Using consumption rate to assess potential predators for biological control of white perch

USGS Publications Warehouse

Gosch, N.J.C.; Pope, K.L.

2011-01-01

Control of undesirable fishes is important in aquatic systems, and using predation as a tool for biological control is an attractive option to fishery biologists. However, determining the appropriate predators for biological control is critical for success. The objective of this study was to evaluate the utility of consumption rate as an index to determine the most effective predators for biological control of an invasive fish. Consumption rate values were calculated for nine potential predators that prey on white perch Morone americana in Branched Oak and Pawnee reservoirs, Nebraska. The consumption rate index provided a unique and insightful means of determining the potential effectiveness of each predator species in controlling white perch. Cumulative frequency distributions facilitated interpretation by providing a graphical presentation of consumption rates by all individuals within each predator species. Largemouth bass Micropterus salmoides, walleye Sander vitreus and sauger S. canadensis were the most efficient white perch predators in both reservoirs; however, previous attempts to increase biomass of these predators have failed suggesting that successful biological control is unlikely using existing predator species in these Nebraska reservoirs. ?? 2011 ONEMA.

Laboratory evaluation of two native fishes from tropical North Queensland as biological control agents of subterranean Aedes aegypti.

PubMed

Russell, B M; Wang, J; Williams, Y; Hearnden, M N; Kay, B H

2001-06-01

The ability of 2 freshwater fishes, eastern rainbow fish Melanotaenia splendida splendida and fly-specked hardyhead Craterocephalus stercusmuscarum stercusmuscarum, native to North Queensland to prey on immature Aedes aegypti was evaluated under laboratory conditions. The predation efficiency of the 2 species was compared to the exotic guppy, Poecilia reticulata, which is commonly used as a biological control agent of mosquito larvae. Of the 3 fish species tested, M. s. splendida was shown to be the most promising agent for the biological control of Ae. aegypti that breed in wells. Melanotaenia s. splendida consumed significantly greater numbers of immature Ae. aegypti than P. reticulata, irrespective of developmental stage or light conditions. Unlike C s. stercusmuscarum, M. s. splendida could be handled, transported, and kept in captivity for extended periods with negligible mortality. However, M. s. splendida was also an efficient predator of Litoria caerulea tadpoles, a species of native frog found in wells during the dry season. This result may limit the usefulness of M. s. splendida as a biological control agent of well-breeding Ae. aegypti and suggests that predacious copepods, Mesocyclops spp., are more suitable. However, the use of M. s. splendida as a mosquito control agent in containers that are unlikely to support frog populations (e.g., aquaculture tanks and drinking troughs) should be given serious consideration.

TRIENNIAL LACTATION SYMPOSIUM: Systems biology of regulatory mechanisms of nutrient metabolism in lactation.

PubMed

McNamara, J P

2015-12-01

A major role of the dairy cow is to convert low-quality plant materials into high-quality protein and other nutrients for humans. We must select and manage cows with the goal of having animals of the greatest efficiency matched to their environment. We have increased efficiency tremendously over the years, yet the variation in productive and reproductive efficiency among animals is still large. In part, this is because of a lack of full integration of genetic, nutritional, and reproductive biology into management decisions. However, integration across these disciplines is increasing as the biological research findings show specific control points at which genetics, nutrition, and reproduction interact. An ordered systems biology approach that focuses on why and how cells regulate energy and N use and on how and why organs interact through endocrine and neurocrine mechanisms will speed improvements in efficiency. More sophisticated dairy managers will demand better information to improve the efficiency of their animals. Using genetic improvement and animal management to improve milk productive and reproductive efficiency requires a deeper understanding of metabolic processes throughout the life cycle. Using existing metabolic models, we can design experiments specifically to integrate data from global transcriptional profiling into models that describe nutrient use in farm animals. A systems modeling approach can help focus our research to make faster and larger advances in efficiency and determine how this knowledge can be applied on the farms.

Economic Analysis of Biological Invasions in Forests

Treesearch

Tomas P. Holmes; Julian Aukema; Jeffrey Englin; Robert G. Haight; Kent Kovacs; Brian Leung

2014-01-01

Biological invasions of native forests by nonnative pests result from complex stochastic processes that are difficult to predict. Although economic optimization models describe efficient controls across the stages of an invasion, the ability to calibrate such models is constrained by lack of information on pest population dynamics and consequent economic damages. Here...

The impact on atmospheric CO2 of iron fertilization induced changes in the ocean's biological pump

NASA Astrophysics Data System (ADS)

Jin, X.; Gruber, N.; Frenzel, H.; Doney, S. C.; McWilliams, J. C.

2007-10-01

Using numerical simulations, we quantify the impact of changes in the ocean's biological pump on the air-sea balance of CO2 by fertilizing a small surface patch in the high-nutrient, low-chlorophyll region of the eastern tropical Pacific with iron. Decade-long fertilization experiments are conducted in a basin-scale, eddy-permitting coupled physical biogeochemical ecological model. In contrast to previous studies, we find that most of the dissolved inorganic carbon (DIC) removed from the euphotic zone by the enhanced biological export is replaced by uptake of CO2 from the atmosphere. Atmospheric uptake efficiencies, the ratio of the perturbation in air-sea CO2 flux to the perturbation in export flux across 100 m, are 0.75 to 0.93 in our patch size-scale experiments. The atmospheric uptake efficiency is insensitive to the duration of the experiment. The primary factor controlling the atmospheric uptake efficiency is the vertical distribution of the enhanced biological production. Iron fertilization at the surface tends to induce production anomalies primarily near the surface, leading to high efficiencies. In contrast, mechanisms that induce deep production anomalies (e.g. altered light availability) tend to have a low uptake efficiency, since most of the removed DIC is replaced by lateral and vertical transport and mixing. Despite high atmospheric uptake efficiencies, patch-scale iron fertilization of the ocean's biological pump tends to remove little CO2 from the atmosphere over the decadal timescale considered here.

The impact on atmospheric CO2 of iron fertilization induced changes in the ocean's biological pump

NASA Astrophysics Data System (ADS)

Jin, X.; Gruber, N.; Frenzel, H.; Doney, S. C.; McWilliams, J. C.

2008-03-01

Using numerical simulations, we quantify the impact of changes in the ocean's biological pump on the air-sea balance of CO2 by fertilizing a small surface patch in the high-nutrient, low-chlorophyll region of the eastern tropical Pacific with iron. Decade-long fertilization experiments are conducted in a basin-scale, eddy-permitting coupled physical/biogeochemical/ecological model. In contrast to previous studies, we find that most of the dissolved inorganic carbon (DIC) removed from the euphotic zone by the enhanced biological export is replaced by uptake of CO2 from the atmosphere. Atmospheric uptake efficiencies, the ratio of the perturbation in air-sea CO2 flux to the perturbation in export flux across 100 m, integrated over 10 years, are 0.75 to 0.93 in our patch size-scale experiments. The atmospheric uptake efficiency is insensitive to the duration of the experiment. The primary factor controlling the atmospheric uptake efficiency is the vertical distribution of the enhanced biological production and export. Iron fertilization at the surface tends to induce production anomalies primarily near the surface, leading to high efficiencies. In contrast, mechanisms that induce deep production anomalies (e.g. altered light availability) tend to have a low uptake efficiency, since most of the removed DIC is replaced by lateral and vertical transport and mixing. Despite high atmospheric uptake efficiencies, patch-scale iron fertilization of the ocean's biological pump tends to remove little CO2 from the atmosphere over the decadal timescale considered here.

Synthetic biology: tools to design microbes for the production of chemicals and fuels.

PubMed

Seo, Sang Woo; Yang, Jina; Min, Byung Eun; Jang, Sungho; Lim, Jae Hyung; Lim, Hyun Gyu; Kim, Seong Cheol; Kim, Se Yeon; Jeong, Jun Hong; Jung, Gyoo Yeol

2013-11-01

The engineering of biological systems to achieve specific purposes requires design tools that function in a predictable and quantitative manner. Recent advances in the field of synthetic biology, particularly in the programmable control of gene expression at multiple levels of regulation, have increased our ability to efficiently design and optimize biological systems to perform designed tasks. Furthermore, implementation of these designs in biological systems highlights the potential of using these tools to build microbial cell factories for the production of chemicals and fuels. In this paper, we review current developments in the design of tools for controlling gene expression at transcriptional, post-transcriptional and post-translational levels, and consider potential applications of these tools. Copyright © 2013 Elsevier Inc. All rights reserved.

Biological pretreatment of corn stover with ligninolytic enzyme for high efficient enzymatic hydrolysis.

PubMed

Wang, Feng-Qin; Xie, Hui; Chen, Wei; Wang, En-Tao; Du, Feng-Guang; Song, An-Dong

2013-09-01

Aiming at increasing the efficiency of transferring corn stover into sugars, a biological pretreatment was developed and investigated in this study. The protocol was characterized by the pretreatment with crude ligninolytic enzymes from Phanerochete chrysosporium and Coridus versicolor to break the lignin structure in corn stover, followed by a washing procedure to eliminate the inhibition of ligninolytic enzyme on cellulase. By a 2 d-pretreatment, sugar yield from corn stover hydrolysis could be increased by 50.2% (up to 323 mg/g) compared with that of the control. X-ray diffractometry and FT-IR analysis revealed that biological pretreatment could partially remove the lignin of corn stover, and consequently enhance the enzymatic hydrolysis efficiency of cellulose and hemeicellulose. In addition, the amount of microbial inhibitors, such as acetic acid and furfural, were much lower in biological pretreatment than that in acid pretreatment. This study provided a promising pretreatment method for biotransformation of corn stovers. Copyright © 2013 Elsevier Ltd. All rights reserved.

Sensitivity analysis of dynamic biological systems with time-delays.

PubMed

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

2010-10-15

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

Observability of Boolean multiplex control networks

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Efficient digital implementation of a conductance-based globus pallidus neuron and the dynamics analysis

NASA Astrophysics Data System (ADS)

Yang, Shuangming; Wei, Xile; Deng, Bin; Liu, Chen; Li, Huiyan; Wang, Jiang

2018-03-01

Balance between biological plausibility of dynamical activities and computational efficiency is one of challenging problems in computational neuroscience and neural system engineering. This paper proposes a set of efficient methods for the hardware realization of the conductance-based neuron model with relevant dynamics, targeting reproducing the biological behaviors with low-cost implementation on digital programmable platform, which can be applied in wide range of conductance-based neuron models. Modified GP neuron models for efficient hardware implementation are presented to reproduce reliable pallidal dynamics, which decode the information of basal ganglia and regulate the movement disorder related voluntary activities. Implementation results on a field-programmable gate array (FPGA) demonstrate that the proposed techniques and models can reduce the resource cost significantly and reproduce the biological dynamics accurately. Besides, the biological behaviors with weak network coupling are explored on the proposed platform, and theoretical analysis is also made for the investigation of biological characteristics of the structured pallidal oscillator and network. The implementation techniques provide an essential step towards the large-scale neural network to explore the dynamical mechanisms in real time. Furthermore, the proposed methodology enables the FPGA-based system a powerful platform for the investigation on neurodegenerative diseases and real-time control of bio-inspired neuro-robotics.

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.

Dynamic optimization of distributed biological systems using robust and efficient numerical techniques.

PubMed

Vilas, Carlos; Balsa-Canto, Eva; García, Maria-Sonia G; Banga, Julio R; Alonso, Antonio A

2012-07-02

Systems biology allows the analysis of biological systems behavior under different conditions through in silico experimentation. The possibility of perturbing biological systems in different manners calls for the design of perturbations to achieve particular goals. Examples would include, the design of a chemical stimulation to maximize the amplitude of a given cellular signal or to achieve a desired pattern in pattern formation systems, etc. Such design problems can be mathematically formulated as dynamic optimization problems which are particularly challenging when the system is described by partial differential equations.This work addresses the numerical solution of such dynamic optimization problems for spatially distributed biological systems. The usual nonlinear and large scale nature of the mathematical models related to this class of systems and the presence of constraints on the optimization problems, impose a number of difficulties, such as the presence of suboptimal solutions, which call for robust and efficient numerical techniques. Here, the use of a control vector parameterization approach combined with efficient and robust hybrid global optimization methods and a reduced order model methodology is proposed. The capabilities of this strategy are illustrated considering the solution of a two challenging problems: bacterial chemotaxis and the FitzHugh-Nagumo model. In the process of chemotaxis the objective was to efficiently compute the time-varying optimal concentration of chemotractant in one of the spatial boundaries in order to achieve predefined cell distribution profiles. Results are in agreement with those previously published in the literature. The FitzHugh-Nagumo problem is also efficiently solved and it illustrates very well how dynamic optimization may be used to force a system to evolve from an undesired to a desired pattern with a reduced number of actuators. The presented methodology can be used for the efficient dynamic optimization of generic distributed biological systems.

Gene Drive for Mosquito Control: Where Did It Come from and Where Are We Headed?

PubMed Central

Macias, Vanessa M.; Ohm, Johanna R.; Rasgon, Jason L.

2017-01-01

Mosquito-borne pathogens place an enormous burden on human health. The existing toolkit is insufficient to support ongoing vector-control efforts towards meeting disease elimination and eradication goals. The perspective that genetic approaches can potentially add a significant set of tools toward mosquito control is not new, but the recent improvements in site-specific gene editing with CRISPR/Cas9 systems have enhanced our ability to both study mosquito biology using reverse genetics and produce genetics-based tools. Cas9-mediated gene-editing is an efficient and adaptable platform for gene drive strategies, which have advantages over innundative release strategies for introgressing desirable suppression and pathogen-blocking genotypes into wild mosquito populations; until recently, an effective gene drive has been largely out of reach. Many considerations will inform the effective use of new genetic tools, including gene drives. Here we review the lengthy history of genetic advances in mosquito biology and discuss both the impact of efficient site-specific gene editing on vector biology and the resulting potential to deploy new genetic tools for the abatement of mosquito-borne disease. PMID:28869513

Apparatus and Methods for Manipulation and Optimization of Biological Systems

NASA Technical Reports Server (NTRS)

Sun, Ren (Inventor); Ho, Chih-Ming (Inventor); Wong, Pak Kin (Inventor); Yu, Fuqu (Inventor)

2014-01-01

The invention provides systems and methods for manipulating biological systems, for example to elicit a more desired biological response from a biological sample, such as a tissue, organ, and/or a cell. In one aspect, the invention operates by efficiently searching through a large parametric space of stimuli and system parameters to manipulate, control, and optimize the response of biological samples sustained in the system. In one aspect, the systems and methods of the invention use at least one optimization algorithm to modify the actuator's control inputs for stimulation, responsive to the sensor's output of response signals. The invention can be used, e.g., to optimize any biological system, e.g., bioreactors for proteins, and the like, small molecules, polysaccharides, lipids, and the like. Another use of the apparatus and methods includes is for the discovery of key parameters in complex biological systems.

