical role in the transmission of microbiota on one’s own body, between individuals, and on environmental surfaces. Effectively measuring the composition of the hand microbiome is important to hand hygiene science, which has implications for human health. Hand hygiene products are evaluated using standard culture-based methods, but standard test methods for culture-independent microbiome characterization are lacking. We sampled the hands of 50 participants using swab-based and glove-based methods prior to and following four hand hygiene treatments (using a nonantimicrobial hand wash, alcohol-based hand sanitizer [ABHS], a 70% ethanol solution, or tap water. We compared results among culture plate counts, 16S rRNA gene sequencing of DNA extracted directly from hands, and sequencing of DNA extracted from culture plates. Glove-based sampling yielded higher numbers of unique operational taxonomic units (OTUs but had less diversity in bacterial community composition than swab-based sampling. We detected treatment-induced changes in diversity only by using swab-based samples (P < 0.001; we were unable to detect changes with glove-based samples. Bacterial cell counts significantly decreased with use of the ABHS (P < 0.05 and ethanol control (P < 0.05. Skin hydration at baseline correlated with bacterial abundances, bacterial community composition, pH, and redness across subjects. The importance of the method choice was substantial. These findings are important to ensure improvement of hand hygiene industry methods and for future hand microbiome studies. On the basis of our results and previously published studies, we propose recommendations for best practices in hand microbiome research.

Analyses of Dynamics in Dairy Products and Identification of Lactic Acid Bacteria Population by Molecular Methods

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Aytül Sofu

2017-01-01

Full Text Available Lactic acid bacteria (LAB with different ecological niches are widely seen in fermented meat, vegetables, dairy products and cereals as well as in fermented beverages. Lactic acid bacteria are the most important group of bacteria in dairy industry due to their probiotic characteristics and fermentation agents as starter culture. In the taxonomy of the lactic acid bacteria; by means of rep-PCR, which is the analysis of repetitive sequences that are based on 16S ribosomal RNA (rRNA gene sequence, it is possible to conduct structural microbial community analyses such as Restriction Fragment Length Polymorphism (RFLP analysis of DNA fragments of different sizes cut with enzymes, Random Amplified Polymorphic DNA (RAPD polymorphic DNA amplified randomly at low temperatures and Amplified Fragment-Length Polymorphism (AFLP-PCR of cut genomic DNA. Besides, in the recent years, non-culture-based molecular methods such as Pulse Field Gel Electrophoresis (PFGE, Denaturing Gradient Gel Electrophoresis (DGGE, Thermal Gradient Gel Electrophoresis (TGGE, and Fluorescence In-situ Hybridization (FISH have replaced classical methods once used for the identification of LAB. Identification of lactic acid bacteria culture independent regardless of the method will be one of the most important methods used in the future pyrosequencing as a Next Generation Sequencing (NGS techniques. This paper reviews molecular-method based studies conducted on the identification of LAB species in dairy products.

Has the use of molecular methods for the characterization of the human oral microbiome changed our understanding of the role of bacteria in the pathogenesis of periodontal disease?

Science.gov (United States)

Wade, William Geoffrey

2011-03-01

Only around half of oral bacteria can be grown in the laboratory using conventional culture methods. Molecular methods based on 16S rRNA gene sequence are now available and are being used to characterize the periodontal microbiota in its entirety. This review describes the cultural characterization of the oral and periodontal microbiotas and explores the influence of the additional data now available from culture-independent molecular analyses on current thinking on the role of bacteria in periodontitis. Culture-independent molecular analysis of the periodontal microbiota has shown it to be far more diverse than previously thought. A number of species including some that have yet to be cultured are as strongly associated with disease as those organisms traditionally regarded as periodontal pathogens. Sequencing of bacterial genomes has revealed a high degree of intra-specific genetic diversity. The use of molecular methods for the characterization of the periodontal microbiome has greatly expanded the range of bacterial species known to colonize this habitat. Understanding the interactions between the human host and its commensal bacterial community at the functional level is a priority. © 2011 John Wiley & Sons A/S.

Developing a complex independent component analysis technique to extract non-stationary patterns from geophysical time-series

Science.gov (United States)

Forootan, Ehsan; Kusche, Jürgen

2016-04-01

Geodetic/geophysical observations, such as the time series of global terrestrial water storage change or sea level and temperature change, represent samples of physical processes and therefore contain information about complex physical interactionswith many inherent time scales. Extracting relevant information from these samples, for example quantifying the seasonality of a physical process or its variability due to large-scale ocean-atmosphere interactions, is not possible by rendering simple time series approaches. In the last decades, decomposition techniques have found increasing interest for extracting patterns from geophysical observations. Traditionally, principal component analysis (PCA) and more recently independent component analysis (ICA) are common techniques to extract statistical orthogonal (uncorrelated) and independent modes that represent the maximum variance of observations, respectively. PCA and ICA can be classified as stationary signal decomposition techniques since they are based on decomposing the auto-covariance matrix or diagonalizing higher (than two)-order statistical tensors from centered time series. However, the stationary assumption is obviously not justifiable for many geophysical and climate variables even after removing cyclic components e.g., the seasonal cycles. In this paper, we present a new decomposition method, the complex independent component analysis (CICA, Forootan, PhD-2014), which can be applied to extract to non-stationary (changing in space and time) patterns from geophysical time series. Here, CICA is derived as an extension of real-valued ICA (Forootan and Kusche, JoG-2012), where we (i) define a new complex data set using a Hilbert transformation. The complex time series contain the observed values in their real part, and the temporal rate of variability in their imaginary part. (ii) An ICA algorithm based on diagonalization of fourth-order cumulants is then applied to decompose the new complex data set in (i

Bio-functions and molecular carbohydrate structure association study in forage with different source origins revealed using non-destructive vibrational molecular spectroscopy techniques.

Science.gov (United States)

Ji, Cuiying; Zhang, Xuewei; Yan, Xiaogang; Mostafizar Rahman, M; Prates, Luciana L; Yu, Peiqiang

2017-08-05

The objectives of this study were to: 1) investigate forage carbohydrate molecular structure profiles; 2) bio-functions in terms of CHO rumen degradation characteristics and hourly effective degradation ratio of N to OM (HED N/OM ), and 3) quantify interactive association between molecular structures, bio-functions and nutrient availability. The vibrational molecular spectroscopy was applied to investigate the structure feature on a molecular basis. Two sourced-origin alfalfa forages were used as modeled forages. The results showed that the carbohydrate molecular structure profiles were highly linked to the bio-functions in terms of rumen degradation characteristics and hourly effective degradation ratio. The molecular spectroscopic technique can be used to detect forage carbohydrate structure features on a molecular basis and can be used to study interactive association between forage molecular structure and bio-functions. Copyright © 2017 Elsevier B.V. All rights reserved.

Cultural Variations in Mothers' Acceptance of and Intent to Use Behavioral Child Management Techniques

Science.gov (United States)

Mah, Janet W. T.; Johnston, Charlotte

2012-01-01

We examined cultural differences in mothers' acceptance of and intent to use behavioral parenting techniques for managing disruptive child behavior, and the possible roles of parenting styles and implicit theories in explaining these cultural differences. A community sample of 117 Euro-Canadian and Chinese-immigrant mothers of boys aged 4- to…

Spheroid Culture of Head and Neck Cancer Cells Reveals an Important Role of EGFR Signalling in Anchorage Independent Survival.

Science.gov (United States)

Braunholz, Diana; Saki, Mohammad; Niehr, Franziska; Öztürk, Merve; Borràs Puértolas, Berta; Konschak, Robert; Budach, Volker; Tinhofer, Ingeborg

2016-01-01

In solid tumours millions of cells are shed into the blood circulation each day. Only a subset of these circulating tumour cells (CTCs) survive, many of them presumable because of their potential to form multi-cellular clusters also named spheroids. Tumour cells within these spheroids are protected from anoikis, which allows them to metastasize to distant organs or re-seed at the primary site. We used spheroid cultures of head and neck squamous cell carcinoma (HNSCC) cell lines as a model for such CTC clusters for determining the role of the epidermal growth factor receptor (EGFR) in cluster formation ability and cell survival after detachment from the extra-cellular matrix. The HNSCC cell lines FaDu, SCC-9 and UT-SCC-9 (UT-SCC-9P) as well as its cetuximab (CTX)-resistant sub-clone (UT-SCC-9R) were forced to grow in an anchorage-independent manner by coating culture dishes with the anti-adhesive polymer poly-2-hydroxyethylmethacrylate (poly-HEMA). The extent of apoptosis, clonogenic survival and EGFR signalling under such culture conditions was evaluated. The potential of spheroid formation in suspension culture was found to be positively correlated with the proliferation rate of HNSCC cell lines as well as their basal EGFR expression levels. CTX and gefitinib blocked, whereas the addition of EGFR ligands promoted anchorage-independent cell survival and spheroid formation. Increased spheroid formation and growth were associated with persistent activation of EGFR and its downstream signalling component (MAPK/ERK). Importantly, HNSCC cells derived from spheroid cultures retained their clonogenic potential in the absence of cell-matrix contact. Addition of CTX under these conditions strongly inhibited colony formation in CTX-sensitive cell lines but not their resistant subclones. Altogether, EGFR activation was identified as crucial factor for anchorage-independent survival of HNSCC cells. Targeting EGFR in CTC cluster formation might represent an attractive anti

Role of non-governmental organizations in formation of non-proliferation culture in new independent countries (NIC)

International Nuclear Information System (INIS)

Sevchik, M.

2000-01-01

Purpose of the report is demonstrate the non-governmental organizations (NGO) role in formation of non-proliferation culture in former Soviet Union. Activity of Center of Non-proliferation Problems Investigation (CNPI) of Monterey Institute of International Investigations and its collaboration with existing in Commonwealth of Independent States (CIS) non-governmental organizations is considered as example. Brief information about CNPI and reasons for it representatives opening of in Kazakhstan and in other CIS-countries, as well as cooperation of NGO in Belarus, Kazakhstan, Russia and Ukraine for creation on Central Asia zone free from nuclear weapon ia given. Some measures which could promote to formation of non-proliferation culture in region are suggested

Multicenter evaluation of molecular and culture-dependent diagnostics for Shigella species and Entero-invasive Escherichia coli in the Netherlands.

Science.gov (United States)

van den Beld, Maaike J C; Friedrich, Alexander W; van Zanten, Evert; Reubsaet, Frans A G; Kooistra-Smid, Mirjam A M D; Rossen, John W A

2016-12-01

An inter-laboratory collaborative trial for the evaluation of diagnostics for detection and identification of Shigella species and Entero-invasive Escherichia coli (EIEC) was performed. Sixteen Medical Microbiological Laboratories (MMLs) participated. MMLs were interviewed about their diagnostic methods and a sample panel, consisting of DNA-extracts and spiked stool samples with different concentrations of Shigella flexneri, was provided to each MML. The results of the trial showed an enormous variety in culture-dependent and molecular diagnostic techniques currently used among MMLs. Despite the various molecular procedures, 15 out of 16 MMLs were able to detect Shigella species or EIEC in all the samples provided, showing that the diversity of methods has no effect on the qualitative detection of Shigella flexneri. In contrast to semi quantitative analysis, the minimum and maximum values per sample differed by approximately five threshold cycles (Ct-value) between the MMLs included in the study. This indicates that defining a uniform Ct-value cut-off for notification to health authorities is not advisable. Copyright © 2016 Elsevier B.V. All rights reserved.

Independent cellular effects of cold ischemia and reperfusion: experimental molecular study.

Science.gov (United States)

Lledó-García, E; Humanes-Sánchez, B; Mojena-Sánchez, M; Rodrígez, J C J; Hernández-Fernández, C; Tejedor-Jorge, A; Fernández, A L

2013-04-01

There is less information available on cell cultures on the exclusive effects of either duration of cold ischemia (CI) or rewarming-reperfusion in the kidney subjected to initial warm ischemia (WI). Therefore, the goals of our work were: (1) to evaluate the consequences on tubular cellular viability of different durations of CI on a kidney after an initial period of WI, and (2) to analyze the additional effect on tubular cell viability of rewarming of the same kidney. Sixteen mini-pig were used. All the animals were performed a right nephrectomy after 45-minute occlusion of the vascular pedicle. The kidneys were then divided into 2 groups (phase 1): cold storage in university of wisconsin (UW) solution for 3 hours (group A, n = 8) at 4°C, or cold storage in UW for 12 hours (group B, n = 8) at 4°C. Four organs of group A and four organs of group B were autotrasplanted (AT) and reperfused for 1 hour (phase 2). Nephrectomy was finally done. Biopsies were taken from all groups to perform cultures of proximal tubule epithelium cells. The biopsies were subjected to studies of cellular morphological viability (contrast phase microscopy [CPM]) and quantitative (confluence cell [CC]) parameters. Phase of pure CI effects (phase 1): Both CC rate and CPM parameters were significantly lower in group B compared with group A, where cell activity reached almost normal results. Phase of CI + AT (phase 2): At produced additional harmful effects in cell cultures compared with those obtained in phase 1, more evident in group B cells. The presence of cold storage followed by rewarming-reperfusion induces independent and cumulative detrimental effects in viability of renal proximal tubule cells. CI periods ≤ 3 hours may ameliorate the injuries secondary to reperfusion in comparison with longer CI periods. Copyright © 2013 Elsevier Inc. All rights reserved.

Bacterial diversity determination using culture-dependent and culture-independent methods

Directory of Open Access Journals (Sweden)

M. Ghiasian

2017-04-01

Full Text Available Mud volcanoes are taken into consideration by geologists and oil industry experts have given their association with oil and gas reserves and methane greenhouse gas production in hydrosphere and atmosphere. Gomishan mud volcano phenomenon in the southeastern edge of the Caspian Sea, given its oil and gas resources, has been studied by some geologists in terms of geology and tectonics but not in terms of microbiology. Accordingly, it seems necessary to study this phenomenon from the perspective of microbiology in order to identify prokaryotes living in this area. Prokaryotes diversity in Mud volcano has been studied by cultivation techniques, fluorescence in situ hybridization, and denaturing gradient gel electrophoresis of PCR-amplified fragments of 16S rRNA genes. Total cell abundance in the mud volcano from 1×101-6×101per milliliter was determined by 4', 6-diamidino-2-phenylindole direct count. The detectable proportion of Archaea to Bacteria in the community by FISH was one to five. High viable counts (1 – 3 × 106 were obtained in culture media. A total of 122 isolates were obtained, 46 colonies were selected based on primarily morphological and physiological traits, and their 16S rRNA sequences were determined. The isolated genera included Halomonas (20%, Arthrobacter (5%, Kocuria (5%, Thalassobacillus (5%, Marinobacter (20%, Paracoccus (5%, Roseovarius (5%, Jeotgalicoccus (5%, Bacillus (15%, and Staphylococcus (15%. Regarding DGGE analysis, selected bands were obtained from the gels, reamplified and sequenced. Overall, 75% of the bacterial sequences were related to Rahnella and 25% related to Serratia.

Nanosecond pulsed electric field incorporation technique to predict molecular mechanisms of teratogenicity and developmental toxicity of estradiol-17β on medaka embryos.

Science.gov (United States)

Yamaguchi, Akemi; Ishibashi, Hiroshi; Kono, Susumu; Iida, Midori; Uchida, Masaya; Arizono, Koji; Tominaga, Nobuaki

2018-05-01

Herein, we propose using a nanosecond pulsed electric field (nsPEF) technique to assess teratogenicity and embryonic developmental toxicity of estradiol-17β (E 2 ) and predict the molecular mechanisms of teratogenicity and embryonic developmental defects caused by E 2 on medaka (Oryzias latipes). The 5 hour post-fertilization embryos were exposed to co-treatment with 10 μm E 2 and nsPEF for 2 hours and then continuously cultured under non-E 2 and nsPEF conditions until hatching. Results documented that the time to hatching of embryos was significantly delayed in comparison to the control group and that typical abnormal embryo development, such as the delay of blood vessel formation, was observed. For DNA microarray analysis, 6 day post-fertilization embryos that had been continuously cultured under the non-E 2 and nsPEF condition after 2 hour co-treatments were used. DNA microarray analysis identified 542 upregulated genes and one downregulated gene in the 6 day post-fertilization embryos. Furthermore, bioinformatic analyses using differentially expressed genes revealed that E 2 exposure affected various gene ontology terms, such as response to hormone stimulus. The network analysis also documented that the estrogen receptor α in the mitogen-activated protein kinase signaling pathway may be involved in regulating several transcription factors, such as FOX, AKT1 and epidermal growth factor receptor. These results suggest that our nsPEF technique is a powerful tool for assessing teratogenicity and embryonic developmental toxicity of E 2 and predict their molecular mechanisms in medaka embryos. Copyright © 2017 John Wiley & Sons, Ltd.

Protection of the cultural environment by nuclear techniques

International Nuclear Information System (INIS)

Ramiere, R.

1982-01-01

The use of gamma radiation in the preservation of the cultural environment, and in particular art objects, is examined. In each branch, the present status of research on, and its application to, the treatment of art objects is described. Two major applications - disinfection and consolidation - are reviewed: (1) Disinfection: The destruction by gamma irradiation of xylophagous insects and of fungi which contaminate paintings, pictorial documents and mummies, is discussed. The effect of gamma-rays on the constituent materials of the infected objects is examined. (2) Consolidation: this process represents an extrapolation to the preservation of cultural objects of research performed over the last 20 years with the aim of improving the mechanical properties of porous materials (by impregnation of the material in a vacuum by a liquid plastic substance which is polymerized by radiation in situ). This technique is currently being used to treat ''uncoated'' wooden objects and, to a more limited extent, ''coated'' wood (polychromy and gilt wood), depending on the fragility of the covering. With regard to stone materials, the enhancement of the mechanical properties of a limestone impregnated with a styrene-polyester resin is described; this resin has been used to treat several sculptures. The use of acrylics and methacrylics has caused some samples to crack during radiation polymerization; theories put forward to explain this phenomenon are discussed. The consolidation of terracotta and bone has also been studied. The consolidation of waterlogged wood (archaeological wood) requires a different impregnation technique (diffusion in liquid). This preservation method has already been used to treat archaeological artifacts. (author)

CATEGORICAL IMAGE COMPONENTS IN THE FORMING SYSTEM OF A MARKETING TECHNIQUES MANAGER’S IMAGE CULTURE

OpenAIRE

Anna Borisovna Cherednyakova

2015-01-01

Based on the understanding of the image culture formation of managers of marketing techniques, as a representative of the social and communication interaction of public structures, categorical apparatus of image culture with an emphasis on the etymology of the image, as an integral component of image culture was analyzed. Categorical components of the image are presented from the standpoint of image culture, as personal new formation, an integral part of the professional activity of the marke...

Nanosecond and femtosecond mass spectroscopic analysis of a molecular beam produced by the spray-jet technique

International Nuclear Information System (INIS)

Yamada, Toshiki; Shinohara, Hidenori; Kamikado, Toshiya; Okuno, Yoshishige; Suzuki, Hitoshi; Mashiko, Shinro; Yokoyama, Shiyoshi

2008-01-01

The spray-jet molecular beam apparatus enabled us to produce a molecular beam of non-volatile molecules under high vacuum from a sprayed mist of sample solutions. The apparatus has been used in spectroscopic studies and as a means of molecular beam deposition. We analyzed the molecular beam, consisting of non-volatile, solvent, and carrier-gas molecules, by using femtosecond- and nanosecond- laser mass spectroscopy. The information thus obtained provided insight into the molecular beam produced by the spray-jet technique

Studies of Phase Transformation in Molecular Crystals Using the Positron Annihilation Technique

DEFF Research Database (Denmark)

Eldrup, Morten Mostgaard; Lightbody, David; Sherwood, John N.

1980-01-01

An examination has been made of the brittle/plastic phase transformation in the molecular crystals cyclohexane, DL-camphene and succinonitrile using the positron annihilation technique. In each material, the transition is characterized by a distinct increase in ortho-positronium lifetime. The inf...

Molecular Diagnosis of Trichomoniasis in Negative Samples Examined by Direct Smear and Culture

Directory of Open Access Journals (Sweden)

Z Valadkhani

2010-12-01

Full Text Available Background: Trichomoniasis is an extremely common sexually transmitted infection (STI world­wide and is associated with important public health problems, including amplification of HIV transmission. This disease is in forms of symptomatic and asymptomatic in women and may de­pend on host as well as parasite variables. Most of the studies reported from females are based on examination of vaginal secretions and urine samples by direct smear and culture in modified Dia­mond's media. The aim of this study was checking the samples, which were negative by direct smear and culture, with PCR technique.Methods: The urine samples and vaginal discharge of patients attending Gynecology Clinics of Ma­zandaran Province, Iran with different symptoms rechecked for Trichomonas vaginalis by PCR technique using primers targeting a conserved region of the beta-tubulin genes of the para­site. Data were analyzed by Epi Info software programResults: Out of 161 negative samples by direct smear and culture, seven samples (4.3% were posi­tive by PCR technique.Conclusion: Diagnosis of trichomoniasis by PCR is a sensitive and specific method that could play important role to help the physicians for properly treatment and control of infection.

Methods in Molecular Biology: Germline Stem Cells | Center for Cancer Research

Science.gov (United States)

The protocols in Germline Stem Cells are intended to present selected genetic, molecular, and cellular techniques used in germline stem cell research. The book is divided into two parts. Part I covers germline stem cell identification and regulation in model organisms. Part II covers current techniques used in in vitro culture and applications of germline stem cells.

Improvement of rice anther culture and application of the technique in mutation breeding

International Nuclear Information System (INIS)

Chen Qiufang; Wang Cailian; Lu Yimei; Jin Wei

2001-01-01

The ability of callus formation and green plant regeneration was very different for different rice type and varieties in anther culture. The differentiation and regeneration of green plants were obviously improved when the rice anthers at about 30 d after culture on induction medium were irradiated with 20 Gy of γ-rays and calli were cultured on the differentiation medium containing 30 mg/L colchicines. The stimulation effect of γ-irradiation combined with colchicines was much better than that of their single use. Mutation frequency and selective efficiency in M 2 were obviously increased by application of the technique

[Detection of Staphylococcus aureus resistant to methicillin (MRSA) by molecular biology (Cepheid GeneXpert IL, GeneOhm BD, Roche LightCycler, Hyplex Evigene I2A) versus screening by culture: Economic and practical strategy for the laboratory].

Science.gov (United States)

Laudat, P; Demondion, E; Jouannet, C; Charron, J; Chillou, C; Salaun, V; Mankikian, B

2012-06-01

Patients admitted in cardiac surgery and cardiac ICU at the Clinic Saint-Gatien (Tours) are screened for MRSA at the entrance by nasal swab and culture on blood agar and selective chromogenic medium made by addition of cefoxitin: BBL CHROMagar MRSA-II BD (result obtained at Day +1). We wanted to assess the molecular biology techniques available to obtain a result at day 0 for the majority of patients and to define an economic and practical strategy for the laboratory. We studied four molecular biology techniques: Cepheid GeneXpert (Cepheid) GeneOhm (BD), LightCycler (Roche) and Hyplex (I2A). Upon reception, nasal swabs were treated by culture, considered as reference, and one of the techniques of molecular biology, according to the manufacturer's notice. We conducted four studies between April 2008 and February 2009 to obtain a significant sample for each of them. By screening we mean a method that allows us to exclude MRSA carriage for patients waiting for surgery, and not to change patient management: for example, lack of isolation measures specific to entrance, no modification of antibiotic prophylaxis during surgery and no isolation measures in the immediate postoperative period. The criteria we considered for this evaluation were: (1) technician time: time to perform one or a series of sample(s) n=10 or more (about 2h for all techniques except GeneXpert 75min), level of skilled competences (no specific training for GeneXpert); (2) results: turnaround time (all molecular biology techniques), ease of reading and results interpretations (no specialized training required for GeneXpert), failure or not (12% of failure of internal controls for GeneOhm); (3) economic: cost for one or a series of sample(s) (n=10 or more), if we considered X as the reference culture cost (10 X Hyplex and LightCycler, 20 X and 40 X for GeneXpert GeneOhm); (4) NPV: 100% for GeneXpert and LightCycler. At same sensitivity, no technique, including culture, can solve alone our problem, which

An optimized protocol for handling and processing fragile acini cultured with the hanging drop technique.

Science.gov (United States)

Snyman, Celia; Elliott, Edith

2011-12-15

The hanging drop three-dimensional culture technique allows cultivation of functional three-dimensional mammary constructs without exogenous extracellular matrix. The fragile acini are, however, difficult to preserve during processing steps for advanced microscopic investigation. We describe adaptations to the protocol for handling of hanging drop cultures to include investigation using confocal, scanning, and electron microscopy, with minimal loss of cell culture components. Copyright © 2011 Elsevier Inc. All rights reserved.

Efficacy of Social Media Adoption on Client Growth for Independent Management Consultants

Science.gov (United States)

2017-02-01

word -of- mouth promotion techniques. Social media also 22 created new opportunities for cultural influences and synthesis of activities and...approach as justification. According to Peters et al. (2013), users of the social media accelerate the potential for viral marketing through word -of- mouth ...denoted how word of mouth (WoM) and social media can benefit independent practices to expand their customer base (Peters, Chen, Kaplan,

Fusarium diversity in soil using a specific molecular approach and a cultural approach.

Science.gov (United States)

Edel-Hermann, Véronique; Gautheron, Nadine; Mounier, Arnaud; Steinberg, Christian

2015-04-01

Fusarium species are ubiquitous in soil. They cause plant and human diseases and can produce mycotoxins. Surveys of Fusarium species diversity in environmental samples usually rely on laborious culture-based methods. In the present study, we have developed a molecular method to analyze Fusarium diversity directly from soil DNA. We designed primers targeting the translation elongation factor 1-alpha (EF-1α) gene and demonstrated their specificity toward Fusarium using a large collection of fungi. We used the specific primers to construct a clone library from three contrasting soils. Sequence analysis confirmed the specificity of the assay, with 750 clones identified as Fusarium and distributed among eight species or species complexes. The Fusarium oxysporum species complex (FOSC) was the most abundant one in the three soils, followed by the Fusarium solani species complex (FSSC). We then compared our molecular approach results with those obtained by isolating Fusarium colonies on two culture media and identifying species by sequencing part of the EF-1α gene. The 750 isolates were distributed into eight species or species complexes, with the same dominant species as with the cloning method. Sequence diversity was much higher in the clone library than in the isolate collection. The molecular approach proved to be a valuable tool to assess Fusarium diversity in environmental samples. Combined with high throughput sequencing, it will allow for in-depth analysis of large numbers of samples. Published by Elsevier B.V.

Practices and Exploration on Competition of Molecular Biological Detection Technology among Students in Food Quality and Safety Major

Science.gov (United States)

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

2017-01-01

With the increasing importance in the application of the molecular biological detection technology in the field of food safety, strengthening education in molecular biology experimental techniques is more necessary for the culture of the students in food quality and safety major. However, molecular biology experiments are not always in curricula…

In vitro culture techniques as a tool of sugarcane bud germination ...

African Journals Online (AJOL)

STORAGESEVER

2008-10-20

Oct 20, 2008 ... and shoot growth under salt stress with different NaCl concentrations (0, 17, 34, 68 and 102 mM) using cultivar NCo310. ... techniques could be used to evaluate salt stress effects in sugarcane at the germination stage. Key words: in vitro culture, .... l'Enseignement Supérieur, de la Formation des Cadres et.

Datafish Multiphase Data Mining Technique to Match Multiple Mutually Inclusive Independent Variables in Large PACS Databases.

Science.gov (United States)

Kelley, Brendan P; Klochko, Chad; Halabi, Safwan; Siegal, Daniel

2016-06-01

Retrospective data mining has tremendous potential in research but is time and labor intensive. Current data mining software contains many advanced search features but is limited in its ability to identify patients who meet multiple complex independent search criteria. Simple keyword and Boolean search techniques are ineffective when more complex searches are required, or when a search for multiple mutually inclusive variables becomes important. This is particularly true when trying to identify patients with a set of specific radiologic findings or proximity in time across multiple different imaging modalities. Another challenge that arises in retrospective data mining is that much variation still exists in how image findings are described in radiology reports. We present an algorithmic approach to solve this problem and describe a specific use case scenario in which we applied our technique to a real-world data set in order to identify patients who matched several independent variables in our institution's picture archiving and communication systems (PACS) database.

Techniques for Maximizing the Performance of Molecular Pathology Testing: Responsibilities of All Pathologists

Directory of Open Access Journals (Sweden)

Evren UZUN

2018-05-01

Full Text Available Molecular pathological analysis has an expanding role in patient diagnosis and management. The performance of these techniques relies on excellent laboratory procedures. However, the crucial step is obtaining the best samples for molecular analysis. Archiving and selection of these are the responsibilities of all pathologists even if they are not working at a center with molecular pathological facilities. This review focuses on the features of different types of materials for molecular pathological analysis. Many steps that might affect the results, including communication between the pathologist and the oncology team, features of different types of materials (cytological, tissue blocks, biopsy, circulating tumor cells (CTCs and cell-free circulating nucleic acids, effects of tissue processing, methods for selecting the best material, and tissue saving and tumor enrichment methods are discussed. The procedures for referral to a center for molecular pathological analysis are also mentioned. Awareness of the importance of the cytopathological and histopathological material of the patients for future molecular pathological analysis by pathologists is of the utmost importance.

Application of Tissue Culture and Transformation Techniques in Model Species Brachypodium distachyon.

Science.gov (United States)

Sogutmaz Ozdemir, Bahar; Budak, Hikmet

2018-01-01

Brachypodium distachyon has recently emerged as a model plant species for the grass family (Poaceae) that includes major cereal crops and forage grasses. One of the important traits of a model species is its capacity to be transformed and ease of growing both in tissue culture and in greenhouse conditions. Hence, plant transformation technology is crucial for improvements in agricultural studies, both for the study of new genes and in the production of new transgenic plant species. In this chapter, we review an efficient tissue culture and two different transformation systems for Brachypodium using most commonly preferred gene transfer techniques in plant species, microprojectile bombardment method (biolistics) and Agrobacterium-mediated transformation.In plant transformation studies, frequently used explant materials are immature embryos due to their higher transformation efficiencies and regeneration capacity. However, mature embryos are available throughout the year in contrast to immature embryos. We explain a tissue culture protocol for Brachypodium using mature embryos with the selected inbred lines from our collection. Embryogenic calluses obtained from mature embryos are used to transform Brachypodium with both plant transformation techniques that are revised according to previously studied protocols applied in the grasses, such as applying vacuum infiltration, different wounding effects, modification in inoculation and cocultivation steps or optimization of bombardment parameters.

Clinical and molecular analyses of Beckwith-Wiedemann syndrome: Comparison between spontaneous conception and assisted reproduction techniques.

