Methods and apparatus for microwave tissue welding for wound closure

NASA Technical Reports Server (NTRS)

Ngo, Phong H. (Inventor); Dusl, John R. (Inventor); Arndt, G. Dickey (Inventor); Phan, Chau T. (Inventor); Byerly, Diane L. (Inventor); Sognier, Marguerite A. (Inventor); Carl, James R. (Inventor)

2013-01-01

Methods and apparatus for joining biological tissue together are provided. In at least one specific embodiment, a method for joining biological tissue together can include applying a biological solder on a wound. A barrier layer can be disposed on the biological solder. An antenna can be located in proximate spatial relationship to the barrier layer. An impedance of the antenna can be matched to an impedance of the wound. Microwaves from a signal generator can be transmitted through the antenna to weld two or more biological tissue pieces of the wound together. A power of the microwaves can be adjusted by a control circuit disposed between the antenna and the signal generator. The heating profile within the tissue may be adjusted and controlled by the placement of metallic microspheres in or around the wound.

Brown spot needle disease--biology and control in Scotch pine plantations.

Treesearch

Darroll D. Skilling; Thomas H. Nicholls

1975-01-01

An application section briefly describes and illustrates the symptoms, hosts, life history of the brown spot needlecast fungus (Scirrhia acicola), and recommends chemical and cultural control methods. A documentation section details the research on the biology and control of the fungus.

Controllability and observability of Boolean networks arising from biology

NASA Astrophysics Data System (ADS)

Li, Rui; Yang, Meng; Chu, Tianguang

2015-02-01

Boolean networks are currently receiving considerable attention as a computational scheme for system level analysis and modeling of biological systems. Studying control-related problems in Boolean networks may reveal new insights into the intrinsic control in complex biological systems and enable us to develop strategies for manipulating biological systems using exogenous inputs. This paper considers controllability and observability of Boolean biological networks. We propose a new approach, which draws from the rich theory of symbolic computation, to solve the problems. Consequently, simple necessary and sufficient conditions for reachability, controllability, and observability are obtained, and algorithmic tests for controllability and observability which are based on the Gröbner basis method are presented. As practical applications, we apply the proposed approach to several different biological systems, namely, the mammalian cell-cycle network, the T-cell activation network, the large granular lymphocyte survival signaling network, and the Drosophila segment polarity network, gaining novel insights into the control and/or monitoring of the specific biological systems.

Rationale for classical biological control of cattle fever ticks and proposed methods for field collection of natural enemies

USDA-ARS?s Scientific Manuscript database

Classical biological control using specialist parasitoids, predators and/or nematodes from the native ranges of cattle fever ticks Rhipicephalus microplus and Rhipicephalus annulatus could complement existing control strategies for this livestock pest in the transboundary region between Mexico and T...

Impact of Release Rates on the Effectiveness of Augmentative Biological Control Agents

PubMed Central

Crowder, David W.

2007-01-01

To access the effect of augmentative biological control agents, 31 articles were reviewed that investigated the impact of release rates of 35 augmentative biological control agents on the control of 42 arthropod pests. In 64% of the cases, the release rate of the biological control agent did not significantly affect the density or mortality of the pest insect. Results where similar when parasitoidsor predators were utilized as the natural enemy. Within any order of natural enemy, there were more cases where release rates did not affect augmentative biological control than cases where release rates were significant. There were more cases in which release rates did not affect augmentative biological control when pests were from the orders Hemiptera, Acari, or Diptera, but not with pests from the order Lepidoptera. In most cases, there was an optimal release rate that produced effective control of a pest species. This was especially true when predators were used as a biological control agent. Increasing the release rate above the optimal rate did not improve control of the pest and thus would be economically detrimental. Lower release rates were of ten optimal when biological control was used in conjunction with insecticides. In many cases, the timing and method of biological control applications were more significant factors impacting the effectiveness of biological control than the release rate. Additional factors that may limit the relative impact of release rates include natural enemy fecundity, establishment rates, prey availability, dispersal, and cannibalism. PMID:20307240

Intelligent nanomedicine integrating diagnosis and therapy

NASA Technical Reports Server (NTRS)

Li, Na (Inventor); Tan, Winny (Inventor)

2012-01-01

A method of controlling the activity of a biologically active compound. The method concerns an oligonucleotide-based compound, comprising a hairpin-forming oligonucleotide, an effector moiety physically associated with the oligonucleotide, where the effector moiety possesses a biological activity, and a regulating moiety physically associated with the oligonucleotide, where the regulating moiety controls the biological activity of the effector moiety by interacting with the effector moiety. The oligonucleotide can assume a hairpin configuration, where the effector and regulating moieties interact, or an open configuration, where the effector and regulating moieties fail to interact. Depending on the nature of the effector and regulating moieties, either configuration can result in the expression of the biological activity of the effector moiety.

Do biological-based strategies hold promise to biofouling control in MBRs?

PubMed

Malaeb, Lilian; Le-Clech, Pierre; Vrouwenvelder, Johannes S; Ayoub, George M; Saikaly, Pascal E

2013-10-01

Biofouling in membrane bioreactors (MBRs) remains a primary challenge for their wider application, despite the growing acceptance of MBRs worldwide. Research studies on membrane fouling are extensive in the literature, with more than 200 publications on MBR fouling in the last 3 years; yet, improvements in practice on biofouling control and management have been remarkably slow. Commonly applied cleaning methods are only partially effective and membrane replacement often becomes frequent. The reason for the slow advancement in successful control of biofouling is largely attributed to the complex interactions of involved biological compounds and the lack of representative-for-practice experimental approaches to evaluate potential effective control strategies. Biofouling is driven by microorganisms and their associated extra-cellular polymeric substances (EPS) and microbial products. Microorganisms and their products convene together to form matrices that are commonly treated as a black box in conventional control approaches. Biological-based antifouling strategies seem to be a promising constituent of an effective integrated control approach since they target the essence of biofouling problems. However, biological-based strategies are in their developmental phase and several questions should be addressed to set a roadmap for translating existing and new information into sustainable and effective control techniques. This paper investigates membrane biofouling in MBRs from the microbiological perspective to evaluate the potential of biological-based strategies in offering viable control alternatives. Limitations of available control methods highlight the importance of an integrated anti-fouling approach including biological strategies. Successful development of these strategies requires detailed characterization of microorganisms and EPS through the proper selection of analytical tools and assembly of results. Existing microbiological/EPS studies reveal a number of implications as well as knowledge gaps, warranting future targeted research. Systematic and representative microbiological studies, complementary utilization of molecular and biofilm characterization tools, standardized experimental methods and validation of successful biological-based antifouling strategies for MBR applications are needed. Specifically, in addition, linking these studies to relevant operational conditions in MBRs is an essential step to ultimately develop a better understanding and more effective and directed control strategy for biofouling. Copyright © 2013 Elsevier Ltd. All rights reserved.

Fifty years of the integrated control concept: moving the model and implementation forward in Arizona††

PubMed Central

Naranjo, Steven E; Ellsworth, Peter C

2009-01-01

Fifty years ago, Stern, Smith, van den Bosch and Hagen outlined a simple but sophisticated idea of pest control predicated on the complementary action of chemical and biological control. This integrated control concept has since been a driving force and conceptual foundation for all integrated pest management (IPM) programs. The four basic elements include thresholds for determining the need for control, sampling to determine critical densities, understanding and conserving the biological control capacity in the system and the use of selective insecticides or selective application methods, when needed, to augment biological control. Here we detail the development, evolution, validation and implementation of an integrated control (IC) program for whitefly, Bemisia tabaci (Genn.), in the Arizona cotton system that provides a rare example of the vision of Stern and his colleagues. Economic thresholds derived from research-based economic injury levels were developed and integrated with rapid and accurate sampling plans into validated decision tools widely adopted by consultants and growers. Extensive research that measured the interplay among pest population dynamics, biological control by indigenous natural enemies and selective insecticides using community ordination methods, predator:prey ratios, predator exclusion and demography validated the critical complementary roles played by chemical and biological control. The term ‘bioresidual’ was coined to describe the extended environmental resistance from biological control and other forces possible when selective insecticides are deployed. The tangible benefits have been a 70% reduction in foliar insecticides, a >$200 million saving in control costs and yield, along with enhanced utilization of ecosystem services over the last 14 years. Published in 2009 by John Wiley & Sons, Ltd. PMID:19834884

Systematic Biological Filter Design with a Desired I/O Filtering Response Based on Promoter-RBS Libraries.

PubMed

Hsu, Chih-Yuan; Pan, Zhen-Ming; Hu, Rei-Hsing; Chang, Chih-Chun; Cheng, Hsiao-Chun; Lin, Che; Chen, Bor-Sen

2015-01-01

In this study, robust biological filters with an external control to match a desired input/output (I/O) filtering response are engineered based on the well-characterized promoter-RBS libraries and a cascade gene circuit topology. In the field of synthetic biology, the biological filter system serves as a powerful detector or sensor to sense different molecular signals and produces a specific output response only if the concentration of the input molecular signal is higher or lower than a specified threshold. The proposed systematic design method of robust biological filters is summarized into three steps. Firstly, several well-characterized promoter-RBS libraries are established for biological filter design by identifying and collecting the quantitative and qualitative characteristics of their promoter-RBS components via nonlinear parameter estimation method. Then, the topology of synthetic biological filter is decomposed into three cascade gene regulatory modules, and an appropriate promoter-RBS library is selected for each module to achieve the desired I/O specification of a biological filter. Finally, based on the proposed systematic method, a robust externally tunable biological filter is engineered by searching the promoter-RBS component libraries and a control inducer concentration library to achieve the optimal reference match for the specified I/O filtering response.

A Correlation of Biology Teachers' Pupil Control Ideology and Their Classroom Teaching Practices.

ERIC Educational Resources Information Center

Jones, Paul L.; Blankenship, Jacob W.

The Pupil Control Ideology Form (PCI Form) and the Biology Classroom Activity Checklist (BCAC) were used to determine the relationship between teachers' stated pupil control ideology and the extent to which their students reported the use of inquiry methods in the classroom. Data were collected from a stratified random sample of 168 teachers and…

United States Department of Agriculture-Agricultural Research Service research on biological control of arthropods.

PubMed

Hopper, Keith R

2003-01-01

During 1999-2001, ARS scientists published over 100 papers on more than 30 species of insect pest and 60 species of predator and parasitoid. These papers address issues crucial to the three strategies of biological control: conservation, augmentation and introduction. Conservation biological control includes both conserving extant populations of natural enemies by using relatively non-toxic pesticides and increasing the abundance of natural enemies in crops by providing or improving refuges for population growth and dispersal into crops. ARS scientists have been very active in determining the effects of pesticides on beneficial arthropods and in studying movement of natural enemies from refuges into crops. Augmentation involves repeated releases of natural enemies in the field, which can be inoculative or inundative. Inoculative releases are used to initiate self-propagating populations at times or in places where they would be slow to colonize. ARS scientists have studied augmentative biological control of a variety of pest insects. The targets are mostly pests in annual crops or other ephemeral habitats, where self-reproducing populations of natural enemies are not sufficiently abundant early enough to keep pest populations in check. ARS research in augmentative biological control centers on methods for rearing large numbers of healthy, effective natural enemies and for releasing them where and when they are needed at a cost less than the value of the reduction in damage to the crop. ARS scientists have researched various aspects of introductions of exotic biological control agents against a diversity of pest insects. The major issues in biological control introductions are accurate identification and adequate systematics of both natural enemies and target pests, exploration for natural enemies, predicting the success of candidates for introduction and the likelihood of non-target impacts, quarantine and rearing methods, and post-introduction evaluation of establishment, control and non-target impacts. ARS scientists have published research on several general issues in biological control. Among the most important are the mechanisms affecting mate- and host-finding and host specificity.

Using Student Self-Assessment of Biological Concepts in an Introductory Biology Course.

ERIC Educational Resources Information Center

Heinze-Fry, Jane Ann

1992-01-01

Describes the author's methods to establish what students enrolled in an introductory biology course for nonmajors know about biology prior to instruction. The project also compared preinstructional knowledge to postinstructional knowledge. Beginning students knew the least about plant transport/chemical control and cellular metabolism. Students…

Identifying Ant-Mirid Spatial Interactions to Improve Biological Control in Cacao-Based Agroforestry System.

PubMed

Bagny Beilhe, Leïla; Piou, Cyril; Tadu, Zéphirin; Babin, Régis

2018-06-06

The use of ants for biological control of insect pests was the first reported case of conservation biological control. Direct and indirect community interactions between ants and pests lead to differential spatial pattern. We investigated spatial interactions between mirids, the major cocoa pest in West Africa and numerically dominant ant species, using bivariate point pattern analysis to identify potential biological control agents. We assume that potential biological control agents should display negative spatial interactions with mirids considering their niche overlap. The mirid/ant data were collected in complex cacao-based agroforestry systems sampled in three agroecological areas over a forest-savannah gradient in Cameroon. Three species, Crematogaster striatula Emery (Hymenoptera: Formicidae), Crematogaster clariventris Mayr (Hymenoptera: Formicidae), and Oecophylla longinoda Latreille (Hymenoptera: Formicidae) with high predator and aggressive behaviors were identified as dominant and showed negative spatial relationships with mirids. The weaver ant, O. longinoda was identified as the only potential biological control agent, considering its ubiquity in the plots, the similarity in niche requirements, and the spatial segregation with mirids resulting probably from exclusion mechanisms. Combining bivariate point pattern analysis to good knowledge of insect ecology was an effective method to identify a potentially good biological control agent.

Green Systems for Wastewater Treatment

ERIC Educational Resources Information Center

Environmental Science and Technology, 1975

1975-01-01

Plants found in marshlands and wetlands in many parts of the world may play an increasing part in a very new, yet very old approach to treatment of water and wastewater--the application of biological methods. Biological water pollution control methods being utilized around the world are examined. (BT)

Nanoscale hybrid systems based on carbon nanotubes for biological sensing and control

PubMed Central

Cho, Youngtak; Shin, Narae; Kim, Daesan; Park, Jae Yeol

2017-01-01

This paper provides a concise review on the recent development of nanoscale hybrid systems based on carbon nanotubes (CNTs) for biological sensing and control. CNT-based hybrid systems have been intensively studied for versatile applications of biological interfaces such as sensing, cell therapy and tissue regeneration. Recent advances in nanobiotechnology not only enable the fabrication of highly sensitive biosensors at nanoscale but also allow the applications in the controls of cell growth and differentiation. This review describes the fabrication methods of such CNT-based hybrid systems and their applications in biosensing and cell controls. PMID:28188158

Possible application of a nematophagous fungus as a biological control agent of parasitic nematodes on commercial sheep farms in South Africa.

PubMed

Faedo, M; Krecek, R C

2002-03-01

Biological control of parasitic nematodes of livestock is currently under development and represents another tool that may be integrated into helminth parasite control strategies. This paper presents a brief introduction to commercial sheep farming in South Africa and currently available nematode parasite control methods. These include the FAMACHA clinical assay, strategies of pasture management, dilution of resistant worm species by introduction of susceptible worms, breed resistant sheep and nutritional supplementation. The purpose of this paper is to outline the principles of biological control using nematophagous fungi and how it may be applied on sheep farms in South Africa.

3D topography of biologic tissue by multiview imaging and structured light illumination

NASA Astrophysics Data System (ADS)

Liu, Peng; Zhang, Shiwu; Xu, Ronald

2014-02-01

Obtaining three-dimensional (3D) information of biologic tissue is important in many medical applications. This paper presents two methods for reconstructing 3D topography of biologic tissue: multiview imaging and structured light illumination. For each method, the working principle is introduced, followed by experimental validation on a diabetic foot model. To compare the performance characteristics of these two imaging methods, a coordinate measuring machine (CMM) is used as a standard control. The wound surface topography of the diabetic foot model is measured by multiview imaging and structured light illumination methods respectively and compared with the CMM measurements. The comparison results show that the structured light illumination method is a promising technique for 3D topographic imaging of biologic tissue.

Biologically Based Methods for Control of Fumonisin-Producing Fusarium Species and Reduction of the Fumonisins.

PubMed

Alberts, Johanna F; van Zyl, Willem H; Gelderblom, Wentzel C A

2016-01-01

Infection by the fumonisin-producing Fusarium spp. and subsequent fumonisin contamination of maize adversely affect international trade and economy with deleterious effects on human and animal health. In developed countries high standards of the major food suppliers and retailers are upheld and regulatory controls deter the importation and local marketing of fumonisin-contaminated food products. In developing countries regulatory measures are either lacking or poorly enforced, due to food insecurity, resulting in an increased mycotoxin exposure. The lack and poor accessibility of effective and environmentally safe control methods have led to an increased interest in practical and biological alternatives to reduce fumonisin intake. These include the application of natural resources, including plants, microbial cultures, genetic material thereof, or clay minerals pre- and post-harvest. Pre-harvest approaches include breeding for resistant maize cultivars, introduction of biocontrol microorganisms, application of phenolic plant extracts, and expression of antifungal proteins and fumonisin degrading enzymes in transgenic maize cultivars. Post-harvest approaches include the removal of fumonisins by natural clay adsorbents and enzymatic degradation of fumonisins through decarboxylation and deamination by recombinant carboxylesterase and aminotransferase enzymes. Although, the knowledge base on biological control methods has expanded, only a limited number of authorized decontamination products and methods are commercially available. As many studies detailed the use of natural compounds in vitro, concepts in reducing fumonisin contamination should be developed further for application in planta and in the field pre-harvest, post-harvest, and during storage and food-processing. In developed countries an integrated approach, involving good agricultural management practices, hazard analysis and critical control point (HACCP) production, and storage management, together with selected biologically based treatments, mild chemical and physical treatments could reduce fumonisin contamination effectively. In rural subsistence farming communities, simple, practical, and culturally acceptable hand-sorting, maize kernel washing, and dehulling intervention methods proved to be effective as a last line of defense for reducing fumonisin exposure. Biologically based methods for control of fumonisin-producing Fusarium spp. and decontamination of the fumonisins could have potential commercial application, while simple and practical intervention strategies could also impact positively on food safety and security, especially in rural populations reliant on maize as a dietary staple.

[Acoustic detection of absorption of millimeter-band electromagnetic waves in biological objects].

PubMed

Polnikov, I G; Putvinskiĭ, A V

1988-01-01

Principles of photoacoustic spectroscopy were applied to elaborate a new method for controlling millimeter electromagnetic waves absorption in biological objects. The method was used in investigations of frequency dependence of millimeter wave power absorption in vitro and in vivo in the commonly used experimental irradiation systems.

The use of continuous culture in systems biology investigations.

PubMed

Winder, Catherine L; Lanthaler, Karin

2011-01-01

When acquiring data for systems biology studies, it is essential to perform the experiments in controlled and reproducible conditions. Advances in the fields of proteomics and metabolomics allow the quantitative analysis of the components of the biological cell. It is essential to include a method in the experimental pipeline to culture the biological system in controlled and reproducible conditions to facilitate the acquisition of high-quality data. The employment of continuous culture methods for the growth of microorganisms is an ideal tool to achieve these objectives. This chapter will review the continuous culture approaches which may be applied in such studies, outline the experimental options which should be considered, and describe the approach applied in the production of steady-state cultures of Saccharomyces cerevisiae. Copyright © 2011 Elsevier Inc. All rights reserved.

Success evaluation of the biological control of Fusarium wilts of cucumber, banana, and tomato since 2000 and future research strategies.

PubMed

Raza, Waseem; Ling, Ning; Zhang, Ruifu; Huang, Qiwei; Xu, Yangchun; Shen, Qirong

2017-03-01

The Fusarium wilt caused by Fusarium oxysporum strains is the most devastating disease of cucumber, banana, and tomato. The biological control of this disease has become an attractive alternative to the chemical fungicides and other conventional control methods. In this review, the research trends and biological control efficiencies (BCE) of different microbial strains since 2000 are reviewed in detail, considering types of microbial genera, inoculum application methods, plant growth medium and conditions, inoculum application with amendments, and co-inoculation of different microbial strains and how those affect the BCE of Fusarium wilt. The data evaluation showed that the BCE of biocontrol agents was higher against the Fusarium wilt of cucumber compared to the Fusarium wilts of banana and tomato. Several biocontrol agents mainly Bacillus, Trichoderma, Pseudomonas, nonpathogenic Fusarium, and Penicillium strains were evaluated to control Fusarium wilt, but still this lethal disease could not be controlled completely. We have discussed different reasons of inconsistent results and recommendations for the betterment of BCE in the future. This review provides knowledge of the biotechnology of biological control of Fusarium wilt of cucumber, banana, and tomato in a nut shell that will provide researchers a beginning line to start and to organize and plan research for the future studies.

Evaluation of recovery and monitoring methods for parasitoids released against emerald ash borer

Treesearch

Michael S. Parisio; Juli R. Gould; John D. Vandenberg; Leah S. Bauer; Melissa K. Fierke

2017-01-01

Emerald ash borer (Agrilus planipennis Fairmaire, EAB) is an invasive forest pest and the target of an extensive biological control program designed to mitigate EAB-caused ash (Fraxinus spp.) mortality. Since 2007, hymenopteran parasitoids of EAB from northeastern Asia have been released as biological control agents in North...

Pre-release biological control agent recommendations for swallow-wort (Vincetoxicum spp.) informed by demographic matrix models

USDA-ARS?s Scientific Manuscript database

Weed biological control workers have advocated for the advance assessment of agent efficacy in order to minimize the release of host-specific but ineffective agents. One method involves demographic matrix modeling of target weed populations in order to identify plant life stage transitions that cont...

Biological control of aflatoxin contamination and pests in U.S. crops using formulations of corn starch-based bioplastic

USDA-ARS?s Scientific Manuscript database

For many years, these laboratories have studied the use of biological control methods to reduce aflatoxin contamination in harvested corn using non-aflatoxigenic Aspergillus flavus isolates in grain-based granule and liquid formulations. More recently, research has focused on using various formulat...

Integrated Pest Management, Preliminary. Curriculum Guide and Instructional Materials for a Secondary School Vo-Ag Program.

ERIC Educational Resources Information Center

Grady County Board of Education, Cairo, GA.

This curriculum guide presents methods to disseminate information to students interested in dealing with pests, or who have concerns about the environmental impacts of modern pest control methods. Options are encouraged for pest control methods using a combination of natural, biological, cultural, and chemical means of control. Specifically…

Modelling malaria control by introduction of larvivorous fish.

PubMed

Lou, Yijun; Zhao, Xiao-Qiang

2011-10-01

Malaria creates serious health and economic problems which call for integrated management strategies to disrupt interactions among mosquitoes, the parasite and humans. In order to reduce the intensity of malaria transmission, malaria vector control may be implemented to protect individuals against infective mosquito bites. As a sustainable larval control method, the use of larvivorous fish is promoted in some circumstances. To evaluate the potential impacts of this biological control measure on malaria transmission, we propose and investigate a mathematical model describing the linked dynamics between the host-vector interaction and the predator-prey interaction. The model, which consists of five ordinary differential equations, is rigorously analysed via theories and methods of dynamical systems. We derive four biologically plausible and insightful quantities (reproduction numbers) that completely determine the community composition. Our results suggest that the introduction of larvivorous fish can, in principle, have important consequences for malaria dynamics, but also indicate that this would require strong predators on larval mosquitoes. Integrated strategies of malaria control are analysed to demonstrate the biological application of our developed theory.

Advances in the application of genetic manipulation methods to apicomplexan parasites.

PubMed

Suarez, C E; Bishop, R P; Alzan, H F; Poole, W A; Cooke, B M

2017-10-01

Apicomplexan parasites such as Babesia, Theileria, Eimeria, Cryptosporidium and Toxoplasma greatly impact animal health globally, and improved, cost-effective measures to control them are urgently required. These parasites have complex multi-stage life cycles including obligate intracellular stages. Major gaps in our understanding of the biology of these relatively poorly characterised parasites and the diseases they cause severely limit options for designing novel control methods. Here we review potentially important shared aspects of the biology of these parasites, such as cell invasion, host cell modification, and asexual and sexual reproduction, and explore the potential of the application of relatively well-established or newly emerging genetic manipulation methods, such as classical transfection or gene editing, respectively, for closing important gaps in our knowledge of the function of specific genes and proteins, and the biology of these parasites. In addition, genetic manipulation methods impact the development of novel methods of control of the diseases caused by these economically important parasites. Transient and stable transfection methods, in conjunction with whole and deep genome sequencing, were initially instrumental in improving our understanding of the molecular biology of apicomplexan parasites and paved the way for the application of the more recently developed gene editing methods. The increasingly efficient and more recently developed gene editing methods, in particular those based on the CRISPR/Cas9 system and previous conceptually similar techniques, are already contributing to additional gene function discovery using reverse genetics and related approaches. However, gene editing methods are only possible due to the increasing availability of in vitro culture, transfection, and genome sequencing and analysis techniques. We envisage that rapid progress in the development of novel gene editing techniques applied to apicomplexan parasites of veterinary interest will ultimately lead to the development of novel and more efficient methods for disease control. Published by Elsevier Ltd.

Green Jobs: Definition and Method of Appraisal of Chemical and Biological Risks

PubMed Central

Cheneval, Erwan; Busque, Marc-Antoine; Ostiguy, Claude; Lavoie, Jacques; Bourbonnais, Robert; Labrèche, France; Bakhiyi, Bouchra; Zayed, Joseph

2016-01-01

In the wake of sustainable development, green jobs are developing rapidly, changing the work environment. However a green job is not automatically a safe job. The aim of the study was to define green jobs, and to establish a preliminary risk assessment of chemical substances and biological agents for workers in Quebec. An operational definition was developed, along with criteria and sustainable development principles to discriminate green jobs from regular jobs. The potential toxicity or hazard associated with their chemical and biological exposures was assessed, and the workers’ exposure appraised using an expert assessment method. A control banding approach was then used to assess risks for workers in selected green jobs. A double entry model allowed us to set priorities in terms of chemical or biological risk. Among jobs that present the highest risk potential, several are related to waste management. The developed method is flexible and could be adapted to better appraise the risks that workers are facing or to propose control measures. PMID:26718400

Biological life-support systems

NASA Technical Reports Server (NTRS)

Shepelev, Y. Y.

1975-01-01

The establishment of human living environments by biologic methods, utilizing the appropriate functions of autotrophic and heterotrophic organisms is examined. Natural biologic systems discussed in terms of modeling biologic life support systems (BLSS), the structure of biologic life support systems, and the development of individual functional links in biologic life support systems are among the factors considered. Experimental modeling of BLSS in order to determine functional characteristics, mechanisms by which stability is maintained, and principles underlying control and regulation is also discussed.

A Study on Simulation Methods in Academic Success with Reference to Teaching Biology for Education Students

ERIC Educational Resources Information Center

Sasikala, P.; Tanyong, Siriwan

2016-01-01

The main objective of this study is to determine the utility of simulation methods in biology teaching for nursing students and academic success. 100 students (50 control, 50 experimental) who studied at Srinivasa Teacher Training School, Kalikiri, Recognised by Sri Venkateswara University, Faculty of Education, Tirupati, AP, India, 2014-215…

Enzymatic control of biological deposits in papermaking.

PubMed

Hatcher, H J

1984-01-01

Deposit control in the pulp and paper industry has traditionally been accomplished by the use of toxic biocides. A method has been found whereby biological deposits can be controlled by the use of an enzyme-based product. Numerous field studies have been conducted successfully and photographs prepared illustrating the process. The dynamics of deposit formation and problems associated with such formations have been the subject of considerable study. Development and control of deposit problems under different paper mill conditions using the chemical-biochemical approach will be discussed.

Strategies for Controlled Delivery of Biologics for Cartilage Repair

PubMed Central

Lam, Johnny; Lu, Steven; Kasper, F. Kurtis; Mikos, Antonios G.

2014-01-01

The delivery of biologics is an important component in the treatment of osteoarthritis and the functional restoration of articular cartilage. Numerous factors have been implicated in the cartilage repair process, but the uncontrolled delivery of these factors may not only reduce their full reparative potential and can also cause unwanted morphological effects. It is therefore imperative to consider the type of biologic to be delivered, the method of delivery, and the temporal as well as spatial presentation of the biologic to achieve the desired effect in cartilage repair. Additionally, the delivery of a single factor may not be sufficient in guiding neo-tissue formation, motivating recent research towards the delivery of multiple factors. This review will discuss the roles of various biologics involved in cartilage repair and the different methods of delivery for appropriate healing responses. A number of spatiotemporal strategies will then be emphasized for the controlled delivery of single and multiple bioactive factors in both in vitro and in vivo cartilage tissue engineering applications. PMID:24993610

Biologically Based Methods for Control of Fumonisin-Producing Fusarium Species and Reduction of the Fumonisins

PubMed Central

Alberts, Johanna F.; van Zyl, Willem H.; Gelderblom, Wentzel C. A.

2016-01-01

Infection by the fumonisin-producing Fusarium spp. and subsequent fumonisin contamination of maize adversely affect international trade and economy with deleterious effects on human and animal health. In developed countries high standards of the major food suppliers and retailers are upheld and regulatory controls deter the importation and local marketing of fumonisin-contaminated food products. In developing countries regulatory measures are either lacking or poorly enforced, due to food insecurity, resulting in an increased mycotoxin exposure. The lack and poor accessibility of effective and environmentally safe control methods have led to an increased interest in practical and biological alternatives to reduce fumonisin intake. These include the application of natural resources, including plants, microbial cultures, genetic material thereof, or clay minerals pre- and post-harvest. Pre-harvest approaches include breeding for resistant maize cultivars, introduction of biocontrol microorganisms, application of phenolic plant extracts, and expression of antifungal proteins and fumonisin degrading enzymes in transgenic maize cultivars. Post-harvest approaches include the removal of fumonisins by natural clay adsorbents and enzymatic degradation of fumonisins through decarboxylation and deamination by recombinant carboxylesterase and aminotransferase enzymes. Although, the knowledge base on biological control methods has expanded, only a limited number of authorized decontamination products and methods are commercially available. As many studies detailed the use of natural compounds in vitro, concepts in reducing fumonisin contamination should be developed further for application in planta and in the field pre-harvest, post-harvest, and during storage and food-processing. In developed countries an integrated approach, involving good agricultural management practices, hazard analysis and critical control point (HACCP) production, and storage management, together with selected biologically based treatments, mild chemical and physical treatments could reduce fumonisin contamination effectively. In rural subsistence farming communities, simple, practical, and culturally acceptable hand-sorting, maize kernel washing, and dehulling intervention methods proved to be effective as a last line of defense for reducing fumonisin exposure. Biologically based methods for control of fumonisin-producing Fusarium spp. and decontamination of the fumonisins could have potential commercial application, while simple and practical intervention strategies could also impact positively on food safety and security, especially in rural populations reliant on maize as a dietary staple. PMID:27199904

How to Identify and Control Water Weeds and Algae.

ERIC Educational Resources Information Center

Applied Biochemists, Inc., Mequon, WI.

Included in this guide to water management are general descriptions of algae, toxic algae, weed problems in lakes, ponds, and canals, and general discussions of mechanical, biological and chemical control methods. In addition, pictures, descriptions, and recommended control methods are given for algae, 6 types of floating weeds, 18 types of…

Apparatus and method to control atmospheric water vapor composition and concentration during dynamic cooling of biological tissues in conjunction with laser irradiations

DOEpatents

Nelson, J. Stuart; Anvari, Bahman; Tanenbaum, B. Samuel; Milner, Thomas E.

1999-01-01

Cryogen spray cooling of skin surface with millisecond cryogen spurts is an effective method for establishing a controlled temperature distribution in tissue and protecting the epidermis from nonspecific thermal injury during laser mediated dermatological procedures. Control of humidity level, spraying distance and cryogen boiling point is material to the resulting surface temperature. Decreasing the ambient humidity level results in less ice formation on the skin surface without altering the surface temperature during the cryogen spurt. For a particular delivery nozzle, increasing the spraying distance to 85 millimeters lowers the surface temperature. The methodology comprises establishing a controlled humidity level in the theater of operation of the irradiation site of the biological tissues before and/or during the cryogenic spray cooling of the biological tissue. At cold temperatures calibration was achieved by mounting a thermistor on a thermoelectric cooler. The thermal electric cooler was cooled from from 20.degree. C. to about -20.degree. C. while measuring its infrared emission.

Insect herbivory stimulates allelopathic exudation by an invasive plant and the suppression of natives

Treesearch

Giles C. Thelen; Jorge M. Vivanco; Beth Newingham; William Good; Harsh P. Bais; Peter Landres; Anthony Caesar; Ragan M. Callaway

2005-01-01

Exotic invasive plants are often subjected to attack from imported insects as a method of biological control. A fundamental, but rarely explicitly tested, assumption of biological control is that damaged plants are less fit and compete poorly. In contrast, we find that one of the most destructive invasive plants in North America, Centaurea maculosa,...

Southern Idaho student "bug crews": Weeds, youth, and biocontrol in the rangelands of Idaho

Treesearch

Sharlyn Gunderson-Izurieta; George P. Markin; Nan Reedy; Becky Frieberg

2009-01-01

Biological control of noxious weeds is an effective and widespread method often used by rangeland managers in the western United States. However, once biological control agents, usually insects, are released onto public and private lands there are few, if any, programs to follow up and monitor the effectiveness of these agents. A technique being used by some...

Evaluation of biologic occupational risk control practices: quality indicators development and validation.

PubMed

Takahashi, Renata Ferreira; Gryschek, Anna Luíza F P L; Izumi Nichiata, Lúcia Yasuko; Lacerda, Rúbia Aparecida; Ciosak, Suely Itsuko; Gir, Elucir; Padoveze, Maria Clara

2010-05-01

There is growing demand for the adoption of qualification systems for health care practices. This study is aimed at describing the development and validation of indicators for evaluation of biologic occupational risk control programs. The study involved 3 stages: (1) setting up a research team, (2) development of indicators, and (3) validation of the indicators by a team of specialists recruited to validate each attribute of the developed indicators. The content validation method was used for the validation, and a psychometric scale was developed for the specialists' assessment. A consensus technique was used, and every attribute that obtained a Content Validity Index of at least 0.75 was approved. Eight indicators were developed for the evaluation of the biologic occupational risk prevention program, with emphasis on accidents caused by sharp instruments and occupational tuberculosis prevention. The indicators included evaluation of the structure, process, and results at the prevention and biologic risk control levels. The majority of indicators achieved a favorable consensus regarding all validated attributes. The developed indicators were considered validated, and the method used for construction and validation proved to be effective. Copyright (c) 2010 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Mosby, Inc. All rights reserved.

Constructing biological pathway models with hybrid functional Petri nets.

PubMed

Doi, Atsushi; Fujita, Sachie; Matsuno, Hiroshi; Nagasaki, Masao; Miyano, Satoru

2004-01-01

In many research projects on modeling and analyzing biological pathways, the Petri net has been recognized as a promising method for representing biological pathways. From the pioneering works by Reddy et al., 1993, and Hofestädt, 1994, that model metabolic pathways by traditional Petri net, several enhanced Petri nets such as colored Petri net, stochastic Petri net, and hybrid Petri net have been used for modeling biological phenomena. Recently, Matsuno et al., 2003b, introduced the hybrid functional Petri net (HFPN) in order to give a more intuitive and natural modeling method for biological pathways than these existing Petri nets. Although the paper demonstrates the effectiveness of HFPN with two examples of gene regulation mechanism for circadian rhythms and apoptosis signaling pathway, there has been no detailed explanation about the method of HFPN construction for these examples. The purpose of this paper is to describe method to construct biological pathways with the HFPN step-by-step. The method is demonstrated by the well-known glycolytic pathway controlled by the lac operon gene regulatory mechanism.