Predator interference effects on biological control: The "paradox" of the generalist predator revisited

NASA Astrophysics Data System (ADS)

Parshad, Rana D.; Bhowmick, Suman; Quansah, Emmanuel; Basheer, Aladeen; Upadhyay, Ranjit Kumar

2016-10-01

An interesting conundrum in biological control questions the efficiency of generalist predators as biological control agents. Theory suggests, generalist predators are poor agents for biological control, primarily due to mutual interference. However field evidence shows they are actually quite effective in regulating pest densities. In this work we provide a plausible answer to this paradox. We analyze a three species model, where a generalist top predator is introduced into an ecosystem as a biological control, to check the population of a middle predator, that in turn is depredating on a prey species. We show that the inclusion of predator interference alone, can cause the solution of the top predator equation to blow-up in finite time, while there is global existence in the no interference case. This result shows that interference could actually cause a population explosion of the top predator, enabling it to control the target species, thus corroborating recent field evidence. Our results might also partially explain the population explosion of certain species, introduced originally for biological control purposes, such as the cane toad (Bufo marinus) in Australia, which now functions as a generalist top predator. We also show both Turing instability and spatio-temporal chaos in the model. Lastly we investigate time delay effects.

Weeds of Hawaii’s lands devoted to watershed protection and biodiversity conservation: Role of biological control as the missing piece in an integrated pest management strategy

USGS Publications Warehouse

Medeiros, Arthur C.; Loope, L.L.

2011-01-01

Despite Hawaii’s reputation as an extinction icon, significant biological resources remain, especially in watersheds, natural areas, and specialized edaphic sites (e.g., lava dry forest, coastal). While direct habitat destruction by humans continues, human-facilitated biological invaders are currently the primary agents of continuing degradation. The ability of invasive plants to have prolific seed production, efficient dispersal systems, and to become established in dense vegetation, complicated by Hawaii’s rugged topography, appears to render mechanical and chemical control as mere holding actions. Costly, ‘environmentally unfriendly’, and often ineffective, strategies using chemical and mechanical control on a large scale, despite the most valiant of efforts, can be viewed simply as attempts to buy time. Without increased levels of safely tested biological control, the seemingly inevitable result is the landscape level transformation of native forests, with potentially catastrophic consequences to cultural, biological, water, and economic resources. Increased levels of effective biological control for certain intractable invasive species appear to comprise a conspicuous ‘missing piece’ in our efforts to protect Hawaiian watersheds and other conservation lands.

Biological Control of Olive Fruit Fly

USDA-ARS?s Scientific Manuscript database

Domestication of olive fruit, Olea europaea L., produced a better host for olive fruit fly, Bactrocera oleae (Gmelin), than wild olives, but fruit domestication reduced natural enemy efficiency. Important factors for selection of natural enemies for control of olive fruit fly include climate matchi...

Is the efficacy of biological control against plant diseases likely to be more durable than that of chemical pesticides?

PubMed Central

Bardin, Marc; Ajouz, Sakhr; Comby, Morgane; Lopez-Ferber, Miguel; Graillot, Benoît; Siegwart, Myriam; Nicot, Philippe C.

2015-01-01

The durability of a control method for plant protection is defined as the persistence of its efficacy in space and time. It depends on (i) the selection pressure exerted by it on populations of plant pathogens and (ii) on the capacity of these pathogens to adapt to the control method. Erosion of effectiveness of conventional plant protection methods has been widely studied in the past. For example, apparition of resistance to chemical pesticides in plant pathogens or pests has been extensively documented. The durability of biological control has often been assumed to be higher than that of chemical control. Results concerning pest management in agricultural systems have shown that this assumption may not always be justified. Resistance of various pests to one or several toxins of Bacillus thuringiensis and apparition of resistance of the codling moth Cydia pomonella to the C. pomonella granulovirus have, for example, been described. In contrast with the situation for pests, the durability of biological control of plant diseases has hardly been studied and no scientific reports proving the loss of efficiency of biological control agents against plant pathogens in practice has been published so far. Knowledge concerning the possible erosion of effectiveness of biological control is essential to ensure a durable efficacy of biological control agents on target plant pathogens. This knowledge will result in identifying risk factors that can foster the selection of strains of plant pathogens resistant to biological control agents. It will also result in identifying types of biological control agents with lower risk of efficacy loss, i.e., modes of action of biological control agents that does not favor the selection of resistant isolates in natural populations of plant pathogens. An analysis of the scientific literature was then conducted to assess the potential for plant pathogens to become resistant to biological control agents. PMID:26284088

Environmental Technology Verification: Supplement to Test/QA Plan for Biological and Aerosol Testing of General Ventilation Air Cleaners; Bioaerosol Inactivation Efficiency by HVAC In-Duct Ultraviolet Light Air Cleaners

EPA Science Inventory

The Air Pollution Control Technology Verification Center has selected general ventilation air cleaners as a technology area. The Generic Verification Protocol for Biological and Aerosol Testing of General Ventilation Air Cleaners is on the Environmental Technology Verification we...

Stepwise flow diagram for the development of formulations of non spore-forming bacteria against foliar pathogens: The case of Lysobacter capsici AZ78.

PubMed

Segarra, Guillem; Puopolo, Gerardo; Giovannini, Oscar; Pertot, Ilaria

2015-12-20

The formulation is a significant step in biopesticide development and is an efficient way to obtain consistency in terms of biological control under field conditions. Nonetheless, there is still a lack of information regarding the processes needed to achieve efficient formulation of non spore-forming bacterial biological control agents. In response to this, we propose a flow diagram made up of six steps including selection of growth parameters, checking of minimum shelf life, selection of protective additives, checking that the additives have no adverse effects, validation of the additive mix under field conditions and choosing whether to use additives as co-formulants or tank mix additives. This diagram is intended to provide guidance and decision-making criteria for the formulation of non spore-forming bacterial biological control agents against foliar pathogens. The diagram was then validated by designing an efficient formulation for a Gram-negative bacterium, Lysobacter capsici AZ78, to control grapevine downy mildew caused by Plasmopara viticola. A harvest of 10(10)L. capsici AZ78cellsml(-1) was obtained in a bench top fermenter. The viability of cells decreased by only one order of magnitude after one year of storage at 4°C. The use of a combination of corn steep liquor, lignosulfonate, and polyethyleneglycol in the formulation improved the survival of L. capsici AZ78 cells living on grapevine leaves under field conditions by one order of magnitude. Furthermore, the use of these additives also guaranteed a reduction of 71% in P. viticola attacks. In conclusion, this work presents a straightforward stepwise flow diagram to help researchers develop formulations for biological control agents that are easy to prepare, stable, not phytotoxic and able to protect the microorganims under field conditions. Copyright © 2015 Elsevier B.V. All rights reserved.

Application of vascular aquatic plants for pollution removal, energy and food production in a biological system

NASA Technical Reports Server (NTRS)

Wolverton, B. C.; Barlow, R. M.; Mcdonald, R. C.

1975-01-01

Vascular aquatic plants such as water hyacinths (Eichhornia crassipes) (Mart.) Solms and alligator weeds (Alternanthera philoxeroides) (Mart.) Griesb., when utilized in a controlled biological system (including a regular program of harvesting to achieve maximum growth and pollution removal efficiency), may represent a remarkably efficient and inexpensive filtration and disposal system for toxic materials and sewage released into waters near urban and industrial areas. The harvested and processed plant materials are sources of energy, fertilizer, animal feed, and human food. Such a system has industrial, municipal, and agricultural applications.

Application of vascular aquatic plants for pollution removal, energy, and food production in a biological system

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

Wolverton, B.C.; Barlow, R.M.; Mcdonald, R.C.

1975-05-12

Vascular aquatic plants such as water hyacinths (Eichhornia crassipes) (Mart.) Solms and alligator weeds (Alternanthera philoxeroides) (Mart.) Griesb., when utilized in a controlled biological system (including a regular program of harvesting to achieve maximum growth and pollution removal efficiency), may represent a remarkably efficient and inexpensive filtration and disposal system for toxic materials and sewage released into waters near urban and industrial areas. The harvested and processed plant materials are sources of energy, fertilizer, animal feed, and human food. Such a system has industrial, municipal, and agricultural applications. (Author) (GRA)

Combination of bioremediation and electrokinetics for the in-situ treatment of diesel polluted soil: A comparison of strategies.

PubMed

Mena Ramírez, Esperanza; Villaseñor Camacho, José; Rodrigo, Manuel A; Cañizares, Pablo

2015-11-15

The aim of this work is to compare different strategies based on electrokinetic soil flushing and bioremediation for the remediation of diesel-polluted soil. Four options were tested at the laboratory scale: single bioremediation (Bio), performed as a control test; a direct combination of electrokinetic soil flushing and biological technologies (EKSF-Bio); EKSF-Bio with daily polarity reversal of the electric field (PR-EKSF-Bio); and a combination of electrokinetic soil flushing and a permeable reactive biological barrier (EKSF-BioPRB). Four batch experiments of 14 days duration were carried out for comparing technologies at room temperature with an electric field of 1.0 V cm(-1) (in EKSF). A diesel degrading microbial consortium was used. The experimental procedure and some specific details, such as the flushing fluids used, varied depending on the strategy. When using the EKSF-Bio option, a high buffer concentration was required to control the pH, causing soil heating, which negatively affected the biological growth and thus the diesel removal. The PR-EKSF-Bio and the EKSF-BioPRB options attained suitable operating conditions and improved the transport processes for biological growth. Polarity reversal was an efficient option for pH, moisture and temperature control. Homogeneous microbial growth was observed, and approximately 20% of the diesel was removed. The BioPRB option was not as efficient as PR-EKSF-Bio in controlling the operating conditions, but the central biobarrier protected the biological activity. Microbial growth was observed not only in the biobarrier but also in a large portion of the soil, and 29% of the diesel was removed in the short remediation test. Copyright © 2015 Elsevier B.V. All rights reserved.

Neuromodulation and Synaptic Plasticity for the Control of Fast Periodic Movement: Energy Efficiency in Coupled Compliant Joints via PCA.

PubMed

Stratmann, Philipp; Lakatos, Dominic; Albu-Schäffer, Alin

2016-01-01

There are multiple indications that the nervous system of animals tunes muscle output to exploit natural dynamics of the elastic locomotor system and the environment. This is an advantageous strategy especially in fast periodic movements, since the elastic elements store energy and increase energy efficiency and movement speed. Experimental evidence suggests that coordination among joints involves proprioceptive input and neuromodulatory influence originating in the brain stem. However, the neural strategies underlying the coordination of fast periodic movements remain poorly understood. Based on robotics control theory, we suggest that the nervous system implements a mechanism to accomplish coordination between joints by a linear coordinate transformation from the multi-dimensional space representing proprioceptive input at the joint level into a one-dimensional controller space. In this one-dimensional subspace, the movements of a whole limb can be driven by a single oscillating unit as simple as a reflex interneuron. The output of the oscillating unit is transformed back to joint space via the same transformation. The transformation weights correspond to the dominant principal component of the movement. In this study, we propose a biologically plausible neural network to exemplify that the central nervous system (CNS) may encode our controller design. Using theoretical considerations and computer simulations, we demonstrate that spike-timing-dependent plasticity (STDP) for the input mapping and serotonergic neuromodulation for the output mapping can extract the dominant principal component of sensory signals. Our simulations show that our network can reliably control mechanical systems of different complexity and increase the energy efficiency of ongoing cyclic movements. The proposed network is simple and consistent with previous biologic experiments. Thus, our controller could serve as a candidate to describe the neural control of fast, energy-efficient, periodic movements involving multiple coupled joints.

Neuromodulation and Synaptic Plasticity for the Control of Fast Periodic Movement: Energy Efficiency in Coupled Compliant Joints via PCA

PubMed Central

Stratmann, Philipp; Lakatos, Dominic; Albu-Schäffer, Alin

2016-01-01

There are multiple indications that the nervous system of animals tunes muscle output to exploit natural dynamics of the elastic locomotor system and the environment. This is an advantageous strategy especially in fast periodic movements, since the elastic elements store energy and increase energy efficiency and movement speed. Experimental evidence suggests that coordination among joints involves proprioceptive input and neuromodulatory influence originating in the brain stem. However, the neural strategies underlying the coordination of fast periodic movements remain poorly understood. Based on robotics control theory, we suggest that the nervous system implements a mechanism to accomplish coordination between joints by a linear coordinate transformation from the multi-dimensional space representing proprioceptive input at the joint level into a one-dimensional controller space. In this one-dimensional subspace, the movements of a whole limb can be driven by a single oscillating unit as simple as a reflex interneuron. The output of the oscillating unit is transformed back to joint space via the same transformation. The transformation weights correspond to the dominant principal component of the movement. In this study, we propose a biologically plausible neural network to exemplify that the central nervous system (CNS) may encode our controller design. Using theoretical considerations and computer simulations, we demonstrate that spike-timing-dependent plasticity (STDP) for the input mapping and serotonergic neuromodulation for the output mapping can extract the dominant principal component of sensory signals. Our simulations show that our network can reliably control mechanical systems of different complexity and increase the energy efficiency of ongoing cyclic movements. The proposed network is simple and consistent with previous biologic experiments. Thus, our controller could serve as a candidate to describe the neural control of fast, energy-efficient, periodic movements involving multiple coupled joints. PMID:27014051

Programming Light-Harvesting Efficiency Using DNA Origami

PubMed Central

2016-01-01

The remarkable performance and quantum efficiency of biological light-harvesting complexes has prompted a multidisciplinary interest in engineering biologically inspired antenna systems as a possible route to novel solar cell technologies. Key to the effectiveness of biological “nanomachines” in light capture and energy transport is their highly ordered nanoscale architecture of photoactive molecules. Recently, DNA origami has emerged as a powerful tool for organizing multiple chromophores with base-pair accuracy and full geometric freedom. Here, we present a programmable antenna array on a DNA origami platform that enables the implementation of rationally designed antenna structures. We systematically analyze the light-harvesting efficiency with respect to number of donors and interdye distances of a ring-like antenna using ensemble and single-molecule fluorescence spectroscopy and detailed Förster modeling. This comprehensive study demonstrates exquisite and reliable structural control over multichromophoric geometries and points to DNA origami as highly versatile platform for testing design concepts in artificial light-harvesting networks. PMID:26906456

Modifying the 5'-Cap for Click Reactions of Eukaryotic mRNA and To Tune Translation Efficiency in Living Cells.

PubMed

Holstein, Josephin M; Anhäuser, Lea; Rentmeister, Andrea

2016-08-26

The 5'-cap is a hallmark of eukaryotic mRNAs and plays fundamental roles in RNA metabolism, ranging from quality control to export and translation. Modifying the 5'-cap may thus enable modulation of the underlying processes and investigation or tuning of several biological functions. A straightforward approach is presented for the efficient production of a range of N7-modified caps based on the highly promiscuous methyltransferase Ecm1. We show that these, as well as N(2) -modified 5'-caps, can be used to tune translation of the respective mRNAs both in vitro and in cells. Appropriate modifications allow subsequent bioorthogonal chemistry, as demonstrated by intracellular live-cell labeling of a target mRNA. The efficient and versatile N7 manipulation of the mRNA cap makes mRNAs amenable to both modulation of their biological function and intracellular labeling, and represents a valuable addition to the chemical biology toolbox. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficient high-throughput biological process characterization: Definitive screening design with the ambr250 bioreactor system.