Science.gov (United States)

Tenorio, Jair; Romanelli, Valeria; Martin-Trujillo, Alex; Fernández, García-Moya; Segovia, Mabel; Perandones, Claudia; Pérez Jurado, Luis A; Esteller, Manel; Fraga, Mario; Arias, Pedro; Gordo, Gema; Dapía, Irene; Mena, Rocío; Palomares, María; Pérez de Nanclares, Guiomar; Nevado, Julián; García-Miñaur, Sixto; Santos-Simarro, Fernando; Martinez-Glez, Víctor; Vallespín, Elena; Monk, David; Lapunzina, Pablo

2016-10-01

Beckwith-Wiedemann syndrome (BWS) is an overgrowth syndrome characterized by an excessive prenatal and postnatal growth, macrosomia, macroglossia, and hemihyperplasia. The molecular basis of this syndrome is complex and heterogeneous, involving genes located at 11p15.5. BWS is correlated with assisted reproductive techniques. BWS in individuals born following assisted reproductive techniques has been found to occur four to nine times higher compared to children with to BWS born after spontaneous conception. Here, we report a series of 187 patients with to BWS born either after assisted reproductive techniques or conceived naturally. Eighty-eight percent of BWS patients born via assisted reproductive techniques had hypomethylation of KCNQ1OT1:TSS-DMR in comparison with 49% for patients with BWS conceived naturally. None of the patients with BWS born via assisted reproductive techniques had hypermethylation of H19/IGF2:IG-DMR, neither CDKN1 C mutations nor patUPD11. We did not find differences in the frequency of multi-locus imprinting disturbances between groups. Patients with BWS born via assisted reproductive techniques had an increased frequency of advanced bone age, congenital heart disease, and decreased frequency of earlobe anomalies but these differences may be explained by the different molecular background compared to those with BWS and spontaneous fertilization. We conclude there is a correlation of the molecular etiology of BWS with the type of conception. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Alignment independent 3D-QSAR, quantum calculations and molecular docking of Mer specific tyrosine kinase inhibitors as anticancer drugs

Directory of Open Access Journals (Sweden)

Fereshteh Shiri

2016-03-01

Full Text Available Mer receptor tyrosine kinase is a promising novel cancer therapeutic target in many human cancers, because abnormal activation of Mer has been implicated in survival signaling and chemoresistance. 3D-QSAR analyses based on alignment independent descriptors were performed on a series of 81 Mer specific tyrosine kinase inhibitors. The fractional factorial design (FFD and the enhanced replacement method (ERM were applied and tested as variable selection algorithms for the selection of optimal subsets of molecular descriptors from a much greater pool of such regression variables. The data set was split into 65 molecules as the training set and 16 compounds as the test set. All descriptors were generated by using the GRid INdependent descriptors (GRIND approach. After variable selection, GRIND were correlated with activity values (pIC50 by PLS regression. Of the two applied variable selection methods, ERM had a noticeable improvement on the statistical parameters of PLS model, and yielded a q2 value of 0.77, an rpred2 of 0.94, and a low RMSEP value of 0.25. The GRIND information contents influencing the affinity on Mer specific tyrosine kinase were also confirmed by docking studies. In a quantum calculation study, the energy difference between HOMO and LUMO (gap implied the high interaction of the most active molecule in the active site of the protein. In addition, the molecular electrostatic potential energy at DFT level confirmed results obtained from the molecular docking. The identified key features obtained from the molecular modeling, enabled us to design novel kinase inhibitors.

Alignment independent 3D-QSAR, quantum calculations and molecular docking of Mer specific tyrosine kinase inhibitors as anticancer drugs.

Science.gov (United States)

Shiri, Fereshteh; Pirhadi, Somayeh; Ghasemi, Jahan B

2016-03-01

Mer receptor tyrosine kinase is a promising novel cancer therapeutic target in many human cancers, because abnormal activation of Mer has been implicated in survival signaling and chemoresistance. 3D-QSAR analyses based on alignment independent descriptors were performed on a series of 81 Mer specific tyrosine kinase inhibitors. The fractional factorial design (FFD) and the enhanced replacement method (ERM) were applied and tested as variable selection algorithms for the selection of optimal subsets of molecular descriptors from a much greater pool of such regression variables. The data set was split into 65 molecules as the training set and 16 compounds as the test set. All descriptors were generated by using the GRid INdependent descriptors (GRIND) approach. After variable selection, GRIND were correlated with activity values (pIC50) by PLS regression. Of the two applied variable selection methods, ERM had a noticeable improvement on the statistical parameters of PLS model, and yielded a q (2) value of 0.77, an [Formula: see text] of 0.94, and a low RMSEP value of 0.25. The GRIND information contents influencing the affinity on Mer specific tyrosine kinase were also confirmed by docking studies. In a quantum calculation study, the energy difference between HOMO and LUMO (gap) implied the high interaction of the most active molecule in the active site of the protein. In addition, the molecular electrostatic potential energy at DFT level confirmed results obtained from the molecular docking. The identified key features obtained from the molecular modeling, enabled us to design novel kinase inhibitors.

Development of molecular markers for zebrafish (Danio rerio) ovarian follicle growth assessment following in-vitro culture in cryopreservation studies.

Science.gov (United States)

Anil, Siji; Rawson, David; Zhang, Tiantian

2018-05-29

Development of in vitro culture protocol for early stage ovarian follicles of zebrafish is important since cryopreserved early stage ovarian follicles would need to be matured in vitro following cryopreservation before they can be fertilised. Development of molecular markers for zebrafish (Danio rerio) ovarian follicle growth assessment following in vitro culture of early stage zebrafish ovarian follicles in ovarian tissue fragments is reported here for the first time although some work has been reported for in vitro culture of isolated early stage zebrafish ovarian follicles. The main aim of the present study was to develop molecular markers in an optimised in vitro culture protocol for stage I and stage II zebrafish ovarian follicles in ovarian tissue fragments. The effect of concentration of the hormones human chorionic gonadotropin and follicle stimulating hormones, and additives such as Foetal Bovine Serum and Bovine Serum Albumin were studied. The results showed that early stage zebrafish ovarian fragments containing stage I and stage II follicles which are cultured in vitro for 24 h in 20% FBS and 100mIU/ml FSH in 90% L-15 medium at 28 °C can grow to the size of stage II and stage III ovarian follicles respectively. More importantly the follicle growth from stage I to stage II and from stage II to stage III were confirmed using molecular markers such as cyp19a1a (also known as P450aromA) and vtg1 genes respectively. However, no follicle growth was observed following cryopreservation and in vitro culture. Copyright © 2018 Elsevier Inc. All rights reserved.

Development of a cell culture surface conversion technique using alginate thin film for evaluating effect upon cellular differentiation

International Nuclear Information System (INIS)

Nakashima, Y.; Tsusu, K.; Minami, K.; Nakanishi, Y.

2014-01-01

Here, we sought to develop a cell culture surface conversion technique that would not damage living cells. An alginate thin film, formed on a glass plate by spin coating of sodium alginate solution and dipping into calcium chloride solution, was used to inhibit adhesion of cells. The film could be removed by ethylenediaminetetraacetate (EDTA) at any time during cell culture, permitting observation of cellular responses to conversion of the culture surface in real time. Additionally, we demonstrated the validity of the alginate thin film coating method and the performance of the film. The thickness of the alginate thin film was controlled by varying the rotation speed during spin coating. Moreover, the alginate thin film completely inhibited the adhesion of cultured cells to the culture surface, irrespective of the thickness of the film. When the alginate thin film was removed from the culture surface by EDTA, the cultured cells adhered to the culture surface, and their morphology changed. Finally, we achieved effective differentiation of C2C12 myoblasts into myotube cells by cell culture on the convertible culture surface, demonstrating the utility of our novel technique

Analysis of Cultural Heritage by Accelerator Techniques and Analytical Imaging

Science.gov (United States)

Ide-Ektessabi, Ari; Toque, Jay Arre; Murayama, Yusuke

2011-12-01

In this paper we present the result of experimental investigation using two very important accelerator techniques: (1) synchrotron radiation XRF and XAFS; and (2) accelerator mass spectrometry and multispectral analytical imaging for the investigation of cultural heritage. We also want to introduce a complementary approach to the investigation of artworks which is noninvasive and nondestructive that can be applied in situ. Four major projects will be discussed to illustrate the potential applications of these accelerator and analytical imaging techniques: (1) investigation of Mongolian Textile (Genghis Khan and Kublai Khan Period) using XRF, AMS and electron microscopy; (2) XRF studies of pigments collected from Korean Buddhist paintings; (3) creating a database of elemental composition and spectral reflectance of more than 1000 Japanese pigments which have been used for traditional Japanese paintings; and (4) visible light-near infrared spectroscopy and multispectral imaging of degraded malachite and azurite. The XRF measurements of the Japanese and Korean pigments could be used to complement the results of pigment identification by analytical imaging through spectral reflectance reconstruction. On the other hand, analysis of the Mongolian textiles revealed that they were produced between 12th and 13th century. Elemental analysis of the samples showed that they contained traces of gold, copper, iron and titanium. Based on the age and trace elements in the samples, it was concluded that the textiles were produced during the height of power of the Mongol empire, which makes them a valuable cultural heritage. Finally, the analysis of the degraded and discolored malachite and azurite demonstrates how multispectral analytical imaging could be used to complement the results of high energy-based techniques.

Quantum chemical approaches: semiempirical molecular orbital and hybrid quantum mechanical/molecular mechanical techniques.

Science.gov (United States)

Bryce, Richard A; Hillier, Ian H

2014-01-01

The use of computational quantum chemical methods to aid drug discovery is surveyed. An overview of the various computational models spanning ab initio, density function theory, semiempirical molecular orbital (MO), and hybrid quantum mechanical (QM)/molecular mechanical (MM) methods is given and their strengths and weaknesses are highlighted, focussing on the challenge of obtaining the accuracy essential for them to make a meaningful contribution to drug discovery. Particular attention is given to hybrid QM/MM and semiempirical MO methods which have the potential to yield the necessary accurate predictions of macromolecular structure and reactivity. These methods are shown to have advanced the study of many aspects of substrate-ligand interactions relevant to drug discovery. Thus, the successful parametrization of semiempirical MO methods and QM/MM methods can be used to model noncovalent substrate-protein interactions, and to lead to improved scoring functions. QM/MM methods can be used in crystal structure refinement and are particularly valuable for modelling covalent protein-ligand interactions and can thus aid the design of transition state analogues. An extensive collection of examples from the areas of metalloenzyme structure, enzyme inhibition, and ligand binding affinities and scoring functions are used to illustrate the power of these techniques.

Semester-long inquiry-based molecular biology laboratory: Transcriptional regulation in yeast.

Science.gov (United States)

Oelkers, Peter M

2017-03-04

A single semester molecular biology laboratory has been developed in which students design and execute a project examining transcriptional regulation in Saccharomyces cerevisiae. Three weeks of planning are allocated to developing a hypothesis through literature searches and use of bioinformatics. Common experimental plans address a cell process and how three genes that encode for proteins involved in that process are transcriptionally regulated in response to changing environmental conditions. Planning includes designing oligonucleotides to amplify the putative promoters of the three genes of interest. After the PCR, each product is cloned proximal to β-galactosidase in a yeast reporter plasmid. Techniques used include agarose electrophoresis, extraction of DNA from agarose, plasmid purification from bacteria, restriction digestion, ligation, and bacterial transformation. This promoter/reporter plasmid is then transformed into yeast. Transformed yeast are cultured in conditions prescribed in the experimental design, lysed and β-galactosidase activity is measured. The course provides an independent research experience in a group setting. Notebooks are maintained on-line with regular feedback. Projects culminate with the presentation of a poster worth 60% of the grade. Over the last three years, about 65% of students met expectations for experimental design, data acquisition, and analysis. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(2):145-151, 2017. © 2016 The International Union of Biochemistry and Molecular Biology.

An in vitro, short-term culture method for mammalian haploid round spermatids amenable for molecular manipulation.

Science.gov (United States)

Dehnugara, Tushna; Dhar, Surbhi; Rao, M R Satyanarayana

2012-01-01

Extensive chromatin remodeling is a characteristic feature of mammalian spermiogenesis. To date, methods for the molecular manipulation of haploid spermatids are not available as there is a lack of a well-established culture system. Biochemical experiments and knockout studies reveal only the final outcome; studying the incremental details of the intricate mechanisms involved is still a challenge. We have established an in vitro culture system for pure haploid round spermatids isolated from rat testes that can be maintained with good viability for up to 72 hr. Changes in cell morphology and flagellar growth were also studied in the cultured spermatids. Further, we have demonstrated that upon treatment of cells with specific histone deacetylase inhibitors, sodium butyrate and trichostatin A, there is an increase in the hyperacetylation status of histone H4, mimicking an important event characteristic of histone replacement process that occurs during later stages of spermiogenesis. We have also tried various methods for introducing DNA and protein into these round spermatids in culture, and report that while DNA transfection is still a challenging task, protein transfection could be achieved using Chariot™ peptide as a transfection reagent. Thus, the method described here sets a stage to study the molecular roles of spermatid-specific proteins and chromatin remodelers in the cellular context. Copyright © 2011 Wiley Periodicals, Inc.

Variation of the Pseudomonas community structure on oak leaf lettuce during storage detected by culture-dependent and -independent methods.

Science.gov (United States)

Nübling, Simone; Schmidt, Herbert; Weiss, Agnes

2016-01-04

The genus Pseudomonas plays an important role in the lettuce leaf microbiota and certain species can induce spoilage. The aim of this study was to investigate the occurrence and diversity of Pseudomonas spp. on oak leaf lettuce and to follow their community shift during a six day cold storage with culture-dependent and culture-independent methods. In total, 21 analysed partial Pseudomonas 16S rRNA gene sequences matched closely (> 98.3%) to the different reference strain sequences, which were distributed among 13 different phylogenetic groups or subgroups within the genus Pseudomonas. It could be shown that all detected Pseudomonas species belonged to the P. fluorescens lineage. In the culture-dependent analysis, 73% of the isolates at day 0 and 79% of the isolates at day 6 belonged to the P. fluorescens subgroup. The second most frequent group, with 12% of the isolates, was the P. koreensis subgroup. This subgroup was only detected at day 0. In the culture-independent analysis the P. fluorescens subgroup and P. extremaustralis could not be differentiated by RFLP. Both groups were most abundant and amounted to approximately 46% at day 0 and 79% at day 6. The phytopathogenic species P. salmonii, P. viridiflava and P. marginalis increased during storage. Both approaches identified the P. fluorescens group as the main phylogenetic group. The results of the present study suggest that pseudomonads found by plating methods indeed represent the most abundant part of the Pseudomonas community on oak leaf lettuce. Copyright © 2015 Elsevier B.V. All rights reserved.

Cross-cultural validation of the Persian version of the Functional Independence Measure for patients with stroke.

Science.gov (United States)

Naghdi, Soofia; Ansari, Noureddin Nakhostin; Raji, Parvin; Shamili, Aryan; Amini, Malek; Hasson, Scott

2016-01-01

To translate and cross-culturally adapt the Functional Independence Measure (FIM) into the Persian language and to test the reliability and validity of the Persian FIM (PFIM) in patients with stroke. In this cross-sectional study carried out in an outpatient stroke rehabilitation center, 40 patients with stroke (mean age 60 years) were participated. A standard forward-backward translation method and expert panel validation was followed to develop the PFIM. Two experienced occupational therapists (OTs) assessed the patients independently in all items of the PFIM in a single session for inter-rater reliability. One of the OTs reassessed the patients after 1 week for intra-rater reliability. There were no floor or ceiling effects for the PFIM. Excellent inter-rater and intra-rater reliability was noted for the PFIM total score, motor and cognitive subscales (ICC(agreement)0.88-0.98). According to the Bland-Altman agreement analysis, there was no systematic bias between raters and within raters. The internal consistency of the PFIM was with Cronbach's alpha from 0.70 to 0.96. The principal component analysis with varimax rotation indicated a three-factor structure: (1) self-care and mobility; (2) sphincter control and (3) cognitive that jointly accounted for 74.8% of the total variance. Construct validity was supported by a significant Pearson correlation between the PFIM and the Persian Barthel Index (r = 0.95; p Persian patients with stroke. The Functional Independence Measure (FIM) is an outcome measure for disability based on the International Classification of Functioning, Disability and Health (ICF). The FIM was cross-culturally adapted and validated into Persian language. The Persian version of the FIM (PFIM) is reliable and valid for assessing functional status of patients with stroke. The PFIM can be used in Persian speaking countries to assess the limitations in activities of daily living of patients with stroke.

Bringing the banjo back to life: The field of dutch independent folk music as participatory culture

OpenAIRE

Poecke, Niels; Michael, Janna

2016-01-01

textabstractIn this paper we investigate factors underlying the production of independent folk music (indie folk) in the Netherlands. By studying the creation, distribution and reception of indie folk music through in-depth interviewing, we argue that the social production of indie folk music is affected by a shift towards 'participatory culture' brought about by the rise of the Internet and Web 2.0. We note how Web 2.0 helps musicians to educate themselves and to develop careers in music. Se...

Molecular features contributing to virus-independent intracellular localization and dynamic behavior of the herpesvirus transport protein US9.

Directory of Open Access Journals (Sweden)

Manuela Pedrazzi

Full Text Available Reaching the right destination is of vital importance for molecules, proteins, organelles, and cargoes. Thus, intracellular traffic is continuously controlled and regulated by several proteins taking part in the process. Viruses exploit this machinery, and viral proteins regulating intracellular transport have been identified as they represent valuable tools to understand and possibly direct molecules targeting and delivery. Deciphering the molecular features of viral proteins contributing to (or determining this dynamic phenotype can eventually lead to a virus-independent approach to control cellular transport and delivery. From this virus-independent perspective we looked at US9, a virion component of Herpes Simplex Virus involved in anterograde transport of the virus inside neurons of the infected host. As the natural cargo of US9-related vesicles is the virus (or its parts, defining its autonomous, virus-independent role in vesicles transport represents a prerequisite to make US9 a valuable molecular tool to study and possibly direct cellular transport. To assess the extent of this autonomous role in vesicles transport, we analyzed US9 behavior in the absence of viral infection. Based on our studies, Us9 behavior appears similar in different cell types; however, as expected, the data we obtained in neurons best represent the virus-independent properties of US9. In these primary cells, transfected US9 mostly recapitulates the behavior of US9 expressed from the viral genome. Additionally, ablation of two major phosphorylation sites (i.e. Y32Y33 and S34ES36 have no effect on protein incorporation on vesicles and on its localization on both proximal and distal regions of the cells. These results support the idea that, while US9 post-translational modification may be important to regulate cargo loading and, consequently, virion export and delivery, no additional viral functions are required for US9 role in intracellular transport.

Clinical Microbiology Laboratories' Adoption of Culture-Independent Diagnostic Tests Is a Threat to Foodborne-Disease Surveillance in the United States.

Science.gov (United States)

Shea, Shari; Kubota, Kristy A; Maguire, Hugh; Gladbach, Stephen; Woron, Amy; Atkinson-Dunn, Robyn; Couturier, Marc Roger; Miller, Melissa B

2017-01-01

INTRODUCTIONIn November 2015, the Centers for Disease Control and Prevention (CDC) sent a letter to state and territorial epidemiologists, state and territorial public health laboratory directors, and state and territorial health officials. In this letter, culture-independent diagnostic tests (CIDTs) for detection of enteric pathogens were characterized as "a serious and current threat to public health surveillance, particularly for Shiga toxin-producing Escherichia coli (STEC) and Salmonella" The document says CDC and its public health partners are approaching this issue, in part, by "reviewing regulatory authority in public health agencies to require culture isolates or specimen submission if CIDTs are used." Large-scale foodborne outbreaks are a continuing threat to public health, and tracking these outbreaks is an important tool in shortening them and developing strategies to prevent them. It is clear that the use of CIDTs for enteric pathogen detection, including both antigen detection and multiplex nucleic acid amplification techniques, is becoming more widespread. Furthermore, some clinical microbiology laboratories will resist the mandate to require submission of culture isolates, since it will likely not improve patient outcomes but may add significant costs. Specimen submission would be less expensive and time-consuming for clinical laboratories; however, this approach would be burdensome for public health laboratories, since those laboratories would need to perform culture isolation prior to typing. Shari Shea and Kristy Kubota from the Association of Public Health Laboratories, along with state public health laboratory officials from Colorado, Missouri, Tennessee, and Utah, will explain the public health laboratories' perspective on why having access to isolates of enteric pathogens is essential for public health surveillance, detection, and tracking of outbreaks and offer potential workable solutions which will allow them to do this. Marc Couturier of

Microbiological characterization of traditional dough fermentation starter (Jiaozi) for steamed bread making by culture-dependent and culture-independent methods.

Science.gov (United States)

Li, Zhijian; Li, Haifeng; Bian, Ke

2016-10-03

In this study, the microbial composition of two types of Jiaozi (a dough fermentation starter in making steamed bread) was investigated using both culture-dependent and culture-independent (PCR-DGGE) methods. The numbers of the cultivable bacteria on MRS at 30°C and yeast on YPD at 28°C in the maize flour Jiaozi (MFJ) were 9.21±0.16 Log CFU/g and 9.18±0.05 Log CFU/g, respectively, which were higher than that in the rice flour Jiaozi (RFJ) (Pyeasts were isolated and identified on the basis of the sequences of their 16S rRNA gene and ITS region. The culture-dependent method showed that Acetobacter tropicalis and Enterococcus durans were the predominant bacteria strains in MFJ, and accounted for 45.7% and 25.7% of the bacteria, and Lactobacillus plantarum and Pediococcus pentosaceus represented 12.8% and 8.6%. In the RFJ sample, the most prominent isolate was P. pentosaceus (38.6%), followed by L. plantarum (24.3%), A. tropicalis (22.8%), and E. durans (5.7%). P. pentosaceus and L. plantarum were also detected in both starters by PCR-DGGE, while some bacteria species such as A. tropicalis and E. durans, recovered as pure cultures, were not detected by direct PCR-DGGE. On the other hand, Lactobacillus brevis, Weissella sp. and Lactobacillus alimentarius detected by PCR-DGGE were not recovered in any of the media and conditions used. In the MFJ sample, the isolated main yeast species were identified as Wickerhamomyces anomalus (67.2%), Saccharomyces cerevisiae (27.9%) and Torulaspora delbrueckii (4.9%). In addition to S. cerevisiae (42.9%), W. anomalus (27.0%) and T. delbrueckii (7.9%), Saccharomycopsis fibuligera was also identified as the predominant isolate in RFJ samples and accounted for 22.2%. PCR-DGGE also indicated the presence of W. anomalus and S. cerevisiae in both MFJ and RFJ starters and S. fibuligera was also detected in RFJ, but T. delbrueckii was not detected in both samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Functional Molecular Junctions Derived from Double Self-Assembled Monolayers.

Science.gov (United States)

Seo, Sohyeon; Hwang, Eunhee; Cho, Yunhee; Lee, Junghyun; Lee, Hyoyoung

2017-09-25

Information processing using molecular junctions is becoming more important as devices are miniaturized to the nanoscale. Herein, we report functional molecular junctions derived from double self-assembled monolayers (SAMs) intercalated between soft graphene electrodes. Newly assembled molecular junctions are fabricated by placing a molecular SAM/(top) electrode on another molecular SAM/(bottom) electrode by using a contact-assembly technique. Double SAMs can provide tunneling conjugation across the van der Waals gap between the terminals of each monolayer and exhibit new electrical functions. Robust contact-assembled molecular junctions can act as platforms for the development of equivalent contact molecular junctions between top and bottom electrodes, which can be applied independently to different kinds of molecules to enhance either the structural complexity or the assembly properties of molecules. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A comparative study of techniques used for porous membrane characterization: pore characterization

NARCIS (Netherlands)

Broek, A.P.; Kim, K.J.; Fane, A.G.; Ben aim, R.; Liu, M.G.; Jonsson, G.; Tessaro, I.C.; Broek, A.P.; Bargeman, D.; Bargeman, D.

1994-01-01

A range of commerical UF membranes have been characterized by thermoporometry, biliquid permporometry and molecular weight cut-off experiments. A comparison of results from these three independent techniques for the same types of membrane shows an indication of the strength and weakness of the

Independent introduction of two lactase-persistence alleles into human populations reflects different history of adaptation to milk culture

DEFF Research Database (Denmark)

Enattah, Nabil Sabri; Jensen, Tine G K; Boyd, Mette

2008-01-01

the same history, probably related to the same cattle domestication event. In contrast, the compound Arab allele shows a different, highly divergent ancestral haplotype, suggesting that these two major global LP alleles have arisen independently, the latter perhaps in response to camel milk consumption....... These results support the convergent evolution of the LP in diverse populations, most probably reflecting different histories of adaptation to milk culture....

Culture Negative Infective Endocarditits: a Changing Paradigm

LENUS (Irish Health Repository)

Daly, A

2016-05-01

Traditionally, the modified Duke\\'s criteria, based primarily on positive blood cultures, is used to diagnose Infective Endocarditis (IE). However, reports demonstrate that 31% of cases are diagnosed as Culture Negative Infective Endocarditis (CNIE)1. Consequently, empiric broad-spectrum antibiotics are prescribed to cover unidentified organisms and, as a result, antibiotic therapy may be compromised. Molecular diagnostic techniques aid with identifying causative organisms in cases of CNIE and we question if the increasing use of such technologies will change the local epidemiology of CNIE. We present the first case of Tropheryma whipplei Infective Endocarditis (TWIE) reported in Ireland.

Molecular basis of structural make-up of feeds in relation to nutrient absorption in ruminants, revealed with advanced molecular spectroscopy: A review on techniques and models

Energy Technology Data Exchange (ETDEWEB)

Rahman, Md. Mostafizar [Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; Yu, Peiqiang [Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada

2017-01-31

Progress in ruminant feed research is no more feasible only based on wet chemical analysis, which is merely able to provide information on chemical composition of feeds regardless of their digestive features and nutritive value in ruminants. Studying internal structural make-up of functional groups/feed nutrients is often vital for understanding the digestive behaviors and nutritive values of feeds in ruminant because the intrinsic structure of feed nutrients is more related to its overall absorption. In this article, the detail information on the recent developments in molecular spectroscopic techniques to reveal microstructural information of feed nutrients and the use of nutrition models in regards to ruminant feed research was reviewed. The emphasis of this review was on (1) the technological progress in the use of molecular spectroscopic techniques in ruminant feed research; (2) revealing spectral analysis of functional groups of biomolecules/feed nutrients; (3) the use of advanced nutrition models for better prediction of nutrient availability in ruminant systems; and (4) the application of these molecular techniques and combination of nutrient models in cereals, co-products and pulse crop research. The information described in this article will promote better insight in the progress of research on molecular structural make-up of feed nutrients in ruminants.

[Application of molecular diagnostic techniques in precision medicine of personalized treatment for colorectal cancer].

Science.gov (United States)

Fu, Ji; Lin, Guole

2016-01-01

Precision medicine is to customize the treatment options for individual patient based on the personal genome information. Colorectal cancer (CRC) is one of the most common cancer worldwide. Molecular heterogeneity of CRC, which includes the MSI phenotype, hypermutation phenotype, and their relationship with clinical preferences, is believed to be one of the main factors responsible for the considerable variability in treatment response. The development of powerful next-generation sequencing (NGS) technologies allows us to further understand the biological behavior of colorectal cancer, and to analyze the prognosis and chemotherapeutic drug reactions by molecular diagnostic techniques, which can guide the clinical treatment. This paper will introduce the new findings in this field. Meanwhile we integrate the new progress of key pathways including EGFR, RAS, PI3K/AKT and VEGF, and the experience in selective patients through associated molecular diagnostic screening who gain better efficacy after target therapy. The technique for detecting circulating tumor DNA (ctDNA) is introduced here as well, which can identify patients with high risk for recurrence, and demonstrate the risk of chemotherapy resistance. Mechanism of tumor drug resistance may be revealed by dynamic observation of gene alteration during treatment.

Mechanistic insights into Mg2+-independent prenylation by CloQ from classical molecular mechanics and hybrid quantum mechanics/molecular mechanics molecular dynamics simulations.

Science.gov (United States)

Bayse, Craig A; Merz, Kenneth M

2014-08-05

Understanding the mechanism of prenyltransferases is important to the design of engineered proteins capable of synthesizing derivatives of naturally occurring therapeutic agents. CloQ is a Mg(2+)-independent aromatic prenyltransferase (APTase) that transfers a dimethylallyl group to 4-hydroxyphenylpyruvate in the biosynthetic pathway for clorobiocin. APTases consist of a common ABBA fold that defines a β-barrel containing the reaction cavity. Positively charged basic residues line the inside of the β-barrel of CloQ to activate the pyrophosphate leaving group to replace the function of the Mg(2+) cofactor in other APTases. Classical molecular dynamics simulations of CloQ, its E281G and F68S mutants, and the related NovQ were used to explore the binding of the 4-hydroxyphenylpyruvate (4HPP) and dimethylallyl diphosphate substrates in the reactive cavity and the role of various conserved residues. Hybrid quantum mechanics/molecular mechanics potential of mean force (PMF) calculations show that the effect of the replacement of the Mg(2+) cofactor with basic residues yields a similar activation barrier for prenylation to Mg(2+)-dependent APTases like NphB. The topology of the binding pocket for 4HPP is important for selective prenylation at the ortho position of the ring. Methylation at this position alters the conformation of the substrate for O-prenylation at the phenol group. Further, a two-dimensional PMF scan shows that a "reverse" prenylation product may be a possible target for protein engineering.

Mise au point d'une technique de culture in vitro d'embryons immatures de Phaseolus

Directory of Open Access Journals (Sweden)

Véronique Schmit

1997-01-01

Full Text Available Development of an in vitro culture technique for immature Phaseolus embryos. In the interspecific crosses Phaseolus polyanthus (or P. coccineus (i? x P. vulgaris, the hybrid embryos abort very early. Therefore, it is essentiel to develop an in vitro culture technique that allows the rescue of beau embryos at globular or early heart-shaped stages. After several trials conceming the salts composition, the sugar rate and the amino acid concentration of différent in vitro culture media, a technique has been developed for heart-shaped Phaseolus embryos. This technique consists of two stages. In a first step, embryos are cultivated under darkness until their germination on a medium containing the salts of Gamborg et al. (1968, 400 mg . 1` (5mM - 1 -' NHNO,, 1 mg . 1-' thiamine HCI, 5 mg . l` nicotinic acid, 0.5 mg - l` pyridoxine, 1,000 mg . l` -glutamine, 1,000 mg . l` casein hydrolysate, 100 mg . l` myo-inositol, 0.028 mg . P N6-benzyladenine, 30 g . l` sucrase, and 8 g -1-' DIFCO agar. After germination, the embryos are cultivated under light on a second medium that does not contain any NHNO, complément and is poorer in amino acids (100 mg • 1-' L-glutamine. Developed with six deys old heart-shaped embryos of the P. vulgaris Bico de Ouro (NI 637 variety, this technique has proved its efficiency with other P. vulgaris and P. polyanthus génotypes. It allows an average régénération rate of 30% from the total number of cultivated embryos.

Development of nonintrusive, scatter-independent techniques for measurement of liquid density inside dense sprays

Science.gov (United States)

Hartfield, Roy

1994-01-01

A nonintrusive optical technique for measuring the liquid density in sprays used to simulate LOX injector flows is under development. This manuscript is a report on work toward that development which is currently in progress. The technique is a scatter-independent, absorption-based approach which depends on the numerical inversion of a collection of absorption profiles. For the case in which visible radiation passes through liquid-gas interfaces so numerous in sprays, substantial reductions and alterations in the signal result from scattering even in the absence of absorption. To avoid these problems, X-Rays will be used as the absorbed radiation. The experimental process is simulated by integrating the absorption spectrum for a known distribution, adding instrument noise to this 'measurement', creating a projection from the 'measurement', filtering the projection, inverting the projection, and comparing the results with the original prescribed distribution.

Application of molecular methods for monitoring transmission stages of malaria parasites

International Nuclear Information System (INIS)

Babiker, Hamza A; Schneider, Petra

2008-01-01

Recent technical advances in malaria research have allowed specific detection of mRNA of genes that are expressed exclusively in sexual stages (gametocytes) of malaria parasites. The specificity and sensitivity of these techniques were validated on cultured laboratory clones of both human malaria parasites (Plasmodium falciparum) and rodent parasites (P. chabaudi). More recently, quantitative molecular techniques have been developed to quantify these sexual stages and used to monitor gametocyte dynamics and their transmission to mosquitoes. Molecular techniques showed that the infectious reservoir for malaria is larger than expected from previous microscopic studies; individual parasite genotypes within an infection can simultaneously produce infectious gametocytes; gametocyte production can be sustained for several months, and is modulated by environmental factors. The above techniques have empowered approaches for in-depth analysis of the biology of the transmission stages of the parasite and epidemiology of malaria transmission

The examination of Hevea brasiliensis plants produced by in vitro culture and mutagenesis by DNA fingerprinting techniques

International Nuclear Information System (INIS)

Low, F.C.; Atan, S.; Jaafar, H.

1998-01-01

Rubber (Hevea brasiliensis) plants derived from anther and ovule culture as well as gamma-irradiated plants were examined by several DNA marker techniques. These include restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPD), sequence tagged microsatellite sites (STMS), DNA amplification fingerprinting (DAF) and amplified fragment length polymorphisms (AFLPs). Compared to control plants produced by vegetative propagation (cutting and budding), plants produced by in vitro culture appeared to have a reduction in the number of rDNA loci. Two RAPD protocols were compared and found to be similar in amplification of the major DNA bands. After confirmation that the RAPD method adopted was reproducible, the technique was applied to the present studies. Eight out of the 60 primers screened were able to elicit polymorphisms between pooled DNA from in vitro culture plants. Variations in DNA patterns were observed between pooled DNA samples of anther-derived plants as well as between anther-derived and ovule-derived plants. Comparisons of RAPD patterns obtained between anther-derived plants exposed to increasing dosages of gamma-irradiation with non irradiated anther-derived plants revealed distinct DNA polymorphisms. The changes in DNA profiles did not appear to be correlated to the dosage of irradiation. Since somaclonal variation was detected, it was difficult to identify changes which were specifically caused by irradiation. Application of the STMS technique to tag micro satellite sequences (GA) n , (TA) n and (TTA) n in the hydroxymethylglutaryl coenzyme A reductase-1 (hmgr-1) gene failed to detect differences between plants derived from anther and ovule culture. Although restriction endonuclease digestions with methylation sensitive enzymes suggested that four in vitro culture plants examined exhibited similar digestion patterns as the controls, a change in cytosine methylation in one anther-derived plant was detected. Examination of

Molecular diversity and tools for deciphering the methanogen community structure and diversity in freshwater sediments.

