Multiscale agent-based cancer modeling.

PubMed

Zhang, Le; Wang, Zhihui; Sagotsky, Jonathan A; Deisboeck, Thomas S

2009-04-01

Agent-based modeling (ABM) is an in silico technique that is being used in a variety of research areas such as in social sciences, economics and increasingly in biomedicine as an interdisciplinary tool to study the dynamics of complex systems. Here, we describe its applicability to integrative tumor biology research by introducing a multi-scale tumor modeling platform that understands brain cancer as a complex dynamic biosystem. We summarize significant findings of this work, and discuss both challenges and future directions for ABM in the field of cancer research.

A Free Accessible Individual-Based Simulator Enabling Virtual Experiments on Soil Organic Matter Processes in Classroom

ERIC Educational Resources Information Center

Gras, Anna; Cañadas, Juan Carlos; Ginovart, Marta

2013-01-01

This work addresses and aims to fulfill a very clear need in teaching biosystem engineering. When introducing students to the complexity of soil processes, one of the frustrations that teachers often experience is the impossibility to demonstrate practically, in the lab, some of the concepts and processes discussed in class. Either the experiments…

BIOREMEDIATION OF HAZARDOUS WASTES

EPA Science Inventory

In 1987, the U.S. Environmental Protection Agency's (EPA) Office of Research and Development (ORD) initiated the Biosystems Technology Development Program to anticipate and address research needs in managing our nation's hazardous waste. The Agency believes that bioremediation of...

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.

BIOREMEDIATION OF HAZARDOUS WASTES - RESEARCH, DEVELOPMENT, AND FIELD EVALUATIONS - 1994

EPA Science Inventory

The proceedings of the 1994 Symposium on Bioremediation of Hazardous Wastes, hosted by the Office of Research and Development (ORD) of the EPA in San Francisco, California. The symposium was the seventh annual meeting for the presentation of research conducted by EPA's Biosystem...

Development and validation of an event-specific quantitative PCR method for genetically modified maize MIR162.

PubMed

Takabatake, Reona; Masubuchi, Tomoko; Futo, Satoshi; Minegishi, Yasutaka; Noguchi, Akio; Kondo, Kazunari; Teshima, Reiko; Kurashima, Takeyo; Mano, Junichi; Kitta, Kazumi

2014-01-01

A novel real-time PCR-based analytical method was developed for the event-specific quantification of a genetically modified (GM) maize event, MIR162. We first prepared a standard plasmid for MIR162 quantification. The conversion factor (Cf) required to calculate the genetically modified organism (GMO) amount was empirically determined for two real-time PCR instruments, the Applied Biosystems 7900HT (ABI7900) and the Applied Biosystems 7500 (ABI7500) for which the determined Cf values were 0.697 and 0.635, respectively. To validate the developed method, a blind test was carried out in an interlaboratory study. The trueness and precision were evaluated as the bias and reproducibility of relative standard deviation (RSDr). The determined biases were less than 25% and the RSDr values were less than 20% at all evaluated concentrations. These results suggested that the limit of quantitation of the method was 0.5%, and that the developed method would thus be suitable for practical analyses for the detection and quantification of MIR162.

BIOREMEDIATION OF HAZARDOUS WASTES - RESEARCH, DEVELOPMENT, AND FIELD EVALUATIONS - 1993

EPA Science Inventory

The proceedings of the 1993 Symposium on Bioremediation of Hazardous Wastes, hosted by the Office of Research and Development (ORD) of the EPA in Dallas, Texas The symposium was the sixth annual meeting for the presentation of research conducts (by EPA's Biosystems Technology Dev...

BIOREMEDIATION OF HAZARDOUS WASTES - RESEARCH, DEVELOPMENT AND FIELD EVALUATIONS - 1995

EPA Science Inventory

The proceedings of the 1995 Symposium on Bioremediation of Hazardous Wastes, hosted by the Office of Research and Development (ORD) of the EPA in Rye Brook, New York. he symposium was the eighth annual meeting for the presentation of research conducted by EPA's Biosystems Technol...

Digital microfabrication of user-defined 3D microstructures in cell-laden hydrogels.

PubMed

Soman, Pranav; Chung, Peter H; Zhang, A Ping; Chen, Shaochen

2013-11-01

Complex 3D interfacial arrangements of cells are found in several in vivo biosystems such as blood vasculature, renal glomeruli, and intestinal villi. Current tissue engineering techniques fail to develop suitable 3D microenvironments to evaluate the concurrent effects of complex topography and cell encapsulation. There is a need to develop new fabrication approaches that control cell density and distribution within complex 3D features. In this work, we present a dynamic projection printing process that allows rapid construction of complex 3D structures using custom-defined computer-aided-design (CAD) files. Gelatin-methacrylate (GelMA) constructs featuring user-defined spiral, pyramid, flower, and dome micro-geometries were fabricated with and without encapsulated cells. Encapsulated cells demonstrate good cell viability across all geometries both on the scaffold surface and internal to the structures. Cells respond to geometric cues individually as well as collectively throughout the larger-scale patterns. Time-lapse observations also reveal the dynamic nature of mechanical interactions between cells and micro-geometry. When compared to conventional cell-seeding, cell encapsulation within complex 3D patterned scaffolds provides long-term control over proliferation, cell morphology, and geometric guidance. Overall, this biofabrication technique offers a flexible platform to evaluate cell interactions with complex 3D micro-features, with the ability to scale-up towards high-throughput screening platforms. © 2013 Wiley Periodicals, Inc.

3D bio-etching of a complex composite-like embryonic tissue.

PubMed

Hazar, Melis; Kim, Yong Tae; Song, Jiho; LeDuc, Philip R; Davidson, Lance A; Messner, William C

2015-08-21

Morphogenesis involves a complex series of cell signaling, migration and differentiation events that are coordinated as tissues self-assemble during embryonic development. Collective cell movements such as those that occur during morphogenesis have typically been studied in 2D with single layers of cultured cells adhering to rigid substrates such as glass or plastic. In vivo, the intricacies of the 3D microenvironment and complex 3D responses are pivotal in the formation of functional tissues. To study such processes as collective cell movements within 3D multilayered tissues, we developed a microfluidic technique capable of producing complex 3D laminar multicellular structures. We call this technique "3D tissue-etching" because it is analogous to techniques used in the microelectromechanics (MEMS) field where complex 3D structures are built by successively removing material from a monolithic solid through subtractive manufacturing. We use a custom-designed microfluidic control system to deliver a range of tissue etching reagents (detergents, chelators, proteases, etc.) to specific regions of multilayered tissues. These tissues were previously isolated by microsurgical excision from embryos of the African claw-toed frog, Xenopus laevis. The ability to shape the 3D form of multicellular tissues and to control 3D stimulation will have a high impact on tissue engineering and regeneration applications in bioengineering and medicine as well as provide significant improvements in the synthesis of highly complex 3D integrated multicellular biosystems.

Photonic homeostatics

NASA Astrophysics Data System (ADS)

Liu, Timon C.; Li, Fan-Hui

2010-11-01

Photonic homeostatics is a discipline to study the establishment, maintenance, decay, upgrading and representation of function-specific homoestasis (FSH) by using photonics. FSH is a negative-feedback response of a biosystem to maintain the function-specific fluctuations inside the biosystem so that the function is perfectly performed. A stress may increase sirtuin 1 (SIRT1) activities above FSH-specific SIRT1 activity to induce a function far from its FSH. On the one hand, low level laser irradiation or monochromatic light (LLL) can not modulate a function in its FSH or a stress in its stress-specific homeostasis (StSH), but modulate a function far from its FSH or a stress far from its StSH. On the other hand, the biophotons from a biosystem with its function in its FSH should be less than the one from the biosystem with its function far from its FSH. The non-resonant interaction of low intensity laser irradiation or monochromatic light (LIL) and a kind of membrane protein can be amplified by all the membrane proteins if the function is far from its FSH. This amplification might hold for biophoton emission of the membrane protein so that the photonic spectroscopy can be used to represent the function far from its FSH, which is called photonomics.

DNA-controlled dynamic colloidal nanoparticle systems for mediating cellular interaction

NASA Astrophysics Data System (ADS)

Ohta, Seiichi; Glancy, Dylan; Chan, Warren C. W.

2016-02-01

Precise control of biosystems requires development of materials that can dynamically change physicochemical properties. Inspired by the ability of proteins to alter their conformation to mediate function, we explored the use of DNA as molecular keys to assemble and transform colloidal nanoparticle systems. The systems consist of a core nanoparticle surrounded by small satellites, the conformation of which can be transformed in response to DNA via a toe-hold displacement mechanism. The conformational changes can alter the optical properties and biological interactions of the assembled nanosystem. Photoluminescent signal is altered by changes in fluorophore-modified particle distance, whereas cellular targeting efficiency is increased 2.5 times by changing the surface display of targeting ligands. These concepts provide strategies for engineering dynamic nanotechnology systems for navigating complex biological environments.

Microfluidics for food, agriculture and biosystems industries.

PubMed

Neethirajan, Suresh; Kobayashi, Isao; Nakajima, Mitsutoshi; Wu, Dan; Nandagopal, Saravanan; Lin, Francis

2011-05-07

Microfluidics, a rapidly emerging enabling technology has the potential to revolutionize food, agriculture and biosystems industries. Examples of potential applications of microfluidics in food industry include nano-particle encapsulation of fish oil, monitoring pathogens and toxins in food and water supplies, micro-nano-filtration for improving food quality, detection of antibiotics in dairy food products, and generation of novel food structures. In addition, microfluidics enables applications in agriculture and animal sciences such as nutrients monitoring and plant cells sorting for improving crop quality and production, effective delivery of biopesticides, simplified in vitro fertilization for animal breeding, animal health monitoring, vaccination and therapeutics. Lastly, microfluidics provides new approaches for bioenergy research. This paper synthesizes information of selected microfluidics-based applications for food, agriculture and biosystems industries. © The Royal Society of Chemistry 2011

Evolutionary Models for Simple Biosystems

NASA Astrophysics Data System (ADS)

Bagnoli, Franco

The concept of evolutionary development of structures constituted a real revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of such systems has shown that indeed, systems under a flux of energy or matter can self-organize into complex patterns, think for instance to Rayleigh-Bernard convection, Liesegang rings, patterns formed by granular systems under shear. Following this line, one could characterize life as a state of matter, characterized by the slow, continuous process that we call evolution. In this paper we try to identify the organizational level of life, that spans several orders of magnitude from the elementary constituents to whole ecosystems. Although similar structures can be found in other contexts like ideas (memes) in neural systems and self-replicating elements (computer viruses, worms, etc.) in computer systems, we shall concentrate on biological evolutionary structure, and try to put into evidence the role and the emergence of network structure in such systems.

The role of fractional calculus in modeling biological phenomena: A review

NASA Astrophysics Data System (ADS)

Ionescu, C.; Lopes, A.; Copot, D.; Machado, J. A. T.; Bates, J. H. T.

2017-10-01

This review provides the latest developments and trends in the application of fractional calculus (FC) in biomedicine and biology. Nature has often showed to follow rather simple rules that lead to the emergence of complex phenomena as a result. Of these, the paper addresses the properties in respiratory lung tissue, whose natural solutions arise from the midst of FC in the form of non-integer differ-integral solutions and non-integer parametric models. Diffusion of substances in human body, e.g. drug diffusion, is also a phenomena well known to be captured with such mathematical models. FC has been employed in neuroscience to characterize the generation of action potentials and spiking patters but also in characterizing bio-systems (e.g. vegetable tissues). Despite the natural complexity, biological systems belong as well to this class of systems, where FC has offered parsimonious yet accurate models. This review paper is a collection of results and literature reports who are essential to any versed engineer with multidisciplinary applications and bio-medical in particular.

Landfill gas distribution at the base of passive methane oxidation biosystems: Transient state analysis of several configurations.

PubMed

Ahoughalandari, Bahar; Cabral, Alexandre R

2017-11-01

The design process of passive methane oxidation biosystems needs to include design criteria that account for the effect of unsaturated hydraulic behavior on landfill gas migration, in particular, restrictions to landfill gas flow due to the capillary barrier effect, which can greatly affect methane oxidation rates. This paper reports the results of numerical simulations performed to assess the landfill gas flow behavior of several passive methane oxidation biosystems. The concepts of these biosystems were inspired by selected configurations found in the technical literature. We adopted the length of unrestricted gas migration (LUGM) as the main design criterion in this assessment. LUGM is defined as the length along the interface between the methane oxidation and gas distribution layers, where the pores of the methane oxidation layer material can be considered blocked for all practical purposes. High values of LUGM indicate that landfill gas can flow easily across this interface. Low values of LUGM indicate greater chances of having preferential upward flow and, consequently, finding hotspots on the surface. Deficient designs may result in the occurrence of hotspots. One of the designs evaluated included an alternative to a concept recently proposed where the interface between the methane oxidation and gas distribution layers was jagged (in the form of a see-saw). The idea behind this ingenious concept is to prevent blockage of air-filled pores in the upper areas of the jagged segments. The results of the simulations revealed the extent of the capability of the different scenarios to provide unrestricted and conveniently distributed upward landfill gas flow. They also stress the importance of incorporating an appropriate design criterion in the selection of the methane oxidation layer materials and the geometrical form of passive biosystems. Copyright © 2017 Elsevier Ltd. All rights reserved.

Preschool Inclusion in the United States: A Review of Research from an Ecological Systems Perspective

ERIC Educational Resources Information Center

Odom, Samuel L.; Vitztum, Joann; Wolery, Ruth; Lieber, Joan; Sandall, Susan; Hanson, Marci J.; Beckman, Paula; Schwartz, Ilene; Horn, Eva

2004-01-01

Using an ecological systems conceptual framework proposed by Bronfenbrenner, research on the inclusion of preschool children with disabilities in programs with typically developing children was reviewed. Drawing mainly from studies conducted in the United States, research on child characteristics (biosystem), classroom practices (microsystem),…

SYMPOSIUM OF NATURAL ATTENUATION OF GROUND WATER (EPA/600/R-94/162)

EPA Science Inventory

The U.S. Environmental Protection Agency's (EPA's) Biosystems Technology Development Program and the U.S. Geological Survey (USGS), with sponsorship from the U.S. Air Force (USAF), coordinated a meeting on the Natural Attenuation of Ground Water at the Hyatt Regency in Denver, CO...

Modeling biology with HDL languages: a first step toward a genetic design automation tool inspired from microelectronics.

PubMed

Gendrault, Yves; Madec, Morgan; Lallement, Christophe; Haiech, Jacques

2014-04-01

Nowadays, synthetic biology is a hot research topic. Each day, progresses are made to improve the complexity of artificial biological functions in order to tend to complex biodevices and biosystems. Up to now, these systems are handmade by bioengineers, which require strong technical skills and leads to nonreusable development. Besides, scientific fields that share the same design approach, such as microelectronics, have already overcome several issues and designers succeed in building extremely complex systems with many evolved functions. On the other hand, in systems engineering and more specifically in microelectronics, the development of the domain has been promoted by both the improvement of technological processes and electronic design automation tools. The work presented in this paper paves the way for the adaptation of microelectronics design tools to synthetic biology. Considering the similarities and differences between the synthetic biology and microelectronics, the milestones of this adaptation are described. The first one concerns the modeling of biological mechanisms. To do so, a new formalism is proposed, based on an extension of the generalized Kirchhoff laws to biology. This way, a description of all biological mechanisms can be made with languages widely used in microelectronics. Our approach is therefore successfully validated on specific examples drawn from the literature.

Biological electric fields and rate equations for biophotons.

PubMed

Alvermann, M; Srivastava, Y N; Swain, J; Widom, A

2015-04-01

Biophoton intensities depend upon the squared modulus of the electric field. Hence, we first make some general estimates about the inherent electric fields within various biosystems. Generally, these intensities do not follow a simple exponential decay law. After a brief discussion on the inapplicability of a linear rate equation that leads to strict exponential decay, we study other, nonlinear rate equations that have been successfully used for biosystems along with their physical origins when available.

Evidence of organic matter in the Ocean-Continent Transition of Alpine Tethys from Totalp, Eastern Swiss Alps

NASA Astrophysics Data System (ADS)

Mateeva, Tsvetomila; Kusznir, Nick; Wolff, George; Wheeler, John; Manatschal, Gianreto

2015-04-01

Evidence from ocean ridge drilling and dredging and from the exhumed Tethyan continental margin in the Alps demonstrates that mantle serpentinization occurs at slow-spreading ocean ridges and magma-poor rifted continental margins. Observations at white smokers suggest that methane produced by serpentinization can support methanotrophic bio-systems which use methane as their only source of carbon. An important question is whether such biosystems are more generally pervasive in their association with serpentinized mantle in the subsurface. The answer to this question has important global implications for the importance of the hidden sub-surface bio-systems, the fate of methane and the carbon cycle. We examine whether serpentinized exhumed mantle at magma-poor rifted continental margins shows evidence for methanotrophy. Fieldwork sampling of km scale exposure of orogenically exhumed serpentinized mantle in the eastern Swiss Alps allows 3D mantle sampling not possible at ocean ridges and has the potential to answer the question regarding localized versus pervasive sub-surface methanotrophic biosystems. The Totalp massif in the eastern Swiss Alps has been chosen for an initial study to investigate the presence or absence of methanotrophic biosystem within serpentinized exhumed mantle in the Tethyan OCT. Totalp has little Alpine deformation and its metamorphism is no more than prehnite-pumpellyite grade. Hands specimens and cores have been taken from the Totalp area in order to sample serpentinization and its lithological diversity in the search for presence or absence of biomarkers. Thin sections analysis reveals multiple serpentinization events. XRD analysis shows complete serpentinization of the olivines and orthopyroxenes. The samples for bio-geochemical analysis were cut and ground to powder, processed by soxhlet extraction and then analysed by GC and GCMS in order to determine the full range of biomarkers. Total carbon and total organic carbon was also determined for the samples. Samples collected from the Totalp area show evidence of organic hydrocarbon in the form of alkanes. The majority of the samples contain n-alkanes in the range C20 - C32. Some samples contain isoprenoids in different concentrations dependent on their lithology, for example pristane and phytane are found in Totalp's sediments. The organic molecular distribution is consistent with the temperature history of the basin. Totalp samples are characterized by TC contents of 0.03% to 12.90% and TOC contents of 0.10% to 1.90%. This large range of values correlates with the large lithological diversity of this area. These first results from Totalp showing evidence for preserved organic matter and biosystems in the serpentinized mantle of the ancient Tethyan OCT are encouraging. Much more work is required to understand whether the organic matter is generated from methane-driven biosystems, and if so whether the methane originated from an organic or inorganic source?

Nature versus design: synthetic biology or how to build a biological non-machine.

PubMed

Porcar, M; Peretó, J

2016-04-18

The engineering ideal of synthetic biology presupposes that organisms are composed of standard, interchangeable parts with a predictive behaviour. In one word, organisms are literally recognized as machines. Yet living objects are the result of evolutionary processes without any purposiveness, not of a design by external agents. Biological components show massive overlapping and functional degeneracy, standard-free complexity, intrinsic variation and context dependent performances. However, although organisms are not full-fledged machines, synthetic biologists may still be eager for machine-like behaviours from artificially modified biosystems.

The Value of Career ePortfolios on Job Applicant Performance: Using Data to Determine Effectiveness

ERIC Educational Resources Information Center

Ring, Gail L.; Waugaman, Chelsea; Brackett, Bob

2017-01-01

This research project investigated how the development of an ePortfolio, combined with ePortfolio pedagogies, impacted the interview performance of undergraduate students as they prepared to enter the job market. Participants were students in the Health Sciences and Biosystems Engineering programs at Clemson University, enrolled in…

Preserved Organic Matter in the Alpine Tethyan Ocean Continental Transition (Totalp unit, Eastern Swiss Alps)

NASA Astrophysics Data System (ADS)

Mateeva, T.; Wolff, G. A.; Kusznir, N.; Wheeler, J.; Manatschal, G.

2015-12-01

Observations at hydrothermal systems in modern ocean settings suggest that methane produced by serpentinization can support methanotrophic bio-systems. An important question is whether such bio-systems are localised or are more pervasive in their association with serpentinized mantle in the subsurface. This has implications for the global importance of the hidden sub-surface bio-systems, the fate of methane and the carbon cycle. The Totalp unit, a remnant of a former Ocean Continent Transition (OCT) exposed in Alps of Eastern Switzerland, has been chosen to investigate the presence or absence of methanotrophic biosystems within serpentinized exhumed mantle in the Alpine Tethyan margin. The Totalp unit is made of serpentinized mantle and ophicalcites overlain by Upper Jurassic to Lower Cretaceous post-rift sediments. The Totalp unit has undergone little Alpine deformation and only a low-grade metamorphic overprint (<200°C). Totalp samples are characterized by total carbon contents of 0.02% to 12.90% and organic carbon contents of 1x10-4 % to 8%. This large range of values reflects the large lithological diversity of this area. The serpentinized peridotite, ophicalcite and post-rift sediments contain hydrocarbons in the form of n-alkanes in the range C20 - C40; isoprenoids, for example pristane and phytane are present in sediments. The organic biological marker distribution is consistent with the temperature history of the OCT (i.e.lower maximum temperature than 200°C). First results from Totalp show evidence for preservation of marine organic matter in the serpentinized mantle and overlying sediments, although there is no evidence that any organic matter is generated from methanotrophic bio-systems. Nevertheless, focussing on Tethyan hydrothermal systems and preserved hydrocarbons will be critical in understanding whether methanotrophic biomarkers can be preserved and if so whether the methane originated from serpentenization.

LINEBACKER: LINE-speed Bio-inspired Analysis and Characterization for Event Recognition

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

Oehmen, Christopher S.; Bruillard, Paul J.; Matzke, Brett D.

2016-08-04

The cyber world is a complex domain, with digital systems mediating a wide spectrum of human and machine behaviors. While this is enabling a revolution in the way humans interact with each other and data, it also is exposing previously unreachable infrastructure to a worldwide set of actors. Existing solutions for intrusion detection and prevention that are signature-focused typically seek to detect anomalous and/or malicious activity for the sake of preventing or mitigating negative impacts. But a growing interest in behavior-based detection is driving new forms of analysis that move the emphasis from static indicators (e.g. rule-based alarms or tripwires)more » to behavioral indicators that accommodate a wider contextual perspective. Similar to cyber systems, biosystems have always existed in resource-constrained hostile environments where behaviors are tuned by context. So we look to biosystems as an inspiration for addressing behavior-based cyber challenges. In this paper, we introduce LINEBACKER, a behavior-model based approach to recognizing anomalous events in network traffic and present the design of this approach of bio-inspired and statistical models working in tandem to produce individualized alerting for a collection of systems. Preliminary results of these models operating on historic data are presented along with a plugin to support real-world cyber operations.« less

[Weighted gene co-expression network analysis in biomedicine research].

PubMed

Liu, Wei; Li, Li; Ye, Hua; Tu, Wei

2017-11-25

High-throughput biological technologies are now widely applied in biology and medicine, allowing scientists to monitor thousands of parameters simultaneously in a specific sample. However, it is still an enormous challenge to mine useful information from high-throughput data. The emergence of network biology provides deeper insights into complex bio-system and reveals the modularity in tissue/cellular networks. Correlation networks are increasingly used in bioinformatics applications. Weighted gene co-expression network analysis (WGCNA) tool can detect clusters of highly correlated genes. Therefore, we systematically reviewed the application of WGCNA in the study of disease diagnosis, pathogenesis and other related fields. First, we introduced principle, workflow, advantages and disadvantages of WGCNA. Second, we presented the application of WGCNA in disease, physiology, drug, evolution and genome annotation. Then, we indicated the application of WGCNA in newly developed high-throughput methods. We hope this review will help to promote the application of WGCNA in biomedicine research.

SBROME: a scalable optimization and module matching framework for automated biosystems design.

PubMed

Huynh, Linh; Tsoukalas, Athanasios; Köppe, Matthias; Tagkopoulos, Ilias

2013-05-17

The development of a scalable framework for biodesign automation is a formidable challenge given the expected increase in part availability and the ever-growing complexity of synthetic circuits. To allow for (a) the use of previously constructed and characterized circuits or modules and (b) the implementation of designs that can scale up to hundreds of nodes, we here propose a divide-and-conquer Synthetic Biology Reusable Optimization Methodology (SBROME). An abstract user-defined circuit is first transformed and matched against a module database that incorporates circuits that have previously been experimentally characterized. Then the resulting circuit is decomposed to subcircuits that are populated with the set of parts that best approximate the desired function. Finally, all subcircuits are subsequently characterized and deposited back to the module database for future reuse. We successfully applied SBROME toward two alternative designs of a modular 3-input multiplexer that utilize pre-existing logic gates and characterized biological parts.

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

NASA Astrophysics Data System (ADS)

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

2015-10-01

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

Inverted battery design as ion generator for interfacing with biosystems

DOE PAGES

Wang, Chengwei; Fu, Kun; Dai, Jiaqi; ...

2017-07-24

In a lithium-ion battery, electrons are released from the anode and go through an external electronic circuit to power devices, while ions simultaneously transfer through internal ionic media to meet with electrons at the cathode. Inspired by the fundamental electrochemistry of the lithium-ion battery, we envision a cell that can generate a current of ions instead of electrons, so that ions can be used for potential applications in biosystems. Based on this concept, we report an ‘electron battery’ configuration in which ions travel through an external circuit to interact with the intended biosystem whereas electrons are transported internally. As amore » proof-of-concept, we demonstrate the application of the electron battery by stimulating a monolayer of cultured cells, which fluoresces a calcium ion wave at a controlled ionic current. Electron batteries with the capability to generate a tunable ionic current could pave the way towards precise ion-system control in a broad range of biological applications« less

Inverted battery design as ion generator for interfacing with biosystems

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

Wang, Chengwei; Fu, Kun; Dai, Jiaqi

In a lithium-ion battery, electrons are released from the anode and go through an external electronic circuit to power devices, while ions simultaneously transfer through internal ionic media to meet with electrons at the cathode. Inspired by the fundamental electrochemistry of the lithium-ion battery, we envision a cell that can generate a current of ions instead of electrons, so that ions can be used for potential applications in biosystems. Based on this concept, we report an ‘electron battery’ configuration in which ions travel through an external circuit to interact with the intended biosystem whereas electrons are transported internally. As amore » proof-of-concept, we demonstrate the application of the electron battery by stimulating a monolayer of cultured cells, which fluoresces a calcium ion wave at a controlled ionic current. Electron batteries with the capability to generate a tunable ionic current could pave the way towards precise ion-system control in a broad range of biological applications« less

Inverted battery design as ion generator for interfacing with biosystems

PubMed Central

Wang, Chengwei; Fu, Kun (Kelvin); Dai, Jiaqi; Lacey, Steven D.; Yao, Yonggang; Pastel, Glenn; Xu, Lisha; Zhang, Jianhua; Hu, Liangbing

2017-01-01

In a lithium-ion battery, electrons are released from the anode and go through an external electronic circuit to power devices, while ions simultaneously transfer through internal ionic media to meet with electrons at the cathode. Inspired by the fundamental electrochemistry of the lithium-ion battery, we envision a cell that can generate a current of ions instead of electrons, so that ions can be used for potential applications in biosystems. Based on this concept, we report an ‘electron battery’ configuration in which ions travel through an external circuit to interact with the intended biosystem whereas electrons are transported internally. As a proof-of-concept, we demonstrate the application of the electron battery by stimulating a monolayer of cultured cells, which fluoresces a calcium ion wave at a controlled ionic current. Electron batteries with the capability to generate a tunable ionic current could pave the way towards precise ion-system control in a broad range of biological applications. PMID:28737174

Optogenetic stimulation of multiwell MEA plates for neural and cardiac applications

NASA Astrophysics Data System (ADS)

Clements, Isaac P.; Millard, Daniel C.; Nicolini, Anthony M.; Preyer, Amanda J.; Grier, Robert; Heckerling, Andrew; Blum, Richard A.; Tyler, Phillip; McSweeney, K. M.; Lu, Yi-Fan; Hall, Diana; Ross, James D.

2016-03-01

Microelectrode array (MEA) technology enables advanced drug screening and "disease-in-a-dish" modeling by measuring the electrical activity of cultured networks of neural or cardiac cells. Recent developments in human stem cell technologies, advancements in genetic models, and regulatory initiatives for drug screening have increased the demand for MEA-based assays. In response, Axion Biosystems previously developed a multiwell MEA platform, providing up to 96 MEA culture wells arrayed into a standard microplate format. Multiwell MEA-based assays would be further enhanced by optogenetic stimulation, which enables selective excitation and inhibition of targeted cell types. This capability for selective control over cell culture states would allow finer pacing and probing of cell networks for more reliable and complete characterization of complex network dynamics. Here we describe a system for independent optogenetic stimulation of each well of a 48-well MEA plate. The system enables finely graded control of light delivery during simultaneous recording of network activity in each well. Using human induced pluripotent stem cell (hiPSC) derived cardiomyocytes and rodent primary neuronal cultures, we demonstrate high channel-count light-based excitation and suppression in several proof-of-concept experimental models. Our findings demonstrate advantages of combining multiwell optical stimulation and MEA recording for applications including cardiac safety screening, neural toxicity assessment, and advanced characterization of complex neuronal diseases.

Validation of the Applied Biosystems RapidFinder Shiga Toxin-Producing E. coli (STEC) Detection Workflow.

PubMed

Cloke, Jonathan; Matheny, Sharon; Swimley, Michelle; Tebbs, Robert; Burrell, Angelia; Flannery, Jonathan; Bastin, Benjamin; Bird, Patrick; Benzinger, M Joseph; Crowley, Erin; Agin, James; Goins, David; Salfinger, Yvonne; Brodsky, Michael; Fernandez, Maria Cristina

2016-11-01

The Applied Biosystems™ RapidFinder™ STEC Detection Workflow (Thermo Fisher Scientific) is a complete protocol for the rapid qualitative detection of Escherichia coli (E. coli) O157:H7 and the "Big 6" non-O157 Shiga-like toxin-producing E. coli (STEC) serotypes (defined as serogroups: O26, O45, O103, O111, O121, and O145). The RapidFinder STEC Detection Workflow makes use of either the automated preparation of PCR-ready DNA using the Applied Biosystems PrepSEQ™ Nucleic Acid Extraction Kit in conjunction with the Applied Biosystems MagMAX™ Express 96-well magnetic particle processor or the Applied Biosystems PrepSEQ Rapid Spin kit for manual preparation of PCR-ready DNA. Two separate assays comprise the RapidFinder STEC Detection Workflow, the Applied Biosystems RapidFinder STEC Screening Assay and the Applied Biosystems RapidFinder STEC Confirmation Assay. The RapidFinder STEC Screening Assay includes primers and probes to detect the presence of stx1 (Shiga toxin 1), stx2 (Shiga toxin 2), eae (intimin), and E. coli O157 gene targets. The RapidFinder STEC Confirmation Assay includes primers and probes for the "Big 6" non-O157 STEC and E. coli O157:H7. The use of these two assays in tandem allows a user to detect accurately the presence of the "Big 6" STECs and E. coli O157:H7. The performance of the RapidFinder STEC Detection Workflow was evaluated in a method comparison study, in inclusivity and exclusivity studies, and in a robustness evaluation. The assays were compared to the U.S. Department of Agriculture (USDA), Food Safety and Inspection Service (FSIS) Microbiology Laboratory Guidebook (MLG) 5.09: Detection, Isolation and Identification of Escherichia coli O157:H7 from Meat Products and Carcass and Environmental Sponges for raw ground beef (73% lean) and USDA/FSIS-MLG 5B.05: Detection, Isolation and Identification of Escherichia coli non-O157:H7 from Meat Products and Carcass and Environmental Sponges for raw beef trim. No statistically significant differences were observed between the reference method and the individual or combined kits forming the candidate assay using either of the DNA preparation kits (manual or automated extraction). For the inclusivity and exclusivity evaluation, the RapidFinder STEC Detection Workflow, comprising both RapidFinder STEC screening and confirmation kits, correctly identified all 50 target organism isolates and correctly excluded all 30 nontarget strains for both of the assays evaluated. The results of these studies demonstrate the sensitivity and selectivity of the RapidFinder STEC Detection Workflow for the detection of E. coli O157:H7 and the "Big 6" STEC serotypes in both raw ground beef and beef trim. The robustness testing demonstrated that minor variations in the method parameters did not impact the accuracy of the assay and highlighted the importance of following the correct incubation temperatures.

Reconstruction method for data protection in telemedicine systems

NASA Astrophysics Data System (ADS)

Buldakova, T. I.; Suyatinov, S. I.

2015-03-01

In the report the approach to protection of transmitted data by creation of pair symmetric keys for the sensor and the receiver is offered. Since biosignals are unique for each person, their corresponding processing allows to receive necessary information for creation of cryptographic keys. Processing is based on reconstruction of the mathematical model generating time series that are diagnostically equivalent to initial biosignals. Information about the model is transmitted to the receiver, where the restoration of physiological time series is performed using the reconstructed model. Thus, information about structure and parameters of biosystem model received in the reconstruction process can be used not only for its diagnostics, but also for protection of transmitted data in telemedicine complexes.

Modeling Metabolism and Stage-Specific Growth of Plasmodium falciparum HB3 during the Intraerythrocytic Development Cycle

DTIC Science & Technology

2014-01-01

of these bars represent the simulation results (blue) and experimental data (green). Paper Molecular BioSystems 2530 | Mol. BioSyst., 2014, 10, 2526...glycolysis pathway (including lactate production and secretion) were among the largest, consistent with the well-established fermentative glucose...metabolite i in biomass function j, Wi denotes the molecular weight of the metabolite, and the factor 1000 converts mol into mmol. Simulation environment

Ab initio O(N) elongation-counterpoise method for BSSE-corrected interaction energy analyses in biosystems

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

Orimoto, Yuuichi; Xie, Peng; Liu, Kai

2015-03-14

An Elongation-counterpoise (ELG-CP) method was developed for performing accurate and efficient interaction energy analysis and correcting the basis set superposition error (BSSE) in biosystems. The method was achieved by combining our developed ab initio O(N) elongation method with the conventional counterpoise method proposed for solving the BSSE problem. As a test, the ELG-CP method was applied to the analysis of the DNAs’ inter-strands interaction energies with respect to the alkylation-induced base pair mismatch phenomenon that causes a transition from G⋯C to A⋯T. It was found that the ELG-CP method showed high efficiency (nearly linear-scaling) and high accuracy with a negligiblymore » small energy error in the total energy calculations (in the order of 10{sup −7}–10{sup −8} hartree/atom) as compared with the conventional method during the counterpoise treatment. Furthermore, the magnitude of the BSSE was found to be ca. −290 kcal/mol for the calculation of a DNA model with 21 base pairs. This emphasizes the importance of BSSE correction when a limited size basis set is used to study the DNA models and compare small energy differences between them. In this work, we quantitatively estimated the inter-strands interaction energy for each possible step in the transition process from G⋯C to A⋯T by the ELG-CP method. It was found that the base pair replacement in the process only affects the interaction energy for a limited area around the mismatch position with a few adjacent base pairs. From the interaction energy point of view, our results showed that a base pair sliding mechanism possibly occurs after the alkylation of guanine to gain the maximum possible number of hydrogen bonds between the bases. In addition, the steps leading to the A⋯T replacement accompanied with replications were found to be unfavorable processes corresponding to ca. 10 kcal/mol loss in stabilization energy. The present study indicated that the ELG-CP method is promising for performing effective interaction energy analyses in biosystems.« less

Laser homeostatics on delayed onset muscle soreness

NASA Astrophysics Data System (ADS)

Liu, T. C. Y.; Fu, D. R.; Liu, X. G.; Tian, Z. X.

2011-01-01

Delayed onset muscle soreness (DOMS) and its photobiomodulation were reviewed from the viewpoint of function-specific homeostasis (FSH) in this paper. FSH is a negative-feedback response of a biosystem to maintain the function-specific fluctuations inside the biosystem so that the function is perfectly performed. A stressor may destroy a FSH. A stress is a response of a biosystem to a stressor and may also be in stress-specific homeostasis (StSH). A low level light (LLL) is so defined that it has no effects on a function in its FSH or a stress in its StSH, but it modulate a function far from its FSH or a stress far from its StSH. For DOMS recovery, protein metabolism in the Z-line streaming muscular cell is the essential process, but the inflammation, pain and soreness are non-essential processes. For many DOMS phenomena, protein metabolism in the Z-line streaming muscular cell is in protein metabolism-specific homeostasis (PmSH) so that there are no effects of LLL although the inflammation can be inhibited and the pain can be relieved. An athlete or animal in the dysfunctional conditions such as blood flow restriction and exercise exhaustion is far from PmSH and the protein metabolism can be improved with LLL.

Development of a spreadsheet for SNPs typing using Microsoft EXCEL.

PubMed

Hashiyada, Masaki; Itakura, Yukio; Takahashi, Shirushi; Sakai, Jun; Funayama, Masato

2009-04-01

Single-nucleotide polymorphisms (SNPs) have some characteristics that make them very appropriate for forensic studies and applications. In our institute, SNPs typings were performed by the TaqMan SNP Genotyping Assays using the ABI PRISM 7500 FAST Real-Time PCR System (AppliedBiosystems) and Sequence Detection Software ver.1.4 (AppliedBiosystem). The TaqMan method was desired two positive control (Allele1 and 2) and one negative control to analyze each SNP locus. Therefore, it can be analyzed up to 24 loci of a person on a 96-well-plate at the same time. If SNPs analysis is expected to apply to biometrics authentication, 48 and over loci are required to identify a person. In this study, we designed a spreadsheet package using Microsoft EXCEL, and population data were used from our 120 SNPs population studies. On the spreadsheet, we defined SNP types using 'template files' instead of positive and negative controls. "Template files" consisted of the results of 94 unknown samples and two negative controls of each of 120 SNPs loci we had previously studied. By the use of the files, the spreadsheet could analyze 96 SNPs on a 96-wells-plate simultaneously.

Toxicity prediction of PHDDs and phenols in the light of nucleic acid bases and DNA base pair interaction.

PubMed

Mondal Roy, Sutapa; Roy, Debesh R; Sahoo, Suban K

2015-11-01

The applicability of Density Functional Theory (DFT) based descriptors for the development of quantitative structure-toxicity relationships (QSTR) is assessed for two different series of toxic aromatic compounds, viz., polyhalogenated dibenzo-p-dioxins (PHDDs) and phenols (PHs). A series of 20 compounds each for PHDDs and PHs with their experimental toxicities (IC50 and IGC50) is chosen in the present study to develop DFT based efficient quantum chemical parameters (QCPs) for explaining the toxin potential of the considered compounds. A systematic analysis to find out the electron donation/acceptance nature of these selected compounds with the considered model biosystems, viz., nucleic acid (NA) bases and DNA base pairs, is performed to identify potential QCPs. Accordingly, PHDDs is found to be electron acceptors whereas phenols as donors, during their interaction with biosystems. Two parameter regression model is carried out comprising global charge transfer (ΔN), and local Fukui Function's for nucleophilic attack (fk(+)) for PHDDs and the same for electrophilic attack (fk(-)) in case of PHs. It is heartening to note that our chosen descriptors, viz, charge transfer (ΔN) and Fukui Function (fk(±)) plays a crucial role by explaining more than 90% of the observed toxic behavior (in terms of correlation-coefficient, R) of PHDDs and PHs. The developed QCPs, viz., ΔN and fk(±) can be added as the new descriptors in the QSTR parlance. Copyright © 2015 Elsevier Inc. All rights reserved.

Single-tube, non-isotopic, multiplex PCR/OLA assay and sequence-coded separation for simultaneous screening of 31 cystic fibrosis mutations

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

Brinson, E.C.; Adriano, T.; Bloch, W.

1994-09-01

We have developed a rapid, single-tube, non-isotopic assay that screens a patient sample for the presence of 31 cystic fibrosis (CF) mutations. This assay can identify these mutations in a single reaction tube and a single electrophoresis run. Sample preparation is a simple, boil-and-go procedure, completed in less than an hour. The assay is composed of a 15-plex PCR, followed by a 61-plex oligonucleotide ligation assay (OLA), and incorporates a novel detection scheme, Sequence Coded Separation. Initially, the multiplex PCR amplifies 15 relevant segments of the CFTR gene, simultaneously. These PCR amplicons serve as templates for the multiplex OLA, whichmore » detects the normal or mutant allele at all loci, simultaneously. Each polymorphic site is interrogated by three oligonucleotide probes, a common probe and two allele-specific probes. Each common probe is tagged with a fluorescent dye, and the competing normal and mutant allelic probes incorporate different, non-nucleotide, mobility modifiers. These modifiers are composed of hexaethylene oxide (HEO) units, incorporated as HEO phosphoramidite monomers during automated DNA synthesis. The OLA is based on both probe hybridization and the ability of DNA ligase to discriminate single base mismatches at the junction between paired probes. Each single tube assay is electrophoresed in a single gel lane of a 4-color fluorescent DNA sequencer (Applied Biosystems, Model 373A). Each of the ligation products is identified by its unique combination of electrophoretic mobility and one of three colors. The fourth color is reserved for the in-lane size standard, used by GENESCAN{sup TM} software (Applied Biosystems) to size the OLA electrophoresis products. The Genotyper{sub TM} software (Applied Biosystems) decodes these Sequence-Coded-Separation data to create a patient summary report for all loci tested.« less

Selection of Suitable DNA Extraction Methods for Genetically Modified Maize 3272, and Development and Evaluation of an Event-Specific Quantitative PCR Method for 3272.

PubMed

Takabatake, Reona; Masubuchi, Tomoko; Futo, Satoshi; Minegishi, Yasutaka; Noguchi, Akio; Kondo, Kazunari; Teshima, Reiko; Kurashima, Takeyo; Mano, Junichi; Kitta, Kazumi

2016-01-01

A novel real-time PCR-based analytical method was developed for the event-specific quantification of a genetically modified (GM) maize, 3272. We first attempted to obtain genome DNA from this maize using a DNeasy Plant Maxi kit and a DNeasy Plant Mini kit, which have been widely utilized in our previous studies, but DNA extraction yields from 3272 were markedly lower than those from non-GM maize seeds. However, lowering of DNA extraction yields was not observed with GM quicker or Genomic-tip 20/G. We chose GM quicker for evaluation of the quantitative method. We prepared a standard plasmid for 3272 quantification. The conversion factor (Cf), which is required to calculate the amount of a genetically modified organism (GMO), was experimentally determined for two real-time PCR instruments, the Applied Biosystems 7900HT (the ABI 7900) and the Applied Biosystems 7500 (the ABI7500). The determined Cf values were 0.60 and 0.59 for the ABI 7900 and the ABI 7500, respectively. To evaluate the developed method, a blind test was conducted as part of an interlaboratory study. The trueness and precision were evaluated as the bias and reproducibility of the relative standard deviation (RSDr). The determined values were similar to those in our previous validation studies. The limit of quantitation for the method was estimated to be 0.5% or less, and we concluded that the developed method would be suitable and practical for detection and quantification of 3272.

Respirometric biomonitor for the control of industrial effluent toxicity

NASA Astrophysics Data System (ADS)

Campanella, Luigi; Favero, G.; Mastrofini, D.; Tomassetti, M.

1995-10-01

A yeast cell biosystem has been recently developed for the total toxicity testing of a sample that may contain a number of different polluting species. The method uses an amperometric gas diffusion oxygen sensor as indicating electrode and is based on the perturbation of the respiratory activity of the immobilized yeast Saccharomyces cerevisiae; glucose acts as substrate. Several toxic substances were tested: metal ions, phenol and cationic, anionic or nonionic surfactants. Some results of a monitoring program of an industrial wastewater are also reported and discussed.

Methods of information geometry in computational system biology (consistency between chemical and biological evolution).

PubMed

Astakhov, Vadim

2009-01-01

Interest in simulation of large-scale metabolic networks, species development, and genesis of various diseases requires new simulation techniques to accommodate the high complexity of realistic biological networks. Information geometry and topological formalisms are proposed to analyze information processes. We analyze the complexity of large-scale biological networks as well as transition of the system functionality due to modification in the system architecture, system environment, and system components. The dynamic core model is developed. The term dynamic core is used to define a set of causally related network functions. Delocalization of dynamic core model provides a mathematical formalism to analyze migration of specific functions in biosystems which undergo structure transition induced by the environment. The term delocalization is used to describe these processes of migration. We constructed a holographic model with self-poetic dynamic cores which preserves functional properties under those transitions. Topological constraints such as Ricci flow and Pfaff dimension were found for statistical manifolds which represent biological networks. These constraints can provide insight on processes of degeneration and recovery which take place in large-scale networks. We would like to suggest that therapies which are able to effectively implement estimated constraints, will successfully adjust biological systems and recover altered functionality. Also, we mathematically formulate the hypothesis that there is a direct consistency between biological and chemical evolution. Any set of causal relations within a biological network has its dual reimplementation in the chemistry of the system environment.

Genetic Testing Registry

MedlinePlus

... Splign Vector Alignment Search Tool (VAST) All Data & Software Resources... Domains & Structures BioSystems Cn3D Conserved Domain Database (CDD) Conserved Domain Search Service (CD Search) Structure (Molecular Modeling Database) Vector Alignment ...

Silicon supported lipid-DNA thin film structures at varying temperature studied by energy dispersive X-ray diffraction and neutron reflectivity.

PubMed

Domenici, F; Castellano, C; Dell'Unto, F; Albinati, A; Congiu, A

2011-11-01

Non-viral gene transfection by means of lipid-based nanosystems, such as solid supported lipid assemblies, is often limited due to their lack of stability and the consequent loss of efficiency. Therefore not only a detailed thermo-lyotropic study of these DNA-lipid complexes is necessary to understand their interaction mechanisms, but it can also be considered as a first step in conceiving and developing new transfection biosystems. The aim of our study is a structural characterization of 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC)-dimethyl-dioctadecyl-ammonium bromide (DDAB)-DNA complex at varying temperature using the energy dispersive X-ray diffraction (EDXD) and neutron reflectivity (NR) techniques. We have shown the formation of a novel thermo-lyotropic structure of DOPC/DDAB thin film self-organized in multi-lamellar planes on (100)-oriented silicon support by spin coating, thus enlightening its ability to include DNA strands. Our NR measurements indicate that the DOPC/DDAB/DNA complex forms temperature-dependent structures. At 65°C and relative humidity of 100% DNA fragments are buried between single lamellar leaflets constituting the hydrocarbon core of the lipid bilayers. This finding supports the consistency of the hydrophobic interaction model, which implies that the coupling between lipid tails and hypo-hydrated DNA single strands could be the driving force of DNA-lipid complexation. Upon cooling to 25°C, EDXD analysis points out that full-hydrated DOPC-DDAB-DNA can switch in a different metastable complex supposed to be driven by lipid heads-DNA electrostatic interaction. Thermotropic response analysis also clarifies that DOPC has a pivotal role in promoting the formation of our observed thermophylic silicon supported lipids-DNA assembly. Copyright © 2011 Elsevier B.V. All rights reserved.

Development and evaluation of event-specific quantitative PCR method for genetically modified soybean A2704-12.

PubMed

Takabatake, Reona; Akiyama, Hiroshi; Sakata, Kozue; Onishi, Mari; Koiwa, Tomohiro; Futo, Satoshi; Minegishi, Yasutaka; Teshima, Reiko; Mano, Junichi; Furui, Satoshi; Kitta, Kazumi

2011-01-01

A novel real-time PCR-based analytical method was developed for the event-specific quantification of a genetically modified (GM) soybean event; A2704-12. During the plant transformation, DNA fragments derived from pUC19 plasmid were integrated in A2704-12, and the region was found to be A2704-12 specific. The pUC19-derived DNA sequences were used as primers for the specific detection of A2704-12. We first tried to construct a standard plasmid for A2704-12 quantification using pUC19. However, non-specific signals appeared with both qualitative and quantitative PCR analyses using the specific primers with pUC19 as a template, and we then constructed a plasmid using pBR322. The conversion factor (C(f)), which is required to calculate the amount of the genetically modified organism (GMO), was experimentally determined with two real-time PCR instruments, the Applied Biosystems 7900HT and the Applied Biosystems 7500. The determined C(f) values were both 0.98. The quantitative method was evaluated by means of blind tests in multi-laboratory trials using the two real-time PCR instruments. The limit of quantitation for the method was estimated to be 0.1%. The trueness and precision were evaluated as the bias and reproducibility of relative standard deviation (RSD(R)), and the determined bias and RSD(R) values for the method were each less than 20%. These results suggest that the developed method would be suitable for practical analyses for the detection and quantification of A2704-12.

Performance of Identifiler Direct and PowerPlex 16 HS on the Applied Biosystems 3730 DNA Analyzer for processing biological samples archived on FTA cards.

PubMed

Laurin, Nancy; DeMoors, Anick; Frégeau, Chantal

2012-09-01

Direct amplification of STR loci from biological samples collected on FTA cards without prior DNA purification was evaluated using Identifiler Direct and PowerPlex 16 HS in conjunction with the use of a high throughput Applied Biosystems 3730 DNA Analyzer. In order to reduce the overall sample processing cost, reduced PCR volumes combined with various FTA disk sizes were tested. Optimized STR profiles were obtained using a 0.53 mm disk size in 10 μL PCR volume for both STR systems. These protocols proved effective in generating high quality profiles on the 3730 DNA Analyzer from both blood and buccal FTA samples. Reproducibility, concordance, robustness, sample stability and profile quality were assessed using a collection of blood and buccal samples on FTA cards from volunteer donors as well as from convicted offenders. The new developed protocols offer enhanced throughput capability and cost effectiveness without compromising the robustness and quality of the STR profiles obtained. These results support the use of these protocols for processing convicted offender samples submitted to the National DNA Data Bank of Canada. Similar protocols could be applied to the processing of casework reference samples or in paternity or family relationship testing. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

National Center for Biotechnology Information

MedlinePlus

... Splign Vector Alignment Search Tool (VAST) All Data & Software Resources... Domains & Structures BioSystems Cn3D Conserved Domain Database (CDD) Conserved Domain Search Service (CD Search) Structure (Molecular Modeling Database) Vector Alignment ...

ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level.

PubMed

Marsili, Simone; Signorini, Giorgio Federico; Chelli, Riccardo; Marchi, Massimo; Procacci, Piero

2010-04-15

We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at http://www.chim.unifi.it/orac. 2009 Wiley Periodicals, Inc.

Conference on Correlations of Aging and Space Effects on Biosystems, Oct. 30-Nov. 1, 1989, Proceedings

NASA Technical Reports Server (NTRS)

Sprott, Richard L. (Editor); Combs, Carol A. (Editor)

1991-01-01

This volume includes papers on correlations between aging effects and space effects on biosystems, with particular attention given to the effects on the cardiovascular system, bone, sleep, cellular systems, immunological system, and genetics. Papers are presented on NASA and NIA plans and opportunities, the age effect on the posture and circulation, the cardiovascular physiology in space flight, and age-related bone changes. Attention is given to research on sleep, circulation rhythms, and aging and its applications to manned spaceflight; sleep and circadian rhythms; altered cell function in microgravity; and the heterogeneity of changes in lymphoproliferative ability with increasing age. Also included is a review of cellular immunosenescence, a paper on the immune response during space flight, and a paper on Caenorhabditis elegans as a model system for space biology studies.

Possible psycho-physiological consequences of human long-term space missions

NASA Astrophysics Data System (ADS)

Belisheva, N. K.; Lammer, H.; Biernat, H. K.; Kachanova, T. L.; Kalashnikova, I. V.

Experiments carried out on the Earth s surface during different years and under contrast periods of solar activity have shown that the functional state of biosystems including the human organisms are controlled by global and local geocosmical agents Our finding have a close relation to space research because they demonstrate the reactions of biosystems on variations of global and local geocosmical agents and the mechanisms of modulations of biosystems state by geocosmical agents We revealed the role of variations of the geomagnetic field for the stimulation of immune systems functional state of peripheral blood human brain growth of microflora skin covers and pathogenic microorganisms The study of the psycho-physiological state of the human organism has demonstrated that an increase of the neutron intensity near the Earth s surface is associated with anxiety decrease of normal and increase of paradox reactions of examinees The analysis of the human brain functional state in dependent on the geomagnetic variation structure dose under exposure to the variations of geomagnetic field in a certain amplitude-frequency range and also the intensity of the nucleon component of secondary cosmic rays showed that the stable and unstable states of the human brain are determined by geomagnetic field variations and the intensity of the nucleon component The stable state of the brain manifested under the periodic oscillations of the geomagnetic field in a certain amplitude-frequency range The low level of geomagnetic activity associated with an

Overview on experimental models of interactions between nanoparticles and the immune system.

PubMed

Najafi-Hajivar, Saeedeh; Zakeri-Milani, Parvin; Mohammadi, Hamed; Niazi, Mehri; Soleymani-Goloujeh, Mehdi; Baradaran, Behzad; Valizadeh, Hadi

2016-10-01

Nanotechnology increasingly plays a significant role in modern medicine development. The clear benefits of using nanomaterials in various biomedical applications are often challenged by concerns about the lack of adequate data regarding their toxicity. Two decades of nanotoxicology research have shown that the interactions between nanoparticles (NPs) and biosystem are remarkably complex. This complexity derives from NPs' ability to bind and interact with biological cells and change their surface characteristics. One area of interest involves the interactions between NPs and the immune component. Immune system's function in the maintenance of tissue homeostasis is to protect the host from unfamiliar agents. This is done through effective surveillance and elimination of foreign substances and abnormal self cells from the body. Research shows that nanomaterials can stimulate and/or suppress the immune responses, and that their compatibility with the immune system is largely determined by their surface properties. NP size, shape, composition, protein binding and administration routes seem to be the main factors that contribute to the interactions of NPs with the immune system. In the present article, we focus on the relationship between effective physiochemical properties of NPs and their immunogenic effects. In addition, we review more details about immunological responses of different types of NPs. Understanding the interactions of nanomaterials with the immune system is essential for the engineering of new NP-based systems for medical applications. Copyright © 2016. Published by Elsevier Masson SAS.

"First generation" automated DNA sequencing technology.

PubMed

Slatko, Barton E; Kieleczawa, Jan; Ju, Jingyue; Gardner, Andrew F; Hendrickson, Cynthia L; Ausubel, Frederick M

2011-10-01

Beginning in the 1980s, automation of DNA sequencing has greatly increased throughput, reduced costs, and enabled large projects to be completed more easily. The development of automation technology paralleled the development of other aspects of DNA sequencing: better enzymes and chemistry, separation and imaging technology, sequencing protocols, robotics, and computational advancements (including base-calling algorithms with quality scores, database developments, and sequence analysis programs). Despite the emergence of high-throughput sequencing platforms, automated Sanger sequencing technology remains useful for many applications. This unit provides background and a description of the "First-Generation" automated DNA sequencing technology. It also includes protocols for using the current Applied Biosystems (ABI) automated DNA sequencing machines. © 2011 by John Wiley & Sons, Inc.

Cell Engineering and Molecular Pharming for Biopharmaceuticals

PubMed Central

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

2008-01-01

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

Time rescaling and pattern formation in biological evolution.

PubMed

Igamberdiev, Abir U

2014-09-01

Biological evolution is analyzed as a process of continuous measurement in which biosystems interpret themselves in the environment resulting in changes of both. This leads to rescaling of internal time (heterochrony) followed by spatial reconstructions of morphology (heterotopy). The logical precondition of evolution is the incompleteness of biosystem's internal description, while the physical precondition is the uncertainty of quantum measurement. The process of evolution is based on perpetual changes in interpretation of information in the changing world. In this interpretation the external biospheric gradients are used for establishment of new features of organization. It is concluded that biological evolution involves the anticipatory epigenetic changes in the interpretation of genetic symbolism which cannot generally be forecasted but can provide canalization of structural transformations defined by the existing organization and leading to predictable patterns of form generation. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

FaSTR DNA: a new expert system for forensic DNA analysis.

PubMed

Power, Timothy; McCabe, Brendan; Harbison, Sally Ann

2008-06-01

The automation of DNA profile analysis of reference and crime samples continues to gain pace driven in part by a realisation by the criminal justice system of the positive impact DNA technology can have in aiding in the solution of crime and the apprehension of suspects. Expert systems to automate the profile analysis component of the process are beginning to be developed. In this paper, we report the validation of a new expert system FaSTR DNA, an expert system suitable for the analysis of DNA profiles from single source reference samples and from crime samples. We compare the performance of FaSTR DNA with that of other equivalent systems, GeneMapper ID v3.2 (Applied Biosystems, Foster City, CA) and FSS-i(3) v4 (The Forensic Science Service((R)) DNA expert System Suite FSS-i(3), Forensic Science Service, Birmingham, UK) with GeneScan Analysis v3.7/Genotyper v3.7 software (Applied Biosystems, Foster City, CA, USA) with manual review. We have shown that FaSTR DNA provides an alternative solution to automating DNA profile analysis and is appropriate for implementation into forensic laboratories. The FaSTR DNA system was demonstrated to be comparable in performance to that of GeneMapper ID v3.2 and superior to that of FSS-i(3) v4 for the analysis of DNA profiles from crime samples.

Changing Conditions in the Arctic: An Analysis of 45 years of Tropospheric Ozone Measurements at Barrow Observatory

NASA Astrophysics Data System (ADS)

McClure-Begley, A.; Petropavlovskikh, I. V.; Crepinsek, S.; Jefferson, A.; Emmons, L. K.; Oltmans, S. J.

2017-12-01

In order to understand the impact of climate on local bio-systems, understanding the changes to the atmospheric composition and processes in the Arctic boundary layer and free troposphere is imperative. In the Arctic, many conditions influence tropospheric ozone variability such as: seasonal halogen caused depletion events, long range transport of pollutants from mid-northern latitudes, compounds released from wildfires, and different meteorological conditions. The Barrow station in Utqiagvik, Alaska has collected continuous measurements of ground-level ozone since 1973. This unique long-term time series allows for analysis of the influence of a rapidly changing climate on ozone conditions in this region. Specifically, this study analyzes the frequency of enhanced ozone episodes over time and provides in depth analysis of periods of positive deviations from the expected conditions. To discern the contribution of different pollutant sources to observed ozone variability, co-located measurements of aerosols, carbon monoxide, and meteorological conditions are used. In addition, the NCAR Mozart-4/MOPITT Chemical Forecast model and NOAA Hysplit back-trajectory analysis provide information on transport patterns to the Arctic and confirmation of the emission sources that influenced the observed conditions. These anthropogenic influences on ozone variability in and below the boundary layer are essential for developing an understanding of the interaction of climate change and the bio-systems in the Arctic.

Mathematical approach to nonlocal interactions using a reaction-diffusion system.

PubMed

Tanaka, Yoshitaro; Yamamoto, Hiroko; Ninomiya, Hirokazu

2017-06-01

In recent years, spatial long range interactions during developmental processes have been introduced as a result of the integration of microscopic information, such as molecular events and signaling networks. They are often called nonlocal interactions. If the profile of a nonlocal interaction is determined by experiments, we can easily investigate how patterns generate by numerical simulations without detailed microscopic events. Thus, nonlocal interactions are useful tools to understand complex biosystems. However, nonlocal interactions are often inconvenient for observing specific mechanisms because of the integration of information. Accordingly, we proposed a new method that could convert nonlocal interactions into a reaction-diffusion system with auxiliary unknown variables. In this review, by introducing biological and mathematical studies related to nonlocal interactions, we will present the heuristic understanding of nonlocal interactions using a reaction-diffusion system. © 2017 Japanese Society of Developmental Biologists.

Aqueous multiphoton lithography with multifunctional silk-centred bio-resists.

PubMed

Sun, Yun-Lu; Li, Qi; Sun, Si-Ming; Huang, Jing-Chun; Zheng, Bo-Yuan; Chen, Qi-Dai; Shao, Zheng-Zhong; Sun, Hong-Bo

2015-10-16

Silk and silk fibroin, the biomaterial from nature, nowadays are being widely utilized in many cutting-edge micro/nanodevices/systems via advanced micro/nanofabrication techniques. Herein, for the first time to our knowledge, we report aqueous multiphoton lithography of diversiform-regenerated-silk-fibroin-centric inks using noncontact and maskless femtosecond laser direct writing (FsLDW). Initially, silk fibroin was FsLDW-crosslinked into arbitrary two/three-dimensional micro/nanostructures with good elastic properties merely using proper photosensitizers. More interestingly, silk/metal composite micro/nanodevices with multidimension-controllable metal content can be FsLDW-customized through laser-induced simultaneous fibroin oxidation/crosslinking and metal photoreduction using the simplest silk/Ag(+) or silk/[AuCl4](-) aqueous resists. Noticeably, during FsLDW, fibroin functions as biological reductant and matrix, while metal ions act as the oxidant. A FsLDW-fabricated prototyping silk/Ag microelectrode exhibited 10(4)-Ω(-1 ) m(-1)-scale adjustable electric conductivity. This work not only provides a powerful development to silk micro/nanoprocessing techniques but also creates a novel way to fabricate multifunctional metal/biomacromolecule complex micro/nanodevices for applications such as micro/nanoscale mechanical and electrical bioengineering and biosystems.

Aqueous multiphoton lithography with multifunctional silk-centred bio-resists

PubMed Central

Sun, Yun-Lu; Li, Qi; Sun, Si-Ming; Huang, Jing-Chun; Zheng, Bo-Yuan; Chen, Qi-Dai; Shao, Zheng-Zhong; Sun, Hong-Bo

2015-01-01

Silk and silk fibroin, the biomaterial from nature, nowadays are being widely utilized in many cutting-edge micro/nanodevices/systems via advanced micro/nanofabrication techniques. Herein, for the first time to our knowledge, we report aqueous multiphoton lithography of diversiform-regenerated-silk-fibroin-centric inks using noncontact and maskless femtosecond laser direct writing (FsLDW). Initially, silk fibroin was FsLDW-crosslinked into arbitrary two/three-dimensional micro/nanostructures with good elastic properties merely using proper photosensitizers. More interestingly, silk/metal composite micro/nanodevices with multidimension-controllable metal content can be FsLDW-customized through laser-induced simultaneous fibroin oxidation/crosslinking and metal photoreduction using the simplest silk/Ag+ or silk/[AuCl4]− aqueous resists. Noticeably, during FsLDW, fibroin functions as biological reductant and matrix, while metal ions act as the oxidant. A FsLDW-fabricated prototyping silk/Ag microelectrode exhibited 104-Ω−1 m−1-scale adjustable electric conductivity. This work not only provides a powerful development to silk micro/nanoprocessing techniques but also creates a novel way to fabricate multifunctional metal/biomacromolecule complex micro/nanodevices for applications such as micro/nanoscale mechanical and electrical bioengineering and biosystems. PMID:26472600

Organic bioelectronics probing conformational changes in surface confined proteins

NASA Astrophysics Data System (ADS)

Macchia, Eleonora; Alberga, Domenico; Manoli, Kyriaki; Mangiatordi, Giuseppe F.; Magliulo, Maria; Palazzo, Gerardo; Giordano, Francesco; Lattanzi, Gianluca; Torsi, Luisa

2016-06-01

The study of proteins confined on a surface has attracted a great deal of attention due to its relevance in the development of bio-systems for laboratory and clinical settings. In this respect, organic bio-electronic platforms can be used as tools to achieve a deeper understanding of the processes involving protein interfaces. In this work, biotin-binding proteins have been integrated in two different organic thin-film transistor (TFT) configurations to separately address the changes occurring in the protein-ligand complex morphology and dipole moment. This has been achieved by decoupling the output current change upon binding, taken as the transducing signal, into its component figures of merit. In particular, the threshold voltage is related to the protein dipole moment, while the field-effect mobility is associated with conformational changes occurring in the proteins of the layer when ligand binding occurs. Molecular Dynamics simulations on the whole avidin tetramer in presence and absence of ligands were carried out, to evaluate how the tight interactions with the ligand affect the protein dipole moment and the conformation of the loops surrounding the binding pocket. These simulations allow assembling a rather complete picture of the studied interaction processes and support the interpretation of the experimental results.

Aqueous multiphoton lithography with multifunctional silk-centred bio-resists

NASA Astrophysics Data System (ADS)

Sun, Yun-Lu; Li, Qi; Sun, Si-Ming; Huang, Jing-Chun; Zheng, Bo-Yuan; Chen, Qi-Dai; Shao, Zheng-Zhong; Sun, Hong-Bo

2015-10-01

Silk and silk fibroin, the biomaterial from nature, nowadays are being widely utilized in many cutting-edge micro/nanodevices/systems via advanced micro/nanofabrication techniques. Herein, for the first time to our knowledge, we report aqueous multiphoton lithography of diversiform-regenerated-silk-fibroin-centric inks using noncontact and maskless femtosecond laser direct writing (FsLDW). Initially, silk fibroin was FsLDW-crosslinked into arbitrary two/three-dimensional micro/nanostructures with good elastic properties merely using proper photosensitizers. More interestingly, silk/metal composite micro/nanodevices with multidimension-controllable metal content can be FsLDW-customized through laser-induced simultaneous fibroin oxidation/crosslinking and metal photoreduction using the simplest silk/Ag+ or silk/[AuCl4]- aqueous resists. Noticeably, during FsLDW, fibroin functions as biological reductant and matrix, while metal ions act as the oxidant. A FsLDW-fabricated prototyping silk/Ag microelectrode exhibited 104-Ω-1 m-1-scale adjustable electric conductivity. This work not only provides a powerful development to silk micro/nanoprocessing techniques but also creates a novel way to fabricate multifunctional metal/biomacromolecule complex micro/nanodevices for applications such as micro/nanoscale mechanical and electrical bioengineering and biosystems.

Organic bioelectronics probing conformational changes in surface confined proteins

PubMed Central

Macchia, Eleonora; Alberga, Domenico; Manoli, Kyriaki; Mangiatordi, Giuseppe F.; Magliulo, Maria; Palazzo, Gerardo; Giordano, Francesco; Lattanzi, Gianluca; Torsi, Luisa

2016-01-01

The study of proteins confined on a surface has attracted a great deal of attention due to its relevance in the development of bio-systems for laboratory and clinical settings. In this respect, organic bio-electronic platforms can be used as tools to achieve a deeper understanding of the processes involving protein interfaces. In this work, biotin-binding proteins have been integrated in two different organic thin-film transistor (TFT) configurations to separately address the changes occurring in the protein-ligand complex morphology and dipole moment. This has been achieved by decoupling the output current change upon binding, taken as the transducing signal, into its component figures of merit. In particular, the threshold voltage is related to the protein dipole moment, while the field-effect mobility is associated with conformational changes occurring in the proteins of the layer when ligand binding occurs. Molecular Dynamics simulations on the whole avidin tetramer in presence and absence of ligands were carried out, to evaluate how the tight interactions with the ligand affect the protein dipole moment and the conformation of the loops surrounding the binding pocket. These simulations allow assembling a rather complete picture of the studied interaction processes and support the interpretation of the experimental results. PMID:27312768

A novel ferrocenyl-naphthalimide as a multichannel probe for the detection of Cu(ii) and Hg(ii) in aqueous media and living cells.

PubMed

Dong, Junyang; Hu, Jianfeng; Baigude, Huricha; Zhang, Hao

2018-01-02

A novel ferrocenyl-naphthalimide multichannel probe 1 was designed and synthesized using a facile method. The color of the solution containing probe 1 changed from yellow to colorless upon the addition of Cu 2+ or Hg 2+ . Interestingly, probe 1 exhibited highly selective fluorescent turn-on for Cu 2+ and turn-off for Hg 2+ in aqueous solution. Probe 1 was an electrochemical Cu 2+ and Hg 2+ ion sensor, in which the Fc/Fc + redox couple was significantly shifted (ΔE 1/2 = 178 mV and ΔE 1/2 = 53 mV, respectively) upon complexation. Therefore, probe 1 can act as a naked-eye chemosensor, as well as an electrochemical and a fluorescent probe for Cu 2+ and Hg 2+ . Furthermore, this is the first reported probe that can be used for the bifunctional fluorescent detection of intracellular Cu 2+ and Hg 2+ by fluorescent imaging studies. These characteristics give this probe considerable potential in the study and analysis of Cu 2+ and Hg 2+ in complex biosystems.

Label-free electrical detection of DNA hybridization using carbon nanotubes and graphene

PubMed Central

Fu, Dongliang; Li, Lain-Jong

2010-01-01

The interface between biosystems and nanomaterials is emerging for detection of various biomolecules and subtle cellular activities. In particular, the development of cost-effective and sequence-selective DNA detection is urgent for the diagnosis of genetic or pathogenic diseases. Graphene-based nanocarbon materials, such as carbon nanotubes and thin graphene layers, have been employed as biosensors because they are biocompatible, extraordinarily sensitive, and promising for large-area detection. Electrical and label-free detection of DNA can be achieved by monitoring the conductance change of devices fabricated from these carbon materials. Here, the recent advances in this research area are briefly reviewed. The key issues and perspectives of future development are also discussed. PMID:22110861

Human Performance and Biosystems

DTIC Science & Technology

2013-03-08

carbon nanotube binding peptides *A mutant laccase designed at UW self- assembles into active crystals Leucine βroll Linker (S) α-helix (H...cognitive functions, bio-molecular repair and bio- resiliency Bioenergy: • Portable H2 Fuel Generated from H2O or Cellulose : - Cheap, self

BIOREMEDIATION OF HAZARDOUS WASTE SITES: PRACTICAL APPROACHES TO IMPLEMENTATION (EPA/625/K-96/001)

EPA Science Inventory

This document contains abstracts and slide hardcopy for the U.S. Environmental Protection Agency's (EPA's) "Seminar Series on Bioremediation of Hazardous Waste Sites: Practical Approaches to Implementation." This technology transfer seminar series, sponsored by EPA's Biosystems ...

Quantitative Biology of Exercise-Induced Signal Transduction Pathways.

PubMed

Liu, Timon Cheng-Yi; Liu, Gang; Hu, Shao-Juan; Zhu, Ling; Yang, Xiang-Bo; Zhang, Quan-Guang

2017-01-01

Exercise is essential in regulating energy metabolism. Exercise activates cellular, molecular, and biochemical pathways with regulatory roles in training response adaptation. Among them, endurance/strength training of an individual has been shown to activate its respective signal transduction pathways in skeletal muscle. This was further studied from the viewpoint of quantitative difference (QD). For the mean values, [Formula: see text], of two sets of data, their QD is defined as [Formula: see text] ([Formula: see text]). The function-specific homeostasis (FSH) of a function of a biosystem is a negative-feedback response of the biosystem to maintain the function-specific conditions inside the biosystem so that the function is perfectly performed. A function in/far from its FSH is called a normal/dysfunctional function. A cellular normal function can resist the activation of other signal transduction pathways so that there are normal function-specific signal transduction pathways which full activation maintains the normal function. An acute endurance/strength training may be dysfunctional, but its regular training may be normal. The normal endurance/strength training of an individual may resist the activation of other signal transduction pathways in skeletal muscle so that there may be normal endurance/strength training-specific signal transduction pathways (NEPs/NSPs) in skeletal muscle. The endurance/strength training may activate NSPs/NEPs, but the QD from the control is smaller than 0.80. The simultaneous activation of both NSPs and NEPs may enhance their respective activation, and the QD from the control is larger than 0.80. The low level laser irradiation pretreatment of rats may promote the activation of NSPs in endurance training skeletal muscle. There may be NEPs/NSPs in skeletal muscle trained by normal endurance/strength training.

Electro-Quasistatic Simulations in Bio-Systems Engineering and Medical Engineering

NASA Astrophysics Data System (ADS)

van Rienen, U.; Flehr, J.; Schreiber, U.; Schulze, S.; Gimsa, U.; Baumann, W.; Weiss, D. G.; Gimsa, J.; Benecke, R.; Pau, H.-W.

2005-05-01

Slowly varying electromagnetic fields play a key role in various applications in bio-systems and medical engineering. Examples are the electric activity of neurons on neurochips used as biosensors, the stimulating electric fields of implanted electrodes used for deep brain stimulation in patients with Morbus Parkinson and the stimulation of the auditory nerves in deaf patients, respectively. In order to simulate the neuronal activity on a chip it is necessary to couple Maxwell's and Hodgkin-Huxley's equations. First numerical results for a neuron coupling to a single electrode are presented. They show a promising qualitative agreement with the experimentally recorded signals. Further, simulations are presented on electrodes for deep brain stimulation in animal experiments where the question of electrode ageing and energy deposition in the surrounding tissue are of major interest. As a last example, electric simulations for a simple cochlea model are presented comparing the field in the skull bones for different electrode types and stimulations in different positions.

[Population data analysis of miniSTR loci: D10S1248, D14S1434 and D22S1045 in the Pomerania-Kujawy region of Poland].

PubMed

Kodroń, Agata; Rychlicka, Edyta; Milewska, Iwona; Woźniak, Marcin; Grzybowski, Tomasz

2010-01-01

This paper presents the allele frequencies and forensic parameters of the three miniSTR loci D10S1248, D14S1434 and D22S1045 in the Pomerania-Kujawy region of Poland. Genomic DNA was extracted by a standard phenol-chloroform extraction procedure. The three miniSTR loci D10S1248, D14S1434 and D22S1045 were amplified in a triplex polymerase chain reaction with the primer sets designed by Coble and Butler in a GeneAmp PCR System 9700 (Applied Biosystems). The amplified products were separated and detected by capillary electrophoresis on an ABI PRISM 3100 Genetic Analyzer (Applied Biosystems).The genotype frequency distributions showed no deviations from Hardy-Weinberg equilibrium expectations. The values of forensic parameters confirm that D10S1248 and D22S1045 are highly informative genetic markers, whereas D14S1434 is a moderately useful for forensic genetic identification purposes.

An intangible energy in the functioning biosystem. I: A search for its fate and a proposed method of delivery.

PubMed

Reid, B L

1995-06-01

This paper treats evidence for an increasing recognition of a force with intangible properties in biosystems with special reference to its ability to transport electrons at near 0 degree Kelvin. It is implied that such force, whose demonstration at these temperatures is an experimental contrivance to emphasise its strictly quantal status, can be operative at room temperature. A discussion is entered as to a mode for delivery of intangible energy from demonstrable non-local origins, locally to the cell to provide for structure and function. Extensive use is made of theory of the structure of the photon from de Broglie and others to accommodate a co-existence of real (electromagnetic) and quantal (intangible) fields within the photon and to discuss how such co-existence may have been copied or otherwise made manifest in a macroscopic structure such as the cell. Cell function is then viewed as concurrent real and intangible effects following stimuli derived from perturbation of the real or electromagnetic component.

A visible-light-excited europium(III) complex-based luminescent probe for visualizing copper ions and hydrogen sulfide in living cells

NASA Astrophysics Data System (ADS)

Wang, Yiren; Wang, Huan; Yang, Mei; Yuan, Jingli; Wu, Jing

2018-01-01

Development of visible-light-excited lanthanide (III) complex-based luminescent probes is highly appealing due to their superiority of less damage to the living biosystems over the conventional UV-light-excited ones. In this work, a visible-light-excited europium (III) complex-based luminescent probe, BPED-BHHCT-Eu3+-BPT, has been designed and synthesized by conjugating the Cu2+-binding N,N-bis(2-pyridylmethyl)ethanediamine (BPED) to a tetradentate β-diketone ligand 4,4‧-bis(1″,1″,1″,2″,2″,3″,3″-heptafluoro-4″,6″-hexanedione-6″-yl)chlorosulfo-o-terphenyl (BHHCT) and coordinating with a coligand 2-(N,N-diethylanilin-4-yl)-4,6-bis(pyrazol-1-yl)-1,3,5-triazine) (BPT) for the time-gated luminescence detection of Cu2+ ions and hydrogen sulfide (H2S) in living cells. BPED-BHHCT-Eu3+-BPT exhibited a sharp excitation peak at 407 nm and a wide excitation window extending to beyond 460 nm. Upon its reaction with Cu2+ ions, the luminescence of BPED-BHHCT-Eu3+-BPT was efficiently quenched, which could be reversibly restored by the addition of H2S due to the strong affinity between Cu2+ ions and H2S. The "on-off-on" type luminescence behavior of BPED-BHHCT-Eu3+-BPT towards Cu2+ ions and H2S enabled the sensing of the two species with high sensitivity and selectivity. The performances of BPED-BHHCT-Eu3+-BPT for visualizing intracellular Cu2+ ions and H2S were investigated, and the results have demonstrated the practical applicability of the probe for molecular imaging of cells.