PubMed

Tai, Mitchell; Ly, Amanda; Leung, Inne; Nayar, Gautam

2015-01-01

The burgeoning pipeline for new biologic drugs has increased the need for high-throughput process characterization to efficiently use process development resources. Breakthroughs in highly automated and parallelized upstream process development have led to technologies such as the 250-mL automated mini bioreactor (ambr250™) system. Furthermore, developments in modern design of experiments (DoE) have promoted the use of definitive screening design (DSD) as an efficient method to combine factor screening and characterization. Here we utilize the 24-bioreactor ambr250™ system with 10-factor DSD to demonstrate a systematic experimental workflow to efficiently characterize an Escherichia coli (E. coli) fermentation process for recombinant protein production. The generated process model is further validated by laboratory-scale experiments and shows how the strategy is useful for quality by design (QbD) approaches to control strategies for late-stage characterization. © 2015 American Institute of Chemical Engineers.

Bio-Defense Now: 56 Suggestions for Immediate Improvements

DTIC Science & Technology

2005-05-01

Air Education and Training Command HVAC Heating, Ventilation and Air Conditioning ICAM Improved Chemical Agent Monitor ICD-9-CM Internal...conditioning ( HVAC ) system capabilities, making a big difference in removal of many BW agents. High Efficiency Particulate Air (HEPA) filters are also...agents. This program has developed biological sensor-activated heating, ventilation, and air conditioning ( HVAC ) control sys- tems, high efficiency

Bioengineering approaches to controlled protein delivery.

PubMed

Kobsa, Serge; Saltzman, W Mark

2008-05-01

Proteins are of crucial importance in all biologic organisms, in terms of both structure and function. Their deficits play central roles in many pathologic states, and their potential as powerful therapeutic agents has been widely recognized. Many issues, however, exist in delivery of biologically active proteins to target tissues and organs. Recent advances in biomedical engineering have lead to development of advanced techniques for controlled delivery of peptides and proteins, paving the way for their efficient use in treating human injury and disease. With a particular emphasis on most recent advances, this review discusses currently available techniques for controlled delivery of proteins and considers future research directions.

Agent-Based Models and Optimal Control in Biology: A Discrete Approach

DTIC Science & Technology

2012-01-01

different parts of the human body to cure diseases such as hypertension, cancer, or heart disease. And we need to control microbes for the efficient...antelope herd interacts with an aggregated prey agent such as cheetahs or lions, the size of each may expand or contract accordingly). Of course, such

Evidence-based economic analysis demonstrates that ecosystem service benefits of water hyacinth management greatly exceed research and control costs

PubMed Central

Harms, Nathan E.; Magen, Cedric; Liang, Dong; Nesslage, Genevieve M.; McMurray, Anna M.; Cofrancesco, Al F.

2018-01-01

Invasive species management can be a victim of its own success when decades of effective control cause memories of past harm to fade and raise questions of whether programs should continue. Economic analysis can be used to assess the efficiency of investing in invasive species control by comparing ecosystem service benefits to program costs, but only if appropriate data exist. We used a case study of water hyacinth (Eichhornia crassipes (Mart.) Solms), a nuisance floating aquatic plant, in Louisiana to demonstrate how comprehensive record-keeping supports economic analysis. Using long-term data sets, we developed empirical and spatio-temporal simulation models of intermediate complexity to project invasive species growth for control and no-control scenarios. For Louisiana, we estimated that peak plant cover would be 76% higher without the substantial growth rate suppression (84% reduction) that appeared due primarily to biological control agents. Our economic analysis revealed that combined biological and herbicide control programs, monitored over an unusually long time period (1975–2013), generated a benefit-cost ratio of about 34:1 derived from the relatively modest costs of $124 million ($2013) compared to the $4.2 billion ($2013) in benefits to anglers, waterfowl hunters, boating-dependent businesses, and water treatment facilities over the 38-year analysis period. This work adds to the literature by: (1) providing evidence of the effectiveness of water hyacinth biological control; (2) demonstrating use of parsimonious spatio-temporal models to estimate benefits of invasive species control; and (3) incorporating activity substitution into economic benefit transfer to avoid overstating benefits. Our study suggests that robust and cost-effective economic analysis is enabled by good record keeping and generalizable models that can demonstrate management effectiveness and promote social efficiency of invasive species control. PMID:29844976

Evidence-based economic analysis demonstrates that ecosystem service benefits of water hyacinth management greatly exceed research and control costs.

PubMed

Wainger, Lisa A; Harms, Nathan E; Magen, Cedric; Liang, Dong; Nesslage, Genevieve M; McMurray, Anna M; Cofrancesco, Al F

2018-01-01

Invasive species management can be a victim of its own success when decades of effective control cause memories of past harm to fade and raise questions of whether programs should continue. Economic analysis can be used to assess the efficiency of investing in invasive species control by comparing ecosystem service benefits to program costs, but only if appropriate data exist. We used a case study of water hyacinth ( Eichhornia crassipes (Mart.) Solms), a nuisance floating aquatic plant, in Louisiana to demonstrate how comprehensive record-keeping supports economic analysis. Using long-term data sets, we developed empirical and spatio-temporal simulation models of intermediate complexity to project invasive species growth for control and no-control scenarios. For Louisiana, we estimated that peak plant cover would be 76% higher without the substantial growth rate suppression (84% reduction) that appeared due primarily to biological control agents. Our economic analysis revealed that combined biological and herbicide control programs, monitored over an unusually long time period (1975-2013), generated a benefit-cost ratio of about 34:1 derived from the relatively modest costs of $124 million ($2013) compared to the $4.2 billion ($2013) in benefits to anglers, waterfowl hunters, boating-dependent businesses, and water treatment facilities over the 38-year analysis period. This work adds to the literature by: (1) providing evidence of the effectiveness of water hyacinth biological control; (2) demonstrating use of parsimonious spatio-temporal models to estimate benefits of invasive species control; and (3) incorporating activity substitution into economic benefit transfer to avoid overstating benefits. Our study suggests that robust and cost-effective economic analysis is enabled by good record keeping and generalizable models that can demonstrate management effectiveness and promote social efficiency of invasive species control.

Evaluation of a novel oxidation ditch system for biological nitrogen and phosphorus removal from domestic sewage.

PubMed

Chen, X; Fujiwara, T; Ohtoshi, K; Inamori, S; Nakamachi, K; Tsuno, H

2010-01-01

A novel oxidation ditch system using anaerobic tanks and innovative dual dissolved oxygen (DO) control technology is proposed for biological nitrogen and phosphorus removal from domestic sewage. A continuous bench-scale experiment running for more than 300 days was performed to evaluate the system. Monitoring and controlling the airflow and recirculation flow rate independently using DO values at two points along the ditch permitted maintenance of aerobic and anoxic zone ratios of around 0.30 and 0.50, respectively. The ability to optimize aerobic and anoxic zone ratios using the dual DO control technology meant that a total nitrogen removal efficiency of 83.2-92.9% could be maintained. This remarkable nitrogen removal performance minimized the nitrate recycle to anaerobic tanks inhibiting the phosphorus release. Hence, the total phosphorus removal efficiency was also improved and ranged within 72.6-88.0%. These results demonstrated that stabilization of the aerobic and anoxic zone ratio by dual DO control technology not only resulted in a marked improvement of nitrogen removal, but it also enhanced phosphorus removal.

Risk assessment paradigm: an opportunity for rationalizing the choice of biological indicator during the validation of isolator biodecontamination cycles.

PubMed

Sansoë-Bourget, Emmanuelle

2006-01-01

The use of biological indicators is integral to the validation of isolator decontamination cycles. The difficulty in setting up the initial qualification of the decontamination cycle and especially the successive requalifications may vary as a function of not only the installation to be qualified and the sterilizing agent and generator used, but also as a function of the type of biological indicators used. In this article the manufacture and control of biological indicators are analyzed using the hazard analysis and critical control point (HACCP) approach. The HACCP risk analysis, which must take into account the application of the isolator being qualified or requalified, is an efficient simplification tool for performing a decontamination cycle using either hydrogen peroxide gas or peracetic acid in a reliable, economical, and reproducible way.

7 CFR 520.2 - Definition.

Code of Federal Regulations, 2014 CFR

2014-01-01

... AGRICULTURE PROCEDURES FOR IMPLEMENTING NATIONAL ENVIRONMENTAL POLICY ACT § 520.2 Definition. Control Agents mean biological material or chemicals which are intended to enhance the production efficiency of an agricultural crop or animal such as through elimination of a pest. ...

7 CFR 520.2 - Definition.

Code of Federal Regulations, 2012 CFR

2012-01-01

... AGRICULTURE PROCEDURES FOR IMPLEMENTING NATIONAL ENVIRONMENTAL POLICY ACT § 520.2 Definition. Control Agents mean biological material or chemicals which are intended to enhance the production efficiency of an agricultural crop or animal such as through elimination of a pest. ...

7 CFR 520.2 - Definition.

Code of Federal Regulations, 2011 CFR

2011-01-01

... AGRICULTURE PROCEDURES FOR IMPLEMENTING NATIONAL ENVIRONMENTAL POLICY ACT § 520.2 Definition. Control Agents mean biological material or chemicals which are intended to enhance the production efficiency of an agricultural crop or animal such as through elimination of a pest. ...

7 CFR 520.2 - Definition.

Code of Federal Regulations, 2013 CFR

2013-01-01

... AGRICULTURE PROCEDURES FOR IMPLEMENTING NATIONAL ENVIRONMENTAL POLICY ACT § 520.2 Definition. Control Agents mean biological material or chemicals which are intended to enhance the production efficiency of an agricultural crop or animal such as through elimination of a pest. ...

7 CFR 520.2 - Definition.

Code of Federal Regulations, 2010 CFR

2010-01-01

... AGRICULTURE PROCEDURES FOR IMPLEMENTING NATIONAL ENVIRONMENTAL POLICY ACT § 520.2 Definition. Control Agents mean biological material or chemicals which are intended to enhance the production efficiency of an agricultural crop or animal such as through elimination of a pest. ...

Metal-Ion-Mediated Supramolecular Chirality of l-Phenylalanine Based Hydrogels.

PubMed

Wang, Fang; Feng, Chuan-Liang

2018-05-14

For chiral hydrogels and related applications, one of the critical issues is how to control the chirality of supramolecular systems in an efficient way, including easy operation, efficient transfer of chirality, and so on. Herein, supramolecular chirality of l-phenylalanine based hydrogels can be effectively controlled by using a broad range of metal ions. The degree of twisting (twist pitch) and the diameter of the chiral nanostructures can also be efficiently regulated. These are ascribed to the synergic effect of hydrogen bonding and metal ion coordination. This study may develop a method to design a new class of electronically, optically, and biologically active materials. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

PubMed

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

2017-03-01

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

DNA codes for nanoscience.

PubMed

Samorì, Bruno; Zuccheri, Giampaolo

2005-02-11

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

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

PubMed

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

2013-10-15

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

The Next Generation of Synthetic Biology Chassis: Moving Synthetic Biology from the Laboratory to the Field

DTIC Science & Technology

2016-09-26

toolkit of additional promoters, RBS, and proteolysis tags to control gene expression at the transcrip- tional, translational, and protein levels. CRISPR ...synthetic promoters, high efficiency RBS, and terminators. Furthermore, the CRISPR -Cas system has been investigated for one cyanobacteria species,10 which...Development of a CRISPR -Cas9 toolkit for comprehensive engineer- ing of Bacillus subtilis. Appl. Environ. Microbiol. 82, 01159−01116. (9) Hussein, A. H

Genetic mitigation strategies to tackle agricultural GHG emissions: The case for biological nitrification inhibition technology.

PubMed

Subbarao, G V; Arango, J; Masahiro, K; Hooper, A M; Yoshihashi, T; Ando, Y; Nakahara, K; Deshpande, S; Ortiz-Monasterio, I; Ishitani, M; Peters, M; Chirinda, N; Wollenberg, L; Lata, J C; Gerard, B; Tobita, S; Rao, I M; Braun, H J; Kommerell, V; Tohme, J; Iwanaga, M

2017-09-01

Accelerated soil-nitrifier activity and rapid nitrification are the cause of declining nitrogen-use efficiency (NUE) and enhanced nitrous oxide (N 2 O) emissions from farming. Biological nitrification inhibition (BNI) is the ability of certain plant roots to suppress soil-nitrifier activity, through production and release of nitrification inhibitors. The power of phytochemicals with BNI-function needs to be harnessed to control soil-nitrifier activity and improve nitrogen-cycling in agricultural systems. Transformative biological technologies designed for genetic mitigation are needed, so that BNI-enabled crop-livestock and cropping systems can rein in soil-nitrifier activity, to help reduce greenhouse gas (GHG) emissions and globally make farming nitrogen efficient and less harmful to environment. This will reinforce the adaptation or mitigation impact of other climate-smart agriculture technologies. Copyright © 2017 Elsevier B.V. All rights reserved.

Marine and maritime uses

NASA Technical Reports Server (NTRS)

1975-01-01

Activities related to: (1) understanding, controlling, and using the ocean's biological and physical processes for food and energy production and ship design purposes, and (2) providing navigation, communication, and data transmission technological aids which improve efficiency and enhance safety in maritime operations are disclosed.

Genome-wide association and pathway analysis of feed efficiency in pigs reveal candidate genes and pathways for residual feed intake

PubMed Central

Do, Duy N.; Strathe, Anders B.; Ostersen, Tage; Pant, Sameer D.; Kadarmideen, Haja N.