Science.gov (United States)

Chaudhary, Prem Prashant; Brablcová, Lenka; Buriánková, Iva; Rulík, Martin

2013-09-01

Methanogenic archaeal communities existing in freshwater sediments are responsible for approximately 50 % of the total global emission of methane. This process contributes significantly to global warming and, hence, necessitates interventional control measures to limit its emission. Unfortunately, the diversity and functional interactions of methanogenic populations occurring in these habitats are yet to be fully characterized. Considering several disadvantages of conventional culture-based methodologies, in recent years, impetus is given to molecular biology approaches to determine the community structure of freshwater sedimentary methanogenic archaea. 16S rRNA and methyl coenzyme M reductase (mcrA) gene-based cloning techniques are the first choice for this purpose. In addition, electrophoresis-based (denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and terminal restriction fragment length polymorphism) and quantitative real-time polymerase chain reaction techniques have also found extensive applications. These techniques are highly sensitive, rapid, and reliable as compared to traditional culture-dependent approaches. Molecular diversity studies revealed the dominance of the orders Methanomicrobiales and Methanosarcinales of methanogens in freshwater sediments. The present review discusses in detail the status of the diversity of methanogens and the molecular approaches applied in this area of research.

Diversity of thermophilic bacteria in raw, pasteurized and selectively-cultured milk, as assessed by culturing, PCR-DGGE and pyrosequencing.

Science.gov (United States)

Delgado, Susana; Rachid, Caio T C C; Fernández, Elena; Rychlik, Tomasz; Alegría, Angel; Peixoto, Raquel S; Mayo, Baltasar

2013-10-01

Thermophilic lactic acid bacteria (LAB) species, such as Streptococcus thermophilus, Lactobacillus delbrueckii and Lactobacillus helveticus, enjoy worldwide economic importance as dairy starters. To assess the diversity of thermophilic bacteria in milk, milk samples were enriched in thermophilic organisms through a stepwise procedure which included pasteurization of milk at 63 °C for 30 min (PM samples) and pasteurization followed by incubation at 42 °C for 24 h (IPM samples). The microbial composition of these samples was analyzed by culture-dependent (at 42 °C) and culture-independent (PCR-DGGE and pyrosequencing of 16S rRNA gene amplicons) microbial techniques. The results were then compared to those obtained for their corresponding starting raw milk counterparts (RM samples). Twenty different species were scored by culturing among 352 isolates purified from the counting plates and identified by molecular methods. Mesophilic LAB species (Lactococcus lactis, Lactococcus garvieae) were dominant (87% of the isolates) among the RM samples. However, S. thermophilus and Lb. delbrueckii were found to be the dominant recoverable organisms in both PM and IPM samples. The DGGE profiles of RM and PM samples were found to be very similar; the most prominent bands belonging to Lactococcus, Leuconostoc and Streptococcus species. In contrast, just three DGGE bands were obtained for IPM samples, two of which were assigned to S. thermophilus. The pyrosequencing results scored 95 operational taxonomic units (OTUs) at 3% sequence divergence in an RM sample, while only 13 were encountered in two IPM samples. This technique identified Leuconostoc citreum as the dominant microorganism in the RM sample, while S. thermophilus constituted more than 98% of the reads in the IPM samples. The procedure followed in this study allowed to estimate the bacterial diversity in milk and afford a suitable strategy for the isolation of new thermophilic LAB strains, among which adequate

Comparison of gene expression profile in embryonic mesencephalon and neuronal primary cultures.

Directory of Open Access Journals (Sweden)

Dario Greco

Full Text Available In the mammalian central nervous system (CNS an important contingent of dopaminergic neurons are localized in the substantia nigra and in the ventral tegmental area of the ventral midbrain. They constitute an anatomically and functionally heterogeneous group of cells involved in a variety of regulatory mechanisms, from locomotion to emotional/motivational behavior. Midbrain dopaminergic neuron (mDA primary cultures represent a useful tool to study molecular mechanisms involved in their development and maintenance. Considerable information has been gathered on the mDA neurons development and maturation in vivo, as well as on the molecular features of mDA primary cultures. Here we investigated in detail the gene expression differences between the tissue of origin and ventral midbrain primary cultures enriched in mDA neurons, using microarray technique. We integrated the results based on different re-annotations of the microarray probes. By using knowledge-based gene network techniques and promoter sequence analysis, we also uncovered mechanisms that might regulate the expression of CNS genes involved in the definition of the identity of specific cell types in the ventral midbrain. We integrate bioinformatics and functional genomics, together with developmental neurobiology. Moreover, we propose guidelines for the computational analysis of microarray gene expression data. Our findings help to clarify some molecular aspects of the development and differentiation of DA neurons within the midbrain.

Metabolomics reveals distinct, antibody-independent, molecular signatures of MS, AQP4-antibody and MOG-antibody disease.

Science.gov (United States)

Jurynczyk, Maciej; Probert, Fay; Yeo, Tianrong; Tackley, George; Claridge, Tim D W; Cavey, Ana; Woodhall, Mark R; Arora, Siddharth; Winkler, Torsten; Schiffer, Eric; Vincent, Angela; DeLuca, Gabriele; Sibson, Nicola R; Isabel Leite, M; Waters, Patrick; Anthony, Daniel C; Palace, Jacqueline

2017-12-06

conditions are indeed different at a molecular level. The metabolites identified provide a molecular signature of each condition which is independent of antibody titre and EDSS, with potential use for disease monitoring and diagnosis.

[Molecular diagnostic methods of respiratory infections. Has the scheme diagnosis changed?].

Science.gov (United States)

Vila Estapé, Jordi; Zboromyrska, Yuliya; Vergara Gómez, Andrea; Alejo Cancho, Izaskun; Rubio García, Elisa; Álvarez-Martínez, Miriam José; la Bellacasa Brugada, Jorge Puig de; Marcos Maeso, M Ángeles

2016-07-01

Lower respiratory tract infections remain one of the most common causes of mortality worldwide, which is why early diagnosis is crucial. Traditionally the microbiological diagnosis of these infections has been based on conventional methods including culture on artificial media for isolation of bacteria and fungi and cell cultures for virus and antibody or antigen detection using antigen-antibody reactions. The main drawback of the above mentioned methods is the time needed for an etiological diagnosis of the infection. The techniques based on molecular biology have drawn much attention in recent decades as tools for rapid diagnosis of infections. Some techniques are very expensive, especially those that can detect various microorganisms in the same reaction, therefore the question that arises is whether the cost of such testing is justified by the information obtained and by the clinical impact that its implementation will determine. In this article we make a review of the various techniques of molecular biology applied to the diagnosis of pneumonia and focus primarily on analysing the impact they may have on the management of patients with acute respiratory tract infections. Copyright © 2016 Elsevier España, S.L.U. All rights reserved.

Utility of the molecular biology techniques to the analytical control of the microbiological quality of waters

International Nuclear Information System (INIS)

Codony, F.; Martin Perez, L.; Morato, J.; Dominguez Gual, M. C.

2009-01-01

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.

Project 'Use of nuclear techniques in investigation, conservation and management of the cultural historical patrimony

International Nuclear Information System (INIS)

Kochmann, Sonnia

2000-12-01

This project is aimed at solving problems of conservation of the cultural historical patrimony through the active participation of the member countries of ARCAL by the application of Analytic Nuclear Techniques [es

Gender identification of Grasshopper Sparrows comparing behavioral, morphological, and molecular techniques

Science.gov (United States)

Ammer, F.K.; Wood, P.B.; McPherson, R.J.

2008-01-01

Correct gender identification in monomorphic species is often difficult especially if males and females do not display obvious behavioral and breeding differences. We compared gender specific morphology and behavior with recently developed DNA techniques for gender identification in the monomorphic Grasshopper Sparrow (Ammodramus savannarum). Gender was ascertained with DNA in 213 individuals using the 2550F/2718R primer set and 3% agarose gel electrophoresis. Field observations using behavior and breeding characteristics to identify gender matched DNA analyses with 100% accuracy for adult males and females. Gender was identified with DNA for all captured juveniles that did not display gender specific traits or behaviors in the field. The molecular techniques used offered a high level of accuracy and may be useful in studies of dispersal mechanisms and winter assemblage composition in monomorphic species.

Molecular techniques for the identification and detection of microorganisms relevant for the food industry

NARCIS (Netherlands)

Klijn, N.

1996-01-01

The research described in this thesis concerns the development and application in food microbiology of molecular identification and detection techniques based on 16S rRNA sequences. The technologies developed were applied to study the microbial ecology of two groups of bacteria, namely

Acid protease and formation of multiple forms of glucoamylase in batch and continuous cultures of Aspergillus niger

DEFF Research Database (Denmark)

Aalbæk, Thomas; Reeslev, Morten; Jensen, Bo

2002-01-01

with molecular weights of approx. 91 (GAI), 73 (GAII), and 59 kDa (GAIII). Data from batch fermentations with constant pH 3.0 and 5.0 showed a uniform distribution of extracellular GA forms throughout the fermentations and independent of culture growth phases. Furthermore, steady-state data from chemostat...

Molecular Approaches to Studying Denitrification

Science.gov (United States)

Voytek, M. A.

2001-05-01

Denitrification is carried out by a diverse array of microbes, mainly as an alternative mode of respiration that allows the organisms to respire using oxidized N compounds instead of oxygen. A common approach in biogeochemistry to the study of the regulation of denitrification is to assess activity by mass balance of substrates and products or direct rate measurements and has intrinsically assumed resource regulation of denitrification. Reported rates can vary significantly even among ecosystems characterized by similar environmental conditions, thus indicating that direct control by abiotic factors often is not sufficient to predict denitrification rates accurately in natural environments. Alternatively, a microbiological approach would proceed with the identification of the organisms responsible and an evaluation of the effect of environmental factors on the biochemical pathways involved. Traditional studies have relied on culturing techniques, such as most probable number enrichments, and have failed to assess the role of the predominately uncultivable members of the microbial community. A combination of biogeochemical measurements and the assessment of the microbial community is necessary and becoming increasingly possible with the development and application of molecular techniques. In order to understand how the composition and physiological behavior of the microbial community affects denitrification rates, we use a suite of molecular techniques developed for phylogenetic and metabolic characterization of denitrifying communities. Molecular tools available for quantifying denitrifying bacteria and assessing their diversity and activity are summarized. Their application is illustrated with examples from marine and freshwater environments. Emerging techniques and their application to ground water studies will be discussed.

FEL induced molecular operation on cultured fibroblast and cholesterol ester

International Nuclear Information System (INIS)

Awazu, Kunio; Ogino, Seiji; Nishimura, Eiichi; Tomimasu, Takio; Yasumoto, Masato.

1997-01-01

Free Electron Lasers can be used to molecular operation such as the delivery of a number of molecules into cells or the separation of cholesterol ester. First, cultured NIH3T3 cells are exposed to high-intensity short pulse Free Electron Laser (FEL). The FEL is tuned to an absorption maximum wavelength, 6.1 μm, which was measured by microscopic FTIR. A fluorescence dye in the cell suspension is more absorbed into the cell with the FEL exposure due to the FEL-induced mechanical stress to the cell membrane. A quantitative fluorescence microscopy is used to determine the efficiency of delivery. Second, as a compound in a lipid cell, cholesterol ester was exposed to 5.75 μm FEL. FTIR measurement was done to evaluate the modification of the cholesterol ester. The result showed that the fluorescence intensity of sample cells were higher than that of control cells, and there was significant difference between the control and the sample group. Blebbing and the colony formation of the cells were observed for cells with mechanical stress. As for the cholesterol ester, it can be modified by the FEL irradiation. These results showed that FEL can be used as a molecular operational tool by photo-chemical and photo-mechanical interaction. (author)

Low Fluid Shear Culture of Staphylococcus Aureus Represses hfq Expression and Induces an Attachment-Independent Biofilm Phenotype

Science.gov (United States)

Ott, C. Mark; Castro, S. L.; Nickerson, C. A.; Nelman-Gonzalez, M.

2011-01-01

Background: The opportunistic pathogen, Staphylococcus aureus, experiences fluctuations in fluid shear during infection and colonization of a human host. Colonization frequently occurs at mucus membrane sites such as in the gastrointestinal tract where the bacterium may experience low levels of fluid shear. The response of S. aureus to low fluid shear remains unclear. Methods: S. aureus was cultured to stationary phase using Rotating-Wall Vessel (RWV) bioreactors which produce a physiologically relevant low fluid shear environment. The bacterial aggregates that developed in the RWV were evaluated by electron microscopy as well as for antibiotic resistance and other virulence-associated stressors. Genetic expression profiles for the low-shear cultured S. aureus were determined by microarray analysis and quantitative real-time PCR. Results: Planktonic S. aureus cultures in the low-shear environment formed aggregates completely encased in high amounts of extracellular polymeric substances. In addition, these aggregates demonstrated increased antibiotic resistance indicating attachment-independent biofilm formation. Carotenoid production in the low-shear cultured S. aureus was significantly decreased, and these cultures displayed an increased susceptibility to oxidative stress and killing by whole blood. The hfq gene, associated with low-shear growth in Gram negative organisms, was also found to be down-regulated in S. aureus. Conclusions: Collectively, this data suggests that S. aureus decreases virulence characteristics in favor of a biofilm-dwelling colonization phenotype in response to a low fluid shear environment. Furthermore, the identification of an Hfq response to low-shear culture in S. aureus, in addition to the previously reported responses in Gram negative organisms, strongly suggests an evolutionarily conserved response to mechanical stimuli among structurally diverse prokaryotes.

Mutation breeding for disease resistance using in-vitro culture techniques

International Nuclear Information System (INIS)

1985-07-01

Breeding for disease resistance is a major aspect of plant breeding, which may take at least 20% of a plant breeder's time, effort and budget. Nevertheless, numerous resistance problems remain unsolved and present major constraints to the production of food, feed, fiber and industrial commodities. The application of novel biotechnology and genetic engineering will extend the possibilities of conventional plant breeding. Therefore a meeting of experts in plant protection, plant breeding and in-vitro culture technology was convened by the Joint FAO/IAEA Division in Vienna. The experts were asked to discuss and give advice on prospects of biotechnology, especially plant in-vitro cultures, to contribute towards improved chances of success in mutation breeding for disease resistance. The plant breeder, in searching for resistance to a particular pathogen, like for any other desirable character, needs genetic variation to begin with. In addition he needs an appropriate screening method to detect the desired character. Science has developed so fast that it is now time to apply the existing knowledge of biotechnology to practical problems in agriculture, also in developing countries. In the near future this may be true also for novel techniques of genetic engineering. The usefulness and feasibility of the application of in-vitro techniques for these purposes varies with crops and pathogens, but also depends on the strength of plant breeding and plant pathology and the facilities available in a particular country. The members of the Advisory Group attempted to discuss the various aspects and to reach sound conclusions

X-ray tomographic techniques for the study of cultural heritages

International Nuclear Information System (INIS)

Schillaci, T.

2011-01-01

In recent years, X-ray Computed Tomography (CT) has become an important tool for investigating all kinds of materials. Due to its non-destructive nature, it is especially suitable to investigate samples that may not be altered or damaged during the course of the investigation. CT has been recently introduced in the field of Cultural Heritage diagnostics, where it can be used for the investigation of different works of art, as it preserves the integrity of the object and gives morphological and physical information on its inner structure. This paper describes a methodological approach on the use of the X-ray CT technique to study items belonging to cultural heritage with the aim to obtain information related to their preservation state and therefore, to plan an adequate conservation and restoration procedure. Significant examples of applications are the study of porosity and pore size distribution and their connectivity for different porous materials and the study of kinetics of capillary fluid absorption in sedimentary rocks. Other applications are relevant to the possibility to investigate in a non-destructive way the presence of defects or fractures inside an object and, not last in order of importance, the possibility to study different typologies of woods or waterlogged woods, the presence of an eventual biodegradation state and the possibility to perform a dendrochronology. In this paper, the results of some case studies, obtained through the integrated use of CT systems with different resolutions, are reported. Other expected future developments will be addressed to the integration of CT data with results of compatible non-destructive techniques.

A multiscale simulation technique for molecular electronics: design of a directed self-assembled molecular n-bit shift register memory device

International Nuclear Information System (INIS)

Lambropoulos, Nicholas A; Reimers, Jeffrey R; Crossley, Maxwell J; Hush, Noel S; Silverbrook, Kia

2013-01-01

A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology. (paper)

A multiscale simulation technique for molecular electronics: design of a directed self-assembled molecular n-bit shift register memory device

Science.gov (United States)

Lambropoulos, Nicholas A.; Reimers, Jeffrey R.; Crossley, Maxwell J.; Hush, Noel S.; Silverbrook, Kia

2013-12-01

A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology.

A multiscale simulation technique for molecular electronics: design of a directed self-assembled molecular n-bit shift register memory device.

Science.gov (United States)

Lambropoulos, Nicholas A; Reimers, Jeffrey R; Crossley, Maxwell J; Hush, Noel S; Silverbrook, Kia

2013-12-20

A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology.

Comparing culture and molecular methods for the identification of microorganisms involved in necrotizing soft tissue infections

DEFF Research Database (Denmark)

Rudkjøbing, Vibeke Børsholt; Thomsen, Trine Rolighed; Xu, Yijuan

2016-01-01

BACKGROUND: Necrotizing soft tissue infections (NSTIs) are a group of infections affecting all soft tissues. NSTI involves necrosis of the afflicted tissue and is potentially life threatening due to major and rapid destruction of tissue, which often leads to septic shock and organ failure. The gold...... to culture. Although the molecular methods generally gave concordant results, our results indicate that Microseq may misidentify or overlook microorganisms that can be detected by other molecular methods. Half of the patients were found to be infected with S. pyogenes, but several atypical findings were also...... that clinicians should be prepared to diagnose and treat any combination of microbial pathogens. Some of the tested molecular methods offer a faster turnaround time combined with a high specificity, which makes supplemental use of such methods attractive for identification of microorganisms, especially...

Identification and characterization of lactic acid bacteria and yeasts of PDO Tuscan bread sourdough by culture dependent and independent methods.

Science.gov (United States)

Palla, Michela; Cristani, Caterina; Giovannetti, Manuela; Agnolucci, Monica

2017-06-05

Sourdough fermentation has been increasingly used worldwide, in accordance with the demand of consumers for tasty, natural and healthy food. The high diversity of lactic acid bacteria (LAB) and yeast species, detected in sourdoughs all over the world, may affect nutritional, organoleptic and technological traits of leavened baked goods. A wide regional variety of traditional sourdough breads, over 200 types, has been recorded in Italy, including special types selected as worthy of either Protected Geographical Indication (PGI) or Protected Designation of Origin (PDO), whose sourdough microbiota has been functionally and molecularly characterized. As, due to the very recent designation, the microbiota of Tuscan bread sourdough has not been investigated so far, the aim of the present work was to isolate and characterize the species composition of LAB and yeasts of PDO Tuscan bread sourdough by culture-independent and dependent methods. A total of 130 yeasts from WLN medium and 193 LAB from both mMRS and SDB media were isolated and maintained to constitute the germplasm bank of PDO Tuscan bread. Ninety six LAB from mMRS medium and 68 yeasts from WLN medium were randomly selected and molecularly identified by ARDRA (Amplified Ribosomal DNA Restriction Analysis) and PCR-RFLP analysis of the ITS region, respectively, and sequencing. The yeast identity was confirmed by 26S D1/D2 sequencing. All bacterial isolates showed 99% identity with Lactobacillus sanfranciscensis, 65 yeast isolates were identified as Candida milleri, and 3 as Saccharomyces cerevisiae. Molecular characterization of PDO Tuscan bread sourdough by PCR-DGGE confirmed such data. The distinctive tripartite species association, detected as the microbiota characterizing the sourdough used to produce PDO Tuscan bread, encompassed a large number of L. sanfranciscensis and C. milleri strains, along with a few of S. cerevisiae. The relative composition and specific physiological characteristics of such microbiota

Culture-Negative Endocarditis Diagnosed Using 16S DNA Polymerase Chain Reaction

Directory of Open Access Journals (Sweden)

Stephen Duffett

2012-01-01

Full Text Available 16S DNA polymerase chain reaction (PCR is a molecular amplification technique that can be used to identify bacterial pathogens in culture-negative endocarditis. Bacterial DNA can be isolated from surgically excised valve tissue or from blood collected in EDTA vials. Use of this technique is particularly helpful in identifying the bacterial pathogen in cases of culture-negative endocarditis. A case involving a 48-year-old man who presented with severe aortic regurgitation and a four-month prodrome of low-grade fever is reported. Blood and valve tissue cultures following valve replacement were negative. A valve tissue sample was sent for investigation with 16S DNA PCR, which successfully identified Streptococcus salivarius and was interpreted as the true diagnosis. A review of the literature suggests that 16S DNA PCR from valve tissue is a more sensitive diagnostic test than culture. It is also extremely specific, based on a sequence match of at least 500 base pairs.

Molecular genetic techniques for gene manipulation in Candida albicans.

Science.gov (United States)

Xu, Qiu-Rong; Yan, Lan; Lv, Quan-Zhen; Zhou, Mi; Sui, Xue; Cao, Yong-Bing; Jiang, Yuan-Ying

2014-05-15

Candida albicans is one of the most common fungal pathogen in humans due to its high frequency as an opportunistic and pathogenic fungus causing superficial as well as invasive infections in immunocompromised patients. An understanding of gene function in C. albicans is necessary to study the molecular basis of its pathogenesis, virulence and drug resistance. Several manipulation techniques have been used for investigation of gene function in C. albicans, including gene disruption, controlled gene expression, protein tagging, gene reintegration, and overexpression. In this review, the main cassettes containing selectable markers used for gene manipulation in C. albicans are summarized; the advantages and limitations of these cassettes are discussed concerning the influences on the target gene expression and the virulence of the mutant strains.

Intestinal microbiota in human health and disease: the impact of probiotics

NARCIS (Netherlands)

Gerritsen, J.; Smidt, H.; Rijkers, G.T.; Vos, de W.M.

2011-01-01

The complex communities of microorganisms that colonise the human gastrointestinal tract play an important role in human health. The development of culture-independent molecular techniques has provided new insights in the composition and diversity of the intestinal microbiota. Here, we summarise the

Molecular diagnostic methods for invasive fungal disease: the horizon draws nearer?

Science.gov (United States)

Halliday, C L; Kidd, S E; Sorrell, T C; Chen, S C-A

2015-04-01

Rapid, accurate diagnostic laboratory tests are needed to improve clinical outcomes of invasive fungal disease (IFD). Traditional direct microscopy, culture and histological techniques constitute the 'gold standard' against which newer tests are judged. Molecular diagnostic methods, whether broad-range or fungal-specific, have great potential to enhance sensitivity and speed of IFD diagnosis, but have varying specificities. The use of PCR-based assays, DNA sequencing, and other molecular methods including those incorporating proteomic approaches such as matrix-assisted laser desorption ionisation-time of flight mass spectroscopy (MALDI-TOF MS) have shown promising results. These are used mainly to complement conventional methods since they require standardisation before widespread implementation can be recommended. None are incorporated into diagnostic criteria for defining IFD. Commercial assays may assist standardisation. This review provides an update of molecular-based diagnostic approaches applicable to biological specimens and fungal cultures in microbiology laboratories. We focus on the most common pathogens, Candida and Aspergillus, and the mucormycetes. The position of molecular-based approaches in the detection of azole and echinocandin antifungal resistance is also discussed.

Molecular Phylogenetic Exploration of Bacterial Diversity in a Bakreshwar (India) Hot Spring and Culture of Shewanella-Related Thermophiles

Science.gov (United States)

Ghosh, Dhritiman; Bal, Bijay; Kashyap, V. K.; Pal, Subrata

2003-01-01

The bacterial diversity of a hot spring in Bakreshwar, India, was investigated by a culture-independent approach. 16S ribosomal DNA clones derived from the sediment samples were found to be associated with gamma-Proteobacteria, cyanobacteria, and green nonsulfur and low-GC gram-positive bacteria. The first of the above phylotypes cobranches with Shewanella, a well-known iron reducer. This phylogenetic correlation has been exploited to develop culture conditions for thermophilic iron-reducing microorganisms. PMID:12839826

Experimental Methodology used by Cell Cultures Laboratory from INRMFB to assess the therapeutic effect of natural factors

Directory of Open Access Journals (Sweden)

Munteanu Constantin

2010-11-01

Full Text Available The experimental study design on cell cultures allows the direct biological evaluation at the cellular level, of the therapeutic effect that natural factors can play over the organism.Techniques for obtaining cell cultures requires a complex and laborious task that starts from live tissue sampling, continuous with isolation of cells and their preparation for sowing a culture plate. This preparation involves mechanical and enzymatic action from the researcher on biological material. Derived cell cultures are monitored morphologically by high-performance inverted biological microscope, with video camera for image acquisition. In the final stage, the cells are scraped, and through biochemical and molecular techniques, the therapeutic efficiency hypothesis of the investigated natural factor is verified experimentally. The cell cultures can be crioconservated in special containers with liquid nitrogen.

Validation and qualification of surface-applied fibre optic strain sensors using application-independent optical techniques

International Nuclear Information System (INIS)

Schukar, Vivien G; Kadoke, Daniel; Kusche, Nadine; Münzenberger, Sven; Gründer, Klaus-Peter; Habel, Wolfgang R

2012-01-01

Surface-applied fibre optic strain sensors were investigated using a unique validation facility equipped with application-independent optical reference systems. First, different adhesives for the sensor's application were analysed regarding their material properties. Measurements resulting from conventional measurement techniques, such as thermo-mechanical analysis and dynamic mechanical analysis, were compared with measurements resulting from digital image correlation, which has the advantage of being a non-contact technique. Second, fibre optic strain sensors were applied to test specimens with the selected adhesives. Their strain-transfer mechanism was analysed in comparison with conventional strain gauges. Relative movements between the applied sensor and the test specimen were visualized easily using optical reference methods, digital image correlation and electronic speckle pattern interferometry. Conventional strain gauges showed limited opportunities for an objective strain-transfer analysis because they are also affected by application conditions. (paper)

Path integral molecular dynamics within the grand canonical-like adaptive resolution technique: Simulation of liquid water

Energy Technology Data Exchange (ETDEWEB)

Agarwal, Animesh, E-mail: animesh@zedat.fu-berlin.de; Delle Site, Luigi, E-mail: dellesite@fu-berlin.de [Institute for Mathematics, Freie Universität Berlin, Berlin (Germany)

2015-09-07

Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to investigate properties induced by spatial delocalization of atoms; however, computationally this technique is very demanding. The above mentioned limitation implies the restriction of PIMD applications to relatively small systems and short time scales. One of the possible solutions to overcome size and time limitation is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme (AdResS). AdResS requires a relatively small region treated at path integral level and embeds it into a large molecular reservoir consisting of generic spherical coarse grained molecules. It was previously shown that the realization of the idea above, at a simple level, produced reasonable results for toy systems or simple/test systems like liquid parahydrogen. Encouraged by previous results, in this paper, we show the simulation of liquid water at room conditions where AdResS, in its latest and more accurate Grand-Canonical-like version (GC-AdResS), is merged with two of the most relevant PIMD techniques available in the literature. The comparison of our results with those reported in the literature and/or with those obtained from full PIMD simulations shows a highly satisfactory agreement.

Translation Techniques

OpenAIRE

Marcia Pinheiro

2015-01-01

In this paper, we discuss three translation techniques: literal, cultural, and artistic. Literal translation is a well-known technique, which means that it is quite easy to find sources on the topic. Cultural and artistic translation may be new terms. Whilst cultural translation focuses on matching contexts, artistic translation focuses on matching reactions. Because literal translation matches only words, it is not hard to find situations in which we should not use this technique.  Because a...

Agent independent task planning

Science.gov (United States)

Davis, William S.

1990-01-01

Agent-Independent Planning is a technique that allows the construction of activity plans without regard to the agent that will perform them. Once generated, a plan is then validated and translated into instructions for a particular agent, whether a robot, crewmember, or software-based control system. Because Space Station Freedom (SSF) is planned for orbital operations for approximately thirty years, it will almost certainly experience numerous enhancements and upgrades, including upgrades in robotic manipulators. Agent-Independent Planning provides the capability to construct plans for SSF operations, independent of specific robotic systems, by combining techniques of object oriented modeling, nonlinear planning and temporal logic. Since a plan is validated using the physical and functional models of a particular agent, new robotic systems can be developed and integrated with existing operations in a robust manner. This technique also provides the capability to generate plans for crewmembers with varying skill levels, and later apply these same plans to more sophisticated robotic manipulators made available by evolutions in technology.

A Novel Microfluidic Cell Co-culture Platform for the Study of the Molecular Mechanisms of Parkinson's Disease and Other Synucleinopathies.

Science.gov (United States)

Fernandes, João T S; Chutna, Oldriska; Chu, Virginia; Conde, João P; Outeiro, Tiago F

2016-01-01

Although, the precise molecular mechanisms underlying Parkinson's disease (PD) are still elusive, it is now known that spreading of alpha-synuclein (aSyn) pathology and neuroinflammation are important players in disease progression. Here, we developed a novel microfluidic cell-culture platform for studying the communication between two different cell populations, a process of critical importance not only in PD but also in many biological processes. The integration of micro-valves in the device enabled us to control fluid routing, cellular microenvironments, and to simulate paracrine signaling. As proof of concept, two sets of experiments were designed to show how this platform can be used to investigate specific molecular mechanisms associated with PD. In one experiment, naïve H4 neuroglioma cells were co-cultured with cells expressing aSyn tagged with GFP (aSyn-GFP), to study the release and spreading of the protein. In our experimental set up, we induced the release of the contents of aSyn-GFP producing cells to the medium and monitored the protein's diffusion. In another experiment, H4 cells were co-cultured with N9 microglial cells to assess the interplay between two cell lines in response to environmental stimuli. Here, we observed an increase in the levels of reactive oxygen species in H4 cells cultured in the presence of activated N9 cells, confirming the cross talk between different cell populations. In summary, the platform developed in this study affords novel opportunities for the study of the molecular mechanisms involved in PD and other neurodegenerative diseases.

Agricultural production - Phase 2. Indonesia. Rice - azolla - fish culture - use of nuclear technique

International Nuclear Information System (INIS)

Watanabe, Iwao.

1991-01-01

The primary aim of the expert mission was to provide advice on the use of nuclear techniques to study rice-azolla-fish culture. Results of the work performed so far show that basal application of azolla gives similar or better yields of rice than basal application of urea. Fish productivity was also found to be significantly higher when azolla is present. 2 tabs

Study of DNA interactions with bifenthrin by spectroscopic techniques and molecular modeling

Science.gov (United States)

Zhu, Pan; Zhang, Guowen; Ma, Yadi; Zhang, Yepeng; Miao, Hong; Wu, Yongning

2013-08-01

The interaction between bifenthrin (BF) and calf thymus DNA (ctDNA) in physiological buffer (pH 7.4) was investigated by UV-vis absorption, fluorescence, circular dichroism (CD), and Fourier transform infrared (FT-IR) spectroscopy, coupled with viscosity measurements and molecular docking techniques. It was found that BF molecular could intercalate into the base pairs of ctDNA as evidenced by significant increases in absorption intensity, fluorescence polarization and relative viscosity of ctDNA, decrease in iodide quenching effect, and induced CD spectral changes. The association constant of BF with ctDNA was evaluated to be in the order of 104 L mol-1. Thermodynamic analysis of the binding data obtained at different temperatures suggested that the binding process was primarily driven by hydrogen bonds and van der Waals forces, as the values of the enthalpy change (ΔH) and the entropy change (ΔS) were calculated to be -31.13 ± 1.89 kJ mol-1 and -22.79 ± 1.21 J mol-1 K-1, respectively. The results of FT-IR spectra and molecular docking showed that a specific binding mainly existed between BF and adenine and guanine bases.