Constructing biological pathway models with hybrid functional petri nets.

PubMed

Doi, Atsushi; Fujita, Sachie; Matsuno, Hiroshi; Nagasaki, Masao; Miyano, Satoru

2011-01-01

In many research projects on modeling and analyzing biological pathways, the Petri net has been recognized as a promising method for representing biological pathways. From the pioneering works by Reddy et al., 1993, and Hofestädt, 1994, that model metabolic pathways by traditional Petri net, several enhanced Petri nets such as colored Petri net, stochastic Petri net, and hybrid Petri net have been used for modeling biological phenomena. Recently, Matsuno et al., 2003b, introduced the hybrid functional Petri net (HFPN) in order to give a more intuitive and natural modeling method for biological pathways than these existing Petri nets. Although the paper demonstrates the effectiveness of HFPN with two examples of gene regulation mechanism for circadian rhythms and apoptosis signaling pathway, there has been no detailed explanation about the method of HFPN construction for these examples. The purpose of this paper is to describe method to construct biological pathways with the HFPN step-by-step. The method is demonstrated by the well-known glycolytic pathway controlled by the lac operon gene regulatory mechanism.

50 CFR 648.20 - Mid-Atlantic Fishery Management Council ABC control rules.

Code of Federal Regulations, 2014 CFR

2014-10-01

... biology of the stock, fisheries that exploit the stock, and data collection methods; (iv) The stock... SSC to determine the following: (i) Key features of the stock biology, the fisheries that exploit it...

50 CFR 648.20 - Mid-Atlantic Fishery Management Council ABC control rules.

Code of Federal Regulations, 2013 CFR

2013-10-01

... biology of the stock, fisheries that exploit the stock, and data collection methods; (iv) The stock... SSC to determine the following: (i) Key features of the stock biology, the fisheries that exploit it...

50 CFR 648.20 - Mid-Atlantic Fishery Management Council ABC control rules.

Code of Federal Regulations, 2012 CFR

2012-10-01

... biology of the stock, fisheries that exploit the stock, and data collection methods; (iv) The stock... SSC to determine the following: (i) Key features of the stock biology, the fisheries that exploit it...

Measuring indigenous photosynthetic organisms to detect chemical warefare agents in water

DOEpatents

Greenbaum, Elias; Sanders, Charlene A.

2005-11-15

A method of testing water to detect the presence of a chemical or biological warfare agent is disclosed. The method is carried out by establishing control data by providing control water containing indigenous organisms but substantially free of a chemical and a biological warfare agent. Then measuring photosynthetic activity of the control water with a fluorometer to obtain control data to compare with test data to detect the presence of the chemical or agent. The test data is gathered by providing test water comprising the same indigenous organisms as contained in the control water. Further, the test water is suspected of containing the chemical or agent to be tested for. Photosynthetic activity is also measured by fluorescence induction in the test water using a fluorometer.

Study report on guidelines and test procedures for investigating stability of nonlinear cardiovascular control system models

NASA Technical Reports Server (NTRS)

Fitzjerrell, D. G.

1974-01-01

A general study of the stability of nonlinear as compared to linear control systems is presented. The analysis is general and, therefore, applies to other types of nonlinear biological control systems as well as the cardiovascular control system models. Both inherent and numerical stability are discussed for corresponding analytical and graphic methods and numerical methods.

SU-G-TeP3-07: On the Development of Mechano-Biological Assessment of Leukemia Cells Using Optical Tweezers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brost, E; Brooks, J; Piepenburg, J

Purpose: Patients with BCR-ABL (Ph +ve) acute lymphoblastic leukemia are at very high risk of relapse and mortality. In line with the NIH mission to understand the physical and biological processes, we seek to report mechano-biological method to assessment and distinguish treated/untreated leukemia cells. Methods: BCR-ABL leukemia cell populations and silica microspheres were trapped in a 100x magnification optical trapping system (λ=660 nm, 70 mW). Light refracted through the trapped sample was collected in the back focal plane by a quadrant detector to measure the positions of individual cells. The sample was driven at a known frequency and amplitude withmore » a flexure translation stage, and the target’s response was recorded. The measured response was calibrated using the known driving parameters, and information about cell movements due to mechano-biological effects was extracted. Two leukemia cell populations were tested: a control group and a group treated with 2 Gy. Results: The mechano-biological movements of 10 microspheres, control cells, and treated cells were tracked over a ∼30 minute window at 1 minute intervals. The microsphere population did not see significant change in mechano-biological movements over the testing interval and remained constant. The control cell population saw a two-fold rise in activity that peaked around 1200 seconds, then dropped off sharply. The treated cell population saw a two-fold rise in activity that peaked at 400 seconds, and dropped off slowly. Conclusion: The investigated technique allows for direct measurement the movements of a trapped object due to mechano-biological effects such as thermal and extracellular motion. When testing microspheres, the mechano-biological activity remained constant over time due to the lack of biological factors. In both the control and treated cell populations, the mechano-biological activity was increased, possibly due to mitochondrial activation. This extra activity decreased over time, possibly due to cellular damage from trapping radiation.« less

HDBStat!: a platform-independent software suite for statistical analysis of high dimensional biology data.

PubMed

Trivedi, Prinal; Edwards, Jode W; Wang, Jelai; Gadbury, Gary L; Srinivasasainagendra, Vinodh; Zakharkin, Stanislav O; Kim, Kyoungmi; Mehta, Tapan; Brand, Jacob P L; Patki, Amit; Page, Grier P; Allison, David B

2005-04-06

Many efforts in microarray data analysis are focused on providing tools and methods for the qualitative analysis of microarray data. HDBStat! (High-Dimensional Biology-Statistics) is a software package designed for analysis of high dimensional biology data such as microarray data. It was initially developed for the analysis of microarray gene expression data, but it can also be used for some applications in proteomics and other aspects of genomics. HDBStat! provides statisticians and biologists a flexible and easy-to-use interface to analyze complex microarray data using a variety of methods for data preprocessing, quality control analysis and hypothesis testing. Results generated from data preprocessing methods, quality control analysis and hypothesis testing methods are output in the form of Excel CSV tables, graphs and an Html report summarizing data analysis. HDBStat! is a platform-independent software that is freely available to academic institutions and non-profit organizations. It can be downloaded from our website http://www.soph.uab.edu/ssg_content.asp?id=1164.

Conservation Biological Control of Pests in the Molecular Era: New Opportunities to Address Old Constraints

PubMed Central

Gurr, Geoff M.; You, Minsheng

2016-01-01

Biological control has long been considered a potential alternative to pesticidal strategies for pest management but its impact and level of use globally remain modest and inconsistent. A rapidly expanding range of molecular – particularly DNA-related – techniques is currently revolutionizing many life sciences. This review identifies a series of constraints on the development and uptake of conservation biological control and considers the contemporary and likely future influence of molecular methods on these constraints. Molecular approaches are now often used to complement morphological taxonomic methods for the identification and study of biological control agents including microbes. A succession of molecular techniques has been applied to ‘who eats whom’ questions in food-web ecology. Polymerase chain reaction (PCR) approaches have largely superseded immunological approaches such as enzyme-linked immunosorbent assay (ELISA) and now – in turn – are being overtaken by next generation sequencing (NGS)-based approaches that offer unparalleled power at a rapidly diminishing cost. There is scope also to use molecular techniques to manipulate biological control agents, which will be accelerated with the advent of gene editing tools, the CRISPR/Cas9 system in particular. Gene editing tools also offer unparalleled power to both elucidate and manipulate plant defense mechanisms including those that involve natural enemy attraction to attacked plants. Rapid advances in technology will allow the development of still more novel pest management options for which uptake is likely to be limited chiefly by regulatory hurdles. PMID:26793225

A Manual of Mosquito Control Projects and Committee Assignments for 4-H and Scouts Biology Class Projects, Organized Community Service Programs, and Individuals Interested in Environmental Management.

ERIC Educational Resources Information Center

Hart, Richard A.

The mosquito control projects presented in this manual were prepared from an educational viewpoint and are intended for use by students in 4-H and Scouts and as a supplement to high school and college biology course work. The major emphasis of the projects is on integrated pest management, an approach utilizing cost-effective control methods which…

Microbiological control of soil-borne phytopathogenic fungi with special emphasis on wilt-inducing Fusarium oxysporum.

PubMed

Alabouvette, Claude; Olivain, Chantal; Migheli, Quirico; Steinberg, Christian

2009-11-01

Plant diseases induced by soil-borne plant pathogens are among the most difficult to control. In the absence of effective chemical control methods, there is renewed interest in biological control based on application of populations of antagonistic micro-organisms. In addition to Pseudomonas spp. and Trichoderma spp., which are the two most widely studied groups of biological control agents, the protective strains of Fusarium oxysporum represent an original model. These protective strains of F. oxysporum can be used to control wilt induced by pathogenic strains of the same species. Exploring the mechanisms involved in the protective capability of these strains is not only necessary for their development as commercial biocontrol agents but raises many basic questions related to the determinism of pathogenicity versus biocontrol capacity in the F. oxysporum species complex. In this paper, current knowledge regarding the interaction between the plant and the protective strains is reviewed in comparison with interactions between the plant and pathogenic strains. The success of biological control depends not only on plant-microbial interactions but also on the ecological fitness of the biological control agents.

Green Jobs: Definition and Method of Appraisal of Chemical and Biological Risks.

PubMed

Cheneval, Erwan; Busque, Marc-Antoine; Ostiguy, Claude; Lavoie, Jacques; Bourbonnais, Robert; Labrèche, France; Bakhiyi, Bouchra; Zayed, Joseph

2016-04-01

In the wake of sustainable development, green jobs are developing rapidly, changing the work environment. However a green job is not automatically a safe job. The aim of the study was to define green jobs, and to establish a preliminary risk assessment of chemical substances and biological agents for workers in Quebec. An operational definition was developed, along with criteria and sustainable development principles to discriminate green jobs from regular jobs. The potential toxicity or hazard associated with their chemical and biological exposures was assessed, and the workers' exposure appraised using an expert assessment method. A control banding approach was then used to assess risks for workers in selected green jobs. A double entry model allowed us to set priorities in terms of chemical or biological risk. Among jobs that present the highest risk potential, several are related to waste management. The developed method is flexible and could be adapted to better appraise the risks that workers are facing or to propose control measures. © The Author 2015. Published by Oxford University Press on behalf of the British Occupational Hygiene Society.

Understanding the biology and control of the poultry red mite Dermanyssus gallinae: a review.

PubMed

Pritchard, James; Kuster, Tatiana; Sparagano, Olivier; Tomley, Fiona

2015-01-01

Dermanyssus gallinae, the poultry red mite (PRM), is a blood-feeding ectoparasite capable of causing pathology in birds, amongst other animals. It is an increasingly important pathogen in egg layers and is responsible for substantial economic losses to the poultry industry worldwide. Even though PRM poses a serious problem, very little is known about the basic biology of the mite. Here we review the current body of literature describing red mite biology and discuss how this has been, or could be, used to develop methods to control PRM infestations. We focus primarily on the PRM digestive system, salivary glands, nervous system and exoskeleton and also explore areas of PRM biology which have to date received little or no study but have the potential to offer new control targets.

Biology-Inspired Autonomous Control

DTIC Science & Technology

2011-08-31

from load sensing in a turbulent flow field with high levels of plant uncertainty and optical feedback latency. The results of this paper suggest... Mimicry of biological systems, in the form of precise mathematical or physical dynamical modeling, is yielding impressive insight into the underlying...processing and plants , the aerospace industry has been slow to accept adaptive control. In the past decade however, newer methods for design of adaptive

Observability of Boolean multiplex control networks

NASA Astrophysics Data System (ADS)

Wu, Yuhu; Xu, Jingxue; Sun, Xi-Ming; Wang, Wei

2017-04-01

Boolean multiplex (multilevel) networks (BMNs) are currently receiving considerable attention as theoretical arguments for modeling of biological systems and system level analysis. Studying control-related problems in BMNs may not only provide new views into the intrinsic control in complex biological systems, but also enable us to develop a method for manipulating biological systems using exogenous inputs. In this article, the observability of the Boolean multiplex control networks (BMCNs) are studied. First, the dynamical model and structure of BMCNs with control inputs and outputs are constructed. By using of Semi-Tensor Product (STP) approach, the logical dynamics of BMCNs is converted into an equivalent algebraic representation. Then, the observability of the BMCNs with two different kinds of control inputs is investigated by giving necessary and sufficient conditions. Finally, examples are given to illustrate the efficiency of the obtained theoretical results.

Struvite scale formation and control.

PubMed

Parsons, S A; Doyle, J D

2004-01-01

Struvite scale formation is a major operational issue at both conventional and biological nutrient removal wastewater treatment plants. Factors affecting the formation of struvite scales were investigated including supersaturation, pH and pipe material and roughness. A range of control methods have been investigated including low fouling materials, pH control, inhibitor and chemical dosing. Control methods exist to reduce scale formation although each has its advantages and disadvantages.

Science Education Notes.

ERIC Educational Resources Information Center

School Science Review, 1983

1983-01-01

Discusses current topics in science education including increasing adult education through innovation in course planning/recruitment methods, a course in microelectronics/digital control, and need for increased human genetics topics in biology/health education. Also discusses changing role of biology teachers, preschool science, and teaching a…

Population control methods in stochastic extinction and outbreak scenarios.

PubMed

Segura, Juan; Hilker, Frank M; Franco, Daniel

2017-01-01

Adaptive limiter control (ALC) and adaptive threshold harvesting (ATH) are two related control methods that have been shown to stabilize fluctuating populations. Large variations in population abundance can threaten the constancy and the persistence stability of ecological populations, which may impede the success and efficiency of managing natural resources. Here, we consider population models that include biological mechanisms characteristic for causing extinctions on the one hand and pest outbreaks on the other hand. These models include Allee effects and the impact of natural enemies (as is typical of forest defoliating insects). We study the impacts of noise and different levels of biological parameters in three extinction and two outbreak scenarios. Our results show that ALC and ATH have an effect on extinction and outbreak risks only for sufficiently large control intensities. Moreover, there is a clear disparity between the two control methods: in the extinction scenarios, ALC can be effective and ATH can be counterproductive, whereas in the outbreak scenarios the situation is reversed, with ATH being effective and ALC being potentially counterproductive.

A Review of the Tawny Crazy Ant, Nylanderia fulva, an Emergent Ant Invader in the Southern United States: Is Biological Control a Feasible Management Option?

PubMed

Wang, Zinan; Moshman, Lori; Kraus, Emily C; Wilson, Blake E; Acharya, Namoona; Diaz, Rodrigo

2016-12-15

The tawny crazy ant, Nylanderia fulva (Mayr) (Hymenoptera: Formicidae), has invaded states of the U.S. including Texas, Louisiana, Mississippi, Alabama, Florida, and Georgia. Native to South America, N. fulva is considered a pest in the U.S. capable of annoying homeowners and farmers, as well as displacing native ant species. As it continues to expand its range, there is a growing need to develop novel management techniques to control the pest and prevent further spread. Current management efforts rely heavily on chemical control, but these methods have not been successful. A review of the biology, taxonomy, ecology, and distribution of N. fulva , including discussion of ecological and economic consequences of this invasive species, is presented. Options for future management are suggested focusing on biological control, including parasitoid flies in the genus Pseudacteon , the microsporidian parasite Myrmecomorba nylanderiae , and a novel polynucleotide virus as potential biological control agents. We suggest further investigation of natural enemies present in the adventive range, as well as foreign exploration undertaken in the native range including Paraguay, Brazil, and Argentina. We conclude that N. fulva may be a suitable candidate for biological control.

A Review of the Tawny Crazy Ant, Nylanderia fulva, an Emergent Ant Invader in the Southern United States: Is Biological Control a Feasible Management Option?

PubMed Central

Wang, Zinan; Moshman, Lori; Kraus, Emily C.; Wilson, Blake E.; Acharya, Namoona; Diaz, Rodrigo

2016-01-01

The tawny crazy ant, Nylanderia fulva (Mayr) (Hymenoptera: Formicidae), has invaded states of the U.S. including Texas, Louisiana, Mississippi, Alabama, Florida, and Georgia. Native to South America, N. fulva is considered a pest in the U.S. capable of annoying homeowners and farmers, as well as displacing native ant species. As it continues to expand its range, there is a growing need to develop novel management techniques to control the pest and prevent further spread. Current management efforts rely heavily on chemical control, but these methods have not been successful. A review of the biology, taxonomy, ecology, and distribution of N. fulva, including discussion of ecological and economic consequences of this invasive species, is presented. Options for future management are suggested focusing on biological control, including parasitoid flies in the genus Pseudacteon, the microsporidian parasite Myrmecomorba nylanderiae, and a novel polynucleotide virus as potential biological control agents. We suggest further investigation of natural enemies present in the adventive range, as well as foreign exploration undertaken in the native range including Paraguay, Brazil, and Argentina. We conclude that N. fulva may be a suitable candidate for biological control. PMID:27983690

Development and Effectiveness of an Educational Card Game as Supplementary Material in Understanding Selected Topics in Biology

PubMed Central

Gutierrez, Arnel F.

2014-01-01

The complex concepts and vocabulary of biology classes discourage many students. In this study, a pretest–posttest model was used to test the effectiveness of an educational card game in reinforcing biological concepts in comparison with traditional teaching methods. The subjects of this study were two biology classes at Bulacan State University–Sarmiento Campus. Both classes received conventional instruction; however, the experimental group's instruction was supplemented with the card game, while the control group's instruction was reinforced with traditional exercises and assignments. The score increases from pretest to posttest showed that both methods effectively reinforced biological concepts, but a t test showed that the card game is more effective than traditional teaching methods. Additionally, students from the experimental group evaluated the card game using five criteria: goals, design, organization, playability, and usefulness. The students rated the material very satisfactory. PMID:24591506

Development and effectiveness of an educational card game as supplementary material in understanding selected topics in biology.

PubMed

Gutierrez, Arnel F

2014-01-01

The complex concepts and vocabulary of biology classes discourage many students. In this study, a pretest-posttest model was used to test the effectiveness of an educational card game in reinforcing biological concepts in comparison with traditional teaching methods. The subjects of this study were two biology classes at Bulacan State University-Sarmiento Campus. Both classes received conventional instruction; however, the experimental group's instruction was supplemented with the card game, while the control group's instruction was reinforced with traditional exercises and assignments. The score increases from pretest to posttest showed that both methods effectively reinforced biological concepts, but a t test showed that the card game is more effective than traditional teaching methods. Additionally, students from the experimental group evaluated the card game using five criteria: goals, design, organization, playability, and usefulness. The students rated the material very satisfactory.

Microbial-enzymatic-hybrid biological fuel cell with optimized growth conditions for Shewanella oneidensis DSP-10.

PubMed

Roy, Jared N; Luckarift, Heather R; Sizemore, Susan R; Farrington, Karen E; Lau, Carolin; Johnson, Glenn R; Atanassov, Plamen

2013-07-10

In this work we present a biological fuel cell fabricated by combining a Shewanella oneidensis microbial anode and a laccase-modified air-breathing cathode. This concept is devised as an extension to traditional biochemical methods by incorporating diverse biological catalysts with the aim of powering small devices. In preparing the biological fuel cell anode, novel hierarchical-structured architectures and biofilm configurations were investigated. A method for creating an artificial biofilm based on encapsulating microorganisms in a porous, thin film of silica was compared with S. oneidensis biofilms that were allowed to colonize naturally. Results indicate comparable current and power densities for artificial and natural biofilm formations, based on growth characteristics. As a result, this work describes methods for creating controllable and reproducible bio-anodes and demonstrates the versatility of hybrid biological fuel cells. Copyright © 2013 Elsevier Inc. All rights reserved.

Integrative Utilization of Microenvironments, Biomaterials and Computational Techniques for Advanced Tissue Engineering.

PubMed

Shamloo, Amir; Mohammadaliha, Negar; Mohseni, Mina

2015-10-20

This review aims to propose the integrative implementation of microfluidic devices, biomaterials, and computational methods that can lead to a significant progress in tissue engineering and regenerative medicine researches. Simultaneous implementation of multiple techniques can be very helpful in addressing biological processes. Providing controllable biochemical and biomechanical cues within artificial extracellular matrix similar to in vivo conditions is crucial in tissue engineering and regenerative medicine researches. Microfluidic devices provide precise spatial and temporal control over cell microenvironment. Moreover, generation of accurate and controllable spatial and temporal gradients of biochemical factors is attainable inside microdevices. Since biomaterials with tunable properties are a worthwhile option to construct artificial extracellular matrix, in vitro platforms that simultaneously utilize natural, synthetic, or engineered biomaterials inside microfluidic devices are phenomenally advantageous to experimental studies in the field of tissue engineering. Additionally, collaboration between experimental and computational methods is a useful way to predict and understand mechanisms responsible for complex biological phenomena. Computational results can be verified by using experimental platforms. Computational methods can also broaden the understanding of the mechanisms behind the biological phenomena observed during experiments. Furthermore, computational methods are powerful tools to optimize the fabrication of microfluidic devices and biomaterials with specific features. Here we present a succinct review of the benefits of microfluidic devices, biomaterial, and computational methods in the case of tissue engineering and regeneration medicine. Furthermore, some breakthroughs in biological phenomena including the neuronal axon development, cancerous cell migration and blood vessel formation via angiogenesis by virtue of the aforementioned approaches are discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

Black Carp: Biological synopsis and risk assessment of an introduced fish

USGS Publications Warehouse

Nico, L.G.; Williams, J.D.; Jelks, H.L.

2005-01-01

Major subjects addressed are (1) taxonomy, description, and distinguishing characteristics of the species; (2) native distribution; (3) biology and natural history, with emphasis on diet and reproduction; (4) history of the species in world aquaculture; (5) history of introduction within and outside the United States; (6) use as a biological control control agent, including a review of digenetic trematodes and snail-borne parasites of special concern and methods used for control; (7) alternatives to the use of black carp; (8) environmental tolerance and potential geographic range; and (9) risks associated with its introduction. The book also includes substantial information on the other Chinese carp species, including bighead carp, silver carp, and grass carp.

Centrifuge-operated specimen staining method and apparatus

NASA Technical Reports Server (NTRS)

Feeback, Daniel L. (Inventor); Clarke, Mark S. F. (Inventor)

1999-01-01

A method of staining preselected, mounted specimens of either biological or nonbiological material enclosed within a staining chamber where the liquid staining reagents are applied and removed from the staining chamber using hypergravity as the propelling force. In the preferred embodiment, a spacecraft-operated centrifuge and method of diagnosing biological specimens while in orbit, characterized by hermetically sealing a shell assembly. The assembly contains slide stain apparatus with computer control therefor, the operative effect of which is to overcome microgravity, for example on board an International Space Station.

Mutual information estimation reveals global associations between stimuli and biological processes

PubMed Central

Suzuki, Taiji; Sugiyama, Masashi; Kanamori, Takafumi; Sese, Jun

2009-01-01

Background Although microarray gene expression analysis has become popular, it remains difficult to interpret the biological changes caused by stimuli or variation of conditions. Clustering of genes and associating each group with biological functions are often used methods. However, such methods only detect partial changes within cell processes. Herein, we propose a method for discovering global changes within a cell by associating observed conditions of gene expression with gene functions. Results To elucidate the association, we introduce a novel feature selection method called Least-Squares Mutual Information (LSMI), which computes mutual information without density estimaion, and therefore LSMI can detect nonlinear associations within a cell. We demonstrate the effectiveness of LSMI through comparison with existing methods. The results of the application to yeast microarray datasets reveal that non-natural stimuli affect various biological processes, whereas others are no significant relation to specific cell processes. Furthermore, we discover that biological processes can be categorized into four types according to the responses of various stimuli: DNA/RNA metabolism, gene expression, protein metabolism, and protein localization. Conclusion We proposed a novel feature selection method called LSMI, and applied LSMI to mining the association between conditions of yeast and biological processes through microarray datasets. In fact, LSMI allows us to elucidate the global organization of cellular process control. PMID:19208155

Biological control of livestock pests: Pathogens

USDA-ARS?s Scientific Manuscript database

Interest in biological methods for livestock and poultry pest management is largely motivated by the development of resistance to most of the available synthetic pesticides by the major pests. There also has been a marked increase in organic systems, and those that promote animal welfare by reducing...

10 CFR 851.21 - Hazard identification and assessment.

Code of Federal Regulations, 2012 CFR

2012-01-01

.... Procedures must include methods to: (1) Assess worker exposure to chemical, physical, biological, or safety..., biological, and safety workplace hazards using recognized exposure assessment and testing methodologies and... hazards and the established controls within 90 days after identifying such hazards. The Head of DOE Field...

10 CFR 851.21 - Hazard identification and assessment.

Code of Federal Regulations, 2010 CFR

2010-01-01

.... Procedures must include methods to: (1) Assess worker exposure to chemical, physical, biological, or safety..., biological, and safety workplace hazards using recognized exposure assessment and testing methodologies and... hazards and the established controls within 90 days after identifying such hazards. The Head of DOE Field...

10 CFR 851.21 - Hazard identification and assessment.

Code of Federal Regulations, 2011 CFR

2011-01-01

.... Procedures must include methods to: (1) Assess worker exposure to chemical, physical, biological, or safety..., biological, and safety workplace hazards using recognized exposure assessment and testing methodologies and... hazards and the established controls within 90 days after identifying such hazards. The Head of DOE Field...

Constrained target controllability of complex networks

NASA Astrophysics Data System (ADS)

Guo, Wei-Feng; Zhang, Shao-Wu; Wei, Ze-Gang; Zeng, Tao; Liu, Fei; Zhang, Jingsong; Wu, Fang-Xiang; Chen, Luonan

2017-06-01

It is of great theoretical interest and practical significance to study how to control a system by applying perturbations to only a few driver nodes. Recently, a hot topic of modern network researches is how to determine driver nodes that allow the control of an entire network. However, in practice, to control a complex network, especially a biological network, one may know not only the set of nodes which need to be controlled (i.e. target nodes), but also the set of nodes to which only control signals can be applied (i.e. constrained control nodes). Compared to the general concept of controllability, we introduce the concept of constrained target controllability (CTC) of complex networks, which concerns the ability to drive any state of target nodes to their desirable state by applying control signals to the driver nodes from the set of constrained control nodes. To efficiently investigate the CTC of complex networks, we further design a novel graph-theoretic algorithm called CTCA to estimate the ability of a given network to control targets by choosing driver nodes from the set of constrained control nodes. We extensively evaluate the CTC of numerous real complex networks. The results indicate that biological networks with a higher average degree are easier to control than biological networks with a lower average degree, while electronic networks with a lower average degree are easier to control than web networks with a higher average degree. We also show that our CTCA can more efficiently produce driver nodes for target-controlling the networks than existing state-of-the-art methods. Moreover, we use our CTCA to analyze two expert-curated bio-molecular networks and compare to other state-of-the-art methods. The results illustrate that our CTCA can efficiently identify proven drug targets and new potentials, according to the constrained controllability of those biological networks.

Meta-analysis of studies on chemical, physical and biological agents in the control of Aedes aegypti.

PubMed

Lima, Estelita Pereira; Goulart, Marília Oliveira Fonseca; Rolim Neto, Modesto Leite

2015-09-04

Aedes aegypti is a vector of international concern because it can transmit to humans three important arboviral diseases: yellow fever, dengue and chikungunya. Epidemics that are repeated year after year in a variety of urban centers indicate that there are control failures, allowing the vector to continue expanding. To identify the most effective vector control strategies and the factors that contributed to the success or failure of each strategy, we carried out a systematic review with meta-analysis of articles published in 12 databases, from 1974 to the month of December 2013. We evaluated the association between the use of whatever chemical substance, mechanical agent, biological or integrated actions against A. aegypti and the control of the vector, as measured by 10 indicators. We found 2,791 articles, but after careful selection, only 26 studies remained for analysis related to control interventions implemented in 15 countries, with 5 biological, 5 chemical, 3 mechanical and 13 integrated strategies. The comparison among all of them, indicated that the control of A. aegypti is significantly associated with the type of strategy used, and that integrated interventions consist of the most effective method for controlling A. aegypti. The most effective control method was the integrated approach, considering the influence of eco-bio-social determinants in the virus-vector-man epidemiological chain, and community involvement, starting with community empowerment as active agents of vector control.

Proteomic Methods of Detection and Quantification of Protein Toxins.

PubMed

Duracova, Miloslava; Klimentova, Jana; Fucikova, Alena; Dresler, Jiri

2018-02-28

Biological toxins are a heterogeneous group of compounds that share commonalities with biological and chemical agents. Among them, protein toxins represent a considerable, diverse set. They cover a broad range of molecular weights from less than 1000 Da to more than 150 kDa. This review aims to compare conventional detection methods of protein toxins such as in vitro bioassays with proteomic methods, including immunoassays and mass spectrometry-based techniques and their combination. Special emphasis is given to toxins falling into a group of selected agents, according to the Centers for Disease Control and Prevention, such as Staphylococcal enterotoxins , Bacillus anthracis toxins, Clostridium botulinum toxins, Clostridium perfringens epsilon toxin, ricin from Ricinus communis , Abrin from Abrus precatorius or control of trade in dual-use items in the European Union, including lesser known protein toxins such as Viscumin from Viscum album . The analysis of protein toxins and monitoring for biological threats, i.e., the deliberate spread of infectious microorganisms or toxins through water, food, or the air, requires rapid and reliable methods for the early identification of these agents.

Proteomic Methods of Detection and Quantification of Protein Toxins

PubMed Central

Klimentova, Jana; Fucikova, Alena

2018-01-01

Biological toxins are a heterogeneous group of compounds that share commonalities with biological and chemical agents. Among them, protein toxins represent a considerable, diverse set. They cover a broad range of molecular weights from less than 1000 Da to more than 150 kDa. This review aims to compare conventional detection methods of protein toxins such as in vitro bioassays with proteomic methods, including immunoassays and mass spectrometry-based techniques and their combination. Special emphasis is given to toxins falling into a group of selected agents, according to the Centers for Disease Control and Prevention, such as Staphylococcal enterotoxins, Bacillus anthracis toxins, Clostridium botulinum toxins, Clostridium perfringens epsilon toxin, ricin from Ricinus communis, Abrin from Abrus precatorius or control of trade in dual-use items in the European Union, including lesser known protein toxins such as Viscumin from Viscum album. The analysis of protein toxins and monitoring for biological threats, i.e., the deliberate spread of infectious microorganisms or toxins through water, food, or the air, requires rapid and reliable methods for the early identification of these agents. PMID:29495560

Balancing Scientific Publication and National Security Concerns: Issues for Congress

DTIC Science & Technology

2003-01-10

because of its potential relevance to biological weapons of mass destruction. Whether the current method of only using classification to limit the...terrorist groups in developing weapons of mass destruction. In 2000, researchers at the Co-operative Research Centre for the Biological Control of Pest...development of chemical, biological , or nuclear weapons is not made accessible to terrorists or countries of proliferation concern. The resolution

Aquatic Pest Control. Sale Publication 4071.

ERIC Educational Resources Information Center

Wamsley, Mary Ann, Ed.; Vermeire, Donna M., Ed.

The information in this manual applies to control of aquatic pests in recreational waters, agricultural reservoirs, ornamental ponds, coastal bays, estuaries and channels, and drinking water reservoirs. Mechanical, cultural, biological, and chemical control methods are discussed. The majority of the material is devoted to weed control in static…

Recent trends in control methods for bacterial wilt diseases caused by Ralstonia solanacearum.

PubMed

Yuliar; Nion, Yanetri Asi; Toyota, Koki

2015-01-01

Previous studies have described the development of control methods against bacterial wilt diseases caused by Ralstonia solanacearum. This review focused on recent advances in control measures, such as biological, physical, chemical, cultural, and integral measures, as well as biocontrol efficacy and suppression mechanisms. Biological control agents (BCAs) have been dominated by bacteria (90%) and fungi (10%). Avirulent strains of R. solanacearum, Pseudomonas spp., Bacillus spp., and Streptomyces spp. are well-known BCAs. New or uncommon BCAs have also been identified such as Acinetobacter sp., Burkholderia sp., and Paenibacillus sp. Inoculation methods for BCAs affect biocontrol efficacy, such as pouring or drenching soil, dipping of roots, and seed coatings. The amendment of different organic matter, such as plant residue, animal waste, and simple organic compounds, have frequently been reported to suppress bacterial wilt diseases. The combined application of BCAs and their substrates was shown to more effectively suppress bacterial wilt in the tomato. Suppression mechanisms are typically attributed to the antibacterial metabolites produced by BCAs or those present in natural products; however, the number of studies related to host resistance to the pathogen is increasing. Enhanced/modified soil microbial communities are also indirectly involved in disease suppression. New promising types of control measures include biological soil disinfection using substrates that release volatile compounds. This review described recent advances in different control measures. We focused on the importance of integrated pest management (IPM) for bacterial wilt diseases.

Recent Trends in Control Methods for Bacterial Wilt Diseases Caused by Ralstonia solanacearum

PubMed Central

Yuliar; Nion, Yanetri Asi; Toyota, Koki

2015-01-01

Previous studies have described the development of control methods against bacterial wilt diseases caused by Ralstonia solanacearum. This review focused on recent advances in control measures, such as biological, physical, chemical, cultural, and integral measures, as well as biocontrol efficacy and suppression mechanisms. Biological control agents (BCAs) have been dominated by bacteria (90%) and fungi (10%). Avirulent strains of R. solanacearum, Pseudomonas spp., Bacillus spp., and Streptomyces spp. are well-known BCAs. New or uncommon BCAs have also been identified such as Acinetobacter sp., Burkholderia sp., and Paenibacillus sp. Inoculation methods for BCAs affect biocontrol efficacy, such as pouring or drenching soil, dipping of roots, and seed coatings. The amendment of different organic matter, such as plant residue, animal waste, and simple organic compounds, have frequently been reported to suppress bacterial wilt diseases. The combined application of BCAs and their substrates was shown to more effectively suppress bacterial wilt in the tomato. Suppression mechanisms are typically attributed to the antibacterial metabolites produced by BCAs or those present in natural products; however, the number of studies related to host resistance to the pathogen is increasing. Enhanced/modified soil microbial communities are also indirectly involved in disease suppression. New promising types of control measures include biological soil disinfection using substrates that release volatile compounds. This review described recent advances in different control measures. We focused on the importance of integrated pest management (IPM) for bacterial wilt diseases. PMID:25762345

Assessing occupational exposure to sea lamprey pesticides

PubMed Central

Ceballos, Diana M; Beaucham, Catherine C; Kurtz, Kristine; Musolin, Kristin

2015-01-01

Background: Sea lampreys are parasitic fish found in lakes of the United States and Canada. Sea lamprey is controlled through manual application of the pesticides 3-trifluoromethyl-4-nitrophenol (TFM) and BayluscideTM into streams and tributaries. 3-Trifluoromethyl-4-nitrophenol may cause irritation and central nervous system depression and Bayluscide may cause irritation, dermatitis, blisters, cracking, edema, and allergic skin reactions. Objectives: To assess occupational exposures to sea lamprey pesticides. Methods: We developed a wipe method for evaluating surface and skin contamination with these pesticides. This method was field tested at a biological field station and at a pesticide river application. We also evaluated exposures using control banding tools. Results: We verified TFM surface contamination at the biological station. At the river application, we found surfaces and worker’s skin contaminated with pesticides. Conclusion: We recommended minimizing exposures by implementing engineering controls and improved use of personal protective equipment. PMID:25730600

DOE Office of Scientific and Technical Information (OSTI.GOV)

Demirag, N

Purpose: To verify the benefits of the biological cost functions. Methods: TG166 patients were used for the test case scenarios. Patients were planned using Monaco V5.0 (CMS/Elekta, St.Louis, MO) Monaco has 3 biological and 8 physical CFs. In this study the plans were optimized using 3 different scenarios. 1- Biological CFs only 2-Physical CFs only 3- Combination of Physical and Biological CFsMonaco has 3 biological CFs. Target EUD used for the targets, derived from the poisson cell kill model, has an α value that controls the cold spots inside the target. α values used in the optimization were 0.5 andmore » 0.8. if cold spots needs to be penalized α value increased. Serial CF: it's called serial to mimic the behaviour of the serial organs, if a high k value like 12 or 14 is used it controls the maximum dose. Serial CF has a k parameter that is used to shape the whole dvh curve. K value ranges between 1–20. k:1 is used to control the mean dose, lower k value controls the mean dose, higher k value controls the higher dose, using 2 serial CFs with different k values controls the whole DVH. Paralel CF controls the percentage of the volume that tolerates higher doses than the reference dose to mimic the behaviour of the paralel organs. Results: It was possible to achive clinically accepted plans in all 3 scenarios. The benefit of the biological cost functions were to control the mean dose for target and OAR, to shape the DVH curve using one EUD value and one k value simplifies the optimization process. Using the biological CFs alone, it was hard to control the dose at a point. Conclusion: Biological CFs in Monaco doesn't require the ntcp/tcp values from the labs and useful to shape the whole dvh curve. I work as an applications support specialist for Elekta and I am a Ph.D. Student in Istanbul University for radiation therapy physics.« less

Cultural and chemical pest control methods alter habitat suitability for biological control agents: An example from Wisconsin commercial cranberry

USDA-ARS?s Scientific Manuscript database

An integrated pest control program requires an in-depth understanding of the compatibility of all control strategies used. In Wisconsin commercial cranberry production, early-season control strategies may include either a broad-spectrum insecticide application or a corresponding spring flood, along ...