2014-01-01

Residual feed intake (RFI) is a complex trait that is economically important for livestock production; however, the genetic and biological mechanisms regulating RFI are largely unknown in pigs. Therefore, the study aimed to identify single nucleotide polymorphisms (SNPs), candidate genes and biological pathways involved in regulating RFI using Genome-wide association (GWA) and pathway analyses. A total of 596 Yorkshire boars with phenotypes for two different measures of RFI (RFI1 and 2) and 60k genotypic data was used. GWA analysis was performed using a univariate mixed model and 12 and 7 SNPs were found to be significantly associated with RFI1 and RFI2, respectively. Several genes such as xin actin-binding repeat-containing protein 2 (XIRP2),tetratricopeptide repeat domain 29 (TTC29),suppressor of glucose, autophagy associated 1 (SOGA1),MAS1,G-protein-coupled receptor (GPCR) kinase 5 (GRK5),prospero-homeobox protein 1 (PROX1),GPCR 155 (GPR155), and FYVE domain containing the 26 (ZFYVE26) were identified as putative candidates for RFI based on their genomic location in the vicinity of these SNPs. Genes located within 50 kbp of SNPs significantly associated with RFI and RFI2 (q-value ≤ 0.2) were subsequently used for pathway analyses. These analyses were performed by assigning genes to biological pathways and then testing the association of individual pathways with RFI using a Fisher’s exact test. Metabolic pathway was significantly associated with both RFIs. Other biological pathways regulating phagosome, tight junctions, olfactory transduction, and insulin secretion were significantly associated with both RFI traits when relaxed threshold for cut-off p-value was used (p ≤ 0.05). These results implied porcine RFI is regulated by multiple biological mechanisms, although the metabolic processes might be the most important. Olfactory transduction pathway controlling the perception of feed via smell, insulin pathway controlling food intake might be important pathways for RFI. Furthermore, our study revealed key genes and genetic variants that control feed efficiency that could potentially be useful for genetic selection of more feed efficient pigs. PMID:25250046

Forward to the past

PubMed Central

Carlini, Alessandro; Actis-Grosso, Rossana; Stucchi, Natale; Pozzo, Thierry

2012-01-01

Our daily experience shows that the CNS is a highly efficient machine to predict the effect of actions into the future; are we so efficient also in reconstructing the past of an action? Previous studies demonstrated we are more effective in extrapolating the final position of a stimulus moving according to biological kinematic laws. Here we address the complementary question: are we more effective in extrapolating the starting position (SP) of a motion following a biological velocity profile? We presented a dot moving upward and corresponding to vertical arm movements that were masked in the first part of the trajectory. The stimulus could either move according to biological or non-biological kinematic laws of motion. Results show a better efficacy in reconstructing the SP of a natural motion: participants demonstrate to reconstruct coherently only the SP of the biological condition. When the motion violates the biological kinematic law, responses are scattered and show a tendency toward larger errors. Instead, in a control experiment where the full motions were displayed, no-difference between biological and non-biological motions is found. Results are discussed in light of potential mechanisms involved in visual inference. We propose that as soon as the target appears the cortical motor area would generate an internal representation of reaching movement. When the visual input and the stored kinematic template match, the SP is traced back on the basis of this memory template, making more effective the SP reconstruction. PMID:22712012

Salt marsh vegetation promotes efficient tidal channel networks

PubMed Central

Kearney, William S.; Fagherazzi, Sergio

2016-01-01

Tidal channel networks mediate the exchange of water, nutrients and sediment between an estuary and marshes. Biology feeds back into channel morphodynamics through the influence of vegetation on both flow and the cohesive strength of channel banks. Determining how vegetation affects channel networks is essential in understanding the biological functioning of intertidal ecosystems and their ecosystem services. However, the processes that control the formation of an efficient tidal channel network remain unclear. Here we compare the channel networks of vegetated salt marshes in Massachusetts and the Venice Lagoon to unvegetated systems in the arid environments of the Gulf of California and Yemen. We find that the unvegetated systems are dissected by less efficient channel networks than the vegetated salt marshes. These differences in network geometry reflect differences in the branching and meandering of the channels in the network, characteristics that are related to the density of vegetation on the marsh. PMID:27430165

Technology development for lunar base water recycling

NASA Technical Reports Server (NTRS)

Schultz, John R.; Sauer, Richard L.

1992-01-01

This paper will review previous and ongoing work in aerospace water recycling and identify research activities required to support development of a lunar base. The development of a water recycle system for use in the life support systems envisioned for a lunar base will require considerable research work. A review of previous work on aerospace water recycle systems indicates that more efficient physical and chemical processes are needed to reduce expendable and power requirements. Development work on biological processes that can be applied to microgravity and lunar environments also needs to be initiated. Biological processes are inherently more efficient than physical and chemical processes and may be used to minimize resupply and waste disposal requirements. Processes for recovering and recycling nutrients such as nitrogen, phosphorus, and sulfur also need to be developed to support plant growth units. The development of efficient water quality monitors to be used for process control and environmental monitoring also needs to be initiated.

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

PubMed

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

2015-10-01

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

Computational Modeling in Concert with Laboratory Studies: Application to B Cell Differentiation

EPA Science Inventory

Remediation is expensive, so accurate prediction of dose-response is important to help control costs. Dose response is a function of biological mechanisms. Computational models of these mechanisms improve the efficiency of research and provide the capability for prediction.

Population dynamics in controlled unsteady-state systems: An application to the degradation of glyphosate in a sequencing batch reactor

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

Devarakonda, M.S.

1988-01-01

Control over population dynamics and organism selection in a biological waste treatment system provides an effective means of engineering process efficiency. Examples of applications of organism selection include control of filamentous organisms, biological nutrient removal, industrial waste treatment requiring the removal of specific substrates, and hazardous waste treatment. Inherently, full scale biological waste treatment systems are unsteady state systems due to the variations in the waste streams and mass flow rates of the substrates. Some systems, however, have the capacity to impose controlled selective pressures on the biological population by means of their operation. An example of such a systemmore » is the Sequencing Batch Reactor (SBR) which was the experimental system utilized in this research work. The concepts of organism selection were studied in detail for the biodegradation of a herbicide waste stream, with glyphosate as the target compound. The SBR provided a reactor configuration capable of exerting the necessary selective pressures to select and enrich for a glyphosate degrading population. Based on results for bench scale SBRs, a hypothesis was developed to explain population dynamics in glyphosate degrading systems.« less

A Keystone Ant Species Provides Robust Biological Control of the Coffee Berry Borer Under Varying Pest Densities.

PubMed

Morris, Jonathan R; Vandermeer, John; Perfecto, Ivette

2015-01-01

Species' functional traits are an important part of the ecological complexity that determines the provisioning of ecosystem services. In biological pest control, predator response to pest density variation is a dynamic trait that impacts the provision of this service in agroecosystems. When pest populations fluctuate, farmers relying on biocontrol services need to know how natural enemies respond to these changes. Here we test the effect of variation in coffee berry borer (CBB) density on the biocontrol efficiency of a keystone ant species (Azteca sericeasur) in a coffee agroecosystem. We performed exclosure experiments to measure the infestation rate of CBB released on coffee branches in the presence and absence of ants at four different CBB density levels. We measured infestation rate as the number of CBB bored into fruits after 24 hours, quantified biocontrol efficiency (BCE) as the proportion of infesting CBB removed by ants, and estimated functional response from ant attack rates, measured as the difference in CBB infestation between branches. Infestation rates of CBB on branches with ants were significantly lower (71%-82%) than on those without ants across all density levels. Additionally, biocontrol efficiency was generally high and did not significantly vary across pest density treatments. Furthermore, ant attack rates increased linearly with increasing CBB density, suggesting a Type I functional response. These results demonstrate that ants can provide robust biological control of CBB, despite variation in pest density, and that the response of predators to pest density variation is an important factor in the provision of biocontrol services. Considering how natural enemies respond to changes in pest densities will allow for more accurate biocontrol predictions and better-informed management of this ecosystem service in agroecosystems.

A Keystone Ant Species Provides Robust Biological Control of the Coffee Berry Borer Under Varying Pest Densities

PubMed Central

Morris, Jonathan R.; Vandermeer, John; Perfecto, Ivette

2015-01-01

Species’ functional traits are an important part of the ecological complexity that determines the provisioning of ecosystem services. In biological pest control, predator response to pest density variation is a dynamic trait that impacts the provision of this service in agroecosystems. When pest populations fluctuate, farmers relying on biocontrol services need to know how natural enemies respond to these changes. Here we test the effect of variation in coffee berry borer (CBB) density on the biocontrol efficiency of a keystone ant species (Azteca sericeasur) in a coffee agroecosystem. We performed exclosure experiments to measure the infestation rate of CBB released on coffee branches in the presence and absence of ants at four different CBB density levels. We measured infestation rate as the number of CBB bored into fruits after 24 hours, quantified biocontrol efficiency (BCE) as the proportion of infesting CBB removed by ants, and estimated functional response from ant attack rates, measured as the difference in CBB infestation between branches. Infestation rates of CBB on branches with ants were significantly lower (71%-82%) than on those without ants across all density levels. Additionally, biocontrol efficiency was generally high and did not significantly vary across pest density treatments. Furthermore, ant attack rates increased linearly with increasing CBB density, suggesting a Type I functional response. These results demonstrate that ants can provide robust biological control of CBB, despite variation in pest density, and that the response of predators to pest density variation is an important factor in the provision of biocontrol services. Considering how natural enemies respond to changes in pest densities will allow for more accurate biocontrol predictions and better-informed management of this ecosystem service in agroecosystems. PMID:26562676

Effects of predation efficiencies on the dynamics of a tritrophic food chain.

PubMed

Cassinari, Maria Paola; Groppi, Maria; Tebaldi, Claudio

2007-07-01

In this paper the dynamics of a tritrophic food chain (resource, consumer, top predator) is investigated, with particular attention not only to equilibrium states but also to cyclic behaviours that the system may exhibit. The analysis is performed in terms of two bifurcation parameters, denoted by p and q, which measure the efficiencies of the interaction processes. The persistence of the system is discussed, characterizing in the (p; q) plane the regions of existence and stability of biologically significant steady states and those of existence of limit cycles. The bifurcations occurring are discussed, and their implications with reference to biological control problems are considered. Examples of the rich dynamics exhibited by the model, including a chaotic regime, are described.

Mechanical properties of porous and cellular materials

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

Sieradzki, K.; Green, D.J.; Gibson, L.J.

1991-01-01

This symposium successfully brought scientists together from a wide variety of disciplines to focus on the mechanical behavior of porous and cellular solids composed of metals, ceramics, polymers, or biological materials. For cellular materials, papers ranged from processing techniques through microstructure-mechanical property relationships to design. In an overview talk, Mike Ashby (Cambridge Univ.) showed how porous cellular materials can be more efficient than dense materials in designs that require minimum weight. He indicated that many biological materials have been able to accomplish such efficiency but there exists an opportunity to design even more efficient, manmade materials controlling microstructures at differentmore » scale levels. In the area of processing, James Aubert (Sandia National Laboratories) discussed techiques for manipulating polymersolvent phase equilibria to control the microstructure of microcellular foams. Other papers on processing discussed the production of cellular ceramics by CVD, HIPing and sol- gel techniques. Papers on the mechanical behavior of cellular materials considered various ceramics microcellular polymers, conventional polymer foams and apples. There were also contributions that considered optimum design procedures for cellular materials. Steven Cowin (City Univ. of New York) discussed procedures to match the discrete microstructural aspects of cellular materials with the continuum mechanics approach to their elastic behavior.« less

Growth efficiency in transgenic tilapia (Oreochromis sp.) carrying a single copy of an homologous cDNA growth hormone.

PubMed

Martínez, R; Juncal, J; Zaldívar, C; Arenal, A; Guillén, I; Morera, V; Carrillo, O; Estrada, M; Morales, A; Estrada, M P

2000-01-07

Growth hormone (GH) has been shown to have a profound impact on fish physiology and metabolism. However, detailed studies in transgenic fish have not been conducted. We have characterized the food conversion efficiency, protein profile, and biochemical correlates of growth rate in transgenic tilapia expressing the tilapia GH cDNA under the control of human cytomegalovirus regulatory sequences. Transgenic tilapia exhibited about 3.6-fold less food consumption than nontransgenic controls (P < 0.001). The food conversion efficiency was significantly (P < 0.05) higher (290%) in transgenic tilapia (2.3 +/- 0.4) than in the control group (0.8 +/- 0.2). Efficiency of growth, synthesis retention, anabolic stimulation, and average protein synthesis were higher in transgenic than in nontransgenic tilapia. Distinctive metabolic differences were found in transgenic juvenile tilapia. We had found differences in hepatic glucose, and in agreement with previous results we observed differences in the level of enzymatic activities in target organs. We conclude that GH-transgenic juvenile tilapia show altered physiological and metabolic conditions and are biologically more efficient. Copyright 2000 Academic Press.

Removal of iron and manganese using biological roughing up flow filtration technology.

PubMed

Pacini, Virginia Alejandra; María Ingallinella, Ana; Sanguinetti, Graciela

2005-11-01

The removal of iron and manganese from groundwater using biological treatment methods is almost unknown in Latin America. Biological systems used in Europe are based on the process of double rapid biofiltration during which dissolved oxygen and pH need to be strictly controlled in order to limit abiotic iron oxidation. The performance of roughing filter technology in a biological treatment process for the removal of iron and manganese, without the use of chemical agents and under natural pH conditions was studied. Two pilot plants, using two different natural groundwaters, were operated with the following treatment line: aeration, up flow roughing filtration and final filtration (either slow or rapid). Iron and manganese removal efficiencies were found to be between 85% and 95%. The high solid retention capability of the roughing filter means that it is possible to remove iron and manganese simultaneously by biotic and abiotic mechanisms. This system combines simple, low-cost operation and maintenance with high iron and manganese removal efficiencies, thus constituting a technology which is particularly suited to small waterworks.

SNAD: Sequence Name Annotation-based Designer.

PubMed

Sidorov, Igor A; Reshetov, Denis A; Gorbalenya, Alexander E

2009-08-14

A growing diversity of biological data is tagged with unique identifiers (UIDs) associated with polynucleotides and proteins to ensure efficient computer-mediated data storage, maintenance, and processing. These identifiers, which are not informative for most people, are often substituted by biologically meaningful names in various presentations to facilitate utilization and dissemination of sequence-based knowledge. This substitution is commonly done manually that may be a tedious exercise prone to mistakes and omissions. Here we introduce SNAD (Sequence Name Annotation-based Designer) that mediates automatic conversion of sequence UIDs (associated with multiple alignment or phylogenetic tree, or supplied as plain text list) into biologically meaningful names and acronyms. This conversion is directed by precompiled or user-defined templates that exploit wealth of annotation available in cognate entries of external databases. Using examples, we demonstrate how this tool can be used to generate names for practical purposes, particularly in virology. A tool for controllable annotation-based conversion of sequence UIDs into biologically meaningful names and acronyms has been developed and placed into service, fostering links between quality of sequence annotation, and efficiency of communication and knowledge dissemination among researchers.

Characterization of dynamic droplet impaction and deposit formation on leaf surfaces

USDA-ARS?s Scientific Manuscript database

Elucidation of droplet dynamic impaction and deposition formation on leaf surfaces would assist to optimize application strategies, improve biological control efficiency, and minimize pesticide waste. A custom-designed system consisting of two high-speed digital cameras and a uniform-size droplet ge...

Biology doesn't waste energy: that's really smart

NASA Astrophysics Data System (ADS)

Vincent, Julian F. V.; Bogatyreva, Olga; Bogatyrev, Nikolaj

2006-03-01

Biology presents us with answers to design problems that we suspect would be very useful if only we could implement them successfully. We use the Russian theory of problem solving - TRIZ - in a novel way to provide a system for analysis and technology transfer. The analysis shows that whereas technology uses energy as the main means of solving technical problems, biology uses information and structure. Biology is also strongly hierarchical. The suggestion is that smart technology in hierarchical structures can help us to design much more efficient technology. TRIZ also suggests that biological design is autonomous and can be defined by the prefix "self-" with any function. This autonomy extends to the control system, so that the sensor is commonly also the actuator, resulting in simpler systems and greater reliability.