Visible light induced electropolymerization of suspended hydrogel bioscaffolds in a microfluidic chip.

PubMed

Li, Pan; Yu, Haibo; Liu, Na; Wang, Feifei; Lee, Gwo-Bin; Wang, Yuechao; Liu, Lianqing; Li, Wen Jung

2018-05-23

The development of microengineered hydrogels co-cultured with cells in vitro could advance in vivo bio-systems in both structural complexity and functional hierarchy, which holds great promise for applications in regenerative tissues or organs, drug discovery and screening, and bio-sensors or bio-actuators. Traditional hydrogel microfabrication technologies such as ultraviolet (UV) laser or multiphoton laser stereolithography and three-dimensional (3D) printing systems have advanced the development of 3D hydrogel micro-structures but need either expensive and complex equipment, or harsh material selection with limited photoinitiators. Herein, we propose a simple and flexible hydrogel microfabrication method based on a ubiquitous visible-light projection system combined with a custom-designed photosensitive microfluidic chip, to rapidly (typically several to tens of seconds) fabricate various two-dimensional (2D) hydrogel patterns and 3D hydrogel constructs. A theoretical layer-by-layer model that involves continuous polymerizing-delaminating-polymerizing cycles is presented to explain the polymerization and structural formation mechanism of hydrogels. A large area of hydrogel patterns was efficiently fabricated without the usage of costly laser systems or photoinitiators, i.e., a stereoscopic mesh-like hydrogel network with intersecting hydrogel micro-belts was fabricated via a series of dynamic-changing digital light projections. The pores and gaps of the hydrogel network are tunable, which facilitates the supply of nutrients and discharge of waste in the construction of 3D thick bio-models. Cell co-culture experiments showed the effective regulation of cell spreading by hydrogel scaffolds fabricated by the new method presented here. This visible light enabled hydrogel microfabrication method may provide new prospects for designing cell-based units for advanced biomedical studies, e.g., for 3D bio-models or bio-actuators in the future.

Spectroscopic and electrochemical investigation with coordination stabilities: Mononuclear manganese(II) complexes derived from different constituents macrocyclic ligands

NASA Astrophysics Data System (ADS)

Kumar, Rajiv; Chnadra, S.; Mishra, Parashuram

2007-12-01

Since the manganese(II) complexes are known as having a high degree of stability, some of them may be able to play a very important role in biosystems. We prepared manganese(II) complexes with different chromospheres containing macrocyclic ligands bearing N, S and O like functional donor atoms in order to obtain different models of compounds. So these new manganese(II) complexes were derived from macrocyclic ligands by chelating them with metal ions. Thus, two macrocyclic ligands, L 1: 2,4-diphenyl-1,5-diaza-8,12-dioxo-6,7:13,14-dibenzocyclo tetradeca-1,4-diene[N 2O 2]ane; L 2: 2,4,9,11-tetraphenyl-6,13-dimethyl-1,5,8,12-traazacyclotertr-adeca-1,4,8,11-tetraene[N 4]ane; and two more different form first one viz.—L 3: 1,7-diaza-4-monothia-10,14-dioxo-8,9:15,16-cyclohexadecane[N 2O 2S]ane and L 4: 4,13-diaoxa-1,7,10,16-hexazacyclooctadecane[N 4O 2]ane were prepared and their capacity to retain the manganese(II) ion in solid as well as aqueous solution was determined from various physiochemical techniques viz: characterized by elemental analyses, molar conductance measurements, magnetic susceptibility measurements, mass, IR, electronic, ESR spectral studies and cyclic voltammetric measurements.

Joseph Rollin | NREL

Science.gov Websites

, during which time he co-founded two start-up companies, Gate Fuels Inc. and Cell-Free Bioinnovations Inc (2015) New biotechnology paradigm: Cell-free biosystems for biomanufacturing. Green Chem. (2013 ). High-yield production of dihydrogen from xylose by using a synthetic enzyme cascase in a cell-free

Simple scaling of cooperation in donor-recipient games.

PubMed

Berger, Ulrich

2009-09-01

We present a simple argument which proves a general version of the scaling phenomenon recently observed in donor-recipient games by Tanimoto [Tanimoto, J., 2009. A simple scaling of the effectiveness of supporting mutual cooperation in donor-recipient games by various reciprocity mechanisms. BioSystems 96, 29-34].

Report of the In Situ Resources Utilization Workshop

NASA Technical Reports Server (NTRS)

Fairchild, Kyle (Editor); Mendell, Wendell W. (Editor)

1988-01-01

The results of a workshop of 50 representatives from the public and private sector which investigated the potential joint development of the key technologies and mechanisms that will enable the permanent habitation of space are presented. The workshop is an initial step to develop a joint public/private assessment of new technology requirements of future space options, to share knowledge on required technologies that may exist in the private sector, and to investigate potential joint technology development opportunities. The majority of the material was produced in 5 working groups: (1) Construction, Assembly, Automation and Robotics; (2) Prospecting, Mining, and Surface Transportation; (3) Biosystems and Life Support; (4) Materials Processing; and (5) Innovative Ventures. In addition to the results of the working groups, preliminary technology development recommendations to assist in near-term development priority decisions are presented. Finally, steps are outlined for potential new future activities and relationships among the public, private, and academic sectors.

Epidermal Growth Factor Signaling towards Proliferation: Modeling and Logic Inference Using Forward and Backward Search

PubMed Central

Riesco, Adrián; Santos-Buitrago, Beatriz; De Las Rivas, Javier; Knapp, Merrill; Talcott, Carolyn

2017-01-01

In biological systems, pathways define complex interaction networks where multiple molecular elements are involved in a series of controlled reactions producing responses to specific biomolecular signals. These biosystems are dynamic and there is a need for mathematical and computational methods able to analyze the symbolic elements and the interactions between them and produce adequate readouts of such systems. In this work, we use rewriting logic to analyze the cellular signaling of epidermal growth factor (EGF) and its cell surface receptor (EGFR) in order to induce cellular proliferation. Signaling is initiated by binding the ligand protein EGF to the membrane-bound receptor EGFR so as to trigger a reactions path which have several linked elements through the cell from the membrane till the nucleus. We present two different types of search for analyzing the EGF/proliferation system with the help of Pathway Logic tool, which provides a knowledge-based development environment to carry out the modeling of the signaling. The first one is a standard (forward) search. The second one is a novel approach based on narrowing, which allows us to trace backwards the causes of a given final state. The analysis allows the identification of critical elements that have to be activated to provoke proliferation. PMID:28191459

Epigenetics in adaptive evolution and development: the interplay between evolving species and epigenetic mechanisms: extract from Trygve Tollefsbol (ed.) (2011) Handbook of epigenetics--the new molecular and medical genetics. Chapter 26. Amsterdam, USA: Elsevier, pp. 423-446.

PubMed

House, Simon H

2013-04-01

By comparing epigenetics of current species with fossil records across evolutionary transitions, we can gauge the moment of emergence of some novel mechanisms in evolution, and recognize that epigenetic mechanisms have a bearing on mutation. Understanding the complexity and changeability of these mechanisms, as well as the changes they can effect, is both fascinating and of vital practical benefit. Our most serious pandemics of so-called 'non-communicable' diseases - mental and cardiovascular disorders, obesity and diabetes, rooted in the 'metabolic syndrome' - are evidently related to effects on our evolutionary mechanisms of agricultural and food industrialization, modern lifestyle and diet. Pollution affects us directly as well as indirectly by its destruction of ecologically essential biosystems. Evidently such powerful conditions of existence have epigenetic effects on both our health and our continuing evolution. Such effects are most profound during reproductive and developmental processes, when levels of hormones, as affected by stress particularly, may be due to modern cultures in childbearing such as excessive intervention, separation, maternal distress and disruption of bonding. Mechanisms of genomic imprinting seem likely to throw light on problems in assisted reproductive technology, among other transgenerational effects. © The Author(s) 2014.

A hydrophobic organelle probe based on aggregation-induced emission: Nanosuspension preparation and direct use for endoplasmic reticulum imaging in living cells

NASA Astrophysics Data System (ADS)

Zheng, Sichao; Huang, Cuihong; Zhao, Xuyan; Zhang, Yong; Liu, Shuwen; Zhu, Qiuhua

2018-01-01

Organic fluorophores have a wide range of biological uses and are usually needed to be prepared as water-soluble compounds or nanoparticles for applications in aqueous biosystems owing to their hydrophobic properties, which often is a complex, time-consuming and high-cost process. Here, the nanoparticle preparation of hydrophobic fluorophores and their application in cell imaging have been investigated. It was found: a) fetal bovine serum (FBS) shows an excellent dispersion effect on hydrophobic small-molecule organic compounds; b) a hydrophobic C6-unsubstituted tetrahydropyrimidine (Me-THP-Naph) can be prepared as nanosuspensions utilizing cell culture medium with 10% FBS and directly be used as a specific real-time imaging probe for the endoplasmic reticulum (ER), a dynamic organelle playing a crucial role in many cellular processes. Compared with existing ER-targeted organic fluorescent probes, Me-THP-Naph, a product of an efficient five-component reaction that we developed, has unconventional aggregation-induced emission characteristics and shows advantages of low cost, long-term staining, good photostability, high signal-to-noise ratio and excellent biocompatibility, which make it a potential specific probe for real-time ER imaging. More importantly, this work affords a simple strategy for direct application of hydrophobic organic compounds in aqueous biological systems.

Impact of intracellular metallothionein on metal biouptake and partitioning dynamics at bacterial interfaces.

PubMed

Présent, Romain M; Rotureau, Elise; Billard, Patrick; Pagnout, Christophe; Sohm, Bénédicte; Flayac, Justine; Gley, Renaud; Pinheiro, José P; Duval, Jérôme F L

2017-11-08

Genetically engineered microorganisms are alternatives to physicochemical methods for remediation of metal-contaminated aquifers due to their remarkable bioaccumulation capacities. The design of such biosystems would benefit from the elaboration of a sound quantitative connection between performance in terms of metal removal from aqueous solution and dynamics of the multiscale processes leading to metal biouptake. In this work, this elaboration is reported for Escherichia coli cells modified to overexpress intracellular metallothionein (MTc), a strong proteinaceous metal chelator. Depletion kinetics of Cd(ii) from bulk solution following biouptake and intracellular accumulation is addressed as a function of cell volume fraction using electroanalytical probes and ligand exchange-based analyses. It is shown that metal biouptake in the absence and presence of MTc is successfully interpreted on the basis of a formalism recently developed for metal partitioning dynamics at biointerfaces with integration of intracellular metal speciation. The analysis demonstrates how fast sequestration of metals by intracellular MTc bypasses metal excretion (efflux) and enhances the rate of metal depletion to an extent such that complete removal is achieved at sufficiently large cell volume fractions. The magnitude of the stability constant of nanoparticulate metal-MTc complexes, as derived from refined analysis of macroscopic bulk metal depletion data, is further confirmed by independent electrochemical measurement of metal binding by purified MTc extracts.

Epidermal Growth Factor Signaling towards Proliferation: Modeling and Logic Inference Using Forward and Backward Search.

PubMed

Riesco, Adrián; Santos-Buitrago, Beatriz; De Las Rivas, Javier; Knapp, Merrill; Santos-García, Gustavo; Talcott, Carolyn

2017-01-01

In biological systems, pathways define complex interaction networks where multiple molecular elements are involved in a series of controlled reactions producing responses to specific biomolecular signals. These biosystems are dynamic and there is a need for mathematical and computational methods able to analyze the symbolic elements and the interactions between them and produce adequate readouts of such systems. In this work, we use rewriting logic to analyze the cellular signaling of epidermal growth factor (EGF) and its cell surface receptor (EGFR) in order to induce cellular proliferation. Signaling is initiated by binding the ligand protein EGF to the membrane-bound receptor EGFR so as to trigger a reactions path which have several linked elements through the cell from the membrane till the nucleus. We present two different types of search for analyzing the EGF/proliferation system with the help of Pathway Logic tool, which provides a knowledge-based development environment to carry out the modeling of the signaling. The first one is a standard (forward) search. The second one is a novel approach based on narrowing , which allows us to trace backwards the causes of a given final state. The analysis allows the identification of critical elements that have to be activated to provoke proliferation.

Validation of the Applied Biosystems 7500 Fast Instrument for Detection of Listeria Species with the SureTect Listeria Species PCR Assay.

PubMed

Cloke, Jonathan; Arizanova, Julia; Crabtree, David; Simpson, Helen; Evans, Katharine; Vaahtoranta, Laura; Palomäki, Jukka-Pekka; Artimo, Paulus; Huang, Feng; Liikanen, Maria; Koskela, Suvi; Chen, Yi

2016-01-01

The Thermo Scientific™ SureTect™ Listeria species Real-Time PCR Assay was certified during 2013 by the AOAC Research Institute (RI) Performance Tested Methods(SM) program as a rapid method for the detection of Listeria species from a wide range of food matrixes and surface samples. A method modification study was conducted in 2015 to extend the matrix claims of the product to a wider range of food matrixes. This report details the method modification study undertaken to extend the use of this PCR kit to the Applied Biosystems™ 7500 Fast PCR Instrument and Applied Biosystems RapidFinder™ Express 2.0 software allowing use of the assay on a 96-well format PCR cycler in addition to the current workflow, using the 24-well Thermo Scientific PikoReal™ PCR Instrument and Thermo Scientific SureTect software. The method modification study presented in this report was assessed by the AOAC-RI as being a level 2 method modification study, necessitating a method developer study on a representative range of food matrixes covering raw ground turkey, 2% fat pasteurized milk, and bagged lettuce as well as stainless steel surface samples. All testing was conducted in comparison to the reference method detailed in International Organization for Standardization (ISO) 6579:2002. No significant difference by probability of detection statistical analysis was found between the SureTect Listeria species PCR Assay or the ISO reference method methods for any of the three food matrixes and the surface samples analyzed during the study.

Comparison of Enterococcus qPCR analysis results from fresh and marine water samples on two real-time instruments -

EPA Science Inventory

EPA is currently considering a quantitative polymerase chain reaction (qPCR) method, targeting Enterococcus spp., for beach monitoring. Improvements in the method’s cost-effectiveness may be realized by the use of newer instrumentation such as the Applied Biosystems StepOneTM a...

Experiences of Second-Class Citizenship Related to Continued Poor Academic Performance of Minority Xhosa Learners

ERIC Educational Resources Information Center

Dreyer, Lorna M.; Singh, Suzanne A. M.

2016-01-01

This article examines the subjective life experiences of racial minority Xhosa speakers and the factors that contribute to their continued poor academic performance in a previously Whites-only school in South Africa. Vygotskian sociocultural perspective in relation to creating a democratic educational system and Bronfenbrenner's biosystemic theory…

Allele frequency distribution for 21 autosomal STR loci in Bhutan.

PubMed

Kraaijenbrink, Thirsa; van Driem, George L; Tshering of Gaselô, Karma; de Knijff, Peter

2007-07-20

We studied the allele frequency distribution of 21 autosomal STR loci contained in the AmpFlSTR Identifiler (Applied Biosystems), the Powerplex 16 (Promega) and the FFFL (Promega) multiplex PCR kits among 936 individuals from the Royal Kingdom of Bhutan. As such these are the first published autosomal DNA results from this country.

Human Performance and Biosystems (Spring Review)

DTIC Science & Technology

2014-03-01

public release; distribution is unlimited Areas of Emphasis Biofilms/Nanowires – microbe communication, extracellular electron transfer, cyborg ...Artificial Photosynthesis • Algal oil generation • Biofilm, Nanowires, Cyborg Cell • tDCS • Biomarkers 5 Distribution A: Approved for public...release; distribution is unlimited Program Interactions BRI magnetic navigation Microbes/nanowires tDCS/ Cyborg cell Synthetic Biology

New Generation Sequencing Technology Panel at SFAF-Part II

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

Fiske, Haley; Turner, Steve; Rhodes, Michael

2009-05-27

From left to right: Haley Fiske of Illumina Inc., Steve Turner of Pacific Biosciences, Michael Rhodes of Applied Biosystems, Patrice Milos of Helicos Biosciences and Tim Harkins of Roche Diagnostics answer questions in a forum moderated by Bob Fulton at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

New Generation Sequencing Technology Panel at SFAF-Part I

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

Fiske, Haley; Turner, Steve; Rhodes, Michael

2009-05-27

From left to right: Haley Fiske of Illumina Inc., Steve Turner of Pacific Biosciences, Michael Rhodes of Applied Biosystems, Patrice Milos of Helicos Biosciences and Tim Harkins of Roche Diagnostics answer questions in a forum moderated by Bob Fulton at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

Science for Iowa Schools, Grades 4-6.

ERIC Educational Resources Information Center

Nice, Karl; And Others

This guide includes four units for use in each of grades 4 through 6. The fourth grade units are entitled Measurement Systems, Classification Systems, Bio-Control Systems, and Hydrologic Systems; the fifth grade units are Chemical Systems, Force Systems, Bio-Systems, and Astro-Systems; and the sixth grade units are Equilibrium Systems,…

The effects of socioeconomic status, clinical factors, and genetic ancestry on pulmonary tuberculosis disease in northeastern Mexico.

PubMed

Young, Bonnie N; Rendón, Adrian; Rosas-Taraco, Adrian; Baker, Jack; Healy, Meghan; Gross, Jessica M; Long, Jeffrey; Burgos, Marcos; Hunley, Keith L

2014-01-01

Diverse socioeconomic and clinical factors influence susceptibility to tuberculosis (TB) disease in Mexico. The role of genetic factors, particularly those that differ between the parental groups that admixed in Mexico, is unclear. The objectives of this study are to identify the socioeconomic and clinical predictors of the transition from latent TB infection (LTBI) to pulmonary TB disease in an urban population in northeastern Mexico, and to examine whether genetic ancestry plays an independent role in this transition. We recruited 97 pulmonary TB disease patients and 97 LTBI individuals from a public hospital in Monterrey, Nuevo León. Socioeconomic and clinical variables were collected from interviews and medical records, and genetic ancestry was estimated for a subset of 142 study participants from 291,917 single nucleotide polymorphisms (SNPs). We examined crude associations between the variables and TB disease status. Significant predictors from crude association tests were analyzed using multivariable logistic regression. We also compared genetic ancestry between LTBI individuals and TB disease patients at 1,314 SNPs in 273 genes from the TB biosystem in the NCBI BioSystems database. In crude association tests, 12 socioeconomic and clinical variables were associated with TB disease. Multivariable logistic regression analyses indicated that marital status, diabetes, and smoking were independently associated with TB status. Genetic ancestry was not associated with TB disease in either crude or multivariable analyses. Separate analyses showed that LTBI individuals recruited from hospital staff had significantly higher European genetic ancestry than LTBI individuals recruited from the clinics and waiting rooms. Genetic ancestry differed between individuals with LTBI and TB disease at SNPs located in two genes in the TB biosystem. These results indicate that Monterrey may be structured with respect to genetic ancestry, and that genetic differences in TB susceptibility in parental populations may contribute to variation in disease susceptibility in the region.

The Effects of Socioeconomic Status, Clinical Factors, and Genetic Ancestry on Pulmonary Tuberculosis Disease in Northeastern Mexico

PubMed Central

Young, Bonnie N.; Rendón, Adrian; Rosas-Taraco, Adrian; Baker, Jack; Healy, Meghan; Gross, Jessica M.; Long, Jeffrey; Burgos, Marcos; Hunley, Keith L.

2014-01-01

Diverse socioeconomic and clinical factors influence susceptibility to tuberculosis (TB) disease in Mexico. The role of genetic factors, particularly those that differ between the parental groups that admixed in Mexico, is unclear. The objectives of this study are to identify the socioeconomic and clinical predictors of the transition from latent TB infection (LTBI) to pulmonary TB disease in an urban population in northeastern Mexico, and to examine whether genetic ancestry plays an independent role in this transition. We recruited 97 pulmonary TB disease patients and 97 LTBI individuals from a public hospital in Monterrey, Nuevo León. Socioeconomic and clinical variables were collected from interviews and medical records, and genetic ancestry was estimated for a subset of 142 study participants from 291,917 single nucleotide polymorphisms (SNPs). We examined crude associations between the variables and TB disease status. Significant predictors from crude association tests were analyzed using multivariable logistic regression. We also compared genetic ancestry between LTBI individuals and TB disease patients at 1,314 SNPs in 273 genes from the TB biosystem in the NCBI BioSystems database. In crude association tests, 12 socioeconomic and clinical variables were associated with TB disease. Multivariable logistic regression analyses indicated that marital status, diabetes, and smoking were independently associated with TB status. Genetic ancestry was not associated with TB disease in either crude or multivariable analyses. Separate analyses showed that LTBI individuals recruited from hospital staff had significantly higher European genetic ancestry than LTBI individuals recruited from the clinics and waiting rooms. Genetic ancestry differed between individuals with LTBI and TB disease at SNPs located in two genes in the TB biosystem. These results indicate that Monterrey may be structured with respect to genetic ancestry, and that genetic differences in TB susceptibility in parental populations may contribute to variation in disease susceptibility in the region. PMID:24728409

Circadian rhythms in effects of hypnotics and sleep inducers.

PubMed

Reinberg, A

1986-01-01

Chronopharmacology involves the investigation of drug effects as a function of biological time and the investigation of drug effects on rhythm characteristics. Three new concepts must be considered: (a) the chronokinetics of a drug, embracing rhythmic (circadian) changes in drug bioavailability (or pharmacokinetics) and its excretion (urinary among others); (b) the chronaesthesia of a biosystem to a drug, i.e. circadian changes in the susceptibility of any biosystem to a drug (including organ systems, parasites, etc.); skin and bronchial chronaesthesia to various agents have been documented in man; and (c) the chronergy of a drug, taking into consideration its chronokinetics and the chronaesthesia of the involved organismic biosystems. The term chronergy includes rhythmic changes in the overall effects and in the effectiveness of some drugs. Clinical chronopharmacology is useful for solving problems of drug optimization, i.e. enhancing the desired efficiency of a drug and reducing its undesired effects. Circadian rhythms can be demonstrated in various effects of drugs on sleep, anaesthesia and related processes. For example, in the rat the duration of sleep induced by substances such as pentobarbital, hexobarbital, Althesin (alphaxadone and alphadoline in castor oil) is circadian system stage-dependent. Time-dependent changes of liver enzymes (e.g. hexobarbital oxidase) play a role in these circadian rhythms. The clinical chronopharmacokinetics of benzodiazepines have been documented in man. Chronopharmacologic methods can be used to study desired and undesired hypnotic effects of substances. Such is the case of new antihistamines (anti-H1), which do not induce sleepiness, in either acute or chronic administration. Pertinent also is the problem of intolerance to shift-work. Intolerant shift-workers are subject to internal desynchronization between at least two rhythms (e.g. activity-rest cycle and body temperature). Clinically these workers suffer from sleep disturbances, persistent fatigue and are regular users of sleeping pills, which is also a symptom of intolerance. However, over the long-term, these drugs are of no help to intolerant shift-workers.

Preserved organic matter in the Serpentinized Ocean-Continent Transition of Alpine Tethys

NASA Astrophysics Data System (ADS)

Mateeva, T.; Wolff, G. A.; Kusznir, N.; Manatschal, G.; Wheeler, J.

2017-12-01

Serpentinization occurs at slow-spreading ocean ridges and magma-poor rifted continental margins. At modern hydrothermal vents, serpentinization has been observed to support hydrogen-driven microbial environments including methanotrophic biosystems. An important question is: "Are such bio-systems locally restricted to hydrothermal vents or are they more pervasive, being linked with the exhumation of serpentinized mantle at the seafloor?" Fieldwork sampling of km scale exposures of orogenically exhumed serpentinized mantle in the Alps allows 3D mantle sampling that is not possible at ocean ridges and provides an opportunity to investigate the organic matter in an ophiolite sequence relative to the seafloor. Samples from the fossil Tethyan OCT, exhumed during Alpine collisional orogeny, have been examined for the presence or absence of biomarkers typical of methanotrophy within serpentinized exhumed mantle. Samples from the Totalp unit, Tasna nappe and Platta unit of the Eastern Swiss Alps and Chenaillet in the Western Alps from the Tethyan magma-poor OCT were selected for analysis because they have little Alpine deformation and underwent only low-grade Alpine metamorphism. Hand specimens and cores taken from these locations have been analysed to search for the presence or absence of biomarkers in the serpentinite and its overlying lithologies. Thin sections of samples from these OCT locations reveal multiple serpentinization events and calcification phases. All the lithologies sampled show the presence of hydrocarbons such as n-alkanes, low molecular weight polynuclear aromatic hydrocarbons (PAHs, of mixed petrogenic and pyrogenic source), hopanes, steranes (of marine origin), and branched alkanes (pristane and phytane, non-specific marine origin). The identifiable biomarkers and the isotopic data are consistent with organic matter of a marine origin and do not provide any evidence for a methanotrophic bio-system. It is noteworthy that basement mantle rocks still contain marine organic matter 160My after their formation at a rifted margin despite having experienced Alpine obduction.

Biofuels from food processing wastes.

PubMed

Zhang, Zhanying; O'Hara, Ian M; Mundree, Sagadevan; Gao, Baoyu; Ball, Andrew S; Zhu, Nanwen; Bai, Zhihui; Jin, Bo

2016-04-01

Food processing industry generates substantial high organic wastes along with high energy uses. The recovery of food processing wastes as renewable energy sources represents a sustainable option for the substitution of fossil energy, contributing to the transition of food sector towards a low-carbon economy. This article reviews the latest research progress on biofuel production using food processing wastes. While extensive work on laboratory and pilot-scale biosystems for energy production has been reported, this work presents a review of advances in metabolic pathways, key technical issues and bioengineering outcomes in biofuel production from food processing wastes. Research challenges and further prospects associated with the knowledge advances and technology development of biofuel production are discussed. Copyright © 2016. Published by Elsevier Ltd.

Labeled Nucleoside Triphosphates with Reversibly Terminating Aminoalkoxyl Groups

PubMed Central

Hutter, Daniel; Kim, Myong-Jung; Karalkar, Nilesh; Leal, Nicole A.; Chen, Fei; Guggenheim, Evan; Visalakshi, Visa; Olejnik, Jerzy; Gordon, Steven; Benner, Steven A.

2013-01-01

Nucleoside triphosphates having a 3′-ONH2 blocking group have been prepared with and without fluorescent tags on their nucleobases. DNA polymerases were identified that accepted these, adding a single nucleotide to the 3′-end of a primer in a template-directed extension reaction that then stops. Nitrite chemistry was developed to cleave the 3′-ONH2 group under mild conditions to allow continued primer extension. Extension-cleavage-extension cycles in solution were demonstrated with untagged nucleotides and mixtures of tagged and untagged nucleotides. Multiple extension-cleavage-extension cycles were demonstrated on an Intelligent Bio-Systems Sequencer, showing the potential of the 3′-ONH2 blocking group in “next generation sequencing”. PMID:21128174

Perturbing Tandem Energy Transfer in Luminescent Heterobinuclear Lanthanide Coordination Polymer Nanoparticles Enables Real-Time Monitoring of Release of the Anthrax Biomarker from Bacterial Spores.

PubMed

Gao, Nan; Zhang, Yunfang; Huang, Pengcheng; Xiang, Zhehao; Wu, Fang-Ying; Mao, Lanqun

2018-06-05

Lanthanide-based luminescent sensors have been widely used for the detection of the anthrax biomarker dipicolinic acid (DPA). However, mainly based on DPA sensitization to the lanthanide core, most of them failed to realize robust detection of DPA in bacterial spores. We proposed a new strategy for reliable detection of DPA by perturbing a tandem energy transfer in heterobinuclear lanthanide coordination polymer nanoparticles simply constructed by two kinds of lanthanide ions, Tb 3+ and Eu 3+ , and guanosine 5'-monophosphate. This smart luminescent probe was demonstrated to exhibit highly sensitive and selective visual luminescence color change upon exposure to DPA, enabling accurate detection of DPA in complex biosystems such as bacterial spores. DPA release from bacterial spores on physiological germination was also successfully monitored in real time by confocal imaging. This probe is thus expected to be a powerful tool for efficient detection of bacterial spores in responding to anthrax threats.

Sequence-specific inhibition of microRNA-130a gene by CRISPR/Cas9 system in breast cancer cell line

NASA Astrophysics Data System (ADS)

Ainina Abdollah, Nur; Das Kumitaa, Theva; Yusof Narazah, Mohd; Razak, Siti Razila Abdul

2017-05-01

MicroRNAs (miRNAs) are short stranded noncoding RNA that play important roles in apoptosis, cell survival, development and cell proliferation. However, gene expression control via small regulatory RNA, particularly miRNA in breast cancer is still less explored. Therefore, this project aims to develop an approach to target microRNA-130a using the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/Cas9 system in MCF7, breast cancer cell line. The 20 bp sequences target at stem loop, 3ʹ and 5ʹ end of miR130a were cloned into pSpCas9(BB)-2A-GFP (PX458) plasmid, and the positive clones were confirmed by sequencing. A total of 5 μg of PX458-miR130a was transfected to MCF7 using Lipofectamine® 3000 according to manufacturer’s protocol. The transfected cells were maintained in the incubator at 37 °C under humidified 5% CO2. After 48 hours, cells were harvested and total RNA was extracted using miRNeasy Mini Kit (Qiagen). cDNAs were synthesised specific to miR-130a using TaqMan MicroRNA Reverse Transcription Kit (Applied Biosystems). Then, qRT-PCR was carried out using TaqMan Universal Master Mix (Applied Biosystems) to quantify the knockdown level of mature miRNAs in the cells. Result showed that miR-130a-5p was significantly downregulated in MCF7 cell line. However, no significant changes were observed for sequences targeting miR-130a-3p and stem loop. Thus, this study showed that the expression of miR-130a-5p was successfully down-regulated using CRISPR silencing system. This technique may be useful to manipulate the level of miRNA in various cell types to answer clinical questions at the molecular level.

An Ultra-High Discrimination Y Chromosome Short Tandem Repeat Multiplex DNA Typing System

PubMed Central

Hanson, Erin K.; Ballantyne, Jack

2007-01-01

In forensic casework, Y chromosome short tandem repeat markers (Y-STRs) are often used to identify a male donor DNA profile in the presence of excess quantities of female DNA, such as is found in many sexual assault investigations. Commercially available Y-STR multiplexes incorporating 12–17 loci are currently used in forensic casework (Promega's PowerPlex® Y and Applied Biosystems' AmpFlSTR® Yfiler®). Despite the robustness of these commercial multiplex Y-STR systems and the ability to discriminate two male individuals in most cases, the coincidence match probabilities between unrelated males are modest compared with the standard set of autosomal STR markers. Hence there is still a need to develop new multiplex systems to supplement these for those cases where additional discriminatory power is desired or where there is a coincidental Y-STR match between potential male participants. Over 400 Y-STR loci have been identified on the Y chromosome. While these have the potential to increase the discrimination potential afforded by the commercially available kits, many have not been well characterized. In the present work, 91 loci were tested for their relative ability to increase the discrimination potential of the commonly used ‘core’ Y-STR loci. The result of this extensive evaluation was the development of an ultra high discrimination (UHD) multiplex DNA typing system that allows for the robust co-amplification of 14 non-core Y-STR loci. Population studies with a mixed African American and American Caucasian sample set (n = 572) indicated that the overall discriminatory potential of the UHD multiplex was superior to all commercial kits tested. The combined use of the UHD multiplex and the Applied Biosystems' AmpFlSTR® Yfiler® kit resulted in 100% discrimination of all individuals within the sample set, which presages its potential to maximally augment currently available forensic casework markers. It could also find applications in human evolutionary genetics and genetic genealogy. PMID:17668066

Application of Non-Kolmogorovian Probability and Quantum Adaptive Dynamics to Unconscious Inference in Visual Perception Process

NASA Astrophysics Data System (ADS)

Accardi, Luigi; Khrennikov, Andrei; Ohya, Masanori; Tanaka, Yoshiharu; Yamato, Ichiro

2016-07-01

Recently a novel quantum information formalism — quantum adaptive dynamics — was developed and applied to modelling of information processing by bio-systems including cognitive phenomena: from molecular biology (glucose-lactose metabolism for E.coli bacteria, epigenetic evolution) to cognition, psychology. From the foundational point of view quantum adaptive dynamics describes mutual adapting of the information states of two interacting systems (physical or biological) as well as adapting of co-observations performed by the systems. In this paper we apply this formalism to model unconscious inference: the process of transition from sensation to perception. The paper combines theory and experiment. Statistical data collected in an experimental study on recognition of a particular ambiguous figure, the Schröder stairs, support the viability of the quantum(-like) model of unconscious inference including modelling of biases generated by rotation-contexts. From the probabilistic point of view, we study (for concrete experimental data) the problem of contextuality of probability, its dependence on experimental contexts. Mathematically contextuality leads to non-Komogorovness: probability distributions generated by various rotation contexts cannot be treated in the Kolmogorovian framework. At the same time they can be embedded in a “big Kolmogorov space” as conditional probabilities. However, such a Kolmogorov space has too complex structure and the operational quantum formalism in the form of quantum adaptive dynamics simplifies the modelling essentially.

Linking First-Year and Senior Engineering Design Teams: Engaging Early Academic Career Students in Engineering Design

ERIC Educational Resources Information Center

Fox, Garey A.; Weckler, Paul; Thomas, Dan

2015-01-01

In Biosystems Engineering at Oklahoma State University, senior design is a two semester course in which students work on real-world projects provided by clients. First-year (freshmen and trans­fer) students enroll in an introductory engineering course. Historically, these students worked on a team-based analysis project, and the engineering design…

Greenhouse gas (GHG) emission in organic farming. Approximate quantification of its generation at the organic garden of the School of Agricultural, Food and Biosystems Engineering (ETSIAAB) in the Technical University of Madrid (UPM)

NASA Astrophysics Data System (ADS)

Campos, Jorge; Barbado, Elena; Maldonado, Mariano; Andreu, Gemma; López de Fuentes, Pilar

2016-04-01

As it well-known, agricultural soil fertilization increases the rate of greenhouse gas (GHG) emission production such as CO2, CH4 and N2O. Participation share of this activity on the climate change is currently under study, as well as the mitigation possibilities. In this context, we considered that it would be interesting to know how this share is in the case of organic farming. In relation to this, a field experiment was carried out at the organic garden of the School of Agricultural, Food and Biosystems Engineering (ETSIAAB) in the Technical University of Madrid (UPM). The orchard included different management growing areas, corresponding to different schools of organic farming. Soil and gas samples were taken from these different sites. Gas samples were collected throughout the growing season from an accumulated atmosphere inside static chambers inserted into the soil. Then, these samples were carried to the laboratory and there analyzed. The results obtained allow knowing approximately how ecological fertilization contributes to air pollution due to greenhouse gases.

Challenges and Rewards on the Road to Translational Systems Biology in Acute Illness: Four Case Reports from Interdisciplinary Teams

PubMed Central

An, Gary; Hunt, C. Anthony; Clermont, Gilles; Neugebauer, Edmund; Vodovotz, Yoram

2007-01-01

Introduction Translational systems biology approaches can be distinguished from mainstream systems biology in that their goal is to drive novel therapies and streamline clinical trials in critical illness. One systems biology approach, dynamic mathematical modeling (DMM), is increasingly used in dealing with the complexity of the inflammatory response and organ dysfunction. The use of DMM often requires a broadening of research methods and a multidisciplinary team approach that includes bioscientists, mathematicians, engineers, and computer scientists. However, the development of these groups must overcome domain-specific barriers to communication and understanding. Methods We present four case studies of successful translational, interdisciplinary systems biology efforts, which differ by organizational level from an individual to an entire research community. Results Case 1 is a single investigator involved in DMM of the acute inflammatory response at Cook County Hospital, in which extensive translational progress was made using agent-based models of inflammation and organ damage. Case 2 is a community-level effort from the University of Witten-Herdecke in Cologne, whose efforts have led to the formation of the Society for Complexity in Acute Illness. Case 3 is an institution-based group, the Biosystems Group at the University of California, San Francisco, whose work has included a focus on a common lexicon for DMM. Case 4 is an institution-based, trans-disciplinary research group (the Center for Inflammation and Regenerative Modeling at the University of Pittsburgh, whose modeling work has led to internal education efforts, grant support, and commercialization. Conclusion A transdisciplinary approach, which involves team interaction in an iterative fashion to address ambiguity and is supported by educational initiatives, is likely to be necessary for DMM in acute illness. Community-wide organizations such as the Society of Complexity in Acute Illness (SCAI) must strive to facilitate the implementation of DMM in sepsis/trauma research into the research community as a whole. PMID:17548029

Electric Field-Mediated Processing of Biomaterials: Toward Nanostructured Biomimetic Systems. Appendix 3

NASA Technical Reports Server (NTRS)

Bowlin, Gary L.; Simpson, David G.; Lam, Philippe; Wnek, Gary E.

2001-01-01

Significant opportunities exist for the processing of synthetic and biological polymers using electric fields ('electroprocessing'). We review casting of multi-component films and the spinning of fibers in electric fields, and indicate opportunities for the creation of smart polymer systems using these approaches. Applications include 2-D substrates for cell growth and diagnostics, scaffolds for tissue engineering and repair, and electromechanically active biosystems.

Evaluation of the Neuroactivity of ToxCast Compounds Using Multi-well Microelectrode Array Recordings in Primary Cortical Neurons

EPA Science Inventory

Evaluation of the Neuroactivity of ToxCast Compounds Using Multi-well Microelectrode Array Recordings in Primary Cortical Neurons P Valdivia1, M Martin2, WR LeFew3, D Hall3, J Ross1, K Houck2 and TJ Shafer3 1Axion Biosystems, Atlanta GA and 2NCCT, 3ISTD, NHEERL, ORD, US EPA, RT...

National Nanotechnology Initiative: The Initiative and Its Implementation Plan

DTIC Science & Technology

2000-07-01

precisely controlled size and composition and then to assemble them into larger structures with unique properties and functions will revolutionize...thousand pounds could be stripped from a pilotless fighter aircraft , resulting in longer missions, and fighter agility could be dramatically improved...societal impact: $12 million. e. Major themes and new programs in FY 2001 include : • Nano-biotechnology: biosystems, bio-mimetics and composites (priority

Differentiating Ferroelectric and Nonferroelectric Electromechanical Effects with Scanning Probe Microscopy

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

Balke, Nina; Maksymovych, Petro; Jesse, Stephen

Ferroelectricity in functional materials remains one of the most fascinating areas of modern science in the past several decades. In the last several years, the rapid development of piezoresponse force microscopy (PFM) and spectroscopy revealed the presence of electromechanical hysteresis loops and bias-induced remnant polar states in a broad variety of materials including many inorganic oxides, polymers, and biosystems. In many cases, this behavior was interpreted as the ample evidence for ferroelectric nature of the system. Here, we systematically analyze PFM responses on ferroelectric and nonferroelectric materials and demonstrate that mechanisms unrelated to ferroelectricity can induce ferroelectric-like characteristics through chargemore » injection and electrostatic forces on the tip. In this paper, we will focus on similarities and differences in various PFM measurement characteristics to provide an experimental guideline to differentiate between ferroelectric material properties and charge injection. In conclusion, we apply the developed measurement protocols to an unknown ferroelectric material.« less

Differentiating Ferroelectric and Nonferroelectric Electromechanical Effects with Scanning Probe Microscopy

DOE PAGES

Balke, Nina; Maksymovych, Petro; Jesse, Stephen; ...

2015-06-02

Ferroelectricity in functional materials remains one of the most fascinating areas of modern science in the past several decades. In the last several years, the rapid development of piezoresponse force microscopy (PFM) and spectroscopy revealed the presence of electromechanical hysteresis loops and bias-induced remnant polar states in a broad variety of materials including many inorganic oxides, polymers, and biosystems. In many cases, this behavior was interpreted as the ample evidence for ferroelectric nature of the system. Here, we systematically analyze PFM responses on ferroelectric and nonferroelectric materials and demonstrate that mechanisms unrelated to ferroelectricity can induce ferroelectric-like characteristics through chargemore » injection and electrostatic forces on the tip. In this paper, we will focus on similarities and differences in various PFM measurement characteristics to provide an experimental guideline to differentiate between ferroelectric material properties and charge injection. In conclusion, we apply the developed measurement protocols to an unknown ferroelectric material.« less

The application of metabolomics in traditional Chinese medicine opens up a dialogue between Chinese and Western medicine.

PubMed

Cao, Hongxin; Zhang, Aihua; Zhang, Huamin; Sun, Hui; Wang, Xijun

2015-02-01

Metabolomics provides an opportunity to develop the systematic analysis of the metabolites and has been applied to discovering biomarkers and perturbed pathways which can clarify the action mechanism of traditional Chinese medicines (TCM). TCM is a comprehensive system of medical practice that has been used to diagnose, treat and prevent illnesses more than 3000 years. Metabolomics represents a powerful approach that provides a dynamic picture of the phenotype of biosystems through the study of endogenous metabolites, and its methods resemble those of TCM. Recently, metabolomics tools have been used for facilitating interactional effects of both Western medicine and TCM. We describe a protocol for investigating how metabolomics can be used to open up 'dialogue' between Chinese and Western medicine, and facilitate lead compound discovery and development from TCM. Metabolomics will bridge the cultural gap between TCM and Western medicine and improve development of integrative medicine, and maximally benefiting the human. Copyright © 2014 John Wiley & Sons, Ltd.

Synthetic biology for microbial heavy metal biosensors.

PubMed

Kim, Hyun Ju; Jeong, Haeyoung; Lee, Sang Jun

2018-02-01

Using recombinant DNA technology, various whole-cell biosensors have been developed for detection of environmental pollutants, including heavy metal ions. Whole-cell biosensors have several advantages: easy and inexpensive cultivation, multiple assays, and no requirement of any special techniques for analysis. In the era of synthetic biology, cutting-edge DNA sequencing and gene synthesis technologies have accelerated the development of cell-based biosensors. Here, we summarize current technological advances in whole-cell heavy metal biosensors, including the synthetic biological components (bioparts), sensing and reporter modules, genetic circuits, and chassis cells. We discuss several opportunities for improvement of synthetic cell-based biosensors. First, new functional modules must be discovered in genome databases, and this knowledge must be used to upgrade specific bioparts through molecular engineering. Second, modules must be assembled into functional biosystems in chassis cells. Third, heterogeneity of individual cells in the microbial population must be eliminated. In the perspectives, the development of whole-cell biosensors is also discussed in the aspects of cultivation methods and synthetic cells.

Influencing governance of a public-private partnership in plant genomics: The societal interface group as a new instrument for public involvement.

PubMed

Hanssen, Lucien; Gremmen, Bart

2013-08-01

The Centre for BioSystems Genomics (CBSG) is a Dutch public-private partnership in plant genomics active in potato and tomato research and exploitation. Its Societal Interface Group (SIG) has been developed to inform its communication strategy and governance practice. This new instrument identifies and discusses early signals from society by bringing together people from different societal backgrounds with members of CBSG management. This interactive learning process facilitates the inclusion of public concerns and needs in scientific developments in the field of plant genomics, and simultaneously enables genomics scientists to search for more societal aims, meanings, and starting points for their research agenda. Analysis of the SIG sessions revealed that the input of public expertise is not threatening or irrational, but provides the opportunity to harness the creative potential of future users highly relevant for the development of societal practices in which plant genomics plays a role.

Remote sensing investigations of wetland biomass and productivity for global biosystems research

NASA Technical Reports Server (NTRS)

Harkisky, M.; Klemas, V.

1983-01-01

Monitoring biomass of wetlands ecosystems can provide information on net primary production and on the chemical and physical status of wetland soils relative to anaerobic microbial transformation of key elements. Multispectral remote sensing techniques successfully estimated macrophytic biomass in wetlands systems. Regression models developed from ground spectral data for predicting Spartina alterniflora biomass over an entire growing season include seasonal variations in biomass density and illumination intensity. An independent set of biomass and spectral data were collected and the standing crop biomass and net primary productivity were estimated. The improved spatial, radiometric and spectral resolution of th LANDSAT-4 Thematic Mapper over the LANDSAT MSS can greatly enhance multispectral techniques for estimating wetlands biomass over large areas. These techniques can provide the biomass data necessary for global ecology studies.

The start of the Abiogenesis: Preservation of homochirality in proteins as a necessary and sufficient condition for the establishment of the metabolism.

PubMed

Toxvaerd, Søren

2018-08-14

Biosystems contain an almost infinite amount of vital important details, which together ensure their life. There are, however, some common structures and reactions in the systems: the homochirality of carbohydrates and proteins, the metabolism and the genetics. The Abiogenesis, or the origin of life, is probably not a result of a series of single events, but rather the result of a gradual process with increasing complexity of molecules and chemical reactions, and the prebiotic synthesis of molecules might not have left a trace of the establishment of structures and reactions at the beginning of the evolution. But alternatively, one might be able to determine some order in the formation of the chemical denominators in the Abiogenesis. Here we review experimental results and present a model of the start of the Abionenesis, where the spontaneous formation of homochirality in proteins is the precondition for the establishment of homochirality of carbohydrates and for the metabolism at the start of the Abiogenesis. Copyright © 2018 Elsevier Ltd. All rights reserved.

Kinetics of the maintenance of the epidermis

NASA Astrophysics Data System (ADS)

Zhdanov, Vladimir P.; Cho, Nam-Joon

2013-08-01

The epidermis is the outermost layer of skin. It is comprised of keratin-containing cells called keratinocytes. Functionally, the epidermis serves as a physical barrier that can prevent infection and regulate body hydration. Maintenance and repair of the epidermis are important for human health. Mechanistically, these processes occur primarily via proliferation and differentiation of stem cells located in the basal monolayer. These processes are believed to depend on cell-cell communication and spatial constraints but existing kinetic models focus mainly on proliferation and differentiation. To address this issue, we present a mean-field kinetic model that takes these additional factors into account and describes the epidermis at a biosystem level. The corresponding equations operate with the populations of stem cells and differentiated cells in the basal layer. The keratinocytes located above the basal layer are treated at a more coarse-grained level by considering the thickness of the epidermis. The model clarifies the likely role of various negative feedbacks that may control the epidermis and, accordingly, provides insight into the cellular mechanisms underlying complex biological phenomena such as wound healing.

Soft Lithography for Oligonucleotide Arrays Fabrication

DTIC Science & Technology

2001-10-25

adenosine; Abbreviated T, C, G, A respectively), the other synthesis reagents and solvents except oxidation agent (seen in Table 1) were purchased...dried by cold blowing before hybridization. Oligonucleotide arrays were hybridized in 200 nM 3’-TCC TCC GAT TCA GAG AGT CC- HEX (PE Biosystems... citrate buffer), 0.1% SDS in 0.1xSSC respectively. The probe array was scanned on the Scanarray Microarray Systems (Packard Biochip Technologies, USA

AN ENVIRONMENTAL TECHNOLOGY VERIFICATION (ETV) PERFORMANCE TESTING OF THREE RAPID PCR TECHNOLOGIES FOR IDAHO TECHNOLOGY R.A.I.D.® SYSTEM, APPLIED BIOSYSTEMS TAQMAN® E. COLI 0157:H7 DETECTION SYSTEM, AND INVITROGEN CORPORATION PATHALERTTM DETECTION KITS

EPA Science Inventory

The Environmental Technology Verification (ETV) Program, beginning as an initiative of the U.S. Environmental Protection Agency (EPA) in 1995, verifies the performance of commercially available, innovative technologies that can be used to measure environmental quality. The ETV p...

Atypical Opioid Mechanisms of Control of Injury-Induced Cutaneous Pain by Delta Receptors

DTIC Science & Technology

2016-07-01

treat, and current opioids (i.e. mu opioid receptor agonists such as morphine) cause unacceptable side effects including addiction . Injuries suffered...treat, and current opioids that act on mu opioid receptors such as morphine generate significant side effects including addiction . War-related...slides. Slides were then processed for fluorescent in situ hybridization with RNAscope technology (ACD Biosystems) to detect Oprd1 mRNA, as described

Rapid Identification of Key Pathogens in Wound Infection by Molecular Means

DTIC Science & Technology

2006-01-01

diagnosis and monitoring of infectious diseases [4]. Rapid diagnosis can be achieved by the direct detection of characteristic bacterial genes in clinical... System ABI PRISM® 7500 Sequence Detection System (Applied Biosystems, Foster City, Calif.) was purchased, set up and standardized. This system ...integrated system for real-time detection of PCR. The system includes a built-in thermal cycler, a laser to induce fluorescence, CCD (charge-coupled device

Toxicity assessment of untreated/treated electroplating sludge using human and plant bioassay.

PubMed

Orescanin, Visnja; Durgo, Ksenija; Mikelic, Ivanka Lovrencic; Halkijevic, Ivan; Kuspilic, Marin

2018-04-30

The purpose of this work was to assess the risk to the environment arising from the electroplating sludge from both chemical and toxicological point of view. Both approaches were used for the assessment of the treatment efficiency which consisted of CaO based solidification followed by thermal treatment at 400°C. The elemental composition was determined in the bulk samples and the leachates of untreated sludge. The toxicity of the leachate was determined using two human colorectal adenocarcinoma cell lines (Caco-2 and SW 480) and Hordeum vulgare L. based plant bioassay. The same toxicity tests were employed to the leachate of the treated sludge. Untreated sludge showed extremely high cytotoxic effect to both human and plant bio-system in dose-dependent manner. The percentages higher than 0.5% and 0.05% of the leachate caused significant cytotoxic effect on Caco-2 and SW 480 cells, respectively. The percentages of the leachate higher than 0.05% also showed significant toxic effect to H. vulgare L. bio-system with complete arrest of seed germination following the treatment with 100% to 5% of the leachate. The leachate of the treated sludge showed no toxicity to any of the test systems confirming the efficiency and justification of the employed procedures for the detoxification of electroplating sludge.

Microbial community dynamics in anaerobic bioreactors and algal tanks treating piggery wastewater.

PubMed

Patil, Sayali S; Kumar, Martin S; Ball, Andrew S

2010-06-01

Integrated biosystem is becoming a major aspect of wastewater management practice. Microbial communities in piggery wastewater sampled from anaerobic (thermophilic and mesophilic) and aerobic digesters (algal tanks) during waste remediation were analyzed by culture-independent techniques based on polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The use of Muyzer's 314F-GC, 518R bacterial primers, and archaeal A934F, 1309R primers followed by partial 16s rDNA sequence analysis of the main bands from DGGE revealed the presence of unknown and as yet uncultured microorganisms but also showed functional and ecologically significant denitrifying, acetogenic bacteria along with autotrophic, hydrogenotrophic, and acetoclastic methanogen archaea. Thermophilic digesters were dominated by gamma-Proteobacteria, Methanothermobacter sp., while mesophilic digesters showed dominance by Firmicutes, uncultured bacteria, Methanosarcina, and Methanoculleus genera. Under aerobic conditions within algal tanks, pH rose from 7.17 to 9.32, with a significant decrease in total ammonia nitrogen, chemical oxygen demand, and soluble phosphorus levels. PCR-DGGE proved a useful tool for investigating the dynamics of microbial community in the bio-processing of piggery wastewater. Knowledge of the microbial communities involved in digestion of piggery wastewater will allow optimization of integrated biosystem by removing the main pollutants like inorganic ammonium-nitrogen, phosphorus, and pathogens from intensive farming system.

Reviews Book: The 4% Universe: Dark Matter, Dark Energy and the Race to Discover the Rest of Reality Book: Quantitative Understanding of Biosystems: An Introduction to Biophysics Book: Edison's Electric Light: The Art of Invention Book: The Edge of Physics: Dispatches from the Frontiers of Cosmology Equipment: Voicebox Equipment: Tracker 4 Books: Hands-On Introduction to NI LabVIEW with Vernier, and Engineering Projects with NI LabVIEW and Vernier Places to Visit: Discovery Museum Book: Philosophy of Science: A Very Short Introduction Web Watch

NASA Astrophysics Data System (ADS)

2011-11-01

WE RECOMMEND Quantitative Understanding of Biosystems: An Introduction to Biophysics Text applies physics to biology concepts Edison's Electric Light: The Art of Invention Edison's light still shines brightly The Edge of Physics: Dispatches from the Frontiers of Cosmology Anecdotes explore cosmology Voicebox Voicebox kit discovers the physics and evolution of speech Tracker 4 Free software tracks motion analysis Hands-On Introduction to NI LabVIEW with Vernier, and Engineering Projects with NI LabVIEW and Vernier Books support the LabVIEW software Discovery Museum Newcastle museum offers science enjoyment for all Philosophy of Science: A Very Short Introduction Philosophy opens up science questions WORTH A LOOK The 4% Universe: Dark Matter, Dark Energy and the Race to Discover the Rest of Reality Book researches the universe WEB WATCH Superconductivity websites are popular

Photodegradation of major soil microbial biomolecules is comparable to biodegradation: Insights from infrared and diffusion editing NMR spectroscopies

NASA Astrophysics Data System (ADS)

Spence, Adrian; Kelleher, Brian P.

2016-03-01

As a primary decomposition process in terrestrial biosystems, biodegradation has been extensively studied with regard to its impact on soil organic matter transformation. However, the biotransformation of soil microbial biomass (a primary source of soil organic carbon) remains poorly understood, and even less is known about the fate of microbial-derived carbon under photodegradation. Here, we combine infrared and diffusion editing NMR spectroscopies to provide molecular-level information on the photodegradation of major biochemical components in soil microbial biomass and leachates over time. Results indicate a considerable enrichment in aliphatic components, presumably polymethylenic-C [(C-H2)n] and the simultaneous loss of carbohydrate and protein structures in the biomass. An immediate conclusion is that photodegradation increased the conversion of macromolecular carbohydrates and proteins to smaller components. However, further analysis reveals that macromolecular carbohydrates and proteins may be more resistant to photodegradation than initially thought and are found in the leachates. Although attenuated, there is also evidence to suggest that some aliphatic structures persist in the leachates. Overall, the photodegradation pathway reported here is remarkably similar to that of biodegradation, suggesting that under rapidly expanding anthropogenic land disturbances, photodegradation could be an important driver of the transformation of microbial-derived organic matter in terrestrial biosystems.

Different protein profile in amniotic fluid with nervous system malformations by surface-enhanced laser desorption-ionization/time-of-flight mass spectrometry (SELDI-TOF-MS) technology.

PubMed

Ma, Zhe; Liu, Cun; Deng, Biping; Dong, Shaogang; Tao, Guowei; Zhan, Xinfeng; Wang, Chuner; Liu, Shaoping; Qu, Xun

2010-12-01

To detect the distinct proteins in amniotic fluid (AF) between nervous system malformations fetuses and normal fetuses. Surface-enhanced laser desorption-ionization/time-of-flight mass spectrometry was used to characterize AF peptides in AF between nervous system malformations fetuses and normal fetuses. WCX2 protein chips were used to characterize AF peptides in AF. Protein chips were examined in a PBSIIC protein reader, the protein profiling was collected by ProteinChip software version 3.1 (Ciphergen Biosystems, Fremont, CA, USA) and analyzed by Biomarker Wizard software (Ciphergen Biosystems). Nine distinct proteins were identified in AF between nervous system malformations fetuses and normal fetuses. Compared with the control group, three proteins with m/z 4967.5 Da, 5258.0 Da, and 11,717.0 Da were down-regulated, and six proteins with m/z 2540.4 Da, 3107.1 Da, 3396.8 Da, 4590.965 Da, 5589.2 Da and 6429.4 Da up-regulated in nervous system malformations fetuses. The results suggest that there are distinct proteins in protein profiling of AF between nervous system malformations fetuses and normal fetuses. © 2010 The Authors. Journal of Obstetrics and Gynaecology Research © 2010 Japan Society of Obstetrics and Gynecology.

A mass action model of a Fibroblast Growth Factor signaling pathway and its simplification.

PubMed

Gaffney, E A; Heath, J K; Kwiatkowska, M Z

2008-11-01

We consider a kinetic law of mass action model for Fibroblast Growth Factor (FGF) signaling, focusing on the induction of the RAS-MAP kinase pathway via GRB2 binding. Our biologically simple model suffers a combinatorial explosion in the number of differential equations required to simulate the system. In addition to numerically solving the full model, we show that it can be accurately simplified. This requires combining matched asymptotics, the quasi-steady state hypothesis, and the fact subsets of the equations decouple asymptotically. Both the full and simplified models reproduce the qualitative dynamics observed experimentally and in previous stochastic models. The simplified model also elucidates both the qualitative features of GRB2 binding and the complex relationship between SHP2 levels, the rate SHP2 induces dephosphorylation and levels of bound GRB2. In addition to providing insight into the important and redundant features of FGF signaling, such work further highlights the usefulness of numerous simplification techniques in the study of mass action models of signal transduction, as also illustrated recently by Borisov and co-workers (Borisov et al. in Biophys. J. 89, 951-966, 2005, Biosystems 83, 152-166, 2006; Kiyatkin et al. in J. Biol. Chem. 281, 19925-19938, 2006). These developments will facilitate the construction of tractable models of FGF signaling, incorporating further biological realism, such as spatial effects or realistic binding stoichiometries, despite a more severe combinatorial explosion associated with the latter.

Interfacing Nanoparticles and Biology: New Strategies for Biomedicine

PubMed Central

Tonga, Gulen Yesilbag; Saha, Krishnendu; Rotello, Vincent M.

2014-01-01

The exterior surface of nanoparticles (NPs) dictates the behavior of these systems with the outside world. Understanding the interactions of NP surface functionality with biosystems enables the design and fabrication of effective platforms for therapeutics, diagnostics, and imaging agents. In this review, we highlight the role of chemistry in the engineering of nanomaterials, focusing on the fundamental role played by surface chemistry in controlling the interaction of NPs with proteins and cells. PMID:24105763

Biocompatible Surface Chemistry Manipulation of Gold Nanorods Preserves Optical Properties for Bio-Imaging Applications

DTIC Science & Technology

2015-12-18

3. DATES COVERED (From - To) March 2014 – Sept 2014 4. TITLE AND SUBTITLE Biocompatible surface chemistry manipulation of gold nanorods preserves...Due to their anisotropic shape, gold nanorods (GNRs) possess a number of advantages for biosystem use including, enhanced surface area and tunable...intracellular aggregation of MTAB-TA GNRs, and identify them as prime andidates for use in nanobased bio-imaging applications. 15. SUBJECT TERMS Gold

An in vitro synthetic biosystem based on acetate for production of phloroglucinol.

PubMed

Zhang, Rubing; Liu, Wei; Cao, Yujin; Xu, Xin; Xian, Mo; Liu, Huizhou

2017-08-08

Phloroglucinol is an important chemical, and the biosynthesis processes which can convert glucose to phloroglucinol have been established. However, due to approximate 80% of the glucose being transformed into undesirable by-products and biomass, this biosynthesis process only shows a low yield with the highest value of about 0.20 g/g. The industrial applications are usually hindered by the low current productivity and yield and also by the high costs. Generally, several different aspects limit the development of phloroglucinol biosynthesis. The yield of phloroglucinol is one of the most important parameters for its bioconversion especially from economic and ecological points of view. The in vitro biosynthesis of bio-based chemicals, is a flexible alternative with potentially high-yield to in vivo biosynthetic technology. By comparing the activity of acetyl-CoA synthetase (ACS) from Escherichia coli and Acetobacter pasteurianus, the highly active ACS2 was identified in A. pasteurianus. Acetyl-CoA carboxylase (ACC) from Acinetobacter calcoaceticus and phloroglucinol synthase (PhlD) from Pseudomonas fluorescens pf-5 were expressed and purified. Acetate was successfully transformed into phloroglucinol by the combined activity of above-mentioned enzymes and required cofactor. After optimization of the in vitro reaction system, phloroglucinol was then produced with a yield of nearly 0.64 g phloroglucinol/g acetic acid, which was equal to 91.43% of the theoretically possible maximum. In this work, a novel in vitro synthetic system for a highly efficient production of phloroglucinol from acetate was demonstrated. The system's performance suggests that in vitro synthesis of phloroglucinol has some advantages and is potential to become a feasible industrial alternative. Based on the results presented herewith, it is believed that in vitro biosystem will provide a feasible option for production of important industrial chemicals from acetate, which could work as a versatile biosynthetic platform.

Remote sensing investigations of wetland biomass and productivity for global biosystems research

NASA Technical Reports Server (NTRS)

Klemas, V.

1986-01-01

The relationship between spectral radiance and plant canopy biomass was studied in wetlands. Spectroradiometer data was gathered on Thematic Mapper wavebands 3, 4, and 5, and correlated with canopy and edaphic factors determined by harvesting. The relationship between spectral radiance and plant canopy biomass for major salt and brackish canopy types was determined. Algorithms were developed for biomass measurement in mangrove swamps. The influence of latitudinal variability in canopy structure on biomass assessment of selected plants was investigated. Brackish marsh biomass estimates were obtained from low altitude aircraft and compared with ground measurements. Annual net aerial primary productivity estimates computed from spectral radiance data were compiled for a Spartina alterniflora marsh. Spectral radiance data were expressed as vegetation or infrared index values. Biomass estimates computed from models were in close agreement with biomass estimates determined from harvests.

An Ant Colony Optimization and Hybrid Metaheuristics Algorithm to Solve the Split Delivery Vehicle Routing Problem

DTIC Science & Technology

2015-01-01

programming formulation of traveling salesman problems , Journal of the ACM, 7(4), 326-329. Montemanni, R., Gambardella, L. M., Rizzoli, A.E., Donati. A.V... salesman problem . BioSystem, 43(1), 73-81. Dror, M., Trudeau, P., 1989. Savings by split delivery routing. Transportation Science, 23, 141- 145. Dror, M...An Ant Colony Optimization and Hybrid Metaheuristics Algorithm to solve the Split Delivery Vehicle Routing Problem Authors: Gautham Rajappa

Identification of BRCA1 and 2 Other Tumor Suppressor Genes on Chromosome 17 Through Positional Cloning

DTIC Science & Technology

2000-04-01

Genes, LOH Mapping, Chromosome 17, Physical Mapping, Genetic Mapping, CDNA Screening, Humans, Anatomical 81 Samples, Mutation Detection, Breast Cancer...According to the established model for LOH involving tumor suppressor genes, the allele remaining in the tumor sample would harbor the deleterious mutation ...sequencing on an AB1373A sequencer (Applied Biosystems, Foster City, CA). As none of the samples we have sequenced have revealed any mutations , we have

Review of incursive, hyperincursive and anticipatory systems-foundation of anticipation in electromagnetism

NASA Astrophysics Data System (ADS)

Dubois, Daniel M.

2000-05-01

The main purpose of this paper is to show that anticipation is not only a property of biosystems but is also a fundamental property of physical systems. In electromagnetism, the anticipation is related to the Lorentz transform. In this framework the anticipation is a strong anticipation because it is not based on a prediction from a model of the physical system but is embedded in the fundamental system. So, Robert Rosen's anticipatory systems deal with weak anticipation. Contrary to Robert Rosen's affirmation, anticipation is thus not a characteristic of living systems. Finality is implicitly embedded in any system and thus the final cause of Aristotle is implicitly embedded in any physical and biological systems, contrary to what Robert Rosen argued. This paper will review some incursive and hyperincursive systems giving rise to strong anticipation. Space-time incursive parabolic systems show non-local properties. Hyperincursive crisp systems are related to catastrophe theory. Finally it will be shown that incursive and hyperincursive anticipatory systems could model properties of biosystems like free will, game strategy, theorem creation, etc. Anticipation is not only related to predictions but to decisions: hyperincursive systems create multiple choices and a decision process selects one choice. So, anticipation is not a final goal, like in cybernetics and system science, but is a fundamental property of physical and biological systems.

Molecular toxicity of nanomaterials.

PubMed

Chang, Xue-Ling; Yang, Sheng-Tao; Xing, Gengmei

2014-10-01

With the rapid developments in the fields of nanoscience and nanotechnlogy, more and more nanomaterials and their based consumer products have been used into our daily life. The safety concerns of nanomaterials have been well recognized by the scientific community and the public. Molecular mechanism of interactions between nanomaterials and biosystems is the most essential topic and final core of the biosafety. In the last two decades, nanotoxicology developed very fast and toxicity phenomena of nanomaterials have been reported. To achieve better understanding and detoxication of nanomaterials, thorough studies of nanotoxicity at molecular level are important. The interactions between nanomaterials and biomolecules have been widely investigated as the first step toward the molecular nanotoxicology. The consequences of such interactions have been discussed in the literature. Besides this, the chemical mechanism of nanotoxicology is gaining more attention, which would lead to a better design of nontoxic nanomaterials. In this review, we focus on the molecular nanotoxicology and explore the toxicity of nanomaterials at molecular level. The molecular level studies of nanotoxicology are summarized and the published nanotoxicological data are revisited.

Multiscale simulation of molecular processes in cellular environments.

PubMed

Chiricotto, Mara; Sterpone, Fabio; Derreumaux, Philippe; Melchionna, Simone

2016-11-13

We describe the recent advances in studying biological systems via multiscale simulations. Our scheme is based on a coarse-grained representation of the macromolecules and a mesoscopic description of the solvent. The dual technique handles particles, the aqueous solvent and their mutual exchange of forces resulting in a stable and accurate methodology allowing biosystems of unprecedented size to be simulated.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Author(s).

Pair-barcode high-throughput sequencing for large-scale multiplexed sample analysis

PubMed Central

2012-01-01

Background The multiplexing becomes the major limitation of the next-generation sequencing (NGS) in application to low complexity samples. Physical space segregation allows limited multiplexing, while the existing barcode approach only permits simultaneously analysis of up to several dozen samples. Results Here we introduce pair-barcode sequencing (PBS), an economic and flexible barcoding technique that permits parallel analysis of large-scale multiplexed samples. In two pilot runs using SOLiD sequencer (Applied Biosystems Inc.), 32 independent pair-barcoded miRNA libraries were simultaneously discovered by the combination of 4 unique forward barcodes and 8 unique reverse barcodes. Over 174,000,000 reads were generated and about 64% of them are assigned to both of the barcodes. After mapping all reads to pre-miRNAs in miRBase, different miRNA expression patterns are captured from the two clinical groups. The strong correlation using different barcode pairs and the high consistency of miRNA expression in two independent runs demonstrates that PBS approach is valid. Conclusions By employing PBS approach in NGS, large-scale multiplexed pooled samples could be practically analyzed in parallel so that high-throughput sequencing economically meets the requirements of samples which are low sequencing throughput demand. PMID:22276739

Pair-barcode high-throughput sequencing for large-scale multiplexed sample analysis.

PubMed

Tu, Jing; Ge, Qinyu; Wang, Shengqin; Wang, Lei; Sun, Beili; Yang, Qi; Bai, Yunfei; Lu, Zuhong

2012-01-25

The multiplexing becomes the major limitation of the next-generation sequencing (NGS) in application to low complexity samples. Physical space segregation allows limited multiplexing, while the existing barcode approach only permits simultaneously analysis of up to several dozen samples. Here we introduce pair-barcode sequencing (PBS), an economic and flexible barcoding technique that permits parallel analysis of large-scale multiplexed samples. In two pilot runs using SOLiD sequencer (Applied Biosystems Inc.), 32 independent pair-barcoded miRNA libraries were simultaneously discovered by the combination of 4 unique forward barcodes and 8 unique reverse barcodes. Over 174,000,000 reads were generated and about 64% of them are assigned to both of the barcodes. After mapping all reads to pre-miRNAs in miRBase, different miRNA expression patterns are captured from the two clinical groups. The strong correlation using different barcode pairs and the high consistency of miRNA expression in two independent runs demonstrates that PBS approach is valid. By employing PBS approach in NGS, large-scale multiplexed pooled samples could be practically analyzed in parallel so that high-throughput sequencing economically meets the requirements of samples which are low sequencing throughput demand.

Electrochemical aptamer-based nanosensor fabricated on single Au nanowire electrodes for adenosine triphosphate assay.

PubMed

Wang, Dongmei; Xiao, Xiaoqing; Xu, Shen; Liu, Yong; Li, Yongxin

2018-01-15

In this work, single Au nanowire electrodes (AuNWEs) were fabricated by laser-assisted pulling/hydrofluoric acid (HF) etching process, which then were characterized by transmission electron microscopy (TEM), electrochemical method and finite-element simulation. The as-prepared single AuNWEs were used to construct electrochemical aptamer-based nanosensors (E-AB nanosensors) based on the formation of Au-S bond that duplex DNA tagged with methylene blue (MB) was modified on the surface of electrode. In the presence of adenosine triphosphate (ATP), the MB-labeled aptamer dissociated from the duplex DNA due to the strong specific affinity between aptamer and target, which lead to the reduction of MB electrochemical signals. Moreover, BSA was employed to further passivate electrode surface bonding sites for the stable of the sensor. The as-prepared E-AB nanosensor has been used for ATP assay with excellent sensitivity and selectivity, even in a complex system like cerebrospinal fluid of rat brain. Considering the unique properties of good stability, larger surface area and smaller overall dimensions, this E-AB nanosensor should be an ideal platform for widely sensing applications in living bio-system. Copyright © 2017 Elsevier B.V. All rights reserved.

Design of metal cofactors activated by a protein–protein electron transfer system

PubMed Central

Ueno, Takafumi; Yokoi, Norihiko; Unno, Masaki; Matsui, Toshitaka; Tokita, Yuichi; Yamada, Masako; Ikeda-Saito, Masao; Nakajima, Hiroshi; Watanabe, Yoshihito

2006-01-01

Protein-to-protein electron transfer (ET) is a critical process in biological chemistry for which fundamental understanding is expected to provide a wealth of applications in biotechnology. Investigations of protein–protein ET systems in reductive activation of artificial cofactors introduced into proteins remains particularly challenging because of the complexity of interactions between the cofactor and the system contributing to ET. In this work, we construct an artificial protein–protein ET system, using heme oxygenase (HO), which is known to catalyze the conversion of heme to biliverdin. HO uses electrons provided from NADPH/cytochrome P450 reductase (CPR) through protein–protein complex formation during the enzymatic reaction. We report that a FeIII(Schiff-base), in the place of the active-site heme prosthetic group of HO, can be reduced by NADPH/CPR. The crystal structure of the Fe(10-CH2CH2COOH-Schiff-base)·HO composite indicates the presence of a hydrogen bond between the propionic acid carboxyl group and Arg-177 of HO. Furthermore, the ET rate from NADPH/CPR to the composite is 3.5-fold faster than that of Fe(Schiff-base)·HO, although the redox potential of Fe(10-CH2CH2COOH-Schiff-base)·HO (−79 mV vs. NHE) is lower than that of Fe(Schiff-base)·HO (+15 mV vs. NHE), where NHE is normal hydrogen electrode. This work describes a synthetic metal complex activated by means of a protein–protein ET system, which has not previously been reported. Moreover, the result suggests the importance of the hydrogen bond for the ET reaction of HO. Our Fe(Schiff-base)·HO composite model system may provide insights with regard to design of ET biosystems for sensors, catalysts, and electronics devices. PMID:16769893

Molecular Dynamics Simulations, Challenges and Opportunities: A Biologist's Prospective.

PubMed

Kumari, Indu; Sandhu, Padmani; Ahmed, Mushtaq; Akhter, Yusuf

2017-08-30

Molecular dynamics (MD) is a computational technique which is used to study biomolecules in virtual environment. Each of the constituent atoms represents a particle and hence the biomolecule embodies a multi-particle mechanical system analyzed within a simulation box during MD analysis. The potential energies of the atoms are explained by a mathematical expression consisting of different forces and space parameters. There are various software and force fields that have been developed for MD studies of the biomolecules. MD analysis has unravelled the various biological mechanisms (protein folding/unfolding, protein-small molecule interactions, protein-protein interactions, DNA/RNA-protein interactions, proteins embedded in membrane, lipid-lipid interactions, drug transport etc.) operating at the atomic and molecular levels. However, there are still some parameters including torsions in amino acids, carbohydrates (whose structure is extended and not well defined like that of proteins) and single stranded nucleic acids for which the force fields need further improvement, although there are several workers putting in constant efforts in these directions. The existing force fields are not efficient for studying the crowded environment inside the cells, since these interactions involve multiple factors in real time. Therefore, the improved force fields may provide the opportunities for their wider applications on the complex biosystems in diverse cellular conditions. In conclusion, the intervention of MD in the basic sciences involving interdisciplinary approaches will be helpful for understanding many fundamental biological and physiological processes at the molecular levels that may be further applied in various fields including biotechnology, fisheries, sustainable agriculture and biomedical research. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Expression of candidate genes associated with obesity in peripheral white blood cells of Mexican children

PubMed Central

Ulloa-Martínez, Marcela; Burguete-García, Ana I.; Murugesan, Selvasankar; Hoyo-Vadillo, Carlos; Cruz-Lopez, Miguel

2016-01-01

Introduction Obesity is a chronic, complex, and multifactorial disease, characterized by excess body fat. Diverse studies of the human genome have led to the identification of susceptibility genes that contribute to obesity. However, relatively few studies have addressed specifically the association between the level of expression of these genes and obesity. Material and methods We studied 160 healthy and obese unrelated Mexican children aged 6 to 14 years. We measured the transcriptional expression of 20 genes associated with obesity, in addition to the biochemical parameters, in peripheral white blood cells. The detection of mRNA levels was performed using the OpenArray Real-Time PCR System (Applied Biosystems). Results Obese children exhibited higher values of fasting glucose (p = 0.034), fasting insulin (p = 0.004), low-density lipoprotein (p = 0.006), triglycerides (p < 0.001), systolic blood pressure and diastolic blood pressure (p < 0.001), and lower values of high-density lipoprotein (p < 0.001) compared to lean children. Analysis of transcriptional expression data showed a difference for ADRB1 (p = 0.0297), ADIPOR1 (p = 0.0317), GHRL (p = 0.0060) and FTO (p = 0.0348) genes. Conclusions Our results suggest that changes in the expression level of the studied genes are involved in biological processes implicated in the development of childhood obesity. Our study contributes new perspectives for a better understanding of biological processes involved in obesity. The protocol was approved by the National Committee and Ethical Committee Board from the Mexican Social Security Institute (IMSS) (IMSS FIS/IMSS/PRIO/10/011). PMID:27695486

Plant response to gravity: towards a biosystems view of root gravitropism

NASA Astrophysics Data System (ADS)

Palme, Klaus; Volkmann, Dieter; Bennett, Malcolm J.; Gausepohl, Heinrich

2005-10-01

Plants are sessile organisms that originated and evolved in Earth's environment. They monitor a wide range of disparate external and internal signals and compute appropriate developmental responses. How do plant cells process these myriad signals into an appropriate response? How do they integrate these signals to reach a finely balanced decision on how to grow, how to determine the direction of growth and how to develop their organs to exploit the environment? As plant responses are generally irreversible growth responses, their signalling systems must compute each developmental decision with extreme care. One stimulus to which plants are continuously exposed is the gravity vector. Gravity affects adaptive growth responses that reorient organs towards light and nutrient resources. The MAP team was established by ESA to study in the model plant Arabidopsis thaliana the role of the hormone auxin in gravity-mediated growth control. Another goal was to dissect gravity perception and gravity signal transduction pathways.