Estimation of Metabolism Characteristics for Heat-Injured Bacteria Using Dielectrophoretic Impedance Measurement Method

NASA Astrophysics Data System (ADS)

Amako, Eri; Enjoji, Takaharu; Uchida, Satoshi; Tochikubo, Fumiyoshi

Constant monitoring and immediate control of fermentation processes have been required for advanced quality preservation in food industry. In the present work, simple estimation of metabolic states for heat-injured Escherichia coli (E. coli) in a micro-cell was investigated using dielectrophoretic impedance measurement (DEPIM) method. Temporal change in the conductance between micro-gap (ΔG) was measured for various heat treatment temperatures. In addition, the dependence of enzyme activity, growth capacity and membrane situation for E. coli on heat treatment temperature was also analyzed with conventional biological methods. Consequently, a correlation between ΔG and those biological properties was obtained quantitatively. This result suggests that DEPIM method will be available for an effective monitoring technique for complex change in various biological states of microorganisms.

The influence of formulation on Trichoderma biological activity and frosty pod rot disease management in Theobroma cacao

USDA-ARS?s Scientific Manuscript database

Frosty pod rot (FPR), caused by Moniliophthora roreri is responsible for significant losses in Theobroma cacao. Due to the limited options for FPR management, biological control methods using Trichoderma are being studied. Combinations of three formulations and two Trichoderma isolates were studied ...

75 FR 74678 - Medicine Bow-Routt National Forests and Thunder Basin National Grassland; Colorado and Wyoming...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-01

..., mechanical, biological, and ground and aerial herbicide control methods. ``Invasive species'' are defined as... and aerial application of herbicides, mechanical, biological, and cultural weed treatments. The MBRTB... include analysis of the effects of new herbicides, new invasive plant populations, or aerial application...

Effects of biocontrol on short-term nutrient dynamics in a tamarix-invaded riparian ecosystem

USDA-ARS?s Scientific Manuscript database

Background/Question/Methods Saltcedar (Tamarix ramosissima) invasion and subsequent dominance in biologically and functionally diverse riparian ecosystems across the western U.S. has lead to release of the leaf beetle (Diorhabda elongata) as a biological control agent, and has resulted in large-sca...

Synthetic Biology: Tools to Design, Build, and Optimize Cellular Processes

PubMed Central

Young, Eric; Alper, Hal

2010-01-01

The general central dogma frames the emergent properties of life, which make biology both necessary and difficult to engineer. In a process engineering paradigm, each biological process stream and process unit is heavily influenced by regulatory interactions and interactions with the surrounding environment. Synthetic biology is developing the tools and methods that will increase control over these interactions, eventually resulting in an integrative synthetic biology that will allow ground-up cellular optimization. In this review, we attempt to contextualize the areas of synthetic biology into three tiers: (1) the process units and associated streams of the central dogma, (2) the intrinsic regulatory mechanisms, and (3) the extrinsic physical and chemical environment. Efforts at each of these three tiers attempt to control cellular systems and take advantage of emerging tools and approaches. Ultimately, it will be possible to integrate these approaches and realize the vision of integrative synthetic biology when cells are completely rewired for biotechnological goals. This review will highlight progress towards this goal as well as areas requiring further research. PMID:20150964

[The level of available methionine and the biological value of fish protein].

PubMed

Lipka, Z; Ganowiak, Z

1992-01-01

Food value of fish protein in fish canning was evaluated biologically and chemically (by available methionine). High-temperature sterilization (126 degrees) proved the least adequate for it causes the greatest loss in the protein food value. The chemical method by available methionine showing close correlation with biological techniques (NPU and PER rates) is thought demonstrative and convenient for technological control in fish processing industry.

Review of Detection of Brucella sp. by Polymerase Chain Reaction

PubMed Central

Yu, Wei Ling; Nielsen, Klaus

2010-01-01

Here we present a review of most of the currently used polymerase chain reaction (PCR)-based methods for identification of Brucella bacteria in biological samples. We focused in particular on methods using single-pair primers, multiplex primers, real-time PCRs, PCRs for marine Brucella, and PCRs for molecular biotyping. These methods are becoming very important tools for the identification of Brucella, at the species level and recently also at the biovar level. These techniques require minimum biological containment and can provide results in a very short time. In addition, genetic fingerprinting of isolates aid in epidemiological studies of the disease and its control. PCR-based methods are more useful and practical than conventional methods used to identify Brucella spp., and new methods for Brucella spp identification and typing are still being developed. However, the sensitivity, specificity, and issues of quality control and quality assurance using these methods must be fully validated on clinical samples before PCR can be used in routine laboratory testing for brucellosis. PMID:20718083

Pathway analysis from lists of microRNAs: common pitfalls and alternative strategy

PubMed Central

Godard, Patrice; van Eyll, Jonathan

2015-01-01

MicroRNAs (miRNAs) are involved in the regulation of gene expression at a post-transcriptional level. As such, monitoring miRNA expression has been increasingly used to assess their role in regulatory mechanisms of biological processes. In large scale studies, once miRNAs of interest have been identified, the target genes they regulate are often inferred using algorithms or databases. A pathway analysis is then often performed in order to generate hypotheses about the relevant biological functions controlled by the miRNA signature. Here we show that the method widely used in scientific literature to identify these pathways is biased and leads to inaccurate results. In addition to describing the bias and its origin we present an alternative strategy to identify potential biological functions specifically impacted by a miRNA signature. More generally, our study exemplifies the crucial need of relevant negative controls when developing, and using, bioinformatics methods. PMID:25800743

Biological optimization systems for enhancing photosynthetic efficiency and methods of use

DOEpatents

Hunt, Ryan W.; Chinnasamy, Senthil; Das, Keshav C.; de Mattos, Erico Rolim

2012-11-06

Biological optimization systems for enhancing photosynthetic efficiency and methods of use. Specifically, methods for enhancing photosynthetic efficiency including applying pulsed light to a photosynthetic organism, using a chlorophyll fluorescence feedback control system to determine one or more photosynthetic efficiency parameters, and adjusting one or more of the photosynthetic efficiency parameters to drive the photosynthesis by the delivery of an amount of light to optimize light absorption of the photosynthetic organism while providing enough dark time between light pulses to prevent oversaturation of the chlorophyll reaction centers are disclosed.

End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Linshiz, Gregory; Jensen, Erik; Stawski, Nina

Synthetic biology aims to engineer biological systems for desired behaviors. The construction of these systems can be complex, often requiring genetic reprogramming, extensive de novo DNA synthesis, and functional screening. Here, we present a programmable, multipurpose microfluidic platform and associated software and apply the platform to major steps of the synthetic biology research cycle: design, construction, testing, and analysis. We show the platform’s capabilities for multiple automated DNA assembly methods, including a new method for Isothermal Hierarchical DNA Construction, and for Escherichia coli and Saccharomyces cerevisiae transformation. The platform enables the automated control of cellular growth, gene expression induction, andmore » proteogenic and metabolic output analysis. Finally, taken together, we demonstrate the microfluidic platform’s potential to provide end-to-end solutions for synthetic biology research, from design to functional analysis.« less

End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis

DOE PAGES

Linshiz, Gregory; Jensen, Erik; Stawski, Nina; ...

2016-02-02

Synthetic biology aims to engineer biological systems for desired behaviors. The construction of these systems can be complex, often requiring genetic reprogramming, extensive de novo DNA synthesis, and functional screening. Here, we present a programmable, multipurpose microfluidic platform and associated software and apply the platform to major steps of the synthetic biology research cycle: design, construction, testing, and analysis. We show the platform’s capabilities for multiple automated DNA assembly methods, including a new method for Isothermal Hierarchical DNA Construction, and for Escherichia coli and Saccharomyces cerevisiae transformation. The platform enables the automated control of cellular growth, gene expression induction, andmore » proteogenic and metabolic output analysis. Finally, taken together, we demonstrate the microfluidic platform’s potential to provide end-to-end solutions for synthetic biology research, from design to functional analysis.« less

Survey of current and emerging technologies for biological contamination control

NASA Astrophysics Data System (ADS)

Frick, Andreas; Mogul, Rakesh

2012-07-01

This study will survey current and emerging technologies for biological contamination control within the context of planetary protection. Using a systems analysis approach, our objective is to compare various implementation variables across tasks ranging from surface cleaning to full-system sterilization for spacecraft and spacecraft components. Methods reviewed include vapor-phase hydrogen peroxide, plasma-phase sterilants such as oxygen and hydrogen peroxide, dry heat, laser-based techniques, supercritical carbon dioxide-based methods, and advanced bio-barriers. These methods will be evaluated in relation to relevant mission architectures and will address aspects of sample return missions. Results from this study, therefore, will offer new insights into the present-day engineering capabilities and future developmental concerns for missions targeting icy satellites, Mars, and other locations of astrochemical and astrobiological significance.

The role of evolutionary biology in research and control of liver flukes in Southeast Asia.

PubMed

Echaubard, Pierre; Sripa, Banchob; Mallory, Frank F; Wilcox, Bruce A

2016-09-01

Stimulated largely by the availability of new technology, biomedical research at the molecular-level and chemical-based control approaches arguably dominate the field of infectious diseases. Along with this, the proximate view of disease etiology predominates to the exclusion of the ultimate, evolutionary biology-based, causation perspective. Yet, historically and up to today, research in evolutionary biology has provided much of the foundation for understanding the mechanisms underlying disease transmission dynamics, virulence, and the design of effective integrated control strategies. Here we review the state of knowledge regarding the biology of Asian liver Fluke-host relationship, parasitology, phylodynamics, drug-based interventions and liver Fluke-related cancer etiology from an evolutionary biology perspective. We consider how evolutionary principles, mechanisms and research methods could help refine our understanding of clinical disease associated with infection by Liver Flukes as well as their transmission dynamics. We identify a series of questions for an evolutionary biology research agenda for the liver Fluke that should contribute to an increased understanding of liver Fluke-associated diseases. Finally, we describe an integrative evolutionary medicine approach to liver Fluke prevention and control highlighting the need to better contextualize interventions within a broader human health and sustainable development framework. Copyright © 2016 Elsevier B.V. All rights reserved.

The Role of Evolutionary Biology in Research and Control of Liver Flukes in Southeast Asia

PubMed Central

Echaubard, Pierre; Sripa, Banchob; Mallory, Frank F.; Wilcox, Bruce A.

2016-01-01

Stimulated largely by the availability of new technology, biomedical research at the molecular-level and chemical-based control approaches arguably dominate the field of infectious diseases. Along with this, the proximate view of disease etiology predominates to the exclusion of the ultimate, evolutionary biology-based, causation perspective. Yet, historically and up to today, research in evolutionary biology has provided much of the foundation for understanding the mechanisms underlying disease transmission dynamics, virulence, and the design of effective integrated control strategies. Here we review the state of knowledge regarding the biology of Asian liver Fluke-host relationship, parasitology, phylodynamics, drug-based interventions and liver Fluke-related cancer etiology from an evolutionary biology perspective. We consider how evolutionary principles, mechanisms and research methods could help refine our understanding of clinical disease associated with infection by Liver Flukes as well as their transmission dynamics. We identify a series of questions for an evolutionary biology research agenda for the liver Fluke that should contribute to an increased understanding of liver Fluke-associated diseases. Finally, we describe an integrative evolutionary medicine approach to liver Fluke prevention and control highlighting the need to better contextualize interventions within a broader human health and sustainable development framework. PMID:27197053

Recent advances in detection and control of infectious hematopoietic necrosis virus in aquaculture

USGS Publications Warehouse

Winton, James R.

1991-01-01

Infectious hematopoietic necrosis (IHN) is one of the most important viral diseases of salmon and trout reared in culture. The disease remains untreatable with avoidance being the only control measure. Much has been learned about the chemical, physical, and serological characteristics of the rhabdovirus causing IHN, but critical gaps exist in our understanding of the biology of the virus in nature. The tools of molecular biology have provided improved methods for detection of pathogens and new strategies for control of viral diseases. This paper reviews several recent improvements in methods for detecting infectious hematopoietic necrosis virus including the application of enzyme-linked immunosorbent assays, development of monoclonal antibodies and DNA probes, and use of the polymerase chain reaction. New strategies for control of IHN through the use of better water treatment, more resistant fish, antiviral drugs or chemicals, and new generation vaccines are discussed.

Sensitivity analysis of dynamic biological systems with time-delays.

PubMed

Wu, Wu Hsiung; Wang, Feng Sheng; Chang, Maw Shang

2010-10-15

Mathematical modeling has been applied to the study and analysis of complex biological systems for a long time. Some processes in biological systems, such as the gene expression and feedback control in signal transduction networks, involve a time delay. These systems are represented as delay differential equation (DDE) models. Numerical sensitivity analysis of a DDE model by the direct method requires the solutions of model and sensitivity equations with time-delays. The major effort is the computation of Jacobian matrix when computing the solution of sensitivity equations. The computation of partial derivatives of complex equations either by the analytic method or by symbolic manipulation is time consuming, inconvenient, and prone to introduce human errors. To address this problem, an automatic approach to obtain the derivatives of complex functions efficiently and accurately is necessary. We have proposed an efficient algorithm with an adaptive step size control to compute the solution and dynamic sensitivities of biological systems described by ordinal differential equations (ODEs). The adaptive direct-decoupled algorithm is extended to solve the solution and dynamic sensitivities of time-delay systems describing by DDEs. To save the human effort and avoid the human errors in the computation of partial derivatives, an automatic differentiation technique is embedded in the extended algorithm to evaluate the Jacobian matrix. The extended algorithm is implemented and applied to two realistic models with time-delays: the cardiovascular control system and the TNF-α signal transduction network. The results show that the extended algorithm is a good tool for dynamic sensitivity analysis on DDE models with less user intervention. By comparing with direct-coupled methods in theory, the extended algorithm is efficient, accurate, and easy to use for end users without programming background to do dynamic sensitivity analysis on complex biological systems with time-delays.

Neural Correlates of Coherent and Biological Motion Perception in Autism

ERIC Educational Resources Information Center

Koldewyn, Kami; Whitney, David; Rivera, Susan M.

2011-01-01

Recent evidence suggests those with autism may be generally impaired in visual motion perception. To examine this, we investigated both coherent and biological motion processing in adolescents with autism employing both psychophysical and fMRI methods. Those with autism performed as well as matched controls during coherent motion perception but…

An improved method to quantitate mature plant microRNA in biological matrices using periodate treatment and internal control

USDA-ARS?s Scientific Manuscript database

MicroRNAs (miRNAs) ubiquitously exist in microorganisms, plants and animals, and appear to modulate a wide range of critical biological processes. However, no definitive conclusion has been reached regarding the uptake of exogenous dietary small RNAs into mammalian circulation and organs and cross-k...

Coccinellids and the Modern Pest Management

ERIC Educational Resources Information Center

Hodek, Ivo

1970-01-01

Discusses the concept of integrated pest control combining chemical and biological methods. Describes many examples of the successful use of coccinellids beetles to control other insects. Cites ecological and physiological research studies related to predator prey relationships involving coccinellids. (EB)

Application of laser chaos control methods to controlling thyroid-catatonic oscillations and burst firing of dopamine neurons

NASA Astrophysics Data System (ADS)

Duong-van, Minh

1993-11-01

A method of controlling chaotic to laminar flows in the Lorenz equations using fixed points dictated by minimizing the Lyapunov functional was proposed by Singer, Wang and Bau. Using different fixed points, we find that the solutions in a chaotic regime can also be periodic. Since the lasers equations are isomorphic to the Lorenz equations, we use this new method to control chaos when the laser is operated over the pump threshold. Furthermore, by solving the laser equations with an occasional proportional feedback mechanism, we recover the essential lasers controlling features experimentally discovered by Roy, Murphy, Jr., Maier, Gills and Hunt. This method of control chaos is now extended to various medical and biological systems.

Control theory meets synthetic biology

PubMed Central

2016-01-01

The past several years have witnessed an increased presence of control theoretic concepts in synthetic biology. This review presents an organized summary of how these control design concepts have been applied to tackle a variety of problems faced when building synthetic biomolecular circuits in living cells. In particular, we describe success stories that demonstrate how simple or more elaborate control design methods can be used to make the behaviour of synthetic genetic circuits within a single cell or across a cell population more reliable, predictable and robust to perturbations. The description especially highlights technical challenges that uniquely arise from the need to implement control designs within a new hardware setting, along with implemented or proposed solutions. Some engineering solutions employing complex feedback control schemes are also described, which, however, still require a deeper theoretical analysis of stability, performance and robustness properties. Overall, this paper should help synthetic biologists become familiar with feedback control concepts as they can be used in their application area. At the same time, it should provide some domain knowledge to control theorists who wish to enter the rising and exciting field of synthetic biology. PMID:27440256

Control theory meets synthetic biology.

PubMed

Del Vecchio, Domitilla; Dy, Aaron J; Qian, Yili

2016-07-01

The past several years have witnessed an increased presence of control theoretic concepts in synthetic biology. This review presents an organized summary of how these control design concepts have been applied to tackle a variety of problems faced when building synthetic biomolecular circuits in living cells. In particular, we describe success stories that demonstrate how simple or more elaborate control design methods can be used to make the behaviour of synthetic genetic circuits within a single cell or across a cell population more reliable, predictable and robust to perturbations. The description especially highlights technical challenges that uniquely arise from the need to implement control designs within a new hardware setting, along with implemented or proposed solutions. Some engineering solutions employing complex feedback control schemes are also described, which, however, still require a deeper theoretical analysis of stability, performance and robustness properties. Overall, this paper should help synthetic biologists become familiar with feedback control concepts as they can be used in their application area. At the same time, it should provide some domain knowledge to control theorists who wish to enter the rising and exciting field of synthetic biology. © 2016 The Author(s).

Non-woody weed control in pine plantations

Treesearch

Phillip M. Dougherty; Bob Lowery

1986-01-01

The cost and benefits derived from controlling non-woody competitors in pine planations were reviewed. Cost considerations included both the capital cost and biological cost that may be incurred when weed control treatments are applied. Several methods for reducing the cost of herbicide treatments were explored. Cost reduction considerations included adjustments in...

Neural correlates of coherent and biological motion perception in autism.

PubMed

Koldewyn, Kami; Whitney, David; Rivera, Susan M

2011-09-01

Recent evidence suggests those with autism may be generally impaired in visual motion perception. To examine this, we investigated both coherent and biological motion processing in adolescents with autism employing both psychophysical and fMRI methods. Those with autism performed as well as matched controls during coherent motion perception but had significantly higher thresholds for biological motion perception. The autism group showed reduced posterior Superior Temporal Sulcus (pSTS), parietal and frontal activity during a biological motion task while showing similar levels of activity in MT+/V5 during both coherent and biological motion trials. Activity in MT+/V5 was predictive of individual coherent motion thresholds in both groups. Activity in dorsolateral prefrontal cortex (DLPFC) and pSTS was predictive of biological motion thresholds in control participants but not in those with autism. Notably, however, activity in DLPFC was negatively related to autism symptom severity. These results suggest that impairments in higher-order social or attentional networks may underlie visual motion deficits observed in autism. © 2011 Blackwell Publishing Ltd.

Neural correlates of coherent and biological motion perception in autism

PubMed Central

Koldewyn, Kami; Whitney, David; Rivera, Susan M.

2011-01-01

Recent evidence suggests those with autism may be generally impaired in visual motion perception. To examine this, we investigated both coherent and biological motion processing in adolescents with autism employing both psychophysical and fMRI methods. Those with autism performed as well as matched controls during coherent motion perception but had significantly higher thresholds for biological motion perception. The autism group showed reduced posterior Superior Temporal Sulcus (pSTS), parietal and frontal activity during a biological motion task while showing similar levels of activity in MT+/V5 during both coherent and biological motion trials. Activity in MT+/V5 was predictive of individual coherent motion thresholds in both groups. Activity in dorsolateral prefrontal cortex (DLPFC) and pSTS was predictive of biological motion thresholds in control participants but not in those with autism. Notably, however, activity in DLPFC was negatively related to autism symptom severity. These results suggest that impairments in higher-order social or attentional networks may underlie visual motion deficits observed in autism. PMID:21884323

Bio-hybrid cell-based actuators for microsystems.

PubMed

Carlsen, Rika Wright; Sitti, Metin

2014-10-15

As we move towards the miniaturization of devices to perform tasks at the nano and microscale, it has become increasingly important to develop new methods for actuation, sensing, and control. Over the past decade, bio-hybrid methods have been investigated as a promising new approach to overcome the challenges of scaling down robotic and other functional devices. These methods integrate biological cells with artificial components and therefore, can take advantage of the intrinsic actuation and sensing functionalities of biological cells. Here, the recent advancements in bio-hybrid actuation are reviewed, and the challenges associated with the design, fabrication, and control of bio-hybrid microsystems are discussed. As a case study, focus is put on the development of bacteria-driven microswimmers, which has been investigated as a targeted drug delivery carrier. Finally, a future outlook for the development of these systems is provided. The continued integration of biological and artificial components is envisioned to enable the performance of tasks at a smaller and smaller scale in the future, leading to the parallel and distributed operation of functional systems at the microscale. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biologically Based Methods for Pest Management in Agriculture under Changing Climates: Challenges and Future Directions.

PubMed

Chidawanyika, Frank; Mudavanhu, Pride; Nyamukondiwa, Casper

2012-11-09

The current changes in global climatic regimes present a significant societal challenge, affecting in all likelihood insect physiology, biochemistry, biogeography and population dynamics. With the increasing resistance of many insect pest species to chemical insecticides and an increasing organic food market, pest control strategies are slowly shifting towards more sustainable, ecologically sound and economically viable options. Biologically based pest management strategies present such opportunities through predation or parasitism of pests and plant direct or indirect defense mechanisms that can all be important components of sustainable integrated pest management programs. Inevitably, the efficacy of biological control systems is highly dependent on natural enemy-prey interactions, which will likely be modified by changing climates. Therefore, knowledge of how insect pests and their natural enemies respond to climate variation is of fundamental importance in understanding biological insect pest management under global climate change. Here, we discuss biological control, its challenges under climate change scenarios and how increased global temperatures will require adaptive management strategies to cope with changing status of insects and their natural enemies.

Statistical Selection of Biological Models for Genome-Wide Association Analyses.

PubMed

Bi, Wenjian; Kang, Guolian; Pounds, Stanley B

2018-05-24

Genome-wide association studies have discovered many biologically important associations of genes with phenotypes. Typically, genome-wide association analyses formally test the association of each genetic feature (SNP, CNV, etc) with the phenotype of interest and summarize the results with multiplicity-adjusted p-values. However, very small p-values only provide evidence against the null hypothesis of no association without indicating which biological model best explains the observed data. Correctly identifying a specific biological model may improve the scientific interpretation and can be used to more effectively select and design a follow-up validation study. Thus, statistical methodology to identify the correct biological model for a particular genotype-phenotype association can be very useful to investigators. Here, we propose a general statistical method to summarize how accurately each of five biological models (null, additive, dominant, recessive, co-dominant) represents the data observed for each variant in a GWAS study. We show that the new method stringently controls the false discovery rate and asymptotically selects the correct biological model. Simulations of two-stage discovery-validation studies show that the new method has these properties and that its validation power is similar to or exceeds that of simple methods that use the same statistical model for all SNPs. Example analyses of three data sets also highlight these advantages of the new method. An R package is freely available at www.stjuderesearch.org/site/depts/biostats/maew. Copyright © 2018. Published by Elsevier Inc.

Recombinant entomopathogenic agents: a review of biotechnological approaches to pest insect control.

PubMed

Karabörklü, Salih; Azizoglu, Ugur; Azizoglu, Zehra Busra

2017-12-18

Although the use of chemical pesticides has decreased in recent years, it is still a common method of pest control. However, chemical use leads to challenging problems. The harm caused by these chemicals and the length of time that they will remain in the environment is of great concern to the future and safety of humans. Therefore, developing new pest control agents that are safer and environmentally compatible, as well as assuring their widespread use is important. Entomopathogenic agents are microorganisms that play an important role in the biological control of pest insects and are eco-friendly alternatives to chemical control. They consist of viruses (non-cellular organisms), bacteria (prokaryotic organisms), fungi and protists (eukaryotic organisms), and nematodes (multicellular organisms). Genetic modification (recombinant technology) provides potential new methods for developing entomopathogens to manage pests. In this review, we focus on the important roles of recombinant entomopathogens in terms of pest insect control, placing them into perspective with other views to discuss, examine and evaluate the use of entomopathogenic agents in biological control.

Assessing occupational exposure to sea lamprey pesticides.

PubMed

Ceballos, Diana M; Beaucham, Catherine C; Kurtz, Kristine; Musolin, Kristin

2015-01-01

Sea lampreys are parasitic fish found in lakes of the United States and Canada. Sea lamprey is controlled through manual application of the pesticides 3-trifluoromethyl-4-nitrophenol (TFM) and Bayluscide(TM) into streams and tributaries. 3-Trifluoromethyl-4-nitrophenol may cause irritation and central nervous system depression and Bayluscide may cause irritation, dermatitis, blisters, cracking, edema, and allergic skin reactions. To assess occupational exposures to sea lamprey pesticides. We developed a wipe method for evaluating surface and skin contamination with these pesticides. This method was field tested at a biological field station and at a pesticide river application. We also evaluated exposures using control banding tools. We verified TFM surface contamination at the biological station. At the river application, we found surfaces and worker's skin contaminated with pesticides. We recommended minimizing exposures by implementing engineering controls and improved use of personal protective equipment.

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

PubMed

Fischbein, D; Corley, J C

2015-02-01

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

Transport of Bacillus thuringiensis var. kurstaki from an outdoor release into buildings: pathways of infiltration and a rapid method to identify contaminated buildings.

PubMed

Van Cuyk, Sheila; Deshpande, Alina; Hollander, Attelia; Franco, David O; Teclemariam, Nerayo P; Layshock, Julie A; Ticknor, Lawrence O; Brown, Michael J; Omberg, Kristin M

2012-06-01

Understanding the fate and transport of biological agents into buildings will be critical to recovery and restoration efforts after a biological attack in an urban area. As part of the Interagency Biological Restoration Demonstration (IBRD), experiments were conducted in Fairfax County, VA, to study whether a biological agent can be expected to infiltrate into buildings following a wide-area release. Bacillus thuringiensis var. kurstaki is a common organic pesticide that has been sprayed in Fairfax County for a number of years to control the gypsy moth. Because the bacterium shares many physical and biological properties with Bacillus anthracis, the results from these studies can be extrapolated to a bioterrorist release. In 2009, samples were collected from inside buildings located immediately adjacent to a spray block. A combined probabilistic and targeted sampling strategy and modeling were conducted to provide insight into likely methods of infiltration. Both the simulations and the experimental results indicate sampling entryways and heating, ventilation, and air conditioning (HVAC) filters are reasonable methods for "ruling in" a building as contaminated. Following a biological attack, this method is likely to provide significant savings in time and labor compared to more rigorous, statistically based characterization. However, this method should never be used to "rule out," or clear, a building.

Recommendations for accreditation of laboratories in molecular biology of hematologic malignancies.

PubMed

Flandrin-Gresta, Pascale; Cornillet, Pascale; Hayette, Sandrine; Gachard, Nathalie; Tondeur, Sylvie; Mauté, Carole; Cayuela, Jean-Michel

2015-01-01

Over recent years, the development of molecular biology techniques has improved the hematological diseases diagnostic and follow-up. Consequently, these techniques are largely used in the biological screening of these diseases; therefore the Hemato-oncology molecular diagnostics laboratories must be actively involved in the accreditation process according the ISO 15189 standard. The French group of molecular biologists (GBMHM) provides requirements for the implementation of quality assurance for the medical molecular laboratories. This guideline states the recommendations for the pre-analytical, analytical (methods validation procedures, quality controls, reagents), and post-analytical conditions. In addition, herein we state a strategy for the internal quality control management. These recommendations will be regularly updated.

The Florey lecture, 1983. Biological control, as exemplified by smallpox eradication and myxomatosis.

PubMed

Fenner, F

1983-06-22

Biological control is an important method of dealing with plant and insect pests. The control of rabbits by myxomatosis and the eradication of smallpox by vaccination are unusual examples of biological control, in that they involve a vertebrate and a viral pest respectively. Myxomatosis is a benign disease in Sylvilagus rabbits in South America which is transmitted mechanically by mosquitoes. In the European rabbit, Oryctolagus, which is a pest in Australia and England, the virus from Sylvilagus produces a generalized disease that is almost always lethal. Myxomatosis was deliberately introduced into Australia in 1950 and into Europe in 1952. It was at first spectacularly successful in controlling the rabbit pest, but biological adjustments occurred in the virulence of the virus and the genetic resistances of rabbits. After 30 years of interaction, natural selection has resulted in a balance at a fairly high level of viral virulence. Smallpox has been a major scourge of mankind for over 1500 years. It spread from Asia to Europe in the Middle ages and from Europe to Africa and the Americas in the 15th and 16th centuries. Jenner's cowpox vaccine provided a method of control that reduced the severity of the disease during the 19th century but failed to eliminate the disease from many countries before the 1930s. Thereafter it was eradicated from Europe and North America, but remained endemic in South America, Africa and Asia. In 1967 it was still endemic in 33 countries and W.H.O. established a programme for global eradication within 10 years. The goal was achieved in 1977. Problems of the eradication programme and reasons for its success will be described.

Programmable chemical controllers made from DNA.

PubMed

Chen, Yuan-Jyue; Dalchau, Neil; Srinivas, Niranjan; Phillips, Andrew; Cardelli, Luca; Soloveichik, David; Seelig, Georg

2013-10-01

Biological organisms use complex molecular networks to navigate their environment and regulate their internal state. The development of synthetic systems with similar capabilities could lead to applications such as smart therapeutics or fabrication methods based on self-organization. To achieve this, molecular control circuits need to be engineered to perform integrated sensing, computation and actuation. Here we report a DNA-based technology for implementing the computational core of such controllers. We use the formalism of chemical reaction networks as a 'programming language' and our DNA architecture can, in principle, implement any behaviour that can be mathematically expressed as such. Unlike logic circuits, our formulation naturally allows complex signal processing of intrinsically analogue biological and chemical inputs. Controller components can be derived from biologically synthesized (plasmid) DNA, which reduces errors associated with chemically synthesized DNA. We implement several building-block reaction types and then combine them into a network that realizes, at the molecular level, an algorithm used in distributed control systems for achieving consensus between multiple agents.

Programmable chemical controllers made from DNA

NASA Astrophysics Data System (ADS)

Chen, Yuan-Jyue; Dalchau, Neil; Srinivas, Niranjan; Phillips, Andrew; Cardelli, Luca; Soloveichik, David; Seelig, Georg

2013-10-01

Biological organisms use complex molecular networks to navigate their environment and regulate their internal state. The development of synthetic systems with similar capabilities could lead to applications such as smart therapeutics or fabrication methods based on self-organization. To achieve this, molecular control circuits need to be engineered to perform integrated sensing, computation and actuation. Here we report a DNA-based technology for implementing the computational core of such controllers. We use the formalism of chemical reaction networks as a 'programming language' and our DNA architecture can, in principle, implement any behaviour that can be mathematically expressed as such. Unlike logic circuits, our formulation naturally allows complex signal processing of intrinsically analogue biological and chemical inputs. Controller components can be derived from biologically synthesized (plasmid) DNA, which reduces errors associated with chemically synthesized DNA. We implement several building-block reaction types and then combine them into a network that realizes, at the molecular level, an algorithm used in distributed control systems for achieving consensus between multiple agents.

Programmable chemical controllers made from DNA

PubMed Central

Chen, Yuan-Jyue; Dalchau, Neil; Srinivas, Niranjan; Phillips, Andrew; Cardelli, Luca; Soloveichik, David; Seelig, Georg

2014-01-01

Biological organisms use complex molecular networks to navigate their environment and regulate their internal state. The development of synthetic systems with similar capabilities could lead to applications such as smart therapeutics or fabrication methods based on self-organization. To achieve this, molecular control circuits need to be engineered to perform integrated sensing, computation and actuation. Here we report a DNA-based technology for implementing the computational core of such controllers. We use the formalism of chemical reaction networks as a 'programming language', and our DNA architecture can, in principle, implement any behaviour that can be mathematically expressed as such. Unlike logic circuits, our formulation naturally allows complex signal processing of intrinsically analogue biological and chemical inputs. Controller components can be derived from biologically synthesized (plasmid) DNA, which reduces errors associated with chemically synthesized DNA. We implement several building-block reaction types and then combine them into a network that realizes, at the molecular level, an algorithm used in distributed control systems for achieving consensus between multiple agents. PMID:24077029

Elemental Analysis in Biological Matrices Using ICP-MS.

PubMed

Hansen, Matthew N; Clogston, Jeffrey D

2018-01-01

The increasing exploration of metallic nanoparticles for use as cancer therapeutic agents necessitates a sensitive technique to track the clearance and distribution of the material once introduced into a living system. Inductively coupled plasma mass spectrometry (ICP-MS) provides a sensitive and selective tool for tracking the distribution of metal components from these nanotherapeutics. This chapter presents a standardized method for processing biological matrices, ensuring complete homogenization of tissues, and outlines the preparation of appropriate standards and controls. The method described herein utilized gold nanoparticle-treated samples; however, the method can easily be applied to the analysis of other metals.