Apparatus and methods for manipulation and optimization of biological systems

NASA Technical Reports Server (NTRS)

Sun, Ren (Inventor); Ho, Chih-Ming (Inventor); Wong, Pak Kin (Inventor); Yu, Fuqu (Inventor)

2012-01-01

The invention provides systems and methods for manipulating, e.g., optimizing and controlling, biological systems, e.g., for eliciting a more desired biological response of biological sample, such as a tissue, organ, and/or a cell. In one aspect, systems and methods of the invention operate by efficiently searching through a large parametric space of stimuli and system parameters to manipulate, control, and optimize the response of biological samples sustained in the system, e.g., a bioreactor. In alternative aspects, systems include a device for sustaining cells or tissue samples, one or more actuators for stimulating the samples via biochemical, electromagnetic, thermal, mechanical, and/or optical stimulation, one or more sensors for measuring a biological response signal of the samples resulting from the stimulation of the sample. In one aspect, the systems and methods of the invention use at least one optimization algorithm to modify the actuator's control inputs for stimulation, responsive to the sensor's output of response signals. The compositions and methods of the invention can be used, e.g., to for systems optimization of any biological manufacturing or experimental system, e.g., bioreactors for proteins, e.g., therapeutic proteins, polypeptides or peptides for vaccines, and the like, small molecules (e.g., antibiotics), polysaccharides, lipids, and the like. Another use of the apparatus and methods includes combination drug therapy, e.g. optimal drug cocktail, directed cell proliferations and differentiations, e.g. in tissue engineering, e.g. neural progenitor cells differentiation, and discovery of key parameters in complex biological systems.

Native strains of Beauveria bassiana for the control of Rhipicephalus sanguineus sensu lato.

PubMed

Cafarchia, Claudia; Immediato, Davide; Iatta, Roberta; Ramos, Rafael Antonio Nascimento; Lia, Riccardo Paolo; Porretta, Daniele; Figueredo, Luciana Aguiar; Dantas-Torres, Filipe; Otranto, Domenico

2015-02-05

Rhipicephalus sanguineus sensu lato ticks are widespread worldwide due to their adaptability to survive under different environmental conditions. They may act as vectors of a wide range of pathogens to humans and animals and their control is based on the use of chemical products on dogs and in the environment. Alternative control strategies, such as the use of entomopathogenic fungi as bio-control agents have also been investigated. The ability of native strains of Beauveria bassiana sensu lato in causing mortality in different tick species (e.g., Amblyomma cajennense and Rhipicephalus microplus) has been demonstrated. However, limited studies have assessed the use of B. bassiana for the control of R. sanguineus s.l. and none of them have employed native strains of this fungus. Here we investigated the pathogenicity of a native strain of B. bassiana (CD1123) against all developmental stages of R. sanguineus s.l.. Batches of eggs, larvae, nymphs and adult ticks were immersed in a suspension of 10(7) conidia/ml of B. bassiana s.l., isolated from a R. sanguineus s.l. engorged female. All treatment and control groups were observed for 20 days, and the biological parameters (i.e., mortality, hatching, moulting percentage, pre-oviposition period, oviposition period and rate, eggs production efficiency, reproductive efficiency and fitness indexes) were assessed. The effect of the B. bassiana strain tested herein on eggs, larvae, nymphs and adults showed a significantly higher mortality than those of the control groups (p < 0.05) at 5 days post-infection. No infected eggs hatched and no infected larvae moulted. Only 15% of infected nymphs moulted into adults. All biological parameters of treated groups differed significantly (p < 0.001) from those of control groups. This study demonstrates that a suspension containing 10(7) conidia/ml of a native B. bassiana strain is highly virulent towards all life-cycle developmental stages of R. sanguineus s.l. and may be of potential interest as a biological control agent against these ticks.

Influence of denitrification reactor retention time distribution (RTD) on dissolved oxygen control and nitrogen removal efficiency.

PubMed

Raboni, Massimo; Gavasci, Renato; Viotti, Paolo

2015-01-01

Low concentrations of dissolved oxygen (DO) are usually found in biological anoxic pre-denitrification reactors, causing a reduction in nitrogen removal efficiency. Therefore, the reduction of DO in such reactors is fundamental for achieving good nutrient removal. The article shows the results of an experimental study carried out to evaluate the effect of the anoxic reactor hydrodynamic model on both residual DO concentration and nitrogen removal efficiency. In particular, two hydrodynamic models were considered: the single completely mixed reactor and a series of four reactors that resemble plug-flow behaviour. The latter prove to be more effective in oxygen consumption, allowing a lower residual DO concentration than the former. The series of reactors also achieves better specific denitrification rates and higher denitrification efficiency. Moreover, the denitrification food to microrganism (F:M) ratio (F:MDEN) demonstrates a relevant synergic action in both controlling residual DO and improving the denitrification performance.

Biodiversity, ecosystem functioning, and classical biological control.

PubMed

Evans, Edward W

Increasing concern over worldwide loss of biodiversity has led ecologists to focus intently on how ecosystem functioning may depend on diversity. In applied entomology, there is longstanding interest in the issue, especially as regards the importance of natural enemy diversity for pest control. Here I review parallels in interest, conceptual framework, and conclusions concerning biodiversity as it affects ecosystem functioning in general and classical biological control in particular. Whereas the former focuses on implications of loss of diversity, the latter focuses on implications of increase in diversity as additional species of natural enemies are introduced to novel communities in new geographic regions for insect pest and weed control. Many field studies now demonstrate that ecosystem functioning, e.g., as reflected in primary productivity, is enhanced and stabilized over time by high diversity as the community increases in its efficiency in exploiting available resources. Similarly, there is growing field support for the generalization that increasing species and functional diversity of natural enemies leads to increasing pest suppression. Nonetheless a central concern of classical biological control in particular, as it seeks to minimize non-target effects, remains as to whether one or a few species of natural enemies can provide sufficient pest control.

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

PubMed

Mitchell, Sara N; Catteruccia, Flaminia

2017-12-01

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

The Spring of Systems Biology-Driven Breeding.

PubMed

Lavarenne, Jérémy; Guyomarc'h, Soazig; Sallaud, Christophe; Gantet, Pascal; Lucas, Mikaël

2018-05-12

Genetics and molecular biology have contributed to the development of rationalized plant breeding programs. Recent developments in both high-throughput experimental analyses of biological systems and in silico data processing offer the possibility to address the whole gene regulatory network (GRN) controlling a given trait. GRN models can be applied to identify topological features helping to shortlist potential candidate genes for breeding purposes. Time-series data sets can be used to support dynamic modelling of the network. This will enable a deeper comprehension of network behaviour and the identification of the few elements to be genetically rewired to push the system towards a modified phenotype of interest. This paves the way to design more efficient, systems biology-based breeding strategies. Copyright © 2018 Elsevier Ltd. All rights reserved.

study on trace contaminants control assembly for sealed environment chamber

NASA Astrophysics Data System (ADS)

Pang, L. P.; Wang, J.; Liu, L. K.; Liu, H.

The biological and Physicochemical P C life support technologies are all important parts to establish a human Closed Ecological Life Support System CELSS for long-duration mission The latter has the advantages of lower power consumption lower mass and higher efficiency therefore researchers often incorporate the use of biological systems with P C life support technologies to continuously recycle air water and part of the solid waste stream generated such as the Russian BLSS and the NASA-sponsored Lunar-Mars Life Support Test Project LMLSTP In short these tests were very successful in integrating biological and P C life support technologies for long-duration life support Therefore we should use a combination of integrated biological with P C life support technologies in a human CELSS Human construction materials plants animals and soils release much trace toxic gases in a CELSS and they will inhibit plant growth and badly affect human health when their concentrations rise over their threshold levels The effect of biological trace contaminant control technologies is slower especially for a human sealed chamber because human produce much more methane and other contaminants A regenerative Trace Contaminant Control Subsystem TCCS with P C technology is a more important part in this case to control quickly the airborne contaminants levels and assure human in good condition in a sealed chamber This paper describes a trace contaminant control test facility incorporated a 8 m3 sealed environment chamber a regenerative TCCS with P C

High performance biological methanation in a thermophilic anaerobic trickle bed reactor.

PubMed

Strübing, Dietmar; Huber, Bettina; Lebuhn, Michael; Drewes, Jörg E; Koch, Konrad

2017-12-01

In order to enhance energy efficiency of biological methanation of CO 2 and H 2 , this study investigated the performance of a thermophilic (55°C) anaerobic trickle bed reactor (ATBR) (58.1L) at ambient pressure. With a methane production rate of up to 15.4m 3 CH4 /(m 3 trickle bed ·d) at methane concentrations above 98%, the ATBR can easily compete with the performance of other mixed culture methanation reactors. Control of pH and nutrient supply turned out to be crucial for stable operation and was affected significantly by dilution due to metabolic water production, especially during demand-orientated operation. Considering practical applications, inoculation with digested sludge, containing a diverse biocenosis, showed high adaptive capacity due to intrinsic biological diversity. However, no macroscopic biofilm formation was observed at thermophilic conditions even after 313days of operation. The applied approach illustrates the high potential of thermophilic ATBRs as a very efficient energy conversion and storage technology. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nanomaterials at the neural interface.

PubMed

Scaini, Denis; Ballerini, Laura

2018-06-01

Interfacing the nervous system with devices able to efficiently record or modulate the electrical activity of neuronal cells represents the underlying foundation of future theranostic applications in neurology and of current openings in neuroscience research. These devices, usually sensing cell activity via microelectrodes, should be characterized by safe working conditions in the biological milieu together with a well-controlled operation-life. The stable device/neuronal electrical coupling at the interface requires tight interactions between the electrode surface and the cell membrane. This neuro-electrode hybrid represents the hyphen between the soft nature of neural tissue, generating electrical signals via ion motions, and the rigid realm of microelectronics and medical devices, dealing with electrons in motion. Efficient integration of these entities is essential for monitoring, analyzing and controlling neuronal signaling but poses significant technological challenges. Improving the cell/electrode interaction and thus the interface performance requires novel engineering of (nano)materials: tuning at the nanoscale electrode's properties may lead to engineer interfacing probes that better camouflaged with their biological target. In this brief review, we highlight the most recent concepts in nanotechnologies and nanomaterials that might help reducing the mismatch between tissue and electrode, focusing on the device's mechanical properties and its biological integration with the tissue. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genome sequence, assembly and characterization of two Metschnikowia fructicola strains used as biocontrol agents of postharvest diseases

USDA-ARS?s Scientific Manuscript database

The yeast Metschnikowia fructicola was reported as an efficient biological control agent of postharvest diseases of fruits and vegetables. Several mechanism of action by which M. fructicola inhibit postharvest pathogens were suggested including iron-binding compounds, induction of defense signaling...

[The adaptive biological control system with electromyographic feedback in the treatment of Bell's palsy].

PubMed

Lobzin, V S; Tsatskina, N D

1989-01-01

A total of 192 patients with Bell paralysis were studied. In 32 a technique of biofeedback training was applied to accelerate the restoration of mimetic muscles with EMG feedback. Clinical and electrophysiological data confirmed the efficiency of this technique in terms of considerably accelerated rehabilitation.

Entomopathogenic fungi as biological control agents of diamondback moth (Lepidoptera: Plutellidae)and compatibility with chemical insecticides

USDA-ARS?s Scientific Manuscript database

The objectives were to evaluate the efficiency of entomopathogenic fungi against Plutella xylostella (L.) and the compatibility of the most virulent isolates with some of the insecticides registered for use on cabbage crops. Pathogenicity tests used isolates of Beauveria bassiana, Metarhizium rileyi...

Robust control for fractional variable-order chaotic systems with non-singular kernel

NASA Astrophysics Data System (ADS)

Zuñiga-Aguilar, C. J.; Gómez-Aguilar, J. F.; Escobar-Jiménez, R. F.; Romero-Ugalde, H. M.

2018-01-01

This paper investigates the chaos control for a class of variable-order fractional chaotic systems using robust control strategy. The variable-order fractional models of the non-autonomous biological system, the King Cobra chaotic system, the Halvorsen's attractor and the Burke-Shaw system, have been derived using the fractional-order derivative with Mittag-Leffler in the Liouville-Caputo sense. The fractional differential equations and the control law were solved using the Adams-Bashforth-Moulton algorithm. To test the control stability efficiency, different statistical indicators were introduced. Finally, simulation results demonstrate the effectiveness of the proposed robust control.

Flexible automated approach for quantitative liquid handling of complex biological samples.

PubMed

Palandra, Joe; Weller, David; Hudson, Gary; Li, Jeff; Osgood, Sarah; Hudson, Emily; Zhong, Min; Buchholz, Lisa; Cohen, Lucinda H

2007-11-01

A fully automated protein precipitation technique for biological sample preparation has been developed for the quantitation of drugs in various biological matrixes. All liquid handling during sample preparation was automated using a Hamilton MicroLab Star Robotic workstation, which included the preparation of standards and controls from a Watson laboratory information management system generated work list, shaking of 96-well plates, and vacuum application. Processing time is less than 30 s per sample or approximately 45 min per 96-well plate, which is then immediately ready for injection onto an LC-MS/MS system. An overview of the process workflow is discussed, including the software development. Validation data are also provided, including specific liquid class data as well as comparative data of automated vs manual preparation using both quality controls and actual sample data. The efficiencies gained from this automated approach are described.

Real-time product attribute control to manufacture antibodies with defined N-linked glycan levels.

PubMed

Zupke, Craig; Brady, Lowell J; Slade, Peter G; Clark, Philip; Caspary, R Guy; Livingston, Brittney; Taylor, Lisa; Bigham, Kyle; Morris, Arvia E; Bailey, Robert W

2015-01-01

Pressures for cost-effective new therapies and an increased emphasis on emerging markets require technological advancements and a flexible future manufacturing network for the production of biologic medicines. The safety and efficacy of a product is crucial, and consistent product quality is an essential feature of any therapeutic manufacturing process. The active control of product quality in a typical biologic process is challenging because of measurement lags and nonlinearities present in the system. The current study uses nonlinear model predictive control to maintain a critical product quality attribute at a predetermined value during pilot scale manufacturing operations. This approach to product quality control ensures a more consistent product for patients, enables greater manufacturing efficiency, and eliminates the need for extensive process characterization by providing direct measures of critical product quality attributes for real time release of drug product. © 2015 American Institute of Chemical Engineers.

Conformational Control of Ultrafast Molecular Rotor Property: Tuning Viscosity Sensing Efficiency by Twist Angle Variation.

PubMed

Ghosh, Rajib; Kushwaha, Archana; Das, Dipanwita

2017-09-21

Fluorescent molecular rotors find widespread application in sensing and imaging of microscopic viscosity in complex chemical and biological media. Development of viscosity-sensitive ultrafast molecular rotor (UMR) relies upon the understanding of the excited-state dynamics and their implications for viscosity-dependent fluorescence signaling. Unraveling the structure-property relationship of UMR behavior is of significance toward development of an ultrasensitive fluorescence microviscosity sensor. Herein we show that the ground-state equilibrium conformation has an important role in the ultrafast twisting dynamics of UMRs and consequent viscosity sensing efficiency. Synthesis, photophysics, and ultrafast spectroscopic experiments in conjunction with quantum chemical calculation of a series of UMRs based on dimethylaniline donor and benzimidazolium acceptor with predefined ground-state torsion angle led us to unravel that the ultrafast torsional dynamics around the bond connecting donor and acceptor groups profoundly influences the molecular rotor efficiency. This is the first experimental demonstration of conformational control of small-molecule-based UMR efficiencies which can have wider implication toward development of fluorescence sensors based on the UMR principle. Conformation-controlled UMR efficiency has been shown to exhibit commensurate fluorescence enhancement upon DNA binding.