Use of multiple molecular subtyping techniques to investigate a Legionnaires' disease outbreak due to identical strains at two tourist lodges.

Science.gov (United States)

Mamolen, M; Breiman, R F; Barbaree, J M; Gunn, R A; Stone, K M; Spika, J S; Dennis, D T; Mao, S H; Vogt, R L

1993-10-01

A multistate outbreak of Legionnaires' disease occurred among nine tour groups of senior citizens returning from stays at one of two lodges in a Vermont resort in October 1987. Interviews and serologic studies of 383 (85%) of the tour members revealed 17 individuals (attack rate, 4.4%) with radiologically documented pneumonia and laboratory evidence of legionellosis. A survey of tour groups staying at four nearby lodges and of Vermont-area medical facilities revealed no additional cases. Environmental investigation of common tour stops revealed no likely aerosol source of Legionella infection outside the lodges. Legionella pneumophila serogroup 1 was isolated from water sources at both implicated lodges, and the monoclonal antibody subtype matched those of the isolates from six patients from whom clinical isolates were obtained. The cultures reacted with monoclonal antibodies MAB1, MAB2, 33G2, and 144C2 to yield a 1,2,5,7 or a Benidorm 030E pattern. The strains were also identical by alloenzyme electrophoresis and DNA ribotyping techniques. The epidemiologic and laboratory data suggest that concurrent outbreaks occurred following exposures to the same L. pneumophila serogroup 1 strain at two separate lodges. Multiple molecular subtyping techniques can provide essential information for epidemiologic investigations of Legionnaires' disease.

[Molecular classification of breast cancer patients obtained through the technique of chromogenic in situ hybridization (CISH)].

Science.gov (United States)

Fernández, Angel; Reigosa, Aldo

2013-12-01

Breast cancer is a heterogeneous disease composed of a growing number of biological subtypes, with substantial variability of the disease progression within each category. The aim of this research was to classify the samples object of study according to the molecular classes of breast cancer: luminal A, luminal B, HER2 and triple negative, as a result of the state of HER2 amplification obtained by the technique of chromogenic in situ hybridization (CISH). The sample consisted of 200 biopsies fixed in 10% formalin, processed by standard techniques up to paraffin embedding, corresponding to patients diagnosed with invasive ductal carcinoma of the breast. These biopsies were obtained from patients from private practice and the Institute of Oncology "Dr. Miguel Pérez Carreño", for immunohistochemistry (IHC) of hormone receptors and HER2 made in the Hospital Metropolitano del Norte, Valencia, Venezuela. The molecular classification of the patient's tumors considering the expression of estrogen and progesterone receptors by IHC and HER2 amplification by CISH, allowed those cases originally classified as unknown, since they had an indeterminate (2+) outcome for HER2 expression by IHC, to be grouped into the different molecular classes. Also, this classification permitted that some cases, initially considered as belonging to a molecular class, were assigned to another class, after the revaluation of the HER2 status by CISH.

Culture-dependent and -independent approaches establish the complexity of a PAH-degrading microbial consortium

Energy Technology Data Exchange (ETDEWEB)

Vinas, M.; Sabate, J.; Solanas, A.M. [Barcelona Univ., Barcelona (Spain). Dept. of Microbiology; Guasp, C.; Lalucat, J. [Illes Balears Univ., Palma de Mallorca (Spain). Dept. of Biology

2005-11-15

Microbial consortia are used in the decontamination of polluted environmental sites. A microbial consortium obtained by batch enrichment culture is a closed system with controlled conditions in which micro-organisms with a potentially high growth rate are selected and become dominant. The aim of this study was to identify the members of consortium AM, in which earlier batch enrichment work had shown high biodegradation rates of the aromatic fraction of polycyclic aromatic hydrocarbon (PAH). The AM consortium was obtained by sequential enrichment in liquid culture with a PAH mixture of 3- and 4- ringed PAHs as the sole source of carbon and energy. The consortium was examined using a triple approach method based on various cultivation strategies, denaturing gradient electrophoresis (DGGE) and the screening of 16S and 18S rRNA gene clone libraries. Eleven different sequences by culture-dependent techniques and 7 by both DGGE and clone libraries were obtained, yielding 19 different microbial components. Proteobacteria were the dominant group, representing 83 per cent of the total, while the Cytophaga-Flexibactor-Bacteroides group (CFB) was 11 per cent, and Ascomycota fungi were 6 per cent. It was determined that {beta}-Proteobacteria were predominant in the DGGE and clone library methods, whereas they were a minority in culturable strains. The highest diversity and number of noncoincident sequences was achieved by the cultivation method that showed members of the {alpha},{beta}, and {gamma}-Proteobacteria, CFB bacterial group, and Ascomycota fungi. Only 6 of the 11 strains isolated showed PAH-degrading capability. The bacterial strain (AMS7) and the fungal strain (AMF1) achieved the greatest PAH depletion. Results indicated that polyphasic assessment is necessary for a proper understanding of the composition of a microbial consortium. It was concluded that microbial consortia are more complex than previously realized. 54 refs., 3 tabs., 3 figs.

Statistical adjustment of culture-independent diagnostic tests for trend analysis in the Foodborne Diseases Active Surveillance Network (FoodNet), USA.

Science.gov (United States)

Gu, Weidong; Dutta, Vikrant; Patrick, Mary; Bruce, Beau B; Geissler, Aimee; Huang, Jennifer; Fitzgerald, Collette; Henao, Olga

2018-03-19

Culture-independent diagnostic tests (CIDTs) are increasingly used to diagnose Campylobacter infection in the Foodborne Diseases Active Surveillance Network (FoodNet). Because CIDTs have different performance characteristics compared with culture, which has been used historically and is still used to diagnose campylobacteriosis, adjustment of cases diagnosed by CIDT is needed to compare with culture-confirmed cases for monitoring incidence trends. We identified the necessary parameters for CIDT adjustment using culture as the gold standard, and derived formulas to calculate positive predictive values (PPVs). We conducted a literature review and meta-analysis to examine the variability in CIDT performance and Campylobacter prevalence applicable to FoodNet sites. We then developed a Monte Carlo method to estimate test-type and site-specific PPVs with their associated uncertainties. The uncertainty in our estimated PPVs was largely derived from uncertainty about the specificity of CIDTs and low prevalence of Campylobacter in tested samples. Stable CIDT-adjusted incidences of Campylobacter cases from 2012 to 2015 were observed compared with a decline in culture-confirmed incidence. We highlight the lack of data on the total numbers of tested samples as one of main limitations for CIDT adjustment. Our results demonstrate the importance of adjusting CIDTs for understanding trends in Campylobacter incidence in FoodNet.

Gas Source Techniques for Molecular Beam Epitaxy of Highly Mismatched Ge Alloys

Directory of Open Access Journals (Sweden)

Chad A. Stephenson

2016-12-01

Full Text Available Ge and its alloys are attractive candidates for a laser compatible with silicon integrated circuits. Dilute germanium carbide (Ge1−xCx offers a particularly interesting prospect. By using a precursor gas with a Ge4C core, C can be preferentially incorporated in substitutional sites, suppressing interstitial and C cluster defects. We present a method of reproducible and upscalable gas synthesis of tetrakis(germylmethane, or (H3Ge4C, followed by the design of a hybrid gas/solid-source molecular beam epitaxy system and subsequent growth of defect-free Ge1−xCx by molecular beam epitaxy (MBE. Secondary ion mass spectroscopy, transmission electron microscopy and contactless electroreflectance confirm the presence of carbon with very high crystal quality resulting in a decrease in the direct bandgap energy. This technique has broad applicability to growth of highly mismatched alloys by MBE.

Recent research on inherent molecular structure, physiochemical properties, and bio-functions of food and feed-type Avena sativa oats and processing-induced changes revealed with molecular microspectroscopic techniques

Energy Technology Data Exchange (ETDEWEB)

Prates, Luciana Louzada [Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; Yu, Peiqiang [Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada

2017-05-16

Avena sativa oat is a cereal widely used as human food and livestock feed. However, the low metabolized energy and the rapid rumen degradations of protein and starch have limited the use of A. sativa oat grains. To overcome this disadvantage, new A. sativa oat varieties have been developed. Additionally, heat-related processing has been performed to decrease the degradation rate and improve the absorption of amino acids in the small intestine. The nutritive value is reflected by both chemical composition and inherent molecular structure conformation. However, the traditional wet chemical analysis is not able to detect the inherent molecular structures within an intact tissue. The advanced synchrotron-radiation and globar-based molecular microspectroscopy have been developed recently and applied to study internal molecular structures and the processing induced structure changes in A. sativa oats and reveal how molecular structure changes in relation to nutrient availability. This review aimed to obtain the recent information regarding physiochemical properties, molecular structures, metabolic characteristics of protein, and the heat-induced changes in new A. sativa oat varieties. The use of the advanced vibrational molecular spectroscopy was emphasized, synchrotron- and globar-based (micro)spectroscopy, to reveal the inherent structure of A. sativa oats at cellular and molecular levels and to reveal the heat processing effect on the degradation characteristics and the protein molecular structure in A. sativa oats. The relationship between nutrient availability and protein molecular inherent structure was also presented. Information described in this review gives better insight in the physiochemical properties, molecular structure, and the heat-induced changes in A. sativa oat detected with advanced molecular spectroscopic techniques in combinination with conventional nutrition study techniques.

Culture-independent investigation of the microbiome associated with the nematode Acrobeloides maximus.

Directory of Open Access Journals (Sweden)

Jean-Paul Baquiran

Full Text Available BACKGROUND: Symbioses between metazoans and microbes are widespread and vital to many ecosystems. Recent work with several nematode species has suggested that strong associations with microbial symbionts may also be common among members of this phylu. In this work we explore possible symbiosis between bacteria and the free living soil bacteriovorous nematode Acrobeloides maximus. METHODOLOGY: We used a soil microcosm approach to expose A. maximus populations grown monoxenically on RFP labeled Escherichia coli in a soil slurry. Worms were recovered by density gradient separation and examined using both culture-independent and isolation methods. A 16S rRNA gene survey of the worm-associated bacteria was compared to the soil and to a similar analysis using Caenorhabditis elegans N2. Recovered A. maximus populations were maintained on cholesterol agar and sampled to examine the population dynamics of the microbiome. RESULTS: A consistent core microbiome was extracted from A. maximus that differed from those in the bulk soil or the C. elegans associated set. Three genera, Ochrobactrum, Pedobacter, and Chitinophaga, were identified at high levels only in the A. maximus populations, which were less diverse than the assemblage associated with C. elegans. Putative symbiont populations were maintained for at least 4 months post inoculation, although the levels decreased as the culture aged. Fluorescence in situ hybridization (FISH using probes specific for Ochrobactrum and Pedobacter stained bacterial cells in formaldehyde fixed nematode guts. CONCLUSIONS: Three microorganisms were repeatedly observed in association with Acrobeloides maximus when recovered from soil microcosms. We isolated several Ochrobactrum sp. and Pedobacter sp., and demonstrated that they inhabit the nematode gut by FISH. Although their role in A. maximus is not resolved, we propose possible mutualistic roles for these bacteria in protection of the host against pathogens and

Impact of accelerator-based analytical techniques on the knowledge and conservation of cultural heritage

International Nuclear Information System (INIS)

Dran, Jean Claude

2001-01-01

A large set of modern analytical techniques is currently applied to get a better insight on art and archaeological objects as well as to contribute to their conservation and restoration. Because of the precious and sometimes unique character of the works, non-destructive techniques and even those requiring no (or only minute) sampling, are preferred. From this standpoint, ion beam analysis (IBA) constitutes one of the best choices, since it combines quite good analytical performance and non-destructiveness. For over 10 years, an IBA facility has been installed in the Research Laboratory of the Museums of France. Until now it is the only facility of this kind entirely devoted to the study of cultural heritage. A special set-up, namely an external beam line, has been developed which permits the in-air analysis of large or fragile works of art without sampling. This facility is used for both short investigations at the request of museum curators and extensive research works in art history and archaeology. Numerous examples will be given to highlight the impact of this tool on cultural heritage. (author)

Research progress in plant mutation by combining ion beam irradiations and tissue culture

International Nuclear Information System (INIS)

Zhou Linbin; Li Wenjian; Qu Ying; Li Ping

2007-01-01

About a new mutation breeding method which combines plant tissue culture technique with heavy ion beam irradiations were discussed in this paper with the principles, operation steps, molecular mechanisms, etc. The mutation method developed a few advantages coming from plant tissue culture, which can produce offspring by asexual ways. Meanwhile, using this method, the study of biological effects of high energy particles with different linear energy transfer values on plant tissues or cells can be explored and optimized in theory or practice. (authors)

Evolutionary Mechanisms Involved in Emergence of Viral Haemorrhagic Septicaemia Virus (VHSV) into Cultured Rainbow Trout, Oncorhynchus mykiss

DEFF Research Database (Denmark)

Schönherz, Anna A.

virulence, causing extensive losses to the aquacultre industry. Cross-species transmission and subsequent adaptation to cultured raibow trout is observed occasionally. However, the biological background facilitationg VHSV emergense has yet to be identified. In the present PhD project potential mechanisms...... facilitation VHSV emergence into cultured raibow trout were explored. In vivo infection trials and in selico based molecular analysis were performed to independently investigate the first two steps of viral emergence, namely initial introduction to- and subsequent adaptation and establishment within the new...... of genetic variation, and that VHSV emergence into cultured rainbow torut was accompanied by rapid adaptive evolution within the viral glucoprotein...

Capture of cell culture-derived influenza virus by lectins: strain independent, but host cell dependent.

Science.gov (United States)

Opitz, Lars; Zimmermann, Anke; Lehmann, Sylvia; Genzel, Yvonne; Lübben, Holger; Reichl, Udo; Wolff, Michael W

2008-12-01

Strategies to control influenza outbreaks are focused mainly on prophylactic vaccination. Human influenza vaccines are trivalent blends of different virus subtypes. Therefore and due to frequent antigenic drifts, strain independent manufacturing processes are required for vaccine production. This study verifies the strain independency of a capture method based on Euonymus europaeus lectin-affinity chromatography (EEL-AC) for downstream processing of influenza viruses under various culture conditions propagated in MDCK cells. A comprehensive lectin binding screening was conducted for two influenza virus types from the season 2007/2008 (A/Wisconsin/67/2005, B/Malaysia/2506/2004) including a comparison of virus-lectin interaction by surface plasmon resonance technology. EEL-AC resulted in a reproducible high product recovery rate and a high degree of contaminant removal in the case of both MDCK cell-derived influenza virus types demonstrating clearly the general applicability of EEL-AC. In addition, host cell dependency of EEL-AC was studied with two industrial relevant cell lines: Vero and MDCK cells. However, the choice of the host cell lines is known to lead to different product glycosylation profiles. Hence, altered lectin specificities have been observed between the two cell lines, requiring process adaptations between different influenza vaccine production systems.

Implications of recent research on microstructure modifications, through heat-related processing and trait alteration to bio-functions, molecular thermal stability and mobility, metabolic characteristics and nutrition in cool-climate cereal grains and other types of seeds with advanced molecular techniques.

Science.gov (United States)

Ying, Yuguang; Zhang, Huihua; Yu, Peiqiang

2018-02-16

The cutting-edge synchrotron radiation based and globar-sourced vibrational infrared microspectroscopy have recently been developed. These novel techniques are able to reveal structure features at cellular and molecular levels with the tested tissues being intact. However, to date, the advanced techniques are unfamiliar or unknown to food and feed scientists and have not been used to study the molecular structure changes in cool-climate cereal grain seeds and other types of bio-oil and bioenergy seeds. This article aims to provide some recent research in cool-climate cereal grains and other types of seeds on molecular structures and metabolic characteristics of carbohydrate and protein, and implication of microstructure modification through heat-related processing and trait alteration to bio-functions, molecular thermal stability and mobility, and nutrition with advanced molecular techniques- synchrotron radiation based and globar-sourced vibrational infrared microspectroscopy in the areas of (1) Inherent microstructure of cereal grain seeds; (2) The nutritional values of cereal grains; (3) Impact and modification of heat-related processing to cereal grain; (4) Conventional nutrition evaluation methodology; (5) Synchrotron radiation-based and globar-sourced vibrational (micro)-spectroscopy for molecular structure study and molecular thermal stability and mobility, and (6) Recent molecular spectroscopic technique applications in research on raw, traits altered and processed cool-climate cereal grains and other types of seeds. The information described in this article gives better insights of research progress and update in cool-climate cereal grains and other seeds with advanced molecular techniques.

Molecular diagnostics for human leptospirosis.

Science.gov (United States)

Waggoner, Jesse J; Pinsky, Benjamin A

2016-10-01

The definitive diagnosis of leptospirosis, which results from infection with spirochetes of the genus Leptospira, currently relies on the use of culture, serological testing (microscopic agglutination testing), and molecular detection. The purpose of this review is to describe new molecular diagnostics for Leptospira and discuss advancements in the use of available methods. Efforts have been focused on improving the clinical sensitivity of Leptospira detection using molecular methods. In this review, we describe a reoptimized pathogenic species-specific real-time PCR (targeting lipL32) that has demonstrated improved sensitivity, findings by two groups that real-time reverse-transcription PCR assays targeting the 16S rrs gene can improve detection, and two new loop-mediated amplification techniques. Quantitation of leptospiremia, detection in different specimen types, and the complementary roles played by molecular detection and microscopic agglutination testing will be discussed. Finally, a protocol for Leptospira strain subtyping using variable number tandem repeat targets and high-resolution melting will be described. Molecular diagnostics have an established role for the diagnosis of leptospirosis and provide an actionable diagnosis in the acute setting. The use of real-time reverse-transcription PCR for testing serum/plasma and cerebrospinal fluid, when available, may improve the detection of Leptospira without decreasing clinical specificity.

Simplified non-cultured non-trypsinised epidermal cell graft technique followed by psoralen and ultraviolet a light therapy for stable vitiligo

Directory of Open Access Journals (Sweden)

Dilip Kachhawa

2017-01-01

Full Text Available Background and Aims: Stable vitiligo can be treated by various surgical procedures. Non-cultured melanocyte grafting techniques were developed to overcome the time-consuming process of culture while at the same time providing acceptable results. All the techniques using non-cultured melanocyte transfer involve trypsinisation as an integral step. Jodhpur technique used by the author is autologous, non-cultured, non-trypsinised, epidermal cell grafting. Settings and Design: The study was conducted on patients visiting the dermatology outpatient department of a tertiary health centre in Western Rajasthan. Materials and Methods: At the donor site, mupirocin ointment was applied and dermabrasion was done with the help of micromotor dermabrader till pinpoint bleeding was seen. The paste-like material obtained by this procedure containing melanocytes and keratinocytes admixed with the ointment base was harvested with spatula and was subsequently spread over the recipient area. Recipient site was prepared in the same manner by dermabrasion. After 10 days, dressing at both sites was removed taking utmost care at the recipient site as there was a theoretical risk of dislodging epidermal cells. Results: In a study of 437 vitiligo patches, more than 75% re-pigmentation (excellent improvement was seen in 41% of the patches. Lesions on thigh (100%, face (75% and trunk (50% showed maximal excellent improvement, whereas patches on joints and acral areas did not show much improvement. Conclusions: This technique is a simplified, cost effective, less time-consuming alternative to other techniques which involve tryspsinisation of melanocytes and at the same time provides satisfactory uniform pigmentation.

Utilization of Cell-Transfer Technique for Molecular Testing on Hematoxylin-Eosin-Stained Sections: A Viable Option for Small Biopsies That Lack Tumor Tissues in Paraffin Block.

Science.gov (United States)

Wu, Howard H; Jovonovich, Stephen M; Randolph, Melissa; Post, Kristin M; Sen, Joyashree D; Curless, Kendra; Cheng, Liang

2016-12-01

- In some instances the standard method of doing molecular testing from formalin-fixed, paraffin-embedded block is not possible because of limited tissue. Tumor cell-enriched cell-transfer technique has been proven useful for performing immunocytochemistry and molecular testing on cytologic smears. - To establish the cell-transfer technique as a viable option for isolating tumor cells from hematoxylin-eosin (H&E)-stained slides. - Molecular testing was performed by using the cell-transfer technique on 97 archived H&E-stained slides from a variety of different tumors. Results were compared to the conventional method of molecular testing. - Polymerase chain reaction-based molecular testing via the cell-transfer technique was successfully performed on 82 of 97 samples (85%). This included 39 of 47 cases for EGFR, 10 of 11 cases for BRAF, and 33 of 39 cases for KRAS mutations. Eighty-one of 82 cell-transfer technique samples (99%) showed agreement with previous standard method results, including 4 mutations and 35 wild-type alleles for EGFR, 4 mutations and 6 wild-type alleles for BRAF, and 11 mutations and 21 wild-type alleles for KRAS. There was only 1 discrepancy: a cell-transfer technique with a false-negative >KRAS result (wild type versus G12C). - Molecular testing performed on H&E-stained sections via cell-transfer technique is useful when tissue from cell blocks and small surgical biopsy samples is exhausted and the only available material for testing is on H&E-stained slides.

Bacterial diversity of the Colombian fermented milk "Suero Costeño" assessed by culturing and high-throughput sequencing and DGGE analysis of 16S rRNA gene amplicons.

Science.gov (United States)

Motato, Karina Edith; Milani, Christian; Ventura, Marco; Valencia, Francia Elena; Ruas-Madiedo, Patricia; Delgado, Susana

2017-12-01

"Suero Costeño" (SC) is a traditional soured cream elaborated from raw milk in the Northern-Caribbean coast of Colombia. The natural microbiota that characterizes this popular Colombian fermented milk is unknown, although several culturing studies have previously been attempted. In this work, the microbiota associated with SC from three manufacturers in two regions, "Planeta Rica" (Córdoba) and "Caucasia" (Antioquia), was analysed by means of culturing methods in combination with high-throughput sequencing and DGGE analysis of 16S rRNA gene amplicons. The bacterial ecosystem of SC samples was revealed to be composed of lactic acid bacteria belonging to the Streptococcaceae and Lactobacillaceae families; the proportions and genera varying among manufacturers and region of elaboration. Members of the Lactobacillus acidophilus group, Lactocococcus lactis, Streptococcus infantarius and Streptococcus salivarius characterized this artisanal product. In comparison with culturing, the use of molecular in deep culture-independent techniques provides a more realistic picture of the overall bacterial communities residing in SC. Besides the descriptive purpose, these approaches will facilitate a rational strategy to follow (culture media and growing conditions) for the isolation of indigenous strains that allow standardization in the manufacture of SC. Copyright © 2017 Elsevier Ltd. All rights reserved.

Development and assessment of molecular diagnostic tests for 15 enteropathogens causing childhood diarrhoea: a multicentre study.

Science.gov (United States)

Liu, Jie; Kabir, Furqan; Manneh, Jainaba; Lertsethtakarn, Paphavee; Begum, Sharmin; Gratz, Jean; Becker, Steve M; Operario, Darwin J; Taniuchi, Mami; Janaki, Lalitha; Platts-Mills, James A; Haverstick, Doris M; Kabir, Mamun; Sobuz, Shihab U; Nakjarung, Kaewkanya; Sakpaisal, Pimmada; Silapong, Sasikorn; Bodhidatta, Ladaporn; Qureshi, Shahida; Kalam, Adil; Saidi, Queen; Swai, Ndealilia; Mujaga, Buliga; Maro, Athanasia; Kwambana, Brenda; Dione, Michel; Antonio, Martin; Kibiki, Gibson; Mason, Carl J; Haque, Rashidul; Iqbal, Najeeha; Zaidi, Anita K M; Houpt, Eric R

2014-08-01

Childhood diarrhoea can be caused by many pathogens that are difficult to assay in the laboratory. Molecular diagnostic techniques provide a uniform method to detect and quantify candidate enteropathogens. We aimed to develop and assess molecular tests for identification of enteropathogens and their association with disease. We developed and assessed molecular diagnostic tests for 15 enteropathogens across three platforms-PCR-Luminex, multiplex real-time PCR, and TaqMan array card-at five laboratories worldwide. We judged the analytical and clinical performance of these molecular techniques against comparator methods (bacterial culture, ELISA, and PCR) using 867 diarrhoeal and 619 non-diarrhoeal stool specimens. We also measured molecular quantities of pathogens to predict the association with diarrhoea, by univariate logistic regression analysis. The molecular tests showed very good analytical and clinical performance at all five laboratories. Comparator methods had limited sensitivity compared with the molecular techniques (20-85% depending on the target) but good specificity (median 97·3%, IQR 96·5-98·9; mean 95·2%, SD 9·1). Positive samples by comparator methods usually had higher molecular quantities of pathogens than did negative samples, across almost all platforms and for most pathogens (pMolecular diagnostic tests can be implemented successfully and with fidelity across laboratories around the world. In the case of diarrhoea, these techniques can detect pathogens with high sensitivity and ascribe diarrhoeal associations based on quantification, including in mixed infections, providing rich and unprecedented measurements of infectious causes. Bill & Melinda Gates Foundation Next Generation Molecular Diagnostics Project. Copyright © 2014 Elsevier Ltd. All rights reserved.

Determination of arterial input function in dynamic susceptibility contrast MRI using group independent component analysis technique

International Nuclear Information System (INIS)

Chen, S.; Liu, H.-L.; Yang Yihong; Hsu, Y.-Y.; Chuang, K.-S.

2006-01-01

Quantification of cerebral blood flow (CBF) with dynamic susceptibility contrast (DSC) magnetic resonance imaging (MRI) requires the determination of the arterial input function (AIF). The segmentation of surrounding tissue by manual selection is error-prone due to the partial volume artifacts. Independent component analysis (ICA) has the advantage in automatically decomposing the signals into interpretable components. Recently group ICA technique has been applied to fMRI study and showed reduced variance caused by motion artifact and noise. In this work, we investigated the feasibility and efficacy of the use of group ICA technique to extract the AIF. Both simulated and in vivo data were analyzed in this study. The simulation data of eight phantoms were generated using randomized lesion locations and time activity curves. The clinical data were obtained from spin-echo EPI MR scans performed in seven normal subjects. Group ICA technique was applied to analyze data through concatenating across seven subjects. The AIFs were calculated from the weighted average of the signals in the region selected by ICA. Preliminary results of this study showed that group ICA technique could not extract accurate AIF information from regions around the vessel. The mismatched location of vessels within the group reduced the benefits of group study

Use of Tissue Culture Techniques for Producing Virus-Free Plant in Garlic and Their Identification through Real-Time PCR

Directory of Open Access Journals (Sweden)

Hatıra Taşkın

2013-01-01

Full Text Available This study was performed for comparison of meristem culture technique with shoot tip culture technique for obtaining virus-free plant, comparison of micropropagation success of two different nutrient media, and determination of effectiveness of real-time PCR assay for the detection of viruses. Two different garlic species (Allium sativum and Allium tuncelianum and two different nutrient media were used in this experiment. Results showed that Medium 2 was more successful compared to Medium 1 for both A. tuncelianum and A. sativum (Kastamonu garlic clone. In vitro plants obtained via meristem and shoot tip cultures were tested for determination of onion yellow dwarf virus (OYDV and leek yellow stripe virus (LYSV through real-time PCR assay. In garlic plants propagated via meristem culture, we could not detect any virus. OYDV and LYSV viruses were detected in plants obtained via shoot tip culture. OYDV virus was observed in amount of 80% and 73% of tested plants for A. tuncelianum and A. sativum, respectively. LYSV virus was found in amount of 67% of tested plants of A. tuncelianum and in amount of 87% of tested plants of A. sativum in this study.

Cultural pathways through universal development.

Science.gov (United States)

Greenfield, Patricia M; Keller, Heidi; Fuligni, Andrew; Maynard, Ashley

2003-01-01

We focus our review on three universal tasks of human development: relationship formation, knowledge acquisition, and the balance between autonomy and relatedness at adolescence. We present evidence that each task can be addressed through two deeply different cultural pathways through development: the pathways of independence and interdependence. Whereas core theories in developmental psychology are universalistic in their intentions, they in fact presuppose the independent pathway of development. Because the independent pathway is therefore well-known in psychology, we focus a large part of our review on empirically documenting the alternative, interdependent pathway for each developmental task. We also present three theoretical approaches to culture and development: the ecocultural, the sociohistorical, and the cultural values approach. We argue that an understanding of cultural pathways through human development requires all three approaches. We review evidence linking values (cultural values approach), ecological conditions (ecocultural approach), and socialization practices (sociohistorical approach) to cultural pathways through universal developmental tasks.

Sensitivity of field tests, serological and molecular techniques for Plum Pox Virus detection in various tissues

Directory of Open Access Journals (Sweden)

Mojca VIRŠČEK MARN

2015-12-01

Full Text Available Sensitivity of field tests (AgriStrip  and Immunochromato, DAS-ELISA, two step RT-PCR and real-time RT-PCR for Plum pox virus (PPV detection was tested in various tissues of apricot, peach, plum and damson plum trees infected with isolates belonging to PPV-D, PPV-M or PPV-Rec, the three strains present in Slovenia. Flowers of apricot and plum in full bloom proved to be a very good source for detection of PPV. PPV could be detected with all tested techniques in symptomatic parts of leaves in May and with one exception even in the beginning of August, but it was not detected in asymptomatic leaves using field tests, DAS-ELISA and partly also molecular techniques. PPV was detected only in some of the samples of asymptomatic parts of the leaves with symptoms and of stalks by field tests and DAS-ELISA. Infections were not detected in buds in August using field tests or DAS-ELISA. Field tests are useful for confirmation of the PPV infection in symptomatic leaves, but in tissues without symptoms DAS-ELISA should be combined or replaced by molecular techniques.

A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome

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Jaderson Silveira Leite Armanhi

2018-01-01

Full Text Available The soil-plant ecosystem harbors an immense microbial diversity that challenges investigative approaches to study traits underlying plant-microbe association. Studies solely based on culture-dependent techniques have overlooked most microbial diversity. Here we describe the concomitant use of culture-dependent and -independent techniques to target plant-beneficial microbial groups from the sugarcane microbiome. The community-based culture collection (CBC approach was used to access microbes from roots and stalks. The CBC recovered 399 unique bacteria representing 15.9% of the rhizosphere core microbiome and 61.6–65.3% of the endophytic core microbiomes of stalks. By cross-referencing the CBC (culture-dependent with the sugarcane microbiome profile (culture-independent, we designed a synthetic community comprised of naturally occurring highly abundant bacterial groups from roots and stalks, most of which has been poorly explored so far. We then used maize as a model to probe the abundance-based synthetic inoculant. We show that when inoculated in maize plants, members of the synthetic community efficiently colonize plant organs, displace the natural microbiota and dominate at 53.9% of the rhizosphere microbial abundance. As a result, inoculated plants increased biomass by 3.4-fold as compared to uninoculated plants. The results demonstrate that abundance-based synthetic inoculants can be successfully applied to recover beneficial plant microbes from plant microbiota.

EDITORIAL: Molecular Imaging Technology

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Asai, Keisuke; Okamoto, Koji

2006-06-01

'Molecular Imaging Technology' focuses on image-based techniques using nanoscale molecules as sensor probes to measure spatial variations of various species (molecular oxygen, singlet oxygen, carbon dioxide, nitric monoxide, etc) and physical properties (pressure, temperature, skin friction, velocity, mechanical stress, etc). This special feature, starting on page 1237, contains selected papers from The International Workshop on Molecular Imaging for Interdisciplinary Research, sponsored by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) in Japan, which was held at the Sendai Mediatheque, Sendai, Japan, on 8 9 November 2004. The workshop was held as a sequel to the MOSAIC International Workshop that was held in Tokyo in 2003, to summarize the outcome of the 'MOSAIC Project', a five-year interdisciplinary project supported by Techno-Infrastructure Program, the Special Coordination Fund for Promotion of Science Technology to develop molecular sensor technology for aero-thermodynamic research. The workshop focused on molecular imaging technology and its applications to interdisciplinary research areas. More than 110 people attended this workshop from various research fields such as aerospace engineering, automotive engineering, radiotechnology, fluid dynamics, bio-science/engineering and medical engineering. The purpose of this workshop is to stimulate intermixing of these interdisciplinary fields for further development of molecular sensor and imaging technology. It is our pleasure to publish the seven papers selected from our workshop as a special feature in Measurement and Science Technology. We will be happy if this issue inspires people to explore the future direction of molecular imaging technology for interdisciplinary research.