Determination of Trace Level Iodine in Biological and Botanical Reference Materials by Isotope Dilution Mass Spectrometry

PubMed Central

Gramlich, John W.; Murphy, Thomas J.

1989-01-01

A method has been developed for the determination of trace level iodine in biological and botanical materials. The method consists of spiking a sample with 129I, equilibration of the spike with the natural iodine, wet ashing under carefully controlled conditions, and separation of the iodine by co-precipitation with silver chloride. Measurement of the 129I/127I ratio is accomplished by negative thermal ionization mass spectrometry using LaB6 for ionization enhancement. The application of the method to the certification of trace iodine in two Standard Reference Materials is described. PMID:28053411

Epigenetic Effects of Diet on Fruit Fly Lifespan: An Investigation to Teach Epigenetics to Biology Students

ERIC Educational Resources Information Center

Billingsley, James; Carlson, Kimberly A.

2010-01-01

Do our genes exclusively control us, or are other factors at play? Epigenetics can provide a means for students to use inquiry-based methods to understand a complex biological concept. Students research and design an experiment testing whether dietary supplements affect the lifespan of Drosophila melanogaster over multiple generations.

Approaches to Quality Risk Management When Using Single-Use Systems in the Manufacture of Biologics.

PubMed

Ishii-Watabe, Akiko; Hirose, Akihiko; Katori, Noriko; Hashii, Norikata; Arai, Susumu; Awatsu, Hirotoshi; Eiza, Akira; Hara, Yoshiaki; Hattori, Hideshi; Inoue, Tomomi; Isono, Tetsuya; Iwakura, Masahiro; Kajihara, Daisuke; Kasahara, Nobuo; Matsuda, Hiroyuki; Murakami, Sei; Nakagawa, Taishiro; Okumura, Takehiro; Omasa, Takeshi; Takuma, Shinya; Terashima, Iyo; Tsukahara, Masayoshi; Tsutsui, Maiko; Yano, Takahiro; Kawasaki, Nana

2015-10-01

Biologics manufacturing technology has made great progress in the last decade. One of the most promising new technologies is the single-use system, which has improved the efficiency of biologics manufacturing processes. To ensure safety of biologics when employing such single-use systems in the manufacturing process, various issues need to be considered including possible extractables/leachables and particles arising from the components used in single-use systems. Japanese pharmaceutical manufacturers, together with single-use suppliers, members of the academia and regulatory authorities have discussed the risks of using single-use systems and established control strategies for the quality assurance of biologics. In this study, we describe approaches for quality risk management when employing single-use systems in the manufacturing of biologics. We consider the potential impact of impurities related to single-use components on drug safety and the potential impact of the single-use system on other critical quality attributes as well as the stable supply of biologics. We also suggest a risk-mitigating strategy combining multiple control methods which includes the selection of appropriate single-use components, their inspections upon receipt and before releasing for use and qualification of single-use systems. Communication between suppliers of single-use systems and the users, as well as change controls in the facilities both of suppliers and users, are also important in risk-mitigating strategies. Implementing these control strategies can mitigate the risks attributed to the use of single-use systems. This study will be useful in promoting the development of biologics as well as in ensuring their safety, quality and stable supply.

AFLP Variation in Populations of Podisus maculiventris

USDA-ARS?s Scientific Manuscript database

We are developing methods to reduce costs of mass producing beneficial insect species for biological control programs. One of our methods entails selecting beneficials for optimal production traits. Currently we are selecting for increased fecundity. Selection protocols, whether based on phenotyp...

Quantifying control effort of biological and technical movements: an information-entropy-based approach.

PubMed

Haeufle, D F B; Günther, M; Wunner, G; Schmitt, S

2014-01-01

In biomechanics and biorobotics, muscles are often associated with reduced movement control effort and simplified control compared to technical actuators. This is based on evidence that the nonlinear muscle properties positively influence movement control. It is, however, open how to quantify the simplicity aspect of control effort and compare it between systems. Physical measures, such as energy consumption, stability, or jerk, have already been applied to compare biological and technical systems. Here a physical measure of control effort based on information entropy is presented. The idea is that control is simpler if a specific movement is generated with less processed sensor information, depending on the control scheme and the physical properties of the systems being compared. By calculating the Shannon information entropy of all sensor signals required for control, an information cost function can be formulated allowing the comparison of models of biological and technical control systems. Exemplarily applied to (bio-)mechanical models of hopping, the method reveals that the required information for generating hopping with a muscle driven by a simple reflex control scheme is only I=32 bits versus I=660 bits with a DC motor and a proportional differential controller. This approach to quantifying control effort captures the simplicity of a control scheme and can be used to compare completely different actuators and control approaches.

The neurophysiology of biological motion perception in schizophrenia

PubMed Central

Jahshan, Carol; Wynn, Jonathan K; Mathis, Kristopher I; Green, Michael F

2015-01-01

Introduction The ability to recognize human biological motion is a fundamental aspect of social cognition that is impaired in people with schizophrenia. However, little is known about the neural substrates of impaired biological motion perception in schizophrenia. In the current study, we assessed event-related potentials (ERPs) to human and nonhuman movement in schizophrenia. Methods Twenty-four subjects with schizophrenia and 18 healthy controls completed a biological motion task while their electroencephalography (EEG) was simultaneously recorded. Subjects watched clips of point-light animations containing 100%, 85%, or 70% biological motion, and were asked to decide whether the clip resembled human or nonhuman movement. Three ERPs were examined: P1, N1, and the late positive potential (LPP). Results Behaviorally, schizophrenia subjects identified significantly fewer stimuli as human movement compared to healthy controls in the 100% and 85% conditions. At the neural level, P1 was reduced in the schizophrenia group but did not differ among conditions in either group. There were no group differences in N1 but both groups had the largest N1 in the 70% condition. There was a condition × group interaction for the LPP: Healthy controls had a larger LPP to 100% versus 85% and 70% biological motion; there was no difference among conditions in schizophrenia subjects. Conclusions Consistent with previous findings, schizophrenia subjects were impaired in their ability to recognize biological motion. The EEG results showed that biological motion did not influence the earliest stage of visual processing (P1). Although schizophrenia subjects showed the same pattern of N1 results relative to healthy controls, they were impaired at a later stage (LPP), reflecting a dysfunction in the identification of human form in biological versus nonbiological motion stimuli. PMID:25722951

Modern methods and systems for precise control of the quality of agricultural and food production

NASA Astrophysics Data System (ADS)

Bednarjevsky, Sergey S.; Veryasov, Yuri V.; Akinina, Evgeniya V.; Smirnov, Gennady I.

1999-01-01

The results on the modeling of non-linear dynamics of strong continuous and impulse radiation in the laser nephelometry of polydisperse biological systems, important from the viewpoint of applications in biotechnologies, are presented. The processes of nonlinear self-action of the laser radiation by the multiple scattering in the disperse biological agro-media are considered. The simplified algorithms of the calculation of the parameters of the biological media under investigation are indicated and the estimates of the errors of the laser-nephelometric measurements are given. The universal high-informative optical analyzers and the standard etalon specimens of agro- objects make the technological foundation of the considered methods and systems.

Field Monitoring of Drosophila suzukii and Associated Communities in South Eastern France as a Pre-Requisite for Classical Biological Control

PubMed Central

Kremmer, Laurent; Thaon, Marcel; Borowiec, Nicolas; David, Jean; Poirié, Marylène; Ris, Nicolas

2017-01-01

The spotted wing Drosophila, Drosophila suzukii (Ds), became a major economic pest for fruit production since its establishment in Europe and America. Among potential control methods, only classical biological control appears to be a mean of sustainably regulating Ds in both cultivated and natural habitats. In the frame of risk assessment, pre-release surveys were carried out in a restricted but highly heterogeneous area in the south-east of France using traps and deliberate field exposures of Ds and D. melanogaster larvae/pupae. Although Ds abundance varied according to sampling methods, it was found to be pervasive and to produce offspring and adults in most conditions (spatial and seasonal). Its main limits are some specific abiotic conditions (i.e., desiccation) as well as interspecific competition. Indeed, Ds mostly co-occurred with D. busckii and D. hydei, probably due to common phenology and/or ecological requirements. These two species thus deserve more attention for risk assessment. The main indigenous parasitoids collected belonged to two pupal species, Trichopria cf drosophilae and Pachycrepoideus vindemmiae, but their presence was observed late in the autumn and mainly in cultivated areas. Results are discussed in a comparison of the methodological approaches for monitoring Drosophilids and the benefits-risks assessment of classical biological control. PMID:29144440

Comparative study of biological and technological characters in three generations of silkworm Bombyx mori L. ameiotic, parthenogenetically cloned lines.

PubMed

Greiss, H; Vassilieva, J; Petkov, N; Petkov, Z

2004-11-01

Detect any deviation in biologic and technologic characters of eight ameiotic-parthenogenetically cloned lines of Bombyx mori L. from different origins from a normal sexually reproduced control line in three generations. Comparative study of the three generations was conducted in SES, Vratza, unit of the National Center for Agrarian Sciences of Bulgaria after fixing all environmental rearing conditions. The ameiotic-parthen-clones displayed good parthenogenetic development, although total hatchability was significantly less than the sexually reproducing control populations. Survival rates between clones and control were not significantly different. All clones displayed significantly longer larval periods. Slight decline in second generation, and a steeper one in the third generation were observed for all eight cloned lines in cocoon weight, shell weight, and shell ratio and these differences were statistically significant. Cocoon yield was significantly lower than the control throughout the three generations. Our parthen-cloning method has a high rate of success in comparison to other cloning methods, the cloned progeny populations although were weaker technologically (cocoon weight, shell weight, and shell ratio), the biological characters (parthenogenetic development and survival rate) were not compromised. Further study is needed to determine the thermal needs of the cloned embryos and metabolic rate of all stages.

Applications of biological control in resistant host-pathogen systems.

PubMed

White, Steven M; White, K A Jane

2005-09-01

Insect pest species can have devastating effects on crops. Control of these insect pests is usually achieved by using chemical insecticides. However, there has been much cause for concern with their overuse. Consequently, research has been carried out into alternative forms of control, in particular biological control methods. Recent laboratory studies have indicated that these natural forms of control can induce resistant strains of insect pest. In this paper we present a discrete-time host-pathogen model to describe the interaction between a host (insect species) that can develop a resistant strain and a pathogen (biological control) that can be externally applied to the system. For this model we use a single-state variable for the host population. We show that the proportion of resistance in the population impacts on the viability of the host population. Moreover, when the host population does persist, we explore the interaction between host susceptibility and host population levels. The different scenarios which arise are explained ecologically in terms of trade-offs in intrinsic growth rates, disease susceptibility and intraspecific host competition for the resistant subclass.

GenePRIMP: A software quality control tool

ScienceCinema

Amrita Pati

2017-12-09

Amrita Pati of the DOE Joint Genome Institute's Genome Biology group describes the software tool GenePRIMP and how it fits into the quality control pipeline for microbial genomics. Further details regarding GenePRIMP appear in a paper published online May 2, 2010 in Nature Methods.

Augmenting the efficacy of fungal and mycotoxin control via chemosensitization

USDA-ARS?s Scientific Manuscript database

Antimycotic chemosensitization could serve as an effective method for control of fungal pathogens. In a chemo-biological platform to enhance antimycotic susceptibility of fungi or to overcome fungal tolerance to conventional antimycotic agents, the model yeast S. cerevisiae could be a functional too...

Evolutionary game theory for physical and biological scientists. I. Training and validating population dynamics equations.

PubMed

Liao, David; Tlsty, Thea D

2014-08-06

Failure to understand evolutionary dynamics has been hypothesized as limiting our ability to control biological systems. An increasing awareness of similarities between macroscopic ecosystems and cellular tissues has inspired optimism that game theory will provide insights into the progression and control of cancer. To realize this potential, the ability to compare game theoretic models and experimental measurements of population dynamics should be broadly disseminated. In this tutorial, we present an analysis method that can be used to train parameters in game theoretic dynamics equations, used to validate the resulting equations, and used to make predictions to challenge these equations and to design treatment strategies. The data analysis techniques in this tutorial are adapted from the analysis of reaction kinetics using the method of initial rates taught in undergraduate general chemistry courses. Reliance on computer programming is avoided to encourage the adoption of these methods as routine bench activities.

Biologically controlled minerals as potential indicators of life

NASA Technical Reports Server (NTRS)

Schwartz, D. E.; Mancinelli, R. L.; Kaneshiro, E.

1991-01-01

Minerals can be produced and deposited either by abiotic or biologic means. Regardless of their origin, mineral crystals reflect the environment conditions (e.g., temperature, pressure, chemical composition, and redox potential) present during crystal formation. Biologically-produced mineral crystals are grown or reworked under the control of their host organism and reflect an environment different from the abiotic environment. In addition, minerals of either biologic or abiotic origin have great longevities. For these reasons, biologically produced minerals have been proposed as biomarkers. Biomarkers are key morphological, chemical, and isotopic signatures of living systems that can be used to determine if life processes have occurred. Studies of biologically controlled minerals produced by the protist, Paramecium tetraurelia, were initiated since techniques have already been developed to culture them and isolate their crystalline material, and methods are already in place to analyze this material. Two direct crystalline phases were identified. One phase, whose chemical composition is high in Mg, was identified as struvite. The second phase, whose chemical composition is high in Ca, has not been previously found occurring naturally and may be considered a newly discovered material. Analyses are underway to determine the characteristics of these minerals in order to compare them with characteristics of these minerals in order to compare them with characteristics of minerals formed abiotically, but with the same chemical composition.

Assessment and management of soil microbial community structure for disease suppression.

PubMed

Mazzola, Mark

2004-01-01

Identification of the biological properties contributing to the function of suppressive soils is a necessary first step to the management of such systems for use in the control of soilborne diseases. The development and application of molecular methods for the characterization and monitoring of soil microbial properties will enable a more rapid and detailed assessment of the biological nature of soil suppressiveness. Although suppressive soils have provided a wealth of microbial resources that have subsequently been applied for the biological control of soilborne plant pathogens, the full functional capabilities of the phenomena have not been realized in production agricultural ecosystems. Cultural practices, such as the application of soil amendments, have the capacity to enhance disease suppression, though the biological modes of action may vary from that initially resident to the soil. Plants have a distinct impact on characteristics and activity of resident soil microbial communities, and therefore play an important role in determining the development of the disease-suppressive state. Likewise, plant genotype will modulate these same biological communities, and should be considered when developing strategies to exploit the potential of such a natural disease control system. Implementation of consistently effective practices to manage this resource in an economically and environmentally feasible manner will require more detailed investigation of these biologically complex systems and refinement of currently available methodologies.

From systems biology to dynamical neuropharmacology: proposal for a new methodology.

PubMed

Erdi, P; Kiss, T; Tóth, J; Ujfalussy, B; Zalányi, L

2006-07-01

The concepts and methods of systems biology are extended to neuropharmacology in order to test and design drugs for the treatment of neurological and psychiatric disorders. Computational modelling by integrating compartmental neural modelling techniques and detailed kinetic descriptions of pharmacological modulation of transmitter-receptor interaction is offered as a method to test the electrophysiological and behavioural effects of putative drugs. Even more, an inverse method is suggested as a method for controlling a neural system to realise a prescribed temporal pattern. In particular, as an application of the proposed new methodology, a computational platform is offered to analyse the generation and pharmacological modulation of theta rhythm related to anxiety.

Inundative release of Aphthona spp. flea beetles (Coleoptera: Chrysomlidae) as a biological "herbicide" on leafy spurge in riparian areas

Treesearch

R.A. Progar; G. Markin; J. Milan; T. Barbouletos; M.J. Rinella

2010-01-01

Inundative releases of beneficial insects are frequently used to suppress pest insects but not commonly attempted as a method of weed biological control because of the difficulty in obtaining the required large numbers of insects. The successful establishment of a flea beetle complex, mixed Aphthona lacertosa (Rosenhauer) and Aphthona...

Collaborative study for the validation of alternative in vitro potency assays for human tetanus immunoglobulins.

PubMed

Gross, S; Janssen, S W J; de Vries, B; Terao, E; Daas, A; Buchheit, K-H

2010-07-01

An international collaborative study to validate 2 alternative in vitro methods for the potency testing of human tetanus immunoglobulin products was organised by the European Directorate for the Quality of Medicines & HealthCare (EDQM). The study, run in the framework of the Biological Standardisation Programme (BSP) under the aegis of the European Commission and the Council of Europe, involved 21 official medicines control and industry laboratories from 15 countries. Both methods, an enzyme-linked immunoassay (EIA) and a toxoid inhibition assay (TIA), showed good reproducibility, repeatability and precision. EIA and TIA discriminated between low, medium and high potency samples. Potency estimates correlated well and both values were in close agreement with those obtained by in vivo methods. Moreover, these alternative methods allowed to resolve discrepant results between laboratories that were due to product potency loss and reporting errors. The study demonstrated that EIA and TIA are suitable quality control methods for tetanus immunoglobulin, which can be standardised in a control laboratory using a quality assurance system. Consequently, the Group of Experts on Human Blood and Blood Products of the European Pharmacopoeia revised the monograph on human tetanus immunoglobulins to include both the methods as compendial alternatives to the in vivo mouse challenge assay. 2010 The International Association for Biologicals. Published by Elsevier Ltd. All rights reserved.

Wavefront control in adaptive microscopy using Shack-Hartmann sensors with arbitrarily shaped pupils.

PubMed

Dong, Bing; Booth, Martin J

2018-01-22

In adaptive optical microscopy of thick biological tissue, strong scattering and aberrations can change the effective pupil shape by rendering some Shack-Hartmann spots unusable. The change of pupil shape leads to a change of wavefront reconstruction or control matrix that should be updated accordingly. Modified slope and modal wavefront control methods based on measurements of a Shack-Hartmann wavefront sensor are proposed to accommodate an arbitrarily shaped pupil. Furthermore, we present partial wavefront control methods that remove specific aberration modes like tip, tilt and defocus from the control loop. The proposed control methods were investigated and compared by simulation using experimentally obtained aberration data. The performance was then tested experimentally through closed-loop aberration corrections using an obscured pupil.

Autoclave use in dental practice in the Republic of Ireland.

PubMed

Healy, C M; Kearns, H P O; Coulter, W A; Stevenson, M; Burke, F J T

2004-08-01

To assess by postal questionnaire, cross-infection control methods, especially sterilisation procedures, of 700 general dental practitioners in the Republic of Ireland, and to biologically monitor steam pressure sterilisers or autoclaves in their practices. Methods of instrument cleaning and sterilisation, autoclave efficacy. A response rate of 40% with all, except one practitioner, using steam sterilisation. 49% also reported the use of chemical sterilisation with a quarter of these using glutaraldehyde. However, instrument soaking time varied greatly from 2.5 minutes to 74 hours. Methods of instrument cleaning prior to autoclaving were as follows: scrubbing by hand 41.5%, ultrasonic cleaning 7.0%, combination of both 50%. 52.9% of the respondents did not autoclave their dental handpieces and only 44.7% disinfected impressions before sending them to the laboratory. The autoclaves of thirty practitioners (11.3%) did not pass the initial biological test. Following counselling about possible causes of failure, four autoclaves (1.5%) failed a repeat biological test. However, seven practitioners did not return the repeat biological test. Some aspects of recommended cross-infection control procedures are well adhered to, e.g. instrument cleaning, but further education is required in certain key areas, in particular the use of chemical sterilisation, dental handpiece autoclaving and impression disinfection. There is also a need to increase awareness of the importance of routine autoclave servicing and calibration, along with validation and monitoring.

BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates.

PubMed

Goren, Emily; Liu, Peng; Wang, Chao; Wang, Chong

2018-04-19

ChIP-seq experiments that are aimed at detecting DNA-protein interactions require biological replication to draw inferential conclusions, however there is no current consensus on how to analyze ChIP-seq data with biological replicates. Very few methodologies exist for the joint analysis of replicated ChIP-seq data, with approaches ranging from combining the results of analyzing replicates individually to joint modeling of all replicates. Combining the results of individual replicates analyzed separately can lead to reduced peak classification performance compared to joint modeling. Currently available methods for joint analysis may fail to control the false discovery rate at the nominal level. We propose BinQuasi, a peak caller for replicated ChIP-seq data, that jointly models biological replicates using a generalized linear model framework and employs a one-sided quasi-likelihood ratio test to detect peaks. When applied to simulated data and real datasets, BinQuasi performs favorably compared to existing methods, including better control of false discovery rate than existing joint modeling approaches. BinQuasi offers a flexible approach to joint modeling of replicated ChIP-seq data which is preferable to combining the results of replicates analyzed individually. Source code is freely available for download at https://cran.r-project.org/package=BinQuasi, implemented in R. pliu@iastate.edu or egoren@iastate.edu. Supplementary material is available at Bioinformatics online.

Multifunctional ferromagnetic disks for modulating cell function

PubMed Central

Vitol, Elina A.; Novosad, Valentyn; Rozhkova, Elena A.

2013-01-01

In this work, we focus on the methods for controlling cell function with ferromagnetic disk-shaped particles. We will first review the history of magnetically assisted modulation of cell behavior and applications of magnetic particles for studying physical properties of a cell. Then, we consider the biological applications of the microdisks such as the method for induction of cancer cell apoptosis, controlled drug release, hyperthermia and MRI imaging. PMID:23766544

New Weapons in the Toad Toolkit: A Review of Methods to Control and Mitigate the Biodiversity Impacts of Invasive Cane Toads (Rhinella Marina).

PubMed

Tingley, Reid; Ward-Fear, Georgia; Schwarzkopf, Lin; Greenlees, Matthew J; Phillips, Benjamin L; Brown, Gregory; Clulow, Simon; Webb, Jonathan; Capon, Robert; Sheppard, Andy; Strive, Tanja; Tizard, Mark; Shine, Richard

2017-06-01

Our best hope of developing innovative methods to combat invasive species is likely to come from the study of high-profile invaders that have attracted intensive research not only into control, but also basic biology. Here we illustrate that point by reviewing current thinking about novel ways to control one of the world’s most well-studied invasions: that of the cane toad in Australia. Recently developed methods for population suppression include more effective traps based on the toad’s acoustic and pheromonal biology. New tools for containing spread include surveillance technologies (e.g., eDNA sampling and automated call detectors), as well as landscape-level barriers that exploit the toad’s vulnerability to desiccation—a strategy that could be significantly enhanced through the introduction of sedentary, range-core genotypes ahead of the invasion front. New methods to reduce the ecological impacts of toads include conditioned taste aversion in free-ranging predators, gene banking, and targeted gene flow. Lastly, recent advances in gene editing and gene drive technology hold the promise of modifying toad phenotypes in ways that may facilitate control or buffer impact. Synergies between these approaches hold great promise for novel and more effective means to combat the toad invasion and its consequent impacts on biodiversity.

Optical trapping and manipulation of neutral particles using lasers

PubMed Central

Ashkin, Arthur

1997-01-01

The techniques of optical trapping and manipulation of neutral particles by lasers provide unique means to control the dynamics of small particles. These new experimental methods have played a revolutionary role in areas of the physical and biological sciences. This paper reviews the early developments in the field leading to the demonstration of cooling and trapping of neutral atoms in atomic physics and to the first use of optical tweezers traps in biology. Some further major achievements of these rapidly developing methods also are considered. PMID:9144154

Biological Control of Introduced Weeds of Native Hawaiian Forests

Treesearch

George P. Markin; Roddy F. Nagata; Donald E. Gardner

1992-01-01

Among the many threats to the continued existence of the remaining native forests and other native ecosystems of the Hawaiian Islands, the most severe and the most difficult to control are the invasion and replacement by induced species of plants. Because conventional methods of plant management have faild to control this invasion, a multiagency, state and federal...

Finite Set Control Transcription for Optimal Control Applications

DTIC Science & Technology

2009-05-01

Figures 1.1 The Parameters of x . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 2.1 Categories of Optimization Algorithms ...Programming (NLP) algorithm , such as SNOPT2 (hereafter, called the optimizer). The Finite Set Control Transcription (FSCT) method is essentially a...artificial neural networks, ge- netic algorithms , or combinations thereof for analysis.4,5 Indeed, an actual biological neural network is an example of

DNA codes for nanoscience.

PubMed

Samorì, Bruno; Zuccheri, Giampaolo

2005-02-11

The nanometer scale is a special place where all sciences meet and develop a particularly strong interdisciplinarity. While biology is a source of inspiration for nanoscientists, chemistry has a central role in turning inspirations and methods from biological systems to nanotechnological use. DNA is the biological molecule by which nanoscience and nanotechnology is mostly fascinated. Nature uses DNA not only as a repository of the genetic information, but also as a controller of the expression of the genes it contains. Thus, there are codes embedded in the DNA sequence that serve to control recognition processes on the atomic scale, such as the base pairing, and others that control processes taking place on the nanoscale. From the chemical point of view, DNA is the supramolecular building block with the highest informational content. Nanoscience has therefore the opportunity of using DNA molecules to increase the level of complexity and efficiency in self-assembling and self-directing processes.

Impaired Perception of Biological Motion in Parkinson’s Disease

PubMed Central

Jaywant, Abhishek; Shiffrar, Maggie; Roy, Serge; Cronin-Golomb, Alice

2016-01-01

Objective We examined biological motion perception in Parkinson’s disease (PD). Biological motion perception is related to one’s own motor function and depends on the integrity of brain areas affected in PD, including posterior superior temporal sulcus. If deficits in biological motion perception exist, they may be specific to perceiving natural/fast walking patterns that individuals with PD can no longer perform, and may correlate with disease-related motor dysfunction. Method 26 non-demented individuals with PD and 24 control participants viewed videos of point-light walkers and scrambled versions that served as foils, and indicated whether each video depicted a human walking. Point-light walkers varied by gait type (natural, parkinsonian) and speed (0.5, 1.0, 1.5 m/s). Participants also completed control tasks (object motion, coherent motion perception), a contrast sensitivity assessment, and a walking assessment. Results The PD group demonstrated significantly less sensitivity to biological motion than the control group (p<.001, Cohen’s d=1.22), regardless of stimulus gait type or speed, with a less substantial deficit in object motion perception (p=.02, Cohen’s d=.68). There was no group difference in coherent motion perception. Although individuals with PD had slower walking speed and shorter stride length than control participants, gait parameters did not correlate with biological motion perception. Contrast sensitivity and coherent motion perception also did not correlate with biological motion perception. Conclusion PD leads to a deficit in perceiving biological motion, which is independent of gait dysfunction and low-level vision changes, and may therefore arise from difficulty perceptually integrating form and motion cues in posterior superior temporal sulcus. PMID:26949927

Optical micromanipulation methods for controlled rotation, transportation, and microinjection of biological objects.

PubMed

Mohanty, S K; Gupta, P K

2007-01-01

The use of laser microtools for rotation and controlled transport of microscopic biological objects and for microinjection of exogenous material in cells is discussed. We first provide a brief overview of the laser tweezers-based methods for rotation or orientation of microscopic objects. Particular emphasis is placed on the methods that are more suitable for the manipulation of biological objects, and the use of these for two-dimensional (2D) and 3D rotations/orientations of intracellular objects is discussed. We also discuss how a change in the shape of a red blood cell (RBC) suspended in hypertonic buffer leads to its rotation when it is optically tweezed. The potential use of this approach for the diagnosis of malaria is also illustrated. The use of a line tweezers having an asymmetric intensity distribution about the center of its major axis for simultaneous transport of microscopic objects, and the successful use of this approach for induction, enhancement, and guidance of neuronal growth cones is presented next. Finally, we describe laser microbeam-assisted microinjection of impermeable drugs into cells and also briefly discuss possible adverse effects of the laser trap or microbeams on cells.

A New Method Using Single-Particle Mass Spectrometry Data to Distinguish Mineral Dust and Biological Aerosols

NASA Astrophysics Data System (ADS)

Al-Mashat, H.; Kristensen, L.; Sultana, C. M.; Prather, K. A.

2016-12-01

The ability to distinguish types of particles present within a cloud is important for determining accurate inputs to climate models. The chemical composition of particles within cloud liquid droplets and ice crystals can have a significant impact on the timing, location, and amount of precipitation that falls. Precipitation efficiency is increased by the presence of ice crystals in clouds, and both mineral dust and biological aerosols have been shown to be effective ice nucleating particles (INPs) in the atmosphere. A current challenge in aerosol science is distinguishing mineral dust and biological material in the analysis of real-time, ambient, single-particle mass spectral data. Single-particle mass spectrometers are capable of measuring the size-resolved chemical composition of individual atmospheric particles. However, there is no consistent analytical method for distinguishing dust and biological aerosols. Sampling and characterization of control samples (i.e. of known identity) of mineral dust and bacteria were performed by the Aerosol Time-of-Flight Mass Spectrometer (ATOFMS) as part of the Fifth Ice Nucleation (FIN01) Workshop at the Aerosol Interaction and Dynamics in the Atmosphere (AIDA) facility in Karlsruhe, Germany. Using data collected by the ATOFMS of control samples, a new metric has been developed to classify single particles as dust or biological independent of spectral cluster analysis. This method, involving the use of a ratio of mass spectral peak areas for organic nitrogen and silicates, is easily reproducible and does not rely on extensive knowledge of particle chemistry or the ionization characteristics of mass spectrometers. This represents a step toward rapidly distinguishing particle types responsible for ice nucleation activity during real-time sampling in clouds. The ability to distinguish types of particles present within a cloud is important for determining accurate inputs to climate models. The chemical composition of particles within cloud liquid droplets and ice crystals can have a significant impact on the timing, location, and amount of precipitation that falls. Precipitation efficiency is increased by the presence of ice crystals in clouds, and both mineral dust and biological aerosols have been shown to be effective ice nucleating particles (INPs) in the atmosphere. A current challenge in aerosol science is distinguishing mineral dust and biological material in the analysis of real-time, ambient, single-particle mass spectral data. Single-particle mass spectrometers are capable of measuring the size-resolved chemical composition of individual atmospheric particles. However, there is no consistent analytical method for distinguishing dust and biological aerosols. Sampling and characterization of control samples (i.e. of known identity) of mineral dust and bacteria were performed by the Aerosol Time-of-Flight Mass Spectrometer (ATOFMS) as part of the Fifth Ice Nucleation (FIN01) Workshop at the Aerosol Interaction and Dynamics in the Atmosphere (AIDA) facility in Karlsruhe, Germany. Using data collected by the ATOFMS of control samples, a new metric has been developed to classify single particles as dust or biological independent of spectral cluster analysis. This method, involving the use of a ratio of mass spectral peak areas for organic nitrogen and silicates, is easily reproducible and does not rely on extensive knowledge of particle chemistry or the ionization characteristics of mass spectrometers. This represents a step toward rapidly distinguishing particle types responsible for ice nucleation activity during real-time sampling in clouds.

Advantages and Disadvantages of Aquatic Plant Management Techniques

DTIC Science & Technology

2000-09-01

This report provides an overview of the environmental and practical advantages and disadvantages of the major aquatic plant management methods, including biological, chemical, mechanical, and physical control techniques.

Reinforcement learning for a biped robot based on a CPG-actor-critic method.

PubMed

Nakamura, Yutaka; Mori, Takeshi; Sato, Masa-aki; Ishii, Shin

2007-08-01

Animals' rhythmic movements, such as locomotion, are considered to be controlled by neural circuits called central pattern generators (CPGs), which generate oscillatory signals. Motivated by this biological mechanism, studies have been conducted on the rhythmic movements controlled by CPG. As an autonomous learning framework for a CPG controller, we propose in this article a reinforcement learning method we call the "CPG-actor-critic" method. This method introduces a new architecture to the actor, and its training is roughly based on a stochastic policy gradient algorithm presented recently. We apply this method to an automatic acquisition problem of control for a biped robot. Computer simulations show that training of the CPG can be successfully performed by our method, thus allowing the biped robot to not only walk stably but also adapt to environmental changes.

Scaffolded Instruction Improves Student Understanding of the Scientific Method & Experimental Design

ERIC Educational Resources Information Center

D'Costa, Allison R.; Schlueter, Mark A.

2013-01-01

Implementation of a guided-inquiry lab in introductory biology classes, along with scaffolded instruction, improved students' understanding of the scientific method, their ability to design an experiment, and their identification of experimental variables. Pre- and postassessments from experimental versus control sections over three semesters…

Rhipicephalus (Boophilus) microplus resistant to acaricides and ivermectin in cattle farms of Mexico

USDA-ARS?s Scientific Manuscript database

Ticks and the diseases they transmit cause great economic losses to livestock in tropical countries. Non-chemical control alternatives include the use of resistant cattle breeds, biological control, and vaccines. However, the most widely used method is the application of different chemical classes o...

Unification of the macro- and microbiome in trophic ecology

USDA-ARS?s Scientific Manuscript database

Biological control is a key part of virtually any IPM program, and microbial bio-control agents represent particularly effective agents because of their capacity to be applied via conventional spray application methods. We are showing that fungi function just as arthropods do in the food web—the fun...

ALTERNATIVES TO CHLORINATION FOR CONTROL OF CONDENSER TUBE BIO-FOULING

EPA Science Inventory

The report gives results of a study of methods used to reduce free-chlorine residuals in power plant effluents. Most U.S. power plants use chlorine (28,600 tons in 1972) to control biological fouling in their cooling systems, particularly in their condenser tubes. Using chlorine ...

INAA Application for Trace Element Determination in Biological Reference Material

NASA Astrophysics Data System (ADS)

Atmodjo, D. P. D.; Kurniawati, S.; Lestiani, D. D.; Adventini, N.

2017-06-01

Trace element determination in biological samples is often used in the study of health and toxicology. Determination change to its essentiality and toxicity of trace element require an accurate determination method, which implies that a good Quality Control (QC) procedure should be performed. In this study, QC for trace element determination in biological samples was applied by analyzing the Standard Reference Material (SRM) Bovine muscle 8414 NIST using Instrumental Neutron Activation Analysis (INAA). Three selected trace element such as Fe, Zn, and Se were determined. Accuracy of the elements showed as %recovery and precision as %coefficient of variance (%CV). The result showed that %recovery of Fe, Zn, and Se were in the range between 99.4-107%, 92.7-103%, and 91.9-112%, respectively, whereas %CV were 2.92, 3.70, and 5.37%, respectively. These results showed that INAA method is precise and accurate for trace element determination in biological matrices.

Town ants: the beginning of John Moser’s remarkable search for knowledge

Treesearch

J.P. Barnett; D.A. Streett; S.R. Blomquist

2016-01-01

John C. Moser’s career spans over 50 years, and his research has focused on understanding the biology of town ants (Atta texana) and phoretic mites and other associates of ants and pine bark beetles. His approach to developing methods for the control of these pests has been to understand more completely the biology of these organisms. This research...

Inundative release of Aphthona spp. flea beetles (Coleoptera: Chrysomelidae) as a biological "herbicide" on leafy spurge in riparian areas

Treesearch

R. A. Progar; G. Markin; J. Milan; T. Barbouletos; M. J. Rinella

2010-01-01

Inundative releases of beneficial insects are frequently used to suppress pest insects but not commonly attempted as a method of weed biological control because of the difficulty in obtaining the required large numbers of insects. The successful establishment of a flea beetle complex, mixed Aphthona lacertosa (Rosenhauer) and Aphthona nigriscutus Foundras (87 and 13%,...