A dedicated database system for handling multi-level data in systems biology.

PubMed

Pornputtapong, Natapol; Wanichthanarak, Kwanjeera; Nilsson, Avlant; Nookaew, Intawat; Nielsen, Jens

2014-01-01

Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic, incomplete and distributed among public databases. This leads to difficulties in data accessibility and often results in errors when data are merged and integrated from varied resources. Therefore, integration and management of systems biological data remain very challenging. To overcome this, we designed and developed a dedicated database system that can serve and solve the vital issues in data management and hereby facilitate data integration, modeling and analysis in systems biology within a sole database. In addition, a yeast data repository was implemented as an integrated database environment which is operated by the database system. Two applications were implemented to demonstrate extensibility and utilization of the system. Both illustrate how the user can access the database via the web query function and implemented scripts. These scripts are specific for two sample cases: 1) Detecting the pheromone pathway in protein interaction networks; and 2) Finding metabolic reactions regulated by Snf1 kinase. In this study we present the design of database system which offers an extensible environment to efficiently capture the majority of biological entities and relations encountered in systems biology. Critical functions and control processes were designed and implemented to ensure consistent, efficient, secure and reliable transactions. The two sample cases on the yeast integrated data clearly demonstrate the value of a sole database environment for systems biology research.

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

PubMed

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

2017-10-01

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

The export and fate of organic matter in the ocean: New constraints from combining satellite and oceanographic tracer observations

NASA Astrophysics Data System (ADS)

DeVries, Tim; Weber, Thomas

2017-03-01

The ocean's biological pump transfers carbon from the surface euphotic zone into the deep ocean, reducing the atmospheric CO2 concentration. Despite its climatic importance, there are large uncertainties in basic metrics of the biological pump. Previous estimates of the strength of the biological pump, as measured by the amount of organic carbon exported from the euphotic zone, range from about 4 to 12 Pg C yr-1. The fate of exported carbon, in terms of how efficiently it is transferred into the deep ocean, is even more uncertain. Here we present a new model of the biological pump that assimilates satellite and oceanographic tracer observations to constrain rates and patterns of organic matter production, export, and remineralization in the ocean. The data-assimilated model predicts a global particulate organic carbon (POC) flux out of the euphotic zone of ˜9 Pg C yr-1. The particle export ratio (the ratio of POC export to net primary production) is highest at high latitudes and lowest at low latitudes, but low-latitude export is greater than predicted by previous models, in better agreement with observed patterns of long-term carbon export. Particle transfer efficiency (Teff) through the mesopelagic zone is controlled by temperature and oxygen, with highest Teff for high-latitude regions and oxygen minimum zones. In contrast, Teff in the deep ocean (below 1000 m) is controlled by particle sinking speed, with highest deep ocean Teff below the subtropical gyres. These results emphasize the utility of both remote sensing and oceanographic tracer observations for constraining the operation of the biological pump.

An Efficient Computational Model to Predict Protonation at the Amide Nitrogen and Reactivity along the C–N Rotational Pathway

PubMed Central

Szostak, Roman; Aubé, Jeffrey

2015-01-01

N-protonation of amides is critical in numerous biological processes, including amide bonds proteolysis and protein folding, as well as in organic synthesis as a method to activate amide bonds towards unconventional reactivity. A computational model enabling prediction of protonation at the amide bond nitrogen atom along the C–N rotational pathway is reported. Notably, this study provides a blueprint for the rational design and application of amides with a controlled degree of rotation in synthetic chemistry and biology. PMID:25766378

Modeling and simulation of high dimensional stochastic multiscale PDE systems at the exascale

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

Zabaras, Nicolas J.

2016-11-08

Predictive Modeling of multiscale and Multiphysics systems requires accurate data driven characterization of the input uncertainties, and understanding of how they propagate across scales and alter the final solution. This project develops a rigorous mathematical framework and scalable uncertainty quantification algorithms to efficiently construct realistic low dimensional input models, and surrogate low complexity systems for the analysis, design, and control of physical systems represented by multiscale stochastic PDEs. The work can be applied to many areas including physical and biological processes, from climate modeling to systems biology.

Bioinspired Concepts: Unified Theory for Complex Biological and Engineering Systems

DTIC Science & Technology

2006-01-01

i.e., data flows of finite size arrive at the system randomly. For such a system , we propose a modified dual scheduling algorithm that stabilizes ...demon. We compute the efficiency of the controller over finite and infinite time intervals, and since the controller is optimal, this yields hard limits...and highly optimized tolerance. PNAS, 102, 2005. 51. G. N. Nair and R. J. Evans. Stabilizability of stochastic linear systems with finite feedback

Differences between winter oilseed rape (Brassica napus L.) cultivars in nitrogen starvation-induced leaf senescence are governed by leaf-inherent rather than root-derived signals

PubMed Central

Koeslin-Findeklee, Fabian; Becker, Martin A.; van der Graaff, Eric; Roitsch, Thomas; Horst, Walter J.

2015-01-01

Nitrogen (N) efficiency of winter oilseed rape (Brassica napus L.) line-cultivars (cvs.), defined as high grain yield under N limitation, has been primarily attributed to maintained N uptake during reproductive growth (N uptake efficiency) in combination with delayed senescence of the older leaves accompanied with maintained photosynthetic capacity (functional stay-green). However, it is not clear whether genotypic variation in N starvation-induced leaf senescence is due to leaf-inherent factors and/or governed by root-mediated signals. Therefore, the N-efficient and stay-green cvs. NPZ-1 and Apex were reciprocally grafted with the N-inefficient and early-senescing cvs. NPZ-2 and Capitol, respectively and grown in hydroponics. The senescence status of older leaves after 12 days of N starvation assessed by SPAD, photosynthesis and the expression of the senescence-specific cysteine protease gene SAG12-1 revealed that the stay-green phenotype of the cvs. NPZ-1 and Apex under N starvation was primarily under the control of leaf-inherent factors. The same four cultivars were submitted to N starvation for up to 12 days in a time-course experiment. The specific leaf contents of biologically active and inactive cytokinins (CKs) and the expression of genes involved in CK homeostasis revealed that under N starvation leaves of early-senescing cultivars were characterized by inactivation of biologically active CKs, whereas in stay-green cultivars synthesis, activation, binding of and response to biologically active CKs were favoured. These results suggest that the homeostasis of biologically active CKs was the predominant leaf-inherent factor for cultivar differences in N starvation-induced leaf senescence and thus N efficiency. PMID:25944925

Beauveria bassiana strains for biological control of Cosmopolites sordidus (Germ.) (Coleoptera: Curculionidae) in plantain.

PubMed

Fancelli, Marilene; Dias, Alex Batista; Delalibera, Italo; de Jesus, Sandra Cerqueira; do Nascimento, Antonio Souza; Silva, Sebastião de Oliveira e; Caldas, Ranulfo Correa; Ledo, Carlos Alberto da Silva

2013-01-01

The objective of this study was to select strains of Beauveria bassiana for controlling Cosmopolites sordidus (Germ.) in plantain farms (cv. Terra) of the "Recôncavo" and southern regions in the state of Bahia, Brazil. The virulence of 32 B. bassiana isolates against C. sordidus was determined under laboratory conditions. Three isolates (CNPMF 407, CNPMF 218, and CNPMF 416) were selected for evaluation under field conditions in plantations located in the counties of Mutuípe and Wenceslau Guimarães. Population of C. sordidus was estimated every 15 days by using pseudostem traps. The efficiency of the three strains of B. bassiana was compared to chemical control (carbofuran, 4 g/trap) and absence of control. Carbofuran caused around 90% of adult mortality after 12 months, with a reduction in the population of C. sordidus since the first evaluation. A low number of trapped insects was observed in the fungus-treated plots, suggesting the efficiency of the isolates in controlling the C. sordidus population. The strain CNPMF 218 was the most efficient in controlling C. sordidus adults in both locations, causing around 20% mortality, leading to 40% population size reduction after 12 months.

Beauveria bassiana Strains for Biological Control of Cosmopolites sordidus (Germ.) (Coleoptera: Curculionidae) in Plantain

PubMed Central

Dias, Alex Batista; Delalibera Júnior, Italo; de Jesus, Sandra Cerqueira; do Nascimento, Antonio Souza; Silva, Sebastião de Oliveira e; Caldas, Ranulfo Correa; Ledo, Carlos Alberto da Silva

2013-01-01

The objective of this study was to select strains of Beauveria bassiana for controlling Cosmopolites sordidus (Germ.) in plantain farms (cv. Terra) of the “Recôncavo” and southern regions in the state of Bahia, Brazil. The virulence of 32 B. bassiana isolates against C. sordidus was determined under laboratory conditions. Three isolates (CNPMF 407, CNPMF 218, and CNPMF 416) were selected for evaluation under field conditions in plantations located in the counties of Mutuípe and Wenceslau Guimarães. Population of C. sordidus was estimated every 15 days by using pseudostem traps. The efficiency of the three strains of B. bassiana was compared to chemical control (carbofuran, 4g/trap) and absence of control. Carbofuran caused around 90% of adult mortality after 12 months, with a reduction in the population of C. sordidus since the first evaluation. A low number of trapped insects was observed in the fungus-treated plots, suggesting the efficiency of the isolates in controlling the C. sordidus population. The strain CNPMF 218 was the most efficient in controlling C. sordidus adults in both locations, causing around 20% mortality, leading to 40% population size reduction after 12 months. PMID:24187659

Enhancing the stability and ecological safety of mass-reared transgenic strains for field release by redundant conditional lethality systems

USDA-ARS?s Scientific Manuscript database

Advances in the genetic manipulation of agriculturally important insects now allows the development of genetic sexing and male sterility systems for more highly efficient biologically-based population control programs, most notably SIT, in fruit pests throughout the world. Potentially, these condit...

Environmental Technology Verification: Biological Inactivation Efficiency by HVAC In-Duct Ultraviolet Light Systems--American Ultraviolet Corporation, DC24-6-120 [EPA600etv08005

EPA Science Inventory

The Air Pollution Control Technology Verification Center (APCT Center) is operated by RTI International (RTI), in cooperation with EPA's National Risk Management Research Laboratory. The APCT Center conducts verifications of technologies that clean air in ventilation systems, inc...

Optimal surveillance and eradication of invasive species in heterogeneous landscapes

Treesearch

Rebecca S. Epanchin-Niell; Robert G. Haight; Ludek Berec; John M. Kean; Andrew M. Liebhold

2012-01-01

Cost-effective surveillance strategies are needed for efficient responses to biological invasions and must account for the trade-offs between surveillance effort and management costs. Less surveillance may allow greater population growth and spread prior to detection, thereby increasing the costs of damages and control. In addition, surveillance strategies are usually...

Effect of Different Proportions of Agrowaste on Cultivation Yield and Nutritional Composition of the Culinary-Medicinal Jelly Mushroom Auricularia polytricha (Higher Basidiomycetes).

PubMed

Wu, Chiu-Yeh; Liang, Chih-Hung; Wu, Kuan-Jzen; Shih, Hsin-Der; Liang, Zeng-Chin

2017-01-01

In this study, Auricularia polytricha was cultivated on a sawdust basal substrate supplemented with different proportions (30%, 45%, and 60%, respectively) of agrowastes-sugarcane bagasse (SB), rice straw (RS), and rice husk (RH)-to evaluate the alternative substrates. The mycelial growth rate, total colonization time, time to first primordia, biological efficiency, and chemical composition of the fruiting bodies were determined. Results indicated that the 60% SB substrate was the best substrate for mycelial growth of A. polytricha, with a corresponding total colonization period of 35.2 days, followed by the control (35.5 days) and 45% SB (36.2 days) substrates. The most suitable substrate with a high biological efficiency was 60% RS substrate (159.14%), followed by the 45% SB (128.45%), and 20% RH (124.47%) substrates. The nutrient values of fruiting bodies showed the largest amounts of ash, protein, fat, carbohydrates, and energy cultivated on 60% SB, 60% SB, 30% SB, 30% RH, and 30% RH/the control substrates, respectively. The results indicated that 60% RS was an appropriate substrate for A. polytricha cultivation.

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

PubMed

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

1993-02-01

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

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

PubMed

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

2016-03-01

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

Enhancing Bioremediation of Oil-contaminated Soils by Controlling Nutrient Transport using Dual Characteristics of Soil Pore Structure

NASA Astrophysics Data System (ADS)

Mori, Y.; Suetsugu, A.; Matsumoto, Y.; Fujihara, A.; Suyama, K.; Miyamoto, T.

2012-12-01

Soil structure is heterogeneous with cracks or macropores allowing bypass flow, which may lead to applied chemicals avoiding interaction with soil particles or the contaminated area. We investigated the bioremediation efficiency of oil-contaminated soils by applying suction at the bottom of soil columns during bioremediation. Unsaturated flow conditions were investigated so as to avoid bypass flow and achieve sufficient dispersion of chemicals in the soil column. The boundary conditions at the bottom of the soil columns were 0 kPa and -3 kPa, and were applied to a volcanic ash soil with and without macropores. Unsaturated flow was achieved with -3 kPa and an injection rate of 1/10 of the saturated hydraulic conductivity. The resultant biological activities of the effluent increased dramatically in the unsaturated flow with macropores condition. Unsaturated conditions prevented bypass flow and allowed dispersion of the injected nutrients. Unsaturated flow achieved 60-80% of saturation, which enhanced biological activity in the soil column. Remediation results were better for unsaturated conditions because of higher biological activity. Moreover, unsaturated flow with macropores achieved uniform remediation efficiency from upper through lower positions in the column. Finally, taking the applied solution volume into consideration, unsaturated flow with -3 kPa achieved 10 times higher efficiency when compared with conventional saturated flow application. These results suggest that effective use of nutrients or remediation chemicals is possible by avoiding bypass flow and enhancing biological activity using relatively simple and inexpensive techniques.

Collection of biological and non-biological particles by new and used filters made from glass and electrostatically charged synthetic fibers.

PubMed

Raynor, P C; Kim, B G; Ramachandran, G; Strommen, M R; Horns, J H; Streifel, A J

2008-02-01

Synthetic filters made from fibers carrying electrostatic charges and fiberglass filters that do not carry electrostatic charges are both utilized commonly in heating, ventilating, and air-conditioning (HVAC) systems. The pressure drop and efficiency of a bank of fiberglass filters and a bank of electrostatically charged synthetic filters were measured repeatedly for 13 weeks in operating HVAC systems at a hospital. Additionally, the efficiency with which new and used fiberglass and synthetic filters collected culturable biological particles was measured in a test apparatus. Pressure drop measurements adjusted to equivalent flows indicated that the synthetic filters operated with a pressure drop less than half that of the fiberglass filters throughout the test. When measured using total ambient particles, synthetic filter efficiency decreased during the test period for all particle diameters. For particles 0.7-1.0 mum in diameter, efficiency decreased from 92% to 44%. It is hypothesized that this reduction in collection efficiency may be due to charge shielding. Efficiency did not change significantly for the fiberglass filters during the test period. However, when measured using culturable biological particles in the ambient air, efficiency was essentially the same for new filters and filters used for 13 weeks in the hospital for both the synthetic and fiberglass filters. It is hypothesized that the lack of efficiency reduction for culturable particles may be due to their having higher charge than non-biological particles, allowing them to overcome the effects of charge shielding. The type of particles requiring capture may be an important consideration when comparing the relative performance of electrostatically charged synthetic and fiberglass filters. Electrostatically charged synthetic filters with high initial efficiency can frequently replace traditional fiberglass filters with lower efficiency in HVAC systems because properly designed synthetic filters offer less resistance to air flow. Although the efficiency of charged synthetic filters at collecting non-biological particles declined substantially with use, the efficiency of these filters at collecting biological particles remained steady. These findings suggest that the merits of electrostatically charged synthetic HVAC filters relative to fiberglass filters may be more pronounced if collection of biological particles is of primary concern.