Bio-activity of aminosulfonyl ureas in the light of nucleic acid bases and DNA base pair interaction.

PubMed

Mondal Roy, Sutapa

2018-08-01

The quantum chemical descriptors based on density functional theory (DFT) are applied to predict the biological activity (log IC 50 ) of one class of acyl-CoA: cholesterol O-acyltransferase (ACAT) inhibitors, viz. aminosulfonyl ureas. ACAT are very effective agents for reduction of triglyceride and cholesterol levels in human body. Successful two parameter quantitative structure-activity relationship (QSAR) models are developed with a combination of relevant global and local DFT based descriptors for prediction of biological activity of aminosulfonyl ureas. The global descriptors, electron affinity of the ACAT inhibitors (EA) and/or charge transfer (ΔN) between inhibitors and model biosystems (NA bases and DNA base pairs) along with the local group atomic charge on sulfonyl moiety (∑Q Sul ) of the inhibitors reveals more than 90% efficacy of the selected descriptors for predicting the experimental log (IC 50 ) values. Copyright © 2018 Elsevier Ltd. All rights reserved.

Application of structural health monitoring technologies to bio-systems: current status and path forward

NASA Astrophysics Data System (ADS)

Bhalla, Suresh; Srivastava, Shashank; Suresh, Rupali; Moharana, Sumedha; Kaur, Naveet; Gupta, Ashok

2015-03-01

This paper presents a case for extension of structural health monitoring (SHM) technologies to offer solutions for biomedical problems. SHM research has made remarkable progress during the last two/ three decades. These technologies are now being extended for possible applications in the bio-medical field. Especially, smart materials, such as piezoelectric ceramic (PZT) patches and fibre-Bragg grating (FBG) sensors, offer a new set of possibilities to the bio-medical community to augment their conventional set of sensors, tools and equipment. The paper presents some of the recent extensions of SHM, such as condition monitoring of bones, monitoring of dental implant post surgery and foot pressure measurement. Latest developments, such as non-bonded configuration of PZT patches for monitoring bones and possible applications in osteoporosis detection, are also discussed. In essence, there is a whole new gamut of new possibilities for SHM technologies making their foray into the bi-medical sector.

Thiazole derivative-modified upconversion nanoparticles for Hg2+ detection in living cells

NASA Astrophysics Data System (ADS)

Gu, Bin; Zhou, Yi; Zhang, Xiao; Liu, Xiaowang; Zhang, Yuhai; Marks, Robert; Zhang, Hua; Liu, Xiaogang; Zhang, Qichun

2015-12-01

Mercury ion (Hg2+) is an extremely toxic ion, which will accumulate in human bodies and cause severe nervous system damage. Therefore, the sensitive and efficient monitoring of Hg2+ in human bodies is of great importance. Upconversion nanoparticle (UCNPs) based nano probes exhibit no autofluorescence, deep penetration depth and chemical stability in biological samples, as well as a large anti-stokes shift. In this study, we have developed thiazole-derivative-functionalized UCNPs, and employed an upconversion emission intensity ratio of 540 nm to 803 nm (I540/I803) as a ratiometric signal to detect Hg2+ in living cells showing excellent photo stability and high selectivity. Our nano probe was characterized using transmission electron microscopy (TEM) and powder X-ray diffraction (PXRD). The low cytotoxicity of our probe was confirmed by an MTT assay and the UCL test in HeLa cells was carried out by confocal microscopy. Our results demonstrated that organic-dye-functionalized UCNPs should be a good strategy for detecting toxic metal ions when studying cellular biosystems.Mercury ion (Hg2+) is an extremely toxic ion, which will accumulate in human bodies and cause severe nervous system damage. Therefore, the sensitive and efficient monitoring of Hg2+ in human bodies is of great importance. Upconversion nanoparticle (UCNPs) based nano probes exhibit no autofluorescence, deep penetration depth and chemical stability in biological samples, as well as a large anti-stokes shift. In this study, we have developed thiazole-derivative-functionalized UCNPs, and employed an upconversion emission intensity ratio of 540 nm to 803 nm (I540/I803) as a ratiometric signal to detect Hg2+ in living cells showing excellent photo stability and high selectivity. Our nano probe was characterized using transmission electron microscopy (TEM) and powder X-ray diffraction (PXRD). The low cytotoxicity of our probe was confirmed by an MTT assay and the UCL test in HeLa cells was carried out by confocal microscopy. Our results demonstrated that organic-dye-functionalized UCNPs should be a good strategy for detecting toxic metal ions when studying cellular biosystems. Electronic supplementary information (ESI) available: NMR, MALDI-TOF MS spectra, etc. See DOI: 10.1039/c5nr05286f

High-speed event detector for embedded nanopore bio-systems.

PubMed

Huang, Yiyun; Magierowski, Sebastian; Ghafar-Zadeh, Ebrahim; Wang, Chengjie

2015-08-01

Biological measurements of microscopic phenomena often deal with discrete-event signals. The ability to automatically carry out such measurements at high-speed in a miniature embedded system is desirable but compromised by high-frequency noise along with practical constraints on filter quality and sampler resolution. This paper presents a real-time event-detection method in the context of nanopore sensing that helps to mitigate these drawbacks and allows accurate signal processing in an embedded system. Simulations show at least a 10× improvement over existing on-line detection methods.

A comprehensive Y-STR portrait of Yousafzai's population.

PubMed

Tabassum, Sadia; Ilyas, Muhammad; Ullah, Inam; Israr, Muhammad; Ahmad, Habib

2017-09-01

In the current study, 17 Y-Chromosomal short tandem repeats (Y-STRs) included in theAmpFlSTR Y-Filer amplification kit (Applied Biosystems, Foster City, USA) were investigated in 146 unrelated Yousafzai males residing in the Khyber Pakhtunkhwa Province of Pakistan. A total of 94 (89.52%) unique haplotypes were observed. Discrimination capacity was 71.92%. Haplotype diversity ranged from 0.354 (DYS456) to 0.663 (DYS458). Both Rst pairwise analysis and multidimensional scaling plot showed that the genetic structure of the Yousafzais is significantly different from neighbouring populations.

Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs.

PubMed

Quesne, Matthew G; Borowski, Tomasz; de Visser, Sam P

2016-02-18

Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black-box method that is easily applied, but requires careful set-up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work-protocols developed in our groups for running successful QM/MM calculations. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A DNA-based pattern classifier with in vitro learning and associative recall for genomic characterization and biosensing without explicit sequence knowledge.

PubMed

Lee, Ju Seok; Chen, Junghuei; Deaton, Russell; Kim, Jin-Woo

2014-01-01

Genetic material extracted from in situ microbial communities has high promise as an indicator of biological system status. However, the challenge is to access genomic information from all organisms at the population or community scale to monitor the biosystem's state. Hence, there is a need for a better diagnostic tool that provides a holistic view of a biosystem's genomic status. Here, we introduce an in vitro methodology for genomic pattern classification of biological samples that taps large amounts of genetic information from all genes present and uses that information to detect changes in genomic patterns and classify them. We developed a biosensing protocol, termed Biological Memory, that has in vitro computational capabilities to "learn" and "store" genomic sequence information directly from genomic samples without knowledge of their explicit sequences, and that discovers differences in vitro between previously unknown inputs and learned memory molecules. The Memory protocol was designed and optimized based upon (1) common in vitro recombinant DNA operations using 20-base random probes, including polymerization, nuclease digestion, and magnetic bead separation, to capture a snapshot of the genomic state of a biological sample as a DNA memory and (2) the thermal stability of DNA duplexes between new input and the memory to detect similarities and differences. For efficient read out, a microarray was used as an output method. When the microarray-based Memory protocol was implemented to test its capability and sensitivity using genomic DNA from two model bacterial strains, i.e., Escherichia coli K12 and Bacillus subtilis, results indicate that the Memory protocol can "learn" input DNA, "recall" similar DNA, differentiate between dissimilar DNA, and detect relatively small concentration differences in samples. This study demonstrated not only the in vitro information processing capabilities of DNA, but also its promise as a genomic pattern classifier that could access information from all organisms in a biological system without explicit genomic information. The Memory protocol has high potential for many applications, including in situ biomonitoring of ecosystems, screening for diseases, biosensing of pathological features in water and food supplies, and non-biological information processing of memory devices, among many.

Microfluidic Approaches to Synchrotron Radiation-Based Fourier Transform Infrared (SR-FTIR) Spectral Microscopy of Living Biosystems

PubMed Central

Loutherback, Kevin; Birarda, Giovanni; Chen, Liang; Holman, Hoi-Ying N.

2016-01-01

A long-standing desire in biological and biomedical sciences is to be able to probe cellular chemistry as biological processes are happening inside living cells. Synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectral microscopy is a label-free and nondestructive analytical technique that can provide spatiotemporal distributions and relative abundances of biomolecules of a specimen by their characteristic vibrational modes. Despite great progress in recent years, SR-FTIR imaging of living biological systems remains challenging because of the demanding requirements on environmental control and strong infrared absorption of water. To meet this challenge, microfluidic devices have emerged as a method to control the water thickness while providing a hospitable environment to measure cellular processes and responses over many hours or days. This paper will provide an overview of microfluidic device development for SR-FTIR imaging of living biological systems, provide contrast between the various techniques including closed and open-channel designs, and discuss future directions of development within this area. Even as the fundamental science and technological demonstrations develop, other ongoing issues must be addressed; for example, choosing applications whose experimental requirements closely match device capabilities, and developing strategies to efficiently complete the cycle of development. These will require imagination, ingenuity and collaboration. PMID:26732243

Microfluidic approaches to synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectral microscopy of living biosystems

DOE PAGES

Loutherback, Kevin; Birarda, Giovanni; Chen, Liang; ...

2016-02-15

A long-standing desire in biological and biomedical sciences is to be able to probe cellular chemistry as biological processes are happening inside living cells. Synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectral microscopy is a label-free and nondestructive analytical technique that can provide spatiotemporal distributions and relative abundances of biomolecules of a specimen by their characteristic vibrational modes. Despite great progress in recent years, SR-FTIR imaging of living biological systems remains challenging because of the demanding requirements on environmental control and strong infrared absorption of water. To meet this challenge, microfluidic devices have emerged as a method to control the watermore » thickness while providing a hospitable environment to measure cellular processes and responses over many hours or days. This paper will provide an overview of microfluidic device development for SR-FTIR imaging of living biological systems, provide contrast between the various techniques including closed and open-channel designs, and discuss future directions of development within this area. Even as the fundamental science and technological demonstrations develop, other ongoing issues must be addressed; for example, choosing applications whose experimental requirements closely match device capabilities, and developing strategies to efficiently complete the cycle of development. These will require imagination, ingenuity and collaboration.« less

Microfluidic approaches to synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectral microscopy of living biosystems

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

Loutherback, Kevin; Birarda, Giovanni; Chen, Liang

A long-standing desire in biological and biomedical sciences is to be able to probe cellular chemistry as biological processes are happening inside living cells. Synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectral microscopy is a label-free and nondestructive analytical technique that can provide spatiotemporal distributions and relative abundances of biomolecules of a specimen by their characteristic vibrational modes. Despite great progress in recent years, SR-FTIR imaging of living biological systems remains challenging because of the demanding requirements on environmental control and strong infrared absorption of water. To meet this challenge, microfluidic devices have emerged as a method to control the watermore » thickness while providing a hospitable environment to measure cellular processes and responses over many hours or days. This paper will provide an overview of microfluidic device development for SR-FTIR imaging of living biological systems, provide contrast between the various techniques including closed and open-channel designs, and discuss future directions of development within this area. Even as the fundamental science and technological demonstrations develop, other ongoing issues must be addressed; for example, choosing applications whose experimental requirements closely match device capabilities, and developing strategies to efficiently complete the cycle of development. These will require imagination, ingenuity and collaboration.« less

Effects of Cerium Oxide Nanoparticles on Sorghum Plant Traits

NASA Astrophysics Data System (ADS)

Mu, L.; Chen, Y.; Darnault, C. J. G.; Rauh, B.; Kresovich, S.; Korte, C.

2015-12-01

Nanotechnology and nanomaterials are considered as the development of the modern science. However, besides with that wide application, nanoparticles arouse to the side effects on the environment and human health. As the catalyst of ceramics and fuel industry, Cerium (IV) oxide nanoparticles (CeO2 NPs) can be found in the environment following their use and life-cycle. Therefore, it is critical to assess the potential effects that CeO2 NPs found in soils may have on plants. In this study, CeO2 NPs were analyzed for the potential influence on the sorghum [Sorghum bicolor (L.) Moench] (Reg. no. 126) (PI 154844) growth and traits. The objectives of this research were to determine whether CeO2 NPs impact the sorghum germination and growth characteristics. The sorghum was grown in the greenhouse located at Biosystems Research Complex, Clemson University under different CeO2 NPs treatments (0mg; 100mg; 500mg; 1000mg CeO2 NPs/Kg soil) and harvested around each month. At the end of the each growing period, above ground vegetative tissue was air-dried, ground to 2mm particle size and compositional traits estimated using near-infrared spectroscopy. Also, the NPK value of the sorghum tissue was tested by Clemson Agriculture Center. After the first harvest, the result showed that the height of above ground biomass under the nanoparticles stress was higher than that of control group. This difference between the control and the nanoparticles treatments was significant (F>F0.05; LSD). Our results also indicated that some of the compositional traits were impacted by the different treatments, including the presence and/or concentrations of the nanoparticles.

ConvAn: a convergence analyzing tool for optimization of biochemical networks.

PubMed

Kostromins, Andrejs; Mozga, Ivars; Stalidzans, Egils

2012-01-01

Dynamic models of biochemical networks usually are described as a system of nonlinear differential equations. In case of optimization of models for purpose of parameter estimation or design of new properties mainly numerical methods are used. That causes problems of optimization predictability as most of numerical optimization methods have stochastic properties and the convergence of the objective function to the global optimum is hardly predictable. Determination of suitable optimization method and necessary duration of optimization becomes critical in case of evaluation of high number of combinations of adjustable parameters or in case of large dynamic models. This task is complex due to variety of optimization methods, software tools and nonlinearity features of models in different parameter spaces. A software tool ConvAn is developed to analyze statistical properties of convergence dynamics for optimization runs with particular optimization method, model, software tool, set of optimization method parameters and number of adjustable parameters of the model. The convergence curves can be normalized automatically to enable comparison of different methods and models in the same scale. By the help of the biochemistry adapted graphical user interface of ConvAn it is possible to compare different optimization methods in terms of ability to find the global optima or values close to that as well as the necessary computational time to reach them. It is possible to estimate the optimization performance for different number of adjustable parameters. The functionality of ConvAn enables statistical assessment of necessary optimization time depending on the necessary optimization accuracy. Optimization methods, which are not suitable for a particular optimization task, can be rejected if they have poor repeatability or convergence properties. The software ConvAn is freely available on www.biosystems.lv/convan. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Extracting Diffusion Constants from Echo-Time-Dependent PFG NMR Data Using Relaxation-Time Information

NASA Astrophysics Data System (ADS)

Vandusschoten, D.; Dejager, P. A.; Vanas, H.

Heterogeneous (bio)systems are often characterized by several water-containing compartments that differ in relaxation time values and diffusion constants. Because of the relatively small differences among these diffusion constants, nonoptimal measuring conditions easily lead to the conclusion that a single diffusion constant suffices to describe the water mobility in a heterogeneous (bio)system. This paper demonstrates that the combination of a T2 measurement and diffusion measurements at various echo times (TE), based on the PFG MSE sequence, enables the accurate determination of diffusion constants which are less than a factor of 2 apart. This new method gives errors of the diffusion constant below 10% when two fractions are present, while the standard approach of a biexponential fit to the diffusion data in identical circumstances gives larger (>25%) errors. On application of this approach to water in apple parenchyma tissue, the diffusion constant of water in the vacuole of the cells ( D = 1.7 × 10 -9 m 2/s) can be distinguished from that of the cytoplasm ( D = 1.0 × 10 -9 m 2/s). Also, for mung bean seedlings, the cell size determined by PFG MSE measurements increased from 65 to 100 μm when the echo time increased from 150 to 900 ms, demonstrating that the interpretation of PFG SE data used to investigate cell sizes is strongly dependent on the T2 values of the fractions within the sample. Because relaxation times are used to discriminate the diffusion constants, we propose to name this approach diffusion analysis by relaxation- time- separated (DARTS) PFG NMR.

Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry.

PubMed

Maclean, Brendan; Tomazela, Daniela M; Abbatiello, Susan E; Zhang, Shucha; Whiteaker, Jeffrey R; Paulovich, Amanda G; Carr, Steven A; Maccoss, Michael J

2010-12-15

Proteomics experiments based on Selected Reaction Monitoring (SRM, also referred to as Multiple Reaction Monitoring or MRM) are being used to target large numbers of protein candidates in complex mixtures. At present, instrument parameters are often optimized for each peptide, a time and resource intensive process. Large SRM experiments are greatly facilitated by having the ability to predict MS instrument parameters that work well with the broad diversity of peptides they target. For this reason, we investigated the impact of using simple linear equations to predict the collision energy (CE) on peptide signal intensity and compared it with the empirical optimization of the CE for each peptide and transition individually. Using optimized linear equations, the difference between predicted and empirically derived CE values was found to be an average gain of only 7.8% of total peak area. We also found that existing commonly used linear equations fall short of their potential, and should be recalculated for each charge state and when introducing new instrument platforms. We provide a fully automated pipeline for calculating these equations and individually optimizing CE of each transition on SRM instruments from Agilent, Applied Biosystems, Thermo-Scientific and Waters in the open source Skyline software tool ( http://proteome.gs.washington.edu/software/skyline ).

Data series embedding and scale invariant statistics.

PubMed

Michieli, I; Medved, B; Ristov, S

2010-06-01

Data sequences acquired from bio-systems such as human gait data, heart rate interbeat data, or DNA sequences exhibit complex dynamics that is frequently described by a long-memory or power-law decay of autocorrelation function. One way of characterizing that dynamics is through scale invariant statistics or "fractal-like" behavior. For quantifying scale invariant parameters of physiological signals several methods have been proposed. Among them the most common are detrended fluctuation analysis, sample mean variance analyses, power spectral density analysis, R/S analysis, and recently in the realm of the multifractal approach, wavelet analysis. In this paper it is demonstrated that embedding the time series data in the high-dimensional pseudo-phase space reveals scale invariant statistics in the simple fashion. The procedure is applied on different stride interval data sets from human gait measurements time series (Physio-Bank data library). Results show that introduced mapping adequately separates long-memory from random behavior. Smaller gait data sets were analyzed and scale-free trends for limited scale intervals were successfully detected. The method was verified on artificially produced time series with known scaling behavior and with the varying content of noise. The possibility for the method to falsely detect long-range dependence in the artificially generated short range dependence series was investigated. (c) 2009 Elsevier B.V. All rights reserved.

Resolving the Origins of Crystalline Anharmonicity Using Terahertz Time-Domain Spectroscopy and ab Initio Simulations.

PubMed

Ruggiero, Michael T; Zeitler, J Axel

2016-11-17

Anharmonicity has been shown to be an important piece of the fundamental framework that dictates numerous observable phenomena. In particular, anharmonicity is the driving force of vibrational relaxation processes, mechanisms that are integral to the proper function of numerous chemical processes. However, elucidating its origins has proven difficult due to experimental and theoretical challenges, specifically related to separating the anharmonic contributions from other unrelated effects. While no one technique is particularly suited for providing a complete picture of anharmonicity, by combining multiple complementary methods such a characterization can be made. In this study the role of individual atomic interactions on the anharmonic properties of crystalline purine, the building block of many DNA and RNA nucleobases, is studied by experimental terahertz time-domain spectroscopy and first-principles density functional theory (DFT) and ab initio molecular dynamics simulations (AIMD). In particular, the detailed vibrational information provided by the DFT calculations is used to interpret the atomic origins of anharmonic-related effects as determined by the AIMD calculations, which are in good agreement with the experimental data. The results highlight that anharmonicity is especially pronounced in the intermolecular interactions, particularly along the amine hydrogen bond coordinate, and yields valuable insight into what is similarly observed complex biosystems and crystalline solids.

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields.

PubMed

Lagardère, Louis; Jolly, Luc-Henri; Lipparini, Filippo; Aviat, Félix; Stamm, Benjamin; Jing, Zhifeng F; Harger, Matthew; Torabifard, Hedieh; Cisneros, G Andrés; Schnieders, Michael J; Gresh, Nohad; Maday, Yvon; Ren, Pengyu Y; Ponder, Jay W; Piquemal, Jean-Philip

2018-01-28

We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over a single-core computation is observed for the largest systems. The extension of the present CPU implementation of Tinker-HP to other computational platforms is discussed.

The recombination landscape around forensic STRs: Accurate measurement of genetic distances between syntenic STR pairs using HapMap high density SNP data.

PubMed

Phillips, C; Ballard, D; Gill, P; Court, D Syndercombe; Carracedo, A; Lareu, M V

2012-05-01

Family studies can be used to measure the genetic distance between same-chromosome (syntenic) STRs in order to detect physical linkage or linkage disequilibrium. However, family studies are expensive and time consuming, in many cases uninformative, and lack a reliable means to infer the phase of the diplotypes obtained. HapMap provides a more comprehensive and fine-scale estimation of recombination rates using high density multi-point SNP data (average inter-SNP distance: 900 nucleotides). Data at this fine scale detects sub-kilobase genetic distances across the whole recombining human genome. We have used the most recent HapMap SNP data release 22 to measure and compare genetic distances, and by inference fine-scale recombination rates, between 29 syntenic STR pairs identified from 39 validated STRs currently available for forensic use. The 39 STRs comprise 23 core loci: SE33, Penta D & E, 13 CODIS and 7 non-CODIS European Standard Set STRs, plus supplementary STRs in the recently released Promega CS-7™ and Qiagen Investigator HDplex™ kits. Also included were D9S1120, a marker we developed for forensic use unique to chromosome 9, and the novel D6S1043 component STR of SinoFiler™ (Applied Biosystems). The data collated provides reliable estimates of recombination rates between each STR pair, that can then be placed into haplotype frequency calculators for short pedigrees with multiple meiotic inputs and which just requires the addition of allele frequencies. This allows all current STR sets or their combinations to be used in supplemented paternity analyses without the need for further adjustment for physical linkage. The detailed analysis of recombination rates made for autosomal forensic STRs was extended to the more than 50 X chromosome STRs established or in development for complex kinship analyses. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

A lectin HPLC method to enrich selectively-glycosylated peptides from complex biological samples.

PubMed

Johansen, Eric; Schilling, Birgit; Lerch, Michael; Niles, Richard K; Liu, Haichuan; Li, Bensheng; Allen, Simon; Hall, Steven C; Witkowska, H Ewa; Regnier, Fred E; Gibson, Bradford W; Fisher, Susan J; Drake, Penelope M

2009-10-01

Glycans are an important class of post-translational modifications. Typically found on secreted and extracellular molecules, glycan structures signal the internal status of the cell. Glycans on tumor cells tend to have abundant sialic acid and fucose moieties. We propose that these cancer-associated glycan variants be exploited for biomarker development aimed at diagnosing early-stage disease. Accordingly, we developed a mass spectrometry-based workflow that incorporates chromatography on affinity matrices formed from lectins, proteins that bind specific glycan structures. The lectins Sambucus nigra (SNA) and Aleuria aurantia (AAL), which bind sialic acid and fucose, respectively, were covalently coupled to POROS beads (Applied Biosystems) and packed into PEEK columns for high pressure liquid chromatography (HPLC). Briefly, plasma was depleted of the fourteen most abundant proteins using a multiple affinity removal system (MARS-14; Agilent). Depleted plasma was trypsin-digested and separated into flow-through and bound fractions by SNA or AAL HPLC. The fractions were treated with PNGaseF to remove N-linked glycans, and analyzed by LC-MS/MS on a QStar Elite. Data were analyzed using Mascot software. The experimental design included positive controls-fucosylated and sialylated human lactoferrin glycopeptides-and negative controls-high mannose glycopeptides from Saccharomyces cerevisiae-that were used to monitor the specificity of lectin capture. Key features of this workflow include the reproducibility derived from the HPLC format, the positive identification of the captured and PNGaseF-treated glycopeptides from their deamidated Asn-Xxx-Ser/Thr motifs, and quality assessment using glycoprotein standards. Protocol optimization also included determining the appropriate ratio of starting material to column capacity, identifying the most efficient capture and elution buffers, and monitoring the PNGaseF-treatment to ensure full deglycosylation. Future directions include using this workflow to perform mass spectrometry-based discovery experiments on plasma from breast cancer patients and control individuals.

Analysis of amadori-glycated phosphatidylethanolamine in the plasma of healthy subjects and diabetic patients by liquid chromatography-tandem mass spectrometry.

PubMed

Miyazawa, Teruo; Ibusuki, Daigo; Yamashita, Shinji; Nakagawa, Kiyotaka

2008-04-01

Peroxidized phospholipid-mediated cytotoxity, the abnormal increase in the levels of phosphatidylcholine hydroperoxide (PCOOH) found in the plasma of type 2 diabetic patients, is involved in the pathophysiology of many diseases. PCOOH accumulation may be related to Amadori-glycated phosphatidylethanolamine (deoxy-D-fructosyl PE, or Amadori-PE) because Amadori-PE causes oxidative stress. However, the occurrence of lipid glycation products, including Amadori-PE, in vivo remains unclear. We developed a method to analyze Amadori-PE by using quadrupole/linear ion-trap mass spectrometry, the Applied Biosystems 4000 Q TRAP. We found that pyridoxals could easily be condensed with PE before the glucose-PE reaction occurred. The PE-pyridoxal 5'-phosphate adduct was detectable in human red blood cells, and the increased plasma Amadori-PE concentration in streptozotocin-induced diabetic rats was decreased by dietary supplementation with pyridoxal 5'-phosphate. Therefore, it is likely that pyridoxal 5'-phosphate acts as a lipid glycation inhibitor in vivo, and this may contribute to diabetes prevention.

The Chemo-Biological Outreach of Nano-Biomaterials: Implications for Tissue Engineering and Regenerative Medicine.

PubMed

Kumar, Pradeep; Choonara, Yahya E; Khan, Riaz A; Pillay, Viness

2017-01-01

Nanobiomaterials can be defined as materials interacting with and influencing the biological microenvironment at a nanointerface. Recently the basic as well as applied research related to nanobiomaterials - a conjugation of nano-, material- and life-sciences - has immensely evolved for therapeutics and related biotechnology areas. The current overview focused on the potential of nanobiomaterial-based substrates towards the generation of biocompatible surfaces, tissue engineering architectures, and regenerative medicine. Emphasis was given to chemomolecular functionalization of nanobiomaterials, nanobiomaterial composites, and morphomechanically modified nanoarchetypes and their inherent chemo-biological interaction with the biological microenvironment. Additionally, recent developments in nanobiomaterial substrate design and structure, chemo-biological interface related bio-systems uses and further evolving applications in health care, therapeutics and nanomedicine were discussed herein. Furthermore, a special emphasis was placed on the nano-chemo-biological interactions inherent to various nanobiomaterial substrates in close vicinity with biological systems. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Characterization of ZnO nanoparticles grown in presence of Folic acid template

PubMed Central

2012-01-01

Background ZnO nanoparticles (grown in the template of folic acid) are biologically useful, luminescent material. It can be used for multifunctional purposes, e.g., as biosensor, bioimaging, targeted drug delivery and as growth promoting medicine. Methods Sol–gel chemical method was used to develop the uniform ZnO nanoparticles, in a folic acid template at room temperature and pH ~ 7.5. Agglomeration of the particles was prevented due to surface charge density of folic acid in the medium. ZnO nanoparticle was further characterized by different physical methods. Results Nanocrystalline, wurtzite ZnO particles thus prepared show interesting structural as well as band gap properties due to capping with folic acid. Conclusions A rapid, easy and chemical preparative method for the growth of ZnO nanoparticles with important surface physical properties is discussed. Emphatically, after capping with folic acid, its photoluminescence properties are in the visible region. Therefore, the same can be used for monitoring local environmental properties of biosystems. PMID:22788841

A hybrid continuous-wave terahertz imaging system

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

Dolganova, Irina N., E-mail: in.dolganova@gmail.com; Zaytsev, Kirill I., E-mail: kirzay@gmail.ru; Metelkina, Anna A.

2015-11-15

A hybrid (active-passive mode) terahertz (THz) imaging system and an algorithm for imaging synthesis are proposed to enhance the THz image quality. The concept of image contrast is used to compare active and passive THz imaging. Combining the measurement of the self-emitted radiation of the object with the back-scattered source radiation measurement, it becomes possible to use the THz image to retrieve maximum information about the object. The experimental results confirm the advantages of hybrid THz imaging systems, which can be generalized for a wide range of applications in the material sciences, chemical physics, bio-systems, etc.

Thermomicrocapillaries as temperature biosensors in single cells

NASA Astrophysics Data System (ADS)

Herth, Simone; Giesguth, Miriam; Wedel, Waldemar; Reiss, Günther; Dietz, Karl-Josef

2013-03-01

Temperature is an important physical parameter in biology and its deviation from optimum can cause damage in biosystems. Thermocouples based on the Seebeck effect can be structured on glass microcapillaries to obtain thermomicrocapillaries (TMCs) usable in a micromanipulation setup. The suitability of the setup was proven by monitoring the temperature increase upon illumination of leaves and single cells following insertion of the TMC. The increase was 1.5 K in green tissue and 0.75 K in white leaf sections due to lower absorption. In single cells of trichomes, the increase was 0.5 K due to heat dissipation to the surrounding air.

Two-step activation of paper batteries for high power generation: design and fabrication of biofluid- and water-activated paper batteries

NASA Astrophysics Data System (ADS)

Lee, Ki Bang

2006-11-01

Two-step activation of paper batteries has been successfully demonstrated to provide quick activation and to supply high power to credit card-sized biosystems on a plastic chip. A stack of a magnesium layer (an anode), a fluid guide (absorbent paper), a highly doped filter paper with copper chloride (a cathode) and a copper layer as a current collector is laminated between two transparent plastic films into a high power biofluid- and water-activated battery. The battery is activated by two-step activation: (1) after placing a drop of biofluid/water-based solution on the fluid inlet, the surface tension first drives the fluid to soak the fluid guide; (2) the fluid in the fluid guide then penetrates into the heavily doped filter paper with copper chloride to start the battery reaction. The fabricated half credit card-sized battery was activated by saliva, urine and tap water and delivered a maximum voltage of 1.56 V within 10 s after activation and a maximum power of 15.6 mW. When 10 kΩ and 1 KΩ loads are used, the service time with water, urine and saliva is measured as more than 2 h. An in-series battery of 3 V has been successfully tested to power two LEDs (light emitting diodes) and an electric driving circuit. As such, this high power paper battery could be integrated with on-demand credit card-sized biosystems such as healthcare test kits, biochips, lab-on-a-chip, DNA chips, protein chips or even test chips for water quality checking or chemical checking.

Theory favors a stepwise mechanism of porphyrin degradation by a ferric hydroperoxide model of the active species of heme oxygenase.

PubMed

Kumar, Devesh; de Visser, Samuël P; Shaik, Sason

2005-06-08

The report uses density functional theory to address the mechanism of heme degradation by the enzyme heme oxygenase (HO) using a model ferric hydroperoxide complex. HO is known to trap heme molecules and degrade them to maintain iron homeostasis in the biosystem. The degradation is initiated by complexation of the heme, then formation of the iron-hydroperoxo species, which subsequently oxidizes the meso position of the porphyrin by hydroxylation, thereby enabling eventually the cleavage of the porphyrin ring. Kinetic isotope effect studies indicate that the mechanism is assisted by general acid catalysis, via a chain of water molecules, and that all the events occur in concert. However, previous theoretical treatments indicated that the concerted mechanism has a high barrier, much higher than an alternative mechanism that is initiated by O-O bond homolysis of iron-hydroperoxide. The present contribution studies the stepwise and concerted acid-catalyzed mechanisms using H(3)O(+)(H(2)O)(n)(), n = 0-2. The effect of the acid strength is tested using the H(4)N(+)(H(2)O)(2) cluster and a fully protonated ferric hydroperoxide. All the calculations show that a stepwise mechanism that involves proton relay and O-O homolysis, in the rate-determining step, has a much lower barrier (>10 kcal/mol) than the corresponding fully concerted mechanism. The best fit of the calculated solvent kinetic isotope effect, to the experimental data, is obtained for the H(3)O(+)(H(2)O)(2) cluster. The calculated alpha-deuterium secondary kinetic isotope effect is inverse (0.95-0.98), but much less so than the experimental value (0.7). Possible reasons for this quantitative difference are discussed. Some probes are suggested that may enable experiment to distinguish the stepwise from the concerted mechanism.

Polymorphisms in CTNNBL1 in relation to colorectal cancer with evolutionary implications

PubMed Central

Huhn, Stefanie; Ingelfinger, Dierk; Bermejo, Justo Lorenzo; Bevier, Melanie; Pardini, Barbara; Naccarati, Alessio; Steinke, Verena; Rahner, Nils; Holinski-Feder, Elke; Morak, Monika; Schackert, Hans K; Görgens, Heike; Pox, Christian P; Goecke, Timm; Kloor, Matthias; Loeffler, Markus; Büttner, Reinhard; Vodickova, Ludmila; Novotny, Jan; Demir, Kubilay; Cruciat, Cristina-Maria; Renneberg, Rebecca; Huber, Wolfgang; Niehrs, Christof; Boutros, Michael; Propping, Peter; Vodička, Pavel; Hemminki, Kari; Försti, Asta

2011-01-01

Colorectal cancer (CRC) is a complex disease related to environmental and genetic risk factors. Several studies have shown that susceptibility to complex diseases can be mediated by ancestral alleles. Using RNAi screening, CTNNBL1 was identified as a putative regulator of the Wnt signaling pathway, which plays a key role in colorectal carcinogenesis. Recently, single nucleotide polymorphisms (SNPs) in CTNNBL1 have been associated with obesity, a known risk factor for CRC. We investigated whether genetic variation in CTNNBL1 affects susceptibility to CRC and tested for signals of recent selection. We applied a tagging SNP approach that cover all known common variation in CTNNBL1 (allele frequency >5%; r2>0.8). A case-control study was carried out using two well-characterized study populations: a hospital-based Czech population composed of 751 sporadic cases and 755 controls and a family/early onset-based German population (697 cases and 644 controls). Genotyping was performed using allele specific PCR based TaqMan® assays (Applied Biosystems, Weiterstadt, Germany). In the Czech cohort, containing sporadic cases, the ancestral alleles of three SNPs showed evidence of association with CRC: rs2344481 (OR 1.44, 95%CI 1.06-1.95, dominant model), rs2281148 (OR 0.59, 95%CI 0.36-0.96, dominant model) and rs2235460 (OR 1.38, 95%CI 1.01-1.89, AA vs. GG). The associations were less prominent in the family/early onset-based German cohort. Data derived from several databases and statistical tests consistently pointed to a likely shaping of CTNNBL1 by positive selection. Further studies are needed to identify the actual function of CTNNBL1 and to validate the association results in other populations. PMID:21537400

Field-Control, Phase-Transitions, and Life’s Emergence

PubMed Central

Mitra-Delmotte, Gargi; Mitra, A. N.

2012-01-01

Instances of critical-like characteristics in living systems at each organizational level (bio-molecules to ecosystems) as well as the spontaneous emergence of computation (Langton), do suggest the relevance of self-organized criticality (SOC). But extrapolating complex bio-systems to life’s origins, brings up a paradox: how could simple organics – lacking the “soft-matter” response properties of today’s complex bio-molecules – have dissipated energy from primordial reactions (eventually reducing CO2) in a controlled manner for their “ordering”? Nevertheless, a causal link of life’s macroscopic irreversible dynamics to the microscopic reversible laws of statistical mechanics is indicated via the “functional-takeover” of a soft magnetic scaffold by organics (c.f. Cairns-Smith’s “crystal-scaffold”). A field-controlled structure offers a mechanism for boot-strapping – bottom-up assembly with top-down control: its super-paramagnetic colloidal components obey reversible dynamics, but its dissipation of magnetic (H)-field energy for aggregation breaks time-reversal symmetry. The responsive adjustments of the controlled (host) mineral system to environmental changes would bring about mutual coupling between random organic sets supported by it; here the generation of long-range correlations within organic (guest) networks could include SOC-like mechanisms. And, such cooperative adjustments enable the selection of the functional configuration by altering the inorganic dipolar network’s capacity to assist a spontaneous process. A non-equilibrium dynamics could now drive the kinetically oriented system (trimming the phase-space via sterically coupled organics) toward a series of phase-transitions with appropriate organic replacements “taking-over” its functions. Where available, experiments are cited in support of these speculations and for designing appropriate tests. PMID:23060803

Establishment of a Laboratory for Biofuels Research at the University of Kentucky

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

Crocker, Mark; Crofcheck, Czarena; Andrews, Rodney

2013-03-29

This project was aimed at the development of the biofuels industry in Kentucky by establishing a laboratory to develop improved processes for biomass utilization. The facility is based at the University of Kentucky Center for Applied Energy Research and the Department of Biosystems and Agricultural Engineering, and constitutes an “open” laboratory, i.e., its equipment is available to other Kentucky researchers working in the area. The development of this biofuels facility represents a significant expansion of research infrastructure, and will provide a lasting resource for biobased research endeavors at the University of Kentucky. In order to enhance the laboratory's capabilities andmore » contribute to on-going biofuels research at the University of Kentucky, initial research at the laboratory has focused on the following technical areas: (i) the identification of algae strains suitable for oil production, utilizing flue gas from coal-fired power plants as a source of CO 2; (ii) the conversion of algae to biofuels; and (iii) the development of methods for the analysis of lignin and its deconstruction products. Highlights from these activities include the development of catalysts for the upgrading of lipids to hydrocarbons by means of decarboxylation/decarbonylation (deCOx), a study of bio-oil production from the fast pyrolysis of algae (Scenedesmus), and the application of pyrolytic gas chromatography coupled with mass spectrometry (Py-GC-MS) to the characterization of high lignin biomass feedstocks.« less

Surface topography and chemistry shape cellular behavior on wide band-gap semiconductors.

PubMed

Bain, Lauren E; Collazo, Ramon; Hsu, Shu-Han; Latham, Nicole Pfiester; Manfra, Michael J; Ivanisevic, Albena

2014-06-01

The chemical stability and electrical properties of gallium nitride make it a promising material for the development of biocompatible electronics, a range of devices including biosensors as well as interfaces for probing and controlling cellular growth and signaling. To improve the interface formed between the probe material and the cell or biosystem, surface topography and chemistry can be applied to modify the ways in which the device interacts with its environment. PC12 cells are cultured on as-grown planar, unidirectionally polished, etched nanoporous and nanowire GaN surfaces with and without a physisorbed peptide sequence that promotes cell adhesion. While cells demonstrate preferential adhesion to roughened surfaces over as-grown flat surfaces, the topography of that roughness also influences the morphology of cellular adhesion and differentiation in neurotypic cells. Addition of the peptide sequence generally contributes further to cellular adhesion and promotes development of stereotypic long, thin neurite outgrowths over alternate morphologies. The dependence of cell behavior on both the topographic morphology and surface chemistry is thus demonstrated, providing further evidence for the importance of surface modification for modulating bio-inorganic interfaces. Copyright © 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Comprehensive review on phytotechnology: Heavy metals removal by diverse aquatic plants species from wastewater.

PubMed

Rezania, Shahabaldin; Taib, Shazwin Mat; Md Din, Mohd Fadhil; Dahalan, Farrah Aini; Kamyab, Hesam

2016-11-15

Environmental pollution specifically water pollution is alarming both in the developed and developing countries. Heavy metal contamination of water resources is a critical issue which adversely affects humans, plants and animals. Phytoremediation is a cost-effective remediation technology which able to treat heavy metal polluted sites. This environmental friendly method has been successfully implemented in constructed wetland (CWs) which is able to restore the aquatic biosystem naturally. Nowadays, many aquatic plant species are being investigated to determine their potential and effectiveness for phytoremediation application, especially high growth rate plants i.e. macrophytes. Based on the findings, phytofiltration (rhizofiltration) is the sole method which defined as heavy metals removal from water by aquatic plants. Due to specific morphology and higher growth rate, free-floating plants were more efficient to uptake heavy metals in comparison with submerged and emergent plants. In this review, the potential of wide range of aquatic plant species with main focus on four well known species (hyper-accumulators): Pistia stratiotes, Eicchornia spp., Lemna spp. and Salvinia spp. was investigated. Moreover, we discussed about the history, methods and future prospects in phytoremediation of heavy metals by aquatic plants comprehensively. Copyright © 2016. Published by Elsevier B.V.

Enabling personalized implant and controllable biosystem development through 3D printing.

PubMed

Nagarajan, Neerajha; Dupret-Bories, Agnes; Karabulut, Erdem; Zorlutuna, Pinar; Vrana, Nihal Engin

The impact of additive manufacturing in our lives has been increasing constantly. One of the frontiers in this change is the medical devices. 3D printing technologies not only enable the personalization of implantable devices with respect to patient-specific anatomy, pathology and biomechanical properties but they also provide new opportunities in related areas such as surgical education, minimally invasive diagnosis, medical research and disease models. In this review, we cover the recent clinical applications of 3D printing with a particular focus on implantable devices. The current technical bottlenecks in 3D printing in view of the needs in clinical applications are explained and recent advances to overcome these challenges are presented. 3D printing with cells (bioprinting); an exciting subfield of 3D printing, is covered in the context of tissue engineering and regenerative medicine and current developments in bioinks are discussed. Also emerging applications of bioprinting beyond health, such as biorobotics and soft robotics, are introduced. As the technical challenges related to printing rate, precision and cost are steadily being solved, it can be envisioned that 3D printers will become common on-site instruments in medical practice with the possibility of custom-made, on-demand implants and, eventually, tissue engineered organs with active parts developed with biorobotics techniques. Copyright © 2018 Elsevier Inc. All rights reserved.

Micro-nano-biosystems: An overview of European research.

PubMed

Lymberis, Andreas

2010-06-01

New developments in science, technologies and applications are blurring the boundaries between information and communications technology (ICT), micro-nano systems and life sciences, e.g. through miniaturisation and the ability to manipulate matter at the atomic scale and to interface live and man-made systems. Interdisciplinary research towards integrated systems and their applications based on emerging convergence of information & communication technologies, micro-nano and bio technologies is expected to have a direct influence on healthcare, ageing population and well being. Micro-Nano-Bio Systems (MNBS) research and development activities under the European Union's R&D Programs, Information & Communication Technologies priority address miniaturised, smart and integrated systems for in-vitro testing e.g. lab-on-chips and systems interacting with the human e.g. autonomous implants, endoscopic capsules and robotics for minimally invasive surgery. The MNBS group involves hundreds of key public and private international organisations working on system development and validation in diverse applications such as cancer detection and therapy follow-up, minimally invasive surgery, capsular endocsopy, wearable biochemical monitoring and repairing of vital functions with active implant devices. The paper presents MNBS rationale and activities, discusses key research and innovation challenges and proposes R&D directions to achieve the expected impact on healthcare and quality of life.

WISB: Warwick Integrative Synthetic Biology Centre

PubMed Central

McCarthy, John

2016-01-01

Synthetic biology promises to create high-impact solutions to challenges in the areas of biotechnology, human/animal health, the environment, energy, materials and food security. Equally, synthetic biologists create tools and strategies that have the potential to help us answer important fundamental questions in biology. Warwick Integrative Synthetic Biology (WISB) pursues both of these mutually complementary ‘build to apply’ and ‘build to understand’ approaches. This is reflected in our research structure, in which a core theme on predictive biosystems engineering develops underpinning understanding as well as next-generation experimental/theoretical tools, and these are then incorporated into three applied themes in which we engineer biosynthetic pathways, microbial communities and microbial effector systems in plants. WISB takes a comprehensive approach to training, education and outreach. For example, WISB is a partner in the EPSRC/BBSRC-funded U.K. Doctoral Training Centre in synthetic biology, we have developed a new undergraduate module in the subject, and we have established five WISB Research Career Development Fellowships to support young group leaders. Research in Ethical, Legal and Societal Aspects (ELSA) of synthetic biology is embedded in our centre activities. WISB has been highly proactive in building an international research and training network that includes partners in Barcelona, Boston, Copenhagen, Madrid, Marburg, São Paulo, Tartu and Valencia. PMID:27284024

WISB: Warwick Integrative Synthetic Biology Centre.

PubMed

McCarthy, John

2016-06-15

Synthetic biology promises to create high-impact solutions to challenges in the areas of biotechnology, human/animal health, the environment, energy, materials and food security. Equally, synthetic biologists create tools and strategies that have the potential to help us answer important fundamental questions in biology. Warwick Integrative Synthetic Biology (WISB) pursues both of these mutually complementary 'build to apply' and 'build to understand' approaches. This is reflected in our research structure, in which a core theme on predictive biosystems engineering develops underpinning understanding as well as next-generation experimental/theoretical tools, and these are then incorporated into three applied themes in which we engineer biosynthetic pathways, microbial communities and microbial effector systems in plants. WISB takes a comprehensive approach to training, education and outreach. For example, WISB is a partner in the EPSRC/BBSRC-funded U.K. Doctoral Training Centre in synthetic biology, we have developed a new undergraduate module in the subject, and we have established five WISB Research Career Development Fellowships to support young group leaders. Research in Ethical, Legal and Societal Aspects (ELSA) of synthetic biology is embedded in our centre activities. WISB has been highly proactive in building an international research and training network that includes partners in Barcelona, Boston, Copenhagen, Madrid, Marburg, São Paulo, Tartu and Valencia. © 2016 The Author(s).

Cancer: a profit-driven biosystem?

PubMed

Deisboeck, Thomas S

2008-08-01

The argument is made that solid malignant tumors behave as profit-driven biological systems in that they expand their nutrient-uptaking surface to increase energetic revenue, at a comparably low metabolic cost. Within this conceptual framework, cancer cell migration is a critical mechanism as it maximizes systemic surface expansion while minimizing diffusion distance. Treating these tumor systems with adjuvant anti-proliferative regimen only should increase the energetic net gain of the viable cancer cells left behind, hence would facilitate tumor recurrence. Therapeutic attempts to better control tumor (re)growth should therefore aim primarily at containing its surface expansion, thus reducing its energetic revenue, or increasing its metabolic costs or better yet, both.

Cancer: A profit-driven biosystem ?

PubMed Central

Deisboeck, Thomas S.

2008-01-01

The argument is made that solid malignant tumors behave as profit-driven biological systems in that they expand their nutrient-uptaking surface to increase energetic revenue, at a comparably low metabolic cost. Within this conceptual framework, cancer cell migration is a critical mechanism as it maximizes systemic surface expansion while minimizing diffusion distance. Treating these tumor systems with adjuvant anti-proliferative regimen only should increase the energetic net gain of the viable cancer cells left behind, hence would facilitate tumor recurrence. Therapeutic attempts to better control tumor (re)growth should therefore aim primarily at containing its surface expansion, thus reducing its energetic revenue, or increasing its metabolic costs or better yet, both. PMID:18420354

Lung Reference Set A Application: LaszloTakacs - Biosystems (2010) — EDRN Public Portal

Cancer.gov

We would like to access the NCI lung cancer Combined Pre-Validation Reference Set A in order to further validate a lung cancer diagnostic test candidate. Our test is based on a panel of antibodies which have been tested on 4 different cohorts (see below, paragraph “Preliminary Data and Methods”). This Reference Set A, whose clinical setting is “Diagnosis of lung cancer”, will be used to validate the panel of monoclonal antibodies which have been demonstrated by extensive data analysis to provide the best discrimination between controls and Lung Cancer patient plasma samples, sensitivity and specificity values from ROC analyses are superior than 85 %.

Alternative to Ritt's pseudodivision for finding the input-output equations of multi-output models.

PubMed

Meshkat, Nicolette; Anderson, Chris; DiStefano, Joseph J

2012-09-01

Differential algebra approaches to structural identifiability analysis of a dynamic system model in many instances heavily depend upon Ritt's pseudodivision at an early step in analysis. The pseudodivision algorithm is used to find the characteristic set, of which a subset, the input-output equations, is used for identifiability analysis. A simpler algorithm is proposed for this step, using Gröbner Bases, along with a proof of the method that includes a reduced upper bound on derivative requirements. Efficacy of the new algorithm is illustrated with several biosystem model examples. Copyright © 2012 Elsevier Inc. All rights reserved.

Chemical Fixation of CO2 in Coal Combustion Products and Recycling through Biosystems

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

C. Henry Copeland; Paul Pier; Samantha Whitehead

2001-09-30

This Annual Technical Progress Report presents the principle results in enhanced growth of algae using coal combustion products as a catalyst to increase bicarbonate levels in solution. A co-current reactor is present that increases the gas phase to bicarbonate transfer rate by a factor of five to nine. The bicarbonate concentration at a given pH is approximately double that obtained using a control column of similar construction. Algae growth experiments were performed under laboratory conditions to obtain baseline production rates and to perfect experimental methods. The final product of this initial phase in algae production is presented.

Enzymes immobilized on amine-terminated ionic liquid-functionalized carbon nanotube for hydrogen peroxide determination.

PubMed

Liu, Xiuhui; Bu, Caihong; Nan, Zhihan; Zheng, Lichun; Qiu, Yu; Lu, Xiaoquan

2013-02-15

We report on a new approach for the electrochemical detection of hydrogen peroxide (H2O2) based on Cytochrome C (Cyt c) immobilized ionic liquid (IL)-functionalized multi-walled carbon nanotubes (MWCNTs) modified glass carbon electrode (GCE). Functionalization of multi-walled carbon nanotube with amine-terminated ionic liquid materials was characterized using fourier transform infrared spectroscopy (FTIR), UV-vis spectra, and electrochemical impedance spectroscopy (EIS), and the results showed that the covalent modification of MWCNTs with ILs exhibited a high surface area for enzyme immobilization and provided a good microenvironment for Cyt c to retain its bioelectrocatalytic activity toward H2O2. Amperometry was used to evaluate the catalytic activity of the cyt c towards H2O2. The proposed biosensor exhibited a wide linear response range nearly 4 orders of magnitude of H2O2 (4.0 × 10(-8)M-1.0 × 10(-4)M) with a good linearity (0.9980) and a low detection limit of 1.3 × 10(-8)M (based on S/N=3). Furthermore, the biosensor also displays some other excellent characteristics such as high selectivity, good reproducibility and long-term stability. Thus, the biosensor constructed in this study has great potential for detecting H2O2 in the complex biosystems. Copyright © 2012 Elsevier B.V. All rights reserved.

Dynamic modeling of green algae cultivation in a photobioreactor for sustainable biodiesel production.

PubMed

Del Rio-Chanona, Ehecatl A; Liu, Jiao; Wagner, Jonathan L; Zhang, Dongda; Meng, Yingying; Xue, Song; Shah, Nilay

2018-02-01

Biodiesel produced from microalgae has been extensively studied due to its potentially outstanding advantages over traditional transportation fuels. In order to facilitate its industrialization and improve the process profitability, it is vital to construct highly accurate models capable of predicting the complex behavior of the investigated biosystem for process optimization and control, which forms the current research goal. Three original contributions are described in this paper. Firstly, a dynamic model is constructed to simulate the complicated effect of light intensity, nutrient supply and light attenuation on both biomass growth and biolipid production. Secondly, chlorophyll fluorescence, an instantly measurable variable and indicator of photosynthetic activity, is embedded into the model to monitor and update model accuracy especially for the purpose of future process optimal control, and its correlation between intracellular nitrogen content is quantified, which to the best of our knowledge has never been addressed so far. Thirdly, a thorough experimental verification is conducted under different scenarios including both continuous illumination and light/dark cycle conditions to testify the model predictive capability particularly for long-term operation, and it is concluded that the current model is characterized by a high level of predictive capability. Based on the model, the optimal light intensity for algal biomass growth and lipid synthesis is estimated. This work, therefore, paves the way to forward future process design and real-time optimization. © 2017 Wiley Periodicals, Inc.

Spin-vibronic quantum dynamics for ultrafast excited-state processes.

PubMed

Eng, Julien; Gourlaouen, Christophe; Gindensperger, Etienne; Daniel, Chantal

2015-03-17

Ultrafast intersystem crossing (ISC) processes coupled to nuclear relaxation and solvation dynamics play a central role in the photophysics and photochemistry of a wide range of transition metal complexes. These phenomena occurring within a few hundred femtoseconds are investigated experimentally by ultrafast picosecond and femtosecond transient absorption or luminescence spectroscopies, and optical laser pump-X-ray probe techniques using picosecond and femtosecond X-ray pulses. The interpretation of ultrafast structural changes, time-resolved spectra, quantum yields, and time scales of elementary processes or transient lifetimes needs robust theoretical tools combining state-of-the-art quantum chemistry and developments in quantum dynamics for solving the electronic and nuclear problems. Multimode molecular dynamics beyond the Born-Oppenheimer approximation has been successfully applied to many small polyatomic systems. Its application to large molecules containing a transition metal atom is still a challenge because of the nuclear dimensionality of the problem, the high density of electronic excited states, and the spin-orbit coupling effects. Rhenium(I) α-diimine carbonyl complexes, [Re(L)(CO)3(N,N)](n+) are thermally and photochemically robust and highly flexible synthetically. Structural variations of the N,N and L ligands affect the spectroscopy, the photophysics, and the photochemistry of these chromophores easily incorporated into a complex environment. Visible light absorption opens the route to a wide range of applications such as sensors, probes, or emissive labels for imaging biomolecules. Halide complexes [Re(X)(CO)3(bpy)] (X = Cl, Br, or I; bpy = 2,2'-bipyridine) exhibit complex electronic structure and large spin-orbit effects that do not correlate with the heavy atom effects. Indeed, the (1)MLCT → (3)MLCT intersystem crossing (ISC) kinetics is slower than in [Ru(bpy)3](2+) or [Fe(bpy)3](2+) despite the presence of a third-row transition metal. Counterintuitively, singlet excited-state lifetime increases on going from Cl (85 fs) to Br (128 fs) and to I (152 fs). Moreover, correlation between the Re-X stretching mode and the rate of ISC is observed. In this Account, we emphasize on the role of spin-vibronic coupling on the mechanism of ultrafast ISC put in evidence in [Re(Br)(CO)3(bpy)]. For this purpose, we have developed a model Hamiltonian for solving an 11 electronic excited states multimode problem including vibronic and SO coupling within the linear vibronic coupling (LVC) approximation and the assumption of harmonic potentials. The presence of a central metal atom coupled to rigid ligands, such as α-diimine, ensures nuclear motion of small amplitudes and a priori justifies the use of the LVC model. The simulation of the ultrafast dynamics by wavepacket propagations using the multiconfiguration time-dependent Hartree (MCTDH) method is based on density functional theory (DFT), and its time-dependent extension to excited states (TD-DFT) electronic structure data. We believe that the interplay between time-resolved experiments and these pioneering simulations covering the first picoseconds and including spin-vibronic coupling will promote a number of quantum dynamical studies that will contribute to a better understanding of ultrafast processes in a wide range of organic and inorganic chromophores easily incorporated in biosystems or supramolecular devices for specific functions.

Selected developments and medical applications of organic-inorganic hybrid biomaterials based on functionalized spherosilicates.

PubMed

John, Łukasz

2018-07-01

Well-defined and tailor-made spherosilicates and POSS-based (POSS = Polyhedral Oligomeric Silsesquioxanes) (nano)composites with interesting chemical and mechanical properties have applications in the widely-regarded field of innovative biomaterials. They can serve as delivery systems, three-dimensional scaffolds for specific tissue engineering, biomaterials for orthopedic, cardiovascular, and reconstructive surgery, etc. Such organic-inorganic hybrids are much more effective biomaterials than pure polymers, bioglasses, metals, alloys, and ceramics currently used in medical applications and are considered as next-generation systems in innovative medical approaches. This range of applications creates a strong impetus for novel, cheap, and easy-to-scale-up methods for their synthesis. In this review (highlights since 2006), selected biomaterials consisting of various polymeric derivatives such as polymethacrylates, polylactides, polycaprolactones, polyurethanes, etc., which serve as organic side-arms of POSS and can create polymer platforms for precisely localized spherosilicates among organic matrices, are discussed as a new generation of silicon-based biosystems using spherosilicates, promising biomaterials with a particular use in soft- and hard-tissue engineering. Copyright © 2018 Elsevier B.V. All rights reserved.

Looking to the future of organs-on-chips: interview with Professor John Wikswo.

PubMed

Wikswo, John P

2017-06-01

John Wikswo talks to Francesca Lake, Managing Editor: John is the founding Director of the Vanderbilt Institute for Integrative Biosystems Research and Education (VIIBRE). He is also the Gordon A Cain University Professor; a B learned Professor of Living State Physics; and a Professor of Biomedical Engineering, Molecular Physiology and Biophysics, and Physics. John earned his PhD in physics at Stanford University (CA, USA). After serving as a Research Fellow in Cardiology at Stanford, he joined the Department of Physics and Astronomy at Vanderbilt University (TN, USA), where he went on to make the first measurement of the magnetic field of an isolated nerve. He founded VIIBRE at Vanderbilt in 2001 in order to foster and enhance interdisciplinary research in the biophysical sciences, bioengineering and medicine. VIIBRE efforts have led to the development of devices integral to organ-on-chip research. He is focusing on the neurovascular unit-on-a-chip, heart-on-a-chip, a missing organ microformulator, and microfluidic pumps and valves to control and analyze organs-on-chips.

A Hypothesis: Life Initiated from Two Genes, as Deduced from the RNA World Hypothesis and the Characteristics of Life-Like Systems

PubMed Central

Kawamura, Kunio

2016-01-01

RNA played a central role in the emergence of the first life-like system on primitive Earth since RNA molecules contain both genetic information and catalytic activity. However, there are several drawbacks regarding the RNA world hypothesis. Here, I briefly discuss the feasibility of the RNA world hypothesis to deduce the RNA functions that are essential for forming a life-like system. At the same time, I have conducted a conceptual analysis of the characteristics of biosystems as a useful approach to deduce a realistic life-like system in relation to the definition of life. For instance, an RNA-based life-like system should possess enough stability to resist environmental perturbations, by developing a cell-like compartment, for instance. Here, a conceptual viewpoint is summarized to provide a realistic life-like system that is compatible with the primitive Earth environment and the capabilities of RNA molecules. According to the empirical and conceptual analysis, I propose the hypothesis that the first life-like system could have initiated from only two genes. PMID:27490571

Performance testing of a semi-automatic card punch system, using direct STR profiling of DNA from blood samples on FTA™ cards.

PubMed

Ogden, Samantha J; Horton, Jeffrey K; Stubbs, Simon L; Tatnell, Peter J

2015-01-01

The 1.2 mm Electric Coring Tool (e-Core™) was developed to increase the throughput of FTA(™) sample collection cards used during forensic workflows and is similar to a 1.2 mm Harris manual micro-punch for sampling dried blood spots. Direct short tandem repeat (STR) DNA profiling was used to compare samples taken by the e-Core tool with those taken by the manual micro-punch. The performance of the e-Core device was evaluated using a commercially available PowerPlex™ 18D STR System. In addition, an analysis was performed that investigated the potential carryover of DNA via the e-Core punch from one FTA disc to another. This contamination study was carried out using Applied Biosystems AmpflSTR™ Identifiler™ Direct PCR Amplification kits. The e-Core instrument does not contaminate FTA discs when a cleaning punch is used following excision of discs containing samples and generates STR profiles that are comparable to those generated by the manual micro-punch. © 2014 American Academy of Forensic Sciences.

An agent-based model identifies MRI regions of probable tumor invasion in a patient with glioblastoma

NASA Astrophysics Data System (ADS)

Chen, L. Leon; Ulmer, Stephan; Deisboeck, Thomas S.

2010-01-01

We present an application of a previously developed agent-based glioma model (Chen et al 2009 Biosystems 95 234-42) for predicting spatio-temporal tumor progression using a patient-specific MRI lattice derived from apparent diffusion coefficient (ADC) data. Agents representing collections of migrating glioma cells are initialized based upon voxels at the outer border of the tumor identified on T1-weighted (Gd+) MRI at an initial time point. These simulated migratory cells exhibit a specific biologically inspired spatial search paradigm, representing a weighting of the differential contribution from haptotactic permission and biomechanical resistance on the migration decision process. ADC data from 9 months after the initial tumor resection were used to select the best search paradigm for the simulation, which was initiated using data from 6 months after the initial operation. Using this search paradigm, 100 simulations were performed to derive a probabilistic map of tumor invasion locations. The simulation was able to successfully predict a recurrence in the dorsal/posterior aspect long before it was depicted on T1-weighted MRI, 18 months after the initial operation.

An agent-based model identifies MRI regions of probable tumor invasion in a patient with glioblastoma.

PubMed

Chen, L Leon; Ulmer, Stephan; Deisboeck, Thomas S

2010-01-21

We present an application of a previously developed agent-based glioma model (Chen et al 2009 Biosystems 95 234-42) for predicting spatio-temporal tumor progression using a patient-specific MRI lattice derived from apparent diffusion coefficient (ADC) data. Agents representing collections of migrating glioma cells are initialized based upon voxels at the outer border of the tumor identified on T1-weighted (Gd+) MRI at an initial time point. These simulated migratory cells exhibit a specific biologically inspired spatial search paradigm, representing a weighting of the differential contribution from haptotactic permission and biomechanical resistance on the migration decision process. ADC data from 9 months after the initial tumor resection were used to select the best search paradigm for the simulation, which was initiated using data from 6 months after the initial operation. Using this search paradigm, 100 simulations were performed to derive a probabilistic map of tumor invasion locations. The simulation was able to successfully predict a recurrence in the dorsal/posterior aspect long before it was depicted on T1-weighted MRI, 18 months after the initial operation.

An Outlook on Biothermodynamics: Needs, Problems, and New Developments. I. Stability and Hydration of Proteins

NASA Astrophysics Data System (ADS)

Keller, Jürgen U.

2008-12-01

The application of concepts, principles, and methods of thermodynamics of equilibria and processes to bioengineering systems has led to a new and growing field: engineering biothermodynamics. This article, which is meant as the first in a series, gives an outline of basic aspects, changes, and actual examples in this field. After a few introductory remarks, the basic concepts and laws of thermodynamics extended to systems with internal variables, which serve as models for biofluids and other biosystems, are given. The method of thermodynamics is then applied to the problem of thermal stability of aqueous protein solutions, especially to that of myoglobin solutions. After this, the phenomenon of hydration of proteins by adsorption and intrusion of water molecules is considered. Several other phenomena like the adsorption of proteins on solid surfaces or cell membranes and their temperature and pressure-related behavior represented by an equation of state, or the thermodynamics of bacterial solutions including chemical reactions like wine fermentation, etc., will be presented in Parts II and III of this article.

Evolvable social agents for bacterial systems modeling.

PubMed

Paton, Ray; Gregory, Richard; Vlachos, Costas; Saunders, Jon; Wu, Henry

2004-09-01

We present two approaches to the individual-based modeling (IbM) of bacterial ecologies and evolution using computational tools. The IbM approach is introduced, and its important complementary role to biosystems modeling is discussed. A fine-grained model of bacterial evolution is then presented that is based on networks of interactivity between computational objects representing genes and proteins. This is followed by a coarser grained agent-based model, which is designed to explore the evolvability of adaptive behavioral strategies in artificial bacteria represented by learning classifier systems. The structure and implementation of the two proposed individual-based bacterial models are discussed, and some results from simulation experiments are presented, illustrating their adaptive properties.

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc04531j

PubMed Central

Lagardère, Louis; Jolly, Luc-Henri; Lipparini, Filippo; Aviat, Félix; Stamm, Benjamin; Jing, Zhifeng F.; Harger, Matthew; Torabifard, Hedieh; Cisneros, G. Andrés; Schnieders, Michael J.; Gresh, Nohad; Maday, Yvon; Ren, Pengyu Y.; Ponder, Jay W.

2017-01-01

We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over a single-core computation is observed for the largest systems. The extension of the present CPU implementation of Tinker-HP to other computational platforms is discussed. PMID:29732110

High-throughput analysis using non-depletive SPME: challenges and applications to the determination of free and total concentrations in small sample volumes.

PubMed

Boyacı, Ezel; Bojko, Barbara; Reyes-Garcés, Nathaly; Poole, Justen J; Gómez-Ríos, Germán Augusto; Teixeira, Alexandre; Nicol, Beate; Pawliszyn, Janusz

2018-01-18

In vitro high-throughput non-depletive quantitation of chemicals in biofluids is of growing interest in many areas. Some of the challenges facing researchers include the limited volume of biofluids, rapid and high-throughput sampling requirements, and the lack of reliable methods. Coupled to the above, growing interest in the monitoring of kinetics and dynamics of miniaturized biosystems has spurred the demand for development of novel and revolutionary methodologies for analysis of biofluids. The applicability of solid-phase microextraction (SPME) is investigated as a potential technology to fulfill the aforementioned requirements. As analytes with sufficient diversity in their physicochemical features, nicotine, N,N-Diethyl-meta-toluamide, and diclofenac were selected as test compounds for the study. The objective was to develop methodologies that would allow repeated non-depletive sampling from 96-well plates, using 100 µL of sample. Initially, thin film-SPME was investigated. Results revealed substantial depletion and consequent disruption in the system. Therefore, new ultra-thin coated fibers were developed. The applicability of this device to the described sampling scenario was tested by determining the protein binding of the analytes. Results showed good agreement with rapid equilibrium dialysis. The presented method allows high-throughput analysis using small volumes, enabling fast reliable free and total concentration determinations without disruption of system equilibrium.

Development of positive control materials for DNA-based detection of cystic fibrosis: Cloning and sequencing of 31 mutations

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

Iovannisci, D.; Brown, C.; Winn-Deen, E.

1994-09-01

The cloning and sequencing of the gene associated with cystic fibrosis (CF) now provides the opportunity for earlier detection and carrier screening through DNA-based detection schemes. To date, over 300 mutations have been reported to the CF Consortium; however, only 30 mutations have been observed frequently enough world-wide to warrant routine screening. Many of these mutations are not available as cloned material or as established tissue culture cell lines to aid in the development of DNA-based detection assays. We have therefore cloned the 30 most frequently reported mutations, plus the mutation R347H due to its association with male infertility (31more » mutations, total). Two approaches were employed: direct PCR amplification, where mutations were available from patient sources, and site-directed PCR mutagenesis of normal genomic DNA to generate the remaining mutations. After amplification, products were cloned into a sequencing vector, bacterial transformants were screened by a novel method (PCR/oligonucleotide litigation assay/sequence-coded separation), and plamid DNA sequences determined by automated fluorescent methods on the Applied Biosystems 373A. Mixing of the clones allows the construction of artificial genotypes useful as positive control material for assay validation. A second round of mutagenesis, resulting in the construction of plasmids bearing multiple mutations, will be evaluated for their utility as reagent control materials in kit development.« less

Quantitative PCR assay to determine prevalence and intensity of MSX (Haplosporidium nelsoni) in North Carolina and Rhode Island oysters Crassostrea virginica.

PubMed

Wilbur, Ami E; Ford, Susan E; Gauthier, Julie D; Gomez-Chiarri, Marta

2012-12-27

The continuing challenges to the management of both wild and cultured eastern oyster Crassostrea virginica populations resulting from protozoan parasites has stimulated interest in the development of molecular assays for their detection and quantification. For Haplosporidium nelsoni, the causative agent of multinucleated sphere unknown (MSX) disease, diagnostic evaluations depend extensively on traditional but laborious histological approaches and more recently on rapid and sensitive (but not quantitative) end-point polymerase chain reaction (PCR) assays. Here, we describe the development and application of a quantitative PCR (qPCR) assay for H. nelsoni using an Applied Biosystems TaqMan® assay designed with minor groove binder (MGB) probes. The assay was highly sensitive, detecting as few as 20 copies of cloned target DNA. Histologically evaluated parasite density was significantly correlated with the quantification cycle (Cq), regardless of whether quantification was categorical (r2 = 0.696, p < 0.0001) or quantitative (r2 = 0.797, p < 0.0001). Application in field studies conducted in North Carolina, USA (7 locations), revealed widespread occurrence of the parasite with moderate to high intensities noted in some locations. In Rhode Island, USA, application of the assay on oysters from 2 locations resulted in no positives.

The influence of carbon nanotubes on enzyme activity and structure: investigation of different immobilization procedures through enzyme kinetics and circular dichroism studies.

PubMed

Cang-Rong, Jason Teng; Pastorin, Giorgia

2009-06-24

In the last decade, many environmental organizations have devoted their efforts to identifying renewable biosystems, which could provide sustainable fuels and thus enhance energy security. Amidst the myriad of possibilities, some biofuels make use of different types of waste biomasses, and enzymes are often employed to hydrolyze these biomasses and produce sugars that will be subsequently converted into ethanol. In this project, we aimed to bridge nanotechnology and biofuel production: here we report on the activity and structure of the enzyme amyloglucosidase (AMG), physically adsorbed or covalently immobilized onto single-walled carbon nanotubes (SWNTs) and multi-walled carbon nanotubes (MWNTs). In fact, carbon nanotubes (CNTs) present several properties that render them ideal support systems, without the diffusion limitations displayed by porous material and with the advantage of being further functionalizable at their surface. Chemical ligation was achieved both on oxidized nanotubes (via carbodiimide chemistry), as well as on amino-functionalized nanotubes (via periodate-oxidized AMG). Results showed that AMG retained a certain percentage of its specific activity for all enzyme-carbon nanotubes complexes prepared, with the physically adsorbed samples displaying better catalytic efficiency than the covalently immobilized samples. Analysis of the enzyme's structure through circular dichroism (CD) spectroscopy revealed significant structural changes in all samples, the degree of change being consistent with the activity profiles. This study proves that AMG interacts differently with carbon nanotubes depending on the method employed. Due to the higher activity reported by the enzyme physically adsorbed onto CNTs, these samples demonstrated a vast potential for further development. At the same time, the possibility of inducing magnetic properties into CNTs offers the opportunity to easily separate them from the original solution. Hence, substances to which they have been attached can be separated from a reaction medium, or directed by an external magnetic field to achieve efficient biofuel production. This paves the way for future design of efficient CNT-enzyme nanostructure bioreactors.

The influence of carbon nanotubes on enzyme activity and structure: investigation of different immobilization procedures through enzyme kinetics and circular dichroism studies

NASA Astrophysics Data System (ADS)

Cang-Rong, Jason Teng; Pastorin, Giorgia

2009-06-01

In the last decade, many environmental organizations have devoted their efforts to identifying renewable biosystems, which could provide sustainable fuels and thus enhance energy security. Amidst the myriad of possibilities, some biofuels make use of different types of waste biomasses, and enzymes are often employed to hydrolyze these biomasses and produce sugars that will be subsequently converted into ethanol. In this project, we aimed to bridge nanotechnology and biofuel production: here we report on the activity and structure of the enzyme amyloglucosidase (AMG), physically adsorbed or covalently immobilized onto single-walled carbon nanotubes (SWNTs) and multi-walled carbon nanotubes (MWNTs). In fact, carbon nanotubes (CNTs) present several properties that render them ideal support systems, without the diffusion limitations displayed by porous material and with the advantage of being further functionalizable at their surface. Chemical ligation was achieved both on oxidized nanotubes (via carbodiimide chemistry), as well as on amino-functionalized nanotubes (via periodate-oxidized AMG). Results showed that AMG retained a certain percentage of its specific activity for all enzyme-carbon nanotubes complexes prepared, with the physically adsorbed samples displaying better catalytic efficiency than the covalently immobilized samples. Analysis of the enzyme's structure through circular dichroism (CD) spectroscopy revealed significant structural changes in all samples, the degree of change being consistent with the activity profiles. This study proves that AMG interacts differently with carbon nanotubes depending on the method employed. Due to the higher activity reported by the enzyme physically adsorbed onto CNTs, these samples demonstrated a vast potential for further development. At the same time, the possibility of inducing magnetic properties into CNTs offers the opportunity to easily separate them from the original solution. Hence, substances to which they have been attached can be separated from a reaction medium, or directed by an external magnetic field to achieve efficient biofuel production. This paves the way for future design of efficient CNT-enzyme nanostructure bioreactors.

Catechol-O-Methyltransferase Genotypes and Parenting Influence on Long-Term Executive Functioning After Moderate to Severe Early Childhood Traumatic Brain Injury: An Exploratory Study.

PubMed

Kurowski, Brad G; Treble-Barna, Amery; Zang, Huaiyu; Zhang, Nanhua; Martin, Lisa J; Yeates, Keith Owen; Taylor, H Gerry; Wade, Shari L

To examine catechol-O-methyltransferase (COMT) rs4680 genotypes as moderators of the effects of parenting style on postinjury changes in parent behavior ratings of executive dysfunction following moderate to severe early childhood traumatic brain injury. Research was conducted in an outpatient setting. Participants included children admitted to hospital with moderate to severe traumatic brain injury (n = 55) or orthopedic injuries (n = 70) between ages 3 and 7 years. Prospective cohort followed over 7 years postinjury. Parenting Practices Questionnaire and the Behavior Rating Inventory of Executive Functioning obtained at baseline, 6, 12, and 18 months, and 3.5 and 6.8 years postinjury. DNA was collected from saliva samples, purified using the Oragene (DNA Genotek, Ottawa, Ontario, Canada) OG-500 self-collection tubes, and analyzed using TaqMan (Applied Biosystems, Thermo Fisher Scientific, Waltham, Massachusetts) assay protocols to identify the COMT rs4680 polymorphism. Linear mixed models revealed a significant genotype × parenting style × time interaction (F = 5.72, P = .02), which suggested that the adverse effects of authoritarian parenting on postinjury development of executive functioning were buffered by the presence of the COMT AA genotype (lower enzyme activity, higher dopamine levels). There were no significant associations of executive functioning with the interaction between genotype and authoritative or permissive parenting ratings. The lower activity COMT rs4680 genotype may buffer the negative effect of authoritarian parenting on long-term executive functioning following injury in early childhood. The findings provide preliminary evidence for associations of parenting style with executive dysfunction in children and for a complex interplay of genetic and environmental factors as contributors to decreases in these problems after traumatic injuries in children. Further investigation is warranted to understand the interplay among genetic and environmental factors related to recovery after traumatic brain injury in children.

Decreased FOXP3 mRNA expression in children with atopic asthma and IgE-mediated food allergy.

PubMed

Krogulska, Aneta; Polakowska, Ewa; Wąsowska-Królikowska, Krystyna; Małachowska, Beata; Młynarski, Wojciech; Borowiec, Maciej

2015-11-01

The role of T regulatory lymphocytes has been investigated in various allergic diseases. However, the precise relation between the phenotype and severity of allergic diseases and the changes in FOXP3 mRNA expression are not fully understood. To compare the expression of FOXP3 mRNA in children with asthma with and without concomitant food allergy (FA) with healthy children and children with only FA. The study included 82 children: 15 with atopic asthma and IgE-dependent FA, 27 with atopic asthma without FA, 20 with IgE-dependent FA without asthma, and 20 healthy children without atopy. Reverse transcription was performed using a commercially available High Capacity cDNA Archive Kit (Applied Biosystems, Carlsbad, California). Analysis was carried out with a 7900HT real-time polymerase chain reaction system (Applied Biosystems). The average level of the FOXP3 gene expression in children with allergy was significantly lower compared with healthy children (2.2 ± 1.3 vs 4.2 ± 4.2; P = .014). The lowest mean level of FOXP3 mRNA expression (1.9 ± 1.6) was recorded in children with asthma and FA, and the highest level (4.2 ± 4.2) was recorded in healthy children without atopy (P = .036). A milder course of asthma or the degree of allergic reaction after a food challenge was associated with higher FOXP3 mRNA expression. Significantly lower levels of FOXP3 gene expression, observed more commonly in children with asthma and IgE-dependent FA than in healthy controls, were associated with a more severe clinical course. Therefore, FOXP3 expression could serve as an indicator of severe asthma with concomitant atopic conditions such as IgE-dependent FA. Copyright © 2015 American College of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Forces on nuclei moving on autoionizing molecular potential energy surfaces.