Inundative release of Aphthona spp. flea beetles (Coleoptera: Chrysomelidae) as a biological "herbicide" on leafy spurge (Euphorbia esula) in riparian areas

Treesearch

R. A. Progar; G. P. Markin; J. Milan; T. Barbouletos; M. J. Rinella

2013-01-01

Inundative releases of beneficial insects are frequently used to suppress pest insects, but not commonly attempted as a method of weed biological control because of the difficulty in obtaining the required large numbers of insects. The successful establishment of a flea beetle complex, mixed Aphthona lacertosa Rosenhauer and A. nigriscutus Foudras (87% and 13%,...

A review on plants extract mediated synthesis of silver nanoparticles for antimicrobial applications: A green expertise

PubMed Central

Ahmed, Shakeel; Ahmad, Mudasir; Swami, Babu Lal; Ikram, Saiqa

2015-01-01

Metallic nanoparticles are being utilized in every phase of science along with engineering including medical fields and are still charming the scientists to explore new dimensions for their respective worth which is generally attributed to their corresponding small sizes. The up-and-coming researches have proven their antimicrobial significance. Among several noble metal nanoparticles, silver nanoparticles have attained a special focus. Conventionally silver nanoparticles are synthesized by chemical method using chemicals as reducing agents which later on become accountable for various biological risks due to their general toxicity; engendering the serious concern to develop environment friendly processes. Thus, to solve the objective; biological approaches are coming up to fill the void; for instance green syntheses using biological molecules derived from plant sources in the form of extracts exhibiting superiority over chemical and/or biological methods. These plant based biological molecules undergo highly controlled assembly for making them suitable for the metal nanoparticle syntheses. The present review explores the huge plant diversity to be utilized towards rapid and single step protocol preparatory method with green principles over the conventional ones and describes the antimicrobial activities of silver nanoparticles. PMID:26843966

Adaptive filtering in biological signal processing.

PubMed

Iyer, V K; Ploysongsang, Y; Ramamoorthy, P A

1990-01-01

The high dependence of conventional optimal filtering methods on the a priori knowledge of the signal and noise statistics render them ineffective in dealing with signals whose statistics cannot be predetermined accurately. Adaptive filtering methods offer a better alternative, since the a priori knowledge of statistics is less critical, real time processing is possible, and the computations are less expensive for this approach. Adaptive filtering methods compute the filter coefficients "on-line", converging to the optimal values in the least-mean square (LMS) error sense. Adaptive filtering is therefore apt for dealing with the "unknown" statistics situation and has been applied extensively in areas like communication, speech, radar, sonar, seismology, and biological signal processing and analysis for channel equalization, interference and echo canceling, line enhancement, signal detection, system identification, spectral analysis, beamforming, modeling, control, etc. In this review article adaptive filtering in the context of biological signals is reviewed. An intuitive approach to the underlying theory of adaptive filters and its applicability are presented. Applications of the principles in biological signal processing are discussed in a manner that brings out the key ideas involved. Current and potential future directions in adaptive biological signal processing are also discussed.

Detection and quantification of Plectosphaerella cucumerina, a potential biological control agent of potato cyst nematodes, by using conventional PCR, real-time PCR, selective media, and baiting.

PubMed

Atkins, S D; Clark, I M; Sosnowska, D; Hirsch, P R; Kerry, B R

2003-08-01

Potato cyst nematodes (PCN) are serious pests in commercial potato production, causing yield losses valued at approximately $300 million in the European Community. The nematophagous fungus Plectosphaerella cucumerina has demonstrated its potential as a biological control agent against PCN populations by reducing field populations by up to 60% in trials. The use of biological control agents in the field requires the development of specific techniques to monitor the release, population size, spread or decline, and pathogenicity against its host. A range of methods have therefore been developed to monitor P. cucumerina. A species-specific PCR primer set (PcCF1-PcCR1) was designed that was able to detect the presence of P. cucumerina in soil, root, and nematode samples. PCR was combined with a bait method to identify P. cucumerina from infected nematode eggs, confirming the parasitic ability of the fungus. A selective medium was adapted to isolate the fungus from root and soil samples and was used to quantify the fungus from field sites. A second P. cucumerina-specific primer set (PcRTF1-PcRTR1) and a Taqman probe (PcRTP1) were designed for real-time PCR quantification of the fungus and provided a very sensitive means of detecting the fungus from soil. PCR, bait, and culture methods were combined to investigate the presence and abundance of P. cucumerina from two field sites in the United Kingdom where PCN populations were naturally declining. All methods enabled differences in the activity of P. cucumerina to be detected, and the results demonstrated the importance of using a combination of methods to investigate population size and activity of fungi.

Adaptive velocity-based six degree of freedom load control for real-time unconstrained biomechanical testing.

PubMed

Lawless, I M; Ding, B; Cazzolato, B S; Costi, J J

2014-09-22

Robotic biomechanics is a powerful tool for further developing our understanding of biological joints, tissues and their repair. Both velocity-based and hybrid force control methods have been applied to biomechanics but the complex and non-linear properties of joints have limited these to slow or stepwise loading, which may not capture the real-time behaviour of joints. This paper presents a novel force control scheme combining stiffness and velocity based methods aimed at achieving six degree of freedom unconstrained force control at physiological loading rates. Copyright © 2014 Elsevier Ltd. All rights reserved.

The biological control of Pomacea canaliculata population by rice-duck mutualism in paddy fields

Treesearch

Kiang Liang; Jia-en Zhang; Li Fang; Benliang Zaho; Mingzhu Luo; Prem Parajuli; Ying Ouyang

2013-01-01

Duck has been used as a non-chemical control method against Pomacea canaliculata Lamarck, but little is known about its principles that underlie the control of snail populations. An indoor experiment was initially used to observe the predation potential of ducks, followed by replicated field trials. In the indoor studies, ducks effectively preyed on...

Control of Oscillation Patterns in a Symmetric Coupled Biological Oscillator System

NASA Astrophysics Data System (ADS)

Takamatsu, Atsuko; Tanaka, Reiko; Yamamoto, Takatoki; Fujii, Teruo

2003-08-01

A chain of three-oscillator system was constructed with living biological oscillators of phasmodial slime mold, Physarum polycehalum and the oscillation patterns were analyzed by the symmetric Hopf bifurcation theory using group theory. Multi-stability of oscillation patterns was observed, even when the coupling strength was fixed. This suggests that the coupling strength is not an effective parameter to obtain a desired oscillation pattern among the multiple patterns. Here we propose a method to control oscillation patterns using resonance to external stimulus and demonstrate pattern switching induced by frequency resonance given to only one of oscillators in the system.

Regulatory sequence of cupin family gene

DOEpatents

Hood, Elizabeth; Teoh, Thomas

2017-07-25

This invention is in the field of plant biology and agriculture and relates to novel seed specific promoter regions. The present invention further provide methods of producing proteins and other products of interest and methods of controlling expression of nucleic acid sequences of interest using the seed specific promoter regions.

Vesicle-based method for collecting, manipulating, and chemically processing trace macromolecular species

DOEpatents

Davalos, Rafael V [Oakland, CA; Ellis, Christopher R. B. [Oakland, CA

2010-08-17

Disclosed is an apparatus and method for inserting one or several chemical or biological species into phospholipid containers that are controlled within a microfluidic network, wherein individual containers are tracked and manipulated by electric fields and wherein the contained species may be chemically processed.

Vesicle-based method and apparatus for collecting, manipulating, and chemically processing trace macromolecular species

DOEpatents

Davalos, Rafael V [Oakland, CA; Ellis, Christopher R. B. [Oakland, CA

2008-03-04

Disclosed is an apparatus and method for inserting one or several chemical or biological species into phospholipid containers that are controlled within a microfluidic network, wherein individual containers are tracked and manipulated by electric fields and wherein the contained species may be chemically processed.

Hemlock woolly adelgid biological control: molecular methods to distinguish Laricobius nigrinus, L. rubidus, and their hybrids

Treesearch

Nathan P. Havill; Gina Davis; Joanne Klein; Adalgisa Caccone; Scott Salom

2011-01-01

Molecular diagnostics use DNA-based methods to assign unknown organisms to species. As such, they rely on a priori species designation by taxonomists and require validation with enough samples to capture the variation within species for accurately selecting diagnostic characters.

Entomopathogenic Nematodes Combined with Adjuvants Presents a New Potential Biological Control Method for Managing the Wheat Stem Sawfly, Cephus cinctus (Hymenoptera: Cephidae)

PubMed Central

Portman, Scott L.; Krishnankutty, Sindhu M.

2016-01-01

The wheat stem sawfly, (Cephus cinctus Norton) Hymenoptera: Cephidae, has been a major pest of winter wheat and barley in the northern Great Plains for more than 100 years. The insect’s cryptic nature and lack of safe chemical control options make the wheat stem sawfly (WSS) difficult to manage; thus, biological control offers the best hope for sustainable management of WSS. Entomopathogenic nematodes (EPNs) have been used successfully against other above-ground insect pests, and adding adjuvants to sprays containing EPNs has been shown to improve their effectiveness. We tested the hypothesis that adding chemical adjuvants to sprays containing EPNs will increase the ability of EPNs to enter wheat stems and kill diapausing WSS larvae. This is the first study to test the ability of EPNs to infect the WSS, C. cinctus, and test EPNs combined with adjuvants against C. cinctus in both the laboratory and the field. Infection assays showed that three different species of EPNs caused 60–100% mortality to WSS larvae. Adding Penterra, Silwet L-77, Sunspray 11N, or Syl-Tac to solutions containing EPNs resulted in higher WSS mortality than solutions made with water alone. Field tests showed that sprays containing S. feltiae added to 0.1% Penterra increased WSS mortality up to 29.1%. These results indicate a novel control method for WSS, and represent a significant advancement in the biological control of this persistent insect pest. PMID:28006820

Wolbachia: A biological control strategy against arboviral diseases.

PubMed

Mohanty, Ipsita; Rath, Animesha; Mahapatra, Namita; Hazra, Rupenangshu K

2016-01-01

Vector-borne diseases particularly those transmitted by mosquitoes like Dengue are among the leading causes of mortality and morbidity in human population. There are no effective vaccines or treatment against dengue fever till date and the control methods are limited. So, new approaches are urgently in need to reverse these trends. Vector control is currently the primary intervention tool. Strategies that reduce or block pathogen transmission by mosquitoes have been proposed as a means of augmenting current control measures to reduce the growing burden of vector-borne diseases. Wolbachia an endosymbiont of arthropod vectors is being explored as a novel ecofriendly control strategy. Studies in Drosophila have shown that Wolbachia can confer resistance to diverse RNA viruses and protect flies from virus-induced mortality. This review was focused on biology of the Wolbachia and its implication as a control measure for arboviral diseases mainly Dengue and Chikungunya.

Biological Stability of Drinking Water: Controlling Factors, Methods, and Challenges.

PubMed

Prest, Emmanuelle I; Hammes, Frederik; van Loosdrecht, Mark C M; Vrouwenvelder, Johannes S

2016-01-01

Biological stability of drinking water refers to the concept of providing consumers with drinking water of same microbial quality at the tap as produced at the water treatment facility. However, uncontrolled growth of bacteria can occur during distribution in water mains and premise plumbing, and can lead to hygienic (e.g., development of opportunistic pathogens), aesthetic (e.g., deterioration of taste, odor, color) or operational (e.g., fouling or biocorrosion of pipes) problems. Drinking water contains diverse microorganisms competing for limited available nutrients for growth. Bacterial growth and interactions are regulated by factors, such as (i) type and concentration of available organic and inorganic nutrients, (ii) type and concentration of residual disinfectant, (iii) presence of predators, such as protozoa and invertebrates, (iv) environmental conditions, such as water temperature, and (v) spatial location of microorganisms (bulk water, sediment, or biofilm). Water treatment and distribution conditions in water mains and premise plumbing affect each of these factors and shape bacterial community characteristics (abundance, composition, viability) in distribution systems. Improved understanding of bacterial interactions in distribution systems and of environmental conditions impact is needed for better control of bacterial communities during drinking water production and distribution. This article reviews (i) existing knowledge on biological stability controlling factors and (ii) how these factors are affected by drinking water production and distribution conditions. In addition, (iii) the concept of biological stability is discussed in light of experience with well-established and new analytical methods, enabling high throughput analysis and in-depth characterization of bacterial communities in drinking water. We discussed, how knowledge gained from novel techniques will improve design and monitoring of water treatment and distribution systems in order to maintain good drinking water microbial quality up to consumer's tap. A new definition and methodological approach for biological stability is proposed.

Biological Stability of Drinking Water: Controlling Factors, Methods, and Challenges

PubMed Central

Prest, Emmanuelle I.; Hammes, Frederik; van Loosdrecht, Mark C. M.; Vrouwenvelder, Johannes S.

2016-01-01

Biological stability of drinking water refers to the concept of providing consumers with drinking water of same microbial quality at the tap as produced at the water treatment facility. However, uncontrolled growth of bacteria can occur during distribution in water mains and premise plumbing, and can lead to hygienic (e.g., development of opportunistic pathogens), aesthetic (e.g., deterioration of taste, odor, color) or operational (e.g., fouling or biocorrosion of pipes) problems. Drinking water contains diverse microorganisms competing for limited available nutrients for growth. Bacterial growth and interactions are regulated by factors, such as (i) type and concentration of available organic and inorganic nutrients, (ii) type and concentration of residual disinfectant, (iii) presence of predators, such as protozoa and invertebrates, (iv) environmental conditions, such as water temperature, and (v) spatial location of microorganisms (bulk water, sediment, or biofilm). Water treatment and distribution conditions in water mains and premise plumbing affect each of these factors and shape bacterial community characteristics (abundance, composition, viability) in distribution systems. Improved understanding of bacterial interactions in distribution systems and of environmental conditions impact is needed for better control of bacterial communities during drinking water production and distribution. This article reviews (i) existing knowledge on biological stability controlling factors and (ii) how these factors are affected by drinking water production and distribution conditions. In addition, (iii) the concept of biological stability is discussed in light of experience with well-established and new analytical methods, enabling high throughput analysis and in-depth characterization of bacterial communities in drinking water. We discussed, how knowledge gained from novel techniques will improve design and monitoring of water treatment and distribution systems in order to maintain good drinking water microbial quality up to consumer’s tap. A new definition and methodological approach for biological stability is proposed. PMID:26870010

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

PubMed Central

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

2014-01-01

Objective To identify the biological forms, sporozoite rate and molecular characterization of the Anopheles stephensi (An. stephensi) in Hormozgan and Sistan-Baluchistan provinces, the most important malarious areas in Iran. Methods Wild live An. stephensi samples were collected from different malarious areas in southern Iran. The biological forms were identified based on number of egg-ridges. Molecular characterization of biological forms was verified by analysis of the mitochondrial cytochrome oxidase subunit I and II (mtDNA-COI/COII). The Plasmodium infection was examined in the wild female specimens by species-specific nested–PCR method. Results Results showed that all three biological forms including mysorensis, intermediate and type are present in the study areas. Molecular investigations revealed no genetic variation between mtDNA COI/COII sequences of the biological forms and no Plasmodium parasites was detected in the collected mosquito samples. Conclusions Presence of three biological forms with identical sequences showed that the known biological forms belong to a single taxon and the various vectorial capacities reported for these forms are more likely corresponded to other epidemiological factors than to the morphotype of the populations. Lack of malaria parasite infection in An. stephensi, the most important vector of malaria, may be partly due to the success and achievement of ongoing active malaria control program in the region. PMID:24144130

Development of a paper-based carbon nanotube sensing microfluidic device for biological detection.

PubMed

Yang, Shih-I; Lei, Kin Fong; Tsai, Shiao-Wen; Hsu, Hsiao-Ting

2013-01-01

Carbon nanotube (CNT) has been utilized for the biological detection due to its extremely sensitive to biological molecules. A paper-based CNT sensing microfluidic device has been developed for the detection of protein, i.e., biotin-avidin, binding. We have developed a fabrication method that allows controlled deposition of bundled CNTs with well-defined dimensions to form sensors on paper. Then, polydimethyl siloxane (PDMS) was used to pattern the hydrophobic boundary on paper to form the reaction sites. The proposed fabrication method is based on vacuum filtration process with a metal mask covering on a filter paper for the definition of the dimension of sensor. The length, width, and thickness of the CNT-based sensors are readily controlled by the metal mask and the weight of the CNT powder used during the filtration process, respectively. Homogeneous deposition of CNTs with well-defined dimensions can be achieved. The CNT-based sensor on paper has been demonstrated on the detection of the protein binding. Biotin was first immobilized on the CNT's sidewall and avidin suspended solution was applied to the site. The result of the biotin-avidin binding was measured by the resistance change of the sensor, which is a label-free detection method. It showed the CNT is sensitive to the biological molecules and the proposed paper-based CNT sensing device is a possible candidate for point-of-care biosensors. Thus, electrical bio-assays on paper-based microfluidics can be realized to develop low cost, sensitive, and specific diagnostic devices.

[Confrontation of knowledge on alcohol concentration in blood and in exhaled air].

PubMed

Bauer, Miroslav; Bauerová, Jiřina; Šikuta, Ján; Šidlo, Jozef

2015-01-01

The authors of the paper give a brief historical overview of the development of experimental alcohology in the former Czechoslovakia. Enhanced attention is paid to tests of work quality control of toxicological laboratories. Information on results of control tests of blood samples using the method of gas chromatography in Slovakia and within a world-wide study "Eurotox 1990" is presented. There are pointed out the pitfalls related to objective evaluation of the analysis results interpreting alcohol concentration in biological materials and the associated need to eliminate a negative influence of the human factor. The authors recommend performing analyses of alcohol in biological materials only at accredited workplaces and in the case of samples storage to secure a mandatory inhibition of phosphorylation process. There are analysed the reasons of numerical differences of analyses while taking evidence of alcohol in blood and in exhaled air. The authors confirm analysis accuracy using the method of gas chromatography along with breath analysers of exhaled air. They highlight the need for making the analysis results more objective also through confrontation with the results of clinical examination and with examined circumstances. The authors suggest a method of elimination of the human factor, the most frequently responsible for inaccuracy, to a tolerable level (safety factor) and the need of sample analysis by two methods independent of each other or the need of analysis of two biological materials.

Vertebrate Pest Control. Sale Publication 4077.

ERIC Educational Resources Information Center

Stimmann, M. W.; Clark, Dell O.

This guide gives descriptions of common vertebrate pests and guidelines for using some common pesticides. The pests discussed are rats, mice, bats, moles, muskrats, ground squirrels, and gophers. Information is given for each pest on the type of damage the pest can do, the habitat and biology of the pest, and the most effective control methods.…

Invasive Species Guidebook for Department of Defense Installations in the Chesapeake Bay Watershed: Identification, Control, and Restoration

DTIC Science & Technology

2007-11-01

INSTALLATIONS IN THE CHESAPEAKE BAY WATERSHED IDENTIFICATION AND CONTROL METHODS Cogongrass ( Imperata cylindrica ) Description & Biology – A large...Crown vetch Coronilla varia MD, VA 14 Leafy spurge Euphorbia esula VA 15 Ground ivy Glechoma hederacea DC, MD, PA, VA, WV 17 Cogongrass Imperata

78 FR 59712 - Notice of Availability of the Draft Environmental Impact Statement for the 3 Bars Ecosystem and...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-27

... treatment methods would include manual, mechanical, and biological control treatments, prescribed fire or wildland fire for resource benefit, and other management actions. In order to implement the proposed 3 Bars... enhancement, fire and fuels management, control of weeds, woodland and rangeland values, wetland and riparian...

Managing scab diseases of potato and radish caused by Streptomyces spp. using Bacillus amyloliquefaciens BAC03 and other biomaterials

USDA-ARS?s Scientific Manuscript database

Streptomyces spp. cause scab disease in plants like potato and radish. To seek effective control methods of this disease, biologically based materials were examined on their efficacies for disease control. In greenhouse or growth chamber tests, potting soil was infested with Streptomyces scabies (10...

Epidemiologic Study of Malassezia Yeasts in Seborrheic Dermatitis Patients by the Analysis of 26S rDNA PCR-RFLP

PubMed Central

Oh, Byung Ho; Choe, Yong Beom; Ahn, Kyu Joong

2010-01-01

Background This case-control study concerns a molecular biological method based on the data gathered from a group of Korean subjects to examine the distribution of Malassezia yeasts in seborrheic dermatitis (SD) patients. Cultures for Malassezia yeasts were taken from the foreheads, cheeks and chests of 60 patients with SD and in 60 healthy controls of equivalent age. Objective The purpose of this study is to identify the relationship between certain species of Malassezia and SD. This was done by analyzing the differences in the distribution of Malassezia species in terms of age and body parts of the host with healthy controls. Methods 26S rDNA PCR-RFLP, a fast and accurate molecular biological method, was used to overcome the limits of morphological and biochemical methods. Results The positive Malassezia culture rate was 51.7% in patients with SD, which was lower than that of healthy adults (63.9%). M. restricta was dominant in patients with SD (19.5%). Likewise, M. restricta was identified as a common species (20.5%) in healthy controls. In the ages 31~40, M. restricta was found to be the most common species (31.6%) among SD patients. Conclusion According to the results of the study, the most frequently isolated species was M. restricta (19.5%) in patients with SD. There was no statistically significant difference in the distribution of Malassezia species between the SD patients and healthy control groups. PMID:20548904

Biomineralization of unicellular organisms: an unusual membrane biochemistry for the production of inorganic nano- and microstructures.

PubMed

Bäuerlein, Edmund

2003-02-10

With evolution, Nature has ingeniously succeeded in giving rise to an impressive variety of inorganic structures. Every organism that synthesizes biogenic minerals does so in a form that is unique to that species. This biomineralization is apparently biologically controlled. It is thus expected that both the synthesis and the form of every specific biogenic mineral is genetically determined and controlled. An investigation of the mechanism of biomineralization has only become possible with the development of modern methods in molecular biology. Unicellular organisms such as magnetic bacteria, calcareous algae, and diatoms, all of which are amongst the simplest forms of life, are particularly suited to be investigated by these methods. Crystals and composites of proteins and amorphous inorganic polymers are formed as complex structures within these organisms; these structures are not known in conventional inorganic chemistry.

Water-assisted crystallization of mesoporous anatase TiO2 nanospheres

NASA Astrophysics Data System (ADS)

Li, Na; Zhang, Qiao; Joo, Ji Bong; Lu, Zhenda; Dahl, Michael; Gan, Yang; Yin, Yadong

2016-04-01

We report a facile water-assisted crystallization process for the conversion of amorphous sol-gel derived TiO2 into mesoporous anatase nanostructures with a high surface area and well-controlled porosity and crystallinity. As an alternative to conventional calcination methods, this approach works under very mild conditions and is therefore much desired for broad biological, environmental and catalytic applications.We report a facile water-assisted crystallization process for the conversion of amorphous sol-gel derived TiO2 into mesoporous anatase nanostructures with a high surface area and well-controlled porosity and crystallinity. As an alternative to conventional calcination methods, this approach works under very mild conditions and is therefore much desired for broad biological, environmental and catalytic applications. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01892k

The effects of guided inquiry instruction on student achievement in high school biology

NASA Astrophysics Data System (ADS)

Vass, Laszlo

The purpose of this quantitative, quasi-experimental study was to measure the effect of a student-centered instructional method called guided inquiry on the achievement of students in a unit of study in high school biology. The study used a non-random sample of 109 students, the control group of 55 students enrolled in high school one, received teacher centered instruction while the experimental group of 54 students enrolled at high school two received student-centered, guided inquiry instruction. The pretest-posttest design of the study analyzed scores using an independent t-test, a dependent t-test (p = <.001), an ANCOVA (p = .007), mixed method ANOVA (p = .024) and hierarchical linear regression (p = <.001). The experimental group that received guided inquiry instruction had statistically significantly higher achievement than the control group.

Near-optimal experimental design for model selection in systems biology.

PubMed

Busetto, Alberto Giovanni; Hauser, Alain; Krummenacher, Gabriel; Sunnåker, Mikael; Dimopoulos, Sotiris; Ong, Cheng Soon; Stelling, Jörg; Buhmann, Joachim M

2013-10-15

Biological systems are understood through iterations of modeling and experimentation. Not all experiments, however, are equally valuable for predictive modeling. This study introduces an efficient method for experimental design aimed at selecting dynamical models from data. Motivated by biological applications, the method enables the design of crucial experiments: it determines a highly informative selection of measurement readouts and time points. We demonstrate formal guarantees of design efficiency on the basis of previous results. By reducing our task to the setting of graphical models, we prove that the method finds a near-optimal design selection with a polynomial number of evaluations. Moreover, the method exhibits the best polynomial-complexity constant approximation factor, unless P = NP. We measure the performance of the method in comparison with established alternatives, such as ensemble non-centrality, on example models of different complexity. Efficient design accelerates the loop between modeling and experimentation: it enables the inference of complex mechanisms, such as those controlling central metabolic operation. Toolbox 'NearOED' available with source code under GPL on the Machine Learning Open Source Software Web site (mloss.org).

sbv IMPROVER: Modern Approach to Systems Biology.

PubMed

Guryanova, Svetlana; Guryanova, Anna

2017-01-01

The increasing amount and variety of data in biosciences call for innovative methods of visualization, scientific verification, and pathway analysis. Novel approaches to biological networks and research quality control are important because of their role in development of new products, improvement, and acceleration of existing health policies and research for novel ways of solving scientific challenges. One such approach is sbv IMPROVER. It is a platform that uses crowdsourcing and verification to create biological networks with easy public access. It contains 120 networks built in Biological Expression Language (BEL) to interpret data from PubMed articles with high-quality verification available for free on the CBN database. Computable, human-readable biological networks with a structured syntax are a powerful way of representing biological information generated from high-density data. This article presents sbv IMPROVER, a crowd-verification approach for the visualization and expansion of biological networks.

Real-time measurements of airborne biologic particles using fluorescent particle counter to evaluate microbial contamination: results of a comparative study in an operating theater.

PubMed

Dai, Chunyang; Zhang, Yan; Ma, Xiaoling; Yin, Meiling; Zheng, Haiyang; Gu, Xuejun; Xie, Shaoqing; Jia, Hengmin; Zhang, Liang; Zhang, Weijun

2015-01-01

Airborne bacterial contamination poses a risk for surgical site infection, and routine surveillance of airborne bacteria is important. Traditional methods for detecting airborne bacteria are time consuming and strenuous. Measurement of biologic particle concentrations using a fluorescent particle counter is a novel method for evaluating air quality. The current study was to determine whether the number of biologic particles detected by the fluorescent particle counter can be used to indicate airborne bacterial counts in operating rooms. The study was performed in an operating theater at a university hospital in Hefei, China. The number of airborne biologic particles every minute was quantified using a fluorescent particle counter. Microbiologic air sampling was performed every 30 minutes using an Andersen air sampler (Pusong Electronic Instruments, Changzhou, China). Correlations between the 2 different methods were analyzed by Pearson correlation coefficients. A significant correlation was observed between biologic particle and bacterial counts (Pearson correlation coefficient = 0.76), and the counting results from 2 methods both increased substantially between operations, corresponding with human movements in the operating room. Fluorescent particle counters show potential as important tools for monitoring bacterial contamination in operating theatres. Copyright © 2015 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions.

PubMed

Bauler, Patricia; Huber, Gary A; McCammon, J Andrew

2012-04-28

Diffusion is often the rate determining step in many biological processes. Currently, the two main computational methods for studying diffusion are stochastic methods, such as Brownian dynamics, and continuum methods, such as the finite element method. This paper proposes a new hybrid diffusion method that couples the strengths of each of these two methods. The method is derived for a general multidimensional system, and is presented using a basic test case for 1D linear and radially symmetric diffusion systems.

Selection of reference genes for RT-qPCR analysis in a predatory biological control agent, Coleomegilla maculata (Coleoptera: Coccinellidae).

PubMed

Yang, Chunxiao; Pan, Huipeng; Noland, Jeffrey Edward; Zhang, Deyong; Zhang, Zhanhong; Liu, Yong; Zhou, Xuguo

2015-12-10

Reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) is a reliable technique for quantifying gene expression across various biological processes, of which requires a set of suited reference genes to normalize the expression data. Coleomegilla maculata (Coleoptera: Coccinellidae), is one of the most extensively used biological control agents in the field to manage arthropod pest species. In this study, expression profiles of 16 housekeeping genes selected from C. maculata were cloned and investigated. The performance of these candidates as endogenous controls under specific experimental conditions was evaluated by dedicated algorithms, including geNorm, Normfinder, BestKeeper, and ΔCt method. In addition, RefFinder, a comprehensive platform integrating all the above-mentioned algorithms, ranked the overall stability of these candidate genes. As a result, various sets of suitable reference genes were recommended specifically for experiments involving different tissues, developmental stages, sex, and C. maculate larvae treated with dietary double stranded RNA. This study represents the critical first step to establish a standardized RT-qPCR protocol for the functional genomics research in a ladybeetle C. maculate. Furthermore, it lays the foundation for conducting ecological risk assessment of RNAi-based gene silencing biotechnologies on non-target organisms; in this case, a key predatory biological control agent.

MIVOC method with temperature controla)

NASA Astrophysics Data System (ADS)

Takasugi, W.; Wakaisami, M.; Sasaki, N.; Sakuma, T.; Yamamoto, M.; Kitagawa, A.; Muramatsu, M.

2010-02-01

The Heavy Ion Medical Accelerator in Chiba at the National Institute of Radiological Sciences has been used for cancer therapy, physics, and biology experiments since 1994. Its ion sources produce carbon ion for cancer therapy. They also produce various ions (H+-Xe21+) for physics and biology experiments. Most ion species are produced from gases by an 18 GHz electron cyclotron resonance ion source. However, some of ion species is difficult to produce from stable and secure gases. Such ion species are produced by the sputtering method. However, it is necessary to reduce material consumption rate as much as possible in the case of rare and expensive stable isotopes. We have selected "metal ions from volatile compounds method" as a means to solve this problem. We tested a variety of compounds. Since each compound has a suitable temperature to obtain the optimum vapor pressure, we have developed an accurate temperature control system. We have produced ions such as F58e9+, Co9+, Mg5+, Ti10+, Si5+, and Ge12+ with the temperature control.

Chemical copatterning strategies using azlactone-based block copolymers

DOE PAGES

Masigol, Mohammadali; Barua, Niloy; Retterer, Scott T.; ...

2017-09-01

Interfaces can be modified with azlactone-functional polymers in order to manipulate the chemical surface reactivity. Azlactone groups are highly reactive toward amine, thiol, and alcohol nucleophiles, providing a versatile coupling chemistry for secondary surface modification. Azlactone-based surface polymers have been explored in numerous applications, including chemical and biological capture, sensing, and cell culture. These applications often require that the polymer is copatterned within a chemically or biologically inert background; however, common fabrication methods degrade azlactone groups during processing steps or result in polymer films with poorly controlled thicknesses. Here, the authors develop fabrication strategies using parylene lift-off and interface-directed assemblymore » methods to generate microscale patterns of azlactone-based block copolymer in chemically or biologically inert backgrounds. The functionality of azlactone groups was preserved during fabrication, and patterned films appeared as uniform, 80–120nm brushlike films. The authors also develop a patterning approach that uses a novel microcontact stamping method to generate cross-linked, three-dimensional structures of azlactone-based polymers with controllable, microscale thicknesses. The authors identify the benefits of each approach and expect these polymers and patterning strategies to provide a versatile toolbox for developing synthetic interfaces with tuned chemical and physical features for sensing, cell culture, or material capture applications.« less

Chemical copatterning strategies using azlactone-based block copolymers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Masigol, Mohammadali; Barua, Niloy; Retterer, Scott T.

Interfaces can be modified with azlactone-functional polymers in order to manipulate the chemical surface reactivity. Azlactone groups are highly reactive toward amine, thiol, and alcohol nucleophiles, providing a versatile coupling chemistry for secondary surface modification. Azlactone-based surface polymers have been explored in numerous applications, including chemical and biological capture, sensing, and cell culture. These applications often require that the polymer is copatterned within a chemically or biologically inert background; however, common fabrication methods degrade azlactone groups during processing steps or result in polymer films with poorly controlled thicknesses. Here, the authors develop fabrication strategies using parylene lift-off and interface-directed assemblymore » methods to generate microscale patterns of azlactone-based block copolymer in chemically or biologically inert backgrounds. The functionality of azlactone groups was preserved during fabrication, and patterned films appeared as uniform, 80–120nm brushlike films. The authors also develop a patterning approach that uses a novel microcontact stamping method to generate cross-linked, three-dimensional structures of azlactone-based polymers with controllable, microscale thicknesses. The authors identify the benefits of each approach and expect these polymers and patterning strategies to provide a versatile toolbox for developing synthetic interfaces with tuned chemical and physical features for sensing, cell culture, or material capture applications.« less

Enhancing biological relevance of a weighted gene co-expression network for functional module identification.

PubMed

Prom-On, Santitham; Chanthaphan, Atthawut; Chan, Jonathan Hoyin; Meechai, Asawin

2011-02-01

Relationships among gene expression levels may be associated with the mechanisms of the disease. While identifying a direct association such as a difference in expression levels between case and control groups links genes to disease mechanisms, uncovering an indirect association in the form of a network structure may help reveal the underlying functional module associated with the disease under scrutiny. This paper presents a method to improve the biological relevance in functional module identification from the gene expression microarray data by enhancing the structure of a weighted gene co-expression network using minimum spanning tree. The enhanced network, which is called a backbone network, contains only the essential structural information to represent the gene co-expression network. The entire backbone network is decoupled into a number of coherent sub-networks, and then the functional modules are reconstructed from these sub-networks to ensure minimum redundancy. The method was tested with a simulated gene expression dataset and case-control expression datasets of autism spectrum disorder and colorectal cancer studies. The results indicate that the proposed method can accurately identify clusters in the simulated dataset, and the functional modules of the backbone network are more biologically relevant than those obtained from the original approach.

Benefits and Limitations of DNA Barcoding and Metabarcoding in Herbal Product Authentication

PubMed Central

Raclariu, Ancuta Cristina; Heinrich, Michael; Ichim, Mihael Cristin

2017-01-01

Abstract Introduction Herbal medicines play an important role globally in the health care sector and in industrialised countries they are often considered as an alternative to mono‐substance medicines. Current quality and authentication assessment methods rely mainly on morphology and analytical phytochemistry‐based methods detailed in pharmacopoeias. Herbal products however are often highly processed with numerous ingredients, and even if these analytical methods are accurate for quality control of specific lead or marker compounds, they are of limited suitability for the authentication of biological ingredients. Objective To review the benefits and limitations of DNA barcoding and metabarcoding in complementing current herbal product authentication. Method Recent literature relating to DNA based authentication of medicinal plants, herbal medicines and products are summarised to provide a basic understanding of how DNA barcoding and metabarcoding can be applied to this field. Results Different methods of quality control and authentication have varying resolution and usefulness along the value chain of these products. DNA barcoding can be used for authenticating products based on single herbal ingredients and DNA metabarcoding for assessment of species diversity in processed products, and both methods should be used in combination with appropriate hyphenated chemical methods for quality control. Conclusions DNA barcoding and metabarcoding have potential in the context of quality control of both well and poorly regulated supply systems. Standardisation of protocols for DNA barcoding and DNA sequence‐based identification are necessary before DNA‐based biological methods can be implemented as routine analytical approaches and approved by the competent authorities for use in regulated procedures. © 2017 The Authors. Phytochemical Analysis Published by John Wiley & Sons Ltd. PMID:28906059

Biological Control of Appetite: A Daunting Complexity

PubMed Central

MacLean, Paul S.; Blundell, John E.; Mennella, Julie A.; Batterham, Rachel L.