Synergizing Engineering and Biology to Treat and Model Skeletal Muscle Injury and Disease

PubMed Central

Bursac, Nenad; Juhas, Mark; Rando, Thomas A.

2016-01-01

Although skeletal muscle is one of the most regenerative organs in our body, various genetic defects, alterations in extrinsic signaling, or substantial tissue damage can impair muscle function and the capacity for self-repair. The diversity and complexity of muscle disorders have attracted much interest from both cell biologists and, more recently, bioengineers, leading to concentrated efforts to better understand muscle pathology and develop more efficient therapies. This review describes the biological underpinnings of muscle development, repair, and disease, and discusses recent bioengineering efforts to design and control myomimetic environments, both to study muscle biology and function and to aid in the development of new drug, cell, and gene therapies for muscle disorders. The synergy between engineering-aided biological discovery and biology-inspired engineering solutions will be the path forward for translating laboratory results into clinical practice. PMID:26643021

Guiding Classical Biological Control of an Invasive Mealybug Using Integrative Taxonomy

PubMed Central

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

2015-01-01

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

Population control methods in stochastic extinction and outbreak scenarios.

PubMed

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

2017-01-01

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

Is the internal connection more efficient than external connection in mechanical, biological, and esthetical point of views? A systematic review.

PubMed

Goiato, Marcelo Coelho; Pellizzer, Eduardo Piza; da Silva, Emily Vivianne Freitas; Bonatto, Liliane da Rocha; dos Santos, Daniela Micheline

2015-09-01

This systematic review aimed to evaluate if the internal connection is more efficient than the external connection and its associated influencing factors. A specific question was formulated according to the Population, Intervention, Control, and Outcome (PICO): Is internal connection more efficient than external connection in mechanical, biological, and esthetical point of views? An electronic search of the MEDLINE and the Web of Knowledge databases was performed for relevant studies published in English up to November 2013 by two independent reviewers. The keywords used in the search included a combination of "dental implant" and "internal connection" or "Morse connection" or "external connection." Selected studies were randomized clinical trials, prospective or retrospective studies, and in vitro studies with a clear aim of investigating the internal and/or external implant connection use. From an initial screening yield of 674 articles, 64 potentially relevant articles were selected after an evaluation of their titles and abstracts. Full texts of these articles were obtained with 29 articles fulfilling the inclusion criteria. Morse taper connection has the best sealing ability. Concerning crestal bone loss, internal connections presented better results than external connections. The limitation of the present study was the absence of randomized clinical trials that investigated if the internal connection was more efficient than the external connection. The external and internal connections have different mechanical, biological, and esthetical characteristics. Besides all systems that show proper success rates and effectiveness, crestal bone level maintenance is more important around internal connections than external connections. The Morse taper connection seems to be more efficient concerning biological aspects, allowing lower bacterial leakage and bone loss in single implants, including aesthetic regions. Additionally, this connection type can be successfully indicated for fixed partial prostheses and overdenture planning, since it exhibits high mechanical stability.

Apparent synergy among defense mechanisms in subterranean termites (Rhinotermitidae) against epizootic events: limits and potential for biological control.

PubMed

Chouvenc, Thomas; Su, Nan-Yao

2010-08-01

The use of entomopathogens for biological control of subterranean termites (Rhinotermitidae) has attracted attention in the past four decades, and several laboratory studies have shown promising results with fungal agents. This approach was based on the concept of classical biological control with the use of a virulent agent that can self-replicate in a termite nest and be transmitted among individuals, resulting in an epizootic to kill the entire colony. However, the absence of positive results in field studies challenged the potential of fungal pathogens as a realistic approach for subterranean termite control, and the relationship between fungi and subterranean termites remains poorly understood. A multimodal approach of the currently identified defense mechanisms allowed us to show that subterranean termites have the ability to prevent an epizootic from occurring. The defense mechanisms involved in such resistance are reviewed and documented. Finally, the interactions among three major defense mechanisms (grooming, cellular encapsulation, and gut antifungal activity) were analyzed, and it is suggested that these mechanisms act synergistically to produce an efficient defense against the infection of the fungus at the individual and group level so as to protect the colony from epizootics.

Multidisciplinary approaches to solar hydrogen

PubMed Central

Bren, Kara L.

2015-01-01

This review summarizes three different approaches to engineering systems for the solar-driven evolution of hydrogen fuel from water: molecular, nanomaterials and biomolecular. Molecular systems have the advantage of being highly amenable to modification and detailed study and have provided great insight into photophysics, electron transfer and catalytic mechanism. However, they tend to display poor stability. Systems based on nanomaterials are more robust but also are more difficult to synthesize in a controlled manner and to modify and study in detail. Biomolecular systems share many properties with molecular systems and have the advantage of displaying inherently high efficiencies for light absorption, electron–hole separation and catalysis. However, biological systems must be engineered to couple modules that capture and convert solar photons to modules that produce hydrogen fuel. Furthermore, biological systems are prone to degradation when employed in vitro. Advances that use combinations of these three tactics also are described. Multidisciplinary approaches to this problem allow scientists to take advantage of the best features of biological, molecular and nanomaterials systems provided that the components can be coupled for efficient function. PMID:26052425

Whole-genome sequencing of Bacillus subtilis XF-1 reveals mechanisms for biological control and multiple beneficial properties in plants.

PubMed

Guo, Shengye; Li, Xingyu; He, Pengfei; Ho, Honhing; Wu, Yixin; He, Yueqiu

2015-06-01

Bacillus subtilis XF-1 is a gram-positive, plant-associated bacterium that stimulates plant growth and produces secondary metabolites that suppress soil-borne plant pathogens. In particular, it is especially highly efficient at controlling the clubroot disease of cruciferous crops. Its 4,061,186-bp genome contains an estimated 3853 protein-coding sequences and the 1155 genes of XF-1 are present in most genome-sequenced Bacillus strains: 3757 genes in B. subtilis 168, and 1164 in B. amyloliquefaciens FZB42. Analysis using the Cluster of Orthologous Groups database of proteins shows that 60 genes control bacterial mobility, 221 genes are related to cell wall and membrane biosynthesis, and more than 112 are genes associated with secondary metabolites. In addition, the genes contributed to the strain's plant colonization, bio-control and stimulation of plant growth. Sequencing of the genome is a fundamental step for developing a desired strain to serve as an efficient biological control agent and plant growth stimulator. Similar to other members of the taxon, XF-1 has a genome that contains giant gene clusters for the non-ribosomal synthesis of antifungal lipopeptides (surfactin and fengycin), the polyketides (macrolactin and bacillaene), the siderophore bacillibactin, and the dipeptide bacilysin. There are two synthesis pathways for volatile growth-promoting compounds. The expression of biosynthesized antibiotic peptides in XF-1 was revealed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry.

Biological control of Rhizoctonia root rot on bean by phenazine- and cyclic lipopeptide-producing Pseudomonas CMR12a

USDA-ARS?s Scientific Manuscript database

Pseudomonas CMR12a was previously selected as an efficient biocontrol strain producing phenazines and cyclic lipopeptides (CLPs). In this study, biocontrol capacity of Pseudomonas CMR12a against Rhizoctonia root rot of bean and the involvement of phenazines and CLPs in this ability were tested. Two ...

Mammalian designer cells: Engineering principles and biomedical applications.

PubMed

Xie, Mingqi; Fussenegger, Martin

2015-07-01

Biotechnology is a widely interdisciplinary field focusing on the use of living cells or organisms to solve established problems in medicine, food production and agriculture. Synthetic biology, the science of engineering complex biological systems that do not exist in nature, continues to provide the biotechnology industry with tools, technologies and intellectual property leading to improved cellular performance. One key aspect of synthetic biology is the engineering of deliberately reprogrammed designer cells whose behavior can be controlled over time and space. This review discusses the most commonly used techniques to engineer mammalian designer cells; while control elements acting on the transcriptional and translational levels of target gene expression determine the kinetic and dynamic profiles, coupling them to a variety of extracellular stimuli permits their remote control with user-defined trigger signals. Designer mammalian cells with novel or improved biological functions not only directly improve the production efficiency during biopharmaceutical manufacturing but also open the door for cell-based treatment strategies in molecular and translational medicine. In the future, the rational combination of multiple sets of designer cells could permit the construction and regulation of higher-order systems with increased complexity, thereby enabling the molecular reprogramming of tissues, organisms or even populations with highest precision. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Compact and controlled microfluidic mixing and biological particle capture

NASA Astrophysics Data System (ADS)

Ballard, Matthew; Owen, Drew; Mills, Zachary Grant; Hesketh, Peter J.; Alexeev, Alexander

2016-11-01

We use three-dimensional simulations and experiments to develop a multifunctional microfluidic device that performs rapid and controllable microfluidic mixing and specific particle capture. Our device uses a compact microfluidic channel decorated with magnetic features. A rotating magnetic field precisely controls individual magnetic microbeads orbiting around the features, enabling effective continuous-flow mixing of fluid streams over a compact mixing region. We use computer simulations to elucidate the underlying physical mechanisms that lead to effective mixing and compare them with experimental mixing results. We study the effect of various system parameters on microfluidic mixing to design an efficient micromixer. We also experimentally and numerically demonstrate that orbiting microbeads can effectively capture particles transported by the fluid, which has major implications in pre-concentration and detection of biological particles including various cells and bacteria, with applications in areas such as point-of-care diagnostics, biohazard detection, and food safety. Support from NSF and USDA is gratefully acknowledged.

Rapid evolution of regulatory element libraries for tunable transcriptional and translational control of gene expression.

PubMed

Jin, Erqing; Wong, Lynn; Jiao, Yun; Engel, Jake; Holdridge, Benjamin; Xu, Peng

2017-12-01

Engineering cell factories for producing biofuels and pharmaceuticals has spurred great interests to develop rapid and efficient synthetic biology tools customized for modular pathway engineering. Along the way, combinatorial gene expression control through modification of regulatory element offered tremendous opportunity for fine-tuning gene expression and generating digital-like genetic circuits. In this report, we present an efficient evolutionary approach to build a range of regulatory control elements. The reported method allows for rapid construction of promoter, 5'UTR, terminator and trans -activating RNA libraries. Synthetic overlapping oligos with high portion of degenerate nucleotides flanking the regulatory element could be efficiently assembled to a vector expressing fluorescence reporter. This approach combines high mutation rate of the synthetic DNA with the high assembly efficiency of Gibson Mix. Our constructed library demonstrates broad range of transcriptional or translational gene expression dynamics. Specifically, both the promoter library and 5'UTR library exhibits gene expression dynamics spanning across three order of magnitude. The terminator library and trans -activating RNA library displays relatively narrowed gene expression pattern. The reported study provides a versatile toolbox for rapidly constructing a large family of prokaryotic regulatory elements. These libraries also facilitate the implementation of combinatorial pathway engineering principles and the engineering of more efficient microbial cell factory for various biomanufacturing applications.

Coherent optimal control of photosynthetic molecules

NASA Astrophysics Data System (ADS)

Caruso, F.; Montangero, S.; Calarco, T.; Huelga, S. F.; Plenio, M. B.

2012-04-01

We demonstrate theoretically that open-loop quantum optimal control techniques can provide efficient tools for the verification of various quantum coherent transport mechanisms in natural and artificial light-harvesting complexes under realistic experimental conditions. To assess the feasibility of possible biocontrol experiments, we introduce the main settings and derive optimally shaped and robust laser pulses that allow for the faithful preparation of specified initial states (such as localized excitation or coherent superposition, i.e., propagating and nonpropagating states) of the photosystem and probe efficiently the subsequent dynamics. With these tools, different transport pathways can be discriminated, which should facilitate the elucidation of genuine quantum dynamical features of photosystems and therefore enhance our understanding of the role that coherent processes may play in actual biological complexes.

Biological Synthesis of Nanoparticles from Plants and Microorganisms.

PubMed

Singh, Priyanka; Kim, Yu-Jin; Zhang, Dabing; Yang, Deok-Chun

2016-07-01

Nanotechnology has become one of the most promising technologies applied in all areas of science. Metal nanoparticles produced by nanotechnology have received global attention due to their extensive applications in the biomedical and physiochemical fields. Recently, synthesizing metal nanoparticles using microorganisms and plants has been extensively studied and has been recognized as a green and efficient way for further exploiting microorganisms as convenient nanofactories. Here, we explore and detail the potential uses of various biological sources for nanoparticle synthesis and the application of those nanoparticles. Furthermore, we highlight recent milestones achieved for the biogenic synthesis of nanoparticles by controlling critical parameters, including the choice of biological source, incubation period, pH, and temperature. Copyright © 2016 Elsevier Ltd. All rights reserved.

Hypericin-mediated selective photomodification of connective tissues

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

Hovhannisyan, V., E-mail: hovv@phys.ntu.edu.tw; Guo, H. W.; Chen, Y. F., E-mail: yfchen@phys.ntu.edu.tw

2014-12-29

Controllable modification of biological molecules and supramolecular components of connective tissue are important for biophysical and biomedical applications. Through the use of second harmonic generation imaging, two-photon fluorescence microscopy, and spectrofluorimetry, we found that hypericin, a natural pigment, induces photosensitized destruction of collagen fibers but does not affect elastic fibers and lipids in chicken tendon, skin, and blood vessels. We demonstrated the dynamics and efficiency of collagen photomodification and investigated mechanisms of this processes. Our results suggest that hypericin–mediated photoprocesses in biological tissues may be useful in biomedical applications that require selective modification of connective tissues.

Nonlinear electro-optic tuning of plasmonic nano-filter

NASA Astrophysics Data System (ADS)

Kotb, Rehab; Ismail, Yehea; Swillam, Mohamed A.

2015-03-01

Efficient, easy and accurate tuning techniques to a plasmonic nano-filter are investigated. The proposed filter supports both blue and red shift in the resonance wavelength. By varying the refractive index with a very small change (in the order of 10-3), the resonance wavelength can be controlled efficiently. Using Pockels material, an electrical tuning to the response of the filter is demonstrated. In addition, the behavior of the proposed filter can be controlled optically using Kerr material. A new approach of multi-stage electro-optic controlling is introduced. By cascading two stages and filling the first stage with pockels material and the second stage with kerr material, the output response of the second stage can be controlled by controlling the output response of the first stage electrically. Due to the sharp response of the proposed filter, 60nm shift in the resonance wavelength per 10 voltages is achieved. This nano-filter has compact size, low loss, sharp response and wide range of tunabilty which is highly demandable in many biological and sensing applications.