Technique of the 'in vitro' fertilization and the culture of mouse embryos at preimplantation

International Nuclear Information System (INIS)

Kikuchi, Olivia Kimiko; Yamada, Takeshi

1993-03-01

The mammal embryo is an intensive cellular proliferating system, very radiosensitive and therefore adequate to the study of the biological effects of ionizing radiation. The technique of the in vitro fertilization and the culture of mouse embryos at preimplantation period, modified by Yamada et al (1982) to improve the efficiency of more than 95% of blastocyst formation is described. (author)

Independence and Interdependence in Early Childhood Services

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Whitington, Victoria

2004-01-01

It is through culture that children make sense of their worlds (Trevarthen, 1998). Cross- cultural models show that families are likely to primarily foster either independence or interdependence in their children (Gonzalez-Mena, 1997; Greenfield, 1994). Young children are likely to pay the "price of acculturation" when they enter early…

Development of a Semester-Long, Inquiry-Based Laboratory Course in Upper-Level Biochemistry and Molecular Biology

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Murthy, Pushpalatha P. N.; Thompson, Martin; Hungwe, Kedmon

2014-01-01

A semester-long laboratory course was designed and implemented to familiarize students with modern biochemistry and molecular biology techniques. The designed format involved active student participation, evaluation of data, and critical thinking, and guided students to become independent researchers. The first part of the course focused on…

A cell culture technique for human epiretinal membranes to describe cell behavior and membrane contraction in vitro.

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Wertheimer, Christian; Eibl-Lindner, Kirsten H; Compera, Denise; Kueres, Alexander; Wolf, Armin; Docheva, Denitsa; Priglinger, Siegfried G; Priglinger, Claudia; Schumann, Ricarda G

2017-11-01

To introduce a human cell culture technique for investigating in-vitro behavior of primary epiretinal cells and membrane contraction of fibrocellular tissue surgically removed from eyes with idiopathic macular pucker. Human epiretinal membranes were harvested from ten eyes with idiopathic macular pucker during standard vitrectomy. Specimens were fixed on cell culture plastic using small entomological pins to apply horizontal stress to the tissue, and then transferred to standard cell culture conditions. Cell behavior of 400 epiretinal cells from 10 epiretinal membranes was observed in time-lapse microscopy and analyzed in terms of cell migration, cell velocity, and membrane contraction. Immunocytochemistry was performed for cell type-specific antigens. Cell specific differences in migration behavior were observed comprising two phenotypes: (PT1) epiretinal cells moving fast, less directly, with small round phenotype and (PT2) epiretinal cells moving slowly, directly, with elongated large phenotype. No mitosis, no outgrowth and no migration onto the plastic were seen. Horizontal contraction measurements showed variation between specimens. Masses of epiretinal cells with a myofibroblast-like phenotype expressed cytoplasmatic α-SMA stress fibers and correlated with cell behavior characteristics (PT2). Fast moving epiretinal cells (PT1) were identified as microglia by immunostaining. This in-vitro technique using traction application allows for culturing surgically removed epiretinal membranes from eyes with idiopathic macular pucker, demonstrating cell behavior and membrane contraction of primary human epiretinal cells. Our findings emphasize the abundance of myofibroblasts, the presence of microglia and specific differences of cell behavior in these membranes. This technique has the potential to improve the understanding of pathologies at the vitreomacular interface and might be helpful in establishing anti-fibrotic treatment strategies.

Identification of microorganisms involved in nitrogen removal from wastewater treatment systems by means of molecular biology techniques

International Nuclear Information System (INIS)

Figueroa, M.; Alonso-Gutierrez, J.; Campos, J. L.; Mendez, R.; Mosquera-Corral, A.

2010-01-01

The identification of the main bacteria populations present in the granular biomass from a biological reactor treating wastewater has been performed by applying two different molecular biology techniques. By means of the DGGE technique five different genera of heterotrophic bacteria (Thiothrix, Thauera, Cloroflexi, Comamonas y Zoogloea) and one of ammonia oxidizing bacteria (Nitrosomanas) were identified. The FISH technique, based on microscopy, allowed the in situ visualization and quantification of those microorganisms. Special attention was paid to filamentous bacteria distribution (Thiothrix and Cloroflexi) which could exert a structural function in aerobic granular sludge. (Author) 26 refs.

Conceptions of ‘culture' in international communication - Limits to cultural explanations?

DEFF Research Database (Denmark)

Froholdt, Lisa Loloma; Knudsen, Fabienne

2008-01-01

The paper addresses a critical approach to static, objective and context-independent concept of culture. Conceiving of another culture as objective, persistent, and evenly shared features within a nation may bring some basic order while facing an unknown culture, but it may also have unintentional...

Early detection of Pseudomonas aeruginosa – comparison of conventional versus molecular (PCR detection directly from adult patients with cystic fibrosis (CF

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Moore John E

2004-10-01

Full Text Available Abstract Background Pseudomonas aeruginosa (PA is the most important bacterial pathogen in patients with cystic fibrosis (CF patients. Currently, routine bacteriological culture on selective/non- selective culture media is the cornerstone of microbiological detection. The aim of this study was to compare isolation rates of PA by conventional culture and molecular (PCR detection directly from sputum. Methods Adult patients (n = 57 attending the regional adult CF centre in Northern Ireland, provided fresh sputum following airways clearance exercise. Following processing of the specimen with sputasol (1:1 vol, the specimen was examined for the presence of PA by plating onto a combination of culture media (Pseudomonas isolation agar, Blood agar & McConkey agar. In addition, from the same specimen, genomic bacterial DNA was extracted (1 ml and was amplified employing two sequence-specific targets, namely (i the outer membrane protein (oprL gene locus and (ii the exotoxin A (ETA gene locus. Results By sputum culture, there were 30 patients positive for PA, whereas by molecular techniques, there were 35 positive patients. In 39 patients (22 PA +ve & 17 PA -ve, there was complete agreement between molecular and conventional detection and with both PCR gene loci. The oprL locus was more sensitive than the ETA locus, as the former was positive in 10 more patients and there were no patients where the ETA was positive and the oprL target negative. Where a PCR +ve/culture -ve result was recorded (10 patients, we followed these patients and recorded that 5 of these patients converted to being culture-positive at times ranging from 4–17 months later, with a mean lag time of 4.5 months. Conclusions This study indicates that molecular detection of PA in sputum employing the oprL gene target, is a useful technique in the early detection of PA, gaining on average 4.5 months over conventional culture. It now remains to be established whether aggressive antibiotic

Making Mavericks: Preparing Musicians for Independent Artistic Culture

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Canham, Nicole L.

2016-01-01

This essay explores the role that maverick qualities--"independent or unorthodox behaviour" ("The Oxford Dictionary," 2015)--play in developing and sustaining musician employability. Whilst career education for musicians often highlights new career models (Bridgstock, 2005), there is limited evidence of how these concepts work…

Spectroscopic and molecular docking techniques study of the interaction between oxymetholone and human serum albumin

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Madrakian, Tayyebeh, E-mail: madrakian@basu.ac.ir; Bagheri, Habibollah; Afkhami, Abbas; Soleimani, Mohammad

2014-11-15

In this study, the binding of oxymetholone (OXM), a doping drug, to human serum albumin (HSA) was explored at pH 7.40 by spectroscopic methods including spectrofluorimetry, three dimensional excitation–emission matrix (3D EEM), UV–vis absorption, resonance rayleigh scattering (RRS) and molecular docking. The fluorescence results showed that there was a considerable quenching of the intrinsic fluorescence of HSA upon binding to OXM by static quenching mechanism. The Stern–Volmer quenching constants (K{sub SV}) between OXM and HSA at three different temperatures 295, 303, 308 K, were obtained as 4.63×10{sup 4}, 3.05×10{sup 4} and 1.49×10{sup 4} L mol{sup −1}, respectively. Furthermore this interaction was confirmed by UV–vis spectrophotometric and RRS techniques. The binding site number, n, apparent binding constant, K{sub b}, and corresponding thermodynamic parameters (ΔS, ΔH and ΔG) were measured at different temperatures. The Van der Waals and hydrogen-bond forces were found to stabilize OXM–HSA complex. The distance (r) between the donor and acceptor was obtained from Förster's theory of fluorescence resonance energy transfer (FRET) and found to be 1.67 nm. The 3D EEM showed that OXM slightly changes the secondary structure of HSA. Furthermore, the molecular docking was employed for identification of drug binding sites and interaction of OXM with amino acid residues. - Highlights: • The binding of OXM as a doping drug with HSA was studied by different techniques. • The binding constant of HSA–OXM was calculated. • The binding site of OXM on HSA was characterized with molecular docking. • The thermodynamic parameters were calculated according to fluorescence technique.

Culture-dependent and culture-independent analyses reveal no prokaryotic community shifts or recovery of Serratia marcescens in Acropora palmata with white pox disease.

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Lesser, Michael P; Jarett, Jessica K

2014-06-01

Recently, the etiological agent of white pox (WP) disease, also known as acroporid serratiosis, in the endangered coral Acropora palmata is the enteric bacterium Serratia marcescens with the source being localized sewage release onto coastal coral reef communities. Here, we show that both culture-dependent and culture-independent approaches could not recover this bacterium from samples of tissue and mucus from A. palmata colonies affected by WP disease in the Bahamas, or seawater collected adjacent to A. palmata colonies. Additionally, a metagenetic 16S rRNA pyrosequencing study shows no significant difference in the bacterial communities of coral tissues with and without WP lesions. As recent studies have shown for other coral diseases, S. marcescens cannot be identified in all cases of WP disease in several geographically separated populations of A. palmata with the same set of signs. As a result, its identification as the etiological agent of WP disease, and cause of a reverse zoonosis, cannot be broadly supported. However, the prevalence of WP disease associated with S. marcescens does appear to be associated with proximity to population centers, and research efforts should be broadened to examine this association, and to identify other causes of this syndrome. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Long-term culture of rat hippocampal neurons at low density in serum-free medium: combination of the sandwich culture technique with the three-dimensional nanofibrous hydrogel PuraMatrix.

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Kaneko, Ai; Sankai, Yoshiyuki

2014-01-01

The primary culture of neuronal cells plays an important role in neuroscience. There has long been a need for methods enabling the long-term culture of primary neurons at low density, in defined serum-free medium. However, the lower the cell density, the more difficult it is to maintain the cells in culture. Therefore, we aimed to develop a method for long-term culture of neurons at low density, in serum-free medium, without the need for a glial feeder layer. Here, we describe the work leading to our determination of a protocol for long-term (>2 months) primary culture of rat hippocampal neurons in serum-free medium at the low density of 3×10(4) cells/mL (8.9×10(3) cells/cm2) without a glial feeder layer. Neurons were cultured on a three-dimensional nanofibrous hydrogel, PuraMatrix, and sandwiched under a coverslip to reproduce the in vivo environment, including the three-dimensional extracellular matrix, low-oxygen conditions, and exposure to concentrated paracrine factors. We examined the effects of varying PuraMatrix concentrations, the timing and presence or absence of a coverslip, the timing of neuronal isolation from embryos, cell density at plating, medium components, and changing the medium or not on parameters such as developmental pattern, cell viability, neuronal ratio, and neurite length. Using our method of combining the sandwich culture technique with PuraMatrix in Neurobasal medium/B27/L-glutamine for primary neuron culture, we achieved longer neurites (≥3,000 µm), greater cell viability (≥30%) for 2 months, and uniform culture across the wells. We also achieved an average neuronal ratio of 97%, showing a nearly pure culture of neurons without astrocytes. Our method is considerably better than techniques for the primary culture of neurons, and eliminates the need for a glial feeder layer. It also exhibits continued support for axonal elongation and synaptic activity for long periods (>6 weeks).

Long-term culture of rat hippocampal neurons at low density in serum-free medium: combination of the sandwich culture technique with the three-dimensional nanofibrous hydrogel PuraMatrix.

Directory of Open Access Journals (Sweden)

Ai Kaneko

Full Text Available The primary culture of neuronal cells plays an important role in neuroscience. There has long been a need for methods enabling the long-term culture of primary neurons at low density, in defined serum-free medium. However, the lower the cell density, the more difficult it is to maintain the cells in culture. Therefore, we aimed to develop a method for long-term culture of neurons at low density, in serum-free medium, without the need for a glial feeder layer. Here, we describe the work leading to our determination of a protocol for long-term (>2 months primary culture of rat hippocampal neurons in serum-free medium at the low density of 3×10(4 cells/mL (8.9×10(3 cells/cm2 without a glial feeder layer. Neurons were cultured on a three-dimensional nanofibrous hydrogel, PuraMatrix, and sandwiched under a coverslip to reproduce the in vivo environment, including the three-dimensional extracellular matrix, low-oxygen conditions, and exposure to concentrated paracrine factors. We examined the effects of varying PuraMatrix concentrations, the timing and presence or absence of a coverslip, the timing of neuronal isolation from embryos, cell density at plating, medium components, and changing the medium or not on parameters such as developmental pattern, cell viability, neuronal ratio, and neurite length. Using our method of combining the sandwich culture technique with PuraMatrix in Neurobasal medium/B27/L-glutamine for primary neuron culture, we achieved longer neurites (≥3,000 µm, greater cell viability (≥30% for 2 months, and uniform culture across the wells. We also achieved an average neuronal ratio of 97%, showing a nearly pure culture of neurons without astrocytes. Our method is considerably better than techniques for the primary culture of neurons, and eliminates the need for a glial feeder layer. It also exhibits continued support for axonal elongation and synaptic activity for long periods (>6 weeks.

Evaluation of culture-based techniques and 454 pyrosequencing for the analysis of fungal diversity in potting media and organic fertilizers.

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Al-Sadi, A M; Al-Mazroui, S S; Phillips, A J L

2015-08-01

Potting media and organic fertilizers (OFs) are commonly used in agricultural systems. However, there is a lack of studies on the efficiency of culture-based techniques in assessing the level of fungal diversity in these products. A study was conducted to investigate the efficiency of seven culture-based techniques and pyrosequencing for characterizing fungal diversity in potting media and OFs. Fungal diversity was evaluated using serial dilution, direct plating and baiting with carrot slices, potato slices, radish seeds, cucumber seeds and cucumber cotyledons. Identity of all the isolates was confirmed on the basis of the internal transcribed spacer region of the ribosomal RNA (ITS rRNA) sequence data. The direct plating technique was found to be superior over other culture-based techniques in the number of fungal species detected. It was also found to be simple and the least time consuming technique. Comparing the efficiency of direct plating with 454 pyrosequencing revealed that pyrosequencing detected 12 and 15 times more fungal species from potting media and OFs respectively. Analysis revealed that there were differences between potting media and OFs in the dominant phyla, classes, orders, families, genera and species detected. Zygomycota (52%) and Chytridiomycota (60%) were the predominant phyla in potting media and OFs respectively. The superiority of pyrosequencing over cultural methods could be related to the ability to detect obligate fungi, slow growing fungi and fungi that exist at low population densities. The evaluated methods in this study, especially direct plating and pyrosequencing, may be used as tools to help detect and reduce movement of unwanted fungi between countries and regions. © 2015 The Society for Applied Microbiology.

Genetic fallout in biocultural landscapes: molecular imperialism and the cultural politics of (not) seeing transgenes in Mexico.

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Christophe Bonneuil; Foyer, Jean; Wynne, Brian

2014-12-01

This article explores the trajectory of the global controversy over the introgression (or not) of transgenes from genetically modified maize into Mexican indigenous maize landraces. While a plurality of knowledge-making processes were deployed to render transgenes visible or invisible, we analyze how a particular in vitro based DNA-centered knowledge came to marginalize other forms of knowledge, thus obscuring other bio-cultural dimensions key to the understanding of gene flow and maize diversity. We show that dominant molecular norms of proof and standards of detection, which co-developed with the world of industrial monocropping and gene patenting, discarded and externalized non-compliant actors (i.e. complex maize genomes, human dimensions of gene flow). Operating in the name of high science, they hence obscured the complex biological and cultural processes that maintain crop diversity and enacted a cultural-political domination over the world of Mexican landraces and indigenous communities.

The IRIDICA BAC BSI Assay: Rapid, Sensitive and Culture-Independent Identification of Bacteria and Candida in Blood

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Rothman, Richard E.; Peterson, Stephen; Carroll, Karen C.; Zhang, Sean X.; Avornu, Gideon D.; Rounds, Megan A.; Carolan, Heather E.; Toleno, Donna M.; Moore, David; Hall, Thomas A.; Massire, Christian; Richmond, Gregory S.; Gutierrez, Jose R.; Sampath, Rangarajan; Ecker, David J.; Blyn, Lawrence B.

2016-01-01

Bloodstream infection (BSI) and sepsis are rising in incidence throughout the developed world. The spread of multi-drug resistant organisms presents increasing challenges to treatment. Surviving BSI is dependent on rapid and accurate identification of causal organisms, and timely application of appropriate antibiotics. Current culture-based methods used to detect and identify agents of BSI are often too slow to impact early therapy and may fail to detect relevant organisms in many positive cases. Existing methods for direct molecular detection of microbial DNA in blood are limited in either sensitivity (likely the result of small sample volumes) or in breadth of coverage, often because the PCR primers and probes used target only a few specific pathogens. There is a clear unmet need for a sensitive molecular assay capable of identifying the diverse bacteria and yeast associated with BSI directly from uncultured whole blood samples. We have developed a method of extracting DNA from larger volumes of whole blood (5 ml per sample), amplifying multiple widely conserved bacterial and fungal genes using a mismatch- and background-tolerant PCR chemistry, and identifying hundreds of diverse organisms from the amplified fragments on the basis of species-specific genetic signatures using electrospray ionization mass spectrometry (PCR/ESI-MS). We describe the analytical characteristics of the IRIDICA BAC BSI Assay and compare its pre-clinical performance to current standard-of-care methods in a collection of prospectively collected blood specimens from patients with symptoms of sepsis. The assay generated matching results in 80% of culture-positive cases (86% when common contaminants were excluded from the analysis), and twice the total number of positive detections. The described method is capable of providing organism identifications directly from uncultured blood in less than 8 hours. Disclaimer: The IRIDICA BAC BSI Assay is not available in the United States. PMID:27384540

Magnetohydrodynamic shocks in molecular clouds

International Nuclear Information System (INIS)

Chernoff, D.F.

1985-01-01

Part one develops the mathematical and physical theory of one-dimensional, time-independent subalfvenic flow in partially ionized gas with magnetic fields, for application to shocks in molecular clouds. Unlike normal gas-dynamic shocks, the neutral flow may be continuous and cool if the gas radiates efficiently and does not self-ionize. Analytic solutions are given in the limit that the neutral gas is either adiabatic or isothermal (cold). Numerical techniques are developed and applied to find the neutral flow under general circumstances. Part two extends the theory and results of part one in three ways: (1) to faster, superalfvenic flow, (2) to complex gases containing heavy charged particles (grains) in addition to ions, containing heavy charged particles (grains) in addition to ions, electrons and neutrals, and (3) to the entire range in (Omega tau), the ratio of charged particle damping time to gyroperiod, expected in gas flows in molecular clouds

Organotypic Cultures as a Model to Study Adult Neurogenesis in CNS Disorders

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Fabio Cavaliere

2016-01-01

Full Text Available Neural regeneration resides in certain specific regions of adult CNS. Adult neurogenesis occurs throughout life, especially from the subgranular zone of hippocampus and the subventricular zone, and can be modulated in physiological and pathological conditions. Numerous techniques and animal models have been developed to demonstrate and observe neural regeneration but, in order to study the molecular and cellular mechanisms and to characterize multiple types of cell populations involved in the activation of neurogenesis and gliogenesis, investigators have to turn to in vitro models. Organotypic cultures best recapitulate the 3D organization of the CNS and can be explored taking advantage of many techniques. Here, we review the use of organotypic cultures as a reliable and well defined method to study the mechanisms of neurogenesis under normal and pathological conditions. As an example, we will focus on the possibilities these cultures offer to study the pathophysiology of diseases like Alzheimer disease, Parkinson’s disease, and cerebral ischemia.

[Department of the molecular bases of semiotics].

Science.gov (United States)

Ternovyĭ, K S

1995-01-01

Department of molecular basis of semiotics was organized in 1986. The main task of the department was to work out new approaches in estimation of the state of immune and blood system at the tissue, cell and molecular levels, using biochemical, biophysical and molecular biology techniques. There are several main directions of scientific investigations at the department. Most informational methods were collected in "immunological portrait" for differential diagnostic and complex investigation of the immune system of autoimmune patients. This group of techniques was used to study changes in the immune system of Kievites after the Chernobyl disaster. A decrease of complement and thymic serum activity was detected. Antibodies against nuclear components appeared in 20% of donors. And a higher of circulating immune complex of low molecular weight was observed. Low level of thymic serum activity in blood of autoimmune patients with rheumatoid arthritis, lupus erythematosus, diabetes, herpes and other depends on the appearance of zinc-independent timuline inhibitor less then 2000 D. Another kind of thymic hormone inhibitors was detected in thymectomized adult mice. Its effect disappears when zinc added in blood rather due to competition for lymphocyte surface receptors timuline and its inactive analogue than other mechanism. Therapeutic effect of UV irradiation of patients' blood was shown to be closely connected with the changes in thymic serum activity in respect to stabilization of thymic hormone/inhibitor ratio. The immunochemical techniques were used to detect and investigate tumor-associated chromatin antigens in human and animal tumor cells. Antigens not found in normal tissues were detected when using rabbit antibodies against chromatin of rat hepatocarcinoma and human colon and carcinoma.(ABSTRACT TRUNCATED AT 250 WORDS)

Influence of ionizing radiation on synthesis and molecular heterogeneity of catalase in tissue culture of Rauwolfia serpentina

International Nuclear Information System (INIS)

Komov, V.P.; Bespalova, E.V.; Strelkova, M.A.

1998-01-01

Changes in activity and molecular heterogeneity of catalase in tissue culture of Rauwolfia serpentina following irradiation in early growth period at the doses of 8 and 50 Gy has been studied. Ionizing radiation accelerate the synthesis and degradation rates of catalase and total protein. A comparative study of changes in enzyme and protein turnover during growth on irradiated and non-irradiated medium has been made [ru

Car transfer and wheelchair loading techniques in independent drivers with paraplegia

Directory of Open Access Journals (Sweden)

Lisa Lighthall Haubert

2015-09-01

Full Text Available Car transfers and wheelchair (WC loading are crucial for independent community participation in persons with complete paraplegia from spinal cord injury, but are complex, physically demanding, and known to provoke shoulder pain. This study aimed to describe techniques and factors influencing car transfer and WC loading for individuals with paraplegia driving their own vehicles and using their personal WCs. Sedans were the most common vehicle driven (59%. Just over half (52% of drivers place their right leg only into the vehicle prior to transfer. Overall, the leading hand was most frequently placed on the driver’s seat (66% prior to transfer and the trailing hand was most often place on the WC seat (48%. Vehicle height influenced leading hand placement but not leg placement such that driver’s of higher profile vehicles were more likely to place their hand on the driver’s seat than those who drove sedans. Body lift time was negatively correlated with level of injury and age and positively correlated with vehicle height and shoulder abduction strength. Drivers who transferred with their leading hand on the steering wheel had significantly higher levels of shoulder pain than those who placed their hand on the driver’s seat or overhead. The majority of participants used both hands (62% to load their WC frame and, overall, most loaded their fame into the back (62% vs. the front seat. Sedan drivers were more likely to load their frame into the front seat than drivers of higher profile vehicles (53% vs. 17%. Average time to load the WC frame (10.7 seconds was 20% of the total WC loading time and was not related to shoulder strength, frame weight or demographic characteristics. Those who loaded their WC frame into the back seat had significantly weaker right shoulder internal rotators. Understanding car transfers and WC loading in independent drivers is crucial to prevent shoulder pain and injury and preserve community participation.

Impact of changing from staining to culture techniques on detection rates of Campylobacter spp. in routine stool samples in Chile.

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Porte, Lorena; Varela, Carmen; Haecker, Thomas; Morales, Sara; Weitzel, Thomas

2016-05-13

Campylobacter is a leading cause of bacterial gastroenteritis, but sensitive diagnostic methods such as culture are expensive and often not available in resource limited settings. Therefore, direct staining techniques have been developed as a practical and economical alternative. We analyzed the impact of replacing Campylobacter staining with culture for routine stool examinations in a private hospital in Chile. From January to April 2014, a total of 750 consecutive stool samples were examined in parallel by Hucker stain and Campylobacter culture. Isolation rates of Campylobacter were determined and the performance of staining was evaluated against culture as the gold standard. Besides, isolation rates of Campylobacter and other enteric pathogens were compared to those of past years. Campylobacter was isolated by culture in 46 of 750 (6.1 %) stool samples. Direct staining only identified three samples as Campylobacter positive and reached sensitivity and specificity values of 6.5 and 100 %, respectively. In comparison to staining-based detection rates of previous years, we observed a significant increase of Campylobacter cases in our patients. Direct staining technique for Campylobacter had a very low sensitivity compared to culture. Staining methods might lead to a high rate of false negative results and an underestimation of the importance of campylobacteriosis. With the inclusion of Campylobacter culture, this pathogen became a leading cause of intestinal infection in our patient population.

Many Forms of Culture

Science.gov (United States)

Cohen, Adam B.

2009-01-01

Psychologists interested in culture have focused primarily on East-West differences in individualism-collectivism, or independent-interdependent self-construal. As important as this dimension is, there are many other forms of culture with many dimensions of cultural variability. Selecting from among the many understudied cultures in psychology,…

Molecular profiling techniques as tools to detect potential unintended effects in genetically engineered maize

CSIR Research Space (South Africa)

Barros, E

2010-05-01

Full Text Available Molecular Profiling Techniques as Tools to Detect Potential Unintended Effects in Genetically Engineered Maize Eugenia Barros Introduction In the early stages of production and commercialization of foods derived from genetically engineered (GE) plants... systems. In a recent paper published in Plant Biotechnology Journal,4 we compared two transgenic white maize lines with the non-transgenic counterpart to investigate two possible sources of variation: genetic engineering and environmental variation...

Laboratory Approach to the Diagnosis of Culture-Negative Infective Endocarditis.

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Subedi, S; Jennings, Z; Chen, S C-A

2017-08-01

Blood-culture negative endocarditis (BCNE) accounts for up to 35% of all cases of infective endocarditis (IE) and is a serious life-threatening condition with considerable morbidity and mortality. Rapid detection and identification of the causative pathogen is essential for timely, directed therapy. Blood-culture negative endocarditis presents a diagnostic and therapeutic challenge. Causes of BCNE are varied including: treatment with antibiotic agents prior to blood culture collection; sub-optimal specimen collection; and/or infection due to fastidious (eg. nutritionally variant streptococci), intracellular (eg. Coxiella burnetii, Bartonella species) or non-culturable or difficult to culture organisms (eg. Mycobacteria, Tropheryma whipplei and fungi); as well as non-infective aetiologies. Here, we review aetiological and diagnostic approaches to BCNE including newer molecular based techniques, with a brief summary of imaging investigation and treatment principles. Copyright © 2017 Australian and New Zealand Society of Cardiac and Thoracic Surgeons (ANZSCTS) and the Cardiac Society of Australia and New Zealand (CSANZ). Published by Elsevier B.V. All rights reserved.

Photoionization of excited molecular states using multiphoton excitation techniques

International Nuclear Information System (INIS)

Dehmer, P.M.; Pratt, S.T.; Dehmer, J.L.

1984-01-01

Photoelectron spectra are reported for three photon resonant, four photon ionization of H 2 via the B 1 Σ + /sub u/, v = 7 (J = 2,4) and C 1 Pi/sub u/, v = 0-4 (J = 1) levels and of N 2 via the o 3 1 Pi/sub u/, v = 1,2, b 1 Pi/sub u/, v = 3-5, and c 1 Pi/sub u/, v = 0 levels. The results reflect both the spectroscopy and the dynamics of photoionization of excited molecular states and are discussed in terms of the selection rules for photoionization and the relative probabilities of photoionization from Rydberg and valence states. In some cases, in accordance with the Franck-Condon principle, the results demonstrate that resonant multiphoton ionization through Rydberg states may be a powerful technique for the production of electronic, vibrational, and rotational state selected ions. However, in other cases, systematic departures from Franck-Condon factors are observed, which reflect the more subtle dynamics of excited state photoionization

A new crossed molecular beam apparatus using time-sliced ion velocity imaging technique

International Nuclear Information System (INIS)

Wu Guorong; Zhang Weiqing; Pan Huilin; Shuai Quan; Jiang Bo; Dai Dongxu; Yang Xueming

2008-01-01

A new crossed molecular beam apparatus has been constructed for investigating polyatomic chemical reactions using the time-sliced ion velocity map imaging technique. A unique design is adopted for one of the two beam sources and allows us to set up the molecular beam source either horizontally or vertically. This can be conveniently used to produce versatile atomic or radical beams from photodissociation and as well as electric discharge. Intensive H-atom beam source with high speed ratio was produced by photodissociation of the HI molecule and was reacted with the CD 4 molecule. Vibrational-state resolved HD product distribution was measured by detecting the CD 3 product. Preliminary results were also reported on the F+SiH 4 reaction using the discharged F atom beam. These results demonstrate that this new instrument is a powerful tool for investigating chemical dynamics of polyatomic reactions.

Cultural factors in collegiate eating disorder pathology: When family culture clashes with individual culture

OpenAIRE

Tomiyama, AJ; Mann, T

2008-01-01

The authors evaluated the validity of familial enmeshment (extreme proximity in family relationships) as a risk factor for eating disorders across cultural value orientations. They tested the hypothesis that although familial enmeshment may be a risk factor for eating disorder pathology for (1) participants of non-Asian descent or (2) culturally independent participants, enmeshment will not be a risk factor for (1) participants of Asian descent or (2) culturally interdependent participants. P...

Nuclear techniques for the analysis and dating of cultural heritage with the tandetron accelerator at the CEDAD

Directory of Open Access Journals (Sweden)

Lucio Calcagnile

2014-12-01

Full Text Available The Accelerator Mass Spectrometry technique for measuring carbon isotopes and dating artifacts, together with nuclear techniques of ion beam analysis are widely used in the field of cultural heritage owing to the great advantage of their being non-destructive. In Italy, CEDAD - CEntro Di DAtazione e Diagnostica of the University of Salento, with its tandetron accelerator of 3MV, has played a major role for over ten years, in studying materials of cultural assets requiring the determination of their elemental composition and determination of absolute chronology using radiocarbon. This study describes the Accelerator Mass Spectrometry technique used with the accelerator at CEDAD to determine age by means of radiocarbon and PIXE-PIGE techniques, and to determine elements, even in traces, present in materials. Some case studies carried out at CEDAD are reported, including those on the Riace Bronzes and Capitoline Wolf. The latter has been definitively dated to the Middle Ages, 17 centuries later than the previously attributed dating by historians. In addition, an important technical innovation is described, achieved within the framework of the IT@CHA Project enabling organic materials to be dated using only 10 μg of carbon.

Reversible gelling culture media for in-vitro cell culture in three-dimensional matrices

Science.gov (United States)

An, Yuehuei H.; Mironov, Vladimir A.; Gutowska, Anna

2000-01-01

A gelling cell culture medium useful for forming a three dimensional matrix for cell culture in vitro is prepared by copolymerizing an acrylamide derivative with a hydrophilic comonomer to form a reversible (preferably thermally reversible) gelling linear random copolymer in the form of a plurality of linear chains having a plurality of molecular weights greater than or equal to a minimum gelling molecular weight cutoff, mixing the copolymer with an aqueous solvent to form a reversible gelling solution and adding a cell culture medium to the gelling solution to form the gelling cell culture medium. Cells such as chondrocytes or hepatocytes are added to the culture medium to form a seeded culture medium, and temperature of the medium is raised to gel the seeded culture medium and form a three dimensional matrix containing the cells. After propagating the cells in the matrix, the cells may be recovered by lowering the temperature to dissolve the matrix and centrifuging.

Molecular Technique to Understand Deep Microbial Diversity

Science.gov (United States)

Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.