2017-01-01

Objective This review summarizes a portion of the discussions of an NIH Workshop (Bethesda, MD, 2015) entitled, “Self-Regulation of Appetite, It's Complicated,” which focused on the biological aspects of appetite regulation. Methods Here we summarize the key biological inputs of appetite regulation and their implications for body weight regulation. Results These discussions offer an update of the long-held, rigid perspective of an “adipocentric” biological control, taking a broader view that also includes important inputs from the digestive tract, from lean mass, and from the chemical sensory systems underlying taste and smell. We are only beginning to understand how these biological systems are integrated and how this integrated input influences appetite and food eating behaviors. The relevance of these biological inputs was discussed primarily in the context of obesity and the problem of weight regain, touching on topics related to the biological predisposition for obesity and the impact that obesity treatments (dieting, exercise, bariatric surgery, etc.) might have on appetite and weight loss maintenance. Finally, we consider a common theme that pervaded the workshop discussions, which was individual variability. Conclusions It is this individual variability in the predisposition for obesity and in the biological response to weight loss that makes the biological component of appetite regulation so complicated. When this individual biological variability is placed in the context of the diverse environmental and behavioral pressures that also influence food eating behaviors, it is easy to appreciate the daunting complexities that arise with the self-regulation of appetite. PMID:28229538

Exploring a new method for the biological monitoring of plastic workers exposed to the vinyl chloride monomer.

PubMed

Azari, Mansour Rezazadeh; Tayefeh-Rahimian, Raana; Jafari, Mohamad Javad; Souri, Hamid; Shokoohi, Yasser; Tavakol, Alaheh; Yazdanbakhsh, Zahra

2016-12-01

Vinyl chloride monomer (VCM) is widely used in the production of polyvinyl chloride (PVC) plastics. VCM is recognized as a confirmed human and animal carcinogenic compound. Recent studies have reported poor health of plastic workers, even having exposure at concentrations below the permissible limit to VCM. There has not been any study regarding exposed workers to VCM in Iran. Similarly, no information exists as to the biological monitoring of such workers. The main purpose of this study was to conduct a thorough occupational and biological monitoring of Iranian plastic workers exposed to VCM.A total of 100 workers from two plastic manufacturing plants (A and B) in Tehran along with 25 unexposed workers as controls were studied. The personal monitoring of all nonsmoking workers exposed to VCM at two plastic manufacturing plants (A and B) was performed in the morning shift (8 a.m. to 4 p.m.) according to the National Institute For Occupational Safety And Health method no. 1007.Biological monitoring of workers was carried out through collection of exhaled breath of all exposed and control workers in Tedlar bags and with a subsequent analysis using gas chromatography-flame ionization detector.Not only the mean occupational exposure of workers to VCM at plant A was higher than the respective threshold limit value but also the statistical significance was higher than workers at plant B. Similarly, VCM concentration in exhaled breath of workers at plant A was also statistically significantly higher than at plant B. Correlation of occupational exposure of all workers to vinyl chloride with its concentration in exhaled breath was statistically significant.This is the first study on biological monitoring for exposed plastic workers to VCM using exhaled breath. On the basis of the results in this study, a novel method of biological monitoring of plastic workers was proposed. © The Author(s) 2015.

Novel biomaterials: plasma-enabled nanostructures and functions

NASA Astrophysics Data System (ADS)

Levchenko, Igor; Keidar, Michael; Cvelbar, Uroš; Mariotti, Davide; Mai-Prochnow, Anne; Fang, Jinghua; (Ken Ostrikov, Kostya

2016-07-01

Material processing techniques utilizing low-temperature plasmas as the main process tool feature many unique capabilities for the fabrication of various nanostructured materials. As compared with the neutral-gas based techniques and methods, the plasma-based approaches offer higher levels of energy and flux controllability, often leading to higher quality of the fabricated nanomaterials and sometimes to the synthesis of the hierarchical materials with interesting properties. Among others, nanoscale biomaterials attract significant attention due to their special properties towards the biological materials (proteins, enzymes), living cells and tissues. This review briefly examines various approaches based on the use of low-temperature plasma environments to fabricate nanoscale biomaterials exhibiting high biological activity, biological inertness for drug delivery system, and other features of the biomaterials make them highly attractive. In particular, we briefly discuss the plasma-assisted fabrication of gold and silicon nanoparticles for bio-applications; carbon nanoparticles for bioimaging and cancer therapy; carbon nanotube-based platforms for enzyme production and bacteria growth control, and other applications of low-temperature plasmas in the production of biologically-active materials.

Anopheline Reproductive Biology: Impacts on Vectorial Capacity and Potential Avenues for Malaria Control.

PubMed

Mitchell, Sara N; Catteruccia, Flaminia

2017-12-01

Vectorial capacity is a mathematical approximation of the efficiency of vector-borne disease transmission, measured as the number of new infections disseminated per case per day by an insect vector. Multiple elements of mosquito biology govern their vectorial capacity, including survival, population densities, feeding preferences, and vector competence. Intriguingly, biological pathways essential to mosquito reproductive fitness directly or indirectly influence a number of these elements. Here, we explore this complex interaction, focusing on how the interplay between mating and blood feeding in female Anopheles not only shapes their reproductive success but also influences their ability to sustain Plasmodium parasite development. Central to malaria transmission, mosquito reproductive biology has recently become the focus of research strategies aimed at malaria control, and we discuss promising new methods based on the manipulation of key reproductive steps. In light of widespread resistance to all public health-approved insecticides targeting mosquito reproduction may prove crucial to the success of malaria-eradication campaigns. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

p53 as Batman: using a movie plot to understand control of the cell cycle.

PubMed

Gadi, Nikhita; Foley, Sage E; Nowey, Mark; Plopper, George E

2013-04-16

This Teaching Resource provides and describes a two-part classroom exercise to help students understand control of the cell cycle, with a focus on the transcription factor p53, the E3 ubiquitin ligase Mdm2, the Mdm2 inhibitor ARF, the kinases ATM and ATR, the kinase Chk2, and the cell cycle inhibitor p21(Cip1). Students use characters and scenes from the movie The Dark Knight to represent elements of the cell cycle control machinery, then they apply these characters and scenes to translate a primary research article on p53 function into a new movie scene in the "Batman universe." This exercise is appropriate for college-level courses in cell biology and cancer biology and requires students to have a background in introductory cell biology. Explicit learning outcomes and associated assessment methods are provided, as well as slides, student assignments, the primary research article, and an instructor's guide for the exercise.

Preparation and development of block copolypeptide vesicles and hydrogels for biological and medical applications.

PubMed

Deming, Timothy J

2014-01-01

There have been many recent advances in the controlled polymerization of α-amino acid-N-carboxyanhydride (NCA) monomers into well-defined block copolypeptides. Transition metal initiating systems allow block copolypeptide synthesis with excellent control over number and lengths of block segments, chain length distribution, and chain-end functionality. Using this and other methods, block copolypeptides of controlled dimensions have been prepared and their self-assembly into organized structures studied by many research groups. The ability of well-defined block copolypeptides to assemble into supramolecular copolypeptide vesicles and hydrogels has led to the development of these materials for use in biological and medical applications. These assemblies have been found to possess unique properties that are derived from the amino acid building blocks and ordered conformations of the polypeptide segments. Recent work on the incorporation of active and stimulus-responsive functionality in these materials has tremendously increased their potential for use in biological and medical studies. © 2014 Wiley Periodicals, Inc.

Sensitivity to Structure in the Speech Signal by Children with Speech Sound Disorder and Reading Disability

ERIC Educational Resources Information Center

Johnson, Erin Phinney; Pennington, Bruce F.; Lowenstein, Joanna H.; Nittrouer, Susan

2011-01-01

Research Design;Intervention;Biology;Biotechnology;Teaching Methods;Hands on Science;Professional Development;Comparative Analysis;Genetics;Evaluation;Pretests Posttests;Control Groups;Science Education;Science Instruction;Pedagogical Content Knowledge;

Glycan Engineering for Cell and Developmental Biology.

PubMed

Griffin, Matthew E; Hsieh-Wilson, Linda C

2016-01-21

Cell-surface glycans are a diverse class of macromolecules that participate in many key biological processes, including cell-cell communication, development, and disease progression. Thus, the ability to modulate the structures of glycans on cell surfaces provides a powerful means not only to understand fundamental processes but also to direct activity and elicit desired cellular responses. Here, we describe methods to sculpt glycans on cell surfaces and highlight recent successes in which artificially engineered glycans have been employed to control biological outcomes such as the immune response and stem cell fate. Copyright © 2016 Elsevier Ltd. All rights reserved.

Reverse engineering and identification in systems biology: strategies, perspectives and challenges.

PubMed

Villaverde, Alejandro F; Banga, Julio R

2014-02-06

The interplay of mathematical modelling with experiments is one of the central elements in systems biology. The aim of reverse engineering is to infer, analyse and understand, through this interplay, the functional and regulatory mechanisms of biological systems. Reverse engineering is not exclusive of systems biology and has been studied in different areas, such as inverse problem theory, machine learning, nonlinear physics, (bio)chemical kinetics, control theory and optimization, among others. However, it seems that many of these areas have been relatively closed to outsiders. In this contribution, we aim to compare and highlight the different perspectives and contributions from these fields, with emphasis on two key questions: (i) why are reverse engineering problems so hard to solve, and (ii) what methods are available for the particular problems arising from systems biology?

Trends and Controls of inter-annual Variability in the Carbon Budget of Terrestrial Ecosystems

NASA Astrophysics Data System (ADS)

Cescatti, A.; Marcolla, B.

2014-12-01

The climate sensitivity of the terrestrial carbon budget will substantially affect the sign and strength of the land-climate feedbacks and the future climate trajectories. Current trends in the inter-annual variability of terrestrial carbon fluxes (IAV) may contribute to clarify the relative role of physical and biological controls of ecosystem responses to climate change. For this purpose we investigated how recent climate variability has impacted the carbon fluxes at long-term FLUXNET sites. Using a novel method, the IAV has been factored out in climate induced variability (physical control), variability due to changes in ecosystem functioning (biological control) and the interaction of the two terms. The relative control of the main climatic drivers (temperature, water availability) on the physical and biological sources of IAV has been investigated using both site level fluxes and global gridded products generated from the up-scaling of flux data. Results of this analysis highlight the fundamental role of precipitation trends on the pattern of IAV in the last 30 years. Our findings on the spatial/temporal trends of IAV have been finally confirmed using the signal derived from the global network of atmospheric CO2 concentrations measurements.

Will Systems Biology Deliver Its Promise and Contribute to the Development of New or Improved Vaccines? What Really Constitutes the Study of "Systems Biology" and How Might Such an Approach Facilitate Vaccine Design.

PubMed

Germain, Ronald N

2017-10-16

A dichotomy exists in the field of vaccinology about the promise versus the hype associated with application of "systems biology" approaches to rational vaccine design. Some feel it is the only way to efficiently uncover currently unknown parameters controlling desired immune responses or discover what elements actually mediate these responses. Others feel that traditional experimental, often reductionist, methods for incrementally unraveling complex biology provide a more solid way forward, and that "systems" approaches are costly ways to collect data without gaining true insight. Here I argue that both views are inaccurate. This is largely because of confusion about what can be gained from classical experimentation versus statistical analysis of large data sets (bioinformatics) versus methods that quantitatively explain emergent properties of complex assemblies of biological components, with the latter reflecting what was previously called "physiology." Reductionist studies will remain essential for generating detailed insight into the functional attributes of specific elements of biological systems, but such analyses lack the power to provide a quantitative and predictive understanding of global system behavior. But by employing (1) large-scale screening methods for discovery of unknown components and connections in the immune system ( omics ), (2) statistical analysis of large data sets ( bioinformatics ), and (3) the capacity of quantitative computational methods to translate these individual components and connections into models of emergent behavior ( systems biology ), we will be able to better understand how the overall immune system functions and to determine with greater precision how to manipulate it to produce desired protective responses. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Simulation of temperature distribution in tumor Photothermal treatment

NASA Astrophysics Data System (ADS)

Zhang, Xiyang; Qiu, Shaoping; Wu, Shulian; Li, Zhifang; Li, Hui

2018-02-01

The light transmission in biological tissue and the optical properties of biological tissue are important research contents of biomedical photonics. It is of great theoretical and practical significance in medical diagnosis and light therapy of disease. In this paper, the temperature feedback-controller was presented for monitoring photothermal treatment in realtime. Two-dimensional Monte Carlo (MC) and diffuse approximation were compared and analyzed. The results demonstrated that diffuse approximation using extrapolated boundary conditions by finite element method is a good approximation to MC simulation. Then in order to minimize thermal damage, real-time temperature monitoring was appraised by proportional-integral-differential (PID) controller in the process of photothermal treatment.

Fungal Phytotoxins with Potential Herbicidal Activity to Control Chenopodium album.

PubMed

Cimmino, Alessio; Masi, Marco; Evidente, Marco; Evidente, Antonio

2015-06-01

This review deals with the isolation and chemical and biological characterization of phytotoxins produced by Ascochyta caulina and Phoma chenopodiicola proposed as mycoherbicides for the biological control of Chenopodium album, a worldwide spread weed which causes serious problems to some agrarian crops, including sugar beet and maize. Studies on the structure activity relationships and on the modes of actions of toxins isolated are also described, as well as the optimization of analytical methods focused on selection of the best fungal toxin producers. The attempts to scale up production of these phytotoxins aimed to obtain sufficient amounts for their application in greenhouse and field trials are also reported.

Linear control theory for gene network modeling.

PubMed

Shin, Yong-Jun; Bleris, Leonidas

2010-09-16

Systems biology is an interdisciplinary field that aims at understanding complex interactions in cells. Here we demonstrate that linear control theory can provide valuable insight and practical tools for the characterization of complex biological networks. We provide the foundation for such analyses through the study of several case studies including cascade and parallel forms, feedback and feedforward loops. We reproduce experimental results and provide rational analysis of the observed behavior. We demonstrate that methods such as the transfer function (frequency domain) and linear state-space (time domain) can be used to predict reliably the properties and transient behavior of complex network topologies and point to specific design strategies for synthetic networks.

Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future

PubMed Central

Barnes, Stephen; Benton, H. Paul; Casazza, Krista; Cooper, Sara; Cui, Xiangqin; Du, Xiuxia; Engler, Jeffrey; Kabarowski, Janusz H.; Li, Shuzhao; Pathmasiri, Wimal; Prasain, Jeevan K.; Renfrow, Matthew B.; Tiwari, Hemant K.

2017-01-01

Metabolomics, a systems biology discipline representing analysis of known and unknown pathways of metabolism, has grown tremendously over the past 20 years. Because of its comprehensive nature, metabolomics requires careful consideration of the question(s) being asked, the scale needed to answer the question(s), collection and storage of the sample specimens, methods for extraction of the metabolites from biological matrices, the analytical method(s) to be employed and the quality control of the analyses, how collected data are correlated, the statistical methods to determine metabolites undergoing significant change, putative identification of metabolites, and the use of stable isotopes to aid in verifying metabolite identity and establishing pathway connections and fluxes. This second part of a comprehensive description of the methods of metabolomics focuses on data analysis, emerging methods in metabolomics and the future of this discipline. PMID:28239968

An Adaptive Method of Lines with Error Control for Parabolic Equations of the Reaction-Diffusion Type.

DTIC Science & Technology

1984-06-01

space discretization error . 1. I 3 1. INTRODUCTION Reaction- diffusion processes occur in many branches of biology and physical chemistry. Examples...to model reaction- diffusion phenomena. The primary goal of this adaptive method is to keep a particular norm of the space discretization error less...AD-A142 253 AN ADAPTIVE MET6 OFD LNES WITH ERROR CONTROL FOR 1 INST FOR PHYSICAL SCIENCE AND TECH. I BABUSKAAAO C7 EA OH S UMR AN UNVC EEP R

Controlled biological and biomimetic systems for landmine detection.

PubMed

Habib, Maki K

2007-08-30

Humanitarian demining requires to accurately detect, locate and deactivate every single landmine and other buried mine-like objects as safely and as quickly as possible, and in the most non-invasive manner. The quality of landmine detection affects directly the efficiency and safety of this process. Most of the available methods to detect explosives and landmines are limited by their sensitivity and/or operational complexities. All landmines leak with time small amounts of their explosives that can be found on surrounding ground and plant life. Hence, explosive signatures represent the robust primary indicator of landmines. Accordingly, developing innovative technologies and efficient techniques to identify in real-time explosives residue in mined areas represents an attractive and promising approach. Biological and biologically inspired detection technology has the potential to compete with or be used in conjunction with other artificial technology to complement performance strengths. Biological systems are sensitive to many different scents concurrently, a property that has proven difficult to replicate artificially. Understanding biological systems presents unique opportunities for developing new capabilities through direct use of trained bio-systems, integration of living and non-living components, or inspiring new design by mimicking biological capabilities. It is expected that controlled bio-systems, biotechnology and microbial techniques will contribute to the advancement of mine detection and other application domains. This paper provides directions, evaluation and analysis on the progress of controlled biological and biomimetic systems for landmine detection. It introduces and discusses different approaches developed, underlining their relative advantages and limitations, and highlighting trends, safety and ecology concern, and possible future directions.

Biology and Control of Insect and Related Pests of Livestock in Wyoming. MP-23.

ERIC Educational Resources Information Center

Lloyd, John E.

This document provides information that a potential insecticide applicator can utilize to safely and effectively control insects and related pests of livestock. The first section of the manual discusses the general methods of preparation and application of insecticides. The second section concerns itself with the recognition of insect problems,…

The issues of weed infestation with environmentally hazardous plants and methods of their control

NASA Astrophysics Data System (ADS)

Bogdanov, V. L.; Posternak, T. S.; Pasko, O. A.; Kovyazin, V. F.

2016-09-01

The authors analyze expansion of segetal and ruderal vegetation on agricultural lands in Leningrad and Tomsk oblasts, typical for the European and Asian parts of Russia. The spreading conditions, composition of species, biological features and ecological requirements of the most aggressive species are identified. Some effective ways of weed control are suggested.

Benefits and Limitations of DNA Barcoding and Metabarcoding in Herbal Product Authentication.

PubMed

Raclariu, Ancuta Cristina; Heinrich, Michael; Ichim, Mihael Cristin; de Boer, Hugo

2018-03-01

Herbal medicines play an important role globally in the health care sector and in industrialised countries they are often considered as an alternative to mono-substance medicines. Current quality and authentication assessment methods rely mainly on morphology and analytical phytochemistry-based methods detailed in pharmacopoeias. Herbal products however are often highly processed with numerous ingredients, and even if these analytical methods are accurate for quality control of specific lead or marker compounds, they are of limited suitability for the authentication of biological ingredients. To review the benefits and limitations of DNA barcoding and metabarcoding in complementing current herbal product authentication. Recent literature relating to DNA based authentication of medicinal plants, herbal medicines and products are summarised to provide a basic understanding of how DNA barcoding and metabarcoding can be applied to this field. Different methods of quality control and authentication have varying resolution and usefulness along the value chain of these products. DNA barcoding can be used for authenticating products based on single herbal ingredients and DNA metabarcoding for assessment of species diversity in processed products, and both methods should be used in combination with appropriate hyphenated chemical methods for quality control. DNA barcoding and metabarcoding have potential in the context of quality control of both well and poorly regulated supply systems. Standardisation of protocols for DNA barcoding and DNA sequence-based identification are necessary before DNA-based biological methods can be implemented as routine analytical approaches and approved by the competent authorities for use in regulated procedures. © 2017 The Authors. Phytochemical Analysis Published by John Wiley & Sons Ltd. © 2017 The Authors. Phytochemical Analysis Published by John Wiley & Sons Ltd.

Cellular Engineering with Membrane Fusogenic Liposomes to Produce Functionalized Extracellular Vesicles.

PubMed

Lee, Junsung; Lee, Hyoungjin; Goh, Unbyeol; Kim, Jiyoung; Jeong, Moonkyoung; Lee, Jean; Park, Ji-Ho

2016-03-23

Engineering of extracellular vesicles (EVs) without affecting biological functions remains a challenge, limiting the broad applications of EVs in biomedicine. Here, we report a method to equip EVs with various functional agents, including fluorophores, drugs, lipids, and bio-orthogonal chemicals, in an efficient and controlled manner by engineering parental cells with membrane fusogenic liposomes, while keeping the EVs intact. As a demonstration of how this method can be applied, we prepared EVs containing azide-lipids, and conjugated them with targeting peptides using copper-free click chemistry to enhance targeting efficacy to cancer cells. We believe that this liposome-based cellular engineering method will find utility in studying the biological roles of EVs and delivering therapeutic agents through their innate pathway.

Biologic Potential of Calcium Phosphate Biopowders Produced via Decomposition Combustion Synthesis

PubMed Central

Vollmer, N.; King, K.B.; Ayers, R.

2015-01-01

The aim of this research was to evaluate the biologic potential of calcium phosphate (CaP) biopowders produced with a novel reaction synthesis system. Decomposition combustion synthesis (DCS) is a modified combustion synthesis method capable of producing CaP powders for use in bone tissue engineering applications. During DCS, the stoichiometric ratio of reactant salt to fuel was adjusted to alter product chemistry and morphology. In vitro testing methods were utilized to determine the effects of controlling product composition on cytotoxicity, proliferation, biocompatibility and biomineralization. In vitro, human fetal osteoblasts (ATCC, CRL-11372) cultured with CaP powder displayed a flattened morphology, and uniformly encompassed the CaP particulates. Matrix vesicles containing calcium and phosphorous budded from the osteoblast cells. CaP powders produced via DCS are a source of biologically active, synthetic, bone graft substitute materials PMID:26034341

Assessing the Biological Safety Profession's Evaluation and Control of Risks Associated with the Field Collection of Potentially Infectious Specimens.

PubMed

Patlovich, Scott J; Emery, Robert J; Whitehead, Lawrence W; Brown, Eric L; Flores, Rene

2015-03-01

Because the origins of the biological safety profession are rooted in the control and prevention of laboratory-associated infections, the vocation focuses primarily on the safe handling of specimens within the laboratory. But in many cases, the specimens and samples handled in the lab are originally collected in the field where a broader set of possible exposure considerations may be present, each with varying degrees of controllability. The failure to adequately control the risks associated with collecting biological specimens in the field may result in illness or injury, and could have a direct impact on laboratory safety, if infectious specimens were packaged or transported inappropriately, for example. This study developed a web-based survey distributed to practicing biological safety professionals to determine the prevalence of and extent to which biological safety programs consider and evaluate field collection activities. In cases where such issues were considered, the data collected characterize the types of controls and methods of oversight at the institutional level that are employed. Sixty-one percent (61%) of the survey respondents indicated that research involving the field collection of biological specimens is conducted at their institutions. A majority (79%) of these field collection activities occur at academic institutions. Twenty-seven percent (27%) of respondents indicated that their safety committees do not consider issues related to biological specimens collected in the field, and only 25% with an oversight committee charged to review field collection protocols have generated a field research-specific risk assessment form to facilitate the assembly of pertinent information for a project risk assessment review. The results also indicated that most biosafety professionals (73% overall; 71% from institutions conducting field collection activities) have not been formally trained on the topic, but many (64% overall; 87% from institutions conducting field collection activities) indicated that training on field research safety issues would be helpful, and even more (71% overall; 93% from institutions conducting field collection activities) would consider participation in such a training course. Results obtained from this study can be used to develop a field research safety toolkit and associated training curricula specifically targeted to biological safety professionals.

Biological Matrix Effects in Quantitative Tandem Mass Spectrometry-Based Analytical Methods: Advancing Biomonitoring

PubMed Central

Panuwet, Parinya; Hunter, Ronald E.; D’Souza, Priya E.; Chen, Xianyu; Radford, Samantha A.; Cohen, Jordan R.; Marder, M. Elizabeth; Kartavenka, Kostya; Ryan, P. Barry; Barr, Dana Boyd

2015-01-01

The ability to quantify levels of target analytes in biological samples accurately and precisely, in biomonitoring, involves the use of highly sensitive and selective instrumentation such as tandem mass spectrometers and a thorough understanding of highly variable matrix effects. Typically, matrix effects are caused by co-eluting matrix components that alter the ionization of target analytes as well as the chromatographic response of target analytes, leading to reduced or increased sensitivity of the analysis. Thus, before the desired accuracy and precision standards of laboratory data are achieved, these effects must be characterized and controlled. Here we present our review and observations of matrix effects encountered during the validation and implementation of tandem mass spectrometry-based analytical methods. We also provide systematic, comprehensive laboratory strategies needed to control challenges posed by matrix effects in order to ensure delivery of the most accurate data for biomonitoring studies assessing exposure to environmental toxicants. PMID:25562585

Quantitative proteomics in biological research.

PubMed

Wilm, Matthias

2009-10-01

Proteomics has enabled the direct investigation of biological material, at first through the analysis of individual proteins, then of lysates from cell cultures, and finally of extracts from tissues and biopsies from entire organisms. Its latest manifestation - quantitative proteomics - allows deeper insight into biological systems. This article reviews the different methods used to extract quantitative information from mass spectra. It follows the technical developments aimed toward global proteomics, the attempt to characterize every expressed protein in a cell by at least one peptide. When applications of the technology are discussed, the focus is placed on yeast biology. In particular, differential quantitative proteomics, the comparison between an experiment and its control, is very discriminating for proteins involved in the process being studied. When trying to understand biological processes on a molecular level, differential quantitative proteomics tends to give a clearer picture than global transcription analyses. As a result, MS has become an even more indispensable tool for biochemically motivated biological research.

Indirect nontarget effects of host-specific biological control agents: Implications for biological control

Treesearch

Dean E. Pearson; Ragan M. Callaway

2005-01-01

Classical biological control of weeds currently operates under the assumption that biological control agents are safe (i.e., low risk) if they do not directly attack nontarget species. However, recent studies indicate that even highly host-specific biological control agents can impact nontarget species through indirect effects. This finding has profound...

Detecting Rhythms in Time Series with RAIN

PubMed Central

Thaben, Paul F.; Westermark, Pål O.

2014-01-01

A fundamental problem in research on biological rhythms is that of detecting and assessing the significance of rhythms in large sets of data. Classic methods based on Fourier theory are often hampered by the complex and unpredictable characteristics of experimental and biological noise. Robust nonparametric methods are available but are limited to specific wave forms. We present RAIN, a robust nonparametric method for the detection of rhythms of prespecified periods in biological data that can detect arbitrary wave forms. When applied to measurements of the circadian transcriptome and proteome of mouse liver, the sets of transcripts and proteins with rhythmic abundances were significantly expanded due to the increased detection power, when we controlled for false discovery. Validation against independent data confirmed the quality of these results. The large expansion of the circadian mouse liver transcriptomes and proteomes reflected the prevalence of nonsymmetric wave forms and led to new conclusions about function. RAIN was implemented as a freely available software package for R/Bioconductor and is presently also available as a web interface. PMID:25326247

Reusable bi-directional 3ω sensor to measure thermal conductivity of 100-μm thick biological tissues.

PubMed

Lubner, Sean D; Choi, Jeunghwan; Wehmeyer, Geoff; Waag, Bastian; Mishra, Vivek; Natesan, Harishankar; Bischof, John C; Dames, Chris

2015-01-01

Accurate knowledge of the thermal conductivity (k) of biological tissues is important for cryopreservation, thermal ablation, and cryosurgery. Here, we adapt the 3ω method-widely used for rigid, inorganic solids-as a reusable sensor to measure k of soft biological samples two orders of magnitude thinner than conventional tissue characterization methods. Analytical and numerical studies quantify the error of the commonly used "boundary mismatch approximation" of the bi-directional 3ω geometry, confirm that the generalized slope method is exact in the low-frequency limit, and bound its error for finite frequencies. The bi-directional 3ω measurement device is validated using control experiments to within ±2% (liquid water, standard deviation) and ±5% (ice). Measurements of mouse liver cover a temperature ranging from -69 °C to +33 °C. The liver results are independent of sample thicknesses from 3 mm down to 100 μm and agree with available literature for non-mouse liver to within the measurement scatter.

Global analysis of an impulsive delayed Lotka-Volterra competition system

NASA Astrophysics Data System (ADS)

Xia, Yonghui

2011-03-01

In this paper, a retarded impulsive n-species Lotka-Volterra competition system with feedback controls is studied. Some sufficient conditions are obtained to guarantee the global exponential stability and global asymptotic stability of a unique equilibrium for such a high-dimensional biological system. The problem considered in this paper is in many aspects more general and incorporates as special cases various problems which have been extensively studied in the literature. Moreover, applying the obtained results to some special cases, I derive some new criteria which generalize and greatly improve some well known results. A method is proposed to investigate biological systems subjected to the effect of both impulses and delays. The method is based on Banach fixed point theory and matrix's spectral theory as well as Lyapunov function. Moreover, some novel analytic techniques are employed to study GAS and GES. It is believed that the method can be extended to other high-dimensional biological systems and complex neural networks. Finally, two examples show the feasibility of the results.

Reverse engineering of gene regulatory networks.

PubMed

Cho, K H; Choo, S M; Jung, S H; Kim, J R; Choi, H S; Kim, J

2007-05-01

Systems biology is a multi-disciplinary approach to the study of the interactions of various cellular mechanisms and cellular components. Owing to the development of new technologies that simultaneously measure the expression of genetic information, systems biological studies involving gene interactions are increasingly prominent. In this regard, reconstructing gene regulatory networks (GRNs) forms the basis for the dynamical analysis of gene interactions and related effects on cellular control pathways. Various approaches of inferring GRNs from gene expression profiles and biological information, including machine learning approaches, have been reviewed, with a brief introduction of DNA microarray experiments as typical tools for measuring levels of messenger ribonucleic acid (mRNA) expression. In particular, the inference methods are classified according to the required input information, and the main idea of each method is elucidated by comparing its advantages and disadvantages with respect to the other methods. In addition, recent developments in this field are introduced and discussions on the challenges and opportunities for future research are provided.

Prospects for the use of larvivorous fish for malaria control in Ethiopia: search for indigenous species and evaluation of their feeding capacity for mosquito larvae.

PubMed

Fletcher, M; Teklehaimanot, A; Yemane, G; Kassahun, A; Kidane, G; Beyene, Y

1993-02-01

Because of problems with drug and insecticide resistance, the National Organization for the Control of Malaria and other Vectorborne Diseases, Ethiopia, has embarked on a programme of research on alternative malaria control methods, including the use of biological control agents, such as larvivorous fish. The objectives of the study were to identify indigenous larvivorous fish species which could be potential candidates for use as biological control agents; to extend knowledge of their distribution in Ethiopia; and to conduct laboratory tests to determine their feeding capacity. An extensive search resulted in the identification of 11 larvivorous fish species indigenous to Ethiopia, including five species previously unrecorded in the country. Seven species were assessed under standard laboratory conditions for their feeding capacity on larvae of Anopheles gambiae s.l. and Culex andersoni. All species tested were efficient larvivores in the laboratory. However, their larvivorous capacity should be tested further in field trials. Based on the findings of this study, two priority areas for the assessment of biological control using larvivorous fish were identified, the port city of Assab, using the local species Aphanius dispar, and the Ogaden, south-eastern Ethiopia, using the local species Oreochromis spilurus spilurus.

[Establishment of Quality Control System of Nucleic Acid Detection for Ebola Virus in Sierra Leone-China Friendship Biological Safety Laboratory].

PubMed

Wang, Qin; Zhang, Yong; Nie, Kai; Wang, Huanyu; Du, Haijun; Song, Jingdong; Xiao, Kang; Lei, Wenwen; Guo, Jianqiang; Wei, Hejiang; Cai, Kun; Wang, Yanhai; Wu, Jiang; Gerald, Bangura; Kamara, Idrissa Laybohr; Liang, Mifang; Wu, Guizhen; Dong, Xiaoping

2016-03-01

The quality control process throughout the Ebola virus nucleic acid detection in Sierra Leone-China Friendship Biological Safety Laboratory (SLE-CHN Biosafety Lab) was described in detail, in order to comprehensively display the scientific, rigorous, accurate and efficient practice in detection of Ebola virus of first batch detection team in SLE-CHN Biosafety Lab. Firstly, the key points of laboratory quality control system was described, including the managements and organizing, quality control documents and information management, instrument, reagents and supplies, assessment, facilities design and space allocation, laboratory maintenance and biosecurity. Secondly, the application of quality control methods in the whole process of the Ebola virus detection, including before the test, during the test and after the test, was analyzed. The excellent and professional laboratory staffs, the implementation of humanized management are the cornerstone of the success; High-level biological safety protection is the premise for effective quality control and completion of Ebola virus detection tasks. And professional logistics is prerequisite for launching the laboratory diagnosis of Ebola virus. The establishment and running of SLE-CHN Biosafety Lab has landmark significance for the friendship between Sierra Leone and China, and the lab becomes the most important base for Ebola virus laboratory testing in Sierra Leone.

Efficacy of Chaetomium Species as Biological Control Agents against Phytophthora nicotianae Root Rot in Citrus

PubMed Central

Wattanachai, Pongnak; Kasem, Soytong; Poeaim, Supattra

2015-01-01

Thailand is one of the largest citrus producers in Southeast Asia. Pathogenic infection by Phytophthora, however, has become one of major impediments to production. This study identified a pathogenic oomycete isolated from rotted roots of pomelo (Citrus maxima) in Thailand as Phytophthora nicotianae by the internal transcribed spacer ribosomal DNA sequence analysis. Then, we examined the in vitro and in vivo effects of Chaetomium globosum, Chaetomium lucknowense, Chaetomium cupreum and their crude extracts as biological control agents in controlling this P. nicotianae strain. Represent as antagonists in biculture test, the tested Chaetomium species inhibited mycelial growth by 50~56% and parasitized the hyphae, resulting in degradation of P. nicotianae mycelia after 30 days. The crude extracts of these Chaetomium species exhibited antifungal activities against mycelial growth of P. nicotianae, with effective doses of 2.6~101.4 µg/mL. Under greenhouse conditions, application of spores and methanol extracts of these Chaetomium species to pomelo seedlings inoculated with P. nicotianae reduced root rot by 66~71% and increased plant weight by 72~85% compared to that in the control. The method of application of antagonistic spores to control the disease was simple and economical, and it may thus be applicable for large-scale, highly effective biological control of this pathogen. PMID:26539045

Optimization and validation of a label-free MRM method for the quantification of cytochrome P450 isoforms in biological samples.

PubMed

Al Ali, Ahmad; Touboul, David; Le Caër, Jean-Pierre; Schmitz-Afonso, Isabelle; Flinois, Jean-Pierre; Marchetti, Catherine; De Waziers, Isabelle; Brunelle, Alain; Laprévote, Olivier; Beaune, Philippe

2014-08-01

Cytochromes P450 (CYPs) play critical roles in oxidative metabolism of many endogenous and exogenous compounds. Protein expression levels of CYPs in liver provide relevant information for a better understanding of the importance of CYPs in pharmacology and toxicology. This work aimed at establishing a simple method to quantify six CYPs (CYP3A4, CYP3A5, CYP1A2, CYP2D6, CYP2C9, and CYP2J2) in various biological samples without isotopic labeling. The biological matrix was spiked with the standard peptides prior to the digestion step to realize a label-free quantification by mass spectrometry. The method was validated and applied to quantify these six isoforms in both human liver microsomes and mitochondria, but also in recombinant expression systems such as baculosomes and the HepG2 cell line. The results showed intra-assay and interassay accuracy and precision within 16 % and 5 %, respectively, at the low quality control level, and demonstrated the advantages of the method in terms of reproducibility and cost.