PubMed

Moiseyev, Nimrod

2017-01-14

Autoionization of molecular systems occurs in diatomic molecules and in small biochemical systems. Quantum chemistry packages enable calculation of complex potential energy surfaces (CPESs). The imaginary part of the CPES is associated with the autoionization decay rate, which is a function of the molecular structure. Molecular dynamics simulations, within the framework of the Born-Oppenheimer approximation, require the definition of a force field. The ability to calculate the forces on the nuclei in bio-systems when autoionization takes place seems to rely on an understanding of radiative damages in RNA and DNA arising from the release of slow moving electrons which have long de Broglie wavelengths. This work addresses calculation of the real forces on the nuclei moving on the CPES. By using the transformation of the time-dependent Schrödinger equation, previously used by Madelung, we proved that the classical forces on nuclei moving on the CPES correlated with the gradient of the real part of the CPES. It was proved that the force on the nuclei of the metastable molecules is time independent although the probability to detect metastable molecules exponentially decays. The classical force is obtained from the transformed Schrödinger equation when ℏ=0 and the Schrödinger equation is reduced to the classical (Newtonian) equations of motion. The forces on the nuclei regardless on what potential energy surface they move (parent CPES or product real PESs) vary in time due to the autoionization process.

Light scattering optimization of chitin random network in ultrawhite beetle scales

NASA Astrophysics Data System (ADS)

Utel, Francesco; Cortese, Lorenzo; Pattelli, Lorenzo; Burresi, Matteo; Vignolini, Silvia; Wiersma, Diederik

2017-09-01

Among the natural white colored photonics structures, a bio-system has become of great interest in the field of disordered optical media: the scale of the white beetle Chyphochilus. Despite its low thickness, on average 7 μm, and low refractive index, this beetle exhibits extreme high brightness and unique whiteness. These properties arise from the interaction of light with a complex network of chitin nano filaments embedded in the interior of the scales. As it's been recently claimed, this could be a consequence of the peculiar morphology of the filaments network that, by means of high filling fraction (0.61) and structural anisotropy, optimizes the multiple scattering of light. We therefore performed a numerical analysis on the structural properties of the chitin network in order to understand their role in the enhancement of the scale scattering intensity. Modeling the filaments as interconnected rod shaped scattering centers, we numerically generated the spatial coordinates of the network components. Controlling the quantities that are claimed to play a fundamental role in the brightness and whiteness properties of the investigated system (filling fraction and average rods orientation, i.e. the anisotropy of the ensemble of scattering centers), we obtained a set of customized random networks. FDTD simulations of light transport have been performed on these systems, observing high reflectance for all the visible frequencies and proving the implemented algorithm to numerically generate the structures is suitable to investigate the dependence of reflectance by anisotropy.

Pioneering topological methods for network-based drug-target prediction by exploiting a brain-network self-organization theory.

PubMed

Durán, Claudio; Daminelli, Simone; Thomas, Josephine M; Haupt, V Joachim; Schroeder, Michael; Cannistraci, Carlo Vittorio

2017-04-26

The bipartite network representation of the drug-target interactions (DTIs) in a biosystem enhances understanding of the drugs' multifaceted action modes, suggests therapeutic switching for approved drugs and unveils possible side effects. As experimental testing of DTIs is costly and time-consuming, computational predictors are of great aid. Here, for the first time, state-of-the-art DTI supervised predictors custom-made in network biology were compared-using standard and innovative validation frameworks-with unsupervised pure topological-based models designed for general-purpose link prediction in bipartite networks. Surprisingly, our results show that the bipartite topology alone, if adequately exploited by means of the recently proposed local-community-paradigm (LCP) theory-initially detected in brain-network topological self-organization and afterwards generalized to any complex network-is able to suggest highly reliable predictions, with comparable performance with the state-of-the-art-supervised methods that exploit additional (non-topological, for instance biochemical) DTI knowledge. Furthermore, a detailed analysis of the novel predictions revealed that each class of methods prioritizes distinct true interactions; hence, combining methodologies based on diverse principles represents a promising strategy to improve drug-target discovery. To conclude, this study promotes the power of bio-inspired computing, demonstrating that simple unsupervised rules inspired by principles of topological self-organization and adaptiveness arising during learning in living intelligent systems (like the brain) can efficiently equal perform complicated algorithms based on advanced, supervised and knowledge-based engineering. © The Author 2017. Published by Oxford University Press.

Adsorption of insulin peptide on charged single-walled carbon nanotubes: significant role of ordered water molecules.

PubMed

Shen, Jia-Wei; Wu, Tao; Wang, Qi; Kang, Yu; Chen, Xin

2009-06-02

Ordered hydration shells: The more ordered hydration shells outside the charged CNT surfaces prevent more compact adsorption of the peptide in the charged CNT systems [picture: see text], but peptide binding strengths on the charged CNT surfaces are stronger due to the electrostatic interaction.Studies of adsorption dynamics and stability for peptides/proteins on single-walled carbon nanotubes (SWNTs) are of great importance for a better understanding of the properties and nature of nanotube-based biosystems. Herein, the dynamics and mechanism of the adsorption of the insulin chain B peptide on different charged SWNTs are investigated by explicit solvent molecular dynamics simulations. The results show that all types of surfaces effectively attract the model peptide. Water molecules play a significant role in peptide adsorption on the surfaces of charged carbon nanotubes (CNTs). Compared to peptide adsorption on neutral CNT surfaces, the more ordered hydration shells outside the tube prevent more compact adsorption of the peptide in charged CNT systems. This shield effect leads to a smaller conformational change and van der Waals interaction between the peptide and surfaces, but peptide binding strengths on charged CNT surfaces are stronger than those on the neutral CNT surface due to the strong electrostatic interaction. The result of these simulations implies the possibility of improving the binding strength of peptides/proteins on CNT surfaces, as well as keeping the integrity of the peptide/protein conformation in peptide/protein-CNT complexes by charging the CNTs.

Ecosystem growth and development.

PubMed

Fath, Brian D; Jørgensen, Sven E; Patten, Bernard C; Straskraba, Milan

2004-11-01

One of the most important features of biosystems is how they are able to maintain local order (low entropy) within their system boundaries. At the ecosystem scale, this organization can be observed in the thermodynamic parameters that describe it, such that these parameters can be used to track ecosystem growth and development during succession. Thermodynamically, ecosystem growth is the increase of energy throughflow and stored biomass, and ecosystem development is the internal reorganization of these energy mass stores, which affect transfers, transformations, and time lags within the system. Several proposed hypotheses describe thermodynamically the orientation or natural tendency that ecosystems follow during succession, and here, we consider five: minimize specific entropy production, maximize dissipation, maximize exergy storage (includes biomass and information), maximize energy throughflow, and maximize retention time. These thermodynamic orientors were previously all shown to occur to some degree during succession, and here we present a refinement by observing them during different stages of succession. We view ecosystem succession as a series of four growth and development stages: boundary, structural, network, and informational. We demonstrate how each of these ecological thermodynamic orientors behaves during the different growth and development stages, and show that while all apply during some stages only maximizing energy throughflow and maximizing exergy storage are applicable during all four stages. Therefore, we conclude that the movement away from thermodynamic equilibrium, and the subsequent increase in organization during ecosystem growth and development, is a result of system components and configurations that maximize the flux of useful energy and the amount of stored exergy. Empirical data and theoretical models support these conclusions.

Global behavior analysis for stochastic system of 1,3-PD continuous fermentation

NASA Astrophysics Data System (ADS)

Zhu, Xi; Kliemann, Wolfgang; Li, Chunfa; Feng, Enmin; Xiu, Zhilong

2017-12-01

Global behavior for stochastic system of continuous fermentation in glycerol bio-dissimilation to 1,3-propanediol by Klebsiella pneumoniae is analyzed in this paper. This bioprocess cannot avoid the stochastic perturbation caused by internal and external disturbance which reflect on the growth rate. These negative factors can limit and degrade the achievable performance of controlled systems. Based on multiplicity phenomena, the equilibriums and bifurcations of the deterministic system are analyzed. Then, a stochastic model is presented by a bounded Markov diffusion process. In order to analyze the global behavior, we compute the control sets for the associated control system. The probability distributions of relative supports are also computed. The simulation results indicate that how the disturbed biosystem tend to stationary behavior globally.

Multiplex ligation-dependent probe amplification analysis on capillary electrophoresis instruments for a rapid gene copy number study.

PubMed

Jankowski, Stéphane; Currie-Fraser, Erica; Xu, Licen; Coffa, Jordy

2008-09-01

Annotated DNA samples that had been previously analyzed were tested using multiplex ligation-dependent probe amplification (MLPA) assays containing probes targeting BRCA1, BRCA2, and MMR (MLH1/MSH2 genes) and the 9p21 chromosomal region. MLPA polymerase chain reaction products were separated on a capillary electrophoresis platform, and the data were analyzed using GeneMapper v4.0 software (Applied Biosystems, Foster City, CA). After signal normalization, loci regions that had undergone deletions or duplications were identified using the GeneMapper Report Manager and verified using the DyeScale functionality. The results highlight an easy-to-use, optimal sample preparation and analysis workflow that can be used for both small- and large-scale studies.

System-based approach for an advanced drug delivery platform

NASA Astrophysics Data System (ADS)

Kulinsky, Lawrence; Xu, Han; Tsai, Han-Kuan A.; Madou, Marc

2006-03-01

Present study is looking at the problem of integrating drug delivery microcapsule, a bio-sensor, and a control mechanism into a biomedical drug delivery system. A wide range of medical practices from cancer therapy to gastroenterological treatments can benefit from such novel bio-system. Drug release in our drug delivery system is achieved by electrochemically actuating an array of polymeric valves on a set of drug reservoirs. The valves are bi-layer structures, made in the shape of a flap hinged on one side to a valve seat, and consisting of thin films of evaporated gold and electrochemically deposited polypyrrole (PPy). These thin PPy(DBS) bi-layer flaps cover access holes of underlying chambers micromachined in a silicon substrate. Chromium and polyimide layers are applied to implement "differential adhesion" to obtain a voltage induced deflection of the bilayer away from the drug reservoir. The Cr is an adhesion-promoting layer, which is used to strongly bind the gold layer down to the substrate, whereas the gold adheres weakly to polyimide. Drug actives (dry or wet) were pre-stored in the chambers and their release is achieved upon the application of a small bias (~ 1V). Negative voltage causes cation adsorption and volume change in PPy film. This translates into the bending of the PPy/Au bi-layer actuator and release of the drug from reservoirs. This design of the drug delivery module is miniaturized to the dimensions of 200μm valve diameter. Galvanostatic and potentiostatic PPy deposition methods were compared, and potentiostatic deposition method yields film of more uniform thickness. PPy deposition experiments with various pyrrole and NaDBS concentrations were also performed. Glucose biosensor based on glucose oxidase (GOx) embedded in the PPy matrix during elechtrochemical deposition was manufactured and successfully tested. Multiple-drug pulsatile release and continuous linear release patterns can be implemented by controlling the operation of an array of valves. Varying amounts of drugs, together with more complex controlling strategies would allow creation of more complex drug delivery patterns.

Challenges in Characterizing and Controlling Complex Cellular Systems

NASA Astrophysics Data System (ADS)

Wikswo, John

2011-03-01

Multicellular dynamic biological processes such as developmental differentiation, wound repair, disease, aging, and even homeostasis can be represented by trajectories through a phase space whose extent reflects the genetic, post-translational, and metabolic complexity of the process - easily extending to tens of thousands of dimensions. Intra- and inter-cellular sensing and regulatory systems and their nested, redundant, and non-linear feed-forward and feed-back controls create high-dimensioned attractors in this phase space. Metabolism provides free energy to drive non-equilibrium processes and dynamically reconfigure attractors. Studies of single molecules and cells provide only minimalist projections onto a small number of axes. It may be difficult to infer larger-scale emergent behavior from linearized experiments that perform only small amplitude perturbations on a limited number of the dimensions. Complete characterization may succeed for bounded component problems, such as an individual cell cycle or signaling cascade, but larger systems problems will require a coarse-grained approach. Hence a new experimental and analytical framework is needed. Possibly one could utilize high-amplitude, multi-variable driving of the system to infer coarse-grained, effective models, which in turn can be tested by their ability to control systems behavior. Navigation at will between attractors in a high-dimensioned dynamical system will provide not only detailed knowledge of the shape of attractor basins, but also measures of underlying stochastic events such as noise in gene expression or receptor binding and how both affect system stability and robustness. Needed for this are wide-bandwidth methods to sense and actuate large numbers of intracellular and extracellular variables and automatically and rapidly infer dynamic control models. The success of this approach may be determined by how broadly the sensors and actuators can span the full dimensionality of the phase space. Supported by the Defense Threat Reduction Agency HDTRA-09-1-0013, NIH National Institute on Drug Abuse RC2DA028981, the National Academies Keck Futures Initiative, and the Vanderbilt Institute for Integrative Biosystems Research and Education.

Space Product Development: Bringing the Benefits of Space Down to Earth

NASA Technical Reports Server (NTRS)

Allen, Rosalie W.; Tygielski, Andrew; Gabris, Edward A.

1997-01-01

The newly developed microgravity Research Program Office was created to consolidate and integrate NASA's microgravity research efforts, comprised of the microgravity Science and Applications Program and Space Product Development Program. This resulted in an integrated agency program serving the science and industrial research communities, providing leadership, management, direction and overview of all agency microgravity research activities. This paper provides an overview of NASA's microgravity Research Program, with particular emphasis on the Space Product Development Program activities, the potential economic impact and quality of life improvements resulting from this research, and future plans for commercial microgravity research in space. The goal of the Space Product Development Program is to facilitate the use of space for commercial products and services. The unique attributes of space are exploited to conduct industry driven research in the areas of crystallography, bio-systems, agriculture, electronic and non-electronic materials. Industry uses the knowledge gained from focused space research to create new products and processes, to gain economic competitive advantages, to create new jobs and improve the quality of life on earth. The objectives of the program are implemented through NASA's Commercial Space Centers, non-profit consortia of industry, academia and government, that provide the mechanism for communication and technical expert exchange between NASA and industry. Over 200 commercial research activities have been conducted by the Commercial Space Centers and their industrial affiliates over the last four and one-half years during Space Shuttle mission, as well as sounding rocket flights. The results of this research will have a significant impact on competitive products, jobs and quality of life improvements.

Analysis and 3D reconstruction of heterogeneity in malignant brain tumors: an interdisciplinary case study using a novel computational visualization approach.

PubMed

Mojsilovic, Aleksandra; Rogowitz, Bernice; Gomes, Jose; Deisboeck, Thomas S

2002-06-01

To explore how a multidisciplinary approach, combining modern visualization and image processing techniques with innovative experimental studies, can augment the understanding of tumor development. We analyzed histologic sections of a microscopic brain tumor and reconstructed these slices into a 3D representation. We processed these slices to: (1) identify tumor boundaries, (2) isolate proliferating tumor cells, and (3) segment the tumor into regions based on the density of proliferating cells. We then reconstructed the 3D shape of the tumor using a constrained deformable surface approach. This novel method allows the analyst to (1) see specific properties of histologic slices in the 3D environment with animation, (2) switch 2D "views" dynamically, and (3) see relationships between the 3D structure and structure on a plane. Using this method to analyze a specific "case," we were also able to shed light on the limitations of a widely held assumption about the shape of expanding microscopic solid tumors as well as find more indications that such tumors behave as adaptive biosystems. Implications of these case study results, as well as future applications of the method for tumor biology research, are discussed.

Ethanol generation, oxidation and energy production in a cooperative bioelectrochemical system.

PubMed

Pagnoncelli, Kamila C; Pereira, Andressa R; Sedenho, Graziela C; Bertaglia, Thiago; Crespilho, Frank N

2018-08-01

Integrating in situ biofuel production and energy conversion into a single system ensures the production of more robust networks as well as more renewable technologies. For this purpose, identifying and developing new biocatalysts is crucial. Herein, is reported a bioelectrochemical system consisting of alcohol dehydrogenase (ADH) and Saccharomyces cerevisiae, wherein both function cooperatively for ethanol production and its bioelectrochemical oxidation. Here, it is shown that it is possible to produce ethanol and use it as a biofuel in a tandem manner. The strategy is to employ flexible carbon fibres (FCF) electrode that could adsorb both the enzyme and the yeast cells. Glucose is used as a substrate for the yeast for the production of ethanol, while the enzyme is used to catalyse the oxidation of ethanol to acetaldehyde. Regarding the generation of reliable electricity based on electrochemical systems, the biosystem proposed in this study operates at a low temperature and ethanol production is proportional to the generated current. With further optimisation of electrode design, we envision the use of the cooperative biofuel cell for energy conversion and management of organic compounds. Copyright © 2018 Elsevier B.V. All rights reserved.

Informational Closed-Loop Coding-Decoding Control Concept as the Base of the Living or Organized Systems Theory

NASA Astrophysics Data System (ADS)

Kirvelis, Dobilas; Beitas, Kastytis

2008-10-01

The aim of this work is to show that the essence of life and living systems is their organization as bioinformational technology on the base of informational anticipatory control. Principal paradigmatic and structural schemes of functional organization of life (organisms and their systems) are constructed on the basis of systemic analysis and synthesis of main phenomenological features of living world. Life is based on functional elements that implement engineering procedures of closed-loop coding-decoding control (CL-CDC). Phenomenon of natural bioinformational control appeared and developed on the Earth 3-4 bln years ago, when the life originated as a result of chemical and later biological evolution. Informatics paradigm considers the physical and chemical transformations of energy and matter in organized systems as flows that are controlled and the signals as means for purposive informational control programs. The social and technical technological systems as informational control systems are a latter phenomenon engineered by man. The information emerges in organized systems as a necessary component of control technology. Generalized schemes of functional organization on levels of cell, organism and brain neocortex, as the highest biosystem with CL-CDC, are presented. CL-CDC concept expands the understanding of bioinformatics.

Biochemical imaging of tissues by SIMS for biomedical applications

NASA Astrophysics Data System (ADS)

Lee, Tae Geol; Park, Ji-Won; Shon, Hyun Kyong; Moon, Dae Won; Choi, Won Woo; Li, Kapsok; Chung, Jin Ho

2008-12-01

With the development of optimal surface cleaning techniques by cluster ion beam sputtering, certain applications of SIMS for analyzing cells and tissues have been actively investigated. For this report, we collaborated with bio-medical scientists to study bio-SIMS analyses of skin and cancer tissues for biomedical diagnostics. We pay close attention to the setting up of a routine procedure for preparing tissue specimens and treating the surface before obtaining the bio-SIMS data. Bio-SIMS was used to study two biosystems, skin tissues for understanding the effects of photoaging and colon cancer tissues for insight into the development of new cancer diagnostics for cancer. Time-of-flight SIMS imaging measurements were taken after surface cleaning with cluster ion bombardment by Bi n or C 60 under varying conditions. The imaging capability of bio-SIMS with a spatial resolution of a few microns combined with principal component analysis reveal biologically meaningful information, but the lack of high molecular weight peaks even with cluster ion bombardment was a problem. This, among other problems, shows that discourse with biologists and medical doctors are critical to glean any meaningful information from SIMS mass spectrometric and imaging data. For SIMS to be accepted as a routine, daily analysis tool in biomedical laboratories, various practical sample handling methodology such as surface matrix treatment, including nano-metal particles and metal coating, in addition to cluster sputtering, should be studied.

Multiplex Ligation-Dependent Probe Amplification Analysis on Capillary Electrophoresis Instruments for a Rapid Gene Copy Number Study

PubMed Central

Jankowski, Stéphane; Currie-Fraser, Erica; Xu, Licen; Coffa, Jordy

2008-01-01

Annotated DNA samples that had been previously analyzed were tested using multiplex ligation-dependent probe amplification (MLPA) assays containing probes targeting BRCA1, BRCA2, and MMR (MLH1/MSH2 genes) and the 9p21 chromosomal region. MLPA polymerase chain reaction products were separated on a capillary electrophoresis platform, and the data were analyzed using GeneMapper v4.0 software (Applied Biosystems, Foster City, CA). After signal normalization, loci regions that had undergone deletions or duplications were identified using the GeneMapper Report Manager and verified using the DyeScale functionality. The results highlight an easy-to-use, optimal sample preparation and analysis workflow that can be used for both small- and large-scale studies. PMID:19137113

Bioremediation of diesel and lubricant oil-contaminated soils using enhanced landfarming system.

PubMed

Wang, Sih-Yu; Kuo, Yu-Chia; Hong, Andy; Chang, Yu-Min; Kao, Chih-Ming

2016-12-01

Lubricant and diesel oil-polluted sites are difficult to remediate because they have less volatile and biodegradable characteristics. The goal of this research was to evaluate the potential of applying an enhanced landfarming to bioremediate soils polluted by lubricant and diesel. Microcosm study was performed to evaluate the optimal treatment conditions with the addition of different additives (nutrients, addition of activated sludge from oil-refining wastewater facility, compost, TPH-degrading bacteria, and fern chips) to enhance total petroleum hydrocarbon (TPH) removal. To simulate the aerobic landfarming biosystem, air in the microcosm headspace was replaced once a week. Results demonstrate that the additives of activated sludge and compost could result in the increase in soil microbial populations and raise TPH degradation efficiency (up to 83% of TPH removal with 175 days of incubation) with initial (TPH = 4100 mg/kg). The first-order TPH degradation rate reached 0.01 1/d in microcosms with additive of activated sludge (mass ratio of soil to inocula = 50:1). The soil microbial communities were determined by nucleotide sequence analyses and 16S rRNA-based denatured gradient gel electrophoresis. Thirty-four specific TPH-degrading bacteria were detected in microcosm soils. Chromatograph analyses demonstrate that resolved peaks were more biodegradable than unresolved complex mixture. Results indicate that more aggressive remedial measures are required to enhance the TPH biodegradation, which included the increase of (1) microbial population or TPH-degrading bacteria, (2) biodegradable carbon sources, (3) nutrient content, and (4) soil permeability. Copyright © 2016 Elsevier Ltd. All rights reserved.

Influence of capillary barrier effect on biogas distribution at the base of passive methane oxidation biosystems: Parametric study.

PubMed

Ahoughalandari, Bahar; Cabral, Alexandre R

2017-05-01

The efficiency of methane oxidation in passive methane oxidation biosystems (PMOBs) is influenced by, among other things, the intensity and distribution of the CH 4 loading at the base of the methane oxidation layer (MOL). Both the intensity and distribution are affected by the capillary barrier that results from the superposition of the two materials constituting the PMOB, namely the MOL and the gas distribution layer (GDL). The effect of capillary barriers on the unsaturated flow of water has been well documented in the literature. However, its effect on gas flow through PMOBs is still poorly documented. In this study, sets of numerical simulations were performed to evaluate the effect of unsaturated hydraulic characteristics of the MOL material on the value and distribution of moisture and hence, the ease and uniformity in the distribution of the upward flow of biogas along the GDL-MOL interface. The unsaturated hydraulic parameters of the materials used to construct the experimental field plot at the St-Nicephore landfill (Quebec, Canada) were adopted to build the reference simulation of the parametric study. The behavior of the upward flow of biogas for this particular material was analyzed based on its gas intrinsic permeability function, which was obtained in the laboratory. The parameters that most influenced the distribution and the ease of biogas flow at the base of the MOL were the saturated hydraulic conductivity and pore size distribution of the MOL material, whose effects were intensified as the slope of the interface increased. The effect of initial dry density was also assessed herein. Selection of the MOL material must be made bearing in mind that these three parameters are key in the effort to prevent unwanted restriction in the upward flow of biogas, which may result in the redirection of biogas towards the top of the slope, leading to high CH 4 fluxes (hotspots). In a well-designed PMOB, upward flow of biogas across the GDL-MOL interface is unrestricted and moisture distribution is uniform. This paper tries to show how to obtain this. Copyright © 2016 Elsevier Ltd. All rights reserved.

Modification of nucleic acids by azobenzene derivatives and their applications in biotechnology and nanotechnology.

PubMed

Li, Jing; Wang, Xingyu; Liang, Xingguo

2014-12-01

Azobenzene has been widely used as a photoregulator due to its reversible photoisomerization, large structural change between E and Z isomers, high photoisomerization yield, and high chemical stability. On the other hand, some azobenzene derivatives can be used as universal quenchers for many fluorophores. Nucleic acid is a good candidate to be modified because it is not only the template of gene expression but also widely used for building well-organized nanostructures and nanodevices. Because the size and polarity distribution of the azobenzene molecule is similar to a nucleobase pair, the introduction of azobenzene into nucleic acids has been shown to be an ingenious molecular design for constructing light-switching biosystems or light-driven nanomachines. Here we review recent advances in azobenzene-modified nucleic acids and their applications for artificial regulation of gene expression and enzymatic reactions, construction of photoresponsive nanostructures and nanodevices, molecular beacons, as well as obtaining structural information using the introduced azobenzene as an internal probe. In particular, nucleic acids bearing multiple azobenzenes can be used as a novel artificial nanomaterial with merits of high sequence specificity, regular duplex structure, and high photoregulation efficiency. The combination of functional groups with biomolecules may further advance the development of chemical biotechnology and biomolecular engineering. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development of a multiplex real-time PCR for the simultaneous detection of herpes simplex and varicella zoster viruses in cerebrospinal fluid and lesion swab specimens.

PubMed

Wong, Anita A; Pabbaraju, Kanti; Wong, Sallene; Tellier, Raymond

2016-03-01

Herpes simplex viruses (HSV) and varicella zoster virus (VZV) can have very similar and wide-ranging clinical presentations. Rapid identification is necessary for timely antiviral therapy, especially with infections involving the central nervous system, neonates, and immunocompromised individuals. Detection of HSV-1, HSV-2 and VZV was combined into one real-time PCR reaction utilizing hydrolysis probes. The assay was validated on the LightCycler(®) (Roche) and Applied Biosystems 7500 Real-Time PCR System (Thermo Fisher Scientific Inc.) to detect alphaherpesviruses in cerebral spinal fluid (CSF) and lesion swab specimens, respectively. Validation data on blood and tissue samples are also presented. The multiplex assay showed excellent sensitivity, specificity and reproducibility when compared to two singleplex real-time PCR assays for CSF samples and direct fluorescent antigen/culture for lesion swab samples. Implementation of the multiplex assay has facilitated improved sensitivity and accuracy as well as reduced turn-around-times and costs. The results from a large data set of 16,622 prospective samples tested between August 16, 2012 to February 1, 2014 at the Provincial Laboratory for Public Health (Alberta, Canada) are presented here. Copyright © 2015 Elsevier B.V. All rights reserved.

Preparation of non-aggregated fluorescent nanodiamonds (FNDs) by non-covalent coating with a block copolymer and proteins for enhancement of intracellular uptake.

PubMed

Lee, Jong Woo; Lee, Seonju; Jang, Sangmok; Han, Kyu Young; Kim, Younggyu; Hyun, Jaekyung; Kim, Seong Keun; Lee, Yan

2013-05-01

Fluorescent nanodiamonds (FNDs) are very promising fluorophores for use in biosystems due to their high biocompatibility and photostability. To overcome their tendency to aggregate in physiological solutions, which severely limits the biological applications of FNDs, we developed a new non-covalent coating method using a block copolymer, PEG-b-P(DMAEMA-co-BMA), or proteins such as BSA and HSA. By simple mixing of the block copolymer with FNDs, the cationic DMAEMA and hydrophobic BMA moieties can strongly interact with the anionic and hydrophobic moieties on the FND surface, while the PEG block can form a shell to prevent the direct contact between FNDs. The polymer-coated FNDs, along with BSA- and HSA-coated FNDs, showed non-aggregation characteristics and maintained their size at the physiological salt concentration. The well-dispersed, polymer- or protein-coated FNDs in physiological solutions showed enhanced intracellular uptake, which was confirmed by CLSM. In addition, the biocompatibility of the coated FNDs was expressly supported by a cytotoxicity assay. Our simple non-covalent coating with the block copolymer, which can be easily modified by various chemical methods, projects a very promising outlook for future biomedical applications, especially in comparison with covalent coating or protein-based coating.

Comparative analytical evaluation of the respiratory TaqMan Array Card with real-time PCR and commercial multi-pathogen assays.

PubMed

Harvey, John J; Chester, Stephanie; Burke, Stephen A; Ansbro, Marisela; Aden, Tricia; Gose, Remedios; Sciulli, Rebecca; Bai, Jing; DesJardin, Lucy; Benfer, Jeffrey L; Hall, Joshua; Smole, Sandra; Doan, Kimberly; Popowich, Michael D; St George, Kirsten; Quinlan, Tammy; Halse, Tanya A; Li, Zhen; Pérez-Osorio, Ailyn C; Glover, William A; Russell, Denny; Reisdorf, Erik; Whyte, Thomas; Whitaker, Brett; Hatcher, Cynthia; Srinivasan, Velusamy; Tatti, Kathleen; Tondella, Maria Lucia; Wang, Xin; Winchell, Jonas M; Mayer, Leonard W; Jernigan, Daniel; Mawle, Alison C

2016-02-01

In this study, a multicenter evaluation of the Life Technologies TaqMan(®) Array Card (TAC) with 21 custom viral and bacterial respiratory assays was performed on the Applied Biosystems ViiA™ 7 Real-Time PCR System. The goal of the study was to demonstrate the analytical performance of this platform when compared to identical individual pathogen specific laboratory developed tests (LDTs) designed at the Centers for Disease Control and Prevention (CDC), equivalent LDTs provided by state public health laboratories, or to three different commercial multi-respiratory panels. CDC and Association of Public Health Laboratories (APHL) LDTs had similar analytical sensitivities for viral pathogens, while several of the bacterial pathogen APHL LDTs demonstrated sensitivities one log higher than the corresponding CDC LDT. When compared to CDC LDTs, TAC assays were generally one to two logs less sensitive depending on the site performing the analysis. Finally, TAC assays were generally more sensitive than their counterparts in three different commercial multi-respiratory panels. TAC technology allows users to spot customized assays and design TAC layout, simplify assay setup, conserve specimen, dramatically reduce contamination potential, and as demonstrated in this study, analyze multiple samples in parallel with good reproducibility between instruments and operators. Copyright © 2015 Elsevier B.V. All rights reserved.

Development and validation of a D-loop mtDNA SNP assay for the screening of specimens in forensic casework.

PubMed

Chemale, Gustavo; Paneto, Greiciane Gaburro; Menezes, Meiga Aurea Mendes; de Freitas, Jorge Marcelo; Jacques, Guilherme Silveira; Cicarelli, Regina Maria Barretto; Fagundes, Paulo Roberto

2013-05-01

Mitochondrial DNA (mtDNA) analysis is usually a last resort in routine forensic DNA casework. However, it has become a powerful tool for the analysis of highly degraded samples or samples containing too little or no nuclear DNA, such as old bones and hair shafts. The gold standard methodology still constitutes the direct sequencing of polymerase chain reaction (PCR) products or cloned amplicons from the HVS-1 and HVS-2 (hypervariable segment) control region segments. Identifications using mtDNA are time consuming, expensive and can be very complex, depending on the amount and nature of the material being tested. The main goal of this work is to develop a less labour-intensive and less expensive screening method for mtDNA analysis, in order to aid in the exclusion of non-matching samples and as a presumptive test prior to final confirmatory DNA sequencing. We have selected 14 highly discriminatory single nucleotide polymorphisms (SNPs) based on simulations performed by Salas and Amigo (2010) to be typed using SNaPShot(TM) (Applied Biosystems, Foster City, CA, USA). The assay was validated by typing more than 100 HVS-1/HVS-2 sequenced samples. No differences were observed between the SNP typing and DNA sequencing when results were compared, with the exception of allelic dropouts observed in a few haplotypes. Haplotype diversity simulations were performed using 172 mtDNA sequences representative of the Brazilian population and a score of 0.9794 was obtained when the 14 SNPs were used, showing that the theoretical prediction approach for the selection of highly discriminatory SNPs suggested by Salas and Amigo (2010) was confirmed in the population studied. As the main goal of the work is to develop a screening assay to skip the sequencing of all samples in a particular case, a pair-wise comparison of the sequences was done using the selected SNPs. When both HVS-1/HVS-2 SNPs were used for simulations, at least two differences were observed in 93.2% of the comparisons performed. The assay was validated with casework samples. Results show that the method is straightforward and can be used for exclusionary purposes, saving time and laboratory resources. The assay confirms the theoretic prediction suggested by Salas and Amigo (2010). All forensic advantages, such as high sensitivity and power of discrimination, as also the disadvantages, such as the occurrence of allele dropouts, are discussed throughout the article. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Synergetic computer and holonics - information dynamics of a semantic computer

NASA Astrophysics Data System (ADS)

Shimizu, H.; Yamaguchi, Y.

1987-12-01

The dynamics of semantic information in biosystem is studied based on holons, generators of mutual relations. Any biosystem has an internal world, a so-called "self", which has an intrinsic purpose rendering the system continuously alive and developed as much as possible against a fluctuating external world. External signals to the system through sensory organs are classified by the self into two basic categories, semantic information with some meaning and value for the purpose and inputs from background and noise sources. Due to this breaking of semantic symmetry, any input signals are transformed into a figure and background, respectively. As a typical example, the visual perception of vertebrates is studied. For such semantic transformation the external signal is first decomposed and converted into a number of elementary signs named "syntons" which are then transmitted into a sensory area of cortex corresponding to an image synthesizer. The synthesizer is a sort of autonomic parallel processor composed of autonomic units, "holons", which are characterized by many internal modes. Syntons are fed into the holons one by one. A set of the elementary meanings, the so-called "semons", provided to the synton are encoded in the internal modes of the holon; that is, each internal mode encodes a semon. A dynamic information theory for the transformation of external signals to semantic information is developed based on our model which we call holovision. Holovision is a dynamic model of visual perception that processes an autonomic ability to self-organize visual images. Autonomous oscillators are utilized as the line processors to encode line elements with specific orientations in their phases as semons. An information space is defined according to the assembly of holons; the spatial plane on which holons are arranged is a syntactic subspace while the internal modes of the holons span a semantic subspace in the orthogonal direction. In this information space, the image of a figure is self-organized - as a sort of spatiotemporal pattern - by autonomic coordinations of the holons that select relevant internal modes, accompanied with compression of irrelevant syntons that correspond to the background. Holons coded by a synton are relevantly connected by means of coherent relations, i.e., dynamic connections with time-coherence, in order to represent the image that varies in time depending on the instantaneous state of the external object. These connections depend on the internal modes that are cooperatively selectively selected by the holons. The image is regarded as a bridge between the external and internal world that has both external and internal consistency. The meaning of the image, i.e., transformed semantic information, is spontaneously transferred from semantic items that have a coherent relation with the image, and the external signal is perceived by the self through the image. We demonstrate that images are indeed self-organized in holovision in the previously described sense. Simulated processes of the creation of semantic information in holovision are shown to display typical features of the forgoing steps of information compression. Based on these results, we propose quantitative indices that represent the value of semantic information in the image processor as well as in the memory.

Non-complexed four cascade enzyme mixture: simple purification and synergetic co-stabilization.

PubMed

Myung, Suwan; Zhang, Y-H Percival

2013-01-01

Cell-free biosystems comprised of synthetic enzymatic pathways would be a promising biomanufacturing platform due to several advantages, such as high product yield, fast reaction rate, easy control and access, and so on. However, it was essential to produce (purified) enzymes at low costs and stabilize them for a long time so to decrease biocatalyst costs. We studied the stability of the four recombinant enzyme mixtures, all of which originated from thermophilic microorganisms: triosephosphate isomerase (TIM) from Thermus thermophiles, fructose bisphosphate aldolase (ALD) from Thermotoga maritima, fructose bisphosphatase (FBP) from T. maritima, and phosphoglucose isomerase (PGI) from Clostridium thermocellum. It was found that TIM and ALD were very stable at evaluated temperature so that they were purified by heat precipitation followed by gradient ammonia sulfate precipitation. In contrast, PGI was not stable enough for heat treatment. In addition, the stability of a low concentration PGI was enhanced by more than 25 times in the presence of 20 mg/L bovine serum albumin or the other three enzymes. At a practical enzyme loading of 1000 U/L for each enzyme, the half-life time of free PGI was prolong to 433 h in the presence of the other three enzymes, resulting in a great increase in the total turn-over number of PGI to 6.2×10(9) mole of product per mole of enzyme. This study clearly suggested that the presence of other proteins had a strong synergetic effect on the stabilization of the thermolabile enzyme PGI due to in vitro macromolecular crowding effect. Also, this result could be used to explain why not all enzymes isolated from thermophilic microorganisms are stable in vitro because of a lack of the macromolecular crowding environment.

Quantum-Like Model for Decision Making Process in Two Players Game. A Non-Kolmogorovian Model

NASA Astrophysics Data System (ADS)

Asano, Masanari; Ohya, Masanori; Khrennikov, Andrei

2011-03-01

In experiments of games, players frequently make choices which are regarded as irrational in game theory. In papers of Khrennikov (Information Dynamics in Cognitive, Psychological and Anomalous Phenomena. Fundamental Theories of Physics, Kluwer Academic, Norwell, 2004; Fuzzy Sets Syst. 155:4-17, 2005; Biosystems 84:225-241, 2006; Found. Phys. 35(10):1655-1693, 2005; in QP-PQ Quantum Probability and White Noise Analysis, vol. XXIV, pp. 105-117, 2009), it was pointed out that statistics collected in such the experiments have "quantum-like" properties, which can not be explained in classical probability theory. In this paper, we design a simple quantum-like model describing a decision-making process in a two-players game and try to explain a mechanism of the irrational behavior of players. Finally we discuss a mathematical frame of non-Kolmogorovian system in terms of liftings (Accardi and Ohya, in Appl. Math. Optim. 39:33-59, 1999).

[Diffusion and diffusion-osmosis models of the charged macromolecule transfer in barriers of biosystems].

PubMed

Varakin, A I; Mazur, V V; Arkhipova, N V; Serianov, Iu V

2009-01-01

Mathematical models of the transfer of charged macromolecules have been constructed on the basis of the classical equations of electromigration diffusion of Helmholtz-Smolukhovskii, Goldman, and Goldman-Hodgkin-Katz. It was shown that ion transfer in placental (mimicking lipid-protein barriers) and muscle barriers occurs by different mechanisms. In placental barriers, the electromigration diffusion occurs along lipid-protein channels formed due to the conformational deformation of phospholipid and protein molecules with the coefficients of diffusion D = (2.6-3.6) x 10(-8) cm2/s. The transfer in muscle barriers is due to the migration across charged interfibrillar channels with the negative diffusion activation energy, which is explained by changes in the structure of muscle fibers and expenditures of thermal energy for the extrusion of Cl- from channel walls with the diffusion coefficient D = (6.0-10.0) x 10(-6) cm2/s.

The genetic code as a periodic table: algebraic aspects.

PubMed

Bashford, J D; Jarvis, P D

2000-01-01

The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, A=(-1,0), C=(0,-1), G=(0,1), U=(1,0), data can be fitted as low order polynomials of the six coordinates in the 64-dimensional codon weight space. The work confirms and extends the recent studies by Siemion et al. (1995. BioSystems 36, 231-238) of the conformational parameters. Fundamental patterns in the data such as codon periodicities, and related harmonics and reflection symmetries, are here associated with the structure of the set of basis monomials chosen for fitting. Results are plotted using the Siemion one-step mutation ring scheme, and variants thereof. The connections between the present work, and recent studies of the genetic code structure using dynamical symmetry algebras, are pointed out.

[Current aspects of the physiopathology of the infectious process. II. Cybernetic elements in the pathogenetic structure of infectious diseases].

PubMed

Dragomirescu, M; Buzinschi, S

1980-01-01

The authors discuss the applicability of general cybernetic principles (the theory of systems and self-regulated mechanisms based on inversed connections) to the pathophysiologic structure of infections. With reference to concrete examples they outline the following elements: the appartenance of the infectious process to the notion of system (as conceived in the theory of systems), the previsible character of the functional potential of the structured system in the components of infection, and the sequental correspondence between system dynamics and the dynamics of the infectious process. Starting from the mechanism of action of the main microbial toxins, the aptitude of the latter to act upon the functional code of the macroorganism, altering the cellular and supracellular self-regulated biosystems, is demonstrated. Finally, the practical implications of assimilating cybernetic processes in the pathophysiology of infectious diseases are analyzed.

High-throughput real-time quantitative reverse transcription PCR.

PubMed

Bookout, Angie L; Cummins, Carolyn L; Mangelsdorf, David J; Pesola, Jean M; Kramer, Martha F

2006-02-01

Extensive detail on the application of the real-time quantitative polymerase chain reaction (QPCR) for the analysis of gene expression is provided in this unit. The protocols are designed for high-throughput, 384-well-format instruments, such as the Applied Biosystems 7900HT, but may be modified to suit any real-time PCR instrument. QPCR primer and probe design and validation are discussed, and three relative quantitation methods are described: the standard curve method, the efficiency-corrected DeltaCt method, and the comparative cycle time, or DeltaDeltaCt method. In addition, a method is provided for absolute quantification of RNA in unknown samples. RNA standards are subjected to RT-PCR in the same manner as the experimental samples, thus accounting for the reaction efficiencies of both procedures. This protocol describes the production and quantitation of synthetic RNA molecules for real-time and non-real-time RT-PCR applications.

First International Conference between West and East—Leonardo and Lao-Tze. Western Science Meets Eastern Wisdom. Experiences of Scientists and Intellectuals for the Creation of a New Paradigm of Modern Science

PubMed Central

2008-01-01

The Conference was organized and supported by: Nei Dan School (European School of Internal Martial Arts), NIB (Laboratory of Molecular Biology and Stem Cell Bioengineering, National Institute of Biostructures and Biosystems, Institute of Cardiology, S.Orsola-Malpighi Hospital, Bologna), WACIMA (Worldwide Association Chinese Internal Martial Arts), Arti D’Oriente (Magazine of Eastern culture and traditions), Nuovo Orizzonte (Taiji Quan School in Florence), Samurai (Journal on Martial Arts), and Pinus (First National Institute for the Unification of Medical Strategies). Nei Dan School (www.taichineidan.com, neidan@libero.it) was in charge of the organization. Future meetings of the Centro studi ‘Tao and Science’ will take place in spring 2007 in Firenze and in October 2007 in Bologna. For information: E-mail: neidan@libero.it; web site: www.taichineidan.com, www.taoandscience.com PMID:18317548

Mid-infrared spectroscopic analysis of saccharides in aqueous solutions with sodium chloride.

PubMed

Kanou, Mikihito; Kameoka, Takaharu; Suehara, Ken-Ichiro; Hashimoto, Atsushi

2017-04-01

The infrared spectral characteristics of three different types of disaccharides (trehalose, maltose, and sucrose) and four different types of monosaccharides (glucose, mannose, galactose, and fructose) in aqueous solutions with sodium chloride (NaCl) were determined. The infrared spectra were obtained using the FT-IR/ATR method and the absorption intensities respected the interaction between the saccharide and water with NaCl were determined. This study also focused on not only the glycosidic linkage position and the constituent monosaccharides, but also the concentration of the saccharides and NaCl and found that they have a significant influence on the infrared spectroscopic characterization of the disaccharides in an aqueous solution with NaCl. The absorption intensities representing the interaction between a saccharide and water with NaCl were spectroscopically determined. Additionally, the applications of MIR spectroscopy to obtain information about saccharide-NaCl interactions in foods and biosystems were suggested.

Encapsulates for Food Bioconversions and Metabolite Production

NASA Astrophysics Data System (ADS)

Breguet, Véronique; Vojinovic, Vojislav; Marison, Ian W.

The control of production costs in the food industry must be very strict as a result of the relatively low added value of food products. Since a wide variety of enzymes and/or cells are employed in the food industry for starch processing, cheese making, food preservation, lipid hydrolysis and other applications, immobilization of the cells and/or enzymes has been recognized as an attractive approach to improving food processes while minimizing costs. This is due to the fact that biocatalyst immobilization allows for easier separation/purification of the product and reutilization of the biocatalyst. The advantages of the use of immobilized systems are many, and they have a special relevance in the area of food technology, especially because industrial processes using immobilized biosystems are usually characterized by lower capital/energy costs and better logistics. The main applications of immobilization, related to the major processes of food bioconversions and metabolite production, will be described and discussed in this chapter.

Creation of Two-Particle Entanglement in Open Macroscopic Quantum Systems

DOE PAGES

Merkli, M.; Berman, G. P.; Borgonovi, F.; ...

2012-01-01

We considermore » an open quantum system of N not directly interacting spins (qubits) in contact with both local and collective thermal environments. The qubit-environment interactions are energy conserving. We trace out the variables of the thermal environments and N − 2 qubits to obtain the time-dependent reduced density matrix for two arbitrary qubits. We numerically simulate the reduced dynamics and the creation of entanglement (concurrence) as a function of the parameters of the thermal environments and the number of qubits, N . Our results demonstrate that the two-qubit entanglement generally decreases as N increases. We show analytically that, in the limit N → ∞ , no entanglement can be created. This indicates that collective thermal environments cannot create two-qubit entanglement when many qubits are located within a region of the size of the environment coherence length. We discuss possible relevance of our consideration to recent quantum information devices and biosystems.« less

Numerical modelling in biosciences using delay differential equations

NASA Astrophysics Data System (ADS)

Bocharov, Gennadii A.; Rihan, Fathalla A.

2000-12-01

Our principal purposes here are (i) to consider, from the perspective of applied mathematics, models of phenomena in the biosciences that are based on delay differential equations and for which numerical approaches are a major tool in understanding their dynamics, (ii) to review the application of numerical techniques to investigate these models. We show that there are prima facie reasons for using such models: (i) they have a richer mathematical framework (compared with ordinary differential equations) for the analysis of biosystem dynamics, (ii) they display better consistency with the nature of certain biological processes and predictive results. We analyze both the qualitative and quantitative role that delays play in basic time-lag models proposed in population dynamics, epidemiology, physiology, immunology, neural networks and cell kinetics. We then indicate suitable computational techniques for the numerical treatment of mathematical problems emerging in the biosciences, comparing them with those implemented by the bio-modellers.

An eco-sustainable green approach for heavy metals management: two case studies of developing industrial region.

PubMed

Rai, Prabhat Kumar

2012-01-01

Multifaceted issues or paradigm of sustainable development should be appropriately addressed in the discipline of environmental management. Pollution of the biosphere with toxic metals has accelerated dramatically since the beginning of the Industrial Revolution. In present review, comparative assessment of traditional chemical technologies and phytoremediation has been reviewed particularly in the context of cost-effectiveness. The potential of phytoremediation and green chemicals in heavy metals management has been described critically. Further, the review explores our work on phytoremediation as green technology during the last 6 years and hand in hand addresses the various ecological issues, benefits and constraints pertaining to heavy metal pollution of aquatic ecosystems and its phytoremediation as first case study. Second case study demonstrates the possible health implications associated with use of metal contaminated wastewater for irrigation in peri-urban areas of developing world. Our researches revealed wetland plants/macrophytes as ideal bio-system for heavy metals removal in terms of both ecology and economy, when compared with chemical treatments. However, there are several constraints or limitations in the use of aquatic plants for phytoremediation in microcosm as well as mesocosm conditions. On the basis of our past researches, an eco-sustainable model has been proposed in order to resolve the certain constraints imposed in two case studies. In relation to future prospect, phytoremediation technology for enhanced heavy metal accumulation is still in embryonic stage and needs more attention in gene manipulation area. Moreover, harvesting and recycling tools needs more extensive research. A multidisciplinary research effort that integrates the work of natural sciences, environmental engineers and policy makers is essential for greater success of green technologies as a potent tool of heavy metals management.

Global warming effects: future feasibility of current cooling equipment for animal houses

NASA Astrophysics Data System (ADS)

Valiño, V.; Perdigones, A.; García, J. L.; de La Plaza, S.

2009-04-01

Interest in global warming effects on the agricultural systems is currently high, especially in areas which are likely to be more affected by this temperature rising, i.e. the Mediterranean area (IPCC, 2008). According to this report, the model projections of surface warming predict a temperature increase between 0.5°C to 1.5°C in the European area by the period 2020-2029. The aim of the present work was to assess the future consequences of the global warming effect on the feasibility of the cooling equipment in animal houses. Several equipment combinations were compared by means of modelling the inside climate in fattening pig houses, including forced ventilation and cooling pad. The modelling was carried out for six different European locations: Spain, Greece, Italy, The Netherlands, Germany and the United Kingdom, for the today conditions; secondly, the global warming effect in the inside climate was considered in a second set of simulations, and a mean temperature rising of 2°C was taken into account. Climate data. The six European locations were: Madrid (Spain); Aliartos (Greece); Bedford (The United Kingdom); Schipol (The Netherlands); Milan (Italy); and Stuttgart (Germany). From every location, the available climate data were monthly mean temperature (To; °C); monthly mean relative humidity (HRo, %) and monthly mean solar irradiation on horizontal surface (So; W m-2). From these monthly values, hourly means were calculated resulting in 24 data for a typical day, each month. Climate model. In this study, cooling strategies resulted from the combination of natural ventilation, mechanical ventilation and cooling pads. The climate model was developed taking into account the following energy fluxes: solar radiation, ventilation (Seginer, 2002), animal heat losses (Blanes and Pedersen, 2005), and loss of energy due to the cooling pads (Seginer, 2002). Results for the present work, show a comparative scene of the inside climate by using different cooling equipment combinations, from natural ventilation to cooling pads. Simulations which include the effects of climate change show the evolution in cooling technologies which will be necessary in this kind of animal houses, in six European locations, if the global temperature rising continues with the current rate. The necessary changes in cooling technologies of animal houses, will be important in Europe when the outside air temperature rising is greater than or equal to two Celsius degrees. Intergovernmental Panel on the Climate Change. 2008. Climate Change 2007: Synthesis Report. http://www.ipcc.ch/pdf/assessment-report/ar4/syr/ar4syr.pdf I. Seginer. 2002. The Penman-Monteith Evapotranspiration Equation as an Element in Greenhouse Ventilation Design. Biosystems Eng. 82(4): 423-439. doi:10.1006/bioe2002.0086 V. Blanes, S. Pedersen. 2005. Ventilation Flow in Pig Houses measured and calculated by Carbon Dioxide, Moisture and Heat Balance Equations. Biosystems Eng. 92(4): 483-493. doi:10.1006/j.biosystemseng.2005.09.002

A hypothetical mathematical construct explaining the mechanism of biological amplification in an experimental model utilizing picoTesla (PT) electromagnetic fields.

PubMed

Saxena, Anjali; Jacobson, Jerry; Yamanashi, William; Scherlag, Benjamin; Lamberth, John; Saxena, Brij

2003-06-01

We seek to answer the conundrum: What is the fundamental mechanism by which very weak, low frequency Electromagnetic fields influence biosystems? In considering the hydrophobicity of intramembranous protein (IMP) H-bonds which cross the phospholipid bilayer of plasma membranes, and the necessity for photonic recycling in cell surface interactions after dissipation of energetic states, present models lack structure and thermodynamic properties to maintain (DeltaE) sufficient energy sources necessary for amplifications by factors of 10(12). Even though one accepts that the ligand-receptor association alters the conformation of extracellular, extruding portions of IMP's at the cell surface, and that this change can be transmitted to the cytoplasm by the transmembranous helical segments by nonlinear vibrations of proteins with generation of soliton waves, one is still unable to account for repair and balanced function. Indeed, responses of critical molecules to certain magnetic field signals may include enhanced vibrational amplitudes, increased quanta of thermal energies and order inducing interactions. We may accept that microtrabecular reticulum-receptor is associated with actin filaments and ATP molecules which contribute to the activation of the cyclase enzyme system through piezoelectricity. Magnetic fields will pass through the membrane which sharply attenuates the electric field component of an EM field, due to its high impedance. Furthermore, EM oscillations are converted to mechanical vibrations; i.e., photon-phonon transduction, to induce molecular vibrations of frequencies specifically responsible for bioamplifications of weak triggers at the membrane surface, as well as GAP junctions. The hydrogen bonds of considerable importance are those in proteins (10(12)Hz) and DNA (10(11)Hz) and may be viewed as centers of EM radiation emission in the range from the mm microwaves to the far IR. However, classical electrodynamical theory does not yield a model for biomolecular resonant responses which are integrated over time and account for the connection between the phonon field and photons. Jacobson Resonance does supply an initial physical mechanism, as equivalencies in energy to that of Zeeman Resonance (i.e., zero-order magnetic resonance) and cyclotron resonance may be derived from the DeBroglie wave particle equation. For the first time, we view the introduction of Relativity Theory to biology in the expression, mc(2)=BvLq, where m is the mass of a particle in the 'box' or 'string' (molecule in a biosystem), c is the velocity of electromagnetic field in space, independent of its inertial frame of reference, B is the magnetic flux density,v is the velocity of the carrier or 'string' (a one or two dimensional 'box') in which the particle exists, L is its dimension (length) and q represents a unit charge q=1C, by defining electromotive force as energy per unit charge. Equivalencies suggest that qvBL is one of the fundamental expressions of energy of a charged wave-particle in magnetic fields, just as Zeeman and cyclotron resonance energy expressions, gbetaB and qhB/2pim, and is applicable to all charged particles (molecules in biological systems). There may exist spontaneous, independent and incessant interactions of magnetic vector B and particles in biosystems which exert Lorentz forces. Lorentz forces may be transmitted from EM field to gravitational field as a gravity wave which return to the phonon field as microgravitational fluctuations to therein produce quantum vibrational states that increase quanta of thermal energies integrated over time. This may account for the differential of 10(12) between photonic energy of ELF waves and the Boltzman energy kT. Recent data from in vivo controlled studies are included as empirical support for the various hypotheses presented.

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments.

PubMed

MacLean, Brendan; Tomazela, Daniela M; Shulman, Nicholas; Chambers, Matthew; Finney, Gregory L; Frewen, Barbara; Kern, Randall; Tabb, David L; Liebler, Daniel C; MacCoss, Michael J

2010-04-01

Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It is open source and freely available for academic and commercial use. The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected reaction monitoring (SRM). Skyline supports using and creating MS/MS spectral libraries from a wide variety of sources to choose SRM filters and verify results based on previously observed ion trap data. Skyline exports transition lists to and imports the native output files from Agilent, Applied Biosystems, Thermo Fisher Scientific and Waters triple quadrupole instruments, seamlessly connecting mass spectrometer output back to the experimental design document. The fast and compact Skyline file format is easily shared, even for experiments requiring many sample injections. A rich array of graphs displays results and provides powerful tools for inspecting data integrity as data are acquired, helping instrument operators to identify problems early. The Skyline dynamic report designer exports tabular data from the Skyline document model for in-depth analysis with common statistical tools. Single-click, self-updating web installation is available at http://proteome.gs.washington.edu/software/skyline. This web site also provides access to instructional videos, a support board, an issues list and a link to the source code project.

Detection of levamisole exposure in cocaine users by liquid chromatography-tandem mass spectrometry.

PubMed

Lynch, Kara L; Dominy, Stephen S; Graf, Jonathan; Kral, Alexander H

2011-04-01

Levamisole, a veterinary antihelminthic, was recently recognized as an adulterant in cocaine and is known to cause severe adverse reactions in some cocaine users. Because of the health concerns involving levamisole-adulterated cocaine, we developed a liquid chromatography-tandem mass spectrometry (LC-MS-MS) method for the detection of levamisole in urine. This method was used to determine the prevalence of levamisole in cocaine-positive patient samples. All cocaine-positive urine samples that were sent to the San Francisco General Hospital Clinical Laboratory were tested for levamisole for one month. For LC, an Agilent 1200 series was used with a C(18) column and a gradient of mobile phase A (0.05% formic acid) and B (acetonitrile/methanol). Detection was carried out with an Applied Biosystems QTRAP(®) LC-MS-MS. The levamisole LC-MS-MS method was linear over the range of 5-2500 ng/mL (r > 0.996). Interassay and intraassay CVs were < 6%. The lower limit of detection for levamisole was 0.5 ng/mL. Out of 949 total urine drug screens, 20% were positive for benzoylecgonine, and of those, 88% were positive for levamisole. The high prevalence of levamisole-adulterated cocaine and potential toxicity in cocaine users is a serious public health concern. These findings validate the utility of an LC-MS-MS method for the detection of levamisole.

A dynamic metabolic flux analysis of ABE (acetone-butanol-ethanol) fermentation by Clostridium acetobutylicum ATCC 824, with riboflavin as a by-product.

PubMed

Zhao, Xinhe; Kasbi, Mayssa; Chen, Jingkui; Peres, Sabine; Jolicoeur, Mario

2017-12-01

The present study reveals that supplementing sodium acetate (NaAc) strongly stimulates riboflavin production in acetone-butanol-ethanol (ABE) fermentation by Clostridium acetobutylicum ATCC 824 with xylose as carbon source. Riboflavin production increased from undetectable concentrations to ∼0.2 g L -1 (0.53 mM) when supplementing 60 mM NaAc. Of interest, solvents production and biomass yield were also promoted with fivefold acetone, 2.6-fold butanol, and 2.4-fold biomass adding NaAc. A kinetic metabolic model, developed to simulate ABE biosystem, with riboflavin production, revealed from a dynamic metabolic flux analysis (dMFA) simultaneous increase of riboflavin (ribA) and GTP (precursor of riboflavin) (PurM) synthesis flux rates under NaAc supplementation. The model includes 23 fluxes, 24 metabolites, and 72 kinetic parameters. It also suggested that NaAc condition has first stimulated the accumulation of intracellular metabolite intermediates during the acidogenic phase, which have then fed the solventogenic phase leading to increased ABE production. In addition, NaAc resulted in higher intracellular levels of NADH during the whole culture. Moreover, lower GTP-to-adenosine phosphates (ATP, ADP, AMP) ratio under NaAc supplemented condition suggests that GTP may have a minor role in the cell energetic metabolism compared to its contribution to riboflavin synthesis. © 2017 Wiley Periodicals, Inc.

Ion-trap tandem mass spectrometric analysis of Amadori-glycated phosphatidylethanolamine in human plasma with or without diabetes.

PubMed

Nakagawa, Kiyotaka; Oak, Jeong-Ho; Higuchi, Ohki; Tsuzuki, Tsuyoshi; Oikawa, Shinichi; Otani, Haruhisa; Mune, Masatoshi; Cai, Hua; Miyazawa, Teruo

2005-11-01

Peroxidized phospholipid-mediated cytotoxicity is involved in the pathophysiology of diseases [i.e., an abnormal increase of phosphatidylcholine hydroperoxide (PCOOH) in plasma of type 2 diabetic patients]. The PCOOH accumulation may relate to Amadori-glycated phosphatidylethanolamine (Amadori-PE; deoxy-D-fructosyl phosphatidylethanolamine), because Amadori-PE causes oxidative stress. However, the occurrence of lipid glycation products, including Amadori-PE, in vivo is still unclear. Consequently, we developed an analysis method of Amadori-PE using a quadrupole/linear ion-trap mass spectrometer, the Applied Biosystems QTRAP. In positive ion mode, collision-induced dissociation of Amadori-PE produced a well-characterized diglyceride ion ([M+H-303]+) permitting neutral loss scanning and multiple reaction monitoring (MRM). When lipid extract from diabetic plasma was infused directly into the QTRAP, Amadori-PE molecular species could be screened out by neutral loss scanning. Interfacing liquid chromatography with QTRAP mass spectrometry enabled the separation and determination of predominant plasma Amadori-PE species with sensitivity of approximately 0.1 pmol/injection in MRM. The plasma Amadori-PE level was 0.08 mol% of total PE in healthy subjects and 0.15-0.29 mol% in diabetic patients. Furthermore, plasma Amadori-PE levels were positively correlated with PCOOH (a maker for oxidative stress). These results show the involvement between lipid glycation and lipid peroxidation in diabetes pathogenesis.

A Functional Approach towards Understanding the Role of the Mitochondrial Respiratory Chain in an Endomycorrhizal Symbiosis

PubMed Central

Mercy, Louis; Lucic-Mercy, Eva; Nogales, Amaia; Poghosyan, Areg; Schneider, Carolin; Arnholdt-Schmitt, Birgit

2017-01-01

Arbuscular mycorrhizal fungi (AMF) are crucial components of fertile soils, able to provide several ecosystem services for crop production. Current economic, social and legislative contexts should drive the so-called “second green revolution” by better exploiting these beneficial microorganisms. Many challenges still need to be overcome to better understand the mycorrhizal symbiosis, among which (i) the biotrophic nature of AMF, constraining their production, while (ii) phosphate acts as a limiting factor for the optimal mycorrhizal inoculum application and effectiveness. Organism fitness and adaptation to the changing environment can be driven by the modulation of mitochondrial respiratory chain, strongly connected to the phosphorus processing. Nevertheless, the role of the respiratory function in mycorrhiza remains largely unexplored. We hypothesized that the two mitochondrial respiratory chain components, alternative oxidase (AOX) and cytochrome oxidase (COX), are involved in specific mycorrhizal behavior. For this, a complex approach was developed. At the pre-symbiotic phase (axenic conditions), we studied phenotypic responses of Rhizoglomus irregulare spores with two AOX and COX inhibitors [respectively, salicylhydroxamic acid (SHAM) and potassium cyanide (KCN)] and two growth regulators (abscisic acid – ABA and gibberellic acid – Ga3). At the symbiotic phase, we analyzed phenotypic and transcriptomic (genes involved in respiration, transport, and fermentation) responses in Solanum tuberosum/Rhizoglomus irregulare biosystem (glasshouse conditions): we monitored the effects driven by ABA, and explored the modulations induced by SHAM and KCN under five phosphorus concentrations. KCN and SHAM inhibited in vitro spore germination while ABA and Ga3 induced differential spore germination and hyphal patterns. ABA promoted mycorrhizal colonization, strong arbuscule intensity and positive mycorrhizal growth dependency (MGD). In ABA treated plants, R. irregulare induced down-regulation of StAOX gene isoforms and up-regulation of genes involved in plant COX pathway. In all phosphorus (P) concentrations, blocking AOX or COX induced opposite mycorrhizal patterns in planta: KCN induced higher Arum-type arbuscule density, positive MGD but lower root colonization compared to SHAM, which favored Paris-type formation and negative MGD. Following our results and current state-of-the-art knowledge, we discuss metabolic functions linked to respiration that may occur within mycorrhizal behavior. We highlight potential connections between AOX pathways and fermentation, and we propose new research and mycorrhizal application perspectives. PMID:28424712

Polymorphisms of interleukin 6 in Down syndrome individuals: a case-control study.

PubMed

Mattos, M F; Uback, L; Biselli-Chicote, P M; Biselli, J M; Goloni-Bertollo, E M; Pavarino, E C

2017-08-17

Down syndrome (DS) individuals present impaired adaptive immune system. However, the etiology of the immunological deficiency in these individuals is not completely understood. This study investigated the frequency of interleukin 6 polymorphisms (rs1800795, rs1800796, and rs1800797) in individuals with DS and individuals without the syndrome. The study included 282 individuals, 94 with DS attended at the General Genetics Outpatient Service of Hospital de Base, São José do Rio Preto, SP, Brazil, and 188 individuals without DS attended at the Pediatric Service of Hospital de Base de São José do Rio Preto, SP, Brazil. Genotyping was performed by allelic discrimination technique by real-time polymerase chain reaction using TaqMan SNP Genotyping Assays (Applied Biosystems). There was no difference in the genotype frequency between individuals with and without DS for the evaluated polymorphisms (P > 0.05). The frequency of interleukin 6 polymorphisms did not differ significantly between individuals with and without DS in the casuistic analyzed.

Paternity testing in case of brother-sister incest.

PubMed

Macan, Marijana; Uvodić, Petra; Botica, Vladimir

2003-06-01

We performed a paternity test in a case of incest between brother and sister. DNA from blood samples of the alleged parents and their two children was obtained with Chelex DNA extraction method and quantified with Applied Biosystems QuantiBlot quantitation kit. Polymerase chain reaction (PCR) amplification of DNA samples was performed with AmpFlSTR SGM Plus PCR amplification kit and GenePrint PowerPlex PCR amplification kit. The amplified products were separated and detected by using the Perkin Elmer's ABI PRISM trade mark 310 Genetic Analyser. DNA and data analysis of 17 loci and Amelogenin confirmed the suspicion of brother-sister incest. Since both children had inherited all of the obligate alleles from the alleged father, we could confirm with certainty of 99.999999% that the oldest brother in the family was the biological father of both children. Calculated data showed that even in a case of brother-sister incest, paternity could be proved by the analysis of Amelogenin and 17 DNA loci.

A pneumatic device for rapid loading of DNA sequencing gels.

PubMed

Panussis, D A; Cook, M W; Rifkin, L L; Snider, J E; Strong, J T; McGrane, R M; Wilson, R K; Mardis, E R

1998-05-01

This work describes the design and construction of a device that facilitates the loading of DNA samples onto polyacrylamide gels for detection in the Perkin Elmer/Applied Biosystems (PE/ABI) 373 and 377 DNA sequencing instruments. The device is mounted onto the existing gel cassettes and makes the process of loading high-density gels less cumbersome while the associated time and errors are reduced. The principle of operation includes the simultaneous transfer of the entire batch of samples, in which a spring-loaded air cylinder generates positive pressure and flexible silica capillaries transfer the samples. A retractable capillary array carrier allows the delivery ends of the capillaries to be held up clear of the gel during loader attachment on the gel plates, while enabling their insertion in the gel wells once the device is securely mounted. Gel-loading devices capable of simultaneously transferring 72 samples onto the PE/ABI 373 and 377 are currently being used in our production sequencing groups while a 96-sample transfer prototype undergoes testing.

General Formalism of Decision Making Based on Theory of Open Quantum Systems

NASA Astrophysics Data System (ADS)

Asano, M.; Ohya, M.; Basieva, I.; Khrennikov, A.

2013-01-01

We present the general formalism of decision making which is based on the theory of open quantum systems. A person (decision maker), say Alice, is considered as a quantum-like system, i.e., a system which information processing follows the laws of quantum information theory. To make decision, Alice interacts with a huge mental bath. Depending on context of decision making this bath can include her social environment, mass media (TV, newspapers, INTERNET), and memory. Dynamics of an ensemble of such Alices is described by Gorini-Kossakowski-Sudarshan-Lindblad (GKSL) equation. We speculate that in the processes of evolution biosystems (especially human beings) designed such "mental Hamiltonians" and GKSL-operators that any solution of the corresponding GKSL-equation stabilizes to a diagonal density operator (In the basis of decision making.) This limiting density operator describes population in which all superpositions of possible decisions has already been resolved. In principle, this approach can be used for the prediction of the distribution of possible decisions in human populations.

Compartmentalized microchannel array for high-throughput analysis of single cell polarized growth and dynamics

DOE PAGES

Geng, Tao; Bredeweg, Erin L.; Szymanski, Craig J.; ...

2015-11-04

Here, interrogating polarized growth is technologically challenging due to extensive cellular branching and uncontrollable environmental conditions in conventional assays. Here we present a robust and high-performance microfluidic system that enables observations of polarized growth with enhanced temporal and spatial control over prolonged periods. The system has built-in tunability and versatility to accommodate a variety of science applications requiring precisely controlled environments. Using the model filamentous fungus, Neurospora crassa, this microfluidic system enabled direct visualization and analysis of cellular heterogeneity in a clonal fungal cell population, nuclear distribution and dynamics at the subhyphal level, and quantitative dynamics of gene expression withmore » single hyphal compartment resolution in response to carbon source starvation and exchange experiments. Although the microfluidic device is demonstrated on filamentous fungi, our technology is immediately extensible to a wide array of other biosystems that exhibit similar polarized cell growth with applications ranging from bioenergy production to human health.« less

STR-typing of ancient skeletal remains: which multiplex-PCR kit is the best?

PubMed Central

Harder, Melanie; Renneberg, Rebecca; Meyer, Patrick; Krause-Kyora, Ben; von Wurmb-Schwark, Nicole

2012-01-01

Aim To comparatively test nine commercially available short tandem repeat (STR)-multiplex kits (PowerPlex 16, 16HS, ES, ESI17, ESX17, S5 [all Promega]; AmpFiSTR Identifiler, NGM and SEfiler [all Applied Biosystems]) for their efficiency and applicability to analyze ancient and thus highly degraded DNA samples. Methods Fifteen human skeletal remains from the late medieval age were obtained and analyzed using the nine polymerase chain reaction assays with slightly modified protocols. Data were systematically compared to find the most meaningful and sensitive assay. Results The ESI, ESX, and NGM kits showed the best overall results regarding amplification success, detection rate, identification of heterozygous alleles, sex determination, and reproducibility of the obtained data. Conclusion Since application of these three kits enables the employment of different primer sequences for all the investigated amplicons, a combined application is recommended for best possible and – most importantly – reliable genetic analysis of ancient skeletal material or otherwise highly degraded samples, eg, from forensic cases. PMID:23100203

Reciprocity phase in various 2×2 games by agents equipped with two-memory length strategy encouraged by grouping for interaction and adaptation.

PubMed

Wakiyama, Motoya; Tanimoto, Jun

2011-01-01

This paper numerically investigates 2×2 games involving the Prisoner's Dilemma, Chicken, Hero, Leader, Stag Hunt, and Trivial Games in which agents have a strategy expressed by five-bit, two-memory length. Our motivation is to explore how grouping for game interaction and strategy adaptation influence ST reciprocity and R reciprocity (Tanimoto and Sagara, 2007a [Tanimoto, J., Sagara, H., 2007a. A study on emergence of coordinated alternating reciprocity in a 2×2 game with 2-memory length strategy. Biosystems 90(3), 728-737]. Enhanced R reciprocity is observed with the stronger grouping for game interaction when a relatively stronger grouping for strategy adaptation is assumed. On the other hand, enhanced ST reciprocity emerged with the stronger grouping for strategy adaptation when the relatively weaker grouping for game interaction is imposed. Our numerical experiment deals with those two groupings independently and dependently. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

ATP analogues at a glance.

PubMed

Bagshaw, C

2001-02-01

ATP has long been known to play a central role in the energetics of cells both in transduction mechanisms and in metabolic pathways, and is involved in regulation of enzyme, channel and receptor activities. Numerous ATP analogues have been synthesised to probe the role of ATP in biosystems (Yount, 1975; Jameson and Eccleston, 1997; Bagshaw, 1998). In general, two contrasting strategies are employed. Modifications may be introduced deliberately to change the properties of ATP (e.g. making it non-hydrolysable) so as to perturb the chemical steps involved in its action. Typically these involve modification of the phosphate chain. Alternatively, derivatives (e.g. fluorescent probes) are designed to report on the action of ATP but have a minimal effect on its properties. ATP-utilising systems vary enormously in their specificity; so what acts as a good analogue in one case may be very poor in another. The accompanying poster shows a representative selection of derivatives that have been synthesised and summarises their key properties.

Modifications and substitutions of the RNA extraction module in the ViroSeq HIV-1 genotyping system version 2: effects on sensitivity and complexity of the assay.

PubMed

Stürmer, Martin; Berger, Annemarie; Doerr, Hans-Wilhelm

2003-12-01

Genotypic testing for HIV-1 resistance to anti-retroviral drugs has become accepted widely as a routine method to guide anti-retroviral therapy. However, implementation into routine high-throughput laboratory diagnosis is difficult due to the complexity of the assay. A commercially available assay is the ViroSeq HIV-1 Genotyping System (Applied Biosystems, Weiterstadt, Germany). We modified and substituted the RNA extraction module to optimize the proportion of samples amplified successfully as follows: 1 ml plasma was concentrated by ultracentrifugation and extracted according to the manufacturer's instructions (Kit), by substituting the lysis buffer (Roche, Roche Diagnostics GmbH, Mannheim, Germany), and by using the QIAamp Viral RNA Kit (Qiagen GmbH, Hilden, Germany) with elution volumes of 60 (Q60) or 50 micro l (Q50). Overall Q50 showed a higher success rate (97%) than the other extraction modules used (range 88-91%). In samples with a viral load range of 1,000-4,999 copies/ml, Q50 was superior (95 vs. 65% to 83%), while in samples with a viral load range of 5,000-9,999 copies/ml or those with 10,000 or more copies/ml, the success rate of the extraction procedures showed no significant differences. In 18 samples, which were negative using the Kit or Roche extraction, Q60 resulted in 7/18 positive results; in addition the Q50 was successful in amplifying 7/10 of the Q60 negative samples. When investigating samples with a measurable viral load of less than 1,000 copies/ml or lower, Q50 had the highest success rate with 80% compared to the other procedures (33-63%). A statistically significant new cut-off could be defined for Q50 at a value of 250 copies/ml. The results showed clearly that the ViroSeq System is suitable for analyzing the HIV-1 genotype over a wide range of viral loads but could be improved significantly when substituting the RNA extraction module with Q50 without using a nested PCR protocol. This is of great importance as it avoids further time- and cost-intensive steps. Copyright 2003 Wiley-Liss, Inc.

Development and inter-laboratory validation of unlabeled probe melting curve analysis for detection of JAK2 V617F mutation in polycythemia vera.

PubMed

Wu, Zhiyuan; Yuan, Hong; Zhang, Xinju; Liu, Weiwei; Xu, Jinhua; Zhang, Wei; Guan, Ming

2011-01-01

JAK2 V617F, a somatic point mutation that leads to constitutive JAK2 phosphorylation and kinase activation, has been incorporated into the WHO classification and diagnostic criteria of myeloid neoplasms. Although various approaches such as restriction fragment length polymorphism, amplification refractory mutation system and real-time PCR have been developed for its detection, a generic rapid closed-tube method, which can be utilized on routine genetic testing instruments with stability and cost-efficiency, has not been described. Asymmetric PCR for detection of JAK2 V617F with a 3'-blocked unlabeled probe, saturate dye and subsequent melting curve analysis was performed on a Rotor-Gene® Q real-time cycler to establish the methodology. We compared this method to the existing amplification refractory mutation systems and direct sequencing. Hereafter, the broad applicability of this unlabeled probe melting method was also validated on three diverse real-time systems (Roche LightCycler® 480, Applied Biosystems ABI® 7500 and Eppendorf Mastercycler® ep realplex) in two different laboratories. The unlabeled probe melting analysis could genotype JAK2 V617F mutation explicitly with a 3% mutation load detecting sensitivity. At level of 5% mutation load, the intra- and inter-assay CVs of probe-DNA heteroduplex (mutation/wild type) covered 3.14%/3.55% and 1.72%/1.29% respectively. The method could equally discriminate mutant from wild type samples on the other three real-time instruments. With a high detecting sensitivity, unlabeled probe melting curve analysis is more applicable to disclose JAK2 V617F mutation than conventional methodologies. Verified with the favorable inter- and intra-assay reproducibility, unlabeled probe melting analysis provided a generic mutation detecting alternative for real-time instruments.