2012-01-01

Current sequencing-based and DNA microarray techniques to study microbial diversity are based on an initial PCR (polymerase chain reaction) amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of the minor template appears to be suppressed by the exponential amplification of the more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck has overlooked the presence of the less abundant minority population, and underestimated their role in the ecosystem maintenance. To generate PCR amplicons for subsequent diversity analysis, bacterial l6S rRNA genes are amplified by PCR using universal primers. Two distinct PCR regimes are employed in parallel: one using normal and the other using biotinlabeled universal primers. PCR products obtained with biotin-labeled primers are mixed with streptavidin-labeled magnetic beads and selectively captured in the presence of a magnetic field. Less-abundant DNA templates that fail to amplify in this first round of PCR amplification are subjected to a second round of PCR using normal universal primers. These PCR products are then subjected to downstream diversity analyses such as conventional cloning and sequencing. A second round of PCR amplified the minority population and completed the deep diversity picture of the environmental sample.

Sex determination of Pohnpei Micronesian kingfishers using morphological and molecular genetic techniques

Science.gov (United States)

Kesler, Dylan C.; Lopes, I.F.; Haig, Susan M.

2006-01-01

Conservation-oriented studies of Micronesian Kingfishers (Todiramphus cinnamominus) have been hindered by a lack of basic natural history information, despite the status of the Guam subspecies (T. c. cinnamominus) as one of the most endangered species in the world. We used tissue samples and morphometric measures from museum specimens and wild-captured Pohnpei Micronesian Kingfishers (T. c. reichenbachii) to develop methods for sex determination. We present a modified molecular protocol and a discriminant function that yields the probability that a particular individual is male or female. Our results revealed that females were significantly larger than males, and the discriminant function correctly predicted sex in 73% (30/41) of the individuals. The sex of 86% (18/21) of individuals was correctly assigned when a moderate reliability threshold was set. Sex determination using molecular genetic techniques was more reliable than methods based on morphology. Our results will facilitate recovery efforts for the critically endangered Guam Micronesian Kingfisher and provide a basis for sex determination in the 11 other endangered congeners in the Pacific Basin.

Molecular biological and immunohistological characterization of canine dermal papilla cells and the evaluation of culture conditions.

Science.gov (United States)

Kobayashi, Tetsuro; Fujisawa, Akiko; Amagai, Masayuki; Iwasaki, Toshiroh; Ohyama, Manabu

2011-10-01

The dermal papilla (DP) plays pivotal roles in hair follicle morphogenesis and cycling. However, our understanding of the biology of the canine DP is extremely limited. The aim of this study was to elucidate molecular biological and immunohistochemical characteristics of canine DP cells and determine appropriate conditions for in vitro expansion. Histological investigation revealed that the canine DP expressed biomarkers of human and rodent DP, including alkaline phosphatase (ALP) and versican. When microdissected, canine DP, but not fibroblasts, strongly expressed the DP-related genes for alkaline phosphatase, Wnt inhibitory factor 1 and lymphoid enhancer-binding factor 1, confirming successful isolation. The growth rate of isolated canine DP cells was moderate in conventional culture conditions for rodent and human DP; however, AmnioMAX-C100 complete medium allowed more efficient cultivation. Dermal papilla marker gene expression was maintained in early passage cultured DP cells, but gradually lost after the third passage. Approaches to mimic the in vivo DP environment in culture, such as supplementation of keratinocyte-conditioned medium or use of extracellular matrix-coated dishes, moderately ameliorated loss of DP gene expression in canine DP cells. It is possible that constituent factors in AmnioMAX may influence culture. These findings suggested that further refinements of culture conditions may enable DP cell expansion without impairing intrinsic properties and, importantly, demonstrated that AmnioMAX-cultured early passage canine DP cells partly maintained the biological characteristics of in vivo canine DP cells. This study provides crucial information necessary for further optimization of culture conditions of canine DP. © 2011 The Authors. Veterinary Dermatology. © 2011 ESVD and ACVD.

Uncovering the molecular secrets of inflammatory breast cancer biology: an integrated analysis of three distinct affymetrix gene expression datasets.

Science.gov (United States)

Van Laere, Steven J; Ueno, Naoto T; Finetti, Pascal; Vermeulen, Peter; Lucci, Anthony; Robertson, Fredika M; Marsan, Melike; Iwamoto, Takayuki; Krishnamurthy, Savitri; Masuda, Hiroko; van Dam, Peter; Woodward, Wendy A; Viens, Patrice; Cristofanilli, Massimo; Birnbaum, Daniel; Dirix, Luc; Reuben, James M; Bertucci, François

2013-09-01

Inflammatory breast cancer (IBC) is a poorly characterized form of breast cancer. So far, the results of expression profiling in IBC are inconclusive due to various reasons including limited sample size. Here, we present the integration of three Affymetrix expression datasets collected through the World IBC Consortium allowing us to interrogate the molecular profile of IBC using the largest series of IBC samples ever reported. Affymetrix profiles (HGU133-series) from 137 patients with IBC and 252 patients with non-IBC (nIBC) were analyzed using unsupervised and supervised techniques. Samples were classified according to the molecular subtypes using the PAM50-algorithm. Regression models were used to delineate IBC-specific and molecular subtype-independent changes in gene expression, pathway, and transcription factor activation. Four robust IBC-sample clusters were identified, associated with the different molecular subtypes (Pmolecular subtype-independent 79-gene signature, which held independent prognostic value in a series of 871 nIBCs. Functional analysis revealed attenuated TGF-β signaling in IBC. We show that IBC is transcriptionally heterogeneous and that all molecular subtypes described in nIBC are detectable in IBC, albeit with a different frequency. The molecular profile of IBC, bearing molecular traits of aggressive breast tumor biology, shows attenuation of TGF-β signaling, potentially explaining the metastatic potential of IBC tumor cells in an unexpected manner. ©2013 AACR.

Diagnostic performance of automated liquid culture and molecular line probe assay in smear-negative pulmonary tuberculosis.

Science.gov (United States)

Kotwal, Aarti; Biswas, Debasis; Raghuvanshi, Shailendra; Sindhwani, Girish; Kakati, Barnali; Sharma, Shweta

2017-04-01

The diagnosis of smear-negative pulmonary tuberculosis (PTB) is particularly challenging, and automated liquid culture and molecular line probe assays (LPA) may prove particularly useful. The objective of our study was to evaluate the diagnostic potential of automated liquid culture (ALC) technology and commercial LPA in sputum smear-negative PTB suspects. Spot sputum samples were collected from 145 chest-symptomatic smear-negative patients and subjected to ALC, direct drug susceptibility test (DST) testing and LPA, as per manufacturers' instructions. A diagnostic yield of 26.2% was observed among sputum smear-negative TB suspects with 47.4% of the culture isolates being either INH- and/or rifampicin-resistant. Complete agreement was observed between the results of ALC assay and LPA except for two isolates which demonstrated sensitivity to INH and rifampicin at direct DST but were rifampicin-resistant in LPA. Two novel mutations were also detected among the multidrug isolates by LPA. In view of the diagnostic challenges associated with the diagnosis of TB in sputum smear-negative patients, our study demonstrates the applicability of ALC and LPA in establishing diagnostic evidence of TB.

Detection of mycoplasmas in urethral swabs from HIV-1 infected patients and control individuals using culture techniques and polymerase chain reaction

Directory of Open Access Journals (Sweden)

CUNHA Regina Ayr Florio da

1998-01-01

Full Text Available The objective of the present study was to determine the prevalence of certain mycoplasma species, i.e., Mycoplasma hominis, Ureaplasma urealyticum and Mycoplasma penetrans, in urethral swabs from HIV-1 infected patients compared to swabs from a control group. Mycoplasmas were detected by routine culture techniques and by the Polymerase Chain Reaction (PCR technique, using 16SrRNA generic primers of conserved region and Mycoplasma penetrans specific primers. The positivity rates obtained with the two methods were comparable. Nevertheless, PCR was more sensitive, while the culture techniques allowed the quantification of the isolates. The results showed no significant difference (p < 0.05 in positivity rates between the methods used for mycoplasma detection.

Independent random sampling methods

CERN Document Server

Martino, Luca; Míguez, Joaquín

2018-01-01

This book systematically addresses the design and analysis of efficient techniques for independent random sampling. Both general-purpose approaches, which can be used to generate samples from arbitrary probability distributions, and tailored techniques, designed to efficiently address common real-world practical problems, are introduced and discussed in detail. In turn, the monograph presents fundamental results and methodologies in the field, elaborating and developing them into the latest techniques. The theory and methods are illustrated with a varied collection of examples, which are discussed in detail in the text and supplemented with ready-to-run computer code. The main problem addressed in the book is how to generate independent random samples from an arbitrary probability distribution with the weakest possible constraints or assumptions in a form suitable for practical implementation. The authors review the fundamental results and methods in the field, address the latest methods, and emphasize the li...

[Molecular techniques applied in species identification of Toxocara].

Science.gov (United States)

Fogt, Renata

2006-01-01

Toxocarosis is still an important and actual problem in human medicine. It can manifest as visceral (VLM), ocular (OLM) or covert (CT) larva migrans syndroms. Complicated life cycle of Toxocara, lack of easy and practical methods of species differentiation of the adult nematode and embarrassing in recognition of the infection in definitive hosts create difficulties in fighting with the infection. Although studies on human toxocarosis have been continued for over 50 years there is no conclusive answer, which of species--T. canis or T. cati constitutes a greater risk of transmission of the nematode to man. Neither blood serological examinations nor microscopic observations of the morphological features of the nematode give the satisfied answer on the question. Since the 90-ths molecular methods were developed for species identification and became useful tools being widely applied in parasitological diagnosis. This paper cover the survey of methods of DNA analyses used for identification of Toxocara species. The review may be helpful for researchers focused on Toxocara and toxocarosis as well as on detection of new species. The following techniques are described: PCR (Polymerase Chain Reaction), RFLP (Restriction Fragment Length Polymorphism), RAPD (Random Amplified Polymorphic DNA) and SSCP (Single Strand Conformation Polymorphism).

The potential of 3D techniques for cultural heritage object documentation

Science.gov (United States)

Bitelli, Gabriele; Girelli, Valentina A.; Remondino, Fabio; Vittuari, Luca

2007-01-01

The generation of 3D models of objects has become an important research point in many fields of application like industrial inspection, robotics, navigation and body scanning. Recently the techniques for generating photo-textured 3D digital models have interested also the field of Cultural Heritage, due to their capability to combine high precision metrical information with a qualitative and photographic description of the objects. In fact this kind of product is a fundamental support for documentation, studying and restoration of works of art, until a production of replicas by fast prototyping techniques. Close-range photogrammetric techniques are nowadays more and more frequently used for the generation of precise 3D models. With the advent of automated procedures and fully digital products in the 1990s, it has become easier to use and cheaper, and nowadays a wide range of commercial software is available to calibrate, orient and reconstruct objects from images. This paper presents the complete process for the derivation of a photorealistic 3D model of an important basalt stela (about 70 x 60 x 25 cm) discovered in the archaeological site of Tilmen Höyük, in Turkey, dating back to 2nd mill. BC. We will report the modeling performed using passive and active sensors and the comparison of the achieved results.

Strategy for identification & characterization of Bartonella henselae with conventional & molecular methods

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Kavita Diddi

2013-01-01

Full Text Available Background & objectives: Bartonella henselae is a fastidious gram-negative bacterium usually causing self limiting infections in immunocompetent individuals but often causes potentially life threatening infection, such as bacillary angiomatosis in immunocompromised patients. Both diagnosis of infections and research into molecular mechanisms of pathogenesis have been hindered by lack of appropriate and reliable diagnostic techniques. We undertook this study to standardize methods to characterize B. henselae in clinical samples to diagnose Bartonella infection correctly. Methods: B. henselae ATCC 49882 strain was procured from American type culture collection, USA. This strain was revived and maintained in the laboratory, and identification and characterization of this strain was done by conventional and molecular techniques, which included culture on various media, staining by different methods including electron microscopy, biochemical analysis by conventional methods and API, polymerase chain reaction (PCR for amplification of citrate synthase gene followed by restriction fragment length polymorphism (RFLP. Results: This organism was biochemically inert due to slow growth and generated unique identification code with API. The amplification of the citrate-synthase gene with primers yielded a 381 bp product followed by specific RFLP profile for B. henselae. Interpretation & conclusions: Bartonella is fastidious and fragile organism and should be handled carefully. Extra effort and careful observation are required to isolate and characterize this organism.

Space of solitude in culture

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Agnieszka Małgorzata Kulig

2014-04-01

Full Text Available In my article I suggest looking at the phenomenon of solitude in culture not only as an opportunity to study an intimate and individual experience, to which numerous descriptions refer. I would rather consider whether possessing knowledge about this experience we acquire competencies regarding the culture in which this solitude has occurred. The discourse of melancholy, for which the space of solitude and confrontation with the ultimate has been the natural environment, supports me in describing the space of solitude in culture. For the purposes of reflection, I initiate my own definition of solitude as a space between life and death. That space allows the individual to feel the energy of life and the presence of death, even in such moments of human life (youth when the individual is not fully aware of their role in society, and is in the process of crystallizing their identity. In this case, solitude as a space between would be a state of suspension, which, however, prepares for active, independent life in the community. In this article, I refer to the postulate of the German culture researcher Thomas Macho in order to treat the experience of solitude as a context, an opportunity to practise techniques of culture, as well as to heterotopic space as defined by Michel Foucault.

On the assessment of the productivity of suspension cultures of unicellular green algae at defined light conditions

Energy Technology Data Exchange (ETDEWEB)

Seiss, U; Borns, E; Boehm, H

1985-01-01

A description is given of the possibility of a comparison of the production between different suspension cultures of microalgae at equal and defined light conditions. For this, a variant of the turbidostat technique is used by which with the acid of a phototransistor and the filter combination of red filter/opal glass filter a chlorophyll-equivalent signal is applied for control. The equal light conditions are compared and set by the preparation of the respective absorption profiles. From this one can derive the mean level of irradiation within the suspension cultures and use it as the reference value for the light conditions. By this technique it is possible to set equal light conditions in suspension cultures independent of the given cell sizes, cell shapes and dry matter contents.

Molecular and functional analysis of anchorage independent, treatment-evasive neuroblastoma tumorspheres with enhanced malignant properties: A possible explanation for radio-therapy resistance.

Science.gov (United States)

Abou-Antoun, Tamara J; Nazarian, Javad; Ghanem, Anthony; Vukmanovic, Stanislav; Sandler, Anthony D

2018-01-01

Despite significant advances in cancer treatment and management, more than 60% of patients with neuroblastoma present with very poor prognosis in the form of metastatic and aggressive disease. Solid tumors including neuroblastoma are thought to be heterogeneous with a sub-population of stem-like cells that are treatment-evasive with highly malignant characteristics. We previously identified a phenomenon of reversible adaptive plasticity (RAP) between anchorage dependent (AD) cells and anchorage independent (AI) tumorspheres in neuroblastoma cell cultures. To expand our molecular characterization of the AI tumorspheres, we sought to define the comprehensive proteomic profile of murine AD and AI neuroblastoma cells. The proteomic profiles of the two phenotypic cell populations were compared to each other to determine the differential protein expression and molecular pathways of interest. We report exclusive or significant up-regulation of tumorigenic pathways expressed by the AI tumorspheres compared to the AD cancer cells. These pathways govern metastatic potential, enhanced malignancy and epithelial to mesenchymal transition. Furthermore, radio-therapy induced significant up-regulation of specific tumorigenic and proliferative proteins, namely survivin, CDC2 and the enzyme Poly [ADP-ribose] polymerase 1. Bio-functional characteristics of the AI tumorspheres were resistant to sutent inhibition of receptor tyrosine kinases (RTKs) as well as to 2.5 Gy radio-therapy as assessed by cell survival, proliferation, apoptosis and migration. Interestingly, PDGF-BB stimulation of the PDGFRβ led to transactivation of EGFR and VEGFR in AI tumorspheres more potently than in AD cells. Sutent inhibition of PDGFRβ abrogated this transactivation in both cell types. In addition, 48 h sutent treatment significantly down-regulated the protein expression of PDGFRβ, MYCN, SOX2 and Survivin in the AI tumorspheres and inhibited tumorsphere self-renewal. Radio-sensitivity in AI

Effect of Different Concentrations of Growth Regulators on Gardenia jasminoides cv. Veitchii Micropropagation by Tissue Culture Technique

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G. R. Abdullah

2003-01-01

Full Text Available Micropropagation techniques were set up for Gardenia jasminoides c.v. veitchi. Many plantlets were obtained by culturing shoot cuttings in MS nutrient media, 30 g/L Sucrose, 7 g/L Agar Agar, and different concentrations of BAP and IAA. The best concentration was 1mg /L BAP with 0.5 mg/L IAA. This concentration gave the best sprout growth suitable for rooting in primary and secondary culture by reculturing the stuck cutting every 6 weeks and for many times. We also obtained a high rooting percentage up to 98 % of natural rooting in rooting media different from propagation media by reducing mineral salt concentration to half, Sucrose to 20gm/L, and 2gm/L active charcoal, and 1mg/L IAA. Plantlets were transferred to greenhous and subjected for hardening. This technique gave 22 plantlets from one cutting in one year.

Molecular diagnosis of rhino-orbito-cerebral mucormycosis from fresh tissue samples.

Science.gov (United States)

Zaman, Kamran; Rudramurthy, Shivaprakash Mandya; Das, Ashim; Panda, Naresh; Honnavar, Prasanna; Kaur, Harsimran; Chakrabarti, Arunaloke

2017-08-01

We aimed to evaluate a PCR-based technique for the diagnosis of mucormycosis and the identification of fungi from fresh tissue specimens in patients with rhino-orbito-cerebral-mucormycosis (ROCM). Fifty cases of ROCM were included in the study. Conventional identification was performed using microscopy and culture. Molecular diagnosis was performed by amplifying the ribosomal DNA using pan-fungal ITS primers and semi-nested Mucorales-specific primers of the 18S region. The amplified products were sequenced to identify the agents. The utility of PCR-RFLP of the 18S region of rDNA was evaluated to identify the Mucorales. The ROCM cases were diagnosed by the demonstration of aseptate ribbon-like hyphae in biopsy specimens collected from the patients. Isolation was possible in 24 (48 %) samples. The ITS2 PCR confirmed mucormycosis in 27 cases (54 %; CI 59.4-68.2). By comparison, Mucorales-specific PCR was able to amplify DNA and the sequence enabled the identification of Mucorales speciesin all the patients. PCR-RFLP of the 18S region of rDNA could only identify the agent to genus level. The molecular technique was able to identify Mucorales species in 26 (42 %) cases that were negative by culture. Mucorales-specific semi-nested PCR targeting the 18S region is a better technique than ITS2 PCR for diagnosis. PCR-RFLP of the 18S region helps in identification to genus level.

X-ray Constrained Extremely Localized Molecular Orbitals: Theory and Critical Assessment of the New Technique.

Science.gov (United States)

Genoni, Alessandro

2013-07-09

Following the X-ray constrained wave function approach proposed by Jayatilaka, we have devised a new technique that allows to extract molecular orbitals strictly localized on small molecular fragments from sets of experimental X-ray structure factors amplitudes. Since the novel strategy enables to obtain electron distributions that have quantum mechanical features and that can be easily interpreted in terms of traditional chemical concepts, the method can be also considered as a new useful tool for the determination and the analysis of charge densities from high-resolution X-ray experiments. In this paper, we describe in detail the theory of the new technique, which, in comparison to our preliminary work, has been improved both treating the effects of isotropic secondary extinctions and introducing a new protocol to halt the fitting procedure against the experimental X-ray scattering data. The performances of the novel strategy have been studied both in function of the basis-sets flexibility and in function of the quality of the considered crystallographic data. The tests performed on four different systems (α-glycine, l-cysteine, (aminomethyl)phosphonic acid and N-(trifluoromethyl)formamide) have shown that the achievement of good statistical agreements with the experimental measures mainly depends on the quality of the crystal structures (i.e., geometry positions and thermal parameters) used in the X-ray constrained calculations. Finally, given the reliable transferability of the obtained Extremely Localized Molecular Orbitals (ELMOs), we envisage to exploit the novel approach to construct new ELMOs databases suited to the development of linear-scaling methods for the refinement of macromolecular crystal structures.

Design of a tablet computer app for facilitation of a molecular blood culture test in clinical microbiology and preliminary usability evaluation

DEFF Research Database (Denmark)

Samson, Lasse L.; Pape-Haugaard, Louise; Meltzer, Michelle C.

2016-01-01

through specialized applications (apps) while supporting the mobility of the users. The use of apps for mobile phones and tablet computers may support workflow of complex tasks, for example, molecular-based diagnostic tests in clinical microbiology. Multiplex Blood Culture Test (MuxBCT) is a molecular......-based diagnostic test used for rapid identification of pathogens in positive blood cultures. To facilitate the workflow of the MuxBCT, a specialized tablet computer app was developed as an accessory to the diagnostic test. The app aims to reduce the complexity of the test by step-by-step guidance of microscopy...... and to assist users in reaching an exact bacterial or fungal diagnosis based on blood specimen observations and controls. Additionally, the app allows for entry of test results, and communication thereof to the laboratory information system (LIS). OBJECTIVE: The objective of the study was to describe the design...

A correlative study of Papanicolaou smear, fluorescent antibody, and culture for the diagnosis of Chlamydia trachomatis.

Science.gov (United States)

Spence, M R; Barbacci, M; Kappus, E; Quinn, T

1986-11-01

A prospective study of 300 patients undergoing therapeutic termination of pregnancy was conducted. A Papanicolaou smear was obtained and a clinical evaluation of the cervix was made. Specimens from the cervix were examined by both direct fluorescent antibody and culture techniques for the presence of Chlamydia trachomatis. The presence of inflammation on Papanicolaou smear could be correlated with C trachomatis isolation. Papanicolaou smear findings consistent with C trachomatis lacked both sensitivity and specificity when compared with direct fluorescent antibody and/or culture techniques. A correlation was found between the clinical diagnosis of cervicitis and C trachomatis. This interrelationship was absent when the component findings of cervicitis (ectopy, friability, and purulent mucus) were examined independently.

Microbial community analysis of perchlorate-reducing cultures growing on zero-valent iron

International Nuclear Information System (INIS)

Son, Ahjeong; Schmidt, Carl J.; Shin, Hyejin; Cha, Daniel K.

2011-01-01

Anaerobic microbial mixed cultures demonstrated its ability to completely remove perchlorate in the presence of zero-valent iron. In order to understand the major microbial reaction in the iron-supported culture, community analysis comprising of microbial fatty acids and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) techniques was performed for perchlorate reducing cultures. Analysis of fatty acid methyl esters (FAMEs) and subsequent principal component analysis (PCA) showed clear distinctions not only between iron-supported perchlorate reducing culture and seed bacteria, but also among perchlorate-reducing cultures receiving different electron donors. The DGGE pattern targeting the chlorite dismutase (cld) gene showed that iron-supported perchlorate reducing culture is similar to hydrogen-fed cultures as compared to acetate-fed culture. The phylogenetic tree suggested that the dominant microbial reaction may be a combination of the autotrophic and heterotrophic reduction of perchlorate. Both molecular and chemotaxonomic experimental results support further understanding in the function of zero-valent iron as an adequate electron source for enhancing the microbial perchlorate reduction in natural and engineered systems.

Microbial community analysis of perchlorate-reducing cultures growing on zero-valent iron

Energy Technology Data Exchange (ETDEWEB)

Son, Ahjeong, E-mail: ason@auburn.edu [Department of Civil Engineering, Auburn University, Auburn, AL 36849 (United States); Schmidt, Carl J. [Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716 (United States); Shin, Hyejin [Department of Mathematics and Statistics, Auburn University, Auburn, AL 36849 (United States); Cha, Daniel K. [Department of Civil and Environmental Engineering, University of Delaware, Newark, DE 19716 (United States)

2011-01-30

Anaerobic microbial mixed cultures demonstrated its ability to completely remove perchlorate in the presence of zero-valent iron. In order to understand the major microbial reaction in the iron-supported culture, community analysis comprising of microbial fatty acids and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) techniques was performed for perchlorate reducing cultures. Analysis of fatty acid methyl esters (FAMEs) and subsequent principal component analysis (PCA) showed clear distinctions not only between iron-supported perchlorate reducing culture and seed bacteria, but also among perchlorate-reducing cultures receiving different electron donors. The DGGE pattern targeting the chlorite dismutase (cld) gene showed that iron-supported perchlorate reducing culture is similar to hydrogen-fed cultures as compared to acetate-fed culture. The phylogenetic tree suggested that the dominant microbial reaction may be a combination of the autotrophic and heterotrophic reduction of perchlorate. Both molecular and chemotaxonomic experimental results support further understanding in the function of zero-valent iron as an adequate electron source for enhancing the microbial perchlorate reduction in natural and engineered systems.

Molecular identification of Coccidioides spp. in soil samples from Brazil.

Science.gov (United States)

de Macêdo, Regina C L; Rosado, Alexandre S; da Mota, Fabio F; Cavalcante, Maria A S; Eulálio, Kelsen D; Filho, Antônio D; Martins, Liline M S; Lazéra, Márcia S; Wanke, Bodo

2011-05-16

Since 1991 several outbreaks of acute coccidioidomycosis (CM) were diagnosed in the semi-arid Northeast of Brazil, mainly related to disturbance of armadillo burrows caused by hunters while digging them for the capture of these animals. This activity causes dust contaminated with arthroconidia of Coccidioides posadasii, which, once inhaled, cause the mycosis. We report on the identification of C. posadasii in soil samples related to outbreaks of CM. Twenty four soil samples had their DNA extracted and subsequently submitted to a semi-nested PCR technique using specific primers. While only 6 (25%) soil samples were positive for C. posadasii by mice inoculation, all (100%) were positive by the molecular tool. This methodology represents a simple, sensitive and specific molecular technique to determine the environmental distribution of Coccidioides spp. in endemic areas, but cannot distinguish the species. Moreover, it may be useful to identify culture isolates. Key-words: 1. Coccidioidomycosis. 2. Coccidioides spp. 3. C. posadasii. 4. Semi-arid. 5. Semi-nested PCR.

Bacterial diversity analysis of larvae and adult midgut microflora using culture-dependent and culture-independent methods in lab-reared and field-collected Anopheles stephensi-an Asian malarial vector

Directory of Open Access Journals (Sweden)

Adak Tridibesh

2009-05-01

Full Text Available Abstract Background Mosquitoes are intermediate hosts for numerous disease causing organisms. Vector control is one of the most investigated strategy for the suppression of mosquito-borne diseases. Anopheles stephensi is one of the vectors of malaria parasite Plasmodium vivax. The parasite undergoes major developmental and maturation steps within the mosquito midgut and little is known about Anopheles-associated midgut microbiota. Identification and characterization of the mosquito midgut flora is likely to contribute towards better understanding of mosquito biology including longevity, reproduction and mosquito-pathogen interactions that are important to evolve strategies for vector control mechanisms. Results Lab-reared and field-collected A. stephensi male, female and larvae were screened by "culture-dependent and culture-independent" methods. Five 16S rRNA gene library were constructed form lab and field-caught A. stephensi mosquitoes and a total of 115 culturable isolates from both samples were analyzed further. Altogether, 68 genera were identified from midgut of adult and larval A. stephensi, 53 from field-caught and 15 from lab-reared mosquitoes. A total of 171 and 44 distinct phylotypes having 85 to 99% similarity with the closest database matches were detected among field and lab-reared A. stephensi midgut, respectively. These OTUs had a Shannon diversity index value of 1.74–2.14 for lab-reared and in the range of 2.75–3.49 for field-caught A. stephensi mosquitoes. The high species evenness values of 0.93 to 0.99 in field-collected adult and larvae midgut flora indicated the vastness of microbial diversity retrieved by these approaches. The dominant bacteria in field-caught adult male A. stephensi were uncultured Paenibacillaceae while in female and in larvae it was Serratia marcescens, on the other hand in lab-reared mosquitoes, Serratia marcescens and Cryseobacterium meninqosepticum bacteria were found to be abundant. Conclusion

Comparison of group B streptococci colonization in vaginal and rectal specimens by culture method and polymerase chain reaction technique

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Shahrokh Bidgani

2016-03-01

Conclusion: The frequency of GBS culture from rectal samples was higher than vaginal samples. However, the detection percentage of GBS using PCR from vaginal samples was higher than rectal samples. By contrast, the culture is a time-consuming method requiring at least 48 hours for GBS fully identification but PCR is a sensitive and rapid technique in detection of GBS, with the result was acquired during 3 hours.

Photoionization of excited molecular states using multiphoton excitation techniques

International Nuclear Information System (INIS)

Dehmer, P.M.; Pratt, S.T.; Dehmer, J.L.

1984-01-01

Photoelectron spectra are reported for three photon resonant, four photon ionization of H 2 via the B 1 Σ/sub u/ + , v = 7 (J = 2,4) and C 1 π/sub u'/, v = 0-4 (J = 1) levels and of N 2 via the o 3 1 π/sub u'/, v = 1,2, b 1 π/sub u'/, v = 3-5, and c 1 π/sub u'/, v = 0 levels. The results reflect both the spectroscopy and the dynamics of photoionization of excited molecular states and are discussed in terms of the selection rules for photoionization and the relative probabilities of photoionization from Rydberg and valence states. In some cases, in accordance with the Franck-Condon principle, the results demonstrate that resonant multiphoton ionization through Rydberg states may be a powerful technique for the production of electronic, vibrational, and rotational state selected ions. However, in other cases, systematic departures from Franck-Condon factors are observed, which reflect the more subtle dynamics of excited state photoionization. 23 references, 6 figures, 2 tables

Growing Arabidopsis in vitro: cell suspensions, in vitro culture, and regeneration.

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Barkla, Bronwyn J; Vera-Estrella, Rosario; Pantoja, Omar

2014-01-01

An understanding of basic methods in Arabidopsis tissue culture is beneficial for any laboratory working on this model plant. Tissue culture refers to the aseptic growth of cells, organs, or plants in a controlled environment, in which physical, nutrient, and hormonal conditions can all be easily manipulated and monitored. The methodology facilitates the production of a large number of plants that are genetically identical over a relatively short growth period. Techniques, including callus production, cell suspension cultures, and plant regeneration, are all indispensable tools for the study of cellular biochemical and molecular processes. Plant regeneration is a key technology for successful stable plant transformation, while cell suspension cultures can be exploited for metabolite profiling and mining. In this chapter we report methods for the successful and highly efficient in vitro regeneration of plants and production of stable cell suspension lines from leaf explants of both Arabidopsis thaliana and Arabidopsis halleri.

Phylogenetic & Physiological Profiling of Microbial Communities of Contaminated Soils/Sediments: Identifying Microbial consortia...

Energy Technology Data Exchange (ETDEWEB)

Terence L. Marsh

2004-05-26

The goals of this study were: (1) survey the microbial community in soil samples from a site contaminated with heavy metals using new rapid molecular techniques that are culture-independent; (2) identify phylogenetic signatures of microbial populations that correlate with metal ion contamination; and (3) cultivate these diagnostic strains using traditional as well as novel cultivation techniques in order to identify organisms that may be of value in site evaluation/management or bioremediation.

New technique of identifying the hierarchy of dynamic domains in proteins using a method of molecular dynamics simulations

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Yesylevskyy S. O.

2010-04-01

Full Text Available Aim. Despite a large number of existing domain identification techniques there is no universally accepted method, which identifies the hierarchy of dynamic domains using the data of molecular dynamics (MD simulations. The goal of this work is to develop such technique. Methods. The dynamic domains are identified by eliminating systematic motions from MD trajectories recursively in a model-free manner. Results. The technique called the Hierarchical Domain-Wise Alignment (HDWA to identify hierarchically organized dynamic domains in proteins using the MD trajectories has been developed. Conclusion. A new method of domain identification in proteins is proposed

Bacterial population in traditional sourdough evaluated by molecular methods.