A novel algorithm for finding optimal driver nodes to target control complex networks and its applications for drug targets identification.

PubMed

Guo, Wei-Feng; Zhang, Shao-Wu; Shi, Qian-Qian; Zhang, Cheng-Ming; Zeng, Tao; Chen, Luonan

2018-01-19

The advances in target control of complex networks not only can offer new insights into the general control dynamics of complex systems, but also be useful for the practical application in systems biology, such as discovering new therapeutic targets for disease intervention. In many cases, e.g. drug target identification in biological networks, we usually require a target control on a subset of nodes (i.e., disease-associated genes) with minimum cost, and we further expect that more driver nodes consistent with a certain well-selected network nodes (i.e., prior-known drug-target genes). Therefore, motivated by this fact, we pose and address a new and practical problem called as target control problem with objectives-guided optimization (TCO): how could we control the interested variables (or targets) of a system with the optional driver nodes by minimizing the total quantity of drivers and meantime maximizing the quantity of constrained nodes among those drivers. Here, we design an efficient algorithm (TCOA) to find the optional driver nodes for controlling targets in complex networks. We apply our TCOA to several real-world networks, and the results support that our TCOA can identify more precise driver nodes than the existing control-fucus approaches. Furthermore, we have applied TCOA to two bimolecular expert-curate networks. Source code for our TCOA is freely available from http://sysbio.sibcb.ac.cn/cb/chenlab/software.htm or https://github.com/WilfongGuo/guoweifeng . In the previous theoretical research for the full control, there exists an observation and conclusion that the driver nodes tend to be low-degree nodes. However, for target control the biological networks, we find interestingly that the driver nodes tend to be high-degree nodes, which is more consistent with the biological experimental observations. Furthermore, our results supply the novel insights into how we can efficiently target control a complex system, and especially many evidences on the practical strategic utility of TCOA to incorporate prior drug information into potential drug-target forecasts. Thus applicably, our method paves a novel and efficient way to identify the drug targets for leading the phenotype transitions of underlying biological networks.

Practical applications of insects' sexual development for pest control.

PubMed

Koukidou, M; Alphey, L

2014-01-01

Elucidation of the sex differentiation pathway in insects offers an opportunity to understand key aspects of evolutionary developmental biology. In addition, it provides the understanding necessary to manipulate insects in order to develop new synthetic genetics-based tools for the control of pest insects. Considerable progress has been made in this, especially in improvements to the sterile insect technique (SIT). Large scale sex separation is considered highly desirable or essential for most SIT targets. This separation can be provided by genetic methods based on sex-specific gene expression. Investigation of sex determination by many groups has provided molecular components and methods for this. Though the primary sex determination signal varies considerably, key regulatory genes and mechanisms remain surprisingly similar. In most cases studied so far, a primary signal is transmitted to a basal gene at the bottom of the hierarchy (dsx) through an alternative splicing cascade; dsx is itself differentially spliced in males and females. A sex-specific alternative splicing system therefore offers an attractive route to achieve female-specific expression. Experience has shown that alternative splicing modules can be developed with cross-species function; modularity and standardisation and re-use of parts are key principles of synthetic biology. Both female-killing and sex reversal (XX females to phenotypic males) can in principle also be used as efficient alternatives to sterilisation in SIT-like methods. Sexual maturity is yet another area where understanding of sexual development may be applied to insect control programmes. Further detailed understanding of this crucial aspect of insect biology will undoubtedly continue to underpin innovative practical applications. © 2014 S. Karger AG, Basel.

Identifying cooperative transcriptional regulations using protein–protein interactions

PubMed Central

Nagamine, Nobuyoshi; Kawada, Yuji; Sakakibara, Yasubumi

2005-01-01

Cooperative transcriptional activations among multiple transcription factors (TFs) are important to understand the mechanisms of complex transcriptional regulations in eukaryotes. Previous studies have attempted to find cooperative TFs based on gene expression data with gene expression profiles as a measure of similarity of gene regulations. In this paper, we use protein–protein interaction data to infer synergistic binding of cooperative TFs. Our fundamental idea is based on the assumption that genes contributing to a similar biological process are regulated under the same control mechanism. First, the protein–protein interaction networks are used to calculate the similarity of biological processes among genes. Second, we integrate this similarity and the chromatin immuno-precipitation data to identify cooperative TFs. Our computational experiments in yeast show that predictions made by our method have successfully identified eight pairs of cooperative TFs that have literature evidences but could not be identified by the previous method. Further, 12 new possible pairs have been inferred and we have examined the biological relevances for them. However, since a typical problem using protein–protein interaction data is that many false-positive data are contained, we propose a method combining various biological data to increase the prediction accuracy. PMID:16126847

Treatment of laundry wastewater by biological and electrocoagulation methods.

PubMed

Ramcharan, Terelle; Bissessur, Ajay

2017-01-01

The present study describes an improvement in the current electrocoagulation treatment process and focuses on a comparative study for the clean-up of laundry wastewater (LWW) after each wash and rinse cycle by biological and electrocoagulation treatment methods. For biological treatment, the wastewater was treated with a Bacillus strain of aerobic bacteria especially suited for the degradation of fats, lipids, protein, detergents and hydrocarbons. Treatment of the LWW by electrocoagulation involved the oxidation of aluminium metal upon the application of a controlled voltage which produces various aluminium hydroxy species capable of adsorbing pollutants from the wastewater. The efficiency of the clean-up of LWW using each method was assessed by determination of surfactant concentration, chemical oxygen demand and total dissolved solids. A rapid decrease in surfactant concentration was noted within 0.5 hour of electrocoagulation, whereas a notable decrease in the surfactant concentration was observed only after 12 hour of biological treatment. The rapid generation of aluminium hydroxy species in the electrocoagulation cell allowed adsorption of pollutants at a faster rate when compared to the aerobic degradation of the surfactant; hence a reduced period of time is required for treatment of LWW by electrocoagulation.

Illuminating the Chemistry of Life: Design, Synthesis, and Applications of “Caged” and Related Photoresponsive Compounds

PubMed Central

Lee, Hsienming; Larson, Daniel R.; Lawrence, David S.

2009-01-01

Biological systems are characterized by a level of spatial and temporal organization that often lies beyond the grasp of present day methods. Light-modulated bioreagents, including analogs of low molecular weight compounds, peptides, proteins, and nucleic acids, represent a compelling strategy to probe, perturb, or sample biological phenomena with the requisite control to address many of these organizational complexities. Although this technology has created considerable excitement in the chemical community, its application to biological questions has been relatively limited. We describe the challenges associated with the design, synthesis, and use of light-responsive bioreagents, the scope and limitations associated with the instrumentation required for their application, and recent chemical and biological advances in this field. PMID:19298086

Illuminating the chemistry of life: design, synthesis, and applications of "caged" and related photoresponsive compounds.

PubMed

Lee, Hsien-Ming; Larson, Daniel R; Lawrence, David S

2009-06-19

Biological systems are characterized by a level of spatial and temporal organization that often lies beyond the grasp of present day methods. Light-modulated bioreagents, including analogs of low molecular weight compounds, peptides, proteins, and nucleic acids, represent a compelling strategy to probe, perturb, or sample biological phenomena with the requisite control to address many of these organizational complexities. Although this technology has created considerable excitement in the chemical community, its application to biological questions has been relatively limited. We describe the challenges associated with the design, synthesis, and use of light-responsive bioreagents; the scope and limitations associated with the instrumentation required for their application; and recent chemical and biological advances in this field.

Teaching Culture within the Nursing Curriculum Using the Giger-Davidhizar Model of Transcultural Nursing Assessment.

ERIC Educational Resources Information Center

Davidhizar, Ruth; Giger, Joyce Newman

2001-01-01

Presents a method for integrating cultural competence throughout the nursing curriculum. The model contains six cultural phenomena: communication, space, social organization, time, environmental control, and biological variation. Contains 17 references. (SK)

Methods of integrating Islamic values in teaching biology for shaping attitude and character

NASA Astrophysics Data System (ADS)

Listyono; Supardi, K. I.; Hindarto, N.; Ridlo, S.

2018-03-01

Learning is expected to develop the potential of learners to have the spiritual attitude: moral strength, self-control, personality, intelligence, noble character, as well as the skills needed by themselves, society, and nation. Implementation of role and morale in learning is an alternative way which is expected to answer the challenge. The solution offered is to inject student with religious material Islamic in learning biology. The content value of materials teaching biology includes terms of practical value, religious values, daily life value, socio-political value, and the value of art. In Islamic religious values (Qur'an and Hadith) various methods can touch human feelings, souls, and generate motivation. Integrating learning with Islamic value can be done by the deductive or inductive approach. The appropriate method of integration is the amtsal (analog) method, hiwar (dialog) method, targhib & tarhib (encouragement & warning) method, and example method (giving a noble role model / good example). The right strategy in integrating Islamic values is outlined in the design of lesson plan. The integration of Islamic values in lesson plan will facilitate teachers to build students' character because Islamic values can be implemented in every learning steps so students will be accustomed to receiving the character value in this integrated learning.

Effects of crop species richness on pest-natural enemy systems based on an experimental model system using a microlandscape.

PubMed

Zhao, ZiHua; Shi, PeiJian; Men, XingYuan; Ouyang, Fang; Ge, Feng

2013-08-01

The relationship between crop richness and predator-prey interactions as they relate to pest-natural enemy systems is a very important topic in ecology and greatly affects biological control services. The effects of crop arrangement on predator-prey interactions have received much attention as the basis for pest population management. To explore the internal mechanisms and factors driving the relationship between crop richness and pest population management, we designed an experimental model system of a microlandscape that included 50 plots and five treatments. Each treatment had 10 repetitions in each year from 2007 to 2010. The results showed that the biomass of pests and their natural enemies increased with increasing crop biomass and decreased with decreasing crop biomass; however, the effects of plant biomass on the pest and natural enemy biomass were not significant. The relationship between adjacent trophic levels was significant (such as pests and their natural enemies or crops and pests), whereas non-adjacent trophic levels (crops and natural enemies) did not significantly interact with each other. The ratio of natural enemy/pest biomass was the highest in the areas of four crop species that had the best biological control service. Having either low or high crop species richness did not enhance the pest population management service and lead to loss of biological control. Although the resource concentration hypothesis was not well supported by our results, high crop species richness could suppress the pest population, indicating that crop species richness could enhance biological control services. These results could be applied in habitat management aimed at biological control, provide the theoretical basis for agricultural landscape design, and also suggest new methods for integrated pest management.

Reverse engineering and identification in systems biology: strategies, perspectives and challenges

PubMed Central

Villaverde, Alejandro F.; Banga, Julio R.

2014-01-01

The interplay of mathematical modelling with experiments is one of the central elements in systems biology. The aim of reverse engineering is to infer, analyse and understand, through this interplay, the functional and regulatory mechanisms of biological systems. Reverse engineering is not exclusive of systems biology and has been studied in different areas, such as inverse problem theory, machine learning, nonlinear physics, (bio)chemical kinetics, control theory and optimization, among others. However, it seems that many of these areas have been relatively closed to outsiders. In this contribution, we aim to compare and highlight the different perspectives and contributions from these fields, with emphasis on two key questions: (i) why are reverse engineering problems so hard to solve, and (ii) what methods are available for the particular problems arising from systems biology? PMID:24307566

Gene regulatory network inference using fused LASSO on multiple data sets

PubMed Central

Omranian, Nooshin; Eloundou-Mbebi, Jeanne M. O.; Mueller-Roeber, Bernd; Nikoloski, Zoran

2016-01-01

Devising computational methods to accurately reconstruct gene regulatory networks given gene expression data is key to systems biology applications. Here we propose a method for reconstructing gene regulatory networks by simultaneous consideration of data sets from different perturbation experiments and corresponding controls. The method imposes three biologically meaningful constraints: (1) expression levels of each gene should be explained by the expression levels of a small number of transcription factor coding genes, (2) networks inferred from different data sets should be similar with respect to the type and number of regulatory interactions, and (3) relationships between genes which exhibit similar differential behavior over the considered perturbations should be favored. We demonstrate that these constraints can be transformed in a fused LASSO formulation for the proposed method. The comparative analysis on transcriptomics time-series data from prokaryotic species, Escherichia coli and Mycobacterium tuberculosis, as well as a eukaryotic species, mouse, demonstrated that the proposed method has the advantages of the most recent approaches for regulatory network inference, while obtaining better performance and assigning higher scores to the true regulatory links. The study indicates that the combination of sparse regression techniques with other biologically meaningful constraints is a promising framework for gene regulatory network reconstructions. PMID:26864687

Effects of Training on Controllability Attributions of Behavioural Excesses and Deficits Shown by Adults with Down Syndrome and Dementia

ERIC Educational Resources Information Center

Kalsy, Sunny; Heath, Rebecca; Adams, Dawn; Oliver, Chris

2007-01-01

Background: Whereas there is a knowledge base on staff attributions of challenging behaviour, there has been little research on the effects of training, type of behaviour and biological context on staff attributions of controllability in the context of people with intellectual disabilities and dementia. Methods: A mixed design was used to…

Process for control of cell division

NASA Technical Reports Server (NTRS)

Cone, C. D., Jr. (Inventor)

1977-01-01

A method of controlling mitosis of biological cells was developed, which involved inducing a change in the intracellular ionic hierarchy accompanying the cellular electrical transmembrane potential difference (Esubm) of the cells. The ionic hierarchy may be varied by imposing changes on the relative concentrations of Na(+), K(+) and Cl(-), or by directly imposing changes in the physical Esubm level across the cell surface.

Reliability of unstable periodic orbit based control strategies in biological systems.

PubMed

Mishra, Nagender; Hasse, Maria; Biswal, B; Singh, Harinder P

2015-04-01

Presence of recurrent and statistically significant unstable periodic orbits (UPOs) in time series obtained from biological systems is now routinely used as evidence for low dimensional chaos. Extracting accurate dynamical information from the detected UPO trajectories is vital for successful control strategies that either aim to stabilize the system near the fixed point or steer the system away from the periodic orbits. A hybrid UPO detection method from return maps that combines topological recurrence criterion, matrix fit algorithm, and stringent criterion for fixed point location gives accurate and statistically significant UPOs even in the presence of significant noise. Geometry of the return map, frequency of UPOs visiting the same trajectory, length of the data set, strength of the noise, and degree of nonstationarity affect the efficacy of the proposed method. Results suggest that establishing determinism from unambiguous UPO detection is often possible in short data sets with significant noise, but derived dynamical properties are rarely accurate and adequate for controlling the dynamics around these UPOs. A repeat chaos control experiment on epileptic hippocampal slices through more stringent control strategy and adaptive UPO tracking is reinterpreted in this context through simulation of similar control experiments on an analogous but stochastic computer model of epileptic brain slices. Reproduction of equivalent results suggests that far more stringent criteria are needed for linking apparent success of control in such experiments with possible determinism in the underlying dynamics.

Reliability of unstable periodic orbit based control strategies in biological systems

NASA Astrophysics Data System (ADS)

Mishra, Nagender; Hasse, Maria; Biswal, B.; Singh, Harinder P.

2015-04-01

Presence of recurrent and statistically significant unstable periodic orbits (UPOs) in time series obtained from biological systems is now routinely used as evidence for low dimensional chaos. Extracting accurate dynamical information from the detected UPO trajectories is vital for successful control strategies that either aim to stabilize the system near the fixed point or steer the system away from the periodic orbits. A hybrid UPO detection method from return maps that combines topological recurrence criterion, matrix fit algorithm, and stringent criterion for fixed point location gives accurate and statistically significant UPOs even in the presence of significant noise. Geometry of the return map, frequency of UPOs visiting the same trajectory, length of the data set, strength of the noise, and degree of nonstationarity affect the efficacy of the proposed method. Results suggest that establishing determinism from unambiguous UPO detection is often possible in short data sets with significant noise, but derived dynamical properties are rarely accurate and adequate for controlling the dynamics around these UPOs. A repeat chaos control experiment on epileptic hippocampal slices through more stringent control strategy and adaptive UPO tracking is reinterpreted in this context through simulation of similar control experiments on an analogous but stochastic computer model of epileptic brain slices. Reproduction of equivalent results suggests that far more stringent criteria are needed for linking apparent success of control in such experiments with possible determinism in the underlying dynamics.

Biological control of biofilms on membranes by metazoans.

PubMed

Klein, Theresa; Zihlmann, David; Derlon, Nicolas; Isaacson, Carl; Szivak, Ilona; Weissbrodt, David G; Pronk, Wouter

2016-01-01

Traditionally, chemical and physical methods have been used to control biofouling on membranes by inactivating and removing the biofouling layer. Alternatively, the permeability can be increased using biological methods while accepting the presence of the biofouling layer. We have investigated two different types of metazoans for this purpose, the oligochaete Aelosoma hemprichi and the nematode Plectus aquatilis. The addition of these grazing metazoans in biofilm-controlled membrane systems resulted in a flux increase of 50% in presence of the oligochaetes (Aelosoma hemprichi), and a flux increase of 119-164% in presence of the nematodes (Plectus aquatilis) in comparison to the control system operated without metazoans. The change in flux resulted from (1) a change in the biofilm structure, from a homogeneous, cake-like biofilm to a more heterogeneous, porous structure and (2) a significant reduction in the thickness of the basal layer. Pyrosequencing data showed that due to the addition of the predators, also the community composition of the biofilm in terms of protists and bacteria was strongly affected. The results have implications for a range of membrane processes, including ultrafiltration for potable water production, membrane bioreactors and reverse osmosis. Copyright © 2015 Elsevier Ltd. All rights reserved.

[Establishment of biological assess for quality control of Fuzi based on determination of premature ventricular contractions in rats].

PubMed

Zhao, Zhi-Hao; Zhang, Ding-Kun; Wu, Ming-Quan; Li, Chun-Yu; Cao, Li-Juan; Zhang, Ping; Liu, Cui-Zhe; Wang, Jia-Bo; Xiao, Xiao-He

2016-10-01

Aconiti Lateralis Radix (Fuzi) is a toxic traditional Chinese medicine with definite efficacy. In order to improve the quality control of its different prepared products and ensure the security in clinic, it is significant to establish a method of quality evaluation related to clinic adverse effects. Aiming at the important biological marker of early cardiac toxicity reaction, there was no method to detect it. In this manuscript, a novel approach for measuring the minimal toxic dose (MTD) of premature ventricular contractions (PVC) poisoning of rats was established. Then, the determination methodology and conditions were optimized to meet the needs of the quality and biological assessment, including animal sex, weight, stability of standards and test solutions. Using this method, the MTD value of different Fuzi products were determined, such as Heishunpian, Baifupian, Zhengfupian, Baofupian, and Paotianxiong. The results showed that the MTD of Fuzi was significantly decreased after detoxification processed (P<0.05) and the MTD of Heishunpian, Zhengfupian, Baofupian and Baifupian was as much as 15.76, 22.36, 19.65 and 20.97 times to that of unprocessed Shengfuzi. In addition, Paotianxiong could not induce PVC in rats, which indicated that Paotianxiong was nontoxic and safe.This method could appropriately reflects the cardiotoxity of Fuzi and its prepared samples. Together with the chemical composition analysis, the contents of diester alkaloids were explored including aconitine, mesaconitine and hypaconitine as well as monoester alkaloids in Fuzi and its prepared products were significantly associated with PVC. Furthermore, there may be some components undetermined facilitating arrhythmia to be worth exploring. This research provides an overall and comprehensive approach to diagnose early clinical cardiotoxity and control the quality of Fuzi, which could not only be a complementary solution for the chemical evaluation, but a new method to ensure its efficacy and security of clinical application. Copyright© by the Chinese Pharmaceutical Association.

Verification and Optimal Control of Context-Sensitive Probabilistic Boolean Networks Using Model Checking and Polynomial Optimization

PubMed Central

Hiraishi, Kunihiko

2014-01-01

One of the significant topics in systems biology is to develop control theory of gene regulatory networks (GRNs). In typical control of GRNs, expression of some genes is inhibited (activated) by manipulating external stimuli and expression of other genes. It is expected to apply control theory of GRNs to gene therapy technologies in the future. In this paper, a control method using a Boolean network (BN) is studied. A BN is widely used as a model of GRNs, and gene expression is expressed by a binary value (ON or OFF). In particular, a context-sensitive probabilistic Boolean network (CS-PBN), which is one of the extended models of BNs, is used. For CS-PBNs, the verification problem and the optimal control problem are considered. For the verification problem, a solution method using the probabilistic model checker PRISM is proposed. For the optimal control problem, a solution method using polynomial optimization is proposed. Finally, a numerical example on the WNT5A network, which is related to melanoma, is presented. The proposed methods provide us useful tools in control theory of GRNs. PMID:24587766

Assembly of hydrogel units for 3D microenvironment in a poly(dimethylsiloxane) channel

NASA Astrophysics Data System (ADS)

Cho, Chang Hyun; Kwon, Seyong; Park, Je-Kyun

2017-12-01

Construction of three-dimensional (3D) microenvironment become an important issue in recent biological studies due to their biological relevance compared to conventional two-dimensional (2D) microenvironment. Various fabrication techniques have been employed to construct a 3D microenvironment, however, it is difficult to fully satisfy the biological and mechanical properties required for the 3D cell culture system, such as heterogeneous tissue structures generated from the functional differences or diseases. We propose here an assembly method for facile construction of 3D microenvironment in a poly(dimethylsiloxane) (PDMS) channel using hydrogel units. The high-aspect-ratio of hydrogel units was achieved by fabricating these units using a 2D mold. With this approach, 3D heterogeneous hydrogel units were produced and assembled in a PDMS channel by structural hookup. In vivo-like 3D heterogeneous microenvironment in a precisely controllable fluidic system was also demonstrated using a controlled assembly of different types of hydrogel units, which was difficult to obtain from previous methods. By regulating the flow condition, the mechanical stability of the assembled hydrogel units was verified by the flow-induced deformation of hydrogel units. In addition, in vivo-like cell culture environment was demonstrated using an assembly of cell-coated hydrogel units in the fluidic channel. Based on these features, our method expects to provide a beneficial tool for the 3D cell culture module and biomimetic engineering.

RNA sample preparation applied to gene expression profiling for the horse biological passport.

PubMed

Bailly-Chouriberry, Ludovic; Baudoin, Florent; Cormant, Florence; Glavieux, Yohan; Loup, Benoit; Garcia, Patrice; Popot, Marie-Agnès; Bonnaire, Yves

2017-09-01

The improvement of doping control is an ongoing race. Techniques to fight doping are usually based on the direct detection of drugs or their metabolites by analytical methods such as chromatography hyphenated to mass spectrometry after ad hoc sample preparation. Nowadays, omic methods constitute an attractive development and advances have been achieved particularly by application of molecular biology tools for detection of anabolic androgenic steroids (AAS), erythropoiesis-stimulating agent (ESA), or to control human growth hormone misuses. These interesting results across different animal species have suggested that modification of gene expression offers promising new methods of improving the window of detection of banned substances by targeting their effects on blood cell gene expression. In this context, the present study describes the possibility of using a modified version of the dedicated Human IVD (in vitro Diagnostics) PAXgene® Blood RNA Kit for horse gene expression analysis in blood collected on PAXgene® tubes applied to the horse biological passport. The commercial kit was only approved for human blood samples and has required an optimization of specific technical requirements for equine blood samples. Improvements and recommendations were achieved for sample collection, storage and RNA extraction procedure. Following these developments, RNA yield and quality were demonstrated to be suitable for downstream gene expression analysis by qPCR techniques. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Biological Bases of Space Radiation Risk

NASA Technical Reports Server (NTRS)

1997-01-01

In this session, Session JP4, the discussion focuses on the following topics: Hematopoiesis Dynamics in Irradiated Mammals, Mathematical Modeling; Estimating Health Risks in Space from Galactic Cosmic Rays; Failure of Heavy Ions to Affect Physiological Integrity of the Corneal Endothelial Monolayer; Application of an Unbiased Two-Gel CDNA Library Screening Method to Expression Monitoring of Genes in Irradiated Versus Control Cells; Detection of Radiation-Induced DNA Strand Breaks in Mammalian Cells By Enzymatic Post-Labeling; Evaluation of Bleomycin-Induced Chromosome Aberrations Under Microgravity Conditions in Human Lymphocytes, Using "Fish" Techniques; Technical Description of the Space Exposure Biology Assembly Seba on ISS; and Cytogenetic Research in Biological Dosimetry.

Acute and impaired wound healing: pathophysiology and current methods for drug delivery, part 1: normal and chronic wounds: biology, causes, and approaches to care.

PubMed

Demidova-Rice, Tatiana N; Hamblin, Michael R; Herman, Ira M

2012-07-01

This is the first installment of 2 articles that discuss the biology and pathophysiology of wound healing, review the role that growth factors play in this process, and describe current ways of growth factor delivery into the wound bed. Part 1 discusses the latest advances in clinicians' understanding of the control points that regulate wound healing. Importantly, biological similarities and differences between acute and chronic wounds are considered, including the signaling pathways that initiate cellular and tissue responses after injury, which may be impeded during chronic wound healing.

Acute and Impaired Wound Healing: Pathophysiology and Current Methods for Drug Delivery, Part 1: Normal and Chronic Wounds: Biology, Causes, and Approaches to Care

PubMed Central

Demidova-Rice, Tatiana N.; Hamblin, Michael R.; Herman, Ira M.

2012-01-01

This is the first installment of 2 articles that discuss the biology and pathophysiology of wound healing, review the role that growth factors play in this process, and describe current ways of growth factor delivery into the wound bed. Part 1 discusses the latest advances in clinicians’ understanding of the control points that regulate wound healing. Importantly, biological similarities and differences between acute and chronic wounds are considered, including the signaling pathways that initiate cellular and tissue responses after injury, which may be impeded during chronic wound healing. PMID:22713781

DOE Office of Scientific and Technical Information (OSTI.GOV)

Somayaji, Anil B.; Amai, Wendy A.; Walther, Eleanor A.

This reports describes the successful extension of artificial immune systems from the domain of computer security to the domain of real time control systems for robotic vehicles. A biologically-inspired computer immune system was added to the control system of two different mobile robots. As an additional layer in a multi-layered approach, the immune system is complementary to traditional error detection and error handling techniques. This can be thought of as biologically-inspired defense in depth. We demonstrated an immune system can be added with very little application developer effort, resulting in little to no performance impact. The methods described here aremore » extensible to any system that processes a sequence of data through a software interface.« less

Multi-modal Aedes aegypti mosquito reduction interventions and dengue fever prevention.

PubMed

Ballenger-Browning, Kara K; Elder, John P

2009-12-01

To systematically review the effectiveness of biological, chemical and educational dengue fever prevention programs on the reduction of entomologic indicators. Searches of PubMed, GoogleScholar, CabDirect databases and reference lists yielded over 1000 articles containing mosquito abatement interventions. Inclusion criteria were: Vector control programs targeting Aedes aegypti and Aedes albopictus mosquitoes; Studies providing pre- and post-test data. Intervention effectiveness was assessed using Mulla's formula to determine percent reductions for all studies with control groups. Twenty-one studies were reviewed. Twelve dependent variables were presented, however, the Breteau, House and Container indices were the primary measurement tools for monitoring larval populations. Behavioural methods consisting of educational campaigns and maintaining water containers to reduce the mosquito population were applied in eight studies. Eight studies involved the use of biological methods such as predatory organisms or bacteria. Finally, eight studies used chemical control techniques including insecticide sprays, larvicides, insecticide-treated materials, and cleaning water of containers with household chemicals with three studies using a combination of intervention techniques. Post-intervention reduction in entomologic indices ranged from 100% to an increase of 13.9% from baseline. Little evidence exists to support the efficacy of mosquito abatement programs owing to poor study designs and lack of congruent entomologic indices. Creation of a standard entomological index, use of clustered and randomized-controlled trials, and testing the generalizability of proven methods are recommended for future research.

Epidemiologic Study of Malassezia Yeasts in Seborrheic Dermatitis Patients by the Analysis of 26S rDNA PCR-RFLP.

PubMed

Oh, Byung Ho; Lee, Yang Won; Choe, Yong Beom; Ahn, Kyu Joong

2010-05-01

This case-control study concerns a molecular biological method based on the data gathered from a group of Korean subjects to examine the distribution of Malassezia yeasts in seborrheic dermatitis (SD) patients. Cultures for Malassezia yeasts were taken from the foreheads, cheeks and chests of 60 patients with SD and in 60 healthy controls of equivalent age. The purpose of this study is to identify the relationship between certain species of Malassezia and SD. This was done by analyzing the differences in the distribution of Malassezia species in terms of age and body parts of the host with healthy controls. 26S rDNA PCR-RFLP, a fast and accurate molecular biological method, was used to overcome the limits of morphological and biochemical methods. The positive Malassezia culture rate was 51.7% in patients with SD, which was lower than that of healthy adults (63.9%). M. restricta was dominant in patients with SD (19.5%). Likewise, M. restricta was identified as a common species (20.5%) in healthy controls. In the ages 31~40, M. restricta was found to be the most common species (31.6%) among SD patients. According to the results of the study, the most frequently isolated species was M. restricta (19.5%) in patients with SD. There was no statistically significant difference in the distribution of Malassezia species between the SD patients and healthy control groups.

Models for integrated pest control and their biological implications.

PubMed

Tang, Sanyi; Cheke, Robert A

2008-09-01

Successful integrated pest management (IPM) control programmes depend on many factors which include host-parasitoid ratios, starting densities, timings of parasitoid releases, dosages and timings of insecticide applications and levels of host-feeding and parasitism. Mathematical models can help us to clarify and predict the effects of such factors on the stability of host-parasitoid systems, which we illustrate here by extending the classical continuous and discrete host-parasitoid models to include an IPM control programme. The results indicate that one of three control methods can maintain the host level below the economic threshold (ET) in relation to different ET levels, initial densities of host and parasitoid populations and host-parasitoid ratios. The effects of host intrinsic growth rate and parasitoid searching efficiency on host mean outbreak period can be calculated numerically from the models presented. The instantaneous pest killing rate of an insecticide application is also estimated from the models. The results imply that the modelling methods described can help in the design of appropriate control strategies and assist management decision-making. The results also indicate that a high initial density of parasitoids (such as in inundative releases) and high parasitoid inter-generational survival rates will lead to more frequent host outbreaks and, therefore, greater economic damage. The biological implications of this counter intuitive result are discussed.

Bioengineering Spin-Offs from Dynamical Systems Theory

NASA Astrophysics Data System (ADS)

Collins, J. J.

1997-03-01

Recently, there has been considerable interest in applying concepts and techniques from dynamical systems and statistical physics to physiological systems. In this talk, we present work dealing which two active topics in this area: stochastic resonance and (2) chaos control. Stochastic resonance is a phenomenon wherein the response of nonlinear system to a weak input signal is optimally enhanced by the presence of a particular level of noise. Here we demonstrate that noise-based techniques can be used to lower sensory detection thresholds in humans. We discuss how from a bioengineering and clinical standpoint, these developments may be particularly relevant for individuals with elevated sensory thresholds, such as older adults and patients with peripheral neuropathy. Chaos control techniques have been applied to a wide range of experimental systems, including biological preparations. The application of chaos control to biological systems has led to speculations that these methods may be clinically useful. Here we demonstrate that the principles of chaos control can be utilized to stabilize underlying unstable periodic orbits in non-chaotic biological systems. We discuss how from a bioengineering and clinical standpoint, these developments may be important for suppressing or eliminating certain types of cardiac arrhythmias.

The Effects of Using Concept Mapping for Improving Advanced Level Biology Students' Lower- and Higher-Order Cognitive Skills

NASA Astrophysics Data System (ADS)

Bramwell-Lalor, Sharon; Rainford, Marcia

2014-03-01

This paper reports on teachers' use of concept mapping as an alternative assessment strategy in advanced level biology classes and its effects on students' cognitive skills on selected biology concepts. Using a mixed methods approach, the study employed a pre-test/post-test quasi-experimental design involving 156 students and 8 teachers from intact classes. A researcher-constructed Biology Cognitive Skills Test was used to collect the quantitative data. Qualitative data were collected through interviews and students' personal documents. The data showed that the participants utilized concept mapping in various ways and they described positive experiences while being engaged in its use. The main challenge cited by teachers was the limited time available for more consistent use. The results showed that the use of concept mapping in advanced level biology can lead to learning gains that exceed those achieved in classes where mainly traditional methods are used. The students in the concept mapping experimental groups performed significantly better than their peers in the control group on both the lower-order (F(1) = 21.508; p < .001) and higher-order (F(1) = 42.842, p < .001) cognitive items of the biology test. A mean effect size of .56 was calculated representing the contribution of treatment to the students' performance on the test items.

Need for new technologies for detection of adventitious agents in vaccines and other biological products.

PubMed

Mallet, Laurent; Gisonni-Lex, Lucy

2014-01-01

From an industrial perspective, the conventional in vitro and in vivo assays used for detection of viral contaminants have shown their limitations, as illustrated by the unfortunate detection of porcine circovirus contamination in a licensed rotavirus vaccine. This contamination event illustrates the gaps within the existing adventitious agent strategy and the potential use of new broader molecular detection methods. This paper serves to summarize current testing approaches and challenges, along with opportunities for the use of these new technologies. Testing of biological products is required to ensure the safety of patients. Recently, a licensed vaccine was found to be contaminated with a virus. This contamination did not cause a safety concern to the patients; however, it highlights the need for using new testing methods to control our biological products. This paper introduces the benefits of these new tests and outlines the challenges with the current tests. © PDA, Inc. 2014.

Building gene co-expression networks using transcriptomics data for systems biology investigations: Comparison of methods using microarray data

PubMed Central

Kadarmideen, Haja N; Watson-haigh, Nathan S

2012-01-01

Gene co-expression networks (GCN), built using high-throughput gene expression data are fundamental aspects of systems biology. The main aims of this study were to compare two popular approaches to building and analysing GCN. We use real ovine microarray transcriptomics datasets representing four different treatments with Metyrapone, an inhibitor of cortisol biosynthesis. We conducted several microarray quality control checks before applying GCN methods to filtered datasets. Then we compared the outputs of two methods using connectivity as a criterion, as it measures how well a node (gene) is connected within a network. The two GCN construction methods used were, Weighted Gene Co-expression Network Analysis (WGCNA) and Partial Correlation and Information Theory (PCIT) methods. Nodes were ranked based on their connectivity measures in each of the four different networks created by WGCNA and PCIT and node ranks in two methods were compared to identify those nodes which are highly differentially ranked (HDR). A total of 1,017 HDR nodes were identified across one or more of four networks. We investigated HDR nodes by gene enrichment analyses in relation to their biological relevance to phenotypes. We observed that, in contrast to WGCNA method, PCIT algorithm removes many of the edges of the most highly interconnected nodes. Removal of edges of most highly connected nodes or hub genes will have consequences for downstream analyses and biological interpretations. In general, for large GCN construction (with > 20000 genes) access to large computer clusters, particularly those with larger amounts of shared memory is recommended. PMID:23144540

Directional acceleration vector-driven displacement of fluids (DAVD-DOF)

NASA Technical Reports Server (NTRS)

Clarke, Mark S. F. (Inventor); Feeback, Daniel L. (Inventor)

2004-01-01

Centrifugal analyzer and method for staining biological or non-biological samples in microgravity, wherein the method utilizes an increase in weight of a fluid sample as a function of g-load, to overcome cohesive and frictional forces from preventing its movement in a preselected direction. Apparatus is characterized by plural specimen reservoirs and channels in a slide, each channel being of differing cross-section, wherein respective samples are selectively dispensed, from the reservoirs in response to an imposed g-factor, precedent to sample staining. Within the method, one thus employs microscope slides which define channels, each being of a differing cross-section dimension relative to others. In combination therewith, centrifugal slide mounting apparatus controllably imposes g-vectors of differing magnitudes within a defined structure of the centrifuge such as a chip array.