Optimizing wind pumps system for crop irrigation based on wind data processing

NASA Astrophysics Data System (ADS)

Ruiz, Fernando; Tarquis, Ana M.; Sanchez, Raúl; Garcia, Jose Luis

2015-04-01

Crop irrigation is a major consumer of energy that can be resolved with renewable ones, such as wind, which has experienced recent developments in the area of power generation. Therefore, wind power can play an interesting role in irrigation projects in different areas [1]. A simple methodology has been developed in previous papers for technical evaluation of windmills for irrigation water pumping [2]. This methodology can determine the feasibility of the technology and the levels of daily irrigation demand satisfied by windmills. The present work compared the possibilities of this methodology adjusting the three-hourly wind velocity to the Weibull II distribution function, without considering the time sequence [2], or processing wind data using time series analysis. The study was applied to practical cases of wind pumps for irrigation of crops, both in the outside (corn) and inside greenhouses (tomato). The analysis showed that the use of three hourly time series analysis supplied a more realistic modelling of the situation with a better optimization of the water storage tank of the wind pump facility taking into account the risk of calm periods in which the pumping is null. A factor to consider in this study is available precision of the wind sampling rate. References [1] Díaz-Méndez, R., Adnan Rasheed, M. Peillón, A. Perdigones, R. Sánchez, A.M. Tarquis, José L. García-Fernández. Wind pumps for irrigating greenhouse crops: comparison in different socio-economical frameworks. Biosystems Engineering, 128, 21-28, 2014. [2] Peillón, M., Sánchez, R., Tarquis, A.M., García, J.L. The use of wind pumps for greenhouse microirrigation: A case study for tomato in Cuba. Agricultural Water Management, 120, 107-114, 2013.

Investigation of the unusual behavior of cesium-137 and other radionuclides in the Florida environment. Progress report, September 1, 1975--August 31, 1976. [Digitaria decumbens, Paspalum notatum

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

Gamble, J.F.

1976-01-01

The most significant development in the contract year was the documentation of the presence of endomycorrhizal, vesicular arbuscular (V-A) mycorrhizae in the pasture systems of south Florida that have the elevated levels of cesium-137 activity. In all samples the V-A hyphal network was well developed and growing throughout the particles of organic matter. The organic particles are held in a loose, aggregate structure by the hyphal network. In improved pastures of Digitaria decumbens (pangola) and Paspalum notatum (bahiagrass) the root infection ranged from 24 to 95 percent. The principle association was Gigaspora and Glomus sp. In the unimproved pastures ofmore » mostly Aristida stricta (wiregrass) and Serenoa repens (saw palmetto) the infection was 70 percent and only Acaulospora laevis was found. Experiments are in progress to show whether there are differences in cesium uptake between mycorrhizal and non-mycorrhizal grass plants. The test grass is pangola. Greenhouse tests involve V-A mycorrhizal control using a fungicide, the infection of grass cuttings with mycorrhizal strains found in the test area. These pot experiments will serve as pilot programs for field experiments. The effects of ectomycorrhizal associations on uptake of cesium in pine seedlings is also being studied. Analysis of the dynamics of organic matter cycling in a mesic hardwood forest shows that the rates of organic matter flow are similar to tropical systems although the plant species are warm temperate. The increased tempo of organic turnover probably contributes to the observed higher-than-expected levels of cesium-137 activity in Florida biosystems.« less

A sensitive and innovative detection method for rapid C-reactive proteins analysis based on a micro-fluxgate sensor system

PubMed Central

Yang, Zhen; Zhi, Shaotao; Feng, Zhu; Lei, Chong; Zhou, Yong

2018-01-01

A sensitive and innovative assay system based on a micro-MEMS-fluxgate sensor and immunomagnetic beads-labels was developed for the rapid analysis of C-reactive proteins (CRP). The fluxgate sensor presented in this study was fabricated through standard micro-electro-mechanical system technology. A multi-loop magnetic core made of Fe-based amorphous ribbon was employed as the sensing element, and 3-D solenoid copper coils were used to control the sensing core. Antibody-conjugated immunomagnetic microbeads were strategically utilized as signal tags to label the CRP via the specific conjugation of CRP to polyclonal CRP antibodies. Separate Au film substrates were applied as immunoplatforms to immobilize CRP-beads labels through classical sandwich assays. Detection and quantification of the CRP at different concentrations were implemented by detecting the stray field of CRP labeled magnetic beads using the newly-developed micro-fluxgate sensor. The resulting system exhibited the required sensitivity, stability, reproducibility, and selectivity. A detection limit as low as 0.002 μg/mL CRP with a linearity range from 0.002 μg/mL to 10 μg/mL was achieved, and this suggested that the proposed biosystem possesses high sensitivity. In addition to the extremely low detection limit, the proposed method can be easily manipulated and possesses a quick response time. The response time of our sensor was less than 5 s, and the entire detection period for CRP analysis can be completed in less than 30 min using the current method. Given the detection performance and other advantages such as miniaturization, excellent stability and specificity, the proposed biosensor can be considered as a potential candidate for the rapid analysis of CRP, especially for point-of-care platforms. PMID:29601593

Liquid chromatography-tandem mass spectrometry method for the measurement of serum mevalonic acid: a novel marker of hydroxymethylglutaryl coenzyme A reductase inhibition by statins.

PubMed

Waldron, Jenna; Webster, Craig

2011-05-01

Mevalonic acid (MVA) is synthesized at an early and rate-limiting step in the biosynthesis of cholesterol by the enzyme hydroxymethylglutaryl coenzyme A (HMG-CoA) reductase, and is a useful measure of statin efficacy or treatment. A liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the measurement of serum MVA has been developed. Following the in vitro conversion of MVA to mevalonic acid lactone (MVAL) in the serum, MVAL and a deuterated internal standard were extracted using an online solid-phase extraction procedure. Chromatographic separation was achieved using a Luna PFP column (Phenomenex), with enhanced selectivity and improved resolution for polar compounds. A gradient system was used, with mobile phase comprising methanol and water (5 mmol/L ammonium formate buffer, pH 2.5). Analysis was performed using an API 5000 tandem mass spectrometer (Applied Biosystems) in positive electrospray ionization mode. The method showed excellent recoveries (98 ± 8%) and imprecision (intra-assay coefficient of variation of 2.2% [6.5 ng/mL] and 2.6% [10.5 ng/mL], and inter-assay coefficient of variation of 9% [10.5 ng/mL]). The assay provides a calibration range up to 50 ng/mL with a limit of detection at 0.1 ng/mL. A simple, rapid and analytically specific method has been developed for the measurement of serum MVA, in the form of MVAL. The high analytical sensitivity of the method allows for accurate quantitation of MVAL in serum samples, both at the endogenous levels found in healthy individuals and in statin-treated patients where normal levels are expected to be greatly reduced through the inhibition of HMG-CoA reductase.

A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments.

PubMed

Moulder, Robert; Filén, Jan-Jonas; Salmi, Jussi; Katajamaa, Mikko; Nevalainen, Olli S; Oresic, Matej; Aittokallio, Tero; Lahesmaa, Riitta; Nyman, Tuula A

2005-07-01

The options available for processing quantitative data from isotope coded affinity tag (ICAT) experiments have mostly been confined to software specific to the instrument of acquisition. However, recent developments with data format conversion have subsequently increased such processing opportunities. In the present study, data sets from ICAT experiments, analysed with liquid chromatography/tandem mass spectrometry (MS/MS), using an Applied Biosystems QSTAR Pulsar quadrupole-TOF mass spectrometer, were processed in triplicate using separate mass spectrometry software packages. The programs Pro ICAT, Spectrum Mill and SEQUEST with XPRESS were employed. Attention was paid towards the extent of common identification and agreement of quantitative results, with additional interest in the flexibility and productivity of these programs. The comparisons were made with data from the analysis of a specifically prepared test mixture, nine proteins at a range of relative concentration ratios from 0.1 to 10 (light to heavy labelled forms), as a known control, and data selected from an ICAT study involving the measurement of cytokine induced protein expression in human lymphoblasts, as an applied example. Dissimilarities were detected in peptide identification that reflected how the associated scoring parameters favoured information from the MS/MS data sets. Accordingly, there were differences in the numbers of peptides and protein identifications, although from these it was apparent that both confirmatory and complementary information was present. In the quantitative results from the three programs, no statistically significant differences were observed.

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

PubMed Central

MacLean, Brendan; Tomazela, Daniela M.; Shulman, Nicholas; Chambers, Matthew; Finney, Gregory L.; Frewen, Barbara; Kern, Randall; Tabb, David L.; Liebler, Daniel C.; MacCoss, Michael J.

2010-01-01

Summary: Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It is open source and freely available for academic and commercial use. The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected reaction monitoring (SRM). Skyline supports using and creating MS/MS spectral libraries from a wide variety of sources to choose SRM filters and verify results based on previously observed ion trap data. Skyline exports transition lists to and imports the native output files from Agilent, Applied Biosystems, Thermo Fisher Scientific and Waters triple quadrupole instruments, seamlessly connecting mass spectrometer output back to the experimental design document. The fast and compact Skyline file format is easily shared, even for experiments requiring many sample injections. A rich array of graphs displays results and provides powerful tools for inspecting data integrity as data are acquired, helping instrument operators to identify problems early. The Skyline dynamic report designer exports tabular data from the Skyline document model for in-depth analysis with common statistical tools. Availability: Single-click, self-updating web installation is available at http://proteome.gs.washington.edu/software/skyline. This web site also provides access to instructional videos, a support board, an issues list and a link to the source code project. Contact: brendanx@u.washington.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20147306

Response of soybean rhizosphere communities to human hygiene water addition as determined by community level physiological profiling (CLPP) and terminal restriction fragment length polymorphism (TRFLP) analysis

NASA Technical Reports Server (NTRS)

Kerkhof, L.; Santoro, M.; Garland, J.

2000-01-01

In this report, we describe an experiment conducted at Kennedy Space Center in the biomass production chamber (BPC) using soybean plants for purification and processing of human hygiene water. Specifically, we tested whether it was possible to detect changes in the root-associated bacterial assemblage of the plants and ultimately to identify the specific microorganism(s) which differed when plants were exposed to hygiene water and other hydroponic media. Plants were grown in hydroponics media corresponding to four different treatments: control (Hoagland's solution), artificial gray water (Hoagland's+surfactant), filtered gray water collected from human subjects on site, and unfiltered gray water. Differences in rhizosphere microbial populations in all experimental treatments were observed when compared to the control treatment using both community level physiological profiles (BIOLOG) and molecular fingerprinting of 16S rRNA genes by terminal restriction fragment length polymorphism analysis (TRFLP). Furthermore, screening of a clonal library of 16S rRNA genes by TRFLP yielded nearly full length SSU genes associated with the various treatments. Most 16S rRNA genes were affiliated with the Klebsiella, Pseudomonas, Variovorax, Burkholderia, Bordetella and Isosphaera groups. This molecular approach demonstrated the ability to rapidly detect and identify microorganisms unique to experimental treatments and provides a means to fingerprint microbial communities in the biosystems being developed at NASA for optimizing advanced life support operations.

pH-switchable electrochemical sensing platform based on chitosan-reduced graphene oxide/concanavalin a layer for assay of glucose and urea.

PubMed

Song, Yonghai; Liu, Hongyu; Tan, Hongliang; Xu, Fugang; Jia, Jianbo; Zhang, Lixue; Li, Zhuang; Wang, Li

2014-02-18

A facile and effective electrochemical sensing platform for the detection of glucose and urea in one sample without separation was developed using chitosan-reduced graphene oxide (CS-rGO)/concanavalin A (Con A) as a sensing layer. The CS-rGO/Con A with pH-dependent surface net charges exhibited pH-switchable response to negatively charged Fe(CN)6(3-). The principle for glucose and urea detection was essentially based on in situ pH-switchable enzyme-catalyzed reaction in which the oxidation of glucose catalyzed by glucose oxidase or the hydrolyzation of urea catalyzed by urease resulted in a pH change of electrolyte solution to give different electrochemical responses toward Fe(CN)6(3-). It was verified by cyclic voltammograms, differential pulse voltammograms, and electrochemical impedance spectroscopy. The resistance to charge transfer or amperometric current changed proportionally toward glucose concentration from 1.0 to 10.0 mM and urea concentration from 1.0 to 7.0 mM. On the basis of human serum experiments, the sensing platform was proved to be suitable for simultaneous assay of glucose and urea in a practical biosystem. This work not only gives a way to detect glucose and urea in one sample without separation but also provides a potential strategy for the detection of nonelectroactive species based on the enzyme-catalyzed reaction and pH-switchable biosensor.

Internal validation of the DNAscan/ANDE™ Rapid DNA Analysis™ platform and its associated PowerPlex® 16 high content DNA biochip cassette for use as an expert system with reference buccal swabs.

PubMed

Moreno, Lilliana I; Brown, Alice L; Callaghan, Thomas F

2017-07-01

Rapid DNA platforms are fully integrated systems capable of producing and analyzing short tandem repeat (STR) profiles from reference sample buccal swabs in less than two hours. The technology requires minimal user interaction and experience making it possible for high quality profiles to be generated outside an accredited laboratory. The automated production of point of collection reference STR profiles could eliminate the time delay for shipment and analysis of arrestee samples at centralized laboratories. Furthermore, point of collection analysis would allow searching against profiles from unsolved crimes during the normal booking process once the infrastructure to immediately search the Combined DNA Index System (CODIS) database from the booking station is established. The DNAscan/ANDE™ Rapid DNA Analysis™ System developed by Network Biosystems was evaluated for robustness and reliability in the production of high quality reference STR profiles for database enrollment and searching applications. A total of 193 reference samples were assessed for concordance of the CODIS 13 loci. Studies to evaluate contamination, reproducibility, precision, stutter, peak height ratio, noise and sensitivity were also performed. The system proved to be robust, consistent and dependable. Results indicated an overall success rate of 75% for the 13 CODIS core loci and more importantly no incorrect calls were identified. The DNAscan/ANDE™ could be confidently used without human interaction in both laboratory and non-laboratory settings to generate reference profiles. Published by Elsevier B.V.

Pichia pastoris: a recombinant microfactory for antibodies and human membrane proteins.

PubMed

Gonçalves, A M; Pedro, A Q; Maia, C; Sousa, F; Queiroz, J A; Passarinha, L A

2013-05-01

During the last few decades, it has become evident that the compatibility of the yeast biochemical environment with the ability to process and translate the RNA transcript, along with its capacity to modify a translated protein, are relevant requirements for selecting this host cell for protein expression in several pharmaceutical and clinical applications. In particular, Pichia pastoris is used as an industrial host for recombinant protein and metabolite production, showing a powerful capacity to meet required biomolecular target production levels in high-throughput assays for functional genomics and drug screening. In addition, there is a great advantage to using P. pastoris for protein secretion, even at high molecular weights, since the recovery and purification steps are simplified owing to relatively low levels of endogenous proteins in the extracellular medium. Clearly, no single microexpression system can provide all of the desired properties for human protein production. Moreover, chemical and physical bioprocess parameters, including culture medium formulation, temperature, pH, agitation, aeration rates, induction, and feeding strategies, can highly influence product yield and quality. In order to benefit from the currently available wide range of biosynthesis strategies using P. pastoris, this mini review focuses on the developments and technological fermentation achievements, providing both a comparative and an overall integration analysis. The main aim is to highlight the relevance and versatility of the P. pastoris biosystem to the design of more cost-effective microfactories to meet the increasing demands for recombinant membrane proteins and clinical antibodies for several therapeutic applications.

Self-Reported Ethnicity and Genetic Ancestry in Relation to Oral Cancer and Pre-Cancer in Puerto Rico

PubMed Central

Erdei, Esther; Sheng, Huiping; Maestas, Erika; Mackey, Amanda; White, Kirsten A.; Li, Lin; Dong, Yan; Taylor, Justin; Berwick, Marianne; Morse, Douglas E.

2011-01-01

Background Hispanics are known to be an extremely diverse and genetically admixed ethnic group. The lack of methodologies to control for ethnicity and the unknown admixture in complex study populations of Hispanics has left a gap in understanding certain cancer disparity issues. Incidence rates for oral and pharyngeal cancer (OPC) in Puerto Rico are among the highest in the Western Hemisphere. We conducted an epidemiological study to examine risk and protective factors, in addition to possible genetic susceptibility components, for oral cancer and precancer in Puerto Rico. Methodology/Principal Findings We recruited 310 Puerto Rico residents who had been diagnosed with either an incident oral squamous cell carcinoma, oral precancer, or benign oral condition. Participants completed an in-person interview and contributed buccal cells for DNA extraction. ABI Biosystem Taqman™ primer sets were used for genotyping 12 ancestry informative markers (AIMs). Ancestral group estimates were generated using maximum likelihood estimation software (LEADMIX), and additional principal component analysis was carried out to detect population substructures. We used unconditional logistic regression to assess the contribution of ancestry to the risk of being diagnosed with either an oral cancer or precancer while controlling for other potential confounders. The maximum likelihood estimates showed that study participants had a group average ancestry contribution of 69.9% European, 24.5% African, and 5.7% detectable Native American. The African and Indigenous American group estimates were significantly higher than anticipated. Neither self-identified ethnicity nor ancestry markers showed any significant associations with oral cancer/precancer risk in our study. Conclusions/Significance The application of ancestry informative markers (AIMs), specifically designed for Hispanics, suggests no hidden population substructure is present based on our sampling and provides a viable approach for the evaluation and control of ancestry in future studies involving Hispanic populations. PMID:21897864

Phylogenetic Network Analysis Revealed the Occurrence of Horizontal Gene Transfer of 16S rRNA in the Genus Enterobacter

PubMed Central

Sato, Mitsuharu; Miyazaki, Kentaro

2017-01-01

Horizontal gene transfer (HGT) is a ubiquitous genetic event in bacterial evolution, but it seldom occurs for genes involved in highly complex supramolecules (or biosystems), which consist of many gene products. The ribosome is one such supramolecule, but several bacteria harbor dissimilar and/or chimeric 16S rRNAs in their genomes, suggesting the occurrence of HGT of this gene. However, we know little about whether the genes actually experience HGT and, if so, the frequency of such a transfer. This is primarily because the methods currently employed for phylogenetic analysis (e.g., neighbor-joining, maximum likelihood, and maximum parsimony) of 16S rRNA genes assume point mutation-driven tree-shape evolution as an evolutionary model, which is intrinsically inappropriate to decipher the evolutionary history for genes driven by recombination. To address this issue, we applied a phylogenetic network analysis, which has been used previously for detection of genetic recombination in homologous alleles, to the 16S rRNA gene. We focused on the genus Enterobacter, whose phylogenetic relationships inferred by multi-locus sequence alignment analysis and 16S rRNA sequences are incompatible. All 10 complete genomic sequences were retrieved from the NCBI database, in which 71 16S rRNA genes were included. Neighbor-joining analysis demonstrated that the genes residing in the same genomes clustered, indicating the occurrence of intragenomic recombination. However, as suggested by the low bootstrap values, evolutionary relationships between the clusters were uncertain. We then applied phylogenetic network analysis to representative sequences from each cluster. We found three ancestral 16S rRNA groups; the others were likely created through recursive recombination between the ancestors and chimeric descendants. Despite the large sequence changes caused by the recombination events, the RNA secondary structures were conserved. Successive intergenomic and intragenomic recombination thus shaped the evolution of 16S rRNA genes in the genus Enterobacter. PMID:29180992

Perspectives for the information approach application to natural and artificial ecosystems investigation

NASA Astrophysics Data System (ADS)

Lankin, Yuliy

As a methodological matter, all modern conceptions of life development can be subdivided into the substrate (S), the energetic (E) and the informational (I). The S-conception is based on biochemical, genetic and morphological ideas. The E-conception deals with an idea of development of complicated open systems (COS) which are characterized by energy getting constantly from the outside, by improvement of substance cycles and as speeding-up and increasing of "power" of them as well, and by increasing of energy intensity transformation by the each structure of COS. The I-conception has been developing so far in the main within the frameworks of the traditional both cybernetic ideas and information theory that are convenient for many technical applications but are deficient for investigation of ecoand bio-systems. Situation was changed when the conception of adaptive systems (CAS) based on the ideas of ecology, biology and neurocybernetic (neuroinforamtic) had offered. As a consequence of this, the I-conception based on the CAS well accords with the S- and the E-conceptions and allows to hope to their combine into one the S + E + I conception that will include all virtues of the S-, the E-, and the I-conceptions and eliminate of their limitations. Thanks to relative easiness of hierarchic adaptive nonlinear models making using of the CAS, it is possible overcome effectively both of the problems as the "dimensionality problem" and the "loss of stability" as well for complicated models of ecosystems (CME). Optimization of energy and substance consumption process and adaptation of the CME to changes of current conditions are well realized in ranges given by goal function. A use adaptive networks (including neural nets) in frames of the CAS allows to realize any continuous function in control loops and at information processing. The considered features of the S + E + I proposed approach based on the CAS make it perspective for construction as biosphere models and artificial ecosystems as well for space and earth applications.

Quantifying Environmental Effects on the Decay of Hole Transfer Couplings in Biosystems.

PubMed

Ramos, Pablo; Pavanello, Michele

2014-06-10

In the past two decades, many research groups worldwide have tried to understand and categorize simple regimes in the charge transfer of such biological systems as DNA. Theoretically speaking, the lack of exact theories for electron-nuclear dynamics on one side and poor quality of the parameters needed by model Hamiltonians and nonadiabatic dynamics alike (such as couplings and site energies) on the other are the two main difficulties for an appropriate description of the charge transfer phenomena. In this work, we present an application of a previously benchmarked and linear-scaling subsystem density functional theory (DFT) method for the calculation of couplings, site energies, and superexchange decay factors (β) of several biological donor-acceptor dyads, as well as double stranded DNA oligomers composed of up to five base pairs. The calculations are all-electron and provide a clear view of the role of the environment on superexchange couplings in DNA-they follow experimental trends and confirm previous semiempirical calculations. The subsystem DFT method is proven to be an excellent tool for long-range, bridge-mediated coupling and site energy calculations of embedded molecular systems.

Photo-switchable microbial fuel-cells.

PubMed

Schlesinger, Orr; Dandela, Rambabu; Bhagat, Ashok; Adepu, Raju; Meijler, Michael M; Xia, Lin; Alfonta, Lital

2018-05-01

Regulation of Bio-systems in a clean, simple, and efficient way is important for the design of smart bio-interfaces and bioelectronic devices. Light as a non-invasive mean to control the activity of a protein enables spatial and temporal control far superior to other chemical and physical methods. The ability to regulate the activity of a catalytic enzyme in a biofuel-cell reduces the waste of resources and energy and turns the fuel-cell into a smart and more efficient device for power generation. Here we present a microbial-fuel-cell based on a surface displayed, photo-switchable alcohol dehydrogenase. The enzyme was modified near the active site using non-canonical amino acids and a small photo-reactive molecule, which enables reversible control of enzymatic activity. Depending on the modification site, the enzyme exhibits reversible behavior upon irradiation with UV and visible light, in both biochemical, and electrochemical assays. The change observed in power output of a microbial fuel cell utilizing the modified enzyme was almost five-fold, between inactive and active states. © 2018 Wiley Periodicals, Inc.

Database resources of the National Center for Biotechnology Information.

PubMed

Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bolton, Evan; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; Dicuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Krasnov, Sergey; Landsman, David; Lipman, David J; Lu, Zhiyong; Madden, Thomas L; Madej, Tom; Maglott, Donna R; Marchler-Bauer, Aron; Miller, Vadim; Karsch-Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Wang, Yanli; Wilbur, W John; Yaschenko, Eugene; Ye, Jian

2012-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Website. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Probe, Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Graphene-Based Platform for Infrared Near-Field Nanospectroscopy of Water and Biological Materials in an Aqueous Environment.

PubMed

Khatib, Omar; Wood, Joshua D; McLeod, Alexander S; Goldflam, Michael D; Wagner, Martin; Damhorst, Gregory L; Koepke, Justin C; Doidge, Gregory P; Rangarajan, Aniruddh; Bashir, Rashid; Pop, Eric; Lyding, Joseph W; Thiemens, Mark H; Keilmann, Fritz; Basov, D N

2015-08-25

Scattering scanning near-field optical microscopy (s-SNOM) has emerged as a powerful nanoscale spectroscopic tool capable of characterizing individual biomacromolecules and molecular materials. However, applications of scattering-based near-field techniques in the infrared (IR) to native biosystems still await a solution of how to implement the required aqueous environment. In this work, we demonstrate an IR-compatible liquid cell architecture that enables near-field imaging and nanospectroscopy by taking advantage of the unique properties of graphene. Large-area graphene acts as an impermeable monolayer barrier that allows for nano-IR inspection of underlying molecular materials in liquid. Here, we use s-SNOM to investigate the tobacco mosaic virus (TMV) in water underneath graphene. We resolve individual virus particles and register the amide I and II bands of TMV at ca. 1520 and 1660 cm(-1), respectively, using nanoscale Fourier transform infrared spectroscopy (nano-FTIR). We verify the presence of water in the graphene liquid cell by identifying a spectral feature associated with water absorption at 1610 cm(-1).

Pre-aeration of food waste to augment acidogenic process at higher organic load: Valorizing biohydrogen, volatile fatty acids and biohythane.

PubMed

Sarkar, Omprakash; Venkata Mohan, S

2017-10-01

Application of pre-aeration (AS) to waste prior to feeding was evaluated on acidogenic process in a semi-pilot scale biosystem for the production of biobased products (biohydrogen, volatile fatty acids (VFA) and biohythane) from food waste. Oxygen assisted in pre-hydrolysis of waste along with the suppression of methanogenic activity resulting in enhanced acidogenic product formation. AS operation resulted in 97% improvement in hydrogen conversion efficiency (HCE) and 10% more VFA production than the control. Increasing the organic load (OL) of food waste in association with AS application improved the productivity. The application of AS also influenced concentration and composition of fatty acid. Highest fraction of acetic (5.3g/l), butyric (0.7g/l) and propionic acid (0.84g/l) was achieved at higher OL (100g COD/l) with good degree of acidification (DOA). AS strategy showed positive influence on biofuel (biohydrogen and biohythane) production along with the biosynthesis of short chain fatty acids functioning as a low-cost pretreatment strategy in a single stage bioprocess. Copyright © 2017 Elsevier Ltd. All rights reserved.

Biogas recirculation for simultaneous calcium removal and biogas purification within an expanded granular sludge bed system treating leachate.

PubMed

Luo, Jinghuan; Lu, Xueqin; Liu, Jianyong; Qian, Guangren; Lu, Yongsheng

2014-12-01

Biogas, generated from an expanded granular sludge bed (EGSB) reactor treating municipal solid waste (MSW) leachate, was recirculated for calcium removal from the leachate via a carbonation process with simultaneous biogas purification. Batch trials were performed to optimize the solution pH and imported biogas (CO2) for CaCO3 precipitation. With applicable pH of 10-11 obtained, continuous trials achieved final calcium concentrations of 181-375 mg/L (removal efficiencies≈92.8-96.5%) in the leachate and methane contents of 87.1-91.4% (purification efficiencies≈65.4-82.2%) in the biogas. Calcium-balance study indicates that 23-986 mg Ca/d was released from the bio-system under the carbonized condition where CaCO3 precipitating was moved outside the bioreactor, whereas 7918-9517 mg Ca/d was trapped into the system for the controlled one. These findings demonstrate that carbonation removal of calcium by biogas recirculation could be a promising alternative to pretreat calcium-rich MSW leachate and synergistically to improve methane content. Copyright © 2014 Elsevier Ltd. All rights reserved.

Molecular modeling in structural nano-toxicology: interactions of nano-particles with nano-machinery of cells.

PubMed

Yanamala, Naveena; Kagan, Valerian E; Shvedova, Anna A

2013-12-01

Over the past two decades, nanotechnology has emerged as a key player in various disciplines of science and technology. Some of the most exciting applications are in the field of biomedicine - for theranostics (for combined diagnostic and therapeutic purposes) as well as for exploration of biological systems. A detailed understanding of the molecular interactions between nanoparticles and biological nano-machinery - macromolecules, membranes, and intracellular organelles - is crucial for obtaining adequate information on mechanisms of action of nanomaterials as well as a perspective on the long term effects of these materials and their possible toxicological outcomes. This review focuses on the use of structure-based computational molecular modeling as a tool to understand and to predict the interactions between nanomaterials and nano-biosystems. We review major approaches and provide examples of computational analysis of the structural principles behind such interactions. A rationale on how nanoparticles of different sizes, shape, structure and chemical properties can affect the organization and functions of nano-machinery of cells is also presented. Published by Elsevier B.V.

Developmental validation of the PowerPlex(®) Fusion 6C System.

PubMed

Ensenberger, Martin G; Lenz, Kristy A; Matthies, Learden K; Hadinoto, Gregory M; Schienman, John E; Przech, Angela J; Morganti, Michael W; Renstrom, Daniel T; Baker, Victoria M; Gawrys, Kori M; Hoogendoorn, Marlijn; Steffen, Carolyn R; Martín, Pablo; Alonso, Antonio; Olson, Hope R; Sprecher, Cynthia J; Storts, Douglas R

2016-03-01

The PowerPlex(®) Fusion 6C System is a 27-locus, six-dye, multiplex that includes all markers in the expanded CODIS core loci and increases overlap with STR database standards throughout the world. Additionally, it contains two, rapidly mutating, Y-STRs and is capable of both casework and database workflows, including direct amplification. A multi-laboratory developmental validation study was performed on the PowerPlex(®) Fusion 6C System. Here, we report the results of that study which followed SWGDAM guidelines and includes data for: species specificity, sensitivity, stability, precision, reproducibility and repeatability, case-type samples, concordance, stutter, DNA mixtures, and PCR-based procedures. Where appropriate we report data from both extracted DNA samples and direct amplification samples from various substrates and collection devices. Samples from all studies were separated on both Applied Biosystems 3500 series and 6-dye capable 3130 series Genetic Analyzers and data is reported for each. Together, the data validate the design and demonstrate the performance of the PowerPlex(®) Fusion 6C System. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Quantum formalism as an optimisation procedure of information flows for physical and biological systems.

PubMed

Baladrón, Carlos; Khrennikov, Andrei

2016-12-01

The similarities between biological and physical systems as respectively defined in quantum information biology (QIB) and in a Darwinian approach to quantum mechanics (DAQM) have been analysed. In both theories the processing of information is a central feature characterising the systems. The analysis highlights a mutual support on the thesis contended by each theory. On the one hand, DAQM provides a physical basis that might explain the key role played by quantum information at the macroscopic level for bio-systems in QIB. On the other hand, QIB offers the possibility, acting as a macroscopic testing ground, to analyse the emergence of quantumness from classicality in the terms held by DAQM. As an added result of the comparison, a tentative definition of quantum information in terms of classical information flows has been proposed. The quantum formalism would appear from this comparative analysis between QIB and DAQM as an optimal information scheme that would maximise the stability of biological and physical systems at any scale. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The Role of Carbohydrates at the Origin of Homochirality in Biosystems

NASA Astrophysics Data System (ADS)

Toxvaerd, Søren

2013-10-01

Pasteur has demonstrated that the chiral components in a racemic mixture can separate in homochiral crystals. But with a strong chiral discrimination the chiral components in a concentrated mixture can also phase separate into homochiral fluid domains, and the isomerization kinetics can then perform a symmetry breaking into one thermodynamical stable homochiral system. Glyceraldehyde has a sufficient chiral discrimination to perform such a symmetry breaking. The requirement of a high concentration of the chiral reactant(s) in an aqueous solution in order to perform and maintain homochirality; the appearance of phosphorylation of almost all carbohydrates in the central machinery of life; the basic ideas that the biochemistry and the glycolysis and gluconeogenesis contain the trace of the biochemical evolution, all point in the direction of that homochirality was obtained just after- or at a phosphorylation of the very first products of the formose reaction, at high concentrations of the reactants in phosphate rich compartments in submarine hydrothermal vents. A racemic solution of D,L-glyceraldehyde-3-phosphate could be the template for obtaining homochiral D-glyceraldehyde-3-phosphate(aq) as well as L-amino acids.

Oxygen-Free Biochemistry: The Putative CHN Foundation for Exotic Life in a Hydrocarbon World?

NASA Astrophysics Data System (ADS)

Lv, Kong-Peng; Norman, Lucy; Li, Yi-Liang

2017-11-01

Since Earth's biochemistry is carbon-based and water-borne, the main strategies for searching for life elsewhere are "follow the carbon" and "follow the water." Recently, however, there is a growing focus on the prospect that putative exotic life on other planets could rely on unearthly biochemistries. Here, we hypothesize a novel oxygen-free organic chemistry for supporting potential exotic biosystems, which is named CHN biochemistry. This oxygen-free CHN biochemistry starts from simple oxygen-free species (including hydrocarbons, hydrogen cyanide, and nitriles) and produces a range of functional macromolecules that may function in similar ways to terran macromolecules, such as sugars (cyanosugars), acids (cyanoacids), amino acids (amino cyanoacids), and nucleobases (cyanonucleobases). These CHN macromolecules could further interact with each other to generate higher "cyanoester" and "cyanoprotein" systems. In addition, theoretical calculations indicate that the energy changes of some reactions are consistent with their counterparts in Earth's biochemistry. The CHN biochemistry-based life would be applicable in habitats with a low bioavailability of oxygen, such as the alkane lakes of Titan and non-aquatic liquids on extrasolar bodies.

Database resources of the National Center for Biotechnology Information

PubMed Central

Acland, Abigail; Agarwala, Richa; Barrett, Tanya; Beck, Jeff; Benson, Dennis A.; Bollin, Colleen; Bolton, Evan; Bryant, Stephen H.; Canese, Kathi; Church, Deanna M.; Clark, Karen; DiCuccio, Michael; Dondoshansky, Ilya; Federhen, Scott; Feolo, Michael; Geer, Lewis Y.; Gorelenkov, Viatcheslav; Hoeppner, Marilu; Johnson, Mark; Kelly, Christopher; Khotomlianski, Viatcheslav; Kimchi, Avi; Kimelman, Michael; Kitts, Paul; Krasnov, Sergey; Kuznetsov, Anatoliy; Landsman, David; Lipman, David J.; Lu, Zhiyong; Madden, Thomas L.; Madej, Tom; Maglott, Donna R.; Marchler-Bauer, Aron; Karsch-Mizrachi, Ilene; Murphy, Terence; Ostell, James; O'Sullivan, Christopher; Panchenko, Anna; Phan, Lon; Pruitt, Don Preussm Kim D.; Rubinstein, Wendy; Sayers, Eric W.; Schneider, Valerie; Schuler, Gregory D.; Sequeira, Edwin; Sherry, Stephen T.; Shumway, Martin; Sirotkin, Karl; Siyan, Karanjit; Slotta, Douglas; Soboleva, Alexandra; Soussov, Vladimir; Starchenko, Grigory; Tatusova, Tatiana A.; Trawick, Bart W.; Vakatov, Denis; Wang, Yanli; Ward, Minghong; John Wilbur, W.; Yaschenko, Eugene; Zbicz, Kerry

2014-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, PubReader, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Primer-BLAST, COBALT, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing Registry, Genome and related tools, the Map Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, ClinVar, MedGen, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page. PMID:24259429

A least-squares parameter estimation algorithm for switched hammerstein systems with applications to the VOR

NASA Technical Reports Server (NTRS)

Kukreja, Sunil L.; Kearney, Robert E.; Galiana, Henrietta L.

2005-01-01

A "Multimode" or "switched" system is one that switches between various modes of operation. When a switch occurs from one mode to another, a discontinuity may result followed by a smooth evolution under the new regime. Characterizing the switching behavior of these systems is not well understood and, therefore, identification of multimode systems typically requires a preprocessing step to classify the observed data according to a mode of operation. A further consequence of the switched nature of these systems is that data available for parameter estimation of any subsystem may be inadequate. As such, identification and parameter estimation of multimode systems remains an unresolved problem. In this paper, we 1) show that the NARMAX model structure can be used to describe the impulsive-smooth behavior of switched systems, 2) propose a modified extended least squares (MELS) algorithm to estimate the coefficients of such models, and 3) demonstrate its applicability to simulated and real data from the Vestibulo-Ocular Reflex (VOR). The approach will also allow the identification of other nonlinear bio-systems, suspected of containing "hard" nonlinearities.

Optimized transitory ectopic expression of promastigote surface antigen protein in Nicotiana benthamiana, a potential anti-leishmaniasis vaccine candidate.

PubMed

Lacombe, Séverine; Bangratz, Martine; Brizard, Jean-Paul; Petitdidier, Elodie; Pagniez, Julie; Sérémé, Drissa; Lemesre, Jean-Loup; Brugidou, Christophe

2018-01-01

In recent years, plants have been shown to be an efficient alternative expression system for high-value pharmaceuticals such as vaccines. However, constitutive expression of recombinant protein remains uncertain on their level of production and biological activity. To overcome these problems, transitory expression systems have been developed. Here, a series of experiments were performed to determine the most effective conditions to enhance vaccine antigen transient accumulation in Nicotiana benthamiana leaves using the promastigote surface antigen (PSA) from the parasitic protozoan Leishmania infantum. This protein has been previously identified as the major antigen of a licensed canine anti-leishmaniasis vaccine. The classical prokaryote Escherichia coli biosystem failed in accumulating PSA. Consequently, the standard plant system based on N. benthamiana has been optimized for the production of putatively active PSA. First, the RNA silencing defense mechanism set up by the plant against PSA ectopic expression was abolished by using three viral suppressors acting at different steps of the RNA silencing pathway. Then, we demonstrated that the signal peptide at the N-terminal side of the PSA is required for its accumulation. The PSA ER signaling and retention with the PSA signal peptide and the KDEL motif, respectively were optimized to significantly increase its accumulation. Finally, we demonstrate that the production of recombinant PSA in N. benthamiana leaves allows the conservation of its immunogenic property. These approaches demonstrate that based on these optimizations, plant based systems can be used to effectively produce the biological active PSA protein. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Real-Time Reverse-Transcription Quantitative Polymerase Chain Reaction Assay Is a Feasible Method for the Relative Quantification of Heregulin Expression in Non-Small Cell Lung Cancer Tissue.

PubMed

Kristof, Jessica; Sakrison, Kellen; Jin, Xiaoping; Nakamaru, Kenji; Schneider, Matthias; Beckman, Robert A; Freeman, Daniel; Spittle, Cindy; Feng, Wenqin

2017-01-01

In preclinical studies, heregulin ( HRG ) expression was shown to be the most relevant predictive biomarker for response to patritumab, a fully human anti-epidermal growth factor receptor 3 monoclonal antibody. In support of a phase 2 study of erlotinib ± patritumab in non-small cell lung cancer (NSCLC), a reverse-transcription quantitative polymerase chain reaction (RT-qPCR) assay for relative quantification of HRG expression from formalin-fixed paraffin-embedded (FFPE) NSCLC tissue samples was developed and validated and described herein. Test specimens included matched FFPE normal lung and NSCLC and frozen NSCLC tissue, and HRG -positive and HRG -negative cell lines. Formalin-fixed paraffin-embedded tissue was examined for functional performance. Heregulin distribution was also analyzed across 200 NSCLC commercial samples. Applied Biosystems TaqMan Gene Expression Assays were run on the Bio-Rad CFX96 real-time PCR platform. Heregulin RT-qPCR assay specificity, PCR efficiency, PCR linearity, and reproducibility were demonstrated. The final assay parameters included the Qiagen FFPE RNA Extraction Kit for RNA extraction from FFPE NSCLC tissue, 50 ng of RNA input, and 3 reference (housekeeping) genes ( HMBS, IPO8 , and EIF2B1 ), which had expression levels similar to HRG expression levels and were stable among FFPE NSCLC samples. Using the validated assay, unimodal HRG distribution was confirmed across 185 evaluable FFPE NSCLC commercial samples. Feasibility of an RT-qPCR assay for the quantification of HRG expression in FFPE NSCLC specimens was demonstrated.

Plant-centered biosystems in space environments: technological concepts for developing a plant genetic assessment and control system.

PubMed

Lomax, Terri L; Findlay, Kirk A; White, T J; Winner, William E

2003-06-01

Plants will play an essential role in providing life support for any long-term space exploration or habitation. We are evaluating the feasibility of an adaptable system for measuring the response of plants to any unique space condition and optimizing plant performance under those conditions. The proposed system is based on a unique combination of systems including the rapid advances in the field of plant genomics, microarray technology for measuring gene expression, bioinformatics, gene pathways and networks, physiological measurements in controlled environments, and advances in automation and robotics. The resulting flexible module for monitoring and optimizing plant responses will be able to be inserted as a cassette into a variety of platforms and missions for either experimental or life support purposes. The results from future plant functional genomics projects have great potential to be applied to those plant species most likely to be used in space environments. Eventually, it will be possible to use the plant genetic assessment and control system to optimize the performance of any plant in any space environment. In addition to allowing the effective control of environmental parameters for enhanced plant productivity and other life support functions, the proposed module will also allow the selection or engineering of plants to thrive in specific space environments. The proposed project will advance human exploration of space in the near- and mid-term future on the International Space Station and free-flying satellites and in the far-term for longer duration missions and eventual space habitation.

An ESIPT-based two-photon fluorescent probe detection of hydrogen peroxide in live cells and tissues.

PubMed

Zhou, Liyi; Peng, Yongbo; Wang, Qianqian; Lin, Qinlu

2017-02-01

A variety of diseases associated with human aging, which have a strong oxidative stress, but connecting age-related diseases and oxidative stress of the basic molecular mechanisms still insufficiently understood. Oxidative stress origins from the unregulated production of reactive oxygen species (ROS), and oxidative damaging to tissues and organs from subsequent oxidation-reduction chemistry by cellular mismanagement. In particular, H 2 O 2 is a major by-product of ROS in live organisms and a common marker for oxidative stress, and its dynamic equilibrium can have various physiological and pathological consequences. H 2 O 2 is a small molecule, but it is an essential oxygen metabolite in living systems and acts as an important compound in cellular signal transduction by reversible oxidation of proteins. To quantitatively detect of H 2 O 2 in biosystems, herein, we adopted a 2-(2'-hydroxyphenyl)-4(3H)-quinazolinone (HPQ), a small organic fluorophore known for its luminescence mechanism through excited-state intramolecular proton transfer (ESIPT). HPQ was employed as a precursor to develop a turn-on probe (HPQ-H) for bioimaging applications. After cleavaging the boronic ester moiety by H 2 O 2 , HPQ-H releases a HPQ fluorophore which shows a 45-fold fluorescence intensity enhancement with high sensitivity and selectivity over other reactive oxygen species (ROS), and a high resolution imaging and large tissue-imaging depth (70-170μm) in living cells and tissues images under two-photon excitation (720nm). Copyright © 2017 Elsevier B.V. All rights reserved.

Development and validation of a LC-MS method with electrospray ionization for the determination of the imidazole H3 antagonist ROS203 in rat plasma.

PubMed

Vacondio, Federica; Silva, Claudia; Fioni, Alessandro; Mor, Marco; Rivara, Mirko; Bordi, Fabrizio; Flammini, Lisa; Ballabeni, Vigilio; Barocelli, Elisabetta

2008-01-07

A rapid, simple and sensitive liquid chromatography-mass spectrometry (LC-MS) method was developed and validated for the determination of the imidazole H(3) antagonist ROS203 in rat plasma, using the superior homologue ROS287 as internal standard. Analyses were performed on an Agilent 1100 Series HPLC system employing a Supelco Ascentis C(18) column and isocratic elution with acetonitrile-10mM ammonium acetate buffer pH 4.0 (30:70, v/v) at a flow rate of 0.25 mL/min. An Applied Biosystems/MDS Sciex 150-EX single quadrupole mass spectrometer, equipped with an electrospray ionization interface was employed, operating in the positive ion mode. Plasma samples were deproteinized with acetonitrile (1:2), evaporated under nitrogen stream, reconstituted in the mobile phase and 5 microL were injected into the system. The retention times of ROS203 and IS were 2.20 and 2.90 min, respectively. Calibration curves in spiked plasma were linear over the concentration range of 2610-2.61 ng/mL with determination coefficients >0.99. The lower limit of quantification (LLOQ) was 2.61 ng/mL. The accuracy of the method was within 15%. Intra- and inter-day relative standard deviations were less or equal to 9.50% or 7.19%, respectively. The applicability of the LC-MS method was tested employing plasma samples obtained after i.p. administration of ROS203 to female Wistar rats to support a behavioral in vivo study. The specificity of the method was confirmed by the absence of interferences from endogenous substances. The reported method can provide the necessary sensitivity, linearity, precision, accuracy and specificity to allow the determination of ROS203 in rat plasma samples to support further pharmacokinetic assays.

Determination of suvorexant in human plasma using 96-well liquid-liquid extraction and HPLC with tandem mass spectrometric detection.

PubMed

Breidinger, S A; Simpson, R C; Mangin, E; Woolf, E J

2015-10-01

A method, using liquid chromatography with tandem mass spectrometric detection (LC-MS/MS), was developed for the determination of suvorexant (MK-4305, Belsomra(®)), a selective dual orexin receptor antagonist for the treatment insomnia, in human plasma over the concentration range of 1-1000ng/mL. Stable isotope labeled (13)C(2)H3-suvorexant was used as an internal standard. The sample preparation procedure utilized liquid-liquid extraction, in the 96-well format, of a 100μL plasma sample with methyl t-butyl ether. The compounds were chromatographed under isocratic conditions on a Waters dC18 (50×2.1mm, 3μm) column with a mobile phase consisting of 30/70 (v/v %) 10mM ammonium formate, pH3/acetonitrile at a flow rate of 0.3mL/min. Multiple reaction monitoring of the precursor-to-product ion pairs for suvorexant (m/z 451→186) and (13)C(2)H3-suvorexant (m/z 455→190) on an Applied Biosystems API 4000 tandem mass spectrometer was used for quantitation. Intraday assay precision, assessed in six different lots of control plasma, was within 10% CV at all concentrations, while assay accuracy ranged from 95.6 to 105.0% of nominal. Quality control (QC) samples in plasma were stored at -20°C. Initial within day analysis of QCs after one freeze-thaw cycle showed accuracy within 9.5% of nominal with precision (CV) of 6.7% or less. The plasma QC samples were demonstrated to be stable for up to 25 months at -20°C. The method described has been used to support clinical studies during Phase I through III of clinical development. Copyright © 2015 Elsevier B.V. All rights reserved.

Determination of PNU-248686A, a novel matrix metalloproteinase inhibitor, in human plasma by liquid chromatography-tandem mass spectrometry, following protein precipitation in the 96-well plate format.

PubMed

Frigerio, E; Cenacchi, V; James, C A

2003-02-14

A sensitive, specific and high-throughput analytical method for the quantitation of PNU-248686A (I), in human plasma has been developed. I, sodium (2R)-3-[[(4'-chloro(1,1'-biphenyl)-4-yl]sulfonyl]-2-hydroxy-2-[(phenylsulfanyl)methyl] propanoate, is an orally active matrix metalloproteinase (MMP) inhibitor developed for the treatment of solid tumors over-expressing MMPs. Concentrations of I, as free acid, were determined in human plasma by LC-MS-MS after plasma protein precipitation in the 96-well plate format. Aliquots of plasma (50 microl) were placed into the plates and 0.2 ml of methanol was added. The plates were shaken for 5 min and centrifuged at 1500 g for 10 min. Aliquots of 10 microl of the supernatants were then directly injected into the LC-MS-MS system. A Symmetry Shield C. column (50 x 2.1 mm, 3.5 microm) was used to perform the chromatographic analysis. The mobile phase was 5 mM ammonium formate buffer solution pH 5.0-acetonitrile (60:40. v/v) with a flow-rate of 0.3 ml/min. Retention time of I was about 1.2 min. Total cycle time was 2.5 min. MS detection used the Applied Biosystems-MDS Sciex API 3000 with TurbolonSpray interface and single reaction monitoring (461 --> 251 m/z transition) operated in negative ion mode. Calibration curves were constructed by plotting the area of the compound (y) against its concentration (x). A weighed linear regression (weighting factor 1/x(2)) was used to calculate I concentrations in quality control and unknown samples. The method was fully validated over the range of 5.0-5000 ng/ml. The suitability and robustness of the method for in vivo samples was confirmed by analysis of plasma samples from a pilot clinical study.

Association of α-, β-, and γ-Synuclein With Diffuse Lewy Body Disease

PubMed Central

Nishioka, Kenya; Wider, Christian; Vilariño-Güell, Carles; Soto-Ortolaza, Alexandra I.; Lincoln, Sarah J.; Kachergus, Jennifer M.; Jasinska-Myga, Barbara; Ross, Owen A.; Rajput, Alex; Robinson, Christopher A.; Ferman, Tanis J.; Wszolek, Zbigniew K.; Dickson, Dennis W.; Farrer, Matthew J.

2016-01-01

Objective To determine the association of the genes that encode α-, β-, and γ-synuclein (SNCA, SNCB, and SNCG, respectively) with diffuse Lewy body disease (DLBD). Design Case-control study. Subjects A total of 172 patients with DLBD consistent with a clinical diagnosis of Parkinson disease dementia/dementia with Lewy bodies and 350 clinically and 97 pathologically normal controls. Interventions Sequencing of SNCA, SNCB, and SNCG and genotyping of single-nucleotide polymorphisms performed on an Applied Biosystems capillary sequencer and a Sequenom MassArray pLEX platform, respectively. Associations were determined using χ2 or Fisher exact tests. Results Initial sequencing studies of the coding regions of each gene in 89 patients with DLBD did not detect any pathogenic substitutions. Nevertheless, genotyping of known polymorphic variability in sequence-conserved regions detected several single-nucleotide polymorphisms in the SNCA and SNCG genes that were significantly associated with disease (P=.05 to <.001). Significant association was also observed for 3 single-nucleotide polymorphisms located in SNCB when comparing DLBD cases and pathologically confirmed normal controls (P=.03-.01); however, this association was not significant for the clinical controls alone or the combined clinical and pathological controls (P>.05). After correction for multiple testing, only 1 single-nucleotide polymorphism in SNCG (rs3750823) remained significant in all of the analyses (P=.05-.009). Conclusion These findings suggest that variants in all 3 members of the synuclein gene family, particularly SNCA and SNCG, affect the risk of developing DLBD and warrant further investigation in larger, pathologically defined data sets as well as clinically diagnosed Parkinson disease/dementia with Lewy bodies case-control series. PMID:20697047

Old tree with new shoots: silver nanoparticles for label-free and colorimetric mercury ions detection

NASA Astrophysics Data System (ADS)

Gao, Shuyan; Jia, Xiaoxia; Chen, Yanli

2013-01-01

Mercury in the environment from global mercury emissions as well as various forms of contamination poses severe threats to both human health and the environment. Long-term exposure to high levels of Hg-based toxins results in serious and irreversible damage of the central nervous system and other organs. Therefore, the development of effective sensing systems for mercury detection becomes an increasing demand. In this article, a yogurt-mediated silver nanostructure is reported to be unprecedentedly used in the naked-eye and label-free detection of mercury. The method relies on the redox reaction resulting from the electrode potential difference between Ag+/Ag (0.7996 V) and Hg2+/Hg2 2+ (0.920 V) that makes colorless Hg2+ ions which oxidize colored silver nanoparticle (AgNP) to colorless Ag+. The labor-intensive modification of AgNPs and expensive labeling are avoided, and the traditional AuNPs are substituted by AgNPs in this Hg2+ ions sensing platform, which makes it facile, low-cost, and particularly useful for home, clinic, or field applications as well as resource-limited conditions. This sensing system achieves a detection limit as low as 10 nM, lower than the toxicity level of Hg2+ ions in drinking water (30 nM) defined by World Health Organization, and exhibits excellent selectivity, largely free from the matrix effect of the real water samples. This visual label-free Hg2+ ions sensing motif shows great promise for sensing Hg2+ ions in terms of sensitivity, selectivity, cost, and maneuverability. It is also a good example for the organic combination of green chemistry and functional materials, which may trigger interest in furthering biosystems for environmental science applications.

The mRNA expression levels of uncoupling proteins 1 and 2 in mononuclear cells from patients with metabolic disorders: obesity and type 2 diabetes mellitus.

PubMed

Margaryan, Sona; Witkowicz, Agata; Partyka, Anna; Yepiskoposyan, Levon; Manukyan, Gayane; Karabon, Lidia

2017-10-19

Type 2 diabetes mellitus (T2DM) and obesity are metabolic disorders whose major hallmark is insulin resistance. Impaired mitochondrial activity, such as reduced ratio of energy production to respiration, has been implicated in the development of insulin resistance. Uncoupling proteins (UCPs) are proton carriers, expressed in the mitochondrial inner membrane, that uncouple oxygen consumption by the respiratory chain from ATP synthesis. The aim of the study was to determine transcriptional levels of UCP1 and UCP2 in peripheral blood mononuclear cells (PBMCs) from patients with metabolic disorders: T2DM, obesity and from healthy individuals. The mRNA levels of UCP1, UCP2 were determined by Real-Time PCR method using Applied Biosystems assays. The UCP1 mRNA expression level was not detectable in the majority of studied samples, while very low expression was found in PBMCs from 3 obese persons. UCP2 mRNA expression level was detectable in all samples. The median mRNA expression of UCP2 was lower in all patients with metabolic disorders as compared to the controls (0.20+0.14 vs. 0.010+0.009, p=0.05). When compared separately, the differences of medians UCP2 mRNA expression level between the obese individuals and the controls as well as between the T2DM patients and the controls did not reach statistical significance. Decreased UCP2 gene expression in mononuclear cells from obese and diabetic patients might contribute to the immunological abnormalities in these metabolic disorders and suggests its role as a candidate gene in future studies of obesity and diabetes.

Detection of Francisella tularensis within infected mouse tissues by using a hand-held PCR thermocycler.

PubMed

Emanuel, Peter A; Bell, Ryan; Dang, Jessica L; McClanahan, Rebecca; David, John C; Burgess, Robert J; Thompson, Joseph; Collins, Lisa; Hadfield, Ted

2003-02-01

The diagnosis of human cases of tularemia often relies upon the demonstration of an antibody response to Francisella tularensis or the direct culturing of the bacteria from the patient. Antibody response is not detectable until 2 weeks or more after infection, and culturing requires special media and suspicion of tularemia. In addition, handling live Francisella poses a risk to laboratory personnel due to the highly infectious nature of this pathogen. In an effort to develop a rapid diagnostic assay for tularemia, we investigated the use of TaqMan 5' hydrolysis fluorogenic PCR to detect the organism in tissues of infected mice. Mice were infected to produce respiratory tularemia. The fopA and tul4 genes of F. tularensis were amplified from infected spleen, lung, liver, and kidney tissues sampled over a 5-day period. The samples were analyzed using the laboratory-based Applied Biosystems International 7900 and the Smiths Detection-Edgewood BioSeeq, a hand-held portable fluorescence thermocycler designed for use in the field. A comparison of culturing and PCR for detection of bacteria in infected tissues shows that culturing was more sensitive than PCR. However, the results for culture take 72 h, whereas PCR results were available within 4 h. PCR was able to detect infection in all the tissues tested. Lung tissue showed the earliest response at 2 days when tested with the ABI 7900 and in 3 days when tested with the BioSeeq. The results were in agreement between the ABI 7900 and the BioSeeq when presented with the same sample. Template preparation may account for the loss of sensitivity compared to culturing techniques. The hand-held BioSeeq thermocycler shows promise as an expedient means of forward diagnosis of infection in the field.

Detection of Francisella tularensis within Infected Mouse Tissues by Using a Hand-Held PCR Thermocycler

PubMed Central

Emanuel, Peter A.; Bell, Ryan; Dang, Jessica L.; McClanahan, Rebecca; David, John C.; Burgess, Robert J.; Thompson, Joseph; Collins, Lisa; Hadfield, Ted

2003-01-01

The diagnosis of human cases of tularemia often relies upon the demonstration of an antibody response to Francisella tularensis or the direct culturing of the bacteria from the patient. Antibody response is not detectable until 2 weeks or more after infection, and culturing requires special media and suspicion of tularemia. In addition, handling live Francisella poses a risk to laboratory personnel due to the highly infectious nature of this pathogen. In an effort to develop a rapid diagnostic assay for tularemia, we investigated the use of TaqMan 5′ hydrolysis fluorogenic PCR to detect the organism in tissues of infected mice. Mice were infected to produce respiratory tularemia. The fopA and tul4 genes of F. tularensis were amplified from infected spleen, lung, liver, and kidney tissues sampled over a 5-day period. The samples were analyzed using the laboratory-based Applied Biosystems International 7900 and the Smiths Detection-Edgewood BioSeeq, a hand-held portable fluorescence thermocycler designed for use in the field. A comparison of culturing and PCR for detection of bacteria in infected tissues shows that culturing was more sensitive than PCR. However, the results for culture take 72 h, whereas PCR results were available within 4 h. PCR was able to detect infection in all the tissues tested. Lung tissue showed the earliest response at 2 days when tested with the ABI 7900 and in 3 days when tested with the BioSeeq. The results were in agreement between the ABI 7900 and the BioSeeq when presented with the same sample. Template preparation may account for the loss of sensitivity compared to culturing techniques. The hand-held BioSeeq thermocycler shows promise as an expedient means of forward diagnosis of infection in the field. PMID:12574268

Imaging mass spectrometry detection of gangliosides species in the mouse brain following transient focal cerebral ischemia and long-term recovery.

PubMed

Whitehead, Shawn N; Chan, Kenneth H N; Gangaraju, Sandhya; Slinn, Jacqueline; Li, Jianjun; Hou, Sheng T

2011-01-01

Gangliosides, a member of the glycosphingolipid family, are heterogeneously expressed in biological membranes and are particularly enriched within the central nervous system. Gangliosides consist of mono- or poly-sialylated oligosaccharide chains of variable lengths attached to a ceramide unit and are found to be intimately involved in brain disease development. The purpose of this study is to examine the spatial profile of ganglioside species using matrix-assisted laser desorption/ionization (MALDI) imaging (IMS) following middle cerebral artery occlusion (MCAO) reperfusion injury in the mouse. IMS is a powerful method to not only discriminate gangliosides by their oligosaccharide components, but also by their carbon length within their sphingosine base. Mice were subjected to a 30 min unilateral MCAO followed by long-term survival (up to 28 days of reperfusion). Brain sections were sprayed with the matrix 5-Chloro-2-mercaptobenzothiazole, scanned and analyzed for a series of ganglioside molecules using an Applied Biosystems 4800 MALDI TOF/TOF. Traditional histological and immunofluorescence techniques were performed to assess brain tissue damage and verification of the expression of gangliosides of interest. Results revealed a unique anatomical profile of GM1, GD1 and GT1b (d18:1, d20:1 as well as other members of the glycosphingolipid family). There was marked variability in the ratio of expression between ipsilateral and contralateral cortices for the various detected ganglioside species following MCAO-reperfusion injury. Most interestingly, MCAO resulted in the transient induction of both GM2 and GM3 signals within the ipsilateral hemisphere; at the border of the infarcted tissue. Taken together, the data suggest that brain region specific expression of gangliosides, particularly with respect to hydrocarbon length, may play a role in neuronal responses to injury.

LANDSCAPE MANAGEMENT FOR SUSTAINABLE SUPPLIES OF BIOENERGY FEEDSTOCK AND ENHANCED SOIL QUALITY

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

Douglas L. Karlen; David J. Muth, Jr.

2012-09-01

Agriculture can simultaneously address global food, feed, fiber, and energy challenges provided our soil, water, and air resources are not compromised in doing so. As we embark on the 19th Triennial Conference of the International Soil and Tillage Research Organization (ISTRO), I am pleased to proclaim that our members are well poised to lead these endeavors because of our comprehensive understanding of soil, water, agricultural and bio-systems engineering processes. The concept of landscape management, as an approach for integrating multiple bioenergy feedstock sources, including biomass residuals, into current crop production systems, is used as the focal point to show howmore » these ever-increasing global challenges can be met in a sustainable manner. Starting with the 2005 Billion Ton Study (BTS) goals, research and technology transfer activities leading to the 2011 U.S. Department of Energy (DOE) Revised Billion Ton Study (BT2) and development of a residue management tool to guide sustainable crop residue harvest will be reviewed. Multi-location USDA-Agricultural Research Service (ARS) Renewable Energy Assessment Project (REAP) team research and on-going partnerships between public and private sector groups will be shared to show the development of landscape management strategies that can simultaneously address the multiple factors that must be balanced to meet the global challenges. Effective landscape management strategies recognize the importance of nature’s diversity and strive to emulate those conditions to sustain multiple critical ecosystem services. To illustrate those services, the soil quality impact of harvesting crop residues are presented to show how careful, comprehensive monitoring of soil, water and air resources must be an integral part of sustainable bioenergy feedstock production systems. Preliminary analyses suggest that to sustain soil resources within the U.S. Corn Belt, corn (Zea mays L.) stover should not be harvested if average grain yields are less than 11 Mg ha-1 (175 bu ac-1) unless more intensive landscape management practices are implemented. Furthermore, although non-irrigated corn grain yields east and west of the primary Corn Belt may not consistently achieve the 11 Mg ha-1 yield levels, corn can still be part of an overall landscape approach for sustainable feedstock production. Another option for producers with consistently high yields (> 12.6 Mg ha-1 or 200 bu ac-1) that may enable them to sustainably harvest even more stover is to decrease their tillage intensity which will reduce fuel use, preserve rhizosphere carbon, and/or help maintain soil structure and soil quality benefits often attributed to no-till production systems. In conclusion, I challenge all ISTRO scientists to critically ask if your research is contributing to improved soil and crop management strategies that effectively address the complexity associated with sustainable food, feed, fiber and fuel production throughout the world.« less

Application of a non-hazardous vital dye for cell counting with automated cell counters.

PubMed

Kim, Soo In; Kim, Hyun Jeong; Lee, Ho-Jae; Lee, Kiwon; Hong, Dongpyo; Lim, Hyunchang; Cho, Keunchang; Jung, Neoncheol; Yi, Yong Weon

2016-01-01

Recent advances in automated cell counters enable us to count cells more easily with consistency. However, the wide use of the traditional vital dye trypan blue (TB) raises environmental and health concerns due to its potential teratogenic effects. To avoid this chemical hazard, it is of importance to introduce an alternative non-hazardous vital dye that is compatible with automated cell counters. Erythrosin B (EB) is a vital dye that is impermeable to biological membranes and is used as a food additive. Similarly to TB, EB stains only nonviable cells with disintegrated membranes. However, EB is less popular than TB and is seldom used with automated cell counters. We found that cell counting accuracy with EB was comparable to that with TB. EB was found to be an effective dye for accurate counting of cells with different viabilities across three different automated cell counters. In contrast to TB, EB was less toxic to cultured HL-60 cells during the cell counting process. These results indicate that replacing TB with EB for use with automated cell counters will significantly reduce the hazardous risk while producing comparable results. Copyright © 2015 Logos Biosystems, Inc. Published by Elsevier Inc. All rights reserved.

Database resources of the National Center for Biotechnology Information

PubMed Central

Sayers, Eric W.; Barrett, Tanya; Benson, Dennis A.; Bolton, Evan; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M.; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Krasnov, Sergey; Landsman, David; Lipman, David J.; Lu, Zhiyong; Madden, Thomas L.; Madej, Tom; Maglott, Donna R.; Marchler-Bauer, Aron; Miller, Vadim; Karsch-Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D.; Schuler, Gregory D.; Sequeira, Edwin; Sherry, Stephen T.; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A.; Wagner, Lukas; Wang, Yanli; Wilbur, W. John; Yaschenko, Eugene; Ye, Jian

2012-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Website. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Probe, Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. PMID:22140104

Oxygen-Free Biochemistry: The Putative CHN Foundation for Exotic Life in a Hydrocarbon World?

PubMed

Lv, Kong-Peng; Norman, Lucy; Li, Yi-Liang

2017-11-01

Since Earth's biochemistry is carbon-based and water-borne, the main strategies for searching for life elsewhere are "follow the carbon" and "follow the water." Recently, however, there is a growing focus on the prospect that putative exotic life on other planets could rely on unearthly biochemistries. Here, we hypothesize a novel oxygen-free organic chemistry for supporting potential exotic biosystems, which is named CHN biochemistry. This oxygen-free CHN biochemistry starts from simple oxygen-free species (including hydrocarbons, hydrogen cyanide, and nitriles) and produces a range of functional macromolecules that may function in similar ways to terran macromolecules, such as sugars (cyanosugars), acids (cyanoacids), amino acids (amino cyanoacids), and nucleobases (cyanonucleobases). These CHN macromolecules could further interact with each other to generate higher "cyanoester" and "cyanoprotein" systems. In addition, theoretical calculations indicate that the energy changes of some reactions are consistent with their counterparts in Earth's biochemistry. The CHN biochemistry-based life would be applicable in habitats with a low bioavailability of oxygen, such as the alkane lakes of Titan and non-aquatic liquids on extrasolar bodies. Key Words: Oxygen-free biochemistry-Titan-Hydrocarbons-Hydrogen cyanide-Nitriles. Astrobiology 17, 1173-1181.

Database resources of the National Center for Biotechnology Information

PubMed Central

2013-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing Registry, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page. PMID:23193264

Database resources of the National Center for Biotechnology Information

PubMed Central

2015-01-01

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (Bookshelf, PubMed Central (PMC) and PubReader); medical genetics (ClinVar, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen); genes and genomics (BioProject, BioSample, dbSNP, dbVar, Epigenomics, Gene, Gene Expression Omnibus (GEO), Genome, HomoloGene, the Map Viewer, Nucleotide, PopSet, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser, Trace Archive and UniGene); and proteins and chemicals (Biosystems, COBALT, the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB), Protein Clusters, Protein and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for many of these databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov. PMID:25398906

Database resources of the National Center for Biotechnology Information

PubMed Central

2016-01-01

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (PubMed Central (PMC), Bookshelf and PubReader), health (ClinVar, dbGaP, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen), genomes (BioProject, Assembly, Genome, BioSample, dbSNP, dbVar, Epigenomics, the Map Viewer, Nucleotide, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser and the Trace Archive), genes (Gene, Gene Expression Omnibus (GEO), HomoloGene, PopSet and UniGene), proteins (Protein, the Conserved Domain Database (CDD), COBALT, Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB) and Protein Clusters) and chemicals (Biosystems and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for most of these databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. PMID:26615191

Self-organization and information in biosystems: a case study.

PubMed

Haken, Hermann

2018-05-01

Eigen's original molecular evolution equations are extended in two ways. (1) By an additional nonlinear autocatalytic term leading to new stability features, their dependence on the relative size of fitness parameters and on initial conditions is discussed in detail. (2) By adding noise terms that represent the spontaneous generation of molecules by mutations of substrate molecules, these terms are taken care of by both Langevin and Fokker-Planck equations. The steady-state solution of the latter provides us with a potential landscape giving a bird's eye view on all stable states (attractors). Two different types of evolutionary processes are suggested: (a) in a fixed attractor landscape and (b) caused by a changed landscape caused by changed fitness parameters. This may be related to Gould's concept of punctuated equilibria. External signals in the form of additional molecules may generate a new initial state within a specific basin of attraction. The corresponding attractor is then reached by self-organization. This approach allows me to define pragmatic information as signals causing a specific reaction of the receiver and to use equations equivalent to (1) as model of (human) pattern recognition as substantiated by the synergetic computer.

Electromagnetism of Bacterial Growth

NASA Astrophysics Data System (ADS)

Ainiwaer, Ailiyasi

2011-10-01

There has been increasing concern from the public about personal health due to the significant rise in the daily use of electrical devices such as cell phones, radios, computers, GPS, video games and television. All of these devices create electromagnetic (EM) fields, which are simply magnetic and electric fields surrounding the appliances that simultaneously affect the human bio-system. Although these can affect the human system, obstacles can easily shield or weaken the electrical fields; however, magnetic fields cannot be weakened and can pass through walls, human bodies and most other objects. The present study was conducted to examine the possible effects of bacteria when exposed to magnetic fields. The results indicate that a strong causal relationship is not clear, since different magnetic fields affect the bacteria differently, with some causing an increase in bacterial cells, and others causing a decrease in the same cells. This phenomenon has yet to be explained, but the current study attempts to offer a mathematical explanation for this occurrence. The researchers added cultures to the magnetic fields to examine any effects to ion transportation. Researchers discovered ions such as potassium and sodium are affected by the magnetic field. A formula is presented in the analysis section to explain this effect.

Two brothers' alleged paternity for a child: who is the father?

PubMed

Dogan, Muhammed; Kara, Umut; Emre, Ramazan; Fung, Wing Kam; Canturk, Kemal Murat

2015-06-01

In paternity cases where individuals are close relatives, it may be necessary to evaluate mother's DNA profile (trio test) and to increase the number of polymorphic STR loci that are analyzed. In our case, two alleged fathers who are brothers and the child (duo case) were analyzed based on 20 STR loci; however, no exclusions could be achieved. Then trio test (with mother) was performed using the Identifiler Plus kit (Applied Biosystems) and no exclusions could be achieved again. Analysis performed with the ESS Plex Plus kit (Qiagen), the paternity of one of the two alleged fathers was rejected only on 2 STR loci. We made the calculations of power of exclusion values to interpret our results more properly. The probability of exclusion (PE) is calculated as 0.9776546 in 15 loci of Identifiler Plus kit without mother. The PE is calculated as 0.9942803, if 5 additional loci from ESS Plex Plus kit are typed. The PE becomes 0.9961048 for the Identifiler Plus kit in trio analysis. If both Identifiler Plus and ESS Plex Plus kits are used for testing, the PE is calculated as 0.999431654, which indicates that the combined kits are highly discriminating.

Multi-Scale Spatio-Temporal Modeling: Lifelines of Microorganisms in Bioreactors and Tracking Molecules in Cells

NASA Astrophysics Data System (ADS)

Lapin, Alexei; Klann, Michael; Reuss, Matthias

Agent-based models are rigorous tools for simulating the interactions of individual entities, such as organisms or molecules within cells and assessing their effects on the dynamic behavior of the system as a whole. In context with bioprocess and biosystems engineering there are several interesting and important applications. This contribution aims at introducing this strategy with the aid of two examples characterized by striking distinctions in the scale of the individual entities and the mode of their interactions. In the first example a structured-segregated model is applied to travel along the lifelines of single cells in the environment of a three-dimensional turbulent field of a stirred bioreactor. The modeling approach is based on an Euler-Lagrange formulation of the system. The strategy permits one to account for the heterogeneity present in real reactors in both the fluid and cellular phases, respectively. The individual response of the cells to local variations in the extracellular concentrations is pictured by a dynamically structured model of the key reactions of the central metabolism. The approach permits analysis of the lifelines of individual cells in space and time.

Target fragmentation in radiobiology

NASA Technical Reports Server (NTRS)

Wilson, John W.; Cucinotta, Francis A.; Shinn, Judy L.; Townsend, Lawrence W.

1993-01-01

Nuclear reactions in biological systems produce low-energy fragments of the target nuclei seen as local high events of linear energy transfer (LET). A nuclear-reaction formalism is used to evaluate the nuclear-induced fields within biosystems and their effects within several biological models. On the basis of direct ionization interaction, one anticipates high-energy protons to have a quality factor and relative biological effectiveness (RBE) of unity. Target fragmentation contributions raise the effective quality factor of 10 GeV protons to 3.3 in reasonable agreement with RBE values for induced micronuclei in bean sprouts. Application of the Katz model indicates that the relative increase in RBE with decreasing exposure observed in cell survival experiments with 160 MeV protons is related solely to target fragmentation events. Target fragment contributions to lens opacity given an RBE of 1.4 for 2 GeV protons in agreement with the work of Lett and Cox. Predictions are made for the effective RBE for Harderian gland tumors induced by high-energy protons. An exposure model for lifetime cancer risk is derived from NCRP 98 risk tables, and protraction effects are examined for proton and helium ion exposures. The implications of dose rate enhancement effects on space radiation protection are considered.

Genome wide analysis in a discordant monozygotic twin with caudal appendage and multiple congenital anomalies.

PubMed

Cogulu, O; Pariltay, E; Koroglu, O A; Aykut, A; Ozyurek, R; Levent, E; Kultursay, N; Ozkinay, F

2013-01-01

Caudal appendage is a rare dysmorphic feature of which etiologic mechanisms are not well understood. Here we report monozygotic (MZ) twin brothers who are discordant for the caudal appendage and multiple congenital anomalies. Twins were the product of a 33 weeks of gestation, monochorionic-diamniotic pregnancy. On admission the proband had micrognathia, beaked nose, hypospadias, caudal appendage and juxtaductal aorta coarctation. At birth, he was small for gestational age and he had transient hypothyroidism which was detected in the newborn period. Karyotype analysis showed 46,XY. Monozygosity was shown by 15 microsatellite markers plus amelogenin (AmpFlSTR Identifiler PCR Amplification Kit, Applied Biosystems). Genome-wide copy number analysis of the twins by DNA-DNA hybridization of whole genomic DNA (NimbleGen Human CGH 385K WG-T v2.0 array) showed a significant difference at two neighboring probes with Log2 ratio: 0.72088 which are located on chromosome 3p12.3. Further analysis by high resolution of chromosome 3 array (Roche NimbleGen Human HG18 CHR3 FT Median Probe Spacing 475 bp) and quantitative PCR analysis did not confirm the deletion.

Abrupt decadal-to-centennial hydroclimate changes in the Mediterranean region since the mid-Holocene

NASA Astrophysics Data System (ADS)

Hu, Hsun-Ming; Shen, Chuan-Chou; Jiang, Xiuyang; Wang, Yongjin; Mii, Horng-Sheng; Michel, Véronique

2016-04-01

A series of severe drought events in the Mediterranean region over the past two decades has posed a threat on both human society and biosystem. Holocene hydrological dynamics can offer valuable clues for understanding future climate and making proper adaption strategy. Here, we present a decadal-resolved stalagmite record documenting various hydroclimatic fluctuations in the north central Mediterranean region since the middle Holocene. The stalagmite δ18O sequence shows dramatic instability, characterized by abrupt shifts between dry and wet conditions <50 years. The timing of regional culture demises, such as the Hittite Kingdom, Mycenaean Greece, Akkadian Empire, Egyptian Old Kingdom, and Uruk, occurred during the drought events, suggesting an important role of climate impact on human civilization. The unstable hydroclimate evolution is related to transferred North Atlantic Oscillation states. Rate of rapid transfer of precipitation patterns, which can be pin-pointed by our good chronology, improves the prediction to future climate changes in North Atlantic region. We also found that a strong correlation between this stalagmite δ18O and sea surface temperatures especially in Pacific Ocean. This agreement suggests a distant interregional climate teleconnection.

Effect of flow velocity on the photoacoustic detection for glucose aqueous solutions

NASA Astrophysics Data System (ADS)

Ren, Zhong; Liu, Guodong; Ding, Yu; Yao, Qingkai

2018-01-01

The blood glucose non-invasive detection has become the research hot-spot. The photoacoustic spectroscopy is a well-promising, high-efficient and noninvasive detection method because it combines the advantages of the pure optic and pure ultrasonic. In practice, the photoacoustic detection of blood glucose is impacted by many factors because the human body is a complicated bio-system. To study the effect of flow velocity in the blood vessel on the photoacoustic detection of blood glucose, a photoacoustic detection system based on optical parameter oscillator (OPO) pulsed laser induced ultrasonic was established. In this system, a 532nm pumped Nd: YAG OPO pulsed laser was used as the excitation source, and the photoacoustic signals of glucose were captured by ultrasonic transducer. Moreover, a set of blood circulation system was built to simulate the real blood flow situation in the human body. The experiments of the photoacoustic detection of glucose aqueous solutions with different concentrations at different flow velocities were experimentally investigated. Experimental results show that the photoacoustic peak-to-peak value linearly increases with the glucose concentration, but it decreases with the increase of the flow velocity although the profiles of photoacoustic signals don't change.

VARiD: a variation detection framework for color-space and letter-space platforms.