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Randazzo, C L; Heilig, H; Restuccia, C; Giudici, P; Caggia, C

2005-01-01

To study the microbial communities in artisanal sourdoughs, manufactured by traditional procedure in different areas of Sicily, and to evaluate the lactic acid bacteria (LAB) population by classical and culture-independent approaches. Forty-five LAB isolates were identified both by phenotypic and molecular methods. The restriction fragment length polymorphism and 16S ribosomal DNA gene sequencing gave evidence of a variety of species with the dominance of Lactobacillus sanfranciscensis and Lactobacillus pentosus, in all sourdoughs tested. Culture-independent method, such as denaturing gradient gel electrophoresis (DGGE) of the V6-V8 regions of the 16S rDNA, was applied for microbial community fingerprint. The DGGE profiles revealed the dominance of L. sanfranciscensis species. In addition, Lactobacillus-specific primers were used to amplify the V1-V3 regions of the 16S rDNA. DGGE profiles flourished the dominance of L. sanfranciscensis and Lactobacillus fermentum in the traditional sourdoughs, and revealed that the closely related species Lactobacillus kimchii and Lactobacillus alimentarius were not discriminated. Lactobacillus-specific PCR-DGGE analysis is a rapid tool for rapid detection of Lactobacillus species in artisanal sourdough. This study reports a characterization of Lactobacillus isolates from artisanal sourdoughs and highlights the value of DGGE approach to detect uncultivable Lactobacillus species.

Next-generation sequencing and culture-based techniques offer complementary insights into fungi and prokaryotes in beach sands.

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Romão, Daniela; Staley, Christopher; Ferreira, Filipa; Rodrigues, Raquel; Sabino, Raquel; Veríssimo, Cristina; Wang, Ping; Sadowsky, Michael; Brandão, João

2017-06-15

A next-generation sequencing (NGS) approach, in conjunction with culture-based methods, was used to examine fungal and prokaryotic communities for the presence of potential pathogens in beach sands throughout Portugal. Culture-based fungal enumeration revealed low and variable concentrations of the species targeted (yeasts and dermatophytes), which were underrepresented in the community characterized by NGS targeting the ITS1 region. Conversely, NGS indicated that the potentially pathogenic species Purpureocillium liliacinum comprised nearly the entire fungal community. Culturable fecal indicator bacterial concentrations were low throughout the study and unrelated to communities characterized by NGS. Notably, the prokaryotic communities characterized revealed a considerable abundance of archaea. Results highlight differences in communities between methods in beach sand monitoring but indicate the techniques offer complementary insights. Thus, there is a need to leverage culture-based methods with NGS methods, using a toolbox approach, to determine appropriate targets and metrics for beach sand monitoring to adequately protect public health. Copyright © 2017. Published by Elsevier Ltd.

Molecular Detection of Streptococcus pneumoniae on Dried Blood Spots from Febrile Nigerian Children Compared to Culture.

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Pui-Ying Iroh Tam

Full Text Available Nigeria has one of the highest burdens of pneumococcal disease in the world, but accurate surveillance is lacking. Molecular detection of infectious pathogens in dried blood spots (DBS is an ideal method for surveillance of infections in resource-limited settings because of its low cost, minimal blood volumes involved, and ease of storage at ambient temperature. Our study aim was to evaluate a Streptococcus pneumoniae real-time polymerase chain reaction (rt-PCR assay on DBS from febrile Nigerian children on Whatman 903 and FTA filter papers, compared to the gold standard of culture.Between September 2011 to May 2015, blood was collected from children 5 years of age or under who presented to six hospital study sites throughout northern and central Nigeria with febrile illness, and inoculated into blood culture bottles or spotted onto Whatman 903 or FTA filter paper. Culture and rt-PCR were performed on all samples.A total of 537 DBS specimens from 535 children were included in the study, of which 15 were culture-positive for S. pneumoniae. The rt-PCR assay detected S. pneumoniae in 12 DBS specimens (2.2%. One positive rt-PCR result was identified in a culture-negative specimen from a high-risk subject, and two positive rt-PCR results were negative on repeat testing. Six culture-confirmed cases of S. pneumoniae bacteremia were missed. Compared to culture, the overall sensitivities of Whatman 903 and FTA DBS for detection of S. pneumoniae were 57.1% (95% CI 18.4-90.1% and 62.5% (95% CI 24.5-91.5%, respectively. Nonspecific amplification was noted in an additional 22 DBS (4.1%. Among these, six were positive for a non-S. pneumoniae pathogen on culture.Rt-PCR was able to detect S. pneumoniae from clinical DBS specimens, including from a culture-negative specimen. Our findings show promise of this approach as a surveillance diagnostic, but also raise important cautionary questions. Several DBS specimens were detected as S. pneumoniae by rt-PCR despite

Molecular Detection of Streptococcus pneumoniae on Dried Blood Spots from Febrile Nigerian Children Compared to Culture.

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Iroh Tam, Pui-Ying; Hernandez-Alvarado, Nelmary; Schleiss, Mark R; Hassan-Hanga, Fatimah; Onuchukwu, Chuma; Umoru, Dominic; Obaro, Stephen K

2016-01-01

Nigeria has one of the highest burdens of pneumococcal disease in the world, but accurate surveillance is lacking. Molecular detection of infectious pathogens in dried blood spots (DBS) is an ideal method for surveillance of infections in resource-limited settings because of its low cost, minimal blood volumes involved, and ease of storage at ambient temperature. Our study aim was to evaluate a Streptococcus pneumoniae real-time polymerase chain reaction (rt-PCR) assay on DBS from febrile Nigerian children on Whatman 903 and FTA filter papers, compared to the gold standard of culture. Between September 2011 to May 2015, blood was collected from children 5 years of age or under who presented to six hospital study sites throughout northern and central Nigeria with febrile illness, and inoculated into blood culture bottles or spotted onto Whatman 903 or FTA filter paper. Culture and rt-PCR were performed on all samples. A total of 537 DBS specimens from 535 children were included in the study, of which 15 were culture-positive for S. pneumoniae. The rt-PCR assay detected S. pneumoniae in 12 DBS specimens (2.2%). One positive rt-PCR result was identified in a culture-negative specimen from a high-risk subject, and two positive rt-PCR results were negative on repeat testing. Six culture-confirmed cases of S. pneumoniae bacteremia were missed. Compared to culture, the overall sensitivities of Whatman 903 and FTA DBS for detection of S. pneumoniae were 57.1% (95% CI 18.4-90.1%) and 62.5% (95% CI 24.5-91.5%), respectively. Nonspecific amplification was noted in an additional 22 DBS (4.1%). Among these, six were positive for a non-S. pneumoniae pathogen on culture. Rt-PCR was able to detect S. pneumoniae from clinical DBS specimens, including from a culture-negative specimen. Our findings show promise of this approach as a surveillance diagnostic, but also raise important cautionary questions. Several DBS specimens were detected as S. pneumoniae by rt-PCR despite growth of

The microbial content of raw and pasteurized cow milk as determined by molecular approaches.

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Quigley, Lisa; McCarthy, Robert; O'Sullivan, Orla; Beresford, Tom P; Fitzgerald, Gerald F; Ross, R Paul; Stanton, Catherine; Cotter, Paul D

2013-08-01

The microbial composition of raw and pasteurized milk is assessed on a daily basis. However, many such tests are culture-dependent, and, thus, bacteria that are present at subdominant levels, or that cannot be easily grown in the laboratory, may be overlooked. To address this potential bias, we have used several culture-independent techniques, including flow cytometry, real-time quantitative PCR, and high-throughput DNA sequencing, to assess the microbial population of milk from a selection of commercial milk producers, pre- and postpasteurization. The combination of techniques employed reveals the presence of a previously unrecognized and diverse bacterial population in unpasteurized cow milk. Most notably, the use of high-throughput DNA sequencing resulted in several bacterial genera being identified in milk samples for the first time. These included Bacteroides, Faecalibacterium, Prevotella, and Catenibacterium. Our culture-independent analyses also indicate that the bacterial population of pasteurized milk is more diverse than previously appreciated, and that nonthermoduric bacteria within these populations are likely to be in a damaged, nonculturable form. It is thus apparent that the application of state-of-the-art approaches can provide a detailed insight into the bacterial composition of milk and could potentially be employed in the future to investigate the factors that influence the composition of these populations. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

A protocol for preparation and transfection of rat entorhinal cortex organotypic cultures for electrophysiological whole-cell recordings

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Nicholas I. Cilz

2017-01-01

Full Text Available Understanding how neuromodulators influence synaptic transmission and intrinsic excitability within the entorhinal cortex (EC is critical to furthering our understanding of the molecular and cellular aspects of this region. Organotypic cultures can provide a cost-effective means to employ selective molecular biological strategies in elucidating cellular mechanisms of neuromodulation in the EC. We therefore adapted our acute slice model for organotypic culture applications and optimized a protocol for the preparation and biolistic transfection of cultured horizontal EC slices. Here, we present our detailed protocol for culturing EC slices. Using an n-methyl-d-glucamine (NMDG-containing cutting solution, we obtain healthy EC slice cultures for electrophysiological recordings. We also present our protocol for the preparation of “bullets” carrying one or more constructs and demonstrate successful transfection of EC slices. We build upon previous methods and highlight specific aspects in our method that greatly improved the quality of our results. We validate our methods using immunohistochemical, imaging, and electrophysiological techniques. The novelty of this method is that it provides a description of culturing and transfection of EC neurons for specifically addressing their functionality. This method will enable researchers interested in entorhinal function to quickly adopt a similar slice culture transfection system for their own investigations.

15th Anniversary of the Molecular Techniques Unit at the Department of Forensic Medicine at Wroclaw Medical University.

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Pluta, Dominika; Tokarski, Miron; Karpiewska, Anna; Dobosz, Tadeusz

2017-01-01

Molecular Techniques Unit at the Department of Forensic Medicine, Wroclaw Medical University has been operating since December 2003. Soon it will be 15 years since its establishment. This anniversary become an inspiration to write down the story of this institution whose origins illustrate the immense changes that have taken place in forensic genetics. The aim of our work was also to consolidate the professional achievements of Professor Tadeusz Dobosz, chief of the Unit, one of the pioneers of introducing DNA testing technology into Polish forensic medicine. The most important achievements of the Unit include participation in two EU research projects, the development of a non-destructive method of extraction of genetic material, research in field of gene therapy and certification of the Laboratory of the Molecular Techniques Unit by the Polish Accreditation Center (PCA) confirming compliance with the requirements of the PN-EN ISO/IEC 17025:2005 standard.

Improvement of the inlet system for the spray-jet technique for use in spectroscopic studies and molecular deposition

International Nuclear Information System (INIS)

Yamada, Toshiki; Shinohara, Hidenori; Mashiko, Shinro

2006-01-01

We previously developed a molecular beam apparatus with a spray-jet technique in order to produce a molecular beam of non-volatile molecules in vacuum from the sprayed mist of a sample solution. The apparatus is for use in spectroscopic studies or a means of molecular deposition. The spray-jet inlet system consisted of an ultrasonic nebulizer, an inlet chamber and a pulsed nozzle. In the present paper, further improvements to the spray-jet inlet system are reported. The main improvement is the introduction of a pneumatic nebulizer to replace the previous ultrasonic nebulizer. The efficiency of molecular beam generation was evaluated on the basis of the signal intensity of the resonantly enhanced multiphoton ionization time-of-flight mass (REMPI-TOFMS) spectra for a Rhodamine B/methanol solution and the amount of sample consumed. The introduction of the pneumatic nebulizer increased the efficiency by a factor of 20

Biological, serological and molecular techniques to xanthomonas axonopodis pv. Ci tri Asymptomatic detection

International Nuclear Information System (INIS)

Peyrou, M.; Del Campo, R.; Russi, P.; Mara, H.; Rigamonti, N.; Larrechart, L.; Perez, E.

2012-01-01

Xanthomonas axonopodis pv. ci tri (X ac) produces citrus canker disease in all citrus commercial species. The bacteria can be disseminated through vegetative propagation material in asymptomatic form. To optimize bacteria detection techniques applicable to asymptomatic citrus plant tissue routine analysis, ELISA, Immunofluorescence, Pcr, qRT P CR and host plant inoculation (bioassay) diagnostic techniques were compared. Tests were made from decimal dilutions between 108 uf6.ml-1 and 102 ufc.mL-1 using a pure culture of 49b strain.The detection level obtained was 1.8 x 102 ufc.mL-1 using Inmunofluorescence; 1.8x104 ufc.mL-1 with indirect ELISA, 1.8 x 103 ufc.mL-1 by means of PCR; 10 ufc.mL-1 through of qRT P CR and 230 ufc.mL-1 in sour orange inoculated plants. The experiment was repeated at least three times for each technique. Considering this result, and taking into account that sensitivity, practicity and cost, are important when a great number of plants need to be tested, the PCR and inoculation in host plants were those that met the best characteristics to be evaluated in asymptomatic plant material

Difference of microbial community stressed in artificial pit muds for Luzhou-flavour liquor brewing revealed by multiphase culture-independent technology.

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Zhang, L; Zhou, R; Niu, M; Zheng, J; Wu, C

2015-11-01

Artificial pit muds (APMs) is produced by peats, aged pit muds, yellow and black clays etc. and is one of essential factors for Luzhou-flavour liquor production. The microbial community of APMs significantly influence the quality of Luzhou-flavour liquor. The aim of this study was to investigate the differences in bacterial, archaeal and fungal community of APMs, starters and materials. Multiphase culture-independent technology were employed in this study, including nested PCR-denaturing gradient gel electrophoresis (nested PCR-DGGE), phospholipid fatty acid (PLFA), phospholipid ether lipids (PLEL) and fluorescence in situ hybridization (FISH) analysis. Results suggested that the microbial diversity significantly changed under environmental stress and different culture patterns during APMs cultivation. The dominant bacteria in APMs mainly fell into Clostridiales, Lactobacillales, Bacteroidales and Rhizobiales, Archaea affiliated with Methanomicrobiales and Methanosarcinales, and fungi belonged to Saccharomycetales and Eurotiales. Furthermore, the microbial community structures of APMs cultured by ground pile pattern were more similar with that of aged pit muds, meanwhile, the relative bands intensities of microbes, which are the main contributors for liquor brewing, increased with the culture times. Not only the niche selection and biogeochemical properties of APMs, but also the mutual collaboration and constraint between different microbes may result in enriching different liquor-brewing microbes into APMs. APM cultivation technology was necessary to promote enriching functional liquor-brewing microbes into APMs. These results may facilitate understanding the microbial succession during APMs manufacture. © 2015 The Society for Applied Microbiology.

Speckle noise reduction technique for Lidar echo signal based on self-adaptive pulse-matching independent component analysis

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Xu, Fan; Wang, Jiaxing; Zhu, Daiyin; Tu, Qi

2018-04-01

Speckle noise has always been a particularly tricky problem in improving the ranging capability and accuracy of Lidar system especially in harsh environment. Currently, effective speckle de-noising techniques are extremely scarce and should be further developed. In this study, a speckle noise reduction technique has been proposed based on independent component analysis (ICA). Since normally few changes happen in the shape of laser pulse itself, the authors employed the laser source as a reference pulse and executed the ICA decomposition to find the optimal matching position. In order to achieve the self-adaptability of algorithm, local Mean Square Error (MSE) has been defined as an appropriate criterion for investigating the iteration results. The obtained experimental results demonstrated that the self-adaptive pulse-matching ICA (PM-ICA) method could effectively decrease the speckle noise and recover the useful Lidar echo signal component with high quality. Especially, the proposed method achieves 4 dB more improvement of signal-to-noise ratio (SNR) than a traditional homomorphic wavelet method.

Non-linear optical techniques and optical properties of condensed molecular systems

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Citroni, Margherita

2013-06-01

Structure, dynamics, and optical properties of molecular systems can be largely modified by the applied pressure, with remarkable consequences on their chemical stability. Several examples of selective reactions yielding technologically attractive products can be cited, which are particularly efficient when photochemical effects are exploited in conjunction with the structural conditions attained at high density. Non-linear optical techniques are a basic tool to unveil key aspects of the chemical reactivity and dynamic properties of molecules. Their application to high-pressure samples is experimentally challenging, mainly because of the small sample dimensions and of the non-linear effects generated in the anvil materials. In this talk I will present results on the electronic spectra of several aromatic crystals obtained through two-photon induced fluorescence and two-photon excitation profiles measured as a function of pressure (typically up to about 25 GPa), and discuss the relationship between the pressure-induced modifications of the electronic structure and the chemical reactivity at high pressure. I will also present the first successful pump-probe infrared measurement performed as a function of pressure on a condensed molecular system. The system under examination is liquid water, in a sapphire anvil cell, up to 1 GPa along isotherms at 298 and 363 K. These measurements give a new enlightening insight into the dynamical properties of low- and high-density water allowing a definition of the two structures.

Bridging Mediterranean cultures in the IYS: A documentary exhibition on irrigation techniques in water scarcity conditions

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Barontini, Stefano; Louki, Amina; Ben Slima, Zied; Ezzahra Ghaouch, Fatima; Labaran, Raisa; Raffelli, Giulia; Peli, Marco; Vitale, Nicola

2015-04-01

Brescia, an industrial city in Northern Italy, is now experiencing a crucial change in its traditional structure. In recent years in fact it has been elected as living and working seat by many foreigners and it is now one of the cities with the greatest percentage of migrants in the Country. This is an important challenge for the city and an opportunity to merge, compare and integrate different cultures to build its future. In this context some students of different Courses (engineering and medicine), belonging both to the Arabian and local community, met together and with researchers in the study team 'Al-B¯i r¯u n¯i , for culture, science and society'. The team aims at organising cultural events in which, starting from the figure of the Persian scientist Ab¯u Raih. ¯a n Al-B¯i r¯u n¯i (about 973, 1051), the contribution of the Arabian and Islamic culture to the development of the European one in the middle ages is investigated. Moving from the initial idea of the study team Al-B¯i r¯u n¯i and from the suggestions of the World Soil Day 2014 and of the International Year of Soils 2015, we built a documentary exhibition entitled 'Irrigation techniques in water scarcity conditions'. The exhibition, which stresses the importance of the irrigation techniques for the soil conservation, is focused on the idea of disseminating two main concepts, i.e. (1) the technological continuity of some water supply systems in countries, around the Mediterranean Sea, affected by similar conditions of water availability, and (2) the possibility of building environments where, due to severe or extreme climatic conditions, the sustainability is reached when the man lives in equilibrium with the nature. The exhibition, which is written in Italian and will move around in the city during all 2015, consists of about twenty posters organized into three main chapters, corresponding to three main classes of water supply systems which are common in most of the countries surrounding

Detection of Candida spp. in the vagina of a cohort of nulliparous pregnant women by culture and molecular methods: Is there an association between maternal vaginal and infant oral colonisation?

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Payne, Matthew S; Cullinane, Meabh; Garland, Suzanne M; Tabrizi, Sepehr N; Donath, Susan M; Bennett, Catherine M; Amir, Lisa H

2016-04-01

Most studies describing vaginal Candida spp. in pregnancy focus on symptomatic vaginitis, rather than asymptomatic colonisation, and solely utilise microbiological culture. The extent to which asymptomatic vaginal carriage may represent a reservoir for infant oral colonisation has been highly debated. This study formed part of the Candida and Staphylococcus Transmission Longitudinal Evaluation (CASTLE) study, in Melbourne, Australia, from 2009 to 2011 and used culture and molecular methods to examine vaginal swabs collected late in the third trimester of pregnancy for Candida spp. Oral swabs from infants were also examined using culture methods. Overall, 80 of 356 (22%) women were positive for Candida spp; the majority being Candida albicans (83%). Candida glabrata and other Candida spp. were also identified, but in much lower numbers. Molecular analysis identified numerous positive samples not detected by culture, including 13 cases of C. albicans. In addition, some positive samples only recorded to genus level by culture were accurately identified as either C. albicans or C. glabrata following molecular analyses. Eighteen infants recorded positive Candida spp. cultures, predominantly C. albicans. However, there were only four (25%) mother/infant dyads where C. albicans was detected. This study provides valuable data on asymptomatic colonisation rates of Candida spp. within an asymptomatic population of women late in pregnancy. The utilisation of molecular methods improved the rate of detection and provided a more accurate means for identification of non-albicans Candida spp. The low mother/infant colonisation rate suggests that non-maternal sources are likely involved in determining infant oral colonisation status. © 2015 The Royal Australian and New Zealand College of Obstetricians and Gynaecologists.

Cell and molecular biology of the spiny dogfish Squalus acanthias and little skate Leucoraja erinacea: insights from in vitro cultured cells.

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Barnes, D W

2012-04-01

Two of the most commonly used elasmobranch experimental model species are the spiny dogfish Squalus acanthias and the little skate Leucoraja erinacea. Comparative biology and genomics with these species have provided useful information in physiology, pharmacology, toxicology, immunology, evolutionary developmental biology and genetics. A wealth of information has been obtained using in vitro approaches to study isolated cells and tissues from these organisms under circumstances in which the extracellular environment can be controlled. In addition to classical work with primary cell cultures, continuously proliferating cell lines have been derived recently, representing the first cell lines from cartilaginous fishes. These lines have proved to be valuable tools with which to explore functional genomic and biological questions and to test hypotheses at the molecular level. In genomic experiments, complementary (c)DNA libraries have been constructed, and c. 8000 unique transcripts identified, with over 3000 representing previously unknown gene sequences. A sub-set of messenger (m)RNAs has been detected for which the 3' untranslated regions show elements that are remarkably well conserved evolutionarily, representing novel, potentially regulatory gene sequences. The cell culture systems provide physiologically valid tools to study functional roles of these sequences and other aspects of elasmobranch molecular cell biology and physiology. Information derived from the use of in vitro cell cultures is valuable in revealing gene diversity and information for genomic sequence assembly, as well as for identification of new genes and molecular markers, construction of gene-array probes and acquisition of full-length cDNA sequences. © 2012 The Author. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

Molecular cardiovascular imaging

International Nuclear Information System (INIS)

Schaefers, M.

2007-01-01

Although huge and long-lasting research efforts have been spent on the development of new diagnostic techniques investigating cardiovascular diseases, still fundamental challenges exist; the main challenge being the diagnosis of a suspected or known coronary artery disease or its consequences (myocardial infarction, heart failure etc.). Beside morphological techniques, functional imaging modalities are available in clinical diagnostic algorithms, whereas molecular cardiovascular imaging techniques are still under development. This review summarizes clinical-diagnostical challenges of modern cardiovascular medicine as well as the potential of new molecular imaging techniques to face these. (orig.)

Using Web-Based Knowledge Extraction Techniques to Support Cultural Modeling

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Smart, Paul R.; Sieck, Winston R.; Shadbolt, Nigel R.

The World Wide Web is a potentially valuable source of information about the cognitive characteristics of cultural groups. However, attempts to use the Web in the context of cultural modeling activities are hampered by the large-scale nature of the Web and the current dominance of natural language formats. In this paper, we outline an approach to support the exploitation of the Web for cultural modeling activities. The approach begins with the development of qualitative cultural models (which describe the beliefs, concepts and values of cultural groups), and these models are subsequently used to develop an ontology-based information extraction capability. Our approach represents an attempt to combine conventional approaches to information extraction with epidemiological perspectives of culture and network-based approaches to cultural analysis. The approach can be used, we suggest, to support the development of models providing a better understanding of the cognitive characteristics of particular cultural groups.

Subtype-independent near full-length HIV-1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical management.

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Grossmann, Sebastian; Nowak, Piotr; Neogi, Ujjwal

2015-01-01

HIV-1 near full-length genome (HIV-NFLG) sequencing from plasma is an attractive multidimensional tool to apply in large-scale population-based molecular epidemiological studies. It also enables genotypic resistance testing (GRT) for all drug target sites allowing effective intervention strategies for control and prevention in high-risk population groups. Thus, the main objective of this study was to develop a simplified subtype-independent, cost- and labour-efficient HIV-NFLG protocol that can be used in clinical management as well as in molecular epidemiological studies. Plasma samples (n=30) were obtained from HIV-1B (n=10), HIV-1C (n=10), CRF01_AE (n=5) and CRF01_AG (n=5) infected individuals with minimum viral load >1120 copies/ml. The amplification was performed with two large amplicons of 5.5 kb and 3.7 kb, sequenced with 17 primers to obtain HIV-NFLG. GRT was validated against ViroSeq™ HIV-1 Genotyping System. After excluding four plasma samples with low-quality RNA, a total of 26 samples were attempted. Among them, NFLG was obtained from 24 (92%) samples with the lowest viral load being 3000 copies/ml. High (>99%) concordance was observed between HIV-NFLG and ViroSeq™ when determining the drug resistance mutations (DRMs). The N384I connection mutation was additionally detected by NFLG in two samples. Our high efficiency subtype-independent HIV-NFLG is a simple and promising approach to be used in large-scale molecular epidemiological studies. It will facilitate the understanding of the HIV-1 pandemic population dynamics and outline effective intervention strategies. Furthermore, it can potentially be applicable in clinical management of drug resistance by evaluating DRMs against all available antiretrovirals in a single assay.

Expressing exogenous functional odorant receptors in cultured olfactory sensory neurons

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Fomina Alla F

2008-09-01

Full Text Available Abstract Background Olfactory discrimination depends on the large numbers of odorant receptor genes and differential ligand-receptor signaling among neurons expressing different receptors. In this study, we describe an in vitro system that enables the expression of exogenous odorant receptors in cultured olfactory sensory neurons. Olfactory sensory neurons in the culture express characteristic signaling molecules and, therefore, provide a system to study receptor function within its intrinsic cellular environment. Results We demonstrate that cultured olfactory sensory neurons express endogenous odorant receptors. Lentiviral vector-mediated gene transfer enables successful ectopic expression of odorant receptors. We show that the ectopically expressed mouse I7 is functional in the cultured olfactory sensory neurons. When two different odorant receptors are ectopically expressed simultaneously, both receptor proteins co-localized in the same olfactory sensory neurons up to 10 days in vitro. Conclusion This culture technique provided an efficient method to culture olfactory sensory neurons whose morphology, molecular characteristics and maturation progression resembled those observed in vivo. Using this system, regulation of odorant receptor expression and its ligand specificity can be studied in its intrinsic cellular environment.

Applications of synchrotron-based micro-imaging techniques for the analysis of Cultural Heritage materials

International Nuclear Information System (INIS)

Cotte, Marine; Chilida, Javier; Walter, Philippe; Taniguchi, Yoko; Susini, Jean

2009-01-01

The analysis of cultural Heritage objects is often technically challenging. When analyzing micro-fragments, the amount of matter is usually very tiny, hence requiring sensitive techniques. These samples, in particular painting fragments, may present multi-layered structures, with layer thickness of ∼10 μm. It leads to favor micro-imaging techniques, with a good lateral resolution (about one micrometer), that manage the discriminative study of each layer. Besides, samples are usually very complex in term of chemistry, as they are made of mineral and organic matters, amorphous and crystallized phases, major and minor elements. Accordingly, a multi-modal approach is generally essential to solve the chemical complexity of such hybrid materials. Different examples will be given, to illustrate the various possibilities of synchrotron-based micro-imaging techniques, such as micro X-ray diffraction, micro X-ray fluorescence, micro X-ray absorption spectroscopy and micro FTIR spectroscopy. Focus will be made on paintings, but the whole range of museum objects (going from soft matter like paper or wood to hard matter like metal and glass) will be also considered.

Multiple simultaneous fabrication of molecular nanowires using nanoscale electrocrystallization

International Nuclear Information System (INIS)

Hasegawa, Hiroyuki; Ueda, Rieko; Kubota, Tohru; Mashiko, Shinro

2006-01-01

We carried out a multiple simultaneous fabrication based on the nanoscale electrocrystallization to simultaneously construct molecular nanowires at two or more positions. This substrate-independent nanoscale electrocrystallization process enables nanowires fabrication at specific positions using AC. We also succeeded in multiple fabrications only at each gap between the electrode tips. We found that π-stack was formed along the long axis of the nanowires obtained by analyzing the selected-area electron diffraction. We believe this technique has the potential for expansion to the novel low-cost and energy-saving fabrication of high-performance nanodevices

Molecular predictors of 3D morphogenesis by breast cancer cell lines in 3D culture.

Directory of Open Access Journals (Sweden)

Ju Han

2010-02-01

Full Text Available Correlative analysis of molecular markers with phenotypic signatures is the simplest model for hypothesis generation. In this paper, a panel of 24 breast cell lines was grown in 3D culture, their morphology was imaged through phase contrast microscopy, and computational methods were developed to segment and represent each colony at multiple dimensions. Subsequently, subpopulations from these morphological responses were identified through consensus clustering to reveal three clusters of round, grape-like, and stellate phenotypes. In some cases, cell lines with particular pathobiological phenotypes clustered together (e.g., ERBB2 amplified cell lines sharing the same morphometric properties as the grape-like phenotype. Next, associations with molecular features were realized through (i differential analysis within each morphological cluster, and (ii regression analysis across the entire panel of cell lines. In both cases, the dominant genes that are predictive of the morphological signatures were identified. Specifically, PPARgamma has been associated with the invasive stellate morphological phenotype, which corresponds to triple-negative pathobiology. PPARgamma has been validated through two supporting biological assays.

Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture

Energy Technology Data Exchange (ETDEWEB)

Han, Ju; Chang, Hang; Giricz, Orsi; Lee, Genee; Baehner, Frederick; Gray, Joe; Bissell, Mina; Kenny, Paraic; Parvin, Bahram

2010-02-01

Correlative analysis of molecular markers with phenotypic signatures is the simplest model for hypothesis generation. In this paper, a panel of 24 breast cell lines was grown in 3D culture, their morphology was imaged through phase contrast microscopy, and computational methods were developed to segment and represent each colony at multiple dimensions. Subsequently, subpopulations from these morphological responses were identified through consensus clustering to reveal three clusters of round, grape-like, and stellate phenotypes. In some cases, cell lines with particular pathobiological phenotypes clustered together (e.g., ERBB2 amplified cell lines sharing the same morphometric properties as the grape-like phenotype). Next, associations with molecular features were realized through (i) differential analysis within each morphological cluster, and (ii) regression analysis across the entire panel of cell lines. In both cases, the dominant genes that are predictive of the morphological signatures were identified. Specifically, PPAR? has been associated with the invasive stellate morphological phenotype, which corresponds to triple-negative pathobiology. PPAR? has been validated through two supporting biological assays.

Examination, characterisation and analysis techniques for the knowledge and the conservation / restoration of cultural heritage - importance of ionising radiation techniques

International Nuclear Information System (INIS)

Boutaine; J. L.

2004-01-01

For the examination, characterisation and analysis of cultural heritage artefacts or art objects and their component materials, the conservation scientist needs a palette of non destructive and non invasive techniques, in order to improve our knowledge concerning their elaboration, their evolution and/or degradation during time, and to give rational basis for their restoration and conservation. A general survey and illustrations showing the usefulness of these techniques will be presented. Among these methods, many are based on the use of ionising radiation. 1. Radiography (using X-rays, gamma rays, beta particles, secondary electrons, neutrons), electron emission radiography, tomodensimetry, 2. Scanning electron microscope associated with X-ray spectrometry, 3. X-ray diffraction, 4. Synchrotron radiation characterisation, 5. X-ray fluorescence analysis, 6. Activation analysis, 7. Ion beam analysis (PIXE, PIGE, RBS, secondary X-ray fluorescence), 8. Thermoluminescence dating, 9. Carbon-14 dating. These methods are used alone or in connection with other analytical methods. Any kind of materials can be encountered, for instance: i. stones, gems, ceramics, terracotta, enamels, glasses, i i. wood, paper, textile, bone, ivory, i i i. metals, jewellery, i v. paint layers, canvas and wooden backings, pigments, dyers, oils, binding media, varnishes, glues. Some examples will be taken, among recent work done at the Centre of Research and Restoration of the Museums of France (C2RMF), from various geographical origins, various ages and different art disciplines. This will illustrate the kind of assistance that science and technology can provide to a better knowledge of mankind's cultural heritage and also to the establishment of rational basis for its better conservation for the future generations. (Author)

Contributions to advances in blend pellet products (BPP) research on molecular structure and molecular nutrition interaction by advanced synchrotron and globar molecular (Micro)spectroscopy.

Science.gov (United States)

Guevara-Oquendo, Víctor H; Zhang, Huihua; Yu, Peiqiang

2018-04-13

To date, advanced synchrotron-based and globar-sourced techniques are almost unknown to food and feed scientists. There has been little application of these advanced techniques to study blend pellet products at a molecular level. This article aims to provide recent research on advanced synchrotron and globar vibrational molecular spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction. How processing induced molecular structure changes in relation to nutrient availability and utilization of the blend pellet products. The study reviews Utilization of co-product components for blend pellet product in North America; Utilization and benefits of inclusion of pulse screenings; Utilization of additives in blend pellet products; Application of pellet processing in blend pellet products; Conventional evaluation techniques and methods for blend pellet products. The study focus on recent applications of cutting-edge vibrational molecular spectroscopy for molecular structure and molecular structure association with nutrient utilization in blend pellet products. The information described in this article gives better insight on how advanced molecular (micro)spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction.