Physicochemical characterization of silver nanoparticles synthesize using Aloe Vera (Aloe barbadensis)

NASA Astrophysics Data System (ADS)

Kuponiyi, Abiola; Kassama, Lamin; Kukhtareva, Tatiana

2014-08-01

Production of silver nanoparticles (AgNPs) using different biological methods is gaining recognition due to their multiple applications. Although, several physical and chemical methods have been used for the synthesis and stabilizing of AgNPs, yet, a green chemistry method is preferable because it is cost effective and environmentally friendly. The synthesis was done using Aloe Vera (AV) extract because it has chemical compounds such as "Antrokinon" that are known for its antibacterial, antivirus and anticancer properties. We hypothesize that AV extract can produce a stable nanoparticles within the 100 nm range and be biologically active. The biological compounds were extracted from AV skin with water and ethanol which was used as the reduction agent for the synthesis of nanoparticles. The biological extract and AgNO3 were blended and heated to synthesize AgNPs. The reaction process was monitored using UV-Visible spectroscopy. Fourier Transfer Infrared spectroscopy (FTIR) was used for the characterization of biological compounds and their substituent groups before and after the reaction process. Dynamic Light scattering (DLS) method was used to characterize particle size of AgNPs and their biomolecular stability. Results showed that biological compounds such as aliphatic amines, alkenes (=C-H), alkanes (C-H), alcohol (O-H) and unsaturated esters(C-O), which has an average particle size of 109 and 215.8 nm and polydispersity index of 0.451 and 0.375 for ethanol and water extract, respectively. According to TEM measurements the size of AgNPs are in the range 5-20 nm The results suggested that ethanol derived AgNPs contained higher yield of organic compounds, thus has better solubility power than water. Ag NPs can be used to control salmonella in poultry industry.

High-throughput immunomagnetic scavenging technique for quantitative analysis of live VX nerve agent in water, hamburger, and soil matrixes.

PubMed

Knaack, Jennifer S; Zhou, Yingtao; Abney, Carter W; Prezioso, Samantha M; Magnuson, Matthew; Evans, Ronald; Jakubowski, Edward M; Hardy, Katelyn; Johnson, Rudolph C

2012-11-20

We have developed a novel immunomagnetic scavenging technique for extracting cholinesterase inhibitors from aqueous matrixes using biological targeting and antibody-based extraction. The technique was characterized using the organophosphorus nerve agent VX. The limit of detection for VX in high-performance liquid chromatography (HPLC)-grade water, defined as the lowest calibrator concentration, was 25 pg/mL in a small, 500 μL sample. The method was characterized over the course of 22 sample sets containing calibrators, blanks, and quality control samples. Method precision, expressed as the mean relative standard deviation, was less than 9.2% for all calibrators. Quality control sample accuracy was 102% and 100% of the mean for VX spiked into HPLC-grade water at concentrations of 2.0 and 0.25 ng/mL, respectively. This method successfully was applied to aqueous extracts from soil, hamburger, and finished tap water spiked with VX. Recovery was 65%, 81%, and 100% from these matrixes, respectively. Biologically based extractions of organophosphorus compounds represent a new technique for sample extraction that provides an increase in extraction specificity and sensitivity.

Focused fluorescence excitation with time-reversed ultrasonically encoded light and imaging in thick scattering media

NASA Astrophysics Data System (ADS)

Lai, Puxiang; Suzuki, Yuta; Xu, Xiao; Wang, Lihong V.

2013-07-01

Scattering dominates light propagation in biological tissue, and therefore restricts both resolution and penetration depth in optical imaging within thick tissue. As photons travel into the diffusive regime, typically 1 mm beneath human skin, their trajectories transition from ballistic to diffusive due to the increased number of scattering events, which makes it impossible to focus, much less track, photon paths. Consequently, imaging methods that rely on controlled light illumination are ineffective in deep tissue. This problem has recently been addressed by a novel method capable of dynamically focusing light in thick scattering media via time reversal of ultrasonically encoded (TRUE) diffused light. Here, using photorefractive materials as phase conjugate mirrors, we show a direct visualization and dynamic control of optical focusing with this light delivery method, and demonstrate its application for focused fluorescence excitation and imaging in thick turbid media. These abilities are increasingly critical for understanding the dynamic interactions of light with biological matter and processes at different system levels, as well as their applications for biomedical diagnosis and therapy.

Assessment of a novel multi-array normalization method based on spike-in control probes suitable for microRNA datasets with global decreases in expression.

PubMed

Sewer, Alain; Gubian, Sylvain; Kogel, Ulrike; Veljkovic, Emilija; Han, Wanjiang; Hengstermann, Arnd; Peitsch, Manuel C; Hoeng, Julia

2014-05-17

High-quality expression data are required to investigate the biological effects of microRNAs (miRNAs). The goal of this study was, first, to assess the quality of miRNA expression data based on microarray technologies and, second, to consolidate it by applying a novel normalization method. Indeed, because of significant differences in platform designs, miRNA raw data cannot be normalized blindly with standard methods developed for gene expression. This fundamental observation motivated the development of a novel multi-array normalization method based on controllable assumptions, which uses the spike-in control probes to adjust the measured intensities across arrays. Raw expression data were obtained with the Exiqon dual-channel miRCURY LNA™ platform in the "common reference design" and processed as "pseudo-single-channel". They were used to apply several quality metrics based on the coefficient of variation and to test the novel spike-in controls based normalization method. Most of the considerations presented here could be applied to raw data obtained with other platforms. To assess the normalization method, it was compared with 13 other available approaches from both data quality and biological outcome perspectives. The results showed that the novel multi-array normalization method reduced the data variability in the most consistent way. Further, the reliability of the obtained differential expression values was confirmed based on a quantitative reverse transcription-polymerase chain reaction experiment performed for a subset of miRNAs. The results reported here support the applicability of the novel normalization method, in particular to datasets that display global decreases in miRNA expression similarly to the cigarette smoke-exposed mouse lung dataset considered in this study. Quality metrics to assess between-array variability were used to confirm that the novel spike-in controls based normalization method provided high-quality miRNA expression data suitable for reliable downstream analysis. The multi-array miRNA raw data normalization method was implemented in an R software package called ExiMiR and deposited in the Bioconductor repository.

Assessment of a novel multi-array normalization method based on spike-in control probes suitable for microRNA datasets with global decreases in expression

PubMed Central

2014-01-01

Background High-quality expression data are required to investigate the biological effects of microRNAs (miRNAs). The goal of this study was, first, to assess the quality of miRNA expression data based on microarray technologies and, second, to consolidate it by applying a novel normalization method. Indeed, because of significant differences in platform designs, miRNA raw data cannot be normalized blindly with standard methods developed for gene expression. This fundamental observation motivated the development of a novel multi-array normalization method based on controllable assumptions, which uses the spike-in control probes to adjust the measured intensities across arrays. Results Raw expression data were obtained with the Exiqon dual-channel miRCURY LNA™ platform in the “common reference design” and processed as “pseudo-single-channel”. They were used to apply several quality metrics based on the coefficient of variation and to test the novel spike-in controls based normalization method. Most of the considerations presented here could be applied to raw data obtained with other platforms. To assess the normalization method, it was compared with 13 other available approaches from both data quality and biological outcome perspectives. The results showed that the novel multi-array normalization method reduced the data variability in the most consistent way. Further, the reliability of the obtained differential expression values was confirmed based on a quantitative reverse transcription–polymerase chain reaction experiment performed for a subset of miRNAs. The results reported here support the applicability of the novel normalization method, in particular to datasets that display global decreases in miRNA expression similarly to the cigarette smoke-exposed mouse lung dataset considered in this study. Conclusions Quality metrics to assess between-array variability were used to confirm that the novel spike-in controls based normalization method provided high-quality miRNA expression data suitable for reliable downstream analysis. The multi-array miRNA raw data normalization method was implemented in an R software package called ExiMiR and deposited in the Bioconductor repository. PMID:24886675

Mechanism and applications of new fluorescent compounds produced by femtosecond laser surgery in biological tissue (Conference Presentation)

NASA Astrophysics Data System (ADS)

Qu, Jianan Y.; Sun, Qiqi

2017-02-01

The single or multi-photon microscopy based on fluorescent labelling and staining is a sensitive and quantitative method that is widely used in molecular biology and medical research for a variety of experimental, analytical, and quality control applications. However, label-free method is highly desirable in biology and medicine when performing long term live imaging of biological system and obtaining instant tissue examination during surgery procedures. Recently, our group found that femtosecond laser surgery turned a variety of biological tissues and protein samples into highly fluorescent substances. The newly formed fluorescent compounds produced during the laser surgery can be excited via single- and two-photon processes over broad wavelength ranges. We developed a combined confocal and two-photon spectroscopic microscope to characterize the fluorescence from the new compound systematically. The structures of the femtosecond laser treated tissue were studied using Raman spectroscopy and transmission electron microscopy. Our study revealed the mechanisms of the fluorescence emission form the new compound. Furthermore, we demonstrated the applications of the fluorescent compounds for instant evaluation of femtosecond laser microsurgery, study of stem cell responses to muscle injury and neuro-regeneration after spinal cord injury.

A Model of Risk Analysis in Analytical Methodology for Biopharmaceutical Quality Control.

PubMed

Andrade, Cleyton Lage; Herrera, Miguel Angel De La O; Lemes, Elezer Monte Blanco

2018-01-01

One key quality control parameter for biopharmaceutical products is the analysis of residual cellular DNA. To determine small amounts of DNA (around 100 pg) that may be in a biologically derived drug substance, an analytical method should be sensitive, robust, reliable, and accurate. In principle, three techniques have the ability to measure residual cellular DNA: radioactive dot-blot, a type of hybridization; threshold analysis; and quantitative polymerase chain reaction. Quality risk management is a systematic process for evaluating, controlling, and reporting of risks that may affects method capabilities and supports a scientific and practical approach to decision making. This paper evaluates, by quality risk management, an alternative approach to assessing the performance risks associated with quality control methods used with biopharmaceuticals, using the tool hazard analysis and critical control points. This tool provides the possibility to find the steps in an analytical procedure with higher impact on method performance. By applying these principles to DNA analysis methods, we conclude that the radioactive dot-blot assay has the largest number of critical control points, followed by quantitative polymerase chain reaction, and threshold analysis. From the analysis of hazards (i.e., points of method failure) and the associated method procedure critical control points, we conclude that the analytical methodology with the lowest risk for performance failure for residual cellular DNA testing is quantitative polymerase chain reaction. LAY ABSTRACT: In order to mitigate the risk of adverse events by residual cellular DNA that is not completely cleared from downstream production processes, regulatory agencies have required the industry to guarantee a very low level of DNA in biologically derived pharmaceutical products. The technique historically used was radioactive blot hybridization. However, the technique is a challenging method to implement in a quality control laboratory: It is laborious, time consuming, semi-quantitative, and requires a radioisotope. Along with dot-blot hybridization, two alternatives techniques were evaluated: threshold analysis and quantitative polymerase chain reaction. Quality risk management tools were applied to compare the techniques, taking into account the uncertainties, the possibility of circumstances or future events, and their effects upon method performance. By illustrating the application of these tools with DNA methods, we provide an example of how they can be used to support a scientific and practical approach to decision making and can assess and manage method performance risk using such tools. This paper discusses, considering the principles of quality risk management, an additional approach to the development and selection of analytical quality control methods using the risk analysis tool hazard analysis and critical control points. This tool provides the possibility to find the method procedural steps with higher impact on method reliability (called critical control points). Our model concluded that the radioactive dot-blot assay has the larger number of critical control points, followed by quantitative polymerase chain reaction and threshold analysis. Quantitative polymerase chain reaction is shown to be the better alternative analytical methodology in residual cellular DNA analysis. © PDA, Inc. 2018.

Out of the picture: a study of family drawings by children from step-, single-parent, and non-step families.

PubMed

Dunn, Judy; O'Connor, Thomas G; Levy, Irit

2002-12-01

Investigated the family drawings of 180 children ages 5 to 7 years in various family settings, including stepfather, single-parent, complex stepfamilies, and 2-parent control families. The relations of family type and biological relatedness to omission of family members and grouping of parents were examined. Children from step- and single-parent families were more likely to exclude family members than children from "control" non-step families, and exclusion was predicted from biological relatedness. Children who were biologically related to both resident parents were also more likely to group their parents together. Omission of family members was found to be associated with children's adjustment (specifically more externalizing and internalizing behavior) as reported by teachers and parents. The results indicate that biological relatedness is a salient aspect of very young children's representations of their families. The association between adjustment and exclusion of family members and grouping of parents indicates that family drawings may be useful research and clinical tools, when used in combination with other methods of assessment.

Differential effects of plant species on a mite pest (Tetranychus utricae) and its predator (Phytoseiulus persimilis): implications for biological control.

PubMed

Skirvin, D J; de Courcy Williams, M

1999-06-01

The influence of plant species on the population dynamics of the spider mite pest, Tetranychus urticae, and its predator, Phytoseiulus persimilis, was examined as a prerequisite to effective biological control on ornamental nursery stock. Experiments have been done to investigate how the development, fecundity and movement of T. urticae, and the movement of P. persimilis were affected by plant species. A novel experimental method, which incorporates plant structure, was used to investigate the functional response of P. persimilis. Development times for T. urticae were consistent with published data and did not differ with plant species in a biologically meaningful way. Plant species was shown to have a major influence on fecundity (P < 0.001) and movement of the pest mite (P < 0.01), but no influence on the movement of the predator. The movement of both pest and predator was shown to be related to the density of the adult pest mites on the plant (P < 0.001). Plant structure affected the functional response, particularly in relation to the ability of the predator to locate prey at low densities. The impact of these findings on the effective use of biological control on ornamental nursery stock is discussed.

CPG-inspired workspace trajectory generation and adaptive locomotion control for quadruped robots.

PubMed

Liu, Chengju; Chen, Qijun; Wang, Danwei

2011-06-01

This paper deals with the locomotion control of quadruped robots inspired by the biological concept of central pattern generator (CPG). A control architecture is proposed with a 3-D workspace trajectory generator and a motion engine. The workspace trajectory generator generates adaptive workspace trajectories based on CPGs, and the motion engine realizes joint motion imputes. The proposed architecture is able to generate adaptive workspace trajectories online by tuning the parameters of the CPG network to adapt to various terrains. With feedback information, a quadruped robot can walk through various terrains with adaptive joint control signals. A quadruped platform AIBO is used to validate the proposed locomotion control system. The experimental results confirm the effectiveness of the proposed control architecture. A comparison by experiments shows the superiority of the proposed method against the traditional CPG-joint-space control method.

UK–South Asian patients’ experiences of and satisfaction toward receiving information about biologics in rheumatoid arthritis

PubMed Central

Kumar, Kanta; Raizada, Sabrina R; Mallen, Christian D; Stack, Rebecca J

2018-01-01

Background Rheumatoid arthritis (RA) causes painful joint inflammation and is incurable, but treatments control RA. Drug regimens are complex, and patients often do not take their medication as expected. Poor medication adherence can lead to poorly controlled disease and worse patient outcomes. Biologics treatments are expensive and require full engagement from patients. We have previously shown that patients from Black ethnic minority backgrounds do not fully engage into treatment plan. This study explored the patients’ experiences in and satisfaction toward receiving information about biologics and future support preferences in South Asian patients with RA. Methods Twenty South Asian patients with RA from Royal Wolverhampton Hospitals NHS Trust and Central Manchester University Hospitals NHS Foundation Trust participated in individual semistructured interviews. Interviews were transcribed and data were analyzed by using thematic analysis approach. Results Four overarching themes describe the patients’ experience in and satisfaction toward receiving information on biologics: 1) current provision of information regarding the “biologics journey” and understanding of RA: in this theme, non-English-speaking patients expressed heightened anxiety about stepping up to biologics; 2) experience and perceptions of biologics: many patients were positive about the biologic experience; however, there were patient-perceived delays in getting on to the biologics; 3) factors influencing willingness to try biologics: in this theme, a number of factors were identified including seeking advice from doctors abroad; and 4) recommendations on the desired information to fully understand the use of biologics: some patients valued group discussions, while others suggested receiving RA and biologic information through a video interaction. Conclusion This novel study provides insight into South Asian RA patients’ experiences in and satisfaction toward receiving information about biologics. South Asian patients with RA reported a range of perceptions about biologics and support preferences, many of which may not be shared with the non-South Asian population. PMID:29670337

Using biological control research in the classroom to promote scientific inquiry and literacy

USDA-ARS?s Scientific Manuscript database

Many scientists who research biological control also teach at universities or more informally through cooperative outreach. The purpose of this paper is to review biological control activities for the classroom in four refereed journals, The American Biology Teacher, Journal of Biological Education...

OMICS-strategies and methods in the fight against doping.

PubMed

Reichel, Christian

2011-12-10

During the past decade OMICS-methods not only continued to have their impact on research strategies in life sciences and in particular molecular biology, but also started to be used for anti-doping control purposes. Research activities were mainly reasoned by the fact that several substances and methods, which were prohibited by the World Anti-Doping Agency (WADA), were or still are difficult to detect by direct methods. Transcriptomics, proteomics, and metabolomics in theory offer ideal platforms for the discovery of biomarkers for the indirect detection of the abuse of these substances and methods. Traditionally, the main focus of transcriptomics and proteomics projects has been on the prolonged detection of the misuse of human growth hormone (hGH), recombinant erythropoietin (rhEpo), and autologous blood transfusion. An additional benefit of the indirect or marker approach would also be that similarly acting substances might then be detected by a single method, without being forced to develop new direct detection methods for new but comparable prohibited substances (as has been the case, e.g. for the various forms of Epo analogs and biosimilars). While several non-OMICS-derived parameters for the indirect detection of doping are currently in use, for example the blood parameters of the hematological module of the athlete's biological passport, the outcome of most non-targeted OMICS-projects led to no direct application in routine doping control so far. The main reason is the inherent complexity of human transcriptomes, proteomes, and metabolomes and their inter-individual variability. The article reviews previous and recent research projects and their results and discusses future strategies for a more efficient application of OMICS-methods in doping control. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Stochastic Control and Numerical Methods with Applications to Communications. Game Theoretic/Subsolution to Importance Sampling for Rare Event Simulation

DTIC Science & Technology

2008-11-01

support to the value of the approach. 9. Scheduling and Control of Mobile Communications Networks with Randomly Time Varying Channels by Stability ...biological systems . Many examples arise in communications and queueing, due to the finite speed of signal transmission, the nonnegligible time required...without delays, the system state takes values in a subset of some finite -dimensional Euclidean space, and the control is a functional of the current

Towards Engineering Biological Systems in a Broader Context.

PubMed

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

2016-02-27

Significant advances have been made in synthetic biology to program information processing capabilities in cells. While these designs can function predictably in controlled laboratory environments, the reliability of these devices in complex, temporally changing environments has not yet been characterized. As human society faces global challenges in agriculture, human health and energy, synthetic biology should develop predictive design principles for biological systems operating in complex environments. Natural biological systems have evolved mechanisms to overcome innumerable and diverse environmental challenges. Evolutionary design rules should be extracted and adapted to engineer stable and predictable ecological function. We highlight examples of natural biological responses spanning the cellular, population and microbial community levels that show promise in synthetic biology contexts. We argue that synthetic circuits embedded in host organisms or designed ecologies informed by suitable measurement of biotic and abiotic environmental parameters could be used as engineering substrates to achieve target functions in complex environments. Successful implementation of these methods will broaden the context in which synthetic biological systems can be applied to solve important problems. Copyright © 2015 Elsevier Ltd. All rights reserved.

Ultrafast and Wide Range Analysis of DNA Molecules Using Rigid Network Structure of Solid Nanowires

PubMed Central

Rahong, Sakon; Yasui, Takao; Yanagida, Takeshi; Nagashima, Kazuki; Kanai, Masaki; Klamchuen, Annop; Meng, Gang; He, Yong; Zhuge, Fuwei; Kaji, Noritada; Kawai, Tomoji; Baba, Yoshinobu

2014-01-01

Analyzing sizes of DNA via electrophoresis using a gel has played an important role in the recent, rapid progress of biology and biotechnology. Although analyzing DNA over a wide range of sizes in a short time is desired, no existing electrophoresis methods have been able to fully satisfy these two requirements. Here we propose a novel method using a rigid 3D network structure composed of solid nanowires within a microchannel. This rigid network structure enables analysis of DNA under applied DC electric fields for a large DNA size range (100 bp–166 kbp) within 13 s, which are much wider and faster conditions than those of any existing methods. The network density is readily varied for the targeted DNA size range by tailoring the number of cycles of the nanowire growth only at the desired spatial position within the microchannel. The rigid dense 3D network structure with spatial density control plays an important role in determining the capability for analyzing DNA. Since the present method allows the spatial location and density of the nanostructure within the microchannels to be defined, this unique controllability offers a new strategy to develop an analytical method not only for DNA but also for other biological molecules. PMID:24918865

Ultrafast and Wide Range Analysis of DNA Molecules Using Rigid Network Structure of Solid Nanowires

NASA Astrophysics Data System (ADS)

Rahong, Sakon; Yasui, Takao; Yanagida, Takeshi; Nagashima, Kazuki; Kanai, Masaki; Klamchuen, Annop; Meng, Gang; He, Yong; Zhuge, Fuwei; Kaji, Noritada; Kawai, Tomoji; Baba, Yoshinobu

2014-06-01

Analyzing sizes of DNA via electrophoresis using a gel has played an important role in the recent, rapid progress of biology and biotechnology. Although analyzing DNA over a wide range of sizes in a short time is desired, no existing electrophoresis methods have been able to fully satisfy these two requirements. Here we propose a novel method using a rigid 3D network structure composed of solid nanowires within a microchannel. This rigid network structure enables analysis of DNA under applied DC electric fields for a large DNA size range (100 bp-166 kbp) within 13 s, which are much wider and faster conditions than those of any existing methods. The network density is readily varied for the targeted DNA size range by tailoring the number of cycles of the nanowire growth only at the desired spatial position within the microchannel. The rigid dense 3D network structure with spatial density control plays an important role in determining the capability for analyzing DNA. Since the present method allows the spatial location and density of the nanostructure within the microchannels to be defined, this unique controllability offers a new strategy to develop an analytical method not only for DNA but also for other biological molecules.

Notochord isolation using laser capture microdissection.

PubMed

Santegoeds, R G C; Yakkioui, Y; Jahanshahi, A; Raven, G; Van Overbeeke, J J; Herrler, A; Temel, Y

2017-03-01

Chordoma are malignant tumors of the axial skeleton, which arise from remnants of the notochord. The Notochord (chorda dorsalis) is an essential embryonic structure involved in the development of the nervous system and axial skeleton. Therefore, the notochord seems to be the most biologically relevant control tissue to study chordoma in molecular biology research. Nevertheless, up to now mainly different tissues but not the notochord have been used as control for chordoma, due to difficulty of isolating notochordal tissue. Here, we describe a fast and precise method of isolating notochordal cells. Examination of human fetuses, with a gestation of 9, 11 and 13 weeks, using (immuno)histochemical methods was performed. To isolate pure notochord cells for further molecular biology investigation five flash frozen fetuses between 9 and 10 weeks of gestation were dissected by microtome slicing. Thereafter pure notochord cells for further molecular biology investigation where harvested by using laser capture microdissection (LCM). RNA was extracted from these samples and used in quantitative PCR. This study illustrates notochord of embryonic spines in three different stages of gestation (9-11-13 weeks). Immunohistochemical staining with brachyury showed strong staining of the notochord, but also weak staining of the intervertebral disc and vertebral body. LCM of notochord slices and subsequent total RNA extraction resulted in a good yield of total RNA. qPCR analysis of two housekeeping genes confirmed the quality of the RNA. LCM is a fast and precise method to isolate notochord and the quality and yield RNA extracted from this tissue is sufficient for qPCR analysis. Therefore early embryo notochord isolated by LCM is suggested to be the gold standard for future research in chordoma development, classification and diagnosis. Copyright © 2016 Elsevier B.V. All rights reserved.

Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future.

PubMed

Barnes, Stephen; Benton, H Paul; Casazza, Krista; Cooper, Sara J; Cui, Xiangqin; Du, Xiuxia; Engler, Jeffrey; Kabarowski, Janusz H; Li, Shuzhao; Pathmasiri, Wimal; Prasain, Jeevan K; Renfrow, Matthew B; Tiwari, Hemant K

2016-08-01

Metabolomics, a systems biology discipline representing analysis of known and unknown pathways of metabolism, has grown tremendously over the past 20 years. Because of its comprehensive nature, metabolomics requires careful consideration of the question(s) being asked, the scale needed to answer the question(s), collection and storage of the sample specimens, methods for extraction of the metabolites from biological matrices, the analytical method(s) to be employed and the quality control of the analyses, how collected data are correlated, the statistical methods to determine metabolites undergoing significant change, putative identification of metabolites and the use of stable isotopes to aid in verifying metabolite identity and establishing pathway connections and fluxes. This second part of a comprehensive description of the methods of metabolomics focuses on data analysis, emerging methods in metabolomics and the future of this discipline. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

The USDA Cranberry Entomology Lab: Highlights from 2011-2017

USDA-ARS?s Scientific Manuscript database

Biological, chemical, and cultural control methods have been investigated as part of the cranberry crop protection program pursued in the USDA Cranberry Entomology Laboratory. Surveys of native entomopathogenic nematodes in Wisconsin have produced a new bio-insecticide agent (Oscheius onirici subsp....

From biological and social network metaphors to coupled bio-social wireless networks

PubMed Central

Barrett, Christopher L.; Eubank, Stephen; Anil Kumar, V.S.; Marathe, Madhav V.

2010-01-01

Biological and social analogies have been long applied to complex systems. Inspiration has been drawn from biological solutions to solve problems in engineering products and systems, ranging from Velcro to camouflage to robotics to adaptive and learning computing methods. In this paper, we present an overview of recent advances in understanding biological systems as networks and use this understanding to design and analyse wireless communication networks. We expand on two applications, namely cognitive sensing and control and wireless epidemiology. We discuss how our work in these two applications is motivated by biological metaphors. We believe that recent advances in computing and communications coupled with advances in health and social sciences raise the possibility of studying coupled bio-social communication networks. We argue that we can better utilise the advances in our understanding of one class of networks to better our understanding of the other. PMID:21643462

Access and benefit sharing (ABS) under the convention on biological diversity (CBD): implications for microbial biological control

USDA-ARS?s Scientific Manuscript database

Researchers and implementers of biological control are confronted with a variety of scientific, regulatory and administrative challenges to their biological control programs. One developing challenge will arise from the implementation of provisions of the Convention on Biological Diversity (CBD) co...

Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery.

PubMed

Bosl, William J

2007-02-15

Expert knowledge in journal articles is an important source of data for reconstructing biological pathways and creating new hypotheses. An important need for medical research is to integrate this data with high throughput sources to build useful models that span several scales. Researchers traditionally use mental models of pathways to integrate information and development new hypotheses. Unfortunately, the amount of information is often overwhelming and these are inadequate for predicting the dynamic response of complex pathways. Hierarchical computational models that allow exploration of semi-quantitative dynamics are useful systems biology tools for theoreticians, experimentalists and clinicians and may provide a means for cross-communication. A novel approach for biological pathway modeling based on hybrid intelligent systems or soft computing technologies is presented here. Intelligent hybrid systems, which refers to several related computing methods such as fuzzy logic, neural nets, genetic algorithms, and statistical analysis, has become ubiquitous in engineering applications for complex control system modeling and design. Biological pathways may be considered to be complex control systems, which medicine tries to manipulate to achieve desired results. Thus, hybrid intelligent systems may provide a useful tool for modeling biological system dynamics and computational exploration of new drug targets. A new modeling approach based on these methods is presented in the context of hedgehog regulation of the cell cycle in granule cells. Code and input files can be found at the Bionet website: www.chip.ord/~wbosl/Software/Bionet. This paper presents the algorithmic methods needed for modeling complicated biochemical dynamics using rule-based models to represent expert knowledge in the context of cell cycle regulation and tumor growth. A notable feature of this modeling approach is that it allows biologists to build complex models from their knowledge base without the need to translate that knowledge into mathematical form. Dynamics on several levels, from molecular pathways to tissue growth, are seamlessly integrated. A number of common network motifs are examined and used to build a model of hedgehog regulation of the cell cycle in cerebellar neurons, which is believed to play a key role in the etiology of medulloblastoma, a devastating childhood brain cancer.

Detection of Patient Subgroups with Differential Expression in Omics Data: A Comprehensive Comparison of Univariate Measures

PubMed Central

Ahrens, Maike; Turewicz, Michael; Casjens, Swaantje; May, Caroline; Pesch, Beate; Stephan, Christian; Woitalla, Dirk; Gold, Ralf; Brüning, Thomas; Meyer, Helmut E.

2013-01-01

Detection of yet unknown subgroups showing differential gene or protein expression is a frequent goal in the analysis of modern molecular data. Applications range from cancer biology over developmental biology to toxicology. Often a control and an experimental group are compared, and subgroups can be characterized by differential expression for only a subgroup-specific set of genes or proteins. Finding such genes and corresponding patient subgroups can help in understanding pathological pathways, diagnosis and defining drug targets. The size of the subgroup and the type of differential expression determine the optimal strategy for subgroup identification. To date, commonly used software packages hardly provide statistical tests and methods for the detection of such subgroups. Different univariate methods for subgroup detection are characterized and compared, both on simulated and on real data. We present an advanced design for simulation studies: Data is simulated under different distributional assumptions for the expression of the subgroup, and performance results are compared against theoretical upper bounds. For each distribution, different degrees of deviation from the majority of observations are considered for the subgroup. We evaluate classical approaches as well as various new suggestions in the context of omics data, including outlier sum, PADGE, and kurtosis. We also propose the new FisherSum score. ROC curve analysis and AUC values are used to quantify the ability of the methods to distinguish between genes or proteins with and without certain subgroup patterns. In general, FisherSum for small subgroups and -test for large subgroups achieve best results. We apply each method to a case-control study on Parkinson's disease and underline the biological benefit of the new method. PMID:24278130

Determination of 18 beta-glycyrrhetinic acid in biological fluids from humans and rats by solid-phase extraction and high-performance liquid chromatography.

PubMed

Hasler, F; Krapf, R; Brenneisen, R; Bourquin, D; Krähenbühl, S

1993-10-22

Methods have been developed and characterized allowing rapid isolation and quantification of 18 beta-glycyrrhetinic acid (GRA) in biological fluids from both humans and rats. Sample preparation includes extraction with urea-methanol for plasma samples, and solid-phase extraction (SPE) for urine and bile samples. Hydrolysis of GRA glucuronides in urine and bile was performed by treatment with beta-glucuronidase. MGRA, the 3-O-methyl derivative of GRA was synthesized as an internal standard resistant to hydrolysis. High-performance liquid chromatography (HPLC) was performed with an isocratic system using methanol-water-acetic acid (83:16.8:0.2, v/v/v) as solvent on a Lichrocart RP-18 column at 30 degrees C with ultraviolet detection. The methods allowed base line separation of GRA and MGRA from all biological fluids tested, with a detection limit of 0.15 mg/l. Validation of the methods included determination of recovery, accuracy and precision in plasma, bile and urine from humans and rats. The methods were further evaluated by investigating the pharmacokinetics of GRA in normal rats and in rats with a bile fistula. Following an intravenous dose of 10 mg/kg, the plasma concentration-time curve of GRA could be fitted to a one compartment model both in control and bile fistula rats. The elimination half life averaged 15.0 +/- 2.2 versus 16.8 +/- 2.4 min in control and bile fistula rats (difference not significant). Within 90 min following administration of GRA, urinary elimination of GRA and GRA glucuronides was less than 1% in both groups whereas biliary elimination averaged 51.3 +/- 3.1%. The results show that the methods developed allow pharmacokinetic studies of GRA in humans and rats.

Maternal attitudes toward DNA collection for gene-environment studies: a qualitative research study.

PubMed

Jenkins, Mary M; Reed-Gross, Erika; Rasmussen, Sonja A; Barfield, Wanda D; Prue, Christine E; Gallagher, Margaret L; Honein, Margaret A

2009-11-01

To assess attitudes toward DNA collection in an epidemiological study, focus groups were assembled in September 2007 with mothers who had participated in a case-control study of birth defects. Each recruited mother previously had completed an interview and had received a mailed kit containing cytobrushes to collect buccal cells for DNA from herself, her infant, and her infant's father during the period July 2004 through July 2007. A total of 38 mothers attended six focus groups comprising: (1) non-Hispanic Black mothers of case infants who participated or (2) did not participate in DNA collection, (3) mothers of any race or ethnicity who had case infants of low birth weight who participated or (4) did not participate in DNA collection, and (5) non-Hispanic Black mothers of control infants who participated or (6) did not participate in DNA collection. Moderator-led discussions probed maternal attitudes toward providing specimens, factors that influenced decision making, and collection method preferences. Biologics participants reported that they provided DNA for altruistic reasons. Biologics nonparticipants voiced concerns about government involvement and how their DNA will be used. Information provided (or not provided) on DNA use, storage, and disposal influenced decision making. Biologics participants and nonparticipants reported that paternal skepticism was a barrier to participation. All mothers were asked to rank DNA collection methods in terms of preference (cytobrushes, saliva, mouthwash, newborn blood spots, and blood collection). Preferred methods were convenient and noninvasive. Better understanding attitudes toward DNA collection and preferred collection methods might allow more inclusive participation and benefit future studies. Copyright 2009 Wiley-Liss, Inc.

[Potency testing of anti-lymphocyte Globulins: In vitro alternatives for the monkey skin-graft assay

PubMed

Conrad, Christoph; Kabelitz, Dieter; Schäffner, Gabriele

1998-01-01

Antilymphocyte globulins (ALG) are immunosuppressive agents of animal origin currently used in clinical transplantation medicine and for the treatment of severe aplastic anemia. The potency of each batch is tested in vivo using primates as hosts for allogeneic skin transplantation. The test is done with a maximum of three animals, one as a control and two after the treatment with ALG. The two in vitro methods in use are a cytotoxic assay and the rosette inhibition assay. These methods are evaluated with the microscope. Besides wellfare aspects these methods require a lot of experience, are subjective, difficult to validate and the information about the biological potency of the sera is questionable. The aim of our study is a better biological characterisation as a prerequisite to subsequently define an in vitro alternative for the potency test in monkeys. Using a competition assay with monoclonal antibodies we can identify several specificities directed against functional molecules on T cells (e.g., CD2, CD3, CD5, CD28), B Cells (CD19), macrophages and natural killer cells (CD16) and nonlineage specificities such as CD18, CD25, CD29, CD95. This method could describe a part of the biological potency and control homogeneity of batches. The cytotoxic capacity of ALG either with or without complement as well as DNA-fragmentation characteristic for apoptosis can be analysed by flowcytometry using propidiumiodide- (PI) incorporation. Immunoprecipitation of cell-lysate with ALG