PubMed

Dalca, Adrian V; Rumble, Stephen M; Levy, Samuel; Brudno, Michael

2010-06-15

High-throughput sequencing (HTS) technologies are transforming the study of genomic variation. The various HTS technologies have different sequencing biases and error rates, and while most HTS technologies sequence the residues of the genome directly, generating base calls for each position, the Applied Biosystem's SOLiD platform generates dibase-coded (color space) sequences. While combining data from the various platforms should increase the accuracy of variation detection, to date there are only a few tools that can identify variants from color space data, and none that can analyze color space and regular (letter space) data together. We present VARiD--a probabilistic method for variation detection from both letter- and color-space reads simultaneously. VARiD is based on a hidden Markov model and uses the forward-backward algorithm to accurately identify heterozygous, homozygous and tri-allelic SNPs, as well as micro-indels. Our analysis shows that VARiD performs better than the AB SOLiD toolset at detecting variants from color-space data alone, and improves the calls dramatically when letter- and color-space reads are combined. The toolset is freely available at http://compbio.cs.utoronto.ca/varid.

Lack of association between the LRRK2 A419V variant and Asian Parkinson's disease.

PubMed

Gopalai, Aroma Agape; Lim, Shen Yang; Aziz, Zariah Abdul; Lim, Soo Kun; Tan, Li Ping; Chong, Yip Boon; Tan, Chong Tin; Puvanarajah, Santhi; Viswanathan, Shanti; Kuppusamy, Rishikesan; Tan, Ai Huey; Lim, Thien Thien; Eow, Gaik Bee; Norlinah, Mohamed Ibrahim; Li, Hui Hua; Zhao, Yi; Ahmad-Annuar, Azlina

2013-05-01

The G2385R and R1628P LRRK2 gene variants have been associated with an increased risk of Parkinson's disease (PD) in the Asian population. Recently, a new LRRK2 gene variant, A419V, was reported to be a third risk variant for PD in Asian patients. Our objective was to investigate this finding in our cohort of Asian subjects. Eight hundred and twenty-eight subjects (404 PD patients, and 424 age and gender-matched control subjects without neurological disorders) were recruited. Genotyping was done by Taqman® allelic discrimination assay on an Applied Biosystems 7500 Fast Real-Time PCR machine. The heterozygous A419V genotype was found in only 1 patient with PD, compared to 3 in the control group (0.4% vs 1.3%), giving an odds ratio of 0.35 (95% confidence interval (CI), 0.01 to 3.79; P = 0.624). A419V is not an important LRRK2 risk variant in our Asian cohort of patients with PD. Our data are further supported by a literature review which showed that 4 out of 6 published studies reported a negative association of this variant in PD.

Multidentate zwitterionic chitosan oligosaccharide modified gold nanoparticles: stability, biocompatibility and cell interactions

NASA Astrophysics Data System (ADS)

Liu, Xiangsheng; Huang, Haoyuan; Liu, Gongyan; Zhou, Wenbo; Chen, Yangjun; Jin, Qiao; Ji, Jian

2013-04-01

Surface engineering of nanoparticles plays an essential role in their colloidal stability, biocompatibility and interaction with biosystems. In this study, a novel multidentate zwitterionic biopolymer derivative is obtained from conjugating dithiolane lipoic acid and zwitterionic acryloyloxyethyl phosphorylcholine to the chitosan oligosaccharide backbone. Gold nanoparticles (AuNPs) modified by this polymer exhibit remarkable colloidal stabilities under extreme conditions including high salt conditions, wide pH range and serum or plasma containing media. The AuNPs also show strong resistance to competition from dithiothreitol (as high as 1.5 M). Moreover, the modified AuNPs demonstrate low cytotoxicity investigated by both MTT and LDH assays, and good hemocompatibility evaluated by hemolysis of human red blood cells. In addition, the intracellular fate of AuNPs was investigated by ICP-MS and TEM. It showed that the AuNPs are uptaken by cells in a concentration dependent manner, and they can escape from endosomes/lysosomes to cytosol and tend to accumulate around the nucleus after 24 h incubation but few of them are excreted out of the cells. Gold nanorods are also stabilized by this ligand, which demonstrates robust dispersion stability and excellent hemocompatibility. This kind of multidentate zwitterionic chitosan derivative could be widely used for stabilizing other inorganic nanoparticles, which will greatly improve their performance in a variety of bio-related applications.Surface engineering of nanoparticles plays an essential role in their colloidal stability, biocompatibility and interaction with biosystems. In this study, a novel multidentate zwitterionic biopolymer derivative is obtained from conjugating dithiolane lipoic acid and zwitterionic acryloyloxyethyl phosphorylcholine to the chitosan oligosaccharide backbone. Gold nanoparticles (AuNPs) modified by this polymer exhibit remarkable colloidal stabilities under extreme conditions including high salt conditions, wide pH range and serum or plasma containing media. The AuNPs also show strong resistance to competition from dithiothreitol (as high as 1.5 M). Moreover, the modified AuNPs demonstrate low cytotoxicity investigated by both MTT and LDH assays, and good hemocompatibility evaluated by hemolysis of human red blood cells. In addition, the intracellular fate of AuNPs was investigated by ICP-MS and TEM. It showed that the AuNPs are uptaken by cells in a concentration dependent manner, and they can escape from endosomes/lysosomes to cytosol and tend to accumulate around the nucleus after 24 h incubation but few of them are excreted out of the cells. Gold nanorods are also stabilized by this ligand, which demonstrates robust dispersion stability and excellent hemocompatibility. This kind of multidentate zwitterionic chitosan derivative could be widely used for stabilizing other inorganic nanoparticles, which will greatly improve their performance in a variety of bio-related applications. Electronic supplementary information (ESI) available: More experimental details for the synthesis of AuNPs and AuNRs. Fig. S1, 1H NMR spectrum of LA-CSO-PC and Fig. S2, FT-IR spectrum of AuNP-LA-CSO-PC. See DOI: 10.1039/c3nr00284e

Genetic polymorphisms of 15 STR loci within Turkish student population living in Sarajevo, Bosnia and Herzegovina.

PubMed

Dogan, Serkan; Kovacević, Lejla; Marjanović, Damir

2013-12-01

Allele frequencies of 15 STRs included in the PowerPlex 16 System (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, VWA, D8S1179, TPOX and FGA) were calculated from the referent sample of 100 unrelated individuals of both sexes from Turkish student population living in Sarajevo, Bosnia and Herzegovina. Buccal swab, as a source of DNA, was collected from the volunteers from whom the informed consent form was obtained. DNA extraction was performed using QIAamp DNA Micro kit by Qiagen. DNA template ranging from 0.5 to 2 ng was used to amplify 15 STR loci by PCR multiplex amplification which was performed by using the PowerPlex 16 kit (Promega Corp., Madison, WI, USA) according to the manufacturer's protocol. The amplifications were carried out in a PE Gene Amp PCR System thermal cycler (Applied Biosystems) and capillary electrophoresis was carried out in an ABI PRISM 310 Genetic Analyzer (Applied Biosystems) in accordance with the manufacturer's recommendations. The frequency of each locus was calculated from the numbers of each observed genotype. Deviation from Hardy-Weinberg equilibrium and observed heterozygosity were calculated. Data were analyzed by using Microsoft Excel workbook template--Powerstats V12 and the power of discrimination (PD), power of exclusion (PE), as well as other population genetic indices for the 15 STR loci were calculated. Obtained results contribute to existing Turkish DNA database, as well as insight of differences and similarities in comparison to population of Bosnia and Herzegovina. In addition, 13 autosomal STR loci frequencies (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSFIPO, Penta D, VWA, D8S1 179, TPOX, and FGA) were studied in 15 different worldwide populations (Turkish, Bosnian, Croatian, Serbian, Montenegrin, Macedonian, Albanian, Kosovan, Greek, Russian, Japanese, Korean, Lithuanian, Iraqi, Belarusian). For the proof of corresponding data, two different Turkish population STR data obtained from previously published articles were compared with our data and this showed that our data correspond to these 2 previously published data. Further, STR allele frequency data for 13 loci for each population were obtained from previous scientific articles and the allele frequencies and genetic diversity among the 15 sample populations were compared. In addition, even though the populations are from different nationalities, the STR data are similar among the geographically close populations. The phylogenetic tree established among worldwide populations and genetic distance values show a great affinity among the 15populations. Our data is useful for anthropological and further comparative genetic studies of populations.

Effect of surfactants on the interaction of phenol with laccase: Molecular docking and molecular dynamics simulation studies.

PubMed

Liu, Yujie; Liu, Zhifeng; Zeng, Guangming; Chen, Ming; Jiang, Yilin; Shao, Binbin; Li, Zhigang; Liu, Yang

2018-05-22

Some surfactants can enhance the removal of phenol by laccase (Lac) in various industrial effluents. Their behavior and function in the biodegradation of phenolic wastewater have been experimentally reported by many researchers, but the underlying molecular mechanism is still unclear. Therefore, the interaction mechanisms of phenol with Lac from Trametes versicolor were investigated in the presence or absence of Triton X-100 (TX100) or rhamnolipid (RL) by molecular docking and molecular dynamics (MD) simulations. The results indicate that phenol contacts with an active site of Lac by hydrogen bonds (HBs) and van der Waals (vdW) interactions in aqueous solution for maintaining its stability. The presence of TX100 or RL results in the significant changes of enzymatic conformations. Meanwhile, the hydrophobic parts of surfactants contact with the outside surface of Lac. These changes lead to the decrease of binding energy between phenol and Lac. The migration behavior of water molecules within hydration shell is also inevitably affected. Therefore, the amphipathic TX100 or RL may influence the phenol degradation ability of Lac by modulating their interactions and water environment. This study offers molecular level of understanding on the function of surfactants in biosystem. Copyright © 2018 Elsevier B.V. All rights reserved.

Constructal approach to cell membranes transport: Amending the ‘Norton-Simon’ hypothesis for cancer treatment

NASA Astrophysics Data System (ADS)

Lucia, Umberto; Ponzetto, Antonio; Deisboeck, Thomas S.

2016-01-01

To investigate biosystems, we propose a new thermodynamic concept that analyses ion, mass and energy flows across the cell membrane. This paradigm-shifting approach has a wide applicability to medically relevant topics including advancing cancer treatment. To support this claim, we revisit ‘Norton-Simon’ and evolving it from an already important anti-cancer hypothesis to a thermodynamic theorem in medicine. We confirm that an increase in proliferation and a reduction in apoptosis trigger a maximum of ATP consumption by the tumor cell. Moreover, we find that positive, membrane-crossing ions lead to a decrease in the energy used by the tumor, supporting the notion of their growth inhibitory effect while negative ions apparently increase the cancer’s consumption of energy hence reflecting a growth promoting impact. Our results not only represent a thermodynamic proof of the original Norton-Simon hypothesis but, more concretely, they also advance the clinically intriguing and experimentally testable, diagnostic hypothesis that observing an increase in negative ions inside a cell in vitro, and inside a diseased tissue in vivo, may indicate growth or recurrence of a tumor. We conclude with providing theoretical evidence that applying electromagnetic field therapy early on in the treatment cycle may maximize its anti-cancer efficacy.

Three-Dimensional Printing of Multifunctional Nanocomposites: Manufacturing Techniques and Applications.

PubMed

Farahani, Rouhollah D; Dubé, Martine; Therriault, Daniel

2016-07-01

The integration of nanotechnology into three-dimensional printing (3DP) offers huge potential and opportunities for the manufacturing of 3D engineered materials exhibiting optimized properties and multifunctionality. The literature relating to different 3DP techniques used to fabricate 3D structures at the macro- and microscale made of nanocomposite materials is reviewed here. The current state-of-the-art fabrication methods, their main characteristics (e.g., resolutions, advantages, limitations), the process parameters, and materials requirements are discussed. A comprehensive review is carried out on the use of metal- and carbon-based nanomaterials incorporated into polymers or hydrogels for the manufacturing of 3D structures, mostly at the microscale, using different 3D-printing techniques. Several methods, including but not limited to micro-stereolithography, extrusion-based direct-write technologies, inkjet-printing techniques, and popular powder-bed technology, are discussed. Various examples of 3D nanocomposite macro- and microstructures manufactured using different 3D-printing technologies for a wide range of domains such as microelectromechanical systems (MEMS), lab-on-a-chip, microfluidics, engineered materials and composites, microelectronics, tissue engineering, and biosystems are reviewed. Parallel advances on materials and techniques are still required in order to employ the full potential of 3D printing of multifunctional nanocomposites. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A differentiable reformulation for E-optimal design of experiments in nonlinear dynamic biosystems.

PubMed

Telen, Dries; Van Riet, Nick; Logist, Flip; Van Impe, Jan

2015-06-01

Informative experiments are highly valuable for estimating parameters in nonlinear dynamic bioprocesses. Techniques for optimal experiment design ensure the systematic design of such informative experiments. The E-criterion which can be used as objective function in optimal experiment design requires the maximization of the smallest eigenvalue of the Fisher information matrix. However, one problem with the minimal eigenvalue function is that it can be nondifferentiable. In addition, no closed form expression exists for the computation of eigenvalues of a matrix larger than a 4 by 4 one. As eigenvalues are normally computed with iterative methods, state-of-the-art optimal control solvers are not able to exploit automatic differentiation to compute the derivatives with respect to the decision variables. In the current paper a reformulation strategy from the field of convex optimization is suggested to circumvent these difficulties. This reformulation requires the inclusion of a matrix inequality constraint involving positive semidefiniteness. In this paper, this positive semidefiniteness constraint is imposed via Sylverster's criterion. As a result the maximization of the minimum eigenvalue function can be formulated in standard optimal control solvers through the addition of nonlinear constraints. The presented methodology is successfully illustrated with a case study from the field of predictive microbiology. Copyright © 2015. Published by Elsevier Inc.

Comparability of automated human induced pluripotent stem cell culture: a pilot study.

PubMed

Archibald, Peter R T; Chandra, Amit; Thomas, Dave; Chose, Olivier; Massouridès, Emmanuelle; Laâbi, Yacine; Williams, David J

2016-12-01

Consistent and robust manufacturing is essential for the translation of cell therapies, and the utilisation automation throughout the manufacturing process may allow for improvements in quality control, scalability, reproducibility and economics of the process. The aim of this study was to measure and establish the comparability between alternative process steps for the culture of hiPSCs. Consequently, the effects of manual centrifugation and automated non-centrifugation process steps, performed using TAP Biosystems' CompacT SelecT automated cell culture platform, upon the culture of a human induced pluripotent stem cell (hiPSC) line (VAX001024c07) were compared. This study, has demonstrated that comparable morphologies and cell diameters were observed in hiPSCs cultured using either manual or automated process steps. However, non-centrifugation hiPSC populations exhibited greater cell yields, greater aggregate rates, increased pluripotency marker expression, and decreased differentiation marker expression compared to centrifugation hiPSCs. A trend for decreased variability in cell yield was also observed after the utilisation of the automated process step. This study also highlights the detrimental effect of the cryopreservation and thawing processes upon the growth and characteristics of hiPSC cultures, and demonstrates that automated hiPSC manufacturing protocols can be successfully transferred between independent laboratories.

In silico analysis of 16S ribosomal RNA gene sequencing‐based methods for identification of medically important anaerobic bacteria

PubMed Central

Woo, Patrick C Y; Chung, Liliane M W; Teng, Jade L L; Tse, Herman; Pang, Sherby S Y; Lau, Veronica Y T; Wong, Vanessa W K; Kam, Kwok‐ling; Lau, Susanna K P; Yuen, Kwok‐Yung

2007-01-01

This study is the first study that provides useful guidelines to clinical microbiologists and technicians on the usefulness of full 16S rRNA sequencing, 5′‐end 527‐bp 16S rRNA sequencing and the existing MicroSeq full and 500 16S rDNA bacterial identification system (MicroSeq, Perkin‐Elmer Applied Biosystems Division, Foster City, California, USA) databases for the identification of all existing medically important anaerobic bacteria. Full and 527‐bp 16S rRNA sequencing are able to identify 52–63% of 130 Gram‐positive anaerobic rods, 72–73% of 86 Gram‐negative anaerobic rods and 78% of 23 anaerobic cocci. The existing MicroSeq databases are able to identify only 19–25% of 130 Gram‐positive anaerobic rods, 38% of 86 Gram‐negative anaerobic rods and 39% of 23 anaerobic cocci. These represent only 45–46% of those that should be confidently identified by full and 527‐bp 16S rRNA sequencing. To improve the usefulness of MicroSeq, bacterial species that should be confidently identified by full and/or 527‐bp 16S rRNA sequencing but not included in the existing MicroSeq databases should be included. PMID:17046845

Database resources of the National Center for Biotechnology Information.

PubMed

Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bolton, Evan; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Landsman, David; Lipman, David J; Lu, Zhiyong; Madden, Thomas L; Madej, Tom; Maglott, Donna R; Marchler-Bauer, Aron; Miller, Vadim; Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Wang, Yanli; Wilbur, W John; Yaschenko, Eugene; Ye, Jian

2011-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), IBIS, Biosystems, Peptidome, OMSSA, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction.

PubMed

Herbert, Zachary T; Kershner, Jamie P; Butty, Vincent L; Thimmapuram, Jyothi; Choudhari, Sulbha; Alekseyev, Yuriy O; Fan, Jun; Podnar, Jessica W; Wilcox, Edward; Gipson, Jenny; Gillaspy, Allison; Jepsen, Kristen; BonDurant, Sandra Splinter; Morris, Krystalynne; Berkeley, Maura; LeClerc, Ashley; Simpson, Stephen D; Sommerville, Gary; Grimmett, Leslie; Adams, Marie; Levine, Stuart S

2018-03-15

Ribosomal RNA (rRNA) comprises at least 90% of total RNA extracted from mammalian tissue or cell line samples. Informative transcriptional profiling using massively parallel sequencing technologies requires either enrichment of mature poly-adenylated transcripts or targeted depletion of the rRNA fraction. The latter method is of particular interest because it is compatible with degraded samples such as those extracted from FFPE and also captures transcripts that are not poly-adenylated such as some non-coding RNAs. Here we provide a cross-site study that evaluates the performance of ribosomal RNA removal kits from Illumina, Takara/Clontech, Kapa Biosystems, Lexogen, New England Biolabs and Qiagen on intact and degraded RNA samples. We find that all of the kits are capable of performing significant ribosomal depletion, though there are differences in their ease of use. All kits were able to remove ribosomal RNA to below 20% with intact RNA and identify ~ 14,000 protein coding genes from the Universal Human Reference RNA sample at >1FPKM. Analysis of differentially detected genes between kits suggests that transcript length may be a key factor in library production efficiency. These results provide a roadmap for labs on the strengths of each of these methods and how best to utilize them.

A new era. Healing the injuries we have inflicted on our planet.

PubMed

Berry, T

1992-03-01

The health of the earth is essential for the well-being of every living creature on the planet; however, our plundering industrial economy has disrupted the earth's biosystems. Such neglect can no longer be accepted. Medicine is in the same situation as the entire range of human activities: All must find a way to exist in harmony with the natural world. We have been so caught up in our scientific capacity to alter the natural world that we have ignored its most basic structure. We must, therefore, enter a new era-the "Ecozoic" era, a period when humans would live on the earth in a mutually enhancing manner. This transition will require changes at a most profound level in human activity. Three principles form the basis for the Ecozoic era: Humans must recognize the universe as a communion of subjects, not a collection of objects. The earth is primary; humans are derivative. The planet will never again function as it has in the past. To enter the Ecozoic era, humans need sciences that create a new way of understanding the natural world as possessing its own unique spontaneities. Especially needed are biological sciences that have a "feel for the organism." This move from anthropology to "earthology" and cosmology is a comprehensive challenge to all our professions.

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

PubMed Central

Valouev, Anton; Ichikawa, Jeffrey; Tonthat, Thaisan; Stuart, Jeremy; Ranade, Swati; Peckham, Heather; Zeng, Kathy; Malek, Joel A.; Costa, Gina; McKernan, Kevin; Sidow, Arend; Fire, Andrew; Johnson, Steven M.

2008-01-01

Using the massively parallel technique of sequencing by oligonucleotide ligation and detection (SOLiD; Applied Biosystems), we have assessed the in vivo positions of more than 44 million putative nucleosome cores in the multicellular genetic model organism Caenorhabditis elegans. These analyses provide a global view of the chromatin architecture of a multicellular animal at extremely high density and resolution. While we observe some degree of reproducible positioning throughout the genome in our mixed stage population of animals, we note that the major chromatin feature in the worm is a diversity of allowed nucleosome positions at the vast majority of individual loci. While absolute positioning of nucleosomes can vary substantially, relative positioning of nucleosomes (in a repeated array structure likely to be maintained at least in part by steric constraints) appears to be a significant property of chromatin structure. The high density of nucleosomal reads enabled a substantial extension of previous analysis describing the usage of individual oligonucleotide sequences along the span of the nucleosome core and linker. We release this data set, via the UCSC Genome Browser, as a resource for the high-resolution analysis of chromatin conformation and DNA accessibility at individual loci within the C. elegans genome. PMID:18477713

Spectroscopic and electrochemical characterization of cytochrome c encapsulated in a bio sol-gel matrix.

PubMed

Deriu, Daniela; Pagnotta, Sara Emanuela; Santucci, Roberto; Rosato, Nicola

2008-08-01

Sol-gel technique represents a remarkably versatile method for protein encapsulation. To enhance sol-gel biocompatibility, systems envisaging the presence of calcium and phosphates in the sol-gel composition were recently prepared and investigated. Unfortunately, the low pH at which solutions were prepared (pH < 2.5) dramatically limited their application to proteins, because the acidic environment induces protein denaturation. In this paper we apply a new protocol based on the introduction of calcium nitrate to the inorganic phase, with formation of a binary bioactive system. In this case protein encapsulation results versatile and secure, being achieved at a pH close to neutrality (pH 6.0); also, the presence of calcium is expected to enhance system biocompatibility. To determine the properties of the salt-doped sol-gel and the influence exerted on entrapped biosystems, the structural and functional properties of embedded cytochrome c have been investigated. Data obtained indicate that the salt-doped sol-gel induces no significant change in the structure and the redox properties of the embedded protein; also, the matrix increases protein stability. Interestingly, the presence of calcium nitrate appears determinant for refolding of the acid-denatured protein. This is of interest in the perspective of future applications in biosensoristic area.

Electrochemistry and spectroelectrochemistry of bioactive hydroxyquinolines: a mechanistic study.

PubMed

Sokolová, Romana; Nycz, Jacek E; Ramešová, Šárka; Fiedler, Jan; Degano, Ilaria; Szala, Marcin; Kolivoška, Viliam; Gál, Miroslav

2015-05-21

The oxidation mechanism of selected hydroxyquinoline carboxylic acids such as 8-hydroxyquinoline-7-carboxylic acid (1), the two positional isomers 2-methyl-8-hydroxyquinoline-7-carboxylic acid (3) and 2-methyl-5-hydroxyquinoline-6-carboxylic acid (4), as well as other hydroxyquinolines were studied in aprotic environment using cyclic voltammetry, controlled potential electrolysis, in situ UV-vis and IR spectroelectrochemistry, and HPLC-MS/MS techniques. IR spectroelectrochemistry showed that oxidation unexpectedly proceeds together with protonation of the starting compound. We proved that the nitrogen atom in the heterocycle of hydroxyquinolines is protonated during the apparent 0.7 electron oxidation process. This was rationalized by the autodeprotonation reaction by another two starting molecules of hydroxyquinoline, so that the overall oxidation mechanism involves two electrons and three starting molecules. Both the electrochemical and spectroelectrochemical results showed that the oxidation mechanism is not influenced by the presence of the carboxylic group in the chemical structure of hydroxyquinolines, as results from oxidation of 2,7-dimethyl-5-hydroxyquinoline (6). In the presence of a strong proton acceptor such as pyridine, the oxidation ECEC process involves two electrons and two protons per one molecule of the hydroxyquinoline derivative. The electron transfer efficiency of hydroxyquinolines in biosystems may be related to protonation of biocompounds containing nitrogen bases. Molecular orbital calculations support the experimental findings.

Effects of Simulated Microgravity on Otolith Growth of Larval Zebrafish using a Rotating-Wall Vessel: Appropriate Rotation Speed and Fish Developmental Stage

NASA Astrophysics Data System (ADS)

Li, Xiaoyan; Anken, Ralf; Liu, Liyue; Wang, Gaohong; Liu, Yongding

2017-02-01

Stimulus dependence is a general feature of developing animal sensory systems. In this respect, it has extensively been shown earlier that fish inner ear otoliths can act as test masses as their growth is strongly affected by altered gravity such as hypergravity obtained using centrifuges, by (real) microgravity achieved during spaceflight or by simulated microgravity using a ground-based facility. Since flight opportunities are scarce, ground-based simulators of microgravity, using a wide variety of physical principles, have been developed to overcome this shortcoming. Not all of them, however, are equally well suited to provide functional weightlessness from the perspective of the biosystem under evaluation. Therefore, the range of applicability of a particular simulator has to be extensively tested. Earlier, we have shown that a Rotating-Wall Vessel (RWV) can be used to provide simulated microgravity for developing Zebrafish regarding the effect of rotation on otolith development. In the present study, we wanted to find the most effective speed of rotation and identify the appropriate developmental stage of Zebrafish, where effects are the largest, in order to provide a methodological basis for future in-depth analyses dedicated to the physiological processes underlying otolith growth at altered gravity. Last not least, we compared data on the effect of simulated microgravity on the size versus the weight of otoliths, since the size usually is measured in related studies due to convenience, but the weight more accurately approximates the physical capacity of an otolith. Maintaining embryos at 10 hours post fertilization for three days in the RWV, we found that 15 revolutions per minute (rpm) yielded the strongest effects on otolith growth. Maintenance of Zebrafish staged at 10 hpf, 1 day post fertilization (dpf), 4 dpf, 7 dpf and 14 dpf for three days at 15 rpm resulted in the most prominent effects in 7 dpf larvae. Weighing versus measuring the size of otoliths yielded basically similar results, but the data gained by weighing were more distinct. Overall, our results clearly support the concept that the environmental gravity vector regulates fish otolith growth in terms of the pendulum model of otolith test masses, and that wall vessel rotation is a valuable means to provide functional weightlessness from the perspective of developing Zebrafish. We recommend that Zebrafish embryos staged 7 dpf (or possibly slightly elder) are rotated at 15 rpm in a Rotating-Wall Vessel as used in the present study for further experiments designed to elucidate the mechanisms underlying (altered gravity affected) otolith growth.

Formation of noble metal nanocrystals in the presence of biomolecules

NASA Astrophysics Data System (ADS)

Burt, Justin Lockheart

One of the most promising, yet least studied routes for producing biocompatible nanostructures involves synthesis in the presence of biomolecules. I hypothesized that globular proteins could provide a suitable framework to regulate the formation of noble metal nanocrystals. As proof of concept, I designed two novel synthesis protocols utilizing bovine serum albumin (BSA) protein to regulate the formation of gold nanocrystals. In the first case, the standard protocol for polyol reduction was modified by replacing ethylene glycol with glycerin, replacing synthetic polymers with BSA as protecting agent, and decreasing the reaction temperature. In the second case, the Brust-Schiffrin two-phase reduction was modified by replacing alkylthiols with BSA as protecting agent, which facilitated a strictly aqueous phase synthesis. Due to superior product yield and rapid reduction at room temperature, the aqueous protocol became the foundation for subsequent studies. I extended this approach to produce well-dispersed ˜2nm silver, gold, and platinum nanocrystals. Having demonstrated the feasibility of BSA-functionalized nanocrystals, some potential uses were explored. BSA-functionalized silver nanocrystals were employed in a broader study on the interaction of silver nanocrystals with HIV. BSA-functionalized gold nanocrystals were utilized for in vivo dosage of a contrast enhancing agent to bacteria. BSA-functionalized platinum nanocrystals were studied as hydrogenation catalysts. Since many intriguing uses for protein-functionalized nanocrystals involve incorporation into biosystems, I sought to enhance biocompatibility by using ascorbic acid as reducing agent. Initial experiments revealed elongated and branched nanocrystals. Such structures were not observed in previous synthesis protocols with BSA, so I hypothesized ascorbic acid was driving their formation. To test my assertion, I reduced ionic gold in an aqueous solution of ascorbic acid, thereby discovering a new method for producing multiply-branched gold nanocrystals. Two conditions were necessary to achieve multiply-branched structures: rapid kinetics, and strongly acidic pH. By exploiting ascorbic acid complexation with BSA to moderate reaction kinetics, and using sodium hydroxide to provide basic pH, the two conditions for branching were negated, and well-dispersed ˜2.5nm gold nanocrystals were obtained. This protocol represents a novel, environmentally benign approach to producing biocompatible nanocrystals, relying on proteins, ascorbic acid, sodium hydroxide, and water, all at ambient temperature.

Real-time quantitative PCR for retrovirus-like particle quantification in CHO cell culture.

PubMed

de Wit, C; Fautz, C; Xu, Y

2000-09-01

Chinese hamster ovary (CHO) cells have been widely used to manufacture recombinant proteins intended for human therapeutic uses. Retrovirus-like particles, which are apparently defective and non-infectious, have been detected in all CHO cells by electron microscopy (EM). To assure viral safety of CHO cell-derived biologicals, quantification of retrovirus-like particles in production cell culture and demonstration of sufficient elimination of such retrovirus-like particles by the down-stream purification process are required for product market registration worldwide. EM, with a detection limit of 1x10(6) particles/ml, is the standard retrovirus-like particle quantification method. The whole process, which requires a large amount of sample (3-6 litres), is labour intensive, time consuming, expensive, and subject to significant assay variability. In this paper, a novel real-time quantitative PCR assay (TaqMan assay) has been developed for the quantification of retrovirus-like particles. Each retrovirus particle contains two copies of the viral genomic particle RNA (pRNA) molecule. Therefore, quantification of retrovirus particles can be achieved by quantifying the pRNA copy number, i.e. every two copies of retroviral pRNA is equivalent to one retrovirus-like particle. The TaqMan assay takes advantage of the 5'-->3' exonuclease activity of Taq DNA polymerase and utilizes the PRISM 7700 Sequence Detection System of PE Applied Biosystems (Foster City, CA, U.S.A.) for automated pRNA quantification through a dual-labelled fluorogenic probe. The TaqMan quantification technique is highly comparable to the EM analysis. In addition, it offers significant advantages over the EM analysis, such as a higher sensitivity of less than 600 particles/ml, greater accuracy and reliability, higher sample throughput, more flexibility and lower cost. Therefore, the TaqMan assay should be used as a substitute for EM analysis for retrovirus-like particle quantification in CHO cell-based production system. Copyright 2000 The International Association for Biologicals.

Genetic variation in IL-16 miRNA target site and time to prostate cancer diagnosis in African American men

PubMed Central

Hughes, Lucinda; Ruth, Karen; Rebbeck, Timothy R.; Giri, Veda N.

2013-01-01

Background Men with a family history of prostate cancer and African American men are at high risk for prostate cancer and in need of personalized risk estimates to inform screening decisions. This study evaluated genetic variants in genes encoding microRNA (miRNA) binding sites for informing of time to prostate cancer diagnosis among ethnically-diverse, high-risk men undergoing prostate cancer screening. Methods The Prostate Cancer Risk Assessment Program (PRAP) is a longitudinal screening program for high-risk men. Eligibility includes men ages 35-69 with a family history of prostate cancer or African descent. Participants with ≥ 1 follow-up visit were included in the analyses (n=477). Genetic variants in regions encoding miRNA binding sites in four target genes (ALOX15, IL-16, IL-18, and RAF1) previously implicated in prostate cancer development were evaluated. Genotyping methods included Taqman® SNP Genotyping Assay (Applied Biosystems) or pyrosequencing. Cox models were used to assess time to prostate cancer diagnosis by risk genotype. Results Among 256 African Americans with ≥ one follow-up visit, the TT genotype at rs1131445 in IL-16 was significantly associated with earlier time to prostate cancer diagnosis vs. the CC/CT genotypes (p=0.013), with a suggestive association after correction for false-discovery (p=0.065). Hazard ratio after controlling for age and PSA for TT vs. CC/CT among African Americans was 3.0 (95% CI 1.26-7.12). No association to time to diagnosis was detected among Caucasians by IL-16 genotype. No association to time to prostate cancer diagnosis was found for the other miRNA target genotypes. Conclusions Genetic variation in IL-16 encoding miRNA target site may be informative of time to prostate cancer diagnosis among African American men enrolled in prostate cancer risk assessment, which may inform individualized prostate cancer screening strategies in the future. PMID:24061634

Interaction between cytokine gene polymorphisms and the effect of physical exercise on clinical and inflammatory parameters in older women: study protocol for a randomized controlled trial.

PubMed

Pereira, Daniele S; Queiroz, Bárbara Z; Mateo, Elvis C C; Assumpção, Alexandra M; Felício, Diogo C; Miranda, Aline S; Anjos, Daniela M C; Jesus-Moraleida, Fabianna; Dias, Rosângela C; Pereira, Danielle A G; Teixeira, Antônio L; Pereira, Leani S M

2012-08-08

Aging is associated with chronic low-grade inflammatory activity with an elevation of cytokine levels. An association between regular physical activity and reduction of blood levels of anti-inflammatory cytokines is demonstrated in the literature pointing to an anti-inflammatory effect related to exercise. However, there is no consensus regarding which type of exercise and which parameters are the most appropriate to influence inflammatory markers. Evidence indicates that the single nucleotide polymorphism (SNP) can influence the synthesis of those cytokines affecting their production. The design of this study is a randomized controlled trial. The aim of this study is to investigate the interaction between the cytokine genes SNP and the effect of physical activity on older women. The main outcomes are: serum levels of sTNFR-1, sTNFR-2, interleukin (IL)-6, IL-10, measured by the ELISA method; genotyping of tumor necrosis factor- (TNF)-alpha (rs1800629), IL6 (rs1800795), IL10 (rs1800896) by the TaqMan Method (Applied Biosystems, Foster City, CA, USA); and physical performance assessed by Timed Up and Go and 10-Meter Walk Tests. Secondary outcomes include: Geriatric Depression Scale, Perceived Stress Scaleand aerobic capacity, assessed by the six-minute walk; and lower limb muscle strength, using an isokinetic dinamometer (Biodex Medical Systems, Inc., Shirley, NY,USA). Both exercise protocols will be performed three times a week for 10 weeks, 30 sessions in total. Investigating the interaction between genetic factors and exercise effects of both protocols of exercise on the levels of inflammatory cytokine levels can contribute to guide clinical practice related to treatment and prevention of functional changes due to chronic inflammatory activity in older adults. This approach could develop new perspectives on preventive and treatment proposals in physical therapy and in the management of the older patient. (ReBEC) RBR9v9cwf.

Disposition of Cannabichromene, Cannabidiol, and Δ9-Tetrahydrocannabinol and its Metabolites in Mouse Brain following Marijuana Inhalation Determined by High-Performance Liquid Chromatography–Tandem Mass Spectrometry

PubMed Central

Poklis, Justin L.; Thompson, Candace C.; Long, Kelly A.; Lichtman, Aron H.; Poklis, Alphonse

2011-01-01

A liquid chromatography–tandem mass spectrometry (LC–MS–MS) method was developed for the analysis of marijuana cannabinoids in mouse brain tissue using an Applied Biosystems 3200 Q trap with a turbo V source for TurbolonSpray attached to a Shimadzu SCL HPLC system. The method included cannabichromene (CBC), cannabidiol (CBD), D9-tetrahydrocannabinol (THC), 11-hydroxytetrahydrocannabinol (11-OH-THC), and 11-nor-D9-tetrahydrocannabinol-9-carboxylic acid (THC-COOH). These compounds were isolated by liquid-liquid extraction using cold acetonitrile. The following transition ions were monitored by multiple reaction monitoring (MRM): m/z 315>193, 315>259 for THC/CBD/CBC; m/z 331>193, 331>105 for 11-OH-THC; m/z 345>299, 345>193 for THC-COOH;c m/z 318>196 for THC-d3; m/z 334>196 for 11-OH-THC-d3, and m/z 348>302 for THCCOOH-d3. Linearity for THC, 1-OH-THC, and THC-COOH was 1-200 ng/g; for CBC and CBD, it was 0.5–20 ng/g. Within-run and between-run precisions for all the analytes yielded coefficients of variation of < 20%. Four C57BL6 mice were sacrificed 20 min after nose-only exposure to the smoke of 200 mg of marijuana containing 0.44 mg CBC, 0.93 mg CBD, and 8.81 mg THC. The mean brain concentrations were 3.9 ± 1.5 ng/g CBC, 21 ± 3.9 ng/g CBD, 364 ± 74 ng/g THC, and 28 ± 5.9 ng/g 11-OH-THC. THCCOOH was not detected. The relative mean brain cannabinoid concentrations correlated to the amounts of the cannabinoids in the inhaled marijuana. PMID:21258613

Search for DQ2.5 and DQ8 alleles using a lower cost technique in patients with type 1 diabetes and celiac disease in a population of southern Brazil.

PubMed

Bastos, Marília D; Kowalski, Thayne W; Puñales, Márcia; Tschiedel, Balduíno; Mariath, Luiza M; Pires, Ana Luiza G; Faccini, Lavínia S; Silveira, Themis R

2017-12-01

To evaluate the frequency of DQ2.5 and DQ8 alleles using the Tag-single-nucleotide polymorphism (Tag-SNP) technique in individuals with type 1 diabetes mellitus (T1DM) and celiac disease (CD) in southern Brazil. In a prospective design, we performed the search for DQA1*0501 and DQB1*0201 alleles for DQ2.5 and DQB1*0302 for DQ8 through Real-Time Polymerase Chain Reaction (RT-PCR) technique, using TaqMan Genotyping Assays (Applied Biosystems, USA). The diagnosis of CD was established by duodenal biopsy and genotypic determination performed by StepOne Software v2.3. Allelic and genotypic frequencies were compared between groups using Chi-square and Fisher's exact tests and the multiple comparisons using Finner's adjustment. Three hundred and sixty two patients with a median age of 14 years were divided into 3 groups: T1DM without CD (264); T1DM with CD (32) and CD without T1DM (66). In 97% of individuals with T1DM and CD and 76% of individuals with CD without T1DM, respectively, the alleles DQ2.5 and/or DQ8 were identified (p < 0.001). DQ2.5 was more common in individuals with CD (p = 0.004) and DQ8 was more common in individuals with type 1 diabetes (p = 0.008). The evaluation of the alleles for DQ2.5 and DQ8 by Tag-SNP technique showed a high negative predictive value among those with T1DM, similar to that described by the conventional technique. The high frequency of DQ8 alleles in individuals with T1DM did not allow differentiating those at higher risk of developing T1DM.

Final Scientific/Technical Report, DE-FG02-06ER64171, Integrated Nucleic Acid System for In-Field Monitoring of Microbial Community Dynamics and Metabolic Activity – Subproject to Co-PI Eric E. Roden

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

Eric E. Roden

2009-07-08

This report summarizes research conducted in conjunction with a project entitled “Integrated Nucleic Acid System for In-Field Monitoring of Microbial Community Dynamics and Metabolic Activity”, which was funded through the Integrative Studies Element of the former NABIR Program (now the Environmental Remediation Sciences Program) within the Office of Biological and Environmental Research. Dr. Darrell Chandler (originally at Argonne National Laboratory, now with Akonni Biosystems) was the overall PI/PD for the project. The overall project goals were to (1) apply a model iron-reducer and sulfate-reducer microarray and instrumentation systems to sediment and groundwater samples from the Scheibe et al. FRC Areamore » 2 field site, UMTRA sediments, and other DOE contaminated sites; (2) continue development and expansion of a 16S rRNA/rDNA¬-targeted probe suite for microbial community dynamics as new sequences are obtained from DOE-relevant sites; and (3) address the fundamental molecular biology and analytical chemistry associated with the extraction, purification and analysis of functional genes and mRNA in environmental samples. Work on the UW subproject focused on conducting detailed batch and semicontinuous culture reactor experiments with uranium-contaminated FRC Area 2 sediment. The reactor experiments were designed to provide coherent geochemical and microbiological data in support of microarray analyses of microbial communities in Area 2 sediments undergoing biostimulation with ethanol. A total of four major experiments were conducted (one batch and three semicontinuous culture), three of which (the batch and two semicontinuous culture) provided samples for DNA microarray analysis. A variety of other molecular analyses (clone libraries, 16S PhyloChip, RT-PCR, and T-RFLP) were conducted on parallel samples from the various experiments in order to provide independent information on microbial community response to biostimulation.« less

Advanced water splitting for green hydrogen gas production through complete oxidation of starch by in vitro metabolic engineering.

PubMed

Kim, Jae-Eung; Kim, Eui-Jin; Chen, Hui; Wu, Chang-Hao; Adams, Michael W W; Zhang, Y-H Percival

2017-11-01

Starch is a natural energy storage compound and is hypothesized to be a high-energy density chemical compound or solar fuel. In contrast to industrial hydrolysis of starch to glucose, an alternative ATP-free phosphorylation of starch was designed to generate cost-effective glucose 6-phosphate by using five thermophilic enzymes (i.e., isoamylase, alpha-glucan phosphorylase, 4-α-glucanotransferase, phosphoglucomutase, and polyphosphate glucokinase). This enzymatic phosphorolysis is energetically advantageous because the energy of α-1,4-glycosidic bonds among anhydroglucose units is conserved in the form of phosphorylated glucose. Furthermore, we demonstrated an in vitro 17-thermophilic enzyme pathway that can convert all glucose units of starch, regardless of branched and linear contents, with water to hydrogen at a theoretic yield (i.e., 12 H 2 per glucose), three times of the theoretical yield from dark microbial fermentation. The use of a biomimetic electron transport chain enabled to achieve a maximum volumetric productivity of 90.2mmol of H 2 /L/h at 20g/L starch. The complete oxidation of starch to hydrogen by this in vitro synthetic (enzymatic) biosystem suggests that starch as a natural solar fuel becomes a high-density hydrogen storage compound with a gravimetric density of more than 14% H 2 -based mass and an electricity density of more than 3000Wh/kg of starch. Copyright © 2017. Published by Elsevier Inc.

16S rRNA partial gene sequencing for the differentiation and molecular subtyping of Listeria species.

PubMed

Hellberg, Rosalee S; Martin, Keely G; Keys, Ashley L; Haney, Christopher J; Shen, Yuelian; Smiley, R Derike

2013-12-01

Use of 16S rRNA partial gene sequencing within the regulatory workflow could greatly reduce the time and labor needed for confirmation and subtyping of Listeria monocytogenes. The goal of this study was to build a 16S rRNA partial gene reference library for Listeria spp. and investigate the potential for 16S rRNA molecular subtyping. A total of 86 isolates of Listeria representing L. innocua, L. seeligeri, L. welshimeri, and L. monocytogenes were obtained for use in building the custom library. Seven non-Listeria species and three additional strains of Listeria were obtained for use in exclusivity and food spiking tests. Isolates were sequenced for the partial 16S rRNA gene using the MicroSeq ID 500 Bacterial Identification Kit (Applied Biosystems). High-quality sequences were obtained for 84 of the custom library isolates and 23 unique 16S sequence types were discovered for use in molecular subtyping. All of the exclusivity strains were negative for Listeria and the three Listeria strains used in food spiking were consistently recovered and correctly identified at the species level. The spiking results also allowed for differentiation beyond the species level, as 87% of replicates for one strain and 100% of replicates for the other two strains consistently matched the same 16S type. Copyright © 2013 Elsevier Ltd. All rights reserved.

Fragman: an R package for fragment analysis.

PubMed

Covarrubias-Pazaran, Giovanny; Diaz-Garcia, Luis; Schlautman, Brandon; Salazar, Walter; Zalapa, Juan

2016-04-21

Determination of microsatellite lengths or other DNA fragment types is an important initial component of many genetic studies such as mutation detection, linkage and quantitative trait loci (QTL) mapping, genetic diversity, pedigree analysis, and detection of heterozygosity. A handful of commercial and freely available software programs exist for fragment analysis; however, most of them are platform dependent and lack high-throughput applicability. We present the R package Fragman to serve as a freely available and platform independent resource for automatic scoring of DNA fragment lengths diversity panels and biparental populations. The program analyzes DNA fragment lengths generated in Applied Biosystems® (ABI) either manually or automatically by providing panels or bins. The package contains additional tools for converting the allele calls to GenAlEx, JoinMap® and OneMap software formats mainly used for genetic diversity and generating linkage maps in plant and animal populations. Easy plotting functions and multiplexing friendly capabilities are some of the strengths of this R package. Fragment analysis using a unique set of cranberry (Vaccinium macrocarpon) genotypes based on microsatellite markers is used to highlight the capabilities of Fragman. Fragman is a valuable new tool for genetic analysis. The package produces equivalent results to other popular software for fragment analysis while possessing unique advantages and the possibility of automation for high-throughput experiments by exploiting the power of R.

Toxicant inhibition in activated sludge: fractionation of the physiological status of bacteria.

PubMed

Foladori, P; Bruni, L; Tamburini, S

2014-09-15

In wastewater treatment plants the sensitivity of activated sludge to a toxicant depends on the toxicity test chosen, and thus the use of more than one test is suggested. The physiological status of bacteria in response to toxicants was analysed by flow cytometry to distinguish intact, permeabilised, active cells and cells disrupted. Results were compared with respirometry and bioluminescence bioassay (Vibrio fischeri). 3,5-Dichlorophenol (DCP) was used as reference xenobiotic. DCP has a strong effect on cellular integrity, causing an increase in permeabilised and disrupted cells. A reduction of 44-80% of intact cells with 6-30 mgDCP/L for 5h was found. Inhibition of active cells was 25-49%, at 6-30 mgDCP/L for 5h. The bioluminescence bioassay resulted oversensitive to DCP compared to tests based on activated sludge, while oxygen uptake rate was affected similarly to intact cells measured by flow cytometry. Landfill leachate was tested: a detrimental impact on both cellular integrity and enzymatic activity was observed. Reduction of intact cells and active cells was by 32% and 61% respectively after addition of 50% (v/v) of leachate for 5h. The flow cytometry analysis proposed here might be widely applicable in the monitoring of various toxicants and in other aquatic biosystems. Copyright © 2014 Elsevier B.V. All rights reserved.

INTRODUCTION: Wetting and dewetting in bio-related systems

NASA Astrophysics Data System (ADS)

Herminghaus, S.

2005-03-01

Research on such genuinely soft-matter related phenomena as wetting and dewetting would not be complete without reminiscence to biological systems. The recent stir around what has been known as the lotus effect, the amazing ultra-hydrophobic properties of many plants, has highlighted the interconnections of wetting with bio-systems. In the first paper of this section (Mock et al), a `biomimetic' system is conceived which imitates the properties of plant leaves with elastic hairs. The synthesis of such a system turns out to be tricky, but the progress is encouraging. The next three papers deal with surfactant layers, as they occur in many biological systems, such as the plasma membrane. Various experimental techniques, such as fluorescence microscopy (Tanaka et al), neutron reflectivity (Steitz et al), and x-ray scattering (Ahrens et al), are demonstrated as powerful tools for their investigation. The last paper (Heim et al) takes us back to where we started: the morphologies emerging upon dewetting of a liquid. This time, the full diversity of patterns is shown which appears in the deposited solute, once the liquid has evaporated. The motivation of this work is the morphology of deposition of DNA on bio-chips, which may affect the readout results of such devices. It is shown that although much can already be understood, a lot of work has still to be done, and many beautiful mechanisms may still be discovered.

Contribution for an African autosomic STR database (AmpF/STR Identifiler and Powerplex 16 System) and a report on genotypic variations.

PubMed

Alves, Cíntia; Gusmão, Leonor; Damasceno, Albertino; Soares, Benilde; Amorim, António

2004-01-28

Allele frequencies, together with some parameters of forensic interest, for 17 STRs included in the AmpF/STR Identifiler (CSF1PO, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, TH01, TPO and VWA) and Powerplex 16 System (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, Penta D, Penta E, TH01, TPO and VWA) were estimated from a sample of 135-144 unrelated individuals from Mozambique. No deviations from Hardy-Weinberg equilibrium were observed with the exception of the FGA locus (using the Bonferroni correction for the number of loci analysed, the departure observed at this locus was not significant). Comparative analyses between our population data and other African databases, namely Promega's African-Americans, AB Applied Biosystems African-Americans and two other population samples from Mozambique and Guiné Bissau, are presented and discussed. Genotype inconsistencies between both commercial kits (for D16S539 and D8S1179) and other genotypic variations (three-banded allele patterns for TPO) are also reported.

Automated Sanger Analysis Pipeline (ASAP): A Tool for Rapidly Analyzing Sanger Sequencing Data with Minimum User Interference.

PubMed

Singh, Aditya; Bhatia, Prateek

2016-12-01

Sanger sequencing platforms, such as applied biosystems instruments, generate chromatogram files. Generally, for 1 region of a sequence, we use both forward and reverse primers to sequence that area, in that way, we have 2 sequences that need to be aligned and a consensus generated before mutation detection studies. This work is cumbersome and takes time, especially if the gene is large with many exons. Hence, we devised a rapid automated command system to filter, build, and align consensus sequences and also optionally extract exonic regions, translate them in all frames, and perform an amino acid alignment starting from raw sequence data within a very short time. In full capabilities of Automated Mutation Analysis Pipeline (ASAP), it is able to read "*.ab1" chromatogram files through command line interface, convert it to the FASTQ format, trim the low-quality regions, reverse-complement the reverse sequence, create a consensus sequence, extract the exonic regions using a reference exonic sequence, translate the sequence in all frames, and align the nucleic acid and amino acid sequences to reference nucleic acid and amino acid sequences, respectively. All files are created and can be used for further analysis. ASAP is available as Python 3.x executable at https://github.com/aditya-88/ASAP. The version described in this paper is 0.28.

Database resources of the National Center for Biotechnology Information.

PubMed

2016-01-04

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (PubMed Central (PMC), Bookshelf and PubReader), health (ClinVar, dbGaP, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen), genomes (BioProject, Assembly, Genome, BioSample, dbSNP, dbVar, Epigenomics, the Map Viewer, Nucleotide, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser and the Trace Archive), genes (Gene, Gene Expression Omnibus (GEO), HomoloGene, PopSet and UniGene), proteins (Protein, the Conserved Domain Database (CDD), COBALT, Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB) and Protein Clusters) and chemicals (Biosystems and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for most of these databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Database resources of the National Center for Biotechnology Information.

PubMed

2015-01-01

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (Bookshelf, PubMed Central (PMC) and PubReader); medical genetics (ClinVar, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen); genes and genomics (BioProject, BioSample, dbSNP, dbVar, Epigenomics, Gene, Gene Expression Omnibus (GEO), Genome, HomoloGene, the Map Viewer, Nucleotide, PopSet, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser, Trace Archive and UniGene); and proteins and chemicals (Biosystems, COBALT, the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB), Protein Clusters, Protein and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for many of these databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Magnetic Fluid Hyperthermia for Bladder Cancer: A Preclinical Dosimetry Study

PubMed Central

Oliveira, Tiago R.; Stauffer, Paul R.; Lee, Chen-Ting; Landon, Chelsea D.; Etienne, Wiguins; Ashcraft, Kathleen A.; McNerny, Katie L.; Mashal, Alireza; Nouls, John; Maccarini, Paolo F.; Beyer, Wayne F.; Inman, Brant; Dewhirst, Mark W.

2014-01-01

Purpose This paper describes a preclinical investigation of the feasibility of thermotherapy treatment of bladder cancer with Magnetic Fluid Hyperthermia (MFH), performed by analyzing the thermal dosimetry of nanoparticle heating in a rat bladder model. Materials and Methods The bladders of twenty-five female rats were instilled with magnetite-based nanoparticles, and hyperthermia was induced using a novel small animal magnetic field applicator (Actium Biosystems, Boulder, CO). We aimed to increase the bladder lumen temperature to 42°C in <10 min and maintain that temperature for 60 min. Temperatures were measured within the bladder lumen and throughout the rat with seven fiberoptic probes (OpSens Technologies, Quebec, Canada). An MRI analysis was used to confirm the effectiveness of the catheterization method to deliver and maintain various nanoparticle volumes within the bladder. Thermal dosimetry measurements recorded the temperature rise of rat tissues for a variety of nanoparticle exposure conditions. Results Thermal dosimetry data demonstrated our ability to raise and control the temperature of rat bladder lumen ≥1°C/min to a steady-state of 42°C with minimal heating of surrounding normal tissues. MRI scans confirmed the homogenous nanoparticle distribution throughout the bladder. Conclusion These data demonstrate that our MFH system with magnetite-based nanoparticles provide well-localized heating of rat bladder lumen with effective control of temperature in the bladder and minimal heating of surrounding tissues. PMID:24050253

Quantitation of tacrolimus in whole blood using high performance liquid chromatography-tandem mass spectrometry (HPLC-MS-MS).

PubMed

Donaldson, Keri J; Shaw, Leslie M

2010-01-01

We describe a multiple reaction monitoring positive ion HPLC/tandem mass spectrometric method for quantification of tacrolimus in human whole blood with online extraction and cleanup. Included in this procedure: API 2000 triple quadrupole mass spectrometer with turbo-ion spray source (Applied Biosystems, Foster City, CA); 10-port diverter/switching valve (Valco, Houston, TX); HPLC system (Agilent Technologies series 1100, Wilmington, DE); 10 mm (C(18)) guard cartridge (Perkin Elmer, Norwalk, CT) used as an extraction column; a Nova-Pak C18 analytical column (2.1 x 150 mm I.D., 4 microm, Waters Corp, Milford, MA); washing solution, methanol: 30 mM ammonium acetate pH 5.1 (80:20); eluting solution, methanol:30 mM ammonium acetate pH 5.1 (97:3); flow rate 0.8 mL/min; and a run-time of 2.8 min. The first and third quadrupoles were set to detect the ammonium adduct ion and a high mass fragment of tacrolimus (m/z 821.5-->768.3), and of an internal standard (ascomycin) (m/z 901.8-->834.4). The lower limit of quantification of this method is 3.75 mg/L. The concentration of drug is determined by comparing peak-area ratios for tacrolimus and internal standard to a standard curve constructed using non-weighted linear through zero regression.

Longitudinal study on patent citations to academic research articles in nanotechnology (1976-2004)

NASA Astrophysics Data System (ADS)

Hu, Daning; Chen, Hsinchun; Huang, Zan; Roco, Mihail C.

2007-08-01

Academic nanoscale science and engineering (NSE) research provides a foundation for nanotechnology innovation reflected in patents. About 60% or about 50,000 of the NSE-related patents identified by "full-text" keyword searching between 1976 and 2004 at the United States Patent and Trademark Office (USPTO) have an average of approximately 18 academic citations. The most cited academic journals, individual researchers, and research articles have been evaluated as sources of technology innovation in the NSE area over the 28-year period. Each of the most influential articles was cited about 90 times on the average, while the most influential author was cited more than 700 times by the NSE-related patents. Thirteen mainstream journals accounted for about 20% of all citations. Science, Nature and Proceedings of the National Academy of Sciences (PNAS) have consistently been the top three most cited journals, with each article being cited three times on average. There is another kind of influential journals, represented by Biosystems and Origin of Life, which have very few articles cited but with exceptionally high frequencies. The number of academic citations per year from ten most cited journals has increased by over 17 times in the interval (1990-1999) as compared to (1976-1989), and again over 3 times in the interval (2000-2004) as compared to (1990-1999). This is an indication of increased used of academic knowledge creation in the NSE-related patents.

Typeability of DNA in Touch Traces Deposited on Paper and Optical Data Discs.

PubMed

Sołtyszewski, Ireneusz; Szeremeta, Michał; Skawrońska, Małgorzata; Niemcunowicz-Janica, Anna; Pepiński, Witold

2015-01-01

Nucleated epithelial cells that are transferred by casual touching and handling of objects are the primary source of biological evidence that is found in high-volume crimes. Cellular material associated with touch traces usually contains low levels of DNA template making it challenging to acquire an informative profile. The main purpose of this study was to examine the efficacy of DNA typing in fingerprints deposited on optical data discs and the office paper. Latent fingerprints were made by 60 subjects of both sexes (30 males and 30 females). A highly effective DNA extraction method with QIAamp DNA Mini Kit (Qiagen) and an increased sensitivity PCR by AmpFlSTR® NGM™ Amplification Kit (Applied Biosystems) carried out at standard 30 cycles and at increased 34 cycles were used. The mean value of total DNA recovery was 0.4 ng from CDs/DVDs and 0.3 ng from the office paper. Amplification of Low Template DNA (LT-DNA) resulted in improved analytical success by increasing the number of PCR cycles from standard 30 to 34. On the other hand, the increased PCR cycles resulted in allele drop-ins showing additional peaks, the majority of which were outside the stutter positions. Rigorous procedures and interpretation guidelines are required during LT-DNA for producing reliable and reproducible DNA profiles for forensic purposes.

Haplotype diversity of 16 Y-chromosomal STRs in three main ethnic populations (Malays, Chinese and Indians) in Malaysia.

PubMed

Chang, Yuet Meng; Perumal, Revathi; Keat, Phoon Yoong; Kuehn, Daniel L C

2007-03-22

We have analyzed 16 Y-STR loci (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635 or Y-GATA C4, DYS392, Y-GATA H4, DYS437, DYS438 and DYS448) from the non-recombining region of the human Y-chromosome in 980 male individuals from three main ethnic populations in Malaysia (Malay, Chinese, Indian) using the AmpFlSTR((R)) Y-filertrade mark (Applied Biosystems, Foster City, CA). The observed 17-loci haplotypes and the individual allele frequencies for each locus were estimated, whilst the locus diversity, haplotype diversity and discrimination capacity were calculated in the three ethnic populations. Analysis of molecular variance indicated that 88.7% of the haplotypic variation is found within population and 11.3% is between populations (fixation index F(ST)=0.113, p=0.000). This study has revealed Y-chromosomes with null alleles at several Y-loci, namely DYS458, DYS392, DYS389I, DYS389II, DYS439, DYS448 and Y-GATA H4; and several occurrences of duplications at the highly polymorphic DYS385 loci. Some of these deleted loci were in regions of the Y(q) arm that have been implicated in the occurrence of male infertility.

Can we trust intraoperative culture results in nonunions?

PubMed

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

2014-07-01

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

Biomanufacturing: history and perspective.

PubMed

Zhang, Yi-Heng Percival; Sun, Jibin; Ma, Yanhe

2017-05-01

Biomanufacturing is a type of manufacturing that utilizes biological systems (e.g., living microorganisms, resting cells, animal cells, plant cells, tissues, enzymes, or in vitro synthetic (enzymatic) systems) to produce commercially important biomolecules for use in the agricultural, food, material, energy, and pharmaceutical industries. History of biomanufacturing could be classified into the three revolutions in terms of respective product types (mainly), production platforms, and research technologies. Biomanufacturing 1.0 focuses on the production of primary metabolites (e.g., butanol, acetone, ethanol, citric acid) by using mono-culture fermentation; biomanufacturing 2.0 focuses on the production of secondary metabolites (e.g., penicillin, streptomycin) by using a dedicated mutant and aerobic submerged liquid fermentation; and biomanufacturing 3.0 focuses on the production of large-size biomolecules-proteins and enzymes (e.g., erythropoietin, insulin, growth hormone, amylase, DNA polymerase) by using recombinant DNA technology and advanced cell culture. Biomanufacturing 4.0 could focus on new products, for example, human tissues or cells made by regenerative medicine, artificial starch made by in vitro synthetic biosystems, isobutanol fermented by metabolic engineering, and synthetic biology-driven microorganisms, as well as exiting products produced by far better approaches. Biomanufacturing 4.0 would help address some of the most important challenges of humankind, such as food security, energy security and sustainability, water crisis, climate change, health issues, and conflict related to the energy, food, and water nexus.

Learning Human Aspects of Collaborative Software Development

ERIC Educational Resources Information Center

Hadar, Irit; Sherman, Sofia; Hazzan, Orit

2008-01-01

Collaboration has become increasingly widespread in the software industry as systems have become larger and more complex, adding human complexity to the technological complexity already involved in developing software systems. To deal with this complexity, human-centric software development methods, such as Extreme Programming and other agile…

Laser tweezer actuated microphotonic array devices for high resolution imaging and analysis in chip-based biosystems

NASA Astrophysics Data System (ADS)

Birkbeck, Aaron L.

A new technology is developed that functionally integrates arrays of lasers and micro-optics into microfluidic systems for the purpose of imaging, analyzing, and manipulating objects and biological cells. In general, the devices and technologies emerging from this area either lack functionality through the reliance on mechanical systems or provide a serial-based, time consuming approach. As compared to the current state of art, our all-optical design methodology has several distinguishing features, such as parallelism, high efficiency, low power, auto-alignment, and high yield fabrication methods, which all contribute to minimizing the cost of the integration process. The potential use of vertical cavity surface emitting lasers (VCSELs) for the creation of two-dimensional arrays of laser optical tweezers that perform independently controlled, parallel capture, and transport of large numbers of individual objects and biological cells is investigated. One of the primary biological applications for which VCSEL array sourced laser optical tweezers are considered is the formation of engineered tissues through the manipulation and spatial arrangement of different types of cells in a co-culture. Creating devices that combine laser optical tweezers with select micro-optical components permits optical imaging and analysis functions to take place inside the microfluidic channel. One such device is a micro-optical spatial filter whose motion and alignment is controlled using a laser optical tweezer. Unlike conventional spatial filter systems, our device utilizes a refractive optical element that is directly incorporated onto the lithographically patterned spatial filter. This allows the micro-optical spatial filter to automatically align itself in three-dimensions to the focal point of the microscope objective, where it then filters out the higher frequency additive noise components present in the laser beam. As a means of performing high resolution imaging in the microfluidic channel, we developed a novel technique that integrates the capacity of a laser tweezer to optically trap and manipulate objects in three-dimensions with the resolution-enhanced imaging capabilities of a solid immersion lens (SIL). In our design, the SIL is a free-floating device whose imaging beam, motion control and alignment is provided by a laser optical tweezer, which allows the microfluidic SIL to image in areas that are inaccessible to traditional solid immersion microscopes.

[Association between rs10938397 polymorphism in GNPDA2 and obesity in children at different stages of development].

PubMed

Gao, L W; Zhang, M X; Wu, L J; Fu, L W; Zhao, X Y; Mi, J

2018-01-10

Objective: To examine the association between rs10938397 polymorphism in glucosamine-6-phosphate deaminase 2 ( GNPDA2 ) and risk of obesity in children at different stages of development and analyze the differences in the association. Methods: A total of 3 503 school-aged children were selected from the Beijing Child and Adolescent Metabolic Syndrome (BCAMS) study in Beijing and their complete anthropometry weight, height, fat mass percentage (FMP), fat mass index (FMI) and free fat mass index (FFMI) and sexual maturation (SM) data were used. The developmental stages were evaluated using male testicular volume and female breast Tanner staging. FMP, FM and FFM were measured by bioelectrical impedance analysis. General obesity and adiposity were respectively defined according to Chinese sex-age-specific body mass index (BMI) cutoffs and sex-age-specific FMP cutoffs. The SNP rs10938397 were genotyped by the TaqMan Allelic Discrimination Assay with the GeneAmp 7900 sequence detection system (Applied Biosystems, Foster city, CA, USA). Relationships between rs10938397 polymorphism and BMI, FMP, FMI and FFMI and different types of obesity were tested using multivariate linear regression and logistic regression models. Results: After age adjustment and correction for multiple testing, the rs10938397-G was associated with BMI and risk of general obesity in boys in early puberty ( β =0.328, P =0.001; OR =1.420, 95% CI : 1.126-1.790), and the rs10938397-G was associated with BMI in girls in late puberty ( β =0.266, P =0.001). The associations of GNPDA2 rs10938397-G with FFMI and FMI were observed in boys in early puberty ( β =0.137, P =0.016; β =0.202, P =0.007) and the associations of rs10938397-G with FMP and FMI were observed in girls in late puberty ( β =0.153, P =0.002; β =0.168, P =0.001). The rs10938397-G was also associated with adiposity in girls in late puberty ( OR =1.339, 95% CI : 1.093-1.637). Conclusion: The rs10938397 polymorphism in GNPDA2 is associated with adiposity in girls, and it is important to use an accurate indicator of obesity in exposing the genuine association between genes and obesity.

Guidelines and Recommendations for Developing Interactive eHealth Apps for Complex Messaging in Health Promotion.

PubMed

Heffernan, Kayla Joanne; Chang, Shanton; Maclean, Skye Tamara; Callegari, Emma Teresa; Garland, Suzanne Marie; Reavley, Nicola Jane; Varigos, George Andrew; Wark, John Dennis

2016-02-09

The now ubiquitous catchphrase, "There's an app for that," rings true owing to the growing number of mobile phone apps. In excess of 97,000 eHealth apps are available in major app stores. Yet the effectiveness of these apps varies greatly. While a minority of apps are developed grounded in theory and in conjunction with health care experts, the vast majority are not. This is concerning given the Hippocratic notion of "do no harm." There is currently no unified formal theory for developing interactive eHealth apps, and development is especially difficult when complex messaging is required, such as in health promotion and prevention. This paper aims to provide insight into the creation of interactive eHealth apps for complex messaging, by leveraging the Safe-D case study, which involved complex messaging required to guide safe but sufficient UV exposure for vitamin D synthesis in users. We aim to create recommendations for developing interactive eHealth apps for complex messages based on the lessons learned during Safe-D app development. For this case study we developed an Apple and Android app, both named Safe-D, to safely improve vitamin D status in young women through encouraging safe ultraviolet radiation exposure. The app was developed through participatory action research involving medical and human computer interaction researchers, subject matter expert clinicians, external developers, and target users. The recommendations for development were created from analysis of the development process. By working with clinicians and implementing disparate design examples from the literature, we developed the Safe-D app. From this development process, recommendations for developing interactive eHealth apps for complex messaging were created: (1) involve a multidisciplinary team in the development process, (2) manage complex messages to engage users, and (3) design for interactivity (tailor recommendations, remove barriers to use, design for simplicity). This research has provided principles for developing interactive eHealth apps for complex messaging as guidelines by aggregating existing design concepts and expanding these concepts and new learnings from our development process. A set of guidelines to develop interactive eHealth apps generally, and specifically those for complex messaging, was previously missing from the literature; this research has contributed these principles. Safe-D delivers complex messaging simply, to aid education, and explicitly, considering user safety.

Guidelines and Recommendations for Developing Interactive eHealth Apps for Complex Messaging in Health Promotion

PubMed Central

Heffernan, Kayla Joanne; Maclean, Skye Tamara; Callegari, Emma Teresa; Garland, Suzanne Marie; Reavley, Nicola Jane; Varigos, George Andrew; Wark, John Dennis

2016-01-01

Background The now ubiquitous catchphrase, “There’s an app for that,” rings true owing to the growing number of mobile phone apps. In excess of 97,000 eHealth apps are available in major app stores. Yet the effectiveness of these apps varies greatly. While a minority of apps are developed grounded in theory and in conjunction with health care experts, the vast majority are not. This is concerning given the Hippocratic notion of “do no harm.” There is currently no unified formal theory for developing interactive eHealth apps, and development is especially difficult when complex messaging is required, such as in health promotion and prevention. Objective This paper aims to provide insight into the creation of interactive eHealth apps for complex messaging, by leveraging the Safe-D case study, which involved complex messaging required to guide safe but sufficient UV exposure for vitamin D synthesis in users. We aim to create recommendations for developing interactive eHealth apps for complex messages based on the lessons learned during Safe-D app development. Methods For this case study we developed an Apple and Android app, both named Safe-D, to safely improve vitamin D status in young women through encouraging safe ultraviolet radiation exposure. The app was developed through participatory action research involving medical and human computer interaction researchers, subject matter expert clinicians, external developers, and target users. The recommendations for development were created from analysis of the development process. Results By working with clinicians and implementing disparate design examples from the literature, we developed the Safe-D app. From this development process, recommendations for developing interactive eHealth apps for complex messaging were created: (1) involve a multidisciplinary team in the development process, (2) manage complex messages to engage users, and (3) design for interactivity (tailor recommendations, remove barriers to use, design for simplicity). Conclusions This research has provided principles for developing interactive eHealth apps for complex messaging as guidelines by aggregating existing design concepts and expanding these concepts and new learnings from our development process. A set of guidelines to develop interactive eHealth apps generally, and specifically those for complex messaging, was previously missing from the literature; this research has contributed these principles. Safe-D delivers complex messaging simply, to aid education, and explicitly, considering user safety. PMID:26860623

Complexity theory in the management of communicable diseases.

PubMed

Simmons, Mike

2003-06-01

In nature, apparently complex behavioural patterns are the result of repetitive simple rules. Complexity science studies the application of these rules and looks for applications in society. Complexity management opportunities have developed from this science and are providing a revolutionary approach in the constantly changing workplace. This article discusses how complexity management techniques have already been applied to communicable disease management in Wales and suggests further developments. A similar approach is recommended to others in the field, while complexity management probably has wider applications in the NHS, not least in relation to the developing managed clinical networks.

Documentation Driven Development for Complex Real-Time Systems

DTIC Science & Technology

2004-12-01

This paper presents a novel approach for development of complex real - time systems , called the documentation-driven development (DDD) approach. This... time systems . DDD will also support automated software generation based on a computational model and some relevant techniques. DDD includes two main...stakeholders to be easily involved in development processes and, therefore, significantly improve the agility of software development for complex real

78 FR 58311 - Complex Issues in Developing Drug and Biological Products for Rare Diseases; Public Workshop...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-23

...] Complex Issues in Developing Drug and Biological Products for Rare Diseases; Public Workshop; Request for... Issues in Developing Drug and Biological Products for Rare Diseases.'' The purpose of the public workshop is twofold: To discuss complex issues in clinical trials for developing drug and biological products...

Automated extraction of DNA from blood and PCR setup using a Tecan Freedom EVO liquid handler for forensic genetic STR typing of reference samples.

PubMed

Stangegaard, Michael; Frøslev, Tobias G; Frank-Hansen, Rune; Hansen, Anders J; Morling, Niels

2011-04-01

We have implemented and validated automated protocols for DNA extraction and PCR setup using a Tecan Freedom EVO liquid handler mounted with the Te-MagS magnetic separation device (Tecan, Männedorf, Switzerland). The protocols were validated for accredited forensic genetic work according to ISO 17025 using the Qiagen MagAttract DNA Mini M48 kit (Qiagen GmbH, Hilden, Germany) from fresh whole blood and blood from deceased individuals. The workflow was simplified by returning the DNA extracts to the original tubes minimizing the risk of misplacing samples. The tubes that originally contained the samples were washed with MilliQ water before the return of the DNA extracts. The PCR was setup in 96-well microtiter plates. The methods were validated for the kits: AmpFℓSTR Identifiler, SGM Plus and Yfiler (Applied Biosystems, Foster City, CA), GenePrint FFFL and PowerPlex Y (Promega, Madison, WI). The automated protocols allowed for extraction and addition of PCR master mix of 96 samples within 3.5h. In conclusion, we demonstrated that (1) DNA extraction with magnetic beads and (2) PCR setup for accredited, forensic genetic short tandem repeat typing can be implemented on a simple automated liquid handler leading to the reduction of manual work, and increased quality and throughput. Copyright © 2011 Society for Laboratory Automation and Screening. Published by Elsevier Inc. All rights reserved.

Performance Evaluation of the Real-Q Cytomegalovirus (CMV) Quantification Kit Using Two Real-Time PCR Systems for Quantifying CMV DNA in Whole Blood.

PubMed

Park, Jong Eun; Kim, Ji Youn; Yun, Sun Ae; Lee, Myoung Keun; Huh, Hee Jae; Kim, Jong Won; Ki, Chang Seok

2016-11-01

Standardized cytomegalovirus (CMV) DNA quantification is important for managing CMV disease. We evaluated the performance of the Real-Q CMV Quantification Kit (Real-Q assay; BioSewoom, Korea) using whole blood (WB), with nucleic acid extraction using MagNA Pure 96 (Roche Diagnostics, Germany). Real-time PCR was performed on two platforms: the 7500 Fast real-time PCR (7500 Fast; Applied Biosystems, USA) and CFX96 real-time PCR detection (CFX96; Bio-Rad, USA) systems. The WHO international standard, diluted with CMV-negative WB, was used to validate the analytical performance. We used 90 WB clinical samples for comparison with the artus CMV RG PCR kit (artus assay; Qiagen, Germany). Limits of detections (LODs) in 7500 Fast and CFX96 were 367 and 479 IU/mL, respectively. The assay was linear from the LOD to 10⁶ IU/mL (R² ≥0.9886). The conversion factors from copies to IU in 7500 Fast and CFX96 were 0.95 and 1.06, respectively. Compared with the artus assay, for values <1,000 copies/mL, 100% of the samples had a variation <0.7 log₁₀ copies/mL; >1,000 copies/mL, 73.3% and 80.6% of samples in 7500 Fast and CFX96, respectively, had <0.5 log₁₀ copies/mL. The Real-Q assay is useful for quantifying CMV in WB with the two real-time PCR platforms.

A Polymorphism in the Retinol Binding Protein 4 Gene is Not Associated with Gestational Diabetes Mellitus in Several Different Ethnic Groups

PubMed Central

Urschitz, Johann; Sultan, Omar; Ward, Kenneth

2011-01-01

Objective Various Asian and Pacifific Islander groups have higher prevalence rates of type 2 diabetes and gestational diabetes. This increased incidence is likely to include genetic factors. Single nucleotide polymorphisms in the retinol binding protein 4 gene have been linked to the occurrence of type 2 diabetes. Hypothesizing a link between retinol binding protein 4 and gestational diabetes, we performed a candidate gene study to look for an association between an important retinol binding protein gene polymorphism (rs3758539) and gestational diabetes. Study Design Blood was collected from Caucasian, Asian, and Pacific Islander women diagnosed with gestational diabetes and from ethnically matched non-diabetic controls. DNA was extracted and real time PCR technology (TaqMan, Applied Biosystems) used to screen for the rs3758539 single nucleotide polymorphism located 5′ of exon 1 of the retinol binding protein 4 gene. Results Genotype and allele frequencies in the controls and gestational diabetes cases were tested using chi-square contingency tests. Genotype frequencies were in Hardy-Weinberg equilibrium. There was no association between the rs3758539 retinol binding protein 4 single nucleotide polymorphism and gestational diabetes in the Caucasian, Filipino, or Pacific Islander groups. Conclusion Interestingly, the rs3758539 retinol binding protein 4 single nucleotide polymorphism was not found to be associated with gestational diabetes. The absence of association suggests that gestational and type 2 diabetes may have more divergent molecular pathophysiology than previously suspected. PMID:21886308

The Asp(327)Asn polymorphism in the sex hormone-binding globulin gene modifies the association of soy food and tea intake with endometrial cancer risk.

PubMed

Xu, Wang Hong; Zheng, Wei; Cai, Qiuyin; Cheng, Jia-Rong; Cai, Hui; Xiang, Yong-Bing; Shu, Xiao Ou

2008-01-01

We evaluated the interactive effect of polymorphisms in the sex hormone-binding globulin (SHBG) gene with soy isoflavones, tea consumption, and dietary fiber on endometrial cancer risk in a population-based, case-control study of 1,199 endometrial cancer patients and 1,212 controls. Genotyping of polymorphisms was performed by using TaqMan (Applied Biosystems, Foster City, CA) assays (rs6259) or the Affymetrix MegAllele Targeted Genotyping System (Affymetrix, Inc., US) (rs13894, rs858521, and rs2955617). Dietary information was obtained using a validated food frequency questionnaire. A logistic regression model was employed to compute adjusted odds ratios (ORs) and 95% confidence intervals (CIs). We found that the Asp(327)Asn (rs6259) polymorphism was associated with decreased risk of endometrial cancer, particularly among postmenopausal women (OR = 0.79, 95% CI = 0.62-1.00). This single nucleotide polymorphism (SNP) modified associations of soy isoflavones and tea consumption but not fiber intake with endometrial cancer, with the inverse association of soy intake and tea consumption being more evident for those with the Asp/Asp genotype of the SHBG gene at Asp(327)Asn (rs6259), particularly premenopausal women (P(interaction) = 0.06 and 0.02, respectively, for soy isoflavones and tea intake). This study suggests that gene-diet interaction may play an important role in the etiology of endometrial cancer risk.