Light and electron microscopic localization of GABAA-receptors on cultured cerebellar granule cells and astrocytes using immunohistochemical techniques

DEFF Research Database (Denmark)

Hansen, Gert Helge; Hösli, E; Belhage, B

1991-01-01

. At the light microscope level specific staining of GABAA-receptors was localized in various types of neurones in explant cultures of rat cerebellum using the indirect peroxidase-antiperoxidase (PAP) technique, whereas no specific staining was found in astrocytes. At the electron microscope level labeling...

Anti-HCV effect of Lentinula edodes mycelia solid culture extracts and low-molecular-weight lignin.

Science.gov (United States)

Matsuhisa, Koji; Yamane, Seiji; Okamoto, Toru; Watari, Akihiro; Kondoh, Masuo; Matsuura, Yoshiharu; Yagi, Kiyohito

2015-06-19

Lentinula edodes mycelia solid culture extract (MSCE) contains several bioactive molecules, including some polyphenolic compounds, which exert immunomodulatory, antitumor, and hepatoprotective effects. In this study, we examined the anti-hepatitis C virus (HCV) activity of MSCE and low-molecular-weight lignin (LM-lignin), which is the active component responsible for the hepatoprotective effect of MSCE. Both MSCE and LM-lignin inhibited the entry of two HCV pseudovirus (HCVpv) types into Huh7.5.1 cells. LM-lignin inhibited HCVpv entry at a lower concentration than MSCE and inhibited the entry of HCV particles in cell culture (HCVcc). MSCE also inhibited HCV subgenome replication. LM-lignin had no effect on HCV replication, suggesting that MSCE contains additional active substances. We demonstrate here for the first time the anti-HCV effects of plant-derived LM-lignin and MSCE. The hepatoprotective effect of LM-lignin suggests that lignin derivatives, which can be produced in abundance from existing plant resources, may be effective in the treatment of HCV-related diseases. Copyright © 2015 Elsevier Inc. All rights reserved.

Comparative evaluation of positive tests to Mycobacterium avium subsp. paratuberculosis in clinically healthy sheep and goats in south-west Greece using molecular techniques, serology, and culture.

Science.gov (United States)

Ikonomopoulos, John; Balaskas, Christos; Kantzoura, Bagia; Fragiadaki, Eirini; Pavlik, Ivo; Bartos, Milan; Lukas, John C; Gazouli, Maria

2007-09-01

Mycobacterium avium subsp. paratuberculosis (MAP) is the cause of paratuberculosis, which affects mainly ruminants although there is a growing concern about its possible implication in Crohn's disease in humans especially in connection with environmental spread and risks to the food chain. Retail cheese may represent a significant source of human exposure to MAP and the aim of this study was to assess MAP status in clinically healthy sheep and goats in Greece, comparing techniques routinely used in the positive diagnosis of the disease. From a total of 30 flocks, 632 sheep and goats had faecal, serum, and whole-blood samples examined by culture, complement fixation test (CFT), and polymerase chain reaction (PCR) targeted at IS900, IS1245, and IS6110. PCR produced positive results in 21% of the animals tested, with 5.6%, 3.9%, and 11.5% being identified as MAP, Mycobacterium avium subsp. avium, and Mycobacterium tuberculosis complex, respectively. CFT produced positive and suspicious results in 4.4% and 14.4% of the cases. Faecal cultures were negative in all but a single case that was identified as restriction fragment length polymorphism (RFLP)-type BC1. Agreement between results obtained by PCR and CFT was poor with isolated cases although an assessment of the MAP positive tests produced similar results for both methods. The findings indicate the need for additional measures of control, although the costs may be substantial if public health protection justifies elimination of MAP from livestock.

Analysis of membrane proteome by data-dependent LC-MS/MS combined with data-independent LC-MSE technique

Directory of Open Access Journals (Sweden)

Joseph Kwon

2010-03-01

Full Text Available Proteomics work resembles the search for a needle in a haystack. The identification of protein biomarker requires the removal of the false protein data from the whole protein mixture. For high quality proteomic data, even a strict filtration step using the false discovery rate (FDR is insufficient for obtaining perfect protein information from the biological samples. In this study, the cyanobacterial whole membrane fraction was applied to the data-dependent analysis (DDA mode of LC-MS/MS, which was used along with the data-independent LC-MSE technique in order to evaluate the membrane proteomic data. Furthermore, the identified MSE-information (MSE-i data based on the peptide mass and the retention time were validated by the other database search, i.e., the probability-based MASCOT and de novo search engine PEAKS. In this present study, 208 cyanobacterial proteins with FDR of 5% were identified using the data-independent nano-UPLC/MSE acquisition with the Protein Lynx Global Server (PLGS, and 56 of these proteins were the predicted membrane proteins. When a total of 208 MSE-i proteomic data were applied to the DDA mode of LC-MS/MS, the number of identified membrane proteins was 26 and 33 from MASCOT and PEAKS with a FDR of 5%, respectively. The number of totally overlapped membrane proteins was 25. Therefore, the data-independent LC-MSE identified more proteins with a high confidence.

Thinking through creativity and culture

DEFF Research Database (Denmark)

Glaveanu, Vlad Petre

Creativity and culture are inherently linked. Society and culture are part and parcel of creativity’s process, outcome, and subjective experience.Equally, creativity does not reside in the individual independent of culture and society. Vlad Petre Glăveanu’s basic framework includes creators and c...

Tissue culture as a plant production technique for horticultural crops ...

African Journals Online (AJOL)

Over 100 years ago, Haberlandt envisioned the concept of plant tissue culture and provided the groundwork for the cultivation of plant cells, tissues and organs in culture. Initially plant tissue cultures arose as a research tool and focused on attempts to culture and study the development of small, isolated cells and segments ...

Project on production of mutants by irradiation of in vitro cultured tissues of coconut and banana and their mass propagation by the tissue culture technique

International Nuclear Information System (INIS)

Guzman, E.V. de

1975-01-01

Fruit pulp tissue, ovary segments with or without ovules and sections from shoot tips of banana were used for studies on growth stimulating or morphogenetic effects of irradiation. Irradiation at 0.1-1.0 kR tended to induce faster callus growth in the otherwise slow-growing cultures. The physical condition and composition of the culture media especially with respect to growth regulators were studied, as were techniques to overcome discoloration of explants, the best choice of plant tissue for explant, and radiation effects on growth and morphogenesis. Due to the difficulty of callus induction with coconut, only the effects of irradiation on embryos cultured in vitro were studied. They were irradiated at various stages of development, i.e. during the early and final stage of liquid culture, and several days after transfer to a solid medium. Adverse effects of irradiation became evident only during the subsequent growth in solid, during the latter stage of which morphological changes were observed. Whereas irradiation of the liquid as well as solid media up to 50 kR had no adverse effect; survival and development became adversely affected at a dose of 1 kR

Culturing of respiratory viruses in well-differentiated pseudostratified human airway epithelium as a tool to detect unknown viruses

Science.gov (United States)

Jazaeri Farsani, Seyed Mohammad; Deijs, Martin; Dijkman, Ronald; Molenkamp, Richard; Jeeninga, Rienk E; Ieven, Margareta; Goossens, Herman; van der Hoek, Lia

2015-01-01

Background Currently, virus discovery is mainly based on molecular techniques. Here, we propose a method that relies on virus culturing combined with state-of-the-art sequencing techniques. The most natural ex vivo culture system was used to enable replication of respiratory viruses. Method Three respiratory clinical samples were tested on well-differentiated pseudostratified tracheobronchial human airway epithelial (HAE) cultures grown at an air–liquid interface, which resemble the airway epithelium. Cells were stained with convalescent serum of the patients to identify infected cells and apical washes were analyzed by VIDISCA-454, a next-generation sequencing virus discovery technique. Results Infected cells were observed for all three samples. Sequencing subsequently indicated that the cells were infected by either human coronavirus OC43, influenzavirus B, or influenzavirus A. The sequence reads covered a large part of the genome (52%, 82%, and 57%, respectively). Conclusion We present here a new method for virus discovery that requires a virus culture on primary cells and an antibody detection. The virus in the harvest can be used to characterize the viral genome sequence and cell tropism, but also provides progeny virus to initiate experiments to fulfill the Koch's postulates. PMID:25482367

The Role of Molecular Biology in the Biomonitoring of Human Exposure to Chemicals

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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.

Cultural models, socialization goals, and parenting ethnotheories: A multicultural analysis

OpenAIRE

Keller, H; Lamm, B; Abels, M; Yovsi, R; Borke, J; Jensen, H; Papaligoura, Z; Holub, C; Lo, W; Tomiyama, AJ; Su, Y; Wang, Y; Chaudhary, N

2006-01-01

This study conceptualizes a cultural model of parenting. It is argued that cultural models are expressed in the degree of familism, which informs socialization goals that are embodied in parenting ethnotheories. Three cultural models were differentiated a priori: independent, interdependent, and autonomous-related. Samples were recruited that were expected to represent these cultural models: German, Euro-American, and Greek middle-class women representing the independent cultural model; Camer...

SEM: A Cultural Change Agent

Science.gov (United States)

Barnes, Bradley; Bourke, Brian

2015-01-01

The authors advance the concept that institutional culture is a purposeful framework by which to view SEM's utility, particularly as a cultural change agent. Through the connection of seemingly independent functions of performance and behavior, implications emerge that deepen the understanding of the influence of culture on performance outcomes…

Historical and contemporary cultural ecosystem service values in the rapidly urbanizing city state of Singapore.

Science.gov (United States)

Thiagarajah, Jharyathri; Wong, Shermaine K M; Richards, Daniel R; Friess, Daniel A

2015-11-01

Cultural ecosystem services are a function of people and place, so may change as a location transitions from rural to urban. Singapore has undergone rapid urbanization after its independence in 1965, with a concomitant decline in natural habitat extent and accessibility. Using coastal mangrove forests as a case study habitat, changing cultural values were explored with a novel array of techniques, including qualitative archival analysis (photographs, oral histories), current sources (publically uploaded social media photographs), and surveys of (a) the general public and (b) visitors to publically accessible mangroves. Cultural value changed through time, with a significant transition from intrinsic, intrapersonal values (spiritual, cultural heritage) to instrumental, interpersonal values (recreation, education). Additionally, cultural value varied between different mangroves depending on their public accessibility, and the evolving degree of human interaction with the ecosystem as urban development occured. Cultural values change as development transitions, though mangroves still play an important cultural role in a heavily urbanized environment.

The Optimization of Molecular Detection of Clinical Isolates of Brucella in Blood Cultures by eryD Transcriptase Gene for Confirmation of Culture-Negative Samples.

Science.gov (United States)

Tabibnejad, Mahsa; Alikhani, Mohammad Yousef; Arjomandzadegan, Mohammad; Hashemi, Seyed Hamid; Naseri, Zahra

2016-04-01

Brucellosis is a zoonosis disease which is widespread across the world. The aim of the present study is the evaluation of culture-negative blood samples. A total of 100 patients with suspected brucellosis were included in this experimental study and given positive serological tests. Diagnosis was performed on patients with clinical symptoms of the disease, followed by the detection of a titer that was equal to or more than 1:160 (in endemic areas) by the standard tube agglutination method. Blood samples were cultured by a BACTEC 9050 system, and subsequently by Brucella agar. At the same time, DNA from all blood samples was extracted by Qiagen Kit Company (Qia Amp Mini Kit). A molecular assay of blood samples was carried out by detection of eryD transcriptase and bcsp 31 genes in specific double PCR reactions. The specificity of the primers was evaluated by DNA from pure and approved Brucella colonies found in the blood samples, by DNA from other bacteria, and by ordinary PCR. DNA extraction from the pure colonies was carried out by both Qiagen Kit and Chelex 100 methods; the two were compared. 39 cases (39%) had positive results when tested by the BACTEC system, and 61 cases (61%) became negative. 23 culture-positive blood samples were randomly selected for PCR reactions; all showed 491 bp for the eryD gene and 223 bp for the bcsp 31 gene. Interestingly, out of 14 culture-negative blood samples, 13 cases showed positive bonds in PCR. The specificity of the PCR method was equal to 100%. DNA extraction from pure cultures was done by both Chelex 100 and Qiagen Kit; these showed the same results for all samples. The results prove that the presented double PCR method could be used to detect positive cases from culture-negative blood samples. The Chelex 100 method is simpler and safer than the use of Qiagen Kit for DNA extraction.

Establishing molecular microbiology facilities in developing countries

Directory of Open Access Journals (Sweden)

Salman S. Ahmed

2015-11-01

Full Text Available Summary: Microbiology laboratories play an important role in epidemiology and infection control programs. Within microbiology laboratories, molecular microbiology techniques have revolutionized the identification and surveillance of infectious diseases. The combination of excellent sensitivity, specificity, low contamination levels and speed has made molecular techniques appealing methods for the diagnosis of many infectious diseases. In a well-equipped microbiology laboratory, the facility designated for molecular techniques remains indiscrete. However, in most developing countries, poor infrastructure and laboratory mismanagement have precipitated hazardous consequences. The establishment of a molecular microbiology facility within a microbiology laboratory remains fragmented. A high-quality laboratory should include both conventional microbiology methods and molecular microbiology techniques for exceptional performance. Furthermore, it should include appropriate laboratory administration, a well-designed facility, laboratory procedure standardization, a waste management system, a code of practice, equipment installation and laboratory personnel training. This manuscript lays out fundamental issues that need to be addressed when establishing a molecular microbiology facility in developing countries. Keywords: Developing country, Molecular technique, Molecular microbiology laboratory

Molecular cloning of the Coch gene of guinea pig inner ear and its expression analysis in cultured fibrocytes of the spiral ligament.

Science.gov (United States)

Li, Lishu; Ikezono, Tetsuo; Sekine, Kuwon; Shindo, Susumu; Matsumura, Tomohiro; Pawankar, Ruby; Ichimiya, Issei; Yagi, Toshiaki

2010-08-01

We have cloned guinea pig Coch cDNA and the sequence information will be useful for future molecular study combined with physiological experiments. Proper Coch gene expression appears to be dependent on the unique extracellular micro-environment of the inner ear in vivo. These results provide insight into the Coch gene expression and its regulation. To characterize the guinea pig Coch gene, we performed molecular cloning and expression analysis in the inner ear and cultured fibrocytes of the spiral ligament. The Coch cDNA was isolated using RACE. Cochlin isofoms were studied by Western blot using three different types of mammalian inner ear. The cochlear fibrocytes were cultured and characterized by immunostaining. Coch gene expression in the fibrocytes was investigated and the influence of cytokine stimulation was evaluated. The full-length 1991 bp Coch cDNA that encodes a 553 amino acid protein was isolated. The sequence had significant homology with other mammals, and the sizes of the Cochlin isoforms were identical. In the cultured fibrocytes, Coch mRNA was expressed in a very small amount and the isoform production was different, compared with the results in vivo. Cytokine stimulation did not alter the level of mRNA expression or isoform formation.

The characterization of artefacts of cultural heritage significance using physical techniques

International Nuclear Information System (INIS)

Creagh, D.C.

2005-01-01

All societies attempt to preserve their cultural heritage because it is this that gives them their identity. How artefacts are identified as being of significance to society, and how to preserve these for posterity, depend on the sophistication of those societies, their wealth, and the determination of members of the societies to preserve their past. If conservation or restoration measures are being undertaken complex analytical experiments must be undertaken beforehand to ensure that the work is being undertaken in an appropriate manner. These investigations may employ electromagnetic (IR, VIS, UV, X-ray, γ-ray) or particulate (electron, proton, neutron, and ion beams) radiation. The use of many of these techniques is described in this paper in experiments on Australian Aboriginal bark paintings, a suit of armour belonging to a famous Australian outlaw, and the degradation of colour motion picture film

SPECT and PET Serve as Molecular Imaging Techniques and in Vivo Biomarkers for Brain Metastases

Science.gov (United States)

Palumbo, Barbara; Buresta, Tommaso; Nuvoli, Susanna; Spanu, Angela; Schillaci, Orazio; Fravolini, Mario Luca; Palumbo, Isabella

2014-01-01

Nuclear medicine techniques (single photon emission computerized tomography, SPECT, and positron emission tomography, PET) represent molecular imaging tools, able to provide in vivo biomarkers of different diseases. To investigate brain tumours and metastases many different radiopharmaceuticals imaged by SPECT and PET can be used. In this review the main and most promising radiopharmaceuticals available to detect brain metastases are reported. Furthermore the diagnostic contribution of the combination of SPECT and PET data with radiological findings (magnetic resonance imaging, MRI) is discussed. PMID:24897023

Laboratory Workflow Analysis of Culture of Periprosthetic Tissues in Blood Culture Bottles.

Science.gov (United States)

Peel, Trisha N; Sedarski, John A; Dylla, Brenda L; Shannon, Samantha K; Amirahmadi, Fazlollaah; Hughes, John G; Cheng, Allen C; Patel, Robin

2017-09-01

Culture of periprosthetic tissue specimens in blood culture bottles is more sensitive than conventional techniques, but the impact on laboratory workflow has yet to be addressed. Herein, we examined the impact of culture of periprosthetic tissues in blood culture bottles on laboratory workflow and cost. The workflow was process mapped, decision tree models were constructed using probabilities of positive and negative cultures drawn from our published study (T. N. Peel, B. L. Dylla, J. G. Hughes, D. T. Lynch, K. E. Greenwood-Quaintance, A. C. Cheng, J. N. Mandrekar, and R. Patel, mBio 7:e01776-15, 2016, https://doi.org/10.1128/mBio.01776-15), and the processing times and resource costs from the laboratory staff time viewpoint were used to compare periprosthetic tissues culture processes using conventional techniques with culture in blood culture bottles. Sensitivity analysis was performed using various rates of positive cultures. Annualized labor savings were estimated based on salary costs from the U.S. Labor Bureau for Laboratory staff. The model demonstrated a 60.1% reduction in mean total staff time with the adoption of tissue inoculation into blood culture bottles compared to conventional techniques (mean ± standard deviation, 30.7 ± 27.6 versus 77.0 ± 35.3 h per month, respectively; P < 0.001). The estimated annualized labor cost savings of culture using blood culture bottles was $10,876.83 (±$337.16). Sensitivity analysis was performed using various rates of culture positivity (5 to 50%). Culture in blood culture bottles was cost-effective, based on the estimated labor cost savings of $2,132.71 for each percent increase in test accuracy. In conclusion, culture of periprosthetic tissue in blood culture bottles is not only more accurate than but is also cost-saving compared to conventional culture methods. Copyright © 2017 American Society for Microbiology.

Adaptation and Cultural Diffusion.

Science.gov (United States)

Ormrod, Richard K.

1992-01-01

Explores the role of adaptation in cultural diffusion. Explains that adaptation theory recognizes the lack of independence between innovations and their environmental settings. Discusses testing and selection, modification, motivation, and cognition. Suggests that adaptation effects are pervasive in cultural diffusion but require a broader, more…

Molecular identification of Coccidioides spp. in soil samples from Brazil

Directory of Open Access Journals (Sweden)

Filho Antônio D

2011-05-01

Full Text Available Abstract Background Since 1991 several outbreaks of acute coccidioidomycosis (CM were diagnosed in the semi-arid Northeast of Brazil, mainly related to disturbance of armadillo burrows caused by hunters while digging them for the capture of these animals. This activity causes dust contaminated with arthroconidia of Coccidioides posadasii, which, once inhaled, cause the mycosis. We report on the identification of C. posadasii in soil samples related to outbreaks of CM. Results Twenty four soil samples had their DNA extracted and subsequently submitted to a semi-nested PCR technique using specific primers. While only 6 (25% soil samples were positive for C. posadasii by mice inoculation, all (100% were positive by the molecular tool. Conclusion This methodology represents a simple, sensitive and specific molecular technique to determine the environmental distribution of Coccidioides spp. in endemic areas, but cannot distinguish the species. Moreover, it may be useful to identify culture isolates. Key-words: 1. Coccidioidomycosis. 2. Coccidioides spp. 3. C. posadasii. 4. Semi-arid. 5. Semi-nested PCR

Effects of Self-Construal Differences on Cognitive Dissonance Examined by Priming the Independent and Interdependent Self

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Jamie Jia Yan Lee

2014-01-01

Full Text Available Prior cross-cultural research on dissonance has relied on cultural stereotypes in assuming that individuals from Western cultures are individualistic and have independent self-construals whereas individuals from Asian cultures are collectivistic and have interdependent self-construals. The current research made use of priming to avoid relying on cultural stereotypes and examined how having an independent or interdependent self-construal accounted for differences in dissonance experienced. A total of 120 participants who were Singapore citizens or permanent residents were randomly assigned to one of four conditions. Participants received either an independent or interdependent prime, and rated and ranked CDs before and after they made a choice between closely valued alternatives either for oneself or a close other. Results indicated that independently primed participants demonstrated significant dissonance when they made choices for themselves and close others whereas interdependently primed participants demonstrated significant dissonance when they made choices for close others but not for themselves. The study’s findings suggest that having either self-construal accounted for differences in dissonance experienced.

Molecular screening for Candida orthopsilosis and Candida metapsilosis among Danish Candida parapsilosis group blood culture isolates: proposal of a new RFLP profile for differentiation

DEFF Research Database (Denmark)

Mirhendi, Hossein; Bruun, Brita; Schønheyder, Henrik Carl

2010-01-01

Candida orthopsilosis and Candida metapsilosis are recently described species phenotypically indistinguishable from Candida parapsilosis . We evaluated phenotyping and molecular methods for the detection of these species among 79 unique blood culture isolates of the C. parapsilosis group obtained...

Mass Spectrometry-Based Proteomics in Molecular Diagnostics: Discovery of Cancer Biomarkers Using Tissue Culture

Directory of Open Access Journals (Sweden)

Debasish Paul

2013-01-01

Full Text Available Accurate diagnosis and proper monitoring of cancer patients remain a key obstacle for successful cancer treatment and prevention. Therein comes the need for biomarker discovery, which is crucial to the current oncological and other clinical practices having the potential to impact the diagnosis and prognosis. In fact, most of the biomarkers have been discovered utilizing the proteomics-based approaches. Although high-throughput mass spectrometry-based proteomic approaches like SILAC, 2D-DIGE, and iTRAQ are filling up the pitfalls of the conventional techniques, still serum proteomics importunately poses hurdle in overcoming a wide range of protein concentrations, and also the availability of patient tissue samples is a limitation for the biomarker discovery. Thus, researchers have looked for alternatives, and profiling of candidate biomarkers through tissue culture of tumor cell lines comes up as a promising option. It is a rich source of tumor cell-derived proteins, thereby, representing a wide array of potential biomarkers. Interestingly, most of the clinical biomarkers in use today (CA 125, CA 15.3, CA 19.9, and PSA were discovered through tissue culture-based system and tissue extracts. This paper tries to emphasize the tissue culture-based discovery of candidate biomarkers through various mass spectrometry-based proteomic approaches.

Mass Spectrometry-Based Proteomics in Molecular Diagnostics: Discovery of Cancer Biomarkers Using Tissue Culture

Science.gov (United States)

Paul, Debasish; Kumar, Avinash; Gajbhiye, Akshada; Santra, Manas K.; Srikanth, Rapole

2013-01-01

Accurate diagnosis and proper monitoring of cancer patients remain a key obstacle for successful cancer treatment and prevention. Therein comes the need for biomarker discovery, which is crucial to the current oncological and other clinical practices having the potential to impact the diagnosis and prognosis. In fact, most of the biomarkers have been discovered utilizing the proteomics-based approaches. Although high-throughput mass spectrometry-based proteomic approaches like SILAC, 2D-DIGE, and iTRAQ are filling up the pitfalls of the conventional techniques, still serum proteomics importunately poses hurdle in overcoming a wide range of protein concentrations, and also the availability of patient tissue samples is a limitation for the biomarker discovery. Thus, researchers have looked for alternatives, and profiling of candidate biomarkers through tissue culture of tumor cell lines comes up as a promising option. It is a rich source of tumor cell-derived proteins, thereby, representing a wide array of potential biomarkers. Interestingly, most of the clinical biomarkers in use today (CA 125, CA 15.3, CA 19.9, and PSA) were discovered through tissue culture-based system and tissue extracts. This paper tries to emphasize the tissue culture-based discovery of candidate biomarkers through various mass spectrometry-based proteomic approaches. PMID:23586059

Generation of organotypic raft cultures from primary human keratinocytes.

Science.gov (United States)

Anacker, Daniel; Moody, Cary

2012-02-22

The development of organotypic epithelial raft cultures has provided researchers with an efficient in vitro system that faithfully recapitulates epithelial differentiation. There are many uses for this system. For instance, the ability to grow three-dimensional organotypic raft cultures of keratinocytes has been an important milestone in the study of human papillomavirus (HPV)(1). The life cycle of HPV is tightly linked to the differentiation of squamous epithelium(2). Organotypic epithelial raft cultures as demonstrated here reproduce the entire papillomavirus life cycle, including virus production(3,4,5). In addition, these raft cultures exhibit dysplastic lesions similar to those observed upon in vivo infection with HPV. Hence this system can also be used to study epithelial cell cancers, as well as the effect of drugs on epithelial cell differentiation in general. Originally developed by Asselineau and Prunieras(6) and modified by Kopan et al.(7), the organotypic epithelial raft culture system has matured into a general, relatively easy culture model, which involves the growth of cells on collagen plugs maintained at an air-liquid interface (Figure 1A). Over the course of 10-14 days, the cells stratify and differentiate, forming a full thickness epithelium that produces differentiation-specific cytokeratins. Harvested rafts can be examined histologically, as well as by standard molecular and biochemical techniques. In this article, we describe a method for the generation of raft cultures from primary human keratinocytes. The same technique can be used with established epithelial cell lines, and can easily be adapted for use with epithelial tissue from normal or diseased biopsies(8). Many viruses target either the cutaneous or mucosal epithelium as part of their replicative life cycle. Over the past several years, the feasibility of using organotypic raft cultures as a method of studying virus-host cell interactions has been shown for several herpesviruses, as

Microbial community dynamics in thermophilic undefined milk starter cultures.

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Parente, Eugenio; Guidone, Angela; Matera, Attilio; De Filippis, Francesca; Mauriello, Gianluigi; Ricciardi, Annamaria

2016-01-18

Model undefined thermophilic starter cultures were produced from raw milk of nine pasta-filata cheesemaking plants using a selective procedure based on pasteurization and incubation at high temperature with the objective of studying the microbial community dynamics and the variability in performances under repeated (7-13) reproduction cycles with backslopping. The traditional culture-dependent approach, based on random isolation and molecular characterization of isolates was coupled to the determination of pH and the evaluation of the ability to produce acid and fermentation metabolites. Moreover, a culture-independent approach based on amplicon-targeted next-generation sequencing was employed. The microbial diversity was evaluated by 16S rRNA gene sequencing (V1-V3 regions), while the microdiversity of Streptococcus thermophilus populations was explored by using novel approach based on sequencing of partial amplicons of the phosphoserine phosphatase gene (serB). In addition, the occurrence of bacteriophages was evaluated by qPCR and by multiplex PCR. Although it was relatively easy to select for a community dominated by thermophilic lactic acid bacteria (LAB) within a single reproduction cycle, final pH, LAB populations and acid production activity fluctuated over reproduction cycles. Both culture-dependent and -independent methods showed that the cultures were dominated by either S. thermophilus or Lactobacillus delbrueckii subsp. lactis or by both species. Nevertheless, subdominant mesophilic species, including lactococci and spoilage organisms, persisted at low levels. A limited number of serB sequence types (ST) were present in S. thermophilus populations. L. delbrueckii and Lactococcus lactis bacteriophages were below the detection limit of the method used and high titres of cos type S. thermophilus bacteriophages were detected in only two cases. In one case a high titre of bacteriophages was concurrent with a S. thermophilus biotype shift in the culture

Mechanical Properties of Nanostructured Materials Determined Through Molecular Modeling Techniques

Science.gov (United States)

Clancy, Thomas C.; Gates, Thomas S.

2005-01-01

The potential for gains in material properties over conventional materials has motivated an effort to develop novel nanostructured materials for aerospace applications. These novel materials typically consist of a polymer matrix reinforced with particles on the nanometer length scale. In this study, molecular modeling is used to construct fully atomistic models of a carbon nanotube embedded in an epoxy polymer matrix. Functionalization of the nanotube which consists of the introduction of direct chemical bonding between the polymer matrix and the nanotube, hence providing a load transfer mechanism, is systematically varied. The relative effectiveness of functionalization in a nanostructured material may depend on a variety of factors related to the details of the chemical bonding and the polymer structure at the nanotube-polymer interface. The objective of this modeling is to determine what influence the details of functionalization of the carbon nanotube with the polymer matrix has on the resulting mechanical properties. By considering a range of degree of functionalization, the structure-property relationships of these materials is examined and mechanical properties of these models are calculated using standard techniques.

Microbial diversity in an Armenian geothermal spring assessed by molecular and culture-based methods.

Science.gov (United States)

Panosyan, Hovik; Birkeland, Nils-Kåre

2014-11-01

The phylogenetic diversity of the prokaryotic community thriving in the Arzakan hot spring in Armenia was studied using molecular and culture-based methods. A sequence analysis of 16S rRNA gene clone libraries demonstrated the presence of a diversity of microorganisms belonging to the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Epsilonproteobacteria, Firmicutes, Bacteroidetes phyla, and Cyanobacteria. Proteobacteria was the dominant group, representing 52% of the bacterial clones. Denaturing gradient gel electrophoresis profiles of the bacterial 16S rRNA gene fragments also indicated the abundance of Proteobacteria, Bacteroidetes, and Cyanobacteria populations. Most of the sequences were most closely related to uncultivated microorganisms and shared less than 96% similarity with their closest matches in GenBank, indicating that this spring harbors a unique community of novel microbial species or genera. The majority of the sequences of an archaeal 16S rRNA gene library, generated from a methanogenic enrichment, were close relatives of members of the genus Methanoculleus. Aerobic endospore-forming bacteria mainly belonging to Bacillus and Geobacillus were detected only by culture-dependent methods. Three isolates were successfully obtained having 99, 96, and 96% 16S rRNA gene sequence similarities to Arcobacter sp., Methylocaldum sp., and Methanoculleus sp., respectively. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Immobilization with Metal Hydroxides as a Means To Concentrate Food-Borne Bacteria for Detection by Cultural and Molecular Methods†

OpenAIRE

Lucore, Lisa A.; Cullison, Mark A.; Jaykus, Lee-Ann

2000-01-01

The application of nucleic acid amplification methods to the detection of food-borne pathogens could be facilitated by concentrating the organisms from the food matrix before detection. This study evaluated the utility of metal hydroxide immobilization for the concentration of bacterial cells from dairy foods prior to detection by cultural and molecular methods. Using reconstituted nonfat dry milk (NFDM) as a model, two food-borne pathogens (Listeria monocytogenes and Salmonella enterica sero...

Expression of human immunodeficiency virus (HIV) in naturally infected peripheral blood mononuclear cells: comparison of a standard co-culture technique with a newly developed microculture method.

Science.gov (United States)

Eberlein, B; Baur, A; Neundorfer, M; Jahn, G

1991-05-01

Peripheral blood mononuclear cells (PBMCs) from 29 patients infected with human immunodeficiency virus (HIV) were cultured by two different methods. One was the standard co-culture technique, the other a newly developed microculture method. In this assay 10(6) PBMCs were cultivated in 250 microliters medium, no activating agents or allogeneic cells were present. P24 antigen production measured by this method was found in 7 out of 11 PBMC cultures of patients in the Walter Reed (WR) stage 1 or 2, whereas only 4 samples were positive by the co-culture procedure. Cultures from patients in the later stages of the disease (WR 5/6) showed a higher p24 production by the co-culture method than by the microculture assay. It is assumed that rapidly growing HIV strains can be better assessed by the co-culture method which may select for these strains. P24 expression can be more easily obtained by the microculture technique even in cases where slowly replicating strains may be present. In conclusion, results from the microculture procedure described may be a useful supplementation to findings observed by the co-culture method.

SPECT and PET Serve as Molecular Imaging Techniques and in Vivo Biomarkers for Brain Metastases

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