SCAT3 changes from baseline and associations with X2 Patch measured head acceleration in amateur Australian football players.

PubMed

Willmott, Catherine; McIntosh, Andrew S; Howard, Teresa; Mitra, Biswadev; Dimech-Betancourt, Bleydy; Donovan, Jarrod; Rosenfeld, Jeffrey V

2018-05-01

To investigate changes from baseline on SCAT3 as a result of football game exposure, and association with X2 Patch measured head acceleration events in amateur Australian footballers. Prospective cohort. Peak linear acceleration (PLA) of the head (>10 g) was measured by wearable head acceleration sensor X2 Biosystems X-Patch in male (n=34) and female (n=19) Australian footballers. SCAT3 was administered at baseline (B) and post-game (PG). 1394 head acceleration events (HEA) >10 g were measured. Mean and median HEA PLA were recorded as 15.2 g (SD=9.2, range=10.0-115.8) and 12.4 g (IQR=11.0-15.6) respectively. No significant difference in median HEA PLA (g) was detected across gender (p=0.55), however, more HEAs were recorded in males (p=0.03). A greater number (p=0.004) and severity (p<0.001) of symptoms were reported PG than at B. No significant association between number of HEA or median PLA, and SCAT3 change scores (p>0.05 for all), was identified for either gender. Increase in symptom severity post game was not associated with X2 measured HEA. Males sustained more HEA, however HEA PLA magnitude did not differ across gender. Further work on the validation of head acceleration sensors is required and their role in sports concussion research and medical management. Copyright © 2017 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

Genetic variation in Tanis was associated with elevating plasma triglyceride level in Chinese nondiabetic subjects

PubMed Central

2013-01-01

Background The association of genetic polymorphisms of Tanis with triglyceride concentration in human has not been thoroughly examined. We aimed to investigate the relationship between triglyceride concentrations and Tanis genetic polymorphisms. Methods All participants (n=1497) selected from subjects participating in the Cardiovascular Risk Survey (CRS) study were divided into two groups according to ethnicity (Han: n=1059; Uygur: n= 438). Four tagging SNPs (rs12910524, rs1384565, rs2101171, rs4965814) of Tanis gene were genotyped using TaqMan® assays from Applied Biosystems following the manufacturer’s suggestions and analyzed in an ABI 7900HT Fast Real-Time PCR System. Results We found that the SNP rs12910524 was associated with triglyceride levels by analyses of a dominant model (P<0.001), recessive model (P <0.001) and additive model (P < 0.001) not only in Han ethnic but also in Uygur ethnic group, and the difference remained significant after the adjustment of sex, age, alcohol intake, smoking, BMI and plasma glucose (GLU) level (All P < 0.001). However, this relationship was not observed in rs1384565, rs2101171, and rs4965814 before and after multivariate adjustment (All P > 0.05). Furthermore, there were significant interactions between rs12910524 and GLU on TG both in Han (P=0.001) and Uygur population (P=2.60×10-4). Conclusion Our results indicated that the rs12910524 in the Tanis gene was associated with triglyceride concentrations in subjects without diabetes in China. PMID:23829426

Highly efficient nuclear DNA typing of the World War II skeletal remains using three new autosomal short tandem repeat amplification kits with the extended European Standard Set of loci

PubMed Central

Zupanič Pajnič, Irena; Gornjak Pogorelc, Barbara; Balažic, Jože; Zupanc, Tomaž; Štefanič, Borut

2012-01-01

Aim To perform an efficiency study of three new amplification kits with the extended European Standard Set (ESS) of loci for autosomal short tandem repeat (STR) typing of skeletal remains excavated from the World War II mass graves in Slovenia. Methods In the beginning of the 2011, we analyzed 102 bones and teeth using the PowerPlex ESX 17 System (Promega), AmpFiSTR NGM PCR Amplification Kit (Applied Biosystems), and Investigator ESSplex Kit (Qiagen). We cleaned the bones and teeth, removed surface contamination, and ground them into a powder using liquid nitrogen. Prior to DNA isolation with Biorobot EZ1 (Qiagen), 0.5 g bone or tooth powder was decalcified. Nuclear DNA of the samples was quantified using real-time polymerase chain reaction. All three kits used the same extract with the amplification conditions recommended by the manufacturers. Results We extracted up to 131 ng DNA/g of powder from the bones and teeth. All three amplification kits showed very similar efficiency, since DNA typing was successful with all amplification kits in 101 out of 102 bones and teeth, which represents a 99% success rate. Conclusion The commercially available ESX 17, ESSplex, and NGM kits are highly reliable for STR typing of World War II skeletal remains with the DNA extraction method optimized in our laboratory. PMID:22351574

Raw hematite based Fe(III) bio-reduction process for humified landfill leachate treatment.

PubMed

Li, Rui; Jiang, Yu; Xi, Beidou; Li, Mingxiao; Meng, Xiaoguang; Feng, Chuanping; Mao, Xuhui; Liu, Hongliang; Jiang, Yonghai

2018-05-03

Microorganisms from paddy soils and raw hematite are used for enhancing natural Fe(III) bio-reduction, in order to remove macromolecular organic pollutants from humified landfill leachate. Based on batch experiments, 60% of refractory organics can be adsorbed by hematite in 12 days. In the presence of Fe(III)-reducing bacteria, 489.60 ± 0.14 mg L -1 of dissolved organic matters can be degraded to 51.90 ± 3.96 mg L -1 within 50 days; twelve types of semi volatile organic compounds can be degraded; hereby, the reaction follows a first-order kinetics. Crystalline Fe(III) is transformed into the amorphous form and reduced to Fe(II), hydroquinone functional groups in the humic acid (HA) are transformed to quinone ones, and the formation of HA-hematite ligands is promoted. Comparing with most of the studies about electron shuttling of HA, the transformation of quinone in the HA to hydroquinone could not be observed in the present bio-system. Based on column evaluations, more than 93% of chemical oxygen demand (influent concentration of 658 ± 19 mg L -1 ) could be removed microbially under flow conditions, when the hydraulic retention time was 45 h. Raw hematite-based Fe(III) bio-reduction has a promising potential for the removal of humic and benzene series in humified landfill leachate. Copyright © 2018. Published by Elsevier B.V.

MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

PubMed

Lee, Wan-Ping; Stromberg, Michael P; Ward, Alistair; Stewart, Chip; Garrison, Erik P; Marth, Gabor T

2014-01-01

MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me).

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

PubMed Central

Lee, Wan-Ping; Stromberg, Michael P.; Ward, Alistair; Stewart, Chip; Garrison, Erik P.; Marth, Gabor T.

2014-01-01

MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me). PMID:24599324

Genetic polymorphisms variants in interleukin-6 and interleukin-1beta patients with obstructive sleep apnea syndrome in East Northern Turkey.

PubMed

Gok, Ilhami; Huseyinoglu, Nergiz; Ilhan, Dogan

2015-08-01

To investigate the relationship of IL-1β and IL-6 cytokine gene polymorphisms with obstructive sleep apnea syndrome (OSAS) in 61 patients admitted to the neurology clinic in Kafkas University Hospital with insomnia problem who were diagnosed with OSAS in sleeping labs, and 80 healthy subjects not associated with the syndrome. METHODS :Blood samples were taken to isolate DNA from patients diagnosed with OSAS based on polysomnography results and healthy controls. DNA amplification of the genes was performed with PCR. Amplification products were cut with the restriction enzymes in order to determine IL-1 gene (TaqI) and IL-6 gene (Lwel) polymorphisms. The cut DNA fragments were carried out in agarose gel electrophoresis, and RFLP analysis was performed by utilizing the images with gel imaging system. PCR products were sequenced with an Applied Biosystems Automated Sequencer. Polymorphic changes were observed for IL-1β gene in 26 of 62 patients (41.9%), and 16 of the 80 (25.8%) in the control group. The incidence of polymorphic changes in IL-6 gene was in seen in seven (of the 62 patients) (11.3%), and in the 16 (20%) controls. The findings on the genomic level in OSAS may provide an important contribution to diagnosis of obstructive sleep apnea syndrome in clinical practice, as well as it helps to obtain the results easily about environmental and genetic interaction of OSAS patients. Copyright© by the Medical Assotiation of Zenica-Doboj Canton.

Carbon-dot-based fluorescent turn-on sensor for selectively detecting sulfide anions in totally aqueous media and imaging inside live cells.

PubMed

Hou, Xianfeng; Zeng, Fang; Du, Fangkai; Wu, Shuizhu

2013-08-23

Sulfide anions are generated not only as a byproduct from industrial processes but also in biosystems. Hence, robust fluorescent sensors for detecting sulfide anions which are fast-responding, water soluble and biocompatible are highly desirable. Herein, we report a carbon-dot-based fluorescent sensor, which features excellent water solubility, low cytotoxicity and a short response time. This sensor is based on the ligand/Cu(II) approach so as to achieve fast sensing of sulfide anions. The carbon dot (CD) serves as the fluorophore as well as the anchoring site for the ligands which bind with copper ions. For this CD-based system, as copper ions bind with the ligands which reside on the surface of the CD, the paramagnetic copper ions efficiently quench the fluorescence of the CD, affording the system a turn-off sensor for copper ions. More importantly, the subsequently added sulfide anions can extract Cu(2+) from the system and form very stable CuS with Cu(2+), resulting in fluorescence enhancement and affording the system a turn-on sensor for sulfide anions. This fast-responding and selective sensor can operate in totally aqueous solution or in physiological milieu with a low detection limit of 0.78 μM. It displays good biocompatibility, and excellent cell membrane permeability, and can be used to monitor S(2-) levels in running water and living cells.

Rapid detection of Shigella and enteroinvasive Escherichia coli in produce enrichments by a conventional multiplex PCR assay.

PubMed

Binet, Rachel; Deer, Deanne M; Uhlfelder, Samantha J

2014-06-01

Faster detection of contaminated foods can prevent adulterated foods from being consumed and minimize the risk of an outbreak of foodborne illness. A sensitive molecular detection method is especially important for Shigella because ingestion of as few as 10 of these bacterial pathogens can cause disease. The objectives of this study were to compare the ability of four DNA extraction methods to detect Shigella in six types of produce, post-enrichment, and to evaluate a new and rapid conventional multiplex assay that targets the Shigella ipaH, virB and mxiC virulence genes. This assay can detect less than two Shigella cells in pure culture, even when the pathogen is mixed with background microflora, and it can also differentiate natural Shigella strains from a control strain and eliminate false positive results due to accidental laboratory contamination. The four DNA extraction methods (boiling, PrepMan Ultra [Applied Biosystems], InstaGene Matrix [Bio-Rad], DNeasy Tissue kit [Qiagen]) detected 1.6 × 10(3)Shigella CFU/ml post-enrichment, requiring ∼18 doublings to one cell in 25 g of produce pre-enrichment. Lower sensitivity was obtained, depending on produce type and extraction method. The InstaGene Matrix was the most consistent and sensitive and the multiplex assay accurately detected Shigella in less than 90 min, outperforming, to the best of our knowledge, molecular assays currently in place for this pathogen. Published by Elsevier Ltd.

Top down and bottom up engineering of bone.

PubMed

Knothe Tate, Melissa L

2011-01-11

The goal of this retrospective article is to place the body of my lab's multiscale mechanobiology work in context of top-down and bottom-up engineering of bone. We have used biosystems engineering, computational modeling and novel experimental approaches to understand bone physiology, in health and disease, and across time (in utero, postnatal growth, maturity, aging and death, as well as evolution) and length scales (a single bone like a femur, m; a sample of bone tissue, mm-cm; a cell and its local environment, μm; down to the length scale of the cell's own skeleton, the cytoskeleton, nm). First we introduce the concept of flow in bone and the three calibers of porosity through which fluid flows. Then we describe, in the context of organ-tissue, tissue-cell and cell-molecule length scales, both multiscale computational models and experimental methods to predict flow in bone and to understand the flow of fluid as a means to deliver chemical and mechanical cues in bone. Addressing a number of studies in the context of multiple length and time scales, the importance of appropriate boundary conditions, site specific material parameters, permeability measures and even micro-nanoanatomically correct geometries are discussed in context of model predictions and their value for understanding multiscale mechanobiology of bone. Insights from these multiscale computational modeling and experimental methods are providing us with a means to predict, engineer and manufacture bone tissue in the laboratory and in the human body. Copyright © 2010 Elsevier Ltd. All rights reserved.

Molecular Recognition and Structural Influences on Function in Bio-nanosystems of Nucleic Acids and Proteins

NASA Astrophysics Data System (ADS)

Sethaphong, Latsavongsakda

This work examines smart material properties of rational self-assembly and molecular recognition found in nano-biosystems. Exploiting the sequence and structural information encoded within nucleic acids and proteins will permit programmed synthesis of nanomaterials and help create molecular machines that may carry out new roles involving chemical catalysis and bioenergy. Responsive to different ionic environments thru self-reorgnization, nucleic acids (NA) are nature's signature smart material; organisms such as viruses and bacteria use features of NAs to react to their environment and orchestrate their lifecycle. Furthermore, nucleic acid systems (both RNA and DNA) are currently exploited as scaffolds; recent applications have been showcased to build bioelectronics and biotemplated nanostructures via directed assembly of multidimensional nanoelectronic devices 1. Since the most stable and rudimentary structure of nucleic acids is the helical duplex, these were modeled in order to examine the influence of the microenvironment, sequence, and cation-dependent perturbations of their canonical forms. Due to their negatively charged phosphate backbone, NA's rely on counterions to overcome the inherent repulsive forces that arise from the assembly of two complementary strands. As a realistic model system, we chose the HIV-TAR helix (PDB ID: 397D) to study specific sequence motifs on cation sequestration. At physiologically relevant concentrations of sodium and potassium ions, we observed sequence based effects where purine stretches were adept in retaining high residency cations. The transitional space between adenine and guanosine nucleotides (ApG step) in a sequence proved the most favorable. This work was the first to directly show these subtle interactions of sequence based cationic sequestration and may be useful for controlling metallization of nucleic acids in conductive nanowires. Extending the study further, we explored the degree to which the structure of NA duplexes alone interacted with cations distinct from a specific sequence. Under physiologically relevant conditions, a duplex of RNA polyguanine-polycitidine was highly responsive and able to sequester cations to the middle of the purine stretches. The least responsive structure was a DNA polyadenine-polythymine duplex. A random sequence DNA duplex contorted into an RNA-like helix resulted in cationic dynamics similar to RNA systems. These studies showed that cation diffusive binding events in nucleic acid duplex structures are sequence specific and heavily influenced by structural aspects helical forms to account for much of the differences observed. Although structural information in nucleic acids is encoded within their sequence, linking amino acid sequence to protein structure is murkier; the structural information within proteins is encoded by the folding process itself: a complex phenomenon driven toward the equilibrium state of the active conformation. Upwards of two thirds of a protein's sequence can be substituted with similar amino acids without significantly perturbing its function; conserved residues of about 10% seem to be vital; since evolutionary selection pressure in proteins operates 3-dimenionally, a linear sequence is partially informative. We explored this problem by folding de-novo the cytosolic portion of the membrane protein, cellulose synthase, CESA1 from upland cotton, Gossypium hirsutum (Ghcesa1). The cytoplasmic region was generated by homology modeling and refined with molecular dynamics. These mutations impair local structural flexibility which likely results in cellulose that is produced at a lower rate and is less crystalline. Additional modeling of fragments of cellulose synthases from the model plant, Arabidopsis thaliana, offered novel insights into the function of conserved cytosolic domains within plant cellulose synthases. Transport mechanisms related to the transmembrane region revealed significant differences between plants and a bacterial complex. These studies generated possible mutations that may allow for the creation of new synthases and identified other avenues of research in order to develop technologies that may alter the crystallinity and other useful properties of cellulose. 1. Karplus, K., SAM-T08, HMM-based protein structure prediction. Nucleic Acids Research, 2009. 37: p. W492-W497.

A Cross-Linguistic Perspective on Syntactic Complexity in L2 Development: Syntactic Elaboration and Diversity

ERIC Educational Resources Information Center

De Clercq, Bastien; Housen, Alex

2017-01-01

Syntactic and linguistic complexity have been studied extensively in applied linguistics as indicators of linguistic performance, development, and proficiency. Recent publications have equally highlighted the reductionist approach taken to syntactic complexity measurement, which often focuses on one or two measures representing complexity at the…

The Complexity of Primary Care Psychology: Theoretical Foundations.

PubMed

Smit, E H; Derksen, J J L

2015-07-01

How does primary care psychology deal with organized complexity? Has it escaped Newtonian science? Has it, as Weaver (1991) suggests, found a way to 'manage problems with many interrelated factors that cannot be dealt by statistical techniques'? Computer simulations and mathematical models in psychology are ongoing positive developments in the study of complex systems. However, the theoretical development of complex systems in psychology lags behind these advances. In this article we use complexity science to develop a theory on experienced complexity in the daily practice of primary care psychologists. We briefly answer the ontological question of what we see (from the perspective of primary care psychology) as reality, the epistemological question of what we can know, the methodological question of how to act, and the ethical question of what is good care. Following our empirical study, we conclude that complexity science can describe the experienced complexity of the psychologist and offer room for personalized client-centered care. Complexity science is slowly filling the gap between the dominant reductionist theory and complex daily practice.

Can complexity science inform physician leadership development?

PubMed

Grady, Colleen Marie

2016-07-04

Purpose The purpose of this paper is to describe research that examined physician leadership development using complexity science principles. Design/methodology/approach Intensive interviewing of 21 participants and document review provided data regarding physician leadership development in health-care organizations using five principles of complexity science (connectivity, interdependence, feedback, exploration-of-the-space-of-possibilities and co-evolution), which were grouped in three areas of inquiry (relationships between agents, patterns of behaviour and enabling functions). Findings Physician leaders are viewed as critical in the transformation of healthcare and in improving patient outcomes, and yet significant challenges exist that limit their development. Leadership in health care continues to be associated with traditional, linear models, which are incongruent with the behaviour of a complex system, such as health care. Physician leadership development remains a low priority for most health-care organizations, although physicians admit to being limited in their capacity to lead. This research was based on five principles of complexity science and used grounded theory methodology to understand how the behaviours of a complex system can provide data regarding leadership development for physicians. The study demonstrated that there is a strong association between physician leadership and patient outcomes and that organizations play a primary role in supporting the development of physician leaders. Findings indicate that a physician's relationship with their patient and their capacity for innovation can be extended as catalytic behaviours in a complex system. The findings also identified limiting factors that impact physicians who choose to lead, such as reimbursement models that do not place value on leadership and medical education that provides minimal opportunity for leadership skill development. Practical Implications This research provides practical applications for physician leadership development and emphasizes that it is incumbent upon physicians and organizations to focus attention on this to achieve improved patient and organizational outcomes. Originality/value This study pairing complexity science and physician leadership represents a unique way to view the development of physician leaders within the context of the complex system that is health care.

Use of the 22C3 anti-PD-L1 antibody to determine PD-L1 expression in multiple automated immunohistochemistry platforms.

PubMed

Ilie, Marius; Khambata-Ford, Shirin; Copie-Bergman, Christiane; Huang, Lingkang; Juco, Jonathan; Hofman, Veronique; Hofman, Paul

2017-01-01

For non-small cell lung cancer (NSCLC), treatment with pembrolizumab is limited to patients with tumours expressing PD-L1 assessed by immunohistochemistry (IHC) using the PD-L1 IHC 22C3 pharmDx (Dako, Inc.) companion diagnostic test, on the Dako Autostainer Link 48 (ASL48) platform. Optimised protocols are urgently needed for use of the 22C3 antibody concentrate to test PD-L1 expression on more widely available IHC autostainers. We evaluated PD-L1 expression using the 22C3 antibody concentrate in the three main commercially available autostainers Dako ASL48, BenchMark ULTRA (Ventana Medical Systems, Inc.), and Bond-III (Leica Biosystems) and compared the staining results with the PD-L1 IHC 22C3 pharmDx kit on the Dako ASL48 platform. Several technical conditions for laboratory-developed tests (LDTs) were evaluated in tonsil specimens and a training set of three NSCLC samples. Optimised protocols were then validated in 120 NSCLC specimens. Optimised protocols were obtained on both the VENTANA BenchMark ULTRA and Dako ASL48 platforms. Significant expression of PD-L1 was obtained on tissue controls with the Leica Bond-III autostainer when high concentrations of the 22C3 antibody were used. It therefore was not tested on the 120 NSCLC specimens. An almost 100% concordance rate for dichotomized tumour proportion score (TPS) results was observed between TPS ratings using the 22C3 antibody concentrate on the Dako ASL48 and VENTANA BenchMark ULTRA platforms relative to the PD-L1 IHC 22C3 pharmDx kit on the Dako ASL48 platform. Interpathologist agreement was high on both LDTs and the PD-L1 IHC 22C3 pharmDx kit on the Dako ASL48 platform. Availability of standardized protocols for determining PD-L1 expression using the 22C3 antibody concentrate on the widely available Dako ASL48 and VENTANA BenchMark ULTRA IHC platforms will expand the number of laboratories able to determine eligibility of patients with NSCLC for treatment with pembrolizumab in a reliable and concordant manner.

About Mass Transfer in Capillaries of Biological Systems under Influence of Vibrations

NASA Astrophysics Data System (ADS)

Prisniakov, K.

Vibrations accompany the flight of the manned spacecraft both at a stage of a orbital injection to an orbit, and during long flights (as noise), rendering undesirable physiological influence on crew, reducing serviceability and creating constant discomfort. The report represents attempt to predict a state of the cosmonaut in conditions of influence of vibrations for the period of start and stay in Space, being based on researches of mass transfer processes in capillary systems. For this purpose the original researches on heat and mass transfer processes with evaporation of liquids in capillary - porous structures in conditions of vibration actions and changes of a direction of action of gravitation are generalized. Report demonstrates the existence of modes at which increased or lowered mass transfer is achieved on border of separation "liquid - gas". The possible mechanism of influence of vibrations on evaporation of a liquid in capillaries is examined. The magnitudes of frequencies and amplitudes are submitted at which minimax characteristics are observed. The opportunity of application of the developed mathematical model of heat and mass transfer in capillary - porous structures to forecasting influence of vibrations for biological processes in capillaries of alive essences is analyzed. Such approach is justified on the mechanical nature of harmful influence of vibrations on an organism of the person. In addition the range of vibration frequencies which arise during space flights, corresponds to own resonant frequencies of a human body and his separate organs. Comparison of these resonant frequencies of a body of the person (5-80 Hertz) with vibration frequencies of optimum modes of heat and mass transfer in capillary - porous structures (20-40 Hertz) is shown their ranges of coverage. It gives the basis to assume existence of similar effects in capillaries of human body. It is supposed, that the difficulty of breath, change of a rhythm of breath, the subsequent weariness under vibration action are attributable to infringements of normal mass transfer between the inhaled air and blood. The opportunity of use of the received laws is discussed for assessment of influence of gravitational fields on intensity mass transfer in capillaries of biosystems also.

Could Neutrophil CD64 Expression Be Used as a Diagnostic Parameter of Bacteremia in Patients with Febrile Neutropenia?

PubMed

Efe İris, Nur; Yıldırmak, Taner; Gedik, Habip; Şimşek, Funda; Aydın, Demet; Demirel, Naciye; Yokuş, Osman

2017-06-05

The aim of this study is to investigate if neutrophil CD64 expression in febrile neutropenia patients could be used as an early indicator of bacteremia. All consecutive patients older than 18 years of age who had developed febrile neutropenia episodes due to hematological malignancies were included in the study. Those patients who had significant growth in their blood cultures constituted the case group, while those who had febrile neutropenia without any growth in their cultures and who did not have any documented infections formed the control group. Blood culture bottles were incubated in the Bact ALERT 3D system (bioMerieux, France), identification and susceptibility testing were performed using an automated broth microdilution method (VITEK 2, bioMerieux), and CD64 expression analysis was performed by the flow cytometry method. C-reactive protein (CRP) was measured by turbidimetric methods (Biosystems, Spain) and erythrocyte sedimentation rate (ESR) was measured by the Wintrobe method. In total, we prospectively evaluated 31 febrile episodes. The case group consisted of 17 patients while the control group included 14 patients. CD64 was found on neutrophils of the case group patients with a mean count of 8006 molecules/cell and of control group with a mean count of 2786 molecules/cell. CD64 levels of the case group were significantly higher than those of the control group (p=0.005). In the differentiation of the case group from the control group, a 2500 cut-off value for CD64 had significant [AUC=0.792 (0.619-0.965)] predictive value (p=0.001). In the prediction of patients with a 2500 cut-off value for CD64, sensitivity was 94.1%, positive predictive value was 76.2%, specificity was 64.3%, and negative predictive value was 90.0%. CRP levels and ESR values did not differ significantly between the groups (p=0.005). Neutrophil CD64 expression could be a good predictor as an immune parameter with high sensitivity and a negative predictive value for bacteremia in febrile neutropenic patients.

AgIIS, Agricultural Irrigation Imaging System, design and application

NASA Astrophysics Data System (ADS)

Haberland, Julio Andres

Remote sensing is a tool that is increasingly used in agriculture for crop management purposes. A ground-based remote sensing data acquisition system was designed, constructed, and implemented to collect high spatial and temporal resolution data in irrigated agriculture. The system was composed of a rail that mounts on a linear move irrigation machine, and a small cart that runs back and forth on the rail. The cart was equipped with a sensors package that measured reflectance in four discrete wavelengths (550 nm, 660 nm, 720 nm, and 810 nm, all 10 nm bandwidth) and an infrared thermometer. A global positioning system and triggers on the rail indicated cart position. The data was postprocessed in order to generate vegetation maps, N and water status maps and other indices relevant for site-specific crop management. A geographic information system (GIS) was used to generate images of the field on any desired day. The system was named AgIIS (A&barbelow;gricultural I&barbelow;rrigation I&barbelow;maging S&barbelow;ystem). This ground based remote sensing acquisition system was developed at the Agricultural and Biosystems Engineering Department at the University of Arizona in conjunction with the U.S. Water Conservation Laboratory in Phoenix, as part of a cooperative study primarily funded by the Idaho National Environmental and Engineering Laboratory. A second phase of the study utilized data acquired with AgIIS during the 1999 cotton growing season to model petiole nitrate (PNO3 -) and total leaf N. A latin square experimental design with optimal and low water and optimal and low N was used to evaluate N status under water and no water stress conditions. Multivariable models were generated with neural networks (NN) and multilinear regression (MLR). Single variable models were generated from chlorophyll meter readings (SPAD) and from the Canopy Chlorophyll Content Index (CCCI). All models were evaluated against observed PNO3- and total leaf N levels. The NN models showed the highest correlation with PNO3- and total leaf N. AgIIS was a reliable and efficient data acquisition system for research and also showed potential for use in commercial farming systems.

Environmental management on the basis of Complex Regional Indicators Concept: case of the Murmansk region

NASA Astrophysics Data System (ADS)

Kozlov, A.; Gutman, S.; Zaychenko, I.; Rytova, E.; Nijinskaya, P.

2015-09-01

The article presents an approach to sustainable environmental development of the Murmansk region of the Russian Federation based on the complex regional indicators as a transformation of a balance scorecard method. The peculiarities of Murmansk region connected with sustainable environmental development are described. The complex regional indicators approach allows to elaborate the general concept of complex regional development taking into consideration economic and non-economic factors with the focus on environmental aspects, accumulated environmental damage in particular. General strategic chart of sustainable environmental development of the Murmansk region worked out on the basis of complex regional indicators concept is composed. The key target indicators of sustainable ecological development of the Murmansk region are presented for the following strategic chart components: regional finance; society and market; industry and entrepreneurship; training, development and innovations. These charts are to be integrated with international environmental monitoring systems.

Application of Intervention Mapping to the Development of a Complex Physical Therapist Intervention.

PubMed

Jones, Taryn M; Dear, Blake F; Hush, Julia M; Titov, Nickolai; Dean, Catherine M

2016-12-01

Physical therapist interventions, such as those designed to change physical activity behavior, are often complex and multifaceted. In order to facilitate rigorous evaluation and implementation of these complex interventions into clinical practice, the development process must be comprehensive, systematic, and transparent, with a sound theoretical basis. Intervention Mapping is designed to guide an iterative and problem-focused approach to the development of complex interventions. The purpose of this case report is to demonstrate the application of an Intervention Mapping approach to the development of a complex physical therapist intervention, a remote self-management program aimed at increasing physical activity after acquired brain injury. Intervention Mapping consists of 6 steps to guide the development of complex interventions: (1) needs assessment; (2) identification of outcomes, performance objectives, and change objectives; (3) selection of theory-based intervention methods and practical applications; (4) organization of methods and applications into an intervention program; (5) creation of an implementation plan; and (6) generation of an evaluation plan. The rationale and detailed description of this process are presented using an example of the development of a novel and complex physical therapist intervention, myMoves-a program designed to help individuals with an acquired brain injury to change their physical activity behavior. The Intervention Mapping framework may be useful in the development of complex physical therapist interventions, ensuring the development is comprehensive, systematic, and thorough, with a sound theoretical basis. This process facilitates translation into clinical practice and allows for greater confidence and transparency when the program efficacy is investigated. © 2016 American Physical Therapy Association.

Complexity, Chaos, and Nonlinear Dynamics: A New Perspective on Career Development Theory

ERIC Educational Resources Information Center

Bloch, Deborah P.

2005-01-01

The author presents a theory of career development drawing on nonlinear dynamics and chaos and complexity theories. Career is presented as a complex adaptive entity, a fractal of the human entity. Characteristics of complex adaptive entities, including (a) autopiesis, or self-regeneration; (b) open exchange; (c) participation in networks; (d)…

A Systematic Review of Conceptual Frameworks of Medical Complexity and New Model Development.

PubMed

Zullig, Leah L; Whitson, Heather E; Hastings, Susan N; Beadles, Chris; Kravchenko, Julia; Akushevich, Igor; Maciejewski, Matthew L

2016-03-01

Patient complexity is often operationalized by counting multiple chronic conditions (MCC) without considering contextual factors that can affect patient risk for adverse outcomes. Our objective was to develop a conceptual model of complexity addressing gaps identified in a review of published conceptual models. We searched for English-language MEDLINE papers published between 1 January 2004 and 16 January 2014. Two reviewers independently evaluated abstracts and all authors contributed to the development of the conceptual model in an iterative process. From 1606 identified abstracts, six conceptual models were selected. One additional model was identified through reference review. Each model had strengths, but several constructs were not fully considered: 1) contextual factors; 2) dynamics of complexity; 3) patients' preferences; 4) acute health shocks; and 5) resilience. Our Cycle of Complexity model illustrates relationships between acute shocks and medical events, healthcare access and utilization, workload and capacity, and patient preferences in the context of interpersonal, organizational, and community factors. This model may inform studies on the etiology of and changes in complexity, the relationship between complexity and patient outcomes, and intervention development to improve modifiable elements of complex patients.

Postural complexity influences development in infants born preterm with brain injury: relating perception-action theory to 3 cases.

PubMed

Dusing, Stacey C; Izzo, Theresa; Thacker, Leroy R; Galloway, James Cole

2014-10-01

Perception-action theory suggests a cyclical relationship between movement and perceptual information. In this case series, changes in postural complexity were used to quantify an infant's action and perception during the development of early motor behaviors. Three infants born preterm with periventricular white matter injury were included. Longitudinal changes in postural complexity (approximate entropy of the center of pressure), head control, reaching, and global development, measured with the Test of Infant Motor Performance and the Bayley Scales of Infant and Toddler Development, were assessed every 0.5 to 3 months during the first year of life. All 3 infants demonstrated altered postural complexity and developmental delays. However, the timing of the altered postural complexity and the type of delays varied among the infants. For infant 1, reduced postural complexity or limited action while learning to control her head in the midline position may have contributed to her motor delay. However, her ability to adapt her postural complexity eventually may have supported her ability to learn from her environment, as reflected in her relative cognitive strength. For infant 2, limited early postural complexity may have negatively affected his learning through action, resulting in cognitive delay. For infant 3, an increase in postural complexity above typical levels was associated with declining neurological status. Postural complexity is proposed as a measure of perception and action in the postural control system during the development of early behaviors. An optimal, intermediate level of postural complexity supports the use of a variety of postural control strategies and enhances the perception-action cycle. Either excessive or reduced postural complexity may contribute to developmental delays in infants born preterm with white matter injury. © 2014 American Physical Therapy Association.

Multigrid Methods for Aerodynamic Problems in Complex Geometries

NASA Technical Reports Server (NTRS)

Caughey, David A.

1995-01-01

Work has been directed at the development of efficient multigrid methods for the solution of aerodynamic problems involving complex geometries, including the development of computational methods for the solution of both inviscid and viscous transonic flow problems. The emphasis is on problems of complex, three-dimensional geometry. The methods developed are based upon finite-volume approximations to both the Euler and the Reynolds-Averaged Navier-Stokes equations. The methods are developed for use on multi-block grids using diagonalized implicit multigrid methods to achieve computational efficiency. The work is focused upon aerodynamic problems involving complex geometries, including advanced engine inlets.

The Development of the Network Examination for Student Socialization (NEXSS) Observational Instrument

ERIC Educational Resources Information Center

Rhoades, Jesse Lee; Hastmann, Tanis Joy

2014-01-01

The complexity of learning has plagued the educational establishment for decades. Recently, ideas of complexity theory and complex adaptive systems have made headway in how we think of institutions of learning. This study developed and tested an instrument for the modeling of underlying social structures, as an element of complexity, within the…

The Development of Second Language Writing Complexity in Groups and Individuals: A Longitudinal Learner Corpus Study

ERIC Educational Resources Information Center

Vyatkina, Nina

2012-01-01

This study explores the development of multiple dimensions of linguistic complexity in the writing of beginning learners of German both as a group and as individuals. The data come from an annotated, longitudinal learner corpus. The development of lexicogrammatical complexity is explored at 2 intersections: (a) between cross-sectional trendlines…

Dynamic Development of Complexity and Accuracy: A Case Study in Second Language Academic Writing

ERIC Educational Resources Information Center

Rosmawati

2014-01-01

This paper reports on the development of complexity and accuracy in English as a Second Language (ESL) academic writing. Although research into complexity and accuracy development in second language (L2) writing has been well established, few studies have assumed the multidimensionality of these two constructs (Norris & Ortega, 2009) or…

Contingency Detection in a Complex World: A Developmental Model and Implications for Atypical Development

ERIC Educational Resources Information Center

Northrup, Jessie Bolz

2017-01-01

The present article proposes a new developmental model of how young infants adapt and respond to complex contingencies in their environment, and how this influences development. The model proposes that typically developing infants adjust to an increasingly complex environment in ways that make it easier for them to allocate limited attentional…

36 CFR 800.14 - Federal agency program alternatives.

Code of Federal Regulations, 2010 CFR

2010-07-01

... program or the resolution of adverse effects from certain complex project situations or multiple... by the agreement. (3) Developing programmatic agreements for complex or multiple undertakings. Consultation to develop a programmatic agreement for dealing with the potential adverse effects of complex...

Prototype of a subsurface drip irrigation emitter: Manufacturing, hydraulic evaluation and experimental analyses

NASA Astrophysics Data System (ADS)

Souza, Wanderley De Jesus; Rodrigues Sinobas, Leonor; Sánchez, Raúl; Arriel Botrel, Tarlei; Duarte Coelho, Rubens

2013-04-01

Root and soil intrusion into the conventional emitters is one of the major disadvantages to obtain a good uniformity of water application in subsurface drip irrigation (SDI). In the last years, there have been different approaches to reduce these problems such as the impregnation of emitters with herbicide, and the search for an emitter geometry impairing the intrusion of small roots. Within the last this study, has developed and evaluated an emitter model which geometry shows specific physical features to prevent emitter clogging. This work was developed at the Biosystems Engineering Department at ESALQ-USP/Brazil, and it is a part of a research in which an innovated emitteŕs model for SDI has been developed to prevent root and soil particles intrusion. An emitter with a mechanical-hydraulic mechanism (opening and closing the water outlet) for SDI was developed and manufactured using a mechanical lathe process. It was composed by a silicon elastic membrane a polyethylene tube and a Vnyl Polychloride membrane protector system. In this study the performance of the developed prototype was assessed in the laboratory and in the field conditions. In the laboratory, uniformity of water application was calculated by the water emission uniformity coefficient (CUE), and the manufacturer's coefficient of variation (CVm). In addition, variation in the membrane diameter submitted to internal pressures; head losses along the membrane, using the energy equation; and, precision and accuracy of the equation model, analyzed by Pearson's correlation coefficient (r), and by Willmott's concordance index (d) were also calculated with samples of the developed emitters. In the field, the emitters were installed in pots with and without sugar cane culture from October 2010 to January 2012. During this time, flow rate in 20 emitters were measured periodically, and the aspects of them about clogging at the end of the experiment. Emitters flow rates were measured quarterly to calculate: relative flow rate (QR); flow disturbance (FD); CUE; and, variation coefficient of relative flow (CVQR). In the laboratory, both "CVm" and "CUE" were small since emitters were manufactured manually, the manufacturing variation was higher than in processed emitters. Variation in the membrane diameter decreased 1/4.5 from the central toward to the emitter end; and, the head loss increased. Estimated pressures were in good agreement to the observed ones with r and d values of 0.95, and 0.85, respectively. In the field tests, coefficients CVQR and QR were variable showing a poor classification according with ABNT (1986) and Solomon (1984). FD values were ranged between 11 and 24%and there was no observed clogging by roots and/or soil intrusion at the end of the experiment. On the other hand, emitter's flows were close to the average, indicating that water application kept according to the initial results. This study shows the suitability of this emitter model to prevent root and soil intrusion within the research conditions however further studies would be needed assessing the membrane performance, emitter physical characteristics, and control of emitter flow rate in order to develop the final prototype.

Unraveling chaotic attractors by complex networks and measurements of stock market complexity

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

Cao, Hongduo; Li, Ying, E-mail: mnsliy@mail.sysu.edu.cn

2014-03-15

We present a novel method for measuring the complexity of a time series by unraveling a chaotic attractor modeled on complex networks. The complexity index R, which can potentially be exploited for prediction, has a similar meaning to the Kolmogorov complexity (calculated from the Lempel–Ziv complexity), and is an appropriate measure of a series' complexity. The proposed method is used to research the complexity of the world's major capital markets. None of these markets are completely random, and they have different degrees of complexity, both over the entire length of their time series and at a level of detail. However,more » developing markets differ significantly from mature markets. Specifically, the complexity of mature stock markets is stronger and more stable over time, whereas developing markets exhibit relatively low and unstable complexity over certain time periods, implying a stronger long-term price memory process.« less

The building blocks of economic complexity

PubMed Central

Hidalgo, César A.; Hausmann, Ricardo

2009-01-01

For Adam Smith, wealth was related to the division of labor. As people and firms specialize in different activities, economic efficiency increases, suggesting that development is associated with an increase in the number of individual activities and with the complexity that emerges from the interactions between them. Here we develop a view of economic growth and development that gives a central role to the complexity of a country's economy by interpreting trade data as a bipartite network in which countries are connected to the products they export, and show that it is possible to quantify the complexity of a country's economy by characterizing the structure of this network. Furthermore, we show that the measures of complexity we derive are correlated with a country's level of income, and that deviations from this relationship are predictive of future growth. This suggests that countries tend to converge to the level of income dictated by the complexity of their productive structures, indicating that development efforts should focus on generating the conditions that would allow complexity to emerge to generate sustained growth and prosperity. PMID:19549871

Transmetallation from CCC-NHC pincer Zr complexes in the synthesis of air-stable CCC-NHC pincer Co(iii) complexes and initial hydroboration trials.

PubMed

Reilly, Sean W; Webster, Charles Edwin; Hollis, T Keith; Valle, Henry U

2016-02-21

Development of CCC-NHC pincer Co complexes via transmetalation from Zr is reported. Formation of these air-stable Co(iii) complexes was achieved through use of a CoCl2 or Co(acac)3in situ or with a discrete CCC-NHC pincer Zr transmetallating agent. Preliminary activity in the hydroboration of styrene is reported. This facile methodology will further the development of CCC-NHC pincer first-row transition metal complexes.

Chromatin Remodeling BAF (SWI/SNF) Complexes in Neural Development and Disorders

PubMed Central

Sokpor, Godwin; Xie, Yuanbin; Rosenbusch, Joachim; Tuoc, Tran

2017-01-01

The ATP-dependent BRG1/BRM associated factor (BAF) chromatin remodeling complexes are crucial in regulating gene expression by controlling chromatin dynamics. Over the last decade, it has become increasingly clear that during neural development in mammals, distinct ontogenetic stage-specific BAF complexes derived from combinatorial assembly of their subunits are formed in neural progenitors and post-mitotic neural cells. Proper functioning of the BAF complexes plays critical roles in neural development, including the establishment and maintenance of neural fates and functionality. Indeed, recent human exome sequencing and genome-wide association studies have revealed that mutations in BAF complex subunits are linked to neurodevelopmental disorders such as Coffin-Siris syndrome, Nicolaides-Baraitser syndrome, Kleefstra's syndrome spectrum, Hirschsprung's disease, autism spectrum disorder, and schizophrenia. In this review, we focus on the latest insights into the functions of BAF complexes during neural development and the plausible mechanistic basis of how mutations in known BAF subunits are associated with certain neurodevelopmental disorders. PMID:28824374

Chromatin Remodeling BAF (SWI/SNF) Complexes in Neural Development and Disorders.

PubMed

Sokpor, Godwin; Xie, Yuanbin; Rosenbusch, Joachim; Tuoc, Tran

2017-01-01

The ATP-dependent BRG1/BRM associated factor (BAF) chromatin remodeling complexes are crucial in regulating gene expression by controlling chromatin dynamics. Over the last decade, it has become increasingly clear that during neural development in mammals, distinct ontogenetic stage-specific BAF complexes derived from combinatorial assembly of their subunits are formed in neural progenitors and post-mitotic neural cells. Proper functioning of the BAF complexes plays critical roles in neural development, including the establishment and maintenance of neural fates and functionality. Indeed, recent human exome sequencing and genome-wide association studies have revealed that mutations in BAF complex subunits are linked to neurodevelopmental disorders such as Coffin-Siris syndrome, Nicolaides-Baraitser syndrome, Kleefstra's syndrome spectrum, Hirschsprung's disease, autism spectrum disorder, and schizophrenia. In this review, we focus on the latest insights into the functions of BAF complexes during neural development and the plausible mechanistic basis of how mutations in known BAF subunits are associated with certain neurodevelopmental disorders.

KRAS detection in colonic tumors by DNA extraction from FTA paper: the molecular touch-prep.

PubMed

Petras, Melissa L; Lefferts, Joel A; Ward, Brian P; Suriawinata, Arief A; Tsongalis, Gregory J

2011-12-01

DNA isolated from formalin-fixed paraffin-embedded (FFPE) tissue is usually more degraded and contains more polymerase chain reaction (PCR) inhibitors than DNA isolated from nonfixed tissue. In addition, the tumor size and cellular heterogeneity found in tissue sections can often impact testing for molecular biomarkers. As a potential remedy to this situation, we evaluated the use of Whatman FTA paper cards for collection of colorectal tumor samples before tissue fixation and for isolation of DNA for use in a real-time PCR-based KRAS mutation assay. Eleven colon tumor samples were collected by making a cut into the fresh tumor and applying the Whatman FTA paper to the cut surface. Matched FFPE tissue blocks from these tumors were also collected for comparison. KRAS mutation analysis was carried out using the Applied Biosystems 7500 Fast Real-time PCR System using 7 independent custom TaqMan PCR assays. Of the 11 colon tumors sampled, 6 were positive for KRAS mutations in both the Whatman FTA paper preparations and corresponding FFPE samples. Whatman FTA paper cards for collection of colorectal tumor samples before tissue fixation and for isolation of DNA have many advantages including ease of use, intrinsic antimicrobial properties, long storage potential (stability of DNA over time), and a faster turnaround time for results. Extracted DNA should be suitable for most molecular diagnostic assays that use PCR techniques. This novel means of DNA preservation from surgical specimens would benefit from additional study and validation as a dependable and practical technique to preserve specimens for molecular testing.

Free Energy Reconstruction from Logarithmic Mean-Force Dynamics Using Multiple Nonequilibrium Trajectories.

PubMed

Morishita, Tetsuya; Yonezawa, Yasushige; Ito, Atsushi M

2017-07-11

Efficient and reliable estimation of the mean force (MF), the derivatives of the free energy with respect to a set of collective variables (CVs), has been a challenging problem because free energy differences are often computed by integrating the MF. Among various methods for computing free energy differences, logarithmic mean-force dynamics (LogMFD) [ Morishita et al., Phys. Rev. E 2012 , 85 , 066702 ] invokes the conservation law in classical mechanics to integrate the MF, which allows us to estimate the free energy profile along the CVs on-the-fly. Here, we present a method called parallel dynamics, which improves the estimation of the MF by employing multiple replicas of the system and is straightforwardly incorporated in LogMFD or a related method. In the parallel dynamics, the MF is evaluated by a nonequilibrium path-ensemble using the multiple replicas based on the Crooks-Jarzynski nonequilibrium work relation. Thanks to the Crooks relation, realizing full-equilibrium states is no longer mandatory for estimating the MF. Additionally, sampling in the hidden subspace orthogonal to the CV space is highly improved with appropriate weights for each metastable state (if any), which is hardly achievable by typical free energy computational methods. We illustrate how to implement parallel dynamics by combining it with LogMFD, which we call logarithmic parallel dynamics (LogPD). Biosystems of alanine dipeptide and adenylate kinase in explicit water are employed as benchmark systems to which LogPD is applied to demonstrate the effect of multiple replicas on the accuracy and efficiency in estimating the free energy profiles using parallel dynamics.

A microsatellite study for determination of allelic variation of Kurdish population-Kurdistan region-Iraq

NASA Astrophysics Data System (ADS)

Murad, Media J.; Amin, Bushra K.

2017-09-01

The purpose of this study was detecting genetic variations for the Kurdish population in Kurdistan region-Iraq, using fifteen autosomal STR loci. Buccal swabs were collected and depositing on Nucleic Card (Copan, Italia Spa) from 302 healthy unrelated Iraqi Kurds in five provinces of Kurdistan region-Iraq. Fifteen autosomal STR loci are D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, FGA and Amelogenin included in the AmpFlSTR Identifiler® Direct PCR Amplification Kit (Applied Biosystems, Foster City, CA, USA). No significant departure from Hardy Weinberg Equilibrium (HWE) expectations were observed in 10 from 15 STR loci analyzed (a 5% significance level was taken). The exceptions were the CSF1PO, D3S1358, D13S317, D16S539 and D2S1338 loci. Statistical parameters of forensic efficiencies were estimated for the loci, based on allelic frequencies. The mean of observed heterozygosity, expected heterozygosity and PIC values across the 15 loci were 0.762, 0.797 and 0.768 respectively, indicating high gene diversity. The combined probability of exclusion, power of discrimination, probability of matching value for all the 15 STR loci were 0.9999968; 0.9999999 and 4.966×10-17, respectively. These parameters indicated the importance of the loci for forensic genetic purposes and paternity testing.

The key role of biogenic manganese oxides in enhanced removal of highly recalcitrant 1,2,4-triazole from bio-treated chemical industrial wastewater.

PubMed

Wu, Ruiqin; Wu, Haobo; Jiang, Xinbai; Shen, Jinyou; Faheem, Muhammad; Sun, Xiuyun; Li, Jiansheng; Han, Weiqing; Wang, Lianjun; Liu, Xiaodong

2017-04-01

The secondary effluent from biological treatment process in chemical industrial plant often contains refractory organic matter, which deserves to be further treated in order to meet the increasingly stringent environmental regulations. In this study, the key role of biogenic manganese oxides (BioMnOx) in enhanced removal of highly recalcitrant 1,2,4-triazole from bio-treated chemical industrial wastewater was investigated. BioMnOx production by acclimated manganese-oxidizing bacterium (MOB) consortium was confirmed through scanning electronic microscopy (SEM), X-ray photoelectron spectroscopy (XPS), and X-ray diffraction (XRD) analysis. Pseudomonas and Bacillus were found to be the most predominant species in acclimated MOB consortium. Mn 2+ could be oxidized optimally at neutral pH and initial Mn 2+ concentration below 33 mg L -1 . However, 1,2,4-triazole removal by BioMnOx produced occurred optimally at slightly acidic pH. High dosage of both Mn 2+ and 1,2,4-triazole resulted in decreased 1,2,4-triazole removal. In a biological aerated filter (BAF) coupled with manganese oxidation, 1,2,4-triazole and total organic carbon removal could be significantly enhanced compared to the control system without the participation of manganese oxidation, confirming the key role of BioMnOx in the removal of highly recalcitrant 1,2,4-triazole. This study demonstrated that the biosystem coupled with manganese oxidation had a potential for the removal of various recalcitrant contaminants from bio-treated chemical industrial wastewater.

Size and surface functionalization of iron oxide nanoparticles influence the composition and dynamic nature of their protein corona.

PubMed

Ashby, Jonathan; Pan, Songqin; Zhong, Wenwan

2014-09-10

Nanoparticles (NPs) adsorb proteins when in the biological matrix, and the resulted protein corona could affect NP-cell interactions. The corona has a dynamic nature with the adsorbed proteins constantly exchanging with the free proteins in the matrix at various rates. The rapidly exchanging proteins compose the soft corona, which responds more dynamically to environment changes than the hard corona established by the ones with slow exchange rates. In the present study, the corona formed on the superparamagnetic iron oxide NPs (SPIONs) in human serum was studied by flow field-flow fractionation and ultracentrifugation, which rapidly differentiated the corona proteins based on their exchange rates. By varying the surface hydrophobicity of the SPIONs with a core size around 10 nm, we found out that, the more hydrophobic surface ligand attracted proteins with higher surface hydrophobicity and formed a more dynamic corona with a larger portion of the involved proteins with fast exchange rates. Increasing the core diameter of the SPIONs but keeping the surface ligand the same could also result in a more dynamic corona. A brief investigation of the effect on the cellular uptake of SPIONs using one selected corona protein, transferrin, was conducted. The result showed that, only the stably bound transferrin could significantly enhance cellular uptake, while transferrin bound in a dynamic nature had negligible impact. Our study has led to a better understanding of the relationship between the particle properties and the dynamic nature of the corona, which can help with design of nanomaterials with higher biocompatibility and higher efficacy in biosystems for biomedical applications.

Size and Surface Functionalization of Iron Oxide Nanoparticles Influence the Composition and Dynamic Nature of Their Protein Corona

PubMed Central

2015-01-01

Nanoparticles (NPs) adsorb proteins when in the biological matrix, and the resulted protein corona could affect NP-cell interactions. The corona has a dynamic nature with the adsorbed proteins constantly exchanging with the free proteins in the matrix at various rates. The rapidly exchanging proteins compose the soft corona, which responds more dynamically to environment changes than the hard corona established by the ones with slow exchange rates. In the present study, the corona formed on the superparamagnetic iron oxide NPs (SPIONs) in human serum was studied by flow field-flow fractionation and ultracentrifugation, which rapidly differentiated the corona proteins based on their exchange rates. By varying the surface hydrophobicity of the SPIONs with a core size around 10 nm, we found out that, the more hydrophobic surface ligand attracted proteins with higher surface hydrophobicity and formed a more dynamic corona with a larger portion of the involved proteins with fast exchange rates. Increasing the core diameter of the SPIONs but keeping the surface ligand the same could also result in a more dynamic corona. A brief investigation of the effect on the cellular uptake of SPIONs using one selected corona protein, transferrin, was conducted. The result showed that, only the stably bound transferrin could significantly enhance cellular uptake, while transferrin bound in a dynamic nature had negligible impact. Our study has led to a better understanding of the relationship between the particle properties and the dynamic nature of the corona, which can help with design of nanomaterials with higher biocompatibility and higher efficacy in biosystems for biomedical applications. PMID:25144382

biochem4j: Integrated and extensible biochemical knowledge through graph databases.

PubMed

Swainston, Neil; Batista-Navarro, Riza; Carbonell, Pablo; Dobson, Paul D; Dunstan, Mark; Jervis, Adrian J; Vinaixa, Maria; Williams, Alan R; Ananiadou, Sophia; Faulon, Jean-Loup; Mendes, Pedro; Kell, Douglas B; Scrutton, Nigel S; Breitling, Rainer

2017-01-01

Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes. What is needed are integrated repositories to catalogue both biological entities and-crucially-the relationships between them. Such a resource should be extensible, such that newly discovered relationships-for example, those between novel, synthetic enzymes and non-natural products-can be added over time. With the introduction of graph databases, the barrier to the rapid generation, extension and querying of such a resource has been lowered considerably. With a particular focus on metabolic engineering as an illustrative application domain, biochem4j, freely available at http://biochem4j.org, is introduced to provide an integrated, queryable database that warehouses chemical, reaction, enzyme and taxonomic data from a range of reliable resources. The biochem4j framework establishes a starting point for the flexible integration and exploitation of an ever-wider range of biological data sources, from public databases to laboratory-specific experimental datasets, for the benefit of systems biologists, biosystems engineers and the wider community of molecular biologists and biological chemists.

biochem4j: Integrated and extensible biochemical knowledge through graph databases

PubMed Central

Batista-Navarro, Riza; Dunstan, Mark; Jervis, Adrian J.; Vinaixa, Maria; Ananiadou, Sophia; Faulon, Jean-Loup; Kell, Douglas B.

2017-01-01

Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes. What is needed are integrated repositories to catalogue both biological entities and–crucially–the relationships between them. Such a resource should be extensible, such that newly discovered relationships–for example, those between novel, synthetic enzymes and non-natural products–can be added over time. With the introduction of graph databases, the barrier to the rapid generation, extension and querying of such a resource has been lowered considerably. With a particular focus on metabolic engineering as an illustrative application domain, biochem4j, freely available at http://biochem4j.org, is introduced to provide an integrated, queryable database that warehouses chemical, reaction, enzyme and taxonomic data from a range of reliable resources. The biochem4j framework establishes a starting point for the flexible integration and exploitation of an ever-wider range of biological data sources, from public databases to laboratory-specific experimental datasets, for the benefit of systems biologists, biosystems engineers and the wider community of molecular biologists and biological chemists. PMID:28708831

Telangiectatic focal nodular hyperplasia: a variant of hepatocellular adenoma.

PubMed

Paradis, Valerie; Benzekri, Asmae; Dargère, Delphine; Bièche, Ivan; Laurendeau, Ingrid; Vilgrain, Valerie; Belghiti, Jacques; Vidaud, Michel; Degott, Claude; Bedossa, Pierre

2004-05-01

"Telangiectatic focal nodular hyperplasia" designate atypical lesions considered as variants of focal nodular hyperplasia (FNH). However, because "telangiectatic FNH" share several morphologic patterns with hepatocellular adenomas, classification of such lesions deserve further clarification. Therefore, the aim of the present study was to reconsider the classification of telangiectatic FNH with the help of a molecular approach. Ten telangiectatic FNH, 6 typical FNH, and 6 hepatocellular adenomas were studied. DNA, RNA, and protein from each lesion were extracted. Clonality was assessed by the study of the X chromosome inactivation pattern (HUMARA assay). Angiopoietin (ANGPT-1 and ANGPT-2) mRNA, genes the expression of which is typically modified in FNH, were quantified by a real-time RT-PCR procedure. Protein profiles were analyzed by SELDI-TOF PROTEINCHIP (Cyphergen Biosystem, Inc., Fremont, CA) technology. Although all informative cases of FNH (5 of 6) and hepatocellular adenomas (6 of 6) were polyclonal and monoclonal, respectively, clonal analysis showed a nonrandom pattern of X chromosome inactivation consistent with a monoclonal lesion in 6 of 8 cases of telangiectatic FNH. The mean value of the ANGPT-1/ANGPT-2 mRNA ratio was 21.4 in FNH, 2.6 in adenomas, and 2.1 in telangiectatic FNH (P

[Correlation analysis of surnames and Y-chromosome genetic heritage in 3 provinces of southwestern Colombia].

PubMed

Gómez, Alberto; Avila, Sandra J; Briceño, Ignacio

2008-09-01

In Colombia, surnames are characters usually passed to the children by the father, and they have been compared to neutral alleles associated with the Y-chromosome. Population frequencies were determined for 17 short tandem repeats (STR) DNA markers on the Y-chromosome to compare the two identity codes and define the correlation between haplotypes and surnames in each individual. DNA was extracted from blood samples from 308 male individuals in provinces of Valle del Cauca, Cauca and Nariño, all in southwestern Colombia. Sample DNA was analyzed with the commercial kit AmpFLSTR Yfiler (Applied Biosystems) and examined for the following 17 Y-chromosome STR markers: DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and Y-GATA-H4. The frequencies of molecular haplotypes were associated with the surname reported by each individual, and a correlation table was constructed. Amerindian and European surnames were associated with the presence of allele DYS19/13, a characteristic of Amerindian populations. Allele frequencies were reported for each of the 17 STR markers in the southwestern region of Colombia-high genetic and haplotypic diversities were obtained. Approximately 40% of lineage inconsistencies were found when the molecular genotype was compared with the European or Amerindian surnames. Surnames must be used as population markers with reservation. The genetic evidence indicates that traditional genealogies based on surnames with or without documental support, may be inconsistant with their biological provenance.

A Thermodynamic Approach to Soil-Plant-Atmosphere Modeling: From Metabolic Biochemical Processes to Water-Carbon-Nitrogen Balance

NASA Astrophysics Data System (ADS)

Clavijo, H. W.

2016-12-01

Modeling the soil-plant-atmosphere continuum has been central part of understanding interrelationships among biogeochemical and hydrological processes. Theory behind of couplings Land Surface Models (LSM) and Dynamical Global Vegetation Models (DGVM) are based on physical and physiological processes connected by input-output interactions mainly. This modeling framework could be improved by the application of non-equilibrium thermodynamic basis that could encompass the majority of biophysical processes in a standard fashion. This study presents an alternative model for plant-water-atmosphere based on energy-mass thermodynamics. The system of dynamic equations derived is based on the total entropy, the total energy balance for the plant, the biomass dynamics at metabolic level and the water-carbon-nitrogen fluxes and balances. One advantage of this formulation is the capability to describe adaptation and evolution of dynamics of plant as a bio-system coupled to the environment. Second, it opens a window for applications on specific conditions from individual plant scale, to watershed scale, to global scale. Third, it enhances the possibility of analyzing anthropogenic impacts on the system, benefiting from the mathematical formulation and its non-linearity. This non-linear model formulation is analyzed under the concepts of qualitative system dynamics theory, for different state-space phase portraits. The attractors and sources are pointed out with its stability analysis. Possibility of bifurcations are explored and reported. Simulations for the system dynamics under different conditions are presented. These results show strong consistency and applicability that validates the use of the non-equilibrium thermodynamic theory.

High prevalence of exon 8 G533C mutation in apparently sporadic medullary thyroid carcinoma in Greece.

PubMed

Sarika, H L; Papathoma, A; Garofalaki, M; Vasileiou, V; Vlassopoulou, B; Anastasiou, E; Alevizaki, M

2012-12-01

Genetic screening for ret mutation has become routine practice in the evaluation of medullary thyroid carcinoma (MTC). Approximately 25% of these tumours are familial, and they occur as components of the multiple endocrine neoplasia type 2 syndromes (MEN 2A and 2B) or familial MTC. In familial cases, the majority of mutations are found in exons 10, 11, 13, 14 or 15 of the ret gene. A rare mutation involving exon 8 (G533C) has recently been reported in familial cases of MTC in Brazil and Greece; some of these cases were originally thought to be sporadic. The aim of this study was to re-evaluate a series of sporadic cases of MTC, with negative family history, and screen them for germline mutations in exon 8. Genomic DNA was extracted from peripheral lymphocytes in 129 unrelated individuals who had previously been characterized as 'sporadic' based on the negative family history and negative screening for ret gene mutations. Samples were analysed in Applied Biosystems 7500 real-time PCR and confirmed by sequencing. The G533C exon 8 mutation was identified in 10 of 129 patients with sporadic MTC. Asymptomatic gene carriers were subsequently identified in other family members. In our study, we found that 7·75% patients with apparently sporadic MTC do carry G533C mutation involving exon 8 of ret. We feel that there is now a need to include exon 8 mutation screening in all patients diagnosed as sporadic MTC, in Greece. © 2012 Blackwell Publishing Ltd.

Stochastic sampling effects in STR typing: Implications for analysis and interpretation.

PubMed

Timken, Mark D; Klein, Sonja B; Buoncristiani, Martin R

2014-07-01

The analysis and interpretation of forensic STR typing results can become more complicated when reduced template amounts are used for PCR amplification due to increased stochastic effects. These effects are typically observed as reduced heterozygous peak-height balance and increased frequency of undetected alleles (allelic "dropout"). To investigate the origins of these effects, a study was performed using the AmpFlSTR(®) Identifiler Plus(®) and MiniFiler(®) kits to amplify replicates from a dilution series of NIST Human DNA Quantitation Standard (SRM(®) 2372A). The resulting amplicons were resolved and detected on two different genetic analyzer platforms, the Applied Biosystems 3130xL and 3500 analyzers. Results from our study show that the four different STR/genetic analyzer combinations exhibited very similar peak-height ratio statistics when normalized for the amount of template DNA in the PCR. Peak-height ratio statistics were successfully modeled using the Poisson distribution to simulate pre-PCR stochastic sampling of the alleles, confirming earlier explanations that sampling is the primary source for peak-height imbalance in reduced template dilutions. In addition, template-based pre-PCR sampling simulations also successfully predicted allelic dropout frequencies, as modeled by logistic regression methods, for the low-template DNA dilutions. We discuss the possibility that an accurately quantified DNA template might be used to characterize the linear signal response for data collected using different STR kits or genetic analyzer platforms, so as to provide a standardized approach for comparing results obtained from different STR/CE combinations and to aid in validation studies. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

[Evaluation of association between 9 genetic polymorphism and myocardial infarction in the Siberian population].

PubMed

Maksimov, V N; Kulikov, I V; Orlov, P S; Gafarov, V V; Maliutina, S K; Romashchenko, A G; Voevoda, M I

2012-01-01

to evaluate association between genetic polymorphism (SNPs) and myocardial infarction (identified in recent GWAS) as markers of high risk of myocardial infarction (MI) in Siberian population. Patients were divided into 2 groups - MI patients and control group (ratio 1:2) and presented the sapmle of population of Novosibirsk (9400 patients, 45-69 years) within international project HAPIEE (Health, Alcohol and Psychosocial factors In Eastern Europe). 200 patients with MI (129 men, 71 women) were included. Control group - individuals without MI (420) matched for age and sex. Genomic DNA was extracted from venous blood by phenol-chloroform extraction. Gene polymorphism of genes tested by real-time PCR according to protocol (probes TaqMan, Applied Biosystems, USA) with the use of ABI 7900HT. The following SNPs were studied: rs28711149, rs499818, rs619203, rs10757278 and rs1333049 (hr. 9), rs1376251, rs2549513, rs4804611, rs17465637. The association of SNP and MI was confirmed for 4 of 9 studied SNPs: rs1333049 (hr. 9), rs10757278 (hr. 9), rs499818 (hr. 6), rs619203 gene ROS1. Heart rate was associated with rs1333049 and rs10757278. Glucose level was associated with rs619203, rs28711149 and rs1376251. Total cholesterol and atherogenic index was associated with rs28711149. For the first time in Russian population the associations of GWAS with myocardial infarction SNPs was detected for rs619203, rs499818, rs1333049 and rs10757278. These genetic markers can be used for assessing the risk of myocardial infarction in Russian population.

The Aristotle score: a complexity-adjusted method to evaluate surgical results.

PubMed

Lacour-Gayet, F; Clarke, D; Jacobs, J; Comas, J; Daebritz, S; Daenen, W; Gaynor, W; Hamilton, L; Jacobs, M; Maruszsewski, B; Pozzi, M; Spray, T; Stellin, G; Tchervenkov, C; Mavroudis And, C

2004-06-01

Quality control is difficult to achieve in Congenital Heart Surgery (CHS) because of the diversity of the procedures. It is particularly needed, considering the potential adverse outcomes associated with complex cases. The aim of this project was to develop a new method based on the complexity of the procedures. The Aristotle project, involving a panel of expert surgeons, started in 1999 and included 50 pediatric surgeons from 23 countries, representing the EACTS, STS, ECHSA and CHSS. The complexity was based on the procedures as defined by the STS/EACTS International Nomenclature and was undertaken in two steps: the first step was establishing the Basic Score, which adjusts only the complexity of the procedures. It is based on three factors: the potential for mortality, the potential for morbidity and the anticipated technical difficulty. A questionnaire was completed by the 50 centers. The second step was the development of the Comprehensive Aristotle Score, which further adjusts the complexity according to the specific patient characteristics. It includes two categories of complexity factors, the procedure dependent and independent factors. After considering the relationship between complexity and performance, the Aristotle Committee is proposing that: Performance = Complexity x Outcome. The Aristotle score, allows precise scoring of the complexity for 145 CHS procedures. One interesting notion coming out of this study is that complexity is a constant value for a given patient regardless of the center where he is operated. The Aristotle complexity score was further applied to 26 centers reporting to the EACTS congenital database. A new display of centers is presented based on the comparison of hospital survival to complexity and to our proposed definition of performance. A complexity-adjusted method named the Aristotle Score, based on the complexity of the surgical procedures has been developed by an international group of experts. The Aristotle score, electronically available, was introduced in the EACTS and STS databases. A validation process evaluating its predictive value is being developed.

Self-Reacting Friction Stir Welding for Aluminum Complex Curvature Applications

NASA Technical Reports Server (NTRS)

Brown, Randy J.; Martin, W.; Schneider, J.; Hartley, P. J.; Russell, Carolyn; Lawless, Kirby; Jones, Chip

2003-01-01

This viewgraph representation provides an overview of sucessful research conducted by Lockheed Martin and NASA to develop an advanced self-reacting friction stir technology for complex curvature aluminum alloys. The research included weld process development for 0.320 inch Al 2219, sucessful transfer from the 'lab' scale to the production scale tool and weld quality exceeding strenght goals. This process will enable development and implementation of large scale complex geometry hardware fabrication. Topics covered include: weld process development, weld process transfer, and intermediate hardware fabrication.

Reconstitution of the Light Harvesting Chlorophyll a/b Pigment-Protein Complex into Developing Chloroplast Membranes Using a Dialyzable Detergent 1

PubMed Central

Darr, Sylvia C.; Arntzen, Charles J.

1986-01-01

Conditions were developed to isolate the light-harvesting chlorophyll-protein complex serving photosystem II (LHC-II) using a dialyzable detergent, octylpolyoxyethylene. This LHC-II was successfully reconstituted into partially developed chloroplast thylakoids of Hordeum vulgare var Morex (barley) seedlings which were deficient in LHC-II. Functional association of LHC-II with the photosystem II (PSII) core complex was measured by two independent functional assays of PSII sensitization by LHC-II. A 3-fold excess of reconstituted LHC-II was required to equal the activity of LHC developing in vivo. We suggest that a linker component may be absent in the partially developed membranes which is required for specific association of the PSII core complex and LHC-II. Images Fig. 1 PMID:16664744

The Roles and Regulation of Polycomb Complexes in Neural Development

PubMed Central

Corley, Matthew; Kroll, Kristen L.

2014-01-01

In the developing mammalian nervous system, common progenitors integrate both cell extrinsic and intrinsic regulatory programs to produce distinct neuronal and glial cell types as development proceeds. This spatiotemporal restriction of neural progenitor differentiation is enforced, in part, by the dynamic reorganization of chromatin into repressive domains by Polycomb Repressive Complexes, effectively limiting the expression of fate-determining genes. Here, we review distinct roles that the Polycomb Repressive Complexes play during neurogenesis and gliogenesis, while also highlighting recent work describing the molecular mechanisms that govern their dynamic activity in neural development. Further investigation of how Polycomb complexes are regulated in neural development will enable more precise manipulation of neural progenitor differentiation, facilitating the efficient generation of specific neuronal and glial cell types for many biological applications. PMID:25367430

Origins of Complex Syntax in Interlanguage Development.

ERIC Educational Resources Information Center

Sato, Charlene J.

1988-01-01

Functional analysis of longitudinal, conversational interlanguage data from two Vietnamese learners of English focused on the emergence of complex syntax in interlanguage development. The interdependence of different linguistic levels in interlanguage development was demonstrated. (Author/CB)

Life history, cognition and the evolution of complex foraging niches.

PubMed

Schuppli, Caroline; Graber, Sereina M; Isler, Karin; van Schaik, Carel P

2016-03-01

Animal species that live in complex foraging niches have, in general, improved access to energy-rich and seasonally stable food sources. Because human food procurement is uniquely complex, we ask here which conditions may have allowed species to evolve into such complex foraging niches, and also how niche complexity is related to relative brain size. To do so, we divided niche complexity into a knowledge-learning and a motor-learning dimension. Using a sample of 78 primate and 65 carnivoran species, we found that two life-history features are consistently correlated with complex niches: slow, conservative development or provisioning of offspring over extended periods of time. Both act to buffer low energy yields during periods of learning, and may thus act as limiting factors for the evolution of complex niches. Our results further showed that the knowledge and motor dimensions of niche complexity were correlated with pace of development in primates only, and with the length of provisioning in only carnivorans. Accordingly, in primates, but not carnivorans, living in a complex foraging niche requires enhanced cognitive abilities, i.e., a large brain. The patterns in these two groups of mammals show that selection favors evolution into complex niches (in either the knowledge or motor dimension) in species that either develop more slowly or provision their young for an extended period of time. These findings help to explain how humans constructed by far the most complex niche: our ancestors managed to combine slow development (as in other primates) with systematic provisioning of immatures and even adults (as in carnivorans). This study also provides strong support for the importance of ecological factors in brain size evolution. Copyright © 2015 Elsevier Ltd. All rights reserved.

Research Methodology on Language Development from a Complex Systems Perspective

ERIC Educational Resources Information Center

Larsen-Freeman, Diane; Cameron, Lynne

2008-01-01

Changes to research methodology motivated by the adoption of a complexity theory perspective on language development are considered. The dynamic, nonlinear, and open nature of complex systems, together with their tendency toward self-organization and interaction across levels and timescales, requires changes in traditional views of the functions…

Infrared Spectroscopic Analysis of Linkage Isomerism in Metal-Thiocyanate Complexes

ERIC Educational Resources Information Center

Baer, Carl; Pike, Jay

2010-01-01

We developed an experiment suitable for an advanced inorganic chemistry laboratory that utilizes a cooperative learning environment, which allows students to develop an empirical method of determining the bonding mode of a series of unknown metal-thiocyanate complexes. Students synthesize the metal-thiocyanate complexes and obtain the FT-IR…

Factors influencing efficient structure of fuel and energy complex

NASA Astrophysics Data System (ADS)

Sidorova, N. G.; Novikova, S. A.

2017-10-01

The development of the Russian fuel-energy complex is a priority for the national economic policy, and the Far East is a link between Russia and the Asia-Pacific region. Large-scale engineering of numerous resources of the Far East will force industrial development, increase living standard and strengthen Russia’s position in the global energy market. So, revealing the factors which influence rational structure of the fuel-energy complex is very urgent nowadays. With the use of depth analysis of development tendencies of the complex and its problems the authors show ways of its efficiency improvement.

Formative feedback and scaffolding for developing complex problem solving and modelling outcomes

NASA Astrophysics Data System (ADS)

Frank, Brian; Simper, Natalie; Kaupp, James

2018-07-01

This paper discusses the use and impact of formative feedback and scaffolding to develop outcomes for complex problem solving in a required first-year course in engineering design and practice at a medium-sized research-intensive Canadian university. In 2010, the course began to use team-based, complex, open-ended contextualised problems to develop problem solving, communications, teamwork, modelling, and professional skills. Since then, formative feedback has been incorporated into: task and process-level feedback on scaffolded tasks in-class, formative assignments, and post-assignment review. Development in complex problem solving and modelling has been assessed through analysis of responses from student surveys, direct criterion-referenced assessment of course outcomes from 2013 to 2015, and an external longitudinal study. The findings suggest that students are improving in outcomes related to complex problem solving over the duration of the course. Most notably, the addition of new feedback and scaffolding coincided with improved student performance.

Using mixed methods to develop and evaluate complex interventions in palliative care research.

PubMed

Farquhar, Morag C; Ewing, Gail; Booth, Sara

2011-12-01

there is increasing interest in combining qualitative and quantitative research methods to provide comprehensiveness and greater knowledge yield. Mixed methods are valuable in the development and evaluation of complex interventions. They are therefore particularly valuable in palliative care research where the majority of interventions are complex, and the identification of outcomes particularly challenging. this paper aims to introduce the role of mixed methods in the development and evaluation of complex interventions in palliative care, and how they may be used in palliative care research. the paper defines mixed methods and outlines why and how mixed methods are used to develop and evaluate complex interventions, with a pragmatic focus on design and data collection issues and data analysis. Useful texts are signposted and illustrative examples provided of mixed method studies in palliative care, including a detailed worked example of the development and evaluation of a complex intervention in palliative care for breathlessness. Key challenges to conducting mixed methods in palliative care research are identified in relation to data collection, data integration in analysis, costs and dissemination and how these might be addressed. the development and evaluation of complex interventions in palliative care benefit from the application of mixed methods. Mixed methods enable better understanding of whether and how an intervention works (or does not work) and inform the design of subsequent studies. However, they can be challenging: mixed method studies in palliative care will benefit from working with agreed protocols, multidisciplinary teams and engaging staff with appropriate skill sets.

Switchable molecular magnets

PubMed Central

SATO, Osamu

2012-01-01

Various molecular magnetic compounds whose magnetic properties can be controlled by external stimuli have been developed, including electrochemically, photochemically, and chemically tunable bulk magnets as well as a phototunable antiferromagnetic phase of single chain magnet. In addition, we present tunable paramagnetic mononuclear complexes ranging from spin crossover complexes and valence tautomeric complexes to Co complexes in which orbital angular momentum can be switched. Furthermore, we recently developed several switchable clusters and one-dimensional coordination polymers. The switching of magnetic properties can be achieved by modulating metals, ligands, and molecules/ions in the second sphere of the complexes. PMID:22728438

Predicting Development of Mathematical Word Problem Solving Across the Intermediate Grades

PubMed Central

Tolar, Tammy D.; Fuchs, Lynn; Cirino, Paul T.; Fuchs, Douglas; Hamlett, Carol L.; Fletcher, Jack M.

2012-01-01

This study addressed predictors of the development of word problem solving (WPS) across the intermediate grades. At beginning of 3rd grade, 4 cohorts of students (N = 261) were measured on computation, language, nonverbal reasoning skills, and attentive behavior and were assessed 4 times from beginning of 3rd through end of 5th grade on 2 measures of WPS at low and high levels of complexity. Language skills were related to initial performance at both levels of complexity and did not predict growth at either level. Computational skills had an effect on initial performance in low- but not high-complexity problems and did not predict growth at either level of complexity. Attentive behavior did not predict initial performance but did predict growth in low-complexity, whereas it predicted initial performance but not growth for high-complexity problems. Nonverbal reasoning predicted initial performance and growth for low-complexity WPS, but only growth for high-complexity WPS. This evidence suggests that although mathematical structure is fixed, different cognitive resources may act as limiting factors in WPS development when the WPS context is varied. PMID:23325985

Developing a Highly Active Blood Anticoagulant—a Heparin Complex with Glutamic Acid—by Simulating Chemical Equilibria Based on pH-Metric Data

NASA Astrophysics Data System (ADS)

Nikolaeva, L. S.; Semenov, A. N.

2018-02-01

The anticoagulant activity of high-molecular-weight heparin is increased by developing a new highly active heparin complex with glutamate using the thermodynamic model of chemical equilibria based on pH-metric data. The anticoagulant activity of the developed complexes is estimated in the pH range of blood plasma according to the drop in the calculated equilibrium Ca2+ concentration associated with the formation of mixed ligand complexes of Ca2+ ions, heparin (Na4hep), and glutamate (H2Glu). A thermodynamic model is calculated by mathematically modelling chemical equilibria in the CaCl2-Na4hep-H2Glu-H2O-NaCl system in the pH range of 2.30 ≤ pH ≤ 10.50 in diluted saline that acts as a background electrolyte (0.154 M NaCl) at 37°C and initial concentrations of the main components of ν × 10-3 M, where n ≤ 4. The thermodynamic model is used to determine the main complex of the monomeric unit of heparin with glutamate (HhepGlu5-) and the most stable mixed ligand complex of Ca2+ with heparin and glutamate (Ca2hepGlu2-) in the pH range of blood plasma (6.80 ≤ pH ≤ 7.40). It is concluded that the Ca2hepGlu2- complex reduces the Ca2+ concentration 107 times more than the Ca2+ complex with pure heparin. The anticoagulant effect of the developed HhepGlu5- complex is confirmed in vitro and in vivo via coagulation tests on the blood plasma of laboratory rats. Additional antithrombotic properties of the developed complex are identified. The new highly active anticoagulant, HhepGlu5- complex with additional antithrombotic properties, is patented.

Complexity analysis of the cost effectiveness of PI-led NASA science missions

NASA Astrophysics Data System (ADS)

Yoshida, J.; Cowdin, M.; Mize, T.; Kellogg, R.; Bearden, D.

For the last 20 years, NASA has allowed Principal Investigators (PIs) to manage the development of many unmanned space projects. Advocates of PI-led projects believe that a PI-led implementation can result in a project being developed at lower cost and shorter schedule than other implementation modes. This paper seeks to test this hypothesis by comparing the actual costs of NASA and other comparable projects developed under different implementation modes. The Aerospace Corporation's Complexity-Based Risk Assessment (CoBRA) analysis tool is used to normalize the projects such that the cost can be compared for equivalent project complexities. The data is examined both by complexity and by launch year. Cost growth will also be examined for any correlation with implementation mode. Defined in many NASA Announcements of Opportunity (AOs), a PI-led project is characterized by a central, single person with full responsibility for assembling a team and for the project's scientific integrity and the implementation and integrity of all other aspects of the mission, while operating under a cost cap. PIs have larger degrees of freedom to achieve the stated goals within NASA guidelines and oversight. This study leverages the definitions and results of previous National Research Council studies of PI-led projects. Aerospace has defined a complexity index, derived from mission performance, mass, power, and technology choices, to arrive at a broad representation of missions for purposes of comparison. Over a decade of research has established a correlation between mission complexity and spacecraft development cost and schedule. This complexity analysis, CoBRA, is applied to compare a PI-led set of New Frontiers, Discovery, Explorers, and Earth System Science Pathfinder missions to the overall NASA mission dataset. This reveals the complexity trends against development costs, cost growth, and development era.

Fluid Mechanics and Complex Variable Theory: Getting Past the 19th Century

ERIC Educational Resources Information Center

Newton, Paul K.

2017-01-01

The subject of fluid mechanics is a rich, vibrant, and rapidly developing branch of applied mathematics. Historically, it has developed hand-in-hand with the elegant subject of complex variable theory. The Westmont College NSF-sponsored workshop on the revitalization of complex variable theory in the undergraduate curriculum focused partly on…

Sibling Curves and Complex Roots 1: Looking Back

ERIC Educational Resources Information Center

Harding, Ansie; Engelbrecht, Johann

2007-01-01

This paper, the first of a two-part article, follows the trail in history of the development of a graphical representation of the complex roots of a function. Root calculation and root representation are traced through millennia, including the development of the notion of complex numbers and subsequent graphical representation thereof. The…

Complexity Leadership: A Theoretical Perspective

ERIC Educational Resources Information Center

Baltaci, Ali; Balci, Ali

2017-01-01

Complex systems are social networks composed of interactive employees interconnected through collaborative, dynamic ties such as shared goals, perspectives and needs. Complex systems are largely based on "the complex system theory". The complex system theory focuses mainly on finding out and developing strategies and behaviours that…

Precursors to Language Development in Typically and Atypically Developing Infants and Toddlers: The Importance of Embracing Complexity

ERIC Educational Resources Information Center

D'Souza, Dean; D'Souza, Hana; Karmiloff-Smith, Annette

2017-01-01

In order to understand how language abilities emerge in typically and atypically developing infants and toddlers, it is important to embrace complexity in development. In this paper, we describe evidence that early language development is an experience-dependent process, shaped by diverse, interconnected, interdependent developmental mechanisms,…

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

Campbell, Philip LaRoche

At the end of his life, Stephen Jay Kline, longtime professor of mechanical engineering at Stanford University, completed a book on how to address complex systems. The title of the book is 'Conceptual Foundations of Multi-Disciplinary Thinking' (1995), but the topic of the book is systems. Kline first establishes certain limits that are characteristic of our conscious minds. Kline then establishes a complexity measure for systems and uses that complexity measure to develop a hierarchy of systems. Kline then argues that our minds, due to their characteristic limitations, are unable to model the complex systems in that hierarchy. Computers aremore » of no help to us here. Our attempts at modeling these complex systems are based on the way we successfully model some simple systems, in particular, 'inert, naturally-occurring' objects and processes, such as what is the focus of physics. But complex systems overwhelm such attempts. As a result, the best we can do in working with these complex systems is to use a heuristic, what Kline calls the 'Guideline for Complex Systems.' Kline documents the problems that have developed due to 'oversimple' system models and from the inappropriate application of a system model from one domain to another. One prominent such problem is the Procrustean attempt to make the disciplines that deal with complex systems be 'physics-like.' Physics deals with simple systems, not complex ones, using Kline's complexity measure. The models that physics has developed are inappropriate for complex systems. Kline documents a number of the wasteful and dangerous fallacies of this type.« less

Zinc complexes developed as metallopharmaceutics for treating diabetes mellitus based on the bio-medicinal inorganic chemistry.

PubMed

Yoshikawa, Yutaka; Yasui, Hiroyuki

2012-01-01

Biological trace metals such as iron, zinc, copper, and manganese are essential to life and health of humans, and the success of platinum drugs in the cancer chemotherapy has rapidly grown interest in developing inorganic pharmaceutical agents in medicinal chemistry, that is, medicinal inorganic chemistry, using essential elements and other biological trace metals. Transition metal complexes with unique chemical structures may be useful alternatives to the drugs available to address some of the incurable diseases. In this review, we emphasize that metal complexes are an expanding of interest in the research field of treatment of diabetes mellitus. Especially, orally active anti-diabetic and anti-metabolic syndrome zinc complexes have been developed and progressed since the discovery in 2001, where several highly potent anti-diabetic zinc complexes with different coordination structures have quite recently been disclosed, using experimental diabetic animals. In all of the complexes discussed, zinc is found to be biologically active and function by interacting with some target proteins related with diabetes mellitus. The design and screening of zinc complexes with higher activity is not efficient without consideration of the translational research. For the development of a clinically useful metallopharmaceutics, the research of zinc complexes on the long-term toxicity including side effects, clear-cut evidence of target molecule for the in vivo pharmacological action, and good pharmacokinetic property are essential in the current and future studies.

Contribution of parenting to complex syntax development in preschool children with developmental delays or typical development.

PubMed

Moody, C T; Baker, B L; Blacher, J

2018-05-10

Despite studies of how parent-child interactions relate to early child language development, few have examined the continued contribution of parenting to more complex language skills through the preschool years. The current study explored how positive and negative parenting behaviours relate to growth in complex syntax learning from child age 3 to age 4 years, for children with typical development or developmental delays (DDs). Participants were children with or without DD (N = 60) participating in a longitudinal study of development. Parent-child interactions were transcribed and coded for parenting domains and child language. Multiple regression analyses were used to identify the contribution of parenting to complex syntax growth in children with typical development or DD. Analyses supported a final model, F(9,50) = 11.90, P < .001, including a significant three-way interaction between positive parenting behaviours, negative parenting behaviours and child delay status. This model explained 68.16% of the variance in children's complex syntax at age 4. Simple two-way interactions indicated differing effects of parenting variables for children with or without DD. Results have implications for understanding of complex syntax acquisition in young children, as well as implications for interventions. © 2018 MENCAP and International Association of the Scientific Study of Intellectual and Developmental Disabilities and John Wiley & Sons Ltd.

A laser-spectroscopy complex for fluorescent diagnostics and photodynamic therapy of age-related macula degeneration

NASA Astrophysics Data System (ADS)

Shevchik, S. A.; Meerovich, Gennadii A.; Budzinskaya, M. V.; Ermakova, N. A.; Kharnas, Sergey S.; Loschenov, Victor B.

2004-06-01

A laser-spectroscopy complex was developed for fluorescent diagnostics and photodynamic therapy of age related macula degeneration using the Russian photosensitizer Photosense. The complex is based on slit lamp which was additionally equipped with an optical adapter, and the video adapter allows to combine the procedure of photodynamic therapy and the control of its carrying in the frame work of one procedure. The sensitivity and spatial resolution of the complex were investigated using a special test object. The availability of the developed complex and Photosense itself was examined on experimental animals.

The sleeping brain as a complex system.

PubMed

Olbrich, Eckehard; Achermann, Peter; Wennekers, Thomas

2011-10-13

'Complexity science' is a rapidly developing research direction with applications in a multitude of fields that study complex systems consisting of a number of nonlinear elements with interesting dynamics and mutual interactions. This Theme Issue 'The complexity of sleep' aims at fostering the application of complexity science to sleep research, because the brain in its different sleep stages adopts different global states that express distinct activity patterns in large and complex networks of neural circuits. This introduction discusses the contributions collected in the present Theme Issue. We highlight the potential and challenges of a complex systems approach to develop an understanding of the brain in general and the sleeping brain in particular. Basically, we focus on two topics: the complex networks approach to understand the changes in the functional connectivity of the brain during sleep, and the complex dynamics of sleep, including sleep regulation. We hope that this Theme Issue will stimulate and intensify the interdisciplinary communication to advance our understanding of the complex dynamics of the brain that underlies sleep and consciousness.

Challenges of Developing New Classes of NASA Self-Managing Mission

NASA Technical Reports Server (NTRS)

Hinchey, M. G.; Rash, J. I.; Truszkowski, W. F.; Rouff, C. A.; Sterritt, R.

2005-01-01

NASA is proposing increasingly complex missions that will require a high degree of autonomy and autonomicity. These missions pose hereto unforeseen problems and raise issues that have not been well-addressed by the community. Assuring success of such missions will require new software development techniques and tools. This paper discusses some of the challenges that NASA and the rest of the software development community are facing in developing these ever-increasingly complex systems. We give an overview of a proposed NASA mission as well as techniques and tools that are being developed to address autonomic management and the complexity issues inherent in these missions.

Navigating Complex Trade-Offs in Conservation and Development: An Integrative Framework

ERIC Educational Resources Information Center

Hirsch, Paul D.; Brosius, J. Peter

2013-01-01

We present a framework that makes space for multiple perspectives and ways of thinking about complex trade-off problems in conservation and development. At the core of the framework are three "integrative lenses" designed to facilitate lines of inquiry according to three unique ways of perceiving complexity. The aim of the framework is…

Development of Morphosyntactic Accuracy and Grammatical Complexity in Dutch School-Age Children with SLI

ERIC Educational Resources Information Center

Zwitserlood, Rob; van Weerdenburg, Marjolijn; Verhoeven, Ludo; Wijnen, Frank

2015-01-01

Purpose: The purpose of this study was to identify the development of morphosyntactic accuracy and grammatical complexity in Dutch school-age children with specific language impairment (SLI). Method: Morphosyntactic accuracy, the use of dummy auxiliaries, and complex syntax were assessed using a narrative task that was administered at three points…

Dynamics of Complexity and Accuracy: A Longitudinal Case Study of Advanced Untutored Development

ERIC Educational Resources Information Center

Polat, Brittany; Kim, Youjin

2014-01-01

This longitudinal case study follows a dynamic systems approach to investigate an under-studied research area in second language acquisition, the development of complexity and accuracy for an advanced untutored learner of English. Using the analytical tools of dynamic systems theory (Verspoor et al. 2011) within the framework of complexity,…

The Development of Complexity, Accuracy and Fluency in the Written Production of L2 French

ERIC Educational Resources Information Center

Gunnarsson, Cecilia

2012-01-01

The present longitudinal case study investigated the development of fluency, complexity and accuracy--and the possible relationships between them--in the written production of L2 French. We assessed fluency and complexity in five intermediate learners by means of conventional indicators for written L2 (cf. Wolfe-Quintero et al. 1998), while…

The Use of Complexity Theory and Strange Attractors to Understand and Explain Information System Development

ERIC Educational Resources Information Center

Tomasino, Arthur P.

2013-01-01

In spite of the best efforts of researchers and practitioners, Information Systems (IS) developers are having problems "getting it right". IS developments are challenged by the emergence of unanticipated IS characteristics undermining managers ability to predict and manage IS change. Because IS are complex, development formulas, best…

PREFACE: Complex dynamics of fluids in disordered and crowded environments Complex dynamics of fluids in disordered and crowded environments

NASA Astrophysics Data System (ADS)

Coslovich, Daniele; Kahl, Gerhard; Krakoviack, Vincent

2011-06-01

Over the past two decades, the dynamics of fluids under nanoscale confinement has attracted much attention. Motivation for this rapidly increasing interest is based on both practical and fundamental reasons. On the practical and rather applied side, problems in a wide range of scientific topics, such as polymer and colloidal sciences, rheology, geology, or biophysics, benefit from a profound understanding of the dynamical behaviour of confined fluids. Further, effects similar to those observed in confinement are expected in fluids whose constituents have strong size or mass asymmetry, and in biological systems where crowding and obstruction phenomena in the cytosol are responsible for clear separations of time scales for macromolecular transport in the cell. In fundamental research, on the other hand, the interest focuses on the complex interplay between confinement and structural relaxation, which is responsible for the emergence of new phenomena in the dynamics of the system: in confinement, geometric constraints associated with the pore shape are imposed to the adsorbed fluids and an additional characteristic length scale, i.e. the pore size, comes into play. For many years, the topic has been mostly experimentally driven. Indeed, a broad spectrum of systems has been investigated by sophisticated experimental techniques, while theoretical and simulation studies were rather scarce due to conceptual and computational issues. In the past few years, however, theory and simulations could largely catch up with experiments. On one side, new theories have been put forward that duly take into account the porosity, the connectivity, and the randomness of the confinement. On the other side, the ever increasing available computational power now allows investigations that were far out of reach a few years ago. Nowadays, instead of isolated state points, systematic investigations on the dynamics of confined fluids, covering a wide range of system parameters, can be realized. In fact, theory and simulations were recently able to predict new and surprising dynamical features, such as the occurrence of sub-diffusive laws, which result from the trapping due to the geometric and topological constraints and/or quenched disorder, the presence of both continuous and discontinuous glass transitions, and diffusion-localization transitions. Together, theory and simulations are thus able to contribute to a deeper insight into the complex dynamical behaviour of fluids in disordered confinement. Still, many yet unsolved problems remain. The fact that theoretical and simulation approaches have caught up with experimental investigations, has motivated us to organize a workshop on the dynamics of fluids confined in disordered environments, so as to bring together the different communities working in this field: theory and simulations, with their recent developments based on the mode-coupling theory of the glass transition, and experiments, with particular emphasis on colloidal systems and novel techniques. In an effort to give credit to recent developments in related problems of biophysical relevance, an entire session of the programme was dedicated to anomalous diffusion in crowded environments. The workshop was thus aimed at providing a deeper understanding of the complex dynamics of fluids in confinement as well as up-to-date perspectives on the interdisciplinary applications of this field of research. We are proud to say that all 32 contacted speakers accepted our invitation. Additional participants were attracted by our scientific programme, contributing poster presentations to the workshop. In total, close to 50 participants were registered, arriving from 11 different countries (including the US, Japan, and Mexico). Thus we conclude that the workshop indeed addressed a highly topical scientific field. From the scientific point of view a broad range of problems was covered, ranging from biophysics over soft matter to fermion systems. From the vivid discussions it became evident that the close scientific contact between theory, simulation and experiment brought along a fruitful and mutually inspiring atmosphere. On the theoretical side, these discussions have allowed clarification of several connections between the dynamics of models of fluids in porous media (quenched-annealed, pinned particles models), those of well-known limiting cases (Lorentz gas), of realistic models of liquids with strong dynamic asymmetry (asymmetric size and mass mixtures, sodium silicates, polymers blends) and even of bulk glass-formers. On the experimental side, it appeared that soft matter systems may provide an excellent test-bed to verify the theoretical predictions. From the concluding discussion it was also clear that addressing related issues relevant to biology still remains an open challenge for the future. In view of all this, it was concluded that within a short time period a workshop with analogous scope should be organized to address the progress made on both fundamental and interdisciplinary aspects. The realization of this workshop was made possible by generous financial support from CECAM, Centre Blaise Pascal-ENS de Lyon, and the ESF network 'Molecular Simulations in Biosystems and Material Science' (SimBioMa). Complex dynamics of fluids in disordered and crowded environments contents Phonon dispersions of cluster crystals Tim Neuhaus and Christos N Likos Challenges in determining anomalous diffusion in crowded fluids Marcel Hellmann, Joseph Klafter, Dieter W Heermann and Matthias Weiss Diffusion of active tracers in fluctuating fields David S Dean and Vincent Démery Self-diffusion of non-interacting hard spheres in particle gels Jean-Christophe Gimel and Taco Nicolai Probing glassy states in binary mixtures of soft interpenetrable colloids E Stiakakis, B M Erwin, D Vlassopoulos, M Cloitre, A Munam, M Gauthier, H Iatrou and N Hadjichristidis Fluids with quenched disorder: scaling of the free energy barrier near critical points T Fischer and R L C Vink Lennard-Jones binary mixture in disordered matrices: exploring the mode coupling scenario at increasing confinement P Gallo and M Rovere Static and dynamic contributions to anomalous chain dynamics in polymer blends Marco Bernabei, Angel J Moreno and J Colmenero Anomalous transport of a tracer on percolating clusters Markus Spanner, Felix Höfling, Gerd E Schröder-Turk, Klaus Mecke and Thomas Franosch Long-wavelength anomalies in the asymptotic behavior of mode-coupling theory S K Schnyder, F Höfling, T Franosch and Th Voigtmann Dynamic arrest of colloids in porous environments: disentangling crowding and confinement Jan Kurzidim, Daniele Coslovich and Gerhard Kahl Slow dynamics, dynamic heterogeneities, and fragility of supercooled liquids confined in random media Kang Kim, Kunimasa Miyazaki and Shinji Saito

Drug Delivery Systems For Anti-Cancer Active Complexes of Some Coinage Metals.

PubMed

Zhang, Ming; Saint-Germain, Camille; He, Guiling; Sun, Raymond Wai-Yin

2018-02-12

Although cisplatin and a number of platinum complexes have widely been used for the treatment of neoplasia, patients receiving these treatments have frequently suffered from their severe toxic side effects, the development of resistance with consequent relapse. In the recent decades, numerous complexes of coinage metals including that of gold, copper and silver have been reported to display promising in vitro and/or in vivo anti-cancer activities as well as potent activities towards cisplatin-resistant tumors. Nevertheless, the medical development of these metal complexes has been hampered by their instability in aqueous solutions and the nonspecific binding in biological systems. One of the approaches to overcome these problems is to design and develop adequate drug delivery systems (DDSs) for the transport of these complexes. By functionalization, encapsulation or formulation of the metal complexes, several types of DDSs have been reported to improve the desired pharmacological profile of the metal complexes, improving their overall stability, bioavailability, anti-cancer activity and reducing their toxicity towards normal cells. In this review, we summarized the recent findings for different DDSs for various anti- cancer active complexes of some coinage metals. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Border control: selectivity of chloroplast protein import and regulation at the TOC-complex.

PubMed

Demarsy, Emilie; Lakshmanan, Ashok M; Kessler, Felix

2014-01-01

Plants have evolved complex and sophisticated molecular mechanisms to regulate their development and adapt to their surrounding environment. Particularly the development of their specific organelles, chloroplasts and other plastid-types, is finely tuned in accordance with the metabolic needs of the cell. The normal development and functioning of plastids require import of particular subsets of nuclear encoded proteins. Most preproteins contain a cleavable sequence at their N terminal (transit peptide) serving as a signal for targeting to the organelle and recognition by the translocation machinery TOC-TIC (translocon of outer membrane complex-translocon of inner membrane complex) spanning the dual membrane envelope. The plastid proteome needs constant remodeling in response to developmental and environmental factors. Therefore selective regulation of preprotein import plays a crucial role in plant development. In this review we describe the diversity of transit peptides and TOC receptor complexes, and summarize the current knowledge and potential directions for future research concerning regulation of the different Toc isoforms.

Realist complex intervention science: Applying realist principles across all phases of the Medical Research Council framework for developing and evaluating complex interventions

PubMed Central

Fletcher, Adam; Jamal, Farah; Moore, Graham; Evans, Rhiannon E.; Murphy, Simon; Bonell, Chris

2016-01-01

The integration of realist evaluation principles within randomised controlled trials (‘realist RCTs’) enables evaluations of complex interventions to answer questions about what works, for whom and under what circumstances. This allows evaluators to better develop and refine mid-level programme theories. However, this is only one phase in the process of developing and evaluating complex interventions. We describe and exemplify how social scientists can integrate realist principles across all phases of the Medical Research Council framework. Intervention development, modelling, and feasibility and pilot studies need to theorise the contextual conditions necessary for intervention mechanisms to be activated. Where interventions are scaled up and translated into routine practice, realist principles also have much to offer in facilitating knowledge about longer-term sustainability, benefits and harms. Integrating a realist approach across all phases of complex intervention science is vital for considering the feasibility and likely effects of interventions for different localities and population subgroups. PMID:27478401

Redox signaling in the growth and development of colonial hydroids.

PubMed

Blackstone, Neil W

2003-02-01

Redox signaling provides a quick and efficient mechanism for clonal or colonial organisms to adapt their growth and development to aspects of the environment, e.g. the food supply. A 'signature' of mitochondrial redox signaling, particularly as mediated by reactive oxygen species (ROS), can be elucidated by experimental manipulation of the electron transport chain. The major sites of ROS formation are found at NADH dehydrogenase of complex I and at the interface between coenzyme Q and complex III. Inhibitors of complex III should thus upregulate ROS from both sites; inhibitors of complex I should upregulate ROS from the first but not the second site, while uncouplers of oxidative phosphorylation should downregulate ROS from both sites. To investigate the possibility of such redox signaling, perturbations of colony growth and development were carried out using the hydroid Podocoryna carnea. Oxygen uptake of colonies was measured to determine comparable physiological doses of antimycin A(1) (an inhibitor of complex III), rotenone (an inhibitor of complex I) and carbonyl cyanide m-chlorophenylhydrazone (CCCP; an uncoupler of oxidative phosphorylation). Using these doses, clear effects on colony growth and development were obtained. Treatment with antimycin A(1) results in 'runner-like' colony growth, with widely spaced polyps and stolon branches, while treatment with CCCP results in 'sheet-like' growth, with closely spaced polyps and stolon branches. Parallel results have been obtained previously with azide, an inhibitor of complex IV, and dinitrophenol, another uncoupler of oxidative phosphorylation. Perhaps surprisingly, rotenone produced effects on colony development similar to those of CCCP. Assays of peroxides using 2',7'-dichlorofluorescin diacetate and fluorescent microscopy suggest a moderate difference in ROS formation between the antimycin and rotenone treatments. The second site of ROS formation (the interface between coenzyme Q and complex III) may thus predominate in the signaling that regulates colony development. The fat-rich, brine shrimp diet of these hydroids may be relevant in this context. Acyl CoA dehydrogenase, which catalyzes the first step in the mitochondrial beta-oxidation of fatty acids, carries electrons to coenzyme Q, thus bypassing complex I. These results support a role for redox signaling, mediated by ROS, in colony development. Nevertheless, other redox sensors between complexes I and III may yet be found.

Transcriptome complexity in cardiac development and diseases--an expanding universe between genome and phenome.

PubMed

Gao, Chen; Wang, Yibin

2014-01-01

With the advancement of transcriptome profiling by micro-arrays and high-throughput RNA-sequencing, transcriptome complexity and its dynamics are revealed at different levels in cardiovascular development and diseases. In this review, we will highlight the recent progress in our knowledge of cardiovascular transcriptome complexity contributed by RNA splicing, RNA editing and noncoding RNAs. The emerging importance of many of these previously under-explored aspects of gene regulation in cardiovascular development and pathology will be discussed.

Complexity of GPs' explanations about mental health problems: development, reliability, and validity of a measure

PubMed Central

Cape, John; Morris, Elena; Burd, Mary; Buszewicz, Marta

2008-01-01

Background How GPs understand mental health problems determines their treatment choices; however, measures describing GPs' thinking about such problems are not currently available. Aim To develop a measure of the complexity of GP explanations of common mental health problems and to pilot its reliability and validity. Design of study A qualitative development of the measure, followed by inter-rater reliability and validation pilot studies. Setting General practices in North London. Method Vignettes of simulated consultations with patients with mental health problems were videotaped, and an anchored measure of complexity of psychosocial explanation in response to these vignettes was developed. Six GPs, four psychologists, and two lay people viewed the vignettes. Their responses were rated for complexity, both using the anchored measure and independently by two experts in primary care mental health. In a second reliability and revalidation study, responses of 50 GPs to two vignettes were rated for complexity. The GPs also completed a questionnaire to determine their interest and training in mental health, and they completed the Depression Attitudes Questionnaire. Results Inter-rater reliability of the measure of complexity of explanation in both pilot studies was satisfactory (intraclass correlation coefficient = 0.78 and 0.72). The measure correlated with expert opinion as to what constitutes a complex explanation, and the responses of psychologists, GPs, and lay people differed in measured complexity. GPs with higher complexity scores had greater interest, more training in mental health, and more positive attitudes to depression. Conclusion Results suggest that the complexity of GPs' psychosocial explanations about common mental health problems can be reliably and validly assessed by this new standardised measure. PMID:18505616

Managing Schools as Complex Adaptive Systems: A Strategic Perspective

ERIC Educational Resources Information Center

Fidan, Tuncer; Balci, Ali

2017-01-01

This conceptual study examines the analogies between schools and complex adaptive systems and identifies strategies used to manage schools as complex adaptive systems. Complex adaptive systems approach, introduced by the complexity theory, requires school administrators to develop new skills and strategies to realize their agendas in an…

Fortuitous phenomena: on complexity, pragmatic randomised controlled trials, and knowledge for evidence-based practice.

PubMed

Thompson, Carl

2004-01-01

Many of the interventions that nurses develop and implement are in themselves complex and have to operate in situations of irreducible complexity and uncertainty. This article argues that the primary means of generating knowledge for the evidence-based deployment of complex interventions should be the pragmatic randomised controlled trial. Randomised controlled trials represent the only research design to adequately deal with that which we know and (far more importantly) that which we do not. Using the example of practice development as an exemplar for complexity, and drawing on the objections often voiced as a response to calls to make use of randomised controlled trials in nursing and nursing research, the article presents a developmental framework and some methodological solutions to problems often encountered. Randomised controlled trials, whilst undoubtedly methodologically and strategically challenging, offer the most robust basis for developing primary research knowledge on the effects of complex interventions in nursing and their active components.

General and craniofacial development are complex adaptive processes influenced by diversity.

PubMed

Brook, A H; O'Donnell, M Brook; Hone, A; Hart, E; Hughes, T E; Smith, R N; Townsend, G C

2014-06-01

Complex systems are present in such diverse areas as social systems, economies, ecosystems and biology and, therefore, are highly relevant to dental research, education and practice. A Complex Adaptive System in biological development is a dynamic process in which, from interacting components at a lower level, higher level phenomena and structures emerge. Diversity makes substantial contributions to the performance of complex adaptive systems. It enhances the robustness of the process, allowing multiple responses to external stimuli as well as internal changes. From diversity comes variation in outcome and the possibility of major change; outliers in the distribution enhance the tipping points. The development of the dentition is a valuable, accessible model with extensive and reliable databases for investigating the role of complex adaptive systems in craniofacial and general development. The general characteristics of such systems are seen during tooth development: self-organization; bottom-up emergence; multitasking; self-adaptation; variation; tipping points; critical phases; and robustness. Dental findings are compatible with the Random Network Model, the Threshold Model and also with the Scale Free Network Model which has a Power Law distribution. In addition, dental development shows the characteristics of Modularity and Clustering to form Hierarchical Networks. The interactions between the genes (nodes) demonstrate Small World phenomena, Subgraph Motifs and Gene Regulatory Networks. Genetic mechanisms are involved in the creation and evolution of variation during development. The genetic factors interact with epigenetic and environmental factors at the molecular level and form complex networks within the cells. From these interactions emerge the higher level tissues, tooth germs and mineralized teeth. Approaching development in this way allows investigation of why there can be variations in phenotypes from identical genotypes; the phenotype is the outcome of perturbations in the cellular systems and networks, as well as of the genotype. Understanding and applying complexity theory will bring about substantial advances not only in dental research and education but also in the organization and delivery of oral health care. © 2014 Australian Dental Association.

The Impact of Adaptive Complex Assessment on the HOT Skill Development of Students

ERIC Educational Resources Information Center

Raiyn, Jamal; Tilchin, Oleg

2016-01-01

In this paper we propose a method for the adaptive complex assessment (ACA) of the higher-order thinking (HOT) skills needed by students for problem solving, and we examine the impact of the method on the development of HOT skills in a problem-based learning (PBL) environment. Complexity in the assessment is provided by initial, formative, and…

Crystallization of bFGF-DNA Aptamer Complexes Using a Sparse Matrix Designed for Protein-Nucleic Acid Complexes

NASA Technical Reports Server (NTRS)

Cannone, Jaime J.; Barnes, Cindy L.; Achari, Aniruddha; Kundrot, Craig E.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

The Sparse Matrix approach for obtaining lead crystallization conditions has proven to be very fruitful for the crystallization of proteins and nucleic acids. Here we report a Sparse Matrix developed specifically for the crystallization of protein-DNA complexes. This method is rapid and economical, typically requiring 2.5 mg of complex to test 48 conditions. The method was originally developed to crystallize basic fibroblast growth factor (bFGF) complexed with DNA sequences identified through in vitro selection, or SELEX, methods. Two DNA aptamers that bind with approximately nanomolar affinity and inhibit the angiogenic properties of bFGF were selected for co-crystallization. The Sparse Matrix produced lead crystallization conditions for both bFGF-DNA complexes.

Harvest: a web-based biomedical data discovery and reporting application development platform.

PubMed

Italia, Michael J; Pennington, Jeffrey W; Ruth, Byron; Wrazien, Stacey; Loutrel, Jennifer G; Crenshaw, E Bryan; Miller, Jeffrey; White, Peter S

2013-01-01

Biomedical researchers share a common challenge of making complex data understandable and accessible. This need is increasingly acute as investigators seek opportunities for discovery amidst an exponential growth in the volume and complexity of laboratory and clinical data. To address this need, we developed Harvest, an open source framework that provides a set of modular components to aid the rapid development and deployment of custom data discovery software applications. Harvest incorporates visual representations of multidimensional data types in an intuitive, web-based interface that promotes a real-time, iterative approach to exploring complex clinical and experimental data. The Harvest architecture capitalizes on standards-based, open source technologies to address multiple functional needs critical to a research and development environment, including domain-specific data modeling, abstraction of complex data models, and a customizable web client.

The murine SNF5/INI1 chromatin remodeling factor is essential for embryonic development and tumor suppression.

PubMed

Klochendler-Yeivin, A; Fiette, L; Barra, J; Muchardt, C; Babinet, C; Yaniv, M

2000-12-01

The assembly of eukaryotic DNA into nucleosomes and derived higher order structures constitutes a barrier for transcription, replication and repair. A number of chromatin remodeling complexes, as well as histone acetylation, were shown to facilitate gene activation. To investigate the function of two closely related mammalian SWI/SNF complexes in vivo, we inactivated the murine SNF5/INI1 gene, a common subunit of these two complexes. Mice lacking SNF5 protein stop developing at the peri-implantation stage, showing that the SWI/SNF complex is essential for early development and viability of early embryonic cells. Furthermore, heterozygous mice develop nervous system and soft tissue sarcomas. In these tumors the wild-type allele was lost, providing further evidence that SNF5 functions as a tumor suppressor gene in certain cell types.

The murine SNF5/INI1 chromatin remodeling factor is essential for embryonic development and tumor suppression

PubMed Central

Klochendler-Yeivin, Agnes; Fiette, Laurence; Barra, Jaqueline; Muchardt, Christian; Babinet, Charles; Yaniv, Moshe

2000-01-01

The assembly of eukaryotic DNA into nucleosomes and derived higher order structures constitutes a barrier for transcription, replication and repair. A number of chromatin remodeling complexes, as well as histone acetylation, were shown to facilitate gene activation. To investigate the function of two closely related mammalian SWI/SNF complexes in vivo, we inactivated the murine SNF5/INI1 gene, a common subunit of these two complexes. Mice lacking SNF5 protein stop developing at the peri-implantation stage, showing that the SWI/SNF complex is essential for early development and viability of early embryonic cells. Furthermore, heterozygous mice develop nervous system and soft tissue sarcomas. In these tumors the wild-type allele was lost, providing further evidence that SNF5 functions as a tumor suppressor gene in certain cell types. PMID:11263494

Soils as relative-age dating tools

USGS Publications Warehouse

Markewich, Helaine Walsh; Pavich, Milan J.; Wysocki, Douglas A.

2017-01-01

Soils develop at the earth's surface via multiple processes that act through time. Precluding burial or disturbance, soil genetic horizons form progressively and reflect the balance among formation processes, surface age, and original substrate composition. Soil morphology provides a key link between process and time (soil age), enabling soils to serve as both relative and numerical dating tools for geomorphic studies and landscape evolution. Five major factors define the contemporary state of all soils: climate, organisms, topography, parent material, and time. Soils developed on similar landforms and parent materials within a given landscape comprise what we term a soil/landform/substrate complex. Soils on such complexes that differ in development as a function of time represent a soil chronosequence. In a soil chronosequence, time constitutes the only independent formation factor; the other factors act through time. Time dictates the variations in soil development or properties (field or laboratory measured) on a soil/landform/substrate complex. Using a dataset within the chronosequence model, we can also formulate various soil development indices based upon one or a combination of soil properties, either for individual soil horizons or for an entire profile. When we evaluate soil data or soil indices mathematically, the resulting equation creates a chronofunction. Chronofunctions help quantify processes and mechanisms involved in soil development, and relate them mathematically to time. These rigorous kinds of comparisons among and within soil/landform complexes constitute an important tool for relative-age dating. After determining one or more absolute ages for a soil/landform complex, we can calculate quantitative soil formation, and or landform-development rates. Multiple dates for several complexes allow rate calculations for soil/landform-chronosequence development and soil-chronofunction calibration.

Development of Novel DNA Cleavage Systems Based on Copper Complexes. Synthesis and Characterisation of Cu(II) Complexes of Hydroxyflavones

PubMed Central

el Amrani, F. Ben-Allal; Perelló, L.; Torres, L.

2000-01-01

Copper(II) complexes of several hydroxyflavones were prepared and characterised through their physico-chemical properties. The nuclease activity of three synthesised complexes is reported. These copper(II) complexes present more nuclease activity than the ligands and the copper(II) ion. PMID:18475969

Measuring the Level of Complexity of Scientific Inquiries: The LCSI Index

ERIC Educational Resources Information Center

Eilam, Efrat

2015-01-01

The study developed and applied an index for measuring the level of complexity of full authentic scientific inquiry. Complexity is a fundamental attribute of real life scientific research. The level of complexity is an overall reflection of complex cognitive and metacognitive processes which are required for navigating the authentic inquiry…

Simplified Interface to Complex Memory Hierarchies 1.x

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

Lang, Michael; Ionkov, Latchesar; Williams, Sean

2017-02-21

Memory systems are expected to get evermore complicated in the coming years, and it isn't clear exactly what form that complexity will take. On the software side, a simple, flexible way of identifying and working with memory pools is needed. Additionally, most developers seek code portability and do not want to learn the intricacies of complex memory. Hence, we believe that a library for interacting with complex memory systems should expose two kinds of abstraction: First, a low-level, mechanism-based interface designed for the runtime or advanced user that wants complete control, with its focus on simplified representation but with allmore » decisions left to the caller. Second, a high-level, policy-based interface designed for ease of use for the application developer, in which we aim for best-practice decisions based on application intent. We have developed such a library, called SICM: Simplified Interface to Complex Memory.« less

Sparse dynamical Boltzmann machine for reconstructing complex networks with binary dynamics

NASA Astrophysics Data System (ADS)

Chen, Yu-Zhong; Lai, Ying-Cheng

2018-03-01

Revealing the structure and dynamics of complex networked systems from observed data is a problem of current interest. Is it possible to develop a completely data-driven framework to decipher the network structure and different types of dynamical processes on complex networks? We develop a model named sparse dynamical Boltzmann machine (SDBM) as a structural estimator for complex networks that host binary dynamical processes. The SDBM attains its topology according to that of the original system and is capable of simulating the original binary dynamical process. We develop a fully automated method based on compressive sensing and a clustering algorithm to construct the SDBM. We demonstrate, for a variety of representative dynamical processes on model and real world complex networks, that the equivalent SDBM can recover the network structure of the original system and simulates its dynamical behavior with high precision.

Stomatal Complex Development and F-Actin Organization in Maize Leaf Epidermis Depend on Cellulose Synthesis.

PubMed

Panteris, Emmanuel; Achlati, Theonymphi; Daras, Gerasimos; Rigas, Stamatis

2018-06-06

Cellulose microfibrils reinforce the cell wall for morphogenesis in plants. Herein, we provide evidence on a series of defects regarding stomatal complex development and F-actin organization in Zea mays leaf epidermis, due to inhibition of cellulose synthesis. Formative cell divisions of stomatal complex ontogenesis were delayed or inhibited, resulting in lack of subsidiary cells and frequently in unicellular stomata, with an atypical stomatal pore. Guard cells failed to acquire a dumbbell shape, becoming rounded, while subsidiary cells, whenever present, exhibited aberrant morphogenesis. F-actin organization was also affected, since the stomatal complex-specific arrays were scarcely observed. At late developmental stages, the overall F-actin network was diminished in all epidermal cells, although thick actin bundles persisted. Taken together, stomatal complex development strongly depends on cell wall mechanical properties. Moreover, F-actin organization exhibits a tight relationship with the cell wall.

Sparse dynamical Boltzmann machine for reconstructing complex networks with binary dynamics.

PubMed

Chen, Yu-Zhong; Lai, Ying-Cheng

2018-03-01

Revealing the structure and dynamics of complex networked systems from observed data is a problem of current interest. Is it possible to develop a completely data-driven framework to decipher the network structure and different types of dynamical processes on complex networks? We develop a model named sparse dynamical Boltzmann machine (SDBM) as a structural estimator for complex networks that host binary dynamical processes. The SDBM attains its topology according to that of the original system and is capable of simulating the original binary dynamical process. We develop a fully automated method based on compressive sensing and a clustering algorithm to construct the SDBM. We demonstrate, for a variety of representative dynamical processes on model and real world complex networks, that the equivalent SDBM can recover the network structure of the original system and simulates its dynamical behavior with high precision.

Photoisomerization of ruthenium(ii) aquo complexes: mechanistic insights and application development.

PubMed

Hirahara, Masanari; Yagi, Masayuki

2017-03-21

Ruthenium(ii) complexes with polypyridyl ligands have been extensively studied as promising functional molecules due to their unique photochemical and photophysical properties as well as redox properties. In this context, we report the photoisomerization of distal-[Ru(tpy)(pynp)OH 2 ] 2+ (d-1) (tpy = 2,2';6',2''-terpyridine, pynp = 2-(2-pyridyl)-1,8-naphthyridine) to proximal-[Ru(tpy)(pynp)OH 2 ] 2+ (p-1), which has not been previously characterized for polypyridyl ruthenium(ii) aquo complexes. Herein, we review recent progress made by our group on the mechanistic insights and application developments related to the photoisomerization of polypyridyl ruthenium(ii) aquo complexes. We report a new strategic synthesis of dinuclear ruthenium(ii) complexes that can act as an active water oxidation catalyst, as well as the development of unique visible-light-responsive giant vesicles, both of which were achieved based on photoisomerization.

Health care organizations as complex systems: new perspectives on design and management.

PubMed

McDaniel, Reuben R; Driebe, Dean J; Lanham, Holly Jordan

2013-01-01

We discuss the impact of complexity science on the design and management of health care organizations over the past decade. We provide an overview of complexity science issues and their impact on thinking about health care systems, particularly with the rising importance of information systems. We also present a complexity science perspective on current issues in today's health care organizations and suggest ways that this perspective might help in approaching these issues. We review selected research, focusing on work in which we participated, to identify specific examples of applications of complexity science. We then take a look at information systems in health care organizations from a complexity viewpoint. Complexity science is a fundamentally different way of understanding nature and has influenced the thinking of scholars and practitioners as they have attempted to understand health care organizations. Many scholars study health care organizations as complex adaptive systems and through this perspective develop new management strategies. Most important, perhaps, is the understanding that attention to relationships and interdependencies is critical for developing effective management strategies. Increased understanding of complexity science can enhance the ability of researchers and practitioners to develop new ways of understanding and improving health care organizations. This analysis opens new vistas for scholars and practitioners attempting to understand health care organizations as complex adaptive systems. The analysis holds value for those already familiar with this approach as well as those who may not be as familiar.

Role of the X-linked gene GPR174 in autoimmune Addison's disease.

PubMed

Napier, C; Mitchell, A L; Gan, E; Wilson, I; Pearce, S H S

2015-01-01

Autoimmune endocrinopathies demonstrate a profound gender bias, but the reasons for this remain obscure. The 1000 genes on the X chromosome are likely to be implicated in this inherent susceptibility; various theories, including skewed X chromosome inactivation and fetal microchimerism, have been proposed. GPR174 is an Xq21 putative purinergic receptor that is widely expressed in lymphoid tissues. A single-nucleotide polymorphism, rs3827440, encoding Ser162Pro, has recently been associated with Graves' disease in Chinese and Polish populations, suggesting a role of this X chromosome gene in autoimmune disease. We investigated the role of rs3827440 in a UK cohort of patients with autoimmune Addison's disease (AAD). Samples from 286 AAD cases and 288 healthy controls were genotyped using TaqMan single-nucleotide polymorphism genotyping assays (C_25954273_10) on the Applied Biosystems 7900HT Fast real-time PCR system. Using a dominant (present/absent) model, the serine-encoding T allele of rs3827440 was present in 189 of 286 AAD patients (66%) compared with 132 of 288 unaffected controls (46%) [P = .010, odds ratio 1.80 (5%-95% confidence interval 1.22-2.67)]. An allele dosage model found a significant excess of the T allele in AAD patients compared with controls [P = .03, odds ratio 1.34 (5%-95% confidence interval 1.07-1.67)]. We have demonstrated a significant association of this X chromosome-encoded immunoreceptor with AAD for the first time. This X-linked gene could have a more generalized role in autoimmunity pathogenesis: G protein-coupled receptors are promising drugable targets, and further work to elucidate the functional role of GPR174 is now warranted.

The use of in vitro technologies coupled with high resolution accurate mass LC-MS for studying drug metabolism in equine drug surveillance.

PubMed

Scarth, James P; Spencer, Holly A; Timbers, Sarah E; Hudson, Simon C; Hillyer, Lynn L

2010-01-01

The detection of drug abuse in horseracing often requires knowledge of drug metabolism, especially if urine is the matrix of choice. In this study, equine liver/lung microsomes/S9 tissue fractions were used to study the phase I metabolism of eight drugs of relevance to equine drug surveillance (acepromazine, azaperone, celecoxib, fentanyl, fluphenazine, mepivacaine, methylphenidate and tripelennamine). In vitro samples were analyzed qualitatively alongside samples originating from in vivo administrations using LC-MS on a high resolution accurate mass Thermo Orbitrap Discovery instrument and by LC-MS/MS on an Applied Biosystems Sciex 5500 Q Trap.Using high resolution accurate mass full-scan analysis on the Orbitrap, the in vitro systems were found to generate at least the two most abundant phase I metabolites observed in vitro for all eight drugs studied. In the majority of cases, in vitro experiments were also able to generate the minor in vivo metabolites and sometimes metabolites that were only observed in vitro. More detailed analyses of fentanyl incubates using LC-MS/MS showed that it was possible to generate good quality spectra from the metabolites generated in vitro. These data support the suggestion of using in vitro incubates as metabolite reference material in place of in vivo post-administration samples in accordance with new qualitative identification guidelines in the 2009 International Laboratory Accreditation Cooperation-G7 (ILAC-G7) document.In summary, the in vitro and in vivo phase I metabolism results reported herein compare well and demonstrate the potential of in vitro studies to compliment, refine and reduce the existing equine in vivo paradigm. © 2010 John Wiley & Sons, Ltd.

Expression differences of circulating microRNAs in metastatic castration resistant prostate cancer and low-risk, localized prostate cancer.

PubMed

Nguyen, Han Christine Ngoc; Xie, Wanling; Yang, Ming; Hsieh, Chen-Lin; Drouin, Sarah; Lee, Gwo-Shu Mary; Kantoff, Philip W

2013-03-01

Recent studies show that microRNAs (miRNAs), small non-coding RNAs that negatively regulate gene expression, may have potential for monitoring cancer status. We investigated circulating miRNAs in prostate cancer that may be associated with the progression of hormone-sensitive primary tumors to metastatic castration resistant prostate cancer (CRPC) after androgen deprivation therapy. Using genome-wide expression profiling by TaqMan Human MicroRNA Arrays (Applied Biosystems) and/or quantitative real-time polymerase chain reaction, we compared the expression levels of miRNAs in serum samples from 28 patients of low-risk localized disease, 30 of high-risk localized disease and 26 of metastatic CRPC. We demonstrated that serum samples from patients of low risk, localized prostate cancer and metastatic CRPC patients exhibit distinct circulating miRNA signatures. MiR-375, miR-378*, and miR-141 were significantly over-expressed in serum from CRPC patients compared with serum from low-risk localized patients, while miR-409-3p was significantly under-expressed. In prostate primary tumor samples, miR-375 and miR-141 also had significantly higher expression levels compared with those in normal prostate tissue. Circulating miRNAs, particularly miR-375, miR-141, miR-378*, and miR-409-3p, are differentially expressed in serum samples from prostate cancer patients. In the search for improved minimally invasive methods to follow cancer pathogenesis, the correlation of disease status with the expression patterns of circulating miRNAs may indicate the potential importance of circulating miRNAs as prognostic markers for prostate cancer progression. Copyright © 2012 Wiley Periodicals, Inc.

Establishing a novel automated magnetic bead-based method for the extraction of DNA from a variety of forensic samples.

PubMed

Witt, Sebastian; Neumann, Jan; Zierdt, Holger; Gébel, Gabriella; Röscheisen, Christiane

2012-09-01

Automated systems have been increasingly utilized for DNA extraction by many forensic laboratories to handle growing numbers of forensic casework samples while minimizing the risk of human errors and assuring high reproducibility. The step towards automation however is not easy: The automated extraction method has to be very versatile to reliably prepare high yields of pure genomic DNA from a broad variety of sample types on different carrier materials. To prevent possible cross-contamination of samples or the loss of DNA, the components of the kit have to be designed in a way that allows for the automated handling of the samples with no manual intervention necessary. DNA extraction using paramagnetic particles coated with a DNA-binding surface is predestined for an automated approach. For this study, we tested different DNA extraction kits using DNA-binding paramagnetic particles with regard to DNA yield and handling by a Freedom EVO(®)150 extraction robot (Tecan) equipped with a Te-MagS magnetic separator. Among others, the extraction kits tested were the ChargeSwitch(®)Forensic DNA Purification Kit (Invitrogen), the PrepFiler™Automated Forensic DNA Extraction Kit (Applied Biosystems) and NucleoMag™96 Trace (Macherey-Nagel). After an extensive test phase, we established a novel magnetic bead extraction method based upon the NucleoMag™ extraction kit (Macherey-Nagel). The new method is readily automatable and produces high yields of DNA from different sample types (blood, saliva, sperm, contact stains) on various substrates (filter paper, swabs, cigarette butts) with no evidence of a loss of magnetic beads or sample cross-contamination. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Flatness-based control in successive loops for stabilization of heart's electrical activity

NASA Astrophysics Data System (ADS)

Rigatos, Gerasimos; Melkikh, Alexey

2016-12-01

The article proposes a new flatness-based control method implemented in successive loops which allows for stabilization of the heart's electrical activity. Heart's pacemaking function is modeled as a set of coupled oscillators which potentially can exhibit chaotic behavior. It is shown that this model satisfies differential flatness properties. Next, the control and stabilization of this model is performed with the use of flatness-based control implemented in cascading loops. By applying a per-row decomposition of the state-space model of the coupled oscillators a set of nonlinear differential equations is obtained. Differential flatness properties are shown to hold for the subsystems associated with the each one of the aforementioned differential equations and next a local flatness-based controller is designed for each subsystem. For the i-th subsystem, state variable xi is chosen to be the flat output and state variable xi+1 is taken to be a virtual control input. Then the value of the virtual control input which eliminates the output tracking error for the i-th subsystem becomes reference setpoint for the i + 1-th subsystem. In this manner the control of the entire state-space model is performed by successive flatness-based control loops. By arriving at the n-th row of the state-space model one computes the control input that can be actually exerted on the aforementioned biosystem. This real control input of the coupled oscillators' system, contains recursively all virtual control inputs associated with the previous n - 1 rows of the state-space model. This control approach achieves asymptotically the elimination of the chaotic oscillation effects and the stabilization of the heart's pulsation rhythm. The stability of the proposed control scheme is proven with the use of Lyapunov analysis.

Exploring the Angstrom Excursion of Au Nanoparticles Excited away from a Metal Surface by an Impulsive Acoustic Perturbation.

PubMed

Kim, Ji-Wan; Kovalenko, Oleksandr; Liu, Yu; Bigot, Jean-Yves

2016-12-27

We report the anharmonic angstrom dynamics of self-assembled Au nanoparticles (Au:NPs) away from a nickel surface on top of which they are coupled by their near-field interaction. The deformation and the oscillatory excursion away from the surface are induced by picosecond acoustic pulses and probed at the surface plasmon resonance with femtosecond laser pulses. The overall dynamics are due to an efficient transfer of translational momentum from the Ni surface to the Au:NPs, therefore avoiding usual thermal effects and energy redistribution among the electronic states. Two modes are clearly revealed by the oscillatory shift of the Au:NPs surface plasmon resonance-the quadrupole deformation mode due to the transient ellipsoid shape and the excursion mode when the Au:NPs bounce away from the surface. We find that, contrary to the quadrupole mode, the excursion mode is sensitive to the distance between Au:NPs and Ni. Importantly, the excursion dynamics display a nonsinusoidal motion that cannot be explained by a standard harmonic potential model. A detailed modeling of the dynamics using a Hamaker-type Lennard-Jones potential between two media is performed, showing that each Au:NPs coherently evolves in a nearly one-dimensional anharmonic potential with a total excursion of ∼1 Å. This excursion induces a shift of the surface plasmon resonance detectable because of the strong near-field interaction. This general method of observing the spatiotemporal dynamics with angstrom and picosecond resolutions can be directly transposed to many nanostructures or biosystems to reveal the interaction and contact mechanism with their surrounding medium while remaining in their fundamental electronic states.

Discovering the Power of Individual-Based Modelling in Teaching and Learning: The Study of a Predator-Prey System

NASA Astrophysics Data System (ADS)

Ginovart, Marta

2014-08-01

The general aim is to promote the use of individual-based models (biological agent-based models) in teaching and learning contexts in life sciences and to make their progressive incorporation into academic curricula easier, complementing other existing modelling strategies more frequently used in the classroom. Modelling activities for the study of a predator-prey system for a mathematics classroom in the first year of an undergraduate program in biosystems engineering have been designed and implemented. These activities were designed to put two modelling approaches side by side, an individual-based model and a set of ordinary differential equations. In order to organize and display this, a system with wolves and sheep in a confined domain was considered and studied. With the teaching material elaborated and a computer to perform the numerical resolutions involved and the corresponding individual-based simulations, the students answered questions and completed exercises to achieve the learning goals set. Students' responses regarding the modelling of biological systems and these two distinct methodologies applied to the study of a predator-prey system were collected via questionnaires, open-ended queries and face-to-face dialogues. Taking into account the positive responses of the students when they were doing these activities, it was clear that using a discrete individual-based model to deal with a predator-prey system jointly with a set of ordinary differential equations enriches the understanding of the modelling process, adds new insights and opens novel perspectives of what can be done with computational models versus other models. The complementary views given by the two modelling approaches were very well assessed by students.

Y-chromosomal diversity of the Valachs from the Czech Republic: model for isolated population in Central Europe

PubMed Central

Ehler, Edvard; Vaněk, Daniel; Stenzl, Vlastimil; Vančata, Václav

2011-01-01

Aim To evaluate Y-chromosomal diversity of the Moravian Valachs of the Czech Republic and compare them with a Czech population sample and other samples from Central and South-Eastern Europe, and to evaluate the effects of genetic isolation and sampling. Methods The first sample set of the Valachs consisted of 94 unrelated male donors from the Valach region in northeastern Czech Republic border-area. The second sample set of the Valachs consisted of 79 men who originated from 7 paternal lineages defined by surname. No close relatives were sampled. The third sample set consisted of 273 unrelated men from the whole of the Czech Republic and was used for comparison, as well as published data for other 27 populations. The total number of samples was 3244. Y-short tandem repeat (STR) markers were typed by standard methods using PowerPlex® Y System (Promega) and Yfiler® Amplification Kit (Applied Biosystems) kits. Y-chromosomal haplogroups were estimated from the haplotype information. Haplotype diversity and other intra- and inter-population statistics were computed. Results The Moravian Valachs showed a lower genetic variability of Y-STR markers than other Central European populations, resembling more to the isolated Balkan populations (Aromuns, Csango, Bulgarian, and Macedonian Roma) than the surrounding populations (Czechs, Slovaks, Poles, Saxons). We illustrated the effect of sampling on Valach paternal lineages, which includes reduction of discrimination capacity and variability inside Y-chromosomal haplogroups. Valach modal haplotype belongs to R1a haplogroup and it was not detected in the Czech population. Conclusion The Moravian Valachs display strong substructure and isolation in their Y chromosomal markers. They represent a unique Central European population model for population genetics. PMID:21674832

Association between ABCG1 polymorphism rs1893590 and high-density lipoprotein (HDL) in an asymptomatic Brazilian population.

PubMed

Zago, V H S; Scherrer, D Z; Parra, E S; Panzoldo, N B; Alexandre, F; Nakandakare, E R; Quintão, E C R; de Faria, E C

2015-03-01

ATP binding cassette transporter G1 (ABCG1) promotes lipidation of nascent high-density lipoprotein (HDL) particles, acting as an intracellular transporter. SNP rs1893590 (c.-204A > C) of ABCG1 gene has been previously studied and reported as functional over plasma HDL-C and lipoprotein lipase activity. This study aimed to investigate the relationships of SNP rs1893590 with plasma lipids and lipoproteins in a large Brazilian population. Were selected 654 asymptomatic and normolipidemic volunteers from both genders. Clinical and anthropometrical data were taken and blood samples were drawn after 12 h fasting. Plasma lipids and lipoproteins, as well as HDL particle size and volume were determined. Genomic DNA was isolated for SNP rs1893590 detection by TaqMan(®) OpenArray(®) Real-Time PCR Plataform (Applied Biosystems). Mann-Whitney U, Chi square and two-way ANOVA were the used statistical tests. No significant differences were found in the comparison analyses between the allele groups for all studied parameters. Conversely, significant interactions were observed between SNP and age over plasma HDL-C, were volunteers under 60 years with AA genotype had increased HDL-C (p = 0.048). Similar results were observed in the group with body mass index (BMI) < 25 kg/m(2), where volunteers with AA genotype had higher HDL-C levels (p = 0.0034), plus an increased HDL particle size (p = 0.01). These findings indicate that SNP rs1893590 of ABCG1 has a significant impact over HDL-C under asymptomatic clinical conditions in an age and BMI dependent way.

Polymorphism of SMAD7 gene (rs2337104) and risk of colorectal cancer in an Iranian population: a case-control study

PubMed Central

Akbari, Zahra; Safari-Alighiarloo, Nahid; Taleghani, Mohammad Yaghoob; Mirfakhar, Farzaneh Sadat; Asadzadeh Aghdaei, Hamid; Vahedi, Mohsen; Irani Shemirani, Atena; Nazemalhosseini-Mojarad, Ehsan; Zali, Mohammad Reza

2014-01-01

Aim: The purpose of this study was to evaluate the influence of intronic polymorphism of the SMAD7 (Mothers Against Decantaplegic Homolog 7) gene (rs2337104) on the risk of colorectal cancer (CRC) and clinicopathological features in an Iranian population. Background: SMAD7 has been identified as an antagonist of transforming growth factor beta (TGF-b)-mediating fibrosis, carcinogenesis, and inflammation. Regarding to the recent genome-wide scan, a risk locus for colorectal cancer at 18q21 has been found, which maps to the SMAD7 gene. Patients and methods: This case-control study was performed on 109 CRC patients and 109 healthy controls recruited in Taleghani Hospital. The genotyping of all samples were done by TaqMan assay via an ABI 7500 Real Time PCR System (Applied Biosystems) with DNA from peripheral blood. The association of this polymorphism with the risk of CRC and clinicopathological features was investigated. Results: Our results indicated that there were no significant association between genotypic and allelic frequencies of SMAD7 polymorphism (rs2337104) and CRC risk in our population. Although the T allele is the most frequent one in this population and its frequency was 86.7% in patients compared with 91.7% in controls (OR=1.705, 95% CI= 0.916–3.172). Also, the SMAD7 genotypes were not associated with any clinicopathological characteristics in CRC patients (P>0.05). Conclusion: For the first time, this study results revealed that this SMAD7 polymorphism couldn’t be a potential risk factor for CRC or a prognostic biomarker for prediction of clinicopathological features in an Iranian population. A large-scale case-control study is needed to validate our results. PMID:25289133

Head Impact Biomechanics in Women's College Soccer.

PubMed

Lynall, Robert C; Clark, Michael D; Grand, Erin E; Stucker, Jaclyn C; Littleton, Ashley C; Aguilar, Alain J; Petschauer, Meredith A; Teel, Elizabeth F; Mihalik, Jason P

2016-09-01

There are limited nonlaboratory soccer head impact biomechanics data. This is surprising given soccer's global popularity. Epidemiological data suggest that female college soccer players are at a greater concussion injury risk than their male counterparts. Therefore, the purposes of our study were to quantify head impact frequency and magnitude during women's soccer practices and games in the National Collegiate Athletic Association and to characterize these data across event type, playing position, year on the team, and segment of game (first and second halves). Head impact biomechanics were collected from female college soccer players (n = 22; mean ± SD age = 19.1 ± 0.1 yr, height = 168.0 ± 3.5 cm, mass = 63.7 ± 6.0 kg). We employed a helmetless head impact measurement device (X2 Biosystems xPatch) before each competition and practice across a single season. Peak linear and rotational accelerations were categorized based on impact magnitude and subsequently analyzed using appropriate nonparametric analyses. Overall, women's college soccer players experience approximately seven impacts per 90 min of game play. The overwhelming majority (~90%) of all head impacts were categorized into our mildest linear acceleration impact classification (10g-20g). Interestingly, a higher percentage of practice impacts in the 20g-40g range compared with games (11% vs 7%) was observed. Head impact biomechanics studies have provided valuable insights into understanding collision sports and for informing evidence-based rule and policy changes. These have included changing the football kickoff, ice hockey body checking ages, and head-to-head hits in both sports. Given soccer's global popularity, and the growing public concern for the potential long-term neurological implications of collision and contact sports, studying soccer has the potential to impact many athletes and the sports medicine professionals caring for them.

p40 (ΔNp63) expression in breast disease and its correlation with p63 immunohistochemistry

PubMed Central

Kim, Sang Kyum; Jung, Woo Hee; Koo, Ja Seung

2014-01-01

p63 protein is widely used to identify myoepithelial cells in breast disease. There have been no comparative studies of the p63 antibodies which detect different isoforms. In this study, we examine the expression profiles of p63 protein in benign proliferative diseases and malignant tumors of the breast using pan-p63 and p40 antibodies, and analyze their diagnostic utility and clinical implications. We selected 32 adenoses, 34 intraductal papillomas, 31 ductal carcinoma in situ (DCIS), 257 invasive ductal carcinoma (IDC), and 36 metaplastic carcinomas, and created tissue microarray blocks from them. Immunohistochemical assays for p63 protein were performed on these samples. We investigated the expression patterns of the pan-p63 (TP63, 4A4, Dako, 1:700), p40 antibody [5-17, CalBiochem/EMD Biosciences, 1:2000, p40 (CB)], and p40 antibody [polyclonal, Diagnostic BioSystems, 1:100, p40 (DB)] in various forms of breast disease. We determined that p63 and p40 (DB) expression in myoepithelial cells was broadly similar and showed cognate clinicopathologic features, unlike p40 (CB). p40 (CB) was more sensitive (99.0%) but less specific (85.8%), and p63 was less sensitive (93.8%) in adenosis, IP, and DCIS. In IDCs, p63 and p40 (DB) had similar expression in cancer cells; p40 (CB) expression, however, was statistically different. In metaplastic carcinomas, both p63 and p40 (DB) had distinct expression profiles, according to their histologic subtypes. We conclude that p40 antibodies as well as pan-p63 antibody are specific and sensitive myoepithelial cell markers. Interpretation of p40 positivity in cancer cells, however, should be considered carefully, due to their relatively lower specificity. PMID:24696720

The ACTN3 R577X genotype is associated with muscle function in a Japanese population.

PubMed

Kikuchi, Naoki; Yoshida, Shou; Min, Seok-ki; Lee, Kihyuk; Sakamaki-Sunaga, Mikako; Okamoto, Takanobu; Nakazato, Koichi

2015-04-01

Homozygosity for the common nonsense polymorphism R577X in the α-actinin-3 gene (ACTN3) causes complete α-actinin-3 deficiency in fast-twitch skeletal muscle fibers. This study investigated whether the ACTN3 R577X polymorphism affects fitness status using a battery of tests in a large Japanese cohort. In the present study, 1227 subjects (age: 25-85 years) were genotyped for the ACTN3 R577X polymorphism (rs1815739) using a TaqMan SNP genotyping assay (Applied Biosystems). All subjects were divided into 2 groups based on their age (<55 years and ≥55 years). All subjects completed a questionnaire about exercise habits and were subjected to a battery of tests to assess their fitness status (including grip strength test, chair stand test, and 8-foot walking test). A significant association between the ACTN3 R577X genotype and chair stand test performance was observed in the group of men ≥55 using ANCOVA adjusted for age and exercise habits (p = 0.036). The ACTN3 R577X genotype accounted for 2.5% of the variability in the results of the chair stand test among men in the ≥55 age group. Moreover, for the ≥55 age group, performance in the chair stand test was lower among those with the XX genotype than among those with the RR genotype (p = 0.024) or RX genotype (p = 0.005), unlike results for the <55 age group. No significant difference was noted for hand grip strength or 8-foot walking time. Thus, our results suggest that the ACTN3 R577X genotype is associated with lower-extremity muscle function in the Japanese population.

Glucokinase gene mutations (MODY 2) in Asian Indians.

PubMed

Kanthimathi, Sekar; Jahnavi, Suresh; Balamurugan, Kandasamy; Ranjani, Harish; Sonya, Jagadesan; Goswami, Soumik; Chowdhury, Subhankar; Mohan, Viswanathan; Radha, Venkatesan

2014-03-01

Heterozygous inactivating mutations in the glucokinase (GCK) gene cause a hyperglycemic condition termed maturity-onset diabetes of the young (MODY) 2 or GCK-MODY. This is characterized by mild, stable, usually asymptomatic, fasting hyperglycemia that rarely requires pharmacological intervention. The aim of the present study was to screen for GCK gene mutations in Asian Indian subjects with mild hyperglycemia. Of the 1,517 children and adolescents of the population-based ORANGE study in Chennai, India, 49 were found to have hyperglycemia. These children along with the six patients referred to our center with mild hyperglycemia were screened for MODY 2 mutations. The GCK gene was bidirectionally sequenced using BigDye(®) Terminator v3.1 (Applied Biosystems, Foster City, CA) chemistry. In silico predictions of the pathogenicity were carried out using the online tools SIFT, Polyphen-2, and I-Mutant 2.0 software programs. Direct sequencing of the GCK gene in the patients referred to our Centre revealed one novel mutation, Thr206Ala (c.616A>G), in exon 6 and one previously described mutation, Met251Thr (c.752T>C), in exon 7. In silico analysis predicted the novel mutation to be pathogenic. The highly conserved nature and critical location of the residue Thr206 along with the clinical course suggests that the Thr206Ala is a MODY 2 mutation. However, we did not find any MODY 2 mutations in the 49 children selected from the population-based study. Hence prevalence of GCK mutations in Chennai is <1:1,517. This is the first study of MODY 2 mutations from India and confirms the importance of considering GCK gene mutation screening in patients with mild early-onset hyperglycemia who are negative for β-cell antibodies.

Growth dynamics of cancer cell colonies and their comparison with noncancerous cells

NASA Astrophysics Data System (ADS)

Huergo, M. A. C.; Pasquale, M. A.; González, P. H.; Bolzán, A. E.; Arvia, A. J.

2012-01-01

The two-dimensional (2D) growth dynamics of HeLa (cervix cancer) cell colonies was studied following both their growth front and the pattern morphology evolutions utilizing large population colonies exhibiting linearly and radially spreading fronts. In both cases, the colony profile fractal dimension was df=1.20±0.05 and the growth fronts displaced at the constant velocity 0.90±0.05 μm min-1. Colonies showed changes in both cell morphology and average size. As time increased, the formation of large cells at the colony front was observed. Accordingly, the heterogeneity of the colony increased and local driving forces that set in began to influence the dynamics of the colony front. The dynamic scaling analysis of rough colony fronts resulted in a roughness exponent α = 0.50±0.05, a growth exponent β = 0.32±0.04, and a dynamic exponent z=1.5±0.2. The validity of this set of scaling exponents extended from a lower cutoff lc≈60 μm upward, and the exponents agreed with those predicted by the standard Kardar-Parisi-Zhang continuous equation. HeLa data were compared with those previously reported for Vero cell colonies. The value of df and the Kardar-Parisi-Zhang-type 2D front growth dynamics were similar for colonies of both cell lines. This indicates that the cell colony growth dynamics is independent of the genetic background and the tumorigenic nature of the cells. However, one can distinguish some differences between both cell lines during the growth of colonies that may result from specific cooperative effects and the nature of each biosystem.

Inverse problem studies of biochemical systems with structure identification of S-systems by embedding training functions in a genetic algorithm.

PubMed

Sarode, Ketan Dinkar; Kumar, V Ravi; Kulkarni, B D

2016-05-01

An efficient inverse problem approach for parameter estimation, state and structure identification from dynamic data by embedding training functions in a genetic algorithm methodology (ETFGA) is proposed for nonlinear dynamical biosystems using S-system canonical models. Use of multiple shooting and decomposition approach as training functions has been shown for handling of noisy datasets and computational efficiency in studying the inverse problem. The advantages of the methodology are brought out systematically by studying it for three biochemical model systems of interest. By studying a small-scale gene regulatory system described by a S-system model, the first example demonstrates the use of ETFGA for the multifold aims of the inverse problem. The estimation of a large number of parameters with simultaneous state and network identification is shown by training a generalized S-system canonical model with noisy datasets. The results of this study bring out the superior performance of ETFGA on comparison with other metaheuristic approaches. The second example studies the regulation of cAMP oscillations in Dictyostelium cells now assuming limited availability of noisy data. Here, flexibility of the approach to incorporate partial system information in the identification process is shown and its effect on accuracy and predictive ability of the estimated model are studied. The third example studies the phenomenological toy model of the regulation of circadian oscillations in Drosophila that follows rate laws different from S-system power-law. For the limited noisy data, using a priori information about properties of the system, we could estimate an alternate S-system model that showed robust oscillatory behavior with predictive abilities. Copyright © 2016 Elsevier Inc. All rights reserved.

PP128. Placental Caspase-3 gene polymorphisms is associated with preeclampsia.

PubMed

Hsu, C-D; Polavarapu, S; Parton, L

2012-07-01

Increased placental trophoblastic apoptosis (programmed cell death) was previously reported in pregnancies complicated by preeclampsia. Caspase-3 is one of the key executioners of apoptosis. Caspase are expressed in many tissues including human placental trophoblast and other tissues. Variations in the promoter area of the Caspase genes may modulate apoptotic signaling, contributing to an increased risk of preeclampsia To determine if gene polymorphisms of Caspase 3 proteins differ between patient with and without preeclampsia. Forty-three singleton placentas were studied. Twenty-two placentas were with preeclampsia and 21 were normotensive controls. DNA was extracted from placentas using QIAAmp DNA Minikit. Genotyping of Caspase 3 +567 was determined by real-time PCR using the Applied Biosystems Prism 7900 HT SDS machine. Chi-square and Fisher's exact tests were used for statistical analysis. There were no significant differences in maternal age, parity or race between the two groups. Preeclamptic placentas had higher frequency of wild type TT of Caspase-3 SNP (+567) as compared with normotensive controls (59% versus 28.5%). Preeclamptic placentas expressed significantly more genotype of TT of Caspase-3 SNP (+567) than normotensive patients when compared to CC (p=0.02). The alle frequencies of the Caspase SNP (+567) in preeclampstic placentas were 0.77 and 0.23 for T and C, respectively, as compared to 0.52 and 0.48, respectively, in placentas from normotensive pregnancies. Immune intolerance of maternal and placental interaction plays an important role in the pathogenesis of preeclampsia. Increased of placental apoptosis was reported in pregnancy complicated with preeclamsia. Our findings indicate placental Caspase 3 (+567) gene polymorphisms is associated with preeclampsia. Altered placental alle frequencies and caspase-3 SNP (+567) in preeclampsia further suggests preeclampsia is a trophoblastic disorder. Copyright © 2012. Published by Elsevier B.V.

A multianalytical approach to evaluate the association of 55 SNPs in 28 genes with obesity risk in North Indian adults.

PubMed

Srivastava, Apurva; Mittal, Balraj; Prakash, Jai; Srivastava, Pranjal; Srivastava, Nimisha; Srivastava, Neena

2017-03-01

The aim of the study was to investigate the association of 55 SNPs in 28 genes with obesity risk in a North Indian population using a multianalytical approach. Overall, 480 subjects from the North Indian population were studied using strict inclusion/exclusion criteria. SNP Genotyping was carried out by Sequenom Mass ARRAY platform (Sequenom, San Diego, CA) and validated Taqman ® allelic discrimination (Applied Biosystems ® ). Statistical analyses were performed using SPSS software version 19.0, SNPStats, GMDR software (version 6) and GENEMANIA. Logistic regression analysis of 55 SNPs revealed significant associations (P < .05) of 49 SNPs with BMI linked obesity risk whereas the remaining 6 SNPs revealed no association (P > .05). The pathway-wise G-score revealed the significant role (P = .0001) of food intake-energy expenditure pathway genes. In CART analysis, the combined genotypes of FTO rs9939609 and TCF7L2 rs7903146 revealed the highest risk for BMI linked obesity. The analysis of the FTO-IRX3 locus revealed high LD and high order gene-gene interactions for BMI linked obesity. The interaction network of all of the associated genes in the present study generated by GENEMANIA revealed direct and indirect connections. In addition, the analysis with centralized obesity revealed that none of the SNPs except for FTO rs17818902 were significantly associated (P < .05). In this multi-analytical approach, FTO rs9939609 and IRX3 rs3751723, along with TCF7L2 rs7903146 and TMEM18 rs6548238, emerged as the major SNPs contributing to BMI linked obesity risk in the North Indian population. © 2016 Wiley Periodicals, Inc.

Haplotype diversity of 17 Y-chromosomal STRs in three native Sarawak populations (Iban, Bidayuh and Melanau) in East Malaysia.

PubMed

Chang, Yuet Meng; Swaran, Yuvaneswari; Phoon, Yoong Keat; Sothirasan, Kavin; Sim, Hang Thiew; Lim, Kong Boon; Kuehn, Daniel

2009-06-01

17 Y-STRs (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635 or Y-GATA C4, DYS392, Y-GATA H4, DYS437, DYS438 and DYS448) have been analyzed in 320 male individuals from Sarawak, an eastern state of Malaysia on the Borneo island using the AmpFlSTR Y-filer (Applied Biosystems, Foster City, CA). These individuals were from three indigenous ethnic groups in Sarawak comprising of 103 Ibans, 113 Bidayuhs and 104 Melanaus. The observed 17-loci haplotypes and the individual allele frequencies for each locus were estimated, whilst the locus diversity, haplotype diversity and discrimination capacity were calculated in the three groups. Analysis of molecular variance (AMOVA) indicated that 87.6% of the haplotypic variation was found within population and 12.4% between populations (fixation index F(ST)=0.124, p=0.000). This study has revealed that the indigenous populations in Sarawak are distinctly different to each other, and to the three major ethnic groups in Malaysia (Malays, Chinese and Indians), with the Melanaus having a strikingly high degree of shared haplotypes within. There are rare unusual variants and microvariants that were not present in Malaysian Malay, Chinese or Indian groups. In addition, occurrences of DYS385 duplications which were only noticeably present in Chinese group previously was also observed in the Iban group whilst null alleles were detected at several Y-loci (namely DYS19, DYS392, DYS389II and DYS448) in the Iban and Melanau groups.

Genetic and clinical risk factors of root resorption associated with orthodontic treatment.

PubMed

Guo, Yujiao; He, Shushu; Gu, Tian; Liu, Yi; Chen, Song

2016-08-01

External apical root resorption (EARR) is a common complication in orthodontic treatment. Despite many studies on EARR, great controversies remain with regard to its risk factors. The objective of this study was to explore the relationship among sex, root movement, IL-1RN single nucleotide polymorphism (SNP) rs419598, IL-6 SNP rs1800796, and EARR associated with orthodontic treatment. Altogether 174 patients (with 174 maxillary left central incisors) were selected for this study. Cone-beam computed tomography was performed before the start of the treatment and at the end of the treatment. Cone-beam computed tomography data were used to reconstruct a 3-dimensional image of each tooth; the volume and the root resorption volume of each tooth were calculated. Three-dimensional matching was used to measure the amount of movement of each root. Genomic DNA was extracted from buccal swabs, and genotypes of SNP rs419598 and SNP rs1800796 of each subject were determined using TaqMan polymerase chain reaction genotyping (Applied Biosystems, Foster City, Calif). The data were analyzed with multiple linear regression analysis. The statistical analysis indicated no relationship between sex, tooth movement amount, and IL-1RN SNP rs419598 with EARR. The IL-6 SNP rs1800796 GC was associated with EARR, and root resorption differed significantly between SNP rs1800796 GC and CC. IL-6 SNP rs1800796 GC is a risk factor for EARR. The amount of root movement, IL-1RN SNP rs419598, and sex as risk factors for EARR need further study. Copyright © 2016 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.