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.

Maximizing root/rhizosphere efficiency to improve crop productivity and nutrient use efficiency in intensive agriculture of China.

PubMed

Shen, Jianbo; Li, Chunjian; Mi, Guohua; Li, Long; Yuan, Lixing; Jiang, Rongfeng; Zhang, Fusuo

2013-03-01

Root and rhizosphere research has been conducted for many decades, but the underlying strategy of root/rhizosphere processes and management in intensive cropping systems remain largely to be determined. Improved grain production to meet the food demand of an increasing population has been highly dependent on chemical fertilizer input based on the traditionally assumed notion of 'high input, high output', which results in overuse of fertilizers but ignores the biological potential of roots or rhizosphere for efficient mobilization and acquisition of soil nutrients. Root exploration in soil nutrient resources and root-induced rhizosphere processes plays an important role in controlling nutrient transformation, efficient nutrient acquisition and use, and thus crop productivity. The efficiency of root/rhizosphere in terms of improved nutrient mobilization, acquisition, and use can be fully exploited by: (1) manipulating root growth (i.e. root development and size, root system architecture, and distribution); (2) regulating rhizosphere processes (i.e. rhizosphere acidification, organic anion and acid phosphatase exudation, localized application of nutrients, rhizosphere interactions, and use of efficient crop genotypes); and (3) optimizing root zone management to synchronize root growth and soil nutrient supply with demand of nutrients in cropping systems. Experiments have shown that root/rhizosphere management is an effective approach to increase both nutrient use efficiency and crop productivity for sustainable crop production. The objectives of this paper are to summarize the principles of root/rhizosphere management and provide an overview of some successful case studies on how to exploit the biological potential of root system and rhizosphere processes to improve crop productivity and nutrient use efficiency.

Bio-inspired spiking neural network for nonlinear systems control.

PubMed

Pérez, Javier; Cabrera, Juan A; Castillo, Juan J; Velasco, Juan M

2018-08-01

Spiking neural networks (SNN) are the third generation of artificial neural networks. SNN are the closest approximation to biological neural networks. SNNs make use of temporal spike trains to command inputs and outputs, allowing a faster and more complex computation. As demonstrated by biological organisms, they are a potentially good approach to designing controllers for highly nonlinear dynamic systems in which the performance of controllers developed by conventional techniques is not satisfactory or difficult to implement. SNN-based controllers exploit their ability for online learning and self-adaptation to evolve when transferred from simulations to the real world. SNN's inherent binary and temporary way of information codification facilitates their hardware implementation compared to analog neurons. Biological neural networks often require a lower number of neurons compared to other controllers based on artificial neural networks. In this work, these neuronal systems are imitated to perform the control of non-linear dynamic systems. For this purpose, a control structure based on spiking neural networks has been designed. Particular attention has been paid to optimizing the structure and size of the neural network. The proposed structure is able to control dynamic systems with a reduced number of neurons and connections. A supervised learning process using evolutionary algorithms has been carried out to perform controller training. The efficiency of the proposed network has been verified in two examples of dynamic systems control. Simulations show that the proposed control based on SNN exhibits superior performance compared to other approaches based on Neural Networks and SNNs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Impact of deletion of the Lymantria dispar nucleopolyhedrovirus PEP gene on viral potency: expression of the green fluorescent protein prevents larval liquefaction

Treesearch

David S. Bischoff; James M. Slavicek

1999-01-01

The Lymantria dispar multicapsid nucleopolyhedrovirus (LdMNPV) is an effective biological control agent of the gypsy moth, L. dispar, but is not in general use because the high cost of production limits availability. In an effort to generate a more cost efficient LdMNPV biopesticide, two...

Gold nanoparticles as nanosources of heat

NASA Astrophysics Data System (ADS)

Baffou, Guillaume

2018-04-01

Under illumination at their plasmonic resonance wavelength, gold nanoparticles can absorb incident light and turn into efficient nanosources of heat remotely controllable by light. This fundamental scheme is at the basis of an active field of research coined thermoplasmonics and encompasses numerous applications in physics, chemistry and biology at the micro and nano scales. Warning, no authors found for 2018Phot........48.

FtsZ Cytoskeletal Filaments as a Template for Metallic Nanowire Fabrication.

PubMed

Ostrov, Nili; Fichman, Galit; Adler-Abramovich, Lihi; Gazit, Ehud

2015-01-01

Supramolecular protein assemblies can serve as templates for the fabrication of inorganic nanowires due to their morphological reproducibility and innate proclivity to form well-ordered structures. Amongst the variety of naturally occurring nano-scale assemblies, cytoskeletal fibers from diverse biological sources represent a unique family of scaffolds for biomimetics as they efficiently self-assemble in vitro in a controllable manner to form stable filaments. Here, we harness the bacterial FtsZ filament system as a scaffold for protein-based metal nanowires, and further demonstrate the control of wire alignment with the use of an external magnetic field. Due to the ease at which the bacterial FtsZ is overexpressed and purified, as well as the extensive studies of its ultrastructural properties and physiological significance, FtsZ filaments are an ideal substrate for large-scale production and chemical manipulation. Using a biologically compatible electroless metal deposition technique initiated by adsorption of platinum as a surface catalyst, we demonstrate the coating of assembled FtsZ filaments with iron, nickel, gold, and copper to fabricate continuous nanowires with diameters ranging from 10-50 nm. Organic-inorganic hybrid wires were analyzed using high-resolution field-emission-gun transmission and scanning electron microscopy, and confirmed by energy-dispersive elemental analysis. We also achieved alignment of ferrofluid-coated FtsZ filaments using an external magnetic field. Overall, we provide evidence for the robustness of the FtsZ filament system as a molecular scaffold, and offer an efficient, biocompatible procedure for facile bottom-up assembly of metallic wires on biological templates. We believe that bottom-up fabrication methods as reported herein significantly contribute to the expanding toolkit available for the incorporation of biological materials in nano-scale devices for electronic and electromechanical applications.

Inferring Biological Structures from Super-Resolution Single Molecule Images Using Generative Models

PubMed Central

Maji, Suvrajit; Bruchez, Marcel P.

2012-01-01

Localization-based super resolution imaging is presently limited by sampling requirements for dynamic measurements of biological structures. Generating an image requires serial acquisition of individual molecular positions at sufficient density to define a biological structure, increasing the acquisition time. Efficient analysis of biological structures from sparse localization data could substantially improve the dynamic imaging capabilities of these methods. Using a feature extraction technique called the Hough Transform simple biological structures are identified from both simulated and real localization data. We demonstrate that these generative models can efficiently infer biological structures in the data from far fewer localizations than are required for complete spatial sampling. Analysis at partial data densities revealed efficient recovery of clathrin vesicle size distributions and microtubule orientation angles with as little as 10% of the localization data. This approach significantly increases the temporal resolution for dynamic imaging and provides quantitatively useful biological information. PMID:22629348

Size variability of the unit building block of peripheral light-harvesting antennas as a strategy for effective functioning of antennas of variable size that is controlled in vivo by light intensity.

PubMed

Taisova, A S; Yakovlev, A G; Fetisova, Z G

2014-03-01

This work continuous a series of studies devoted to discovering principles of organization of natural antennas in photosynthetic microorganisms that generate in vivo large and highly effective light-harvesting structures. The largest antenna is observed in green photosynthesizing bacteria, which are able to grow over a wide range of light intensities and adapt to low intensities by increasing of size of peripheral BChl c/d/e antenna. However, increasing antenna size must inevitably cause structural changes needed to maintain high efficiency of its functioning. Our model calculations have demonstrated that aggregation of the light-harvesting antenna pigments represents one of the universal structural factors that optimize functioning of any antenna and manage antenna efficiency. If the degree of aggregation of antenna pigments is a variable parameter, then efficiency of the antenna increases with increasing size of a single aggregate of the antenna. This means that change in degree of pigment aggregation controlled by light-harvesting antenna size is biologically expedient. We showed in our previous work on the oligomeric chlorosomal BChl c superantenna of green bacteria of the Chloroflexaceae family that this principle of optimization of variable antenna structure, whose size is controlled by light intensity during growth of bacteria, is actually realized in vivo. Studies of this phenomenon are continued in the present work, expanding the number of studied biological materials and investigating optical linear and nonlinear spectra of chlorosomes having different structures. We show for oligomeric chlorosomal superantennas of green bacteria (from two different families, Chloroflexaceae and Oscillochloridaceae) that a single BChl c aggregate is of small size, and the degree of BChl c aggregation is a variable parameter, which is controlled by the size of the entire BChl c superantenna, and the latter, in turn, is controlled by light intensity in the course of cell culture growth.

Fundamentals of microfluidic cell culture in controlled microenvironments†

PubMed Central

Young, Edmond W. K.; Beebe, David J.

2010-01-01

Microfluidics has the potential to revolutionize the way we approach cell biology research. The dimensions of microfluidic channels are well suited to the physical scale of biological cells, and the many advantages of microfluidics make it an attractive platform for new techniques in biology. One of the key benefits of microfluidics for basic biology is the ability to control parameters of the cell microenvironment at relevant length and time scales. Considerable progress has been made in the design and use of novel microfluidic devices for culturing cells and for subsequent treatment and analysis. With the recent pace of scientific discovery, it is becoming increasingly important to evaluate existing tools and techniques, and to synthesize fundamental concepts that would further improve the efficiency of biological research at the microscale. This tutorial review integrates fundamental principles from cell biology and local microenvironments with cell culture techniques and concepts in microfluidics. Culturing cells in microscale environments requires knowledge of multiple disciplines including physics, biochemistry, and engineering. We discuss basic concepts related to the physical and biochemical microenvironments of the cell, physicochemical properties of that microenvironment, cell culture techniques, and practical knowledge of microfluidic device design and operation. We also discuss the most recent advances in microfluidic cell culture and their implications on the future of the field. The goal is to guide new and interested researchers to the important areas and challenges facing the scientific community as we strive toward full integration of microfluidics with biology. PMID:20179823

Copper metallothioneins.

PubMed

Calvo, Jenifer; Jung, Hunmin; Meloni, Gabriele

2017-04-01

Metallothioneins (MTs) are a class of low molecular weight and cysteine-rich metal binding proteins present in all the branches of the tree of life. MTs efficiently bind with high affinity several essential and toxic divalent and monovalent transition metals by forming characteristic polynuclear metal-thiolate clusters within their structure. MTs fulfil multiple biological functions related to their metal binding properties, with essential roles in both Zn(II) and Cu(I) homeostasis as well as metal detoxification. Depending on the organism considered, the primary sequence, and the specific physiological and metabolic status, Cu(I)-bound MT isoforms have been isolated, and their chemistry and biology characterized. Besides the recognized role in the biochemistry of divalent metals, it is becoming evident that unique biological functions in selectively controlling copper levels, its reactivity as well as copper-mediated biochemical processes have evolved in some members of the MT superfamily. Selected examples are reviewed to highlight the peculiar chemical properties and biological functions of copper MTs. © 2016 IUBMB Life, 69(4):236-245, 2017. © 2017 International Union of Biochemistry and Molecular Biology.

Vulnerability of women in southern Africa to infection with HIV: biological determinants and priority health sector interventions.

PubMed

Chersich, Matthew F; Rees, Helen V

2008-12-01

To review biomedical determinants of women's vulnerability to infection with HIV and interventions to counter this, within the southern African context. Apart from number of exposures, if any, several factors influence the efficiency of HIV transmission during sex. Acute HIV infection, with extraordinarily high semen viral load, in conjunction with concurrent partnerships maximizes this efficiency. Delaying sexual debut and avoiding HIV exposure among biologically and socially vulnerable youth is critical. Reducing unintended pregnancies keeps girls in school and prevents vertical (also possibly horizontal) transmission. Female condoms, especially newer versions, are an under-exploited prevention technology. Control of sexually transmitted infections (STI), which facilitate HIV acquisition and transmission, remains important, especially among the most at-risk populations. Pathogens, such as herpes simplex virus type 2, which contribute most to HIV transmission in southern Africa must be targeted, although the importance of bacterial vaginosis and Trichomonas vaginalis is under-recognized. Also, heavy episodic alcohol use affects sexual decision-making and condom skills. Moreover, prevailing social contexts, partly a consequence of poor leadership, constrain the behavioural 'choices' available for girls and women. Priority health sector interventions for preventing HIV are: male and female condom programming; prevention and control of STI; outreach to most vulnerable populations; HIV testing in all patient-provider encounters; male circumcision; and the integration of HIV prevention within sexual and reproductive health services. Future interventions during acute HIV infection and microbicides will reduce women's biological vulnerability. Far-reaching measures, such as sexual equity and alcohol control, create conditions necessary for achieving sustained prevention results. These are, however, contingent on stronger, more informed cultural and political leadership.

The Renilla luciferase gene as a reference gene for normalization of gene expression in transiently transfected cells.

PubMed

Jiwaji, Meesbah; Daly, Rónán; Pansare, Kshama; McLean, Pauline; Yang, Jingli; Kolch, Walter; Pitt, Andrew R

2010-12-31

The importance of appropriate normalization controls in quantitative real-time polymerase chain reaction (qPCR) experiments has become more apparent as the number of biological studies using this methodology has increased. In developing a system to study gene expression from transiently transfected plasmids, it became clear that normalization using chromosomally encoded genes is not ideal, at it does not take into account the transfection efficiency and the significantly lower expression levels of the plasmids. We have developed and validated a normalization method for qPCR using a co-transfected plasmid. The best chromosomal gene for normalization in the presence of the transcriptional activators used in this study, cadmium, dexamethasone, forskolin and phorbol-12-myristate 13-acetate was first identified. qPCR data was analyzed using geNorm, Normfinder and BestKeeper. Each software application was found to rank the normalization controls differently with no clear correlation. Including a co-transfected plasmid encoding the Renilla luciferase gene (Rluc) in this analysis showed that its calculated stability was not as good as the optimised chromosomal genes, most likely as a result of the lower expression levels and transfection variability. Finally, we validated these analyses by testing two chromosomal genes (B2M and ActB) and a co-transfected gene (Rluc) under biological conditions. When analyzing co-transfected plasmids, Rluc normalization gave the smallest errors compared to the chromosomal reference genes. Our data demonstrates that transfected Rluc is the most appropriate normalization reference gene for transient transfection qPCR analysis; it significantly reduces the standard deviation within biological experiments as it takes into account the transfection efficiencies and has easily controllable expression levels. This improves reproducibility, data validity and most importantly, enables accurate interpretation of qPCR data.

Postteneral Protein Feeding may Improve Biological Control Efficiency of Aphytis lingnanensis and Aphytis melinus

PubMed Central

Vanaclocha, Pilar; Papacek, Dan; Verdú, Maria Jesús; Urbaneja, Alberto

2014-01-01

Abstract The augmentative releases of mass-reared Aphytis spp. (Hymenoptera: Aphelinidae) parasitoids are widely used against armored scales. The nutritional status and the initial egg load of Aphytis spp. females are key to their success as biological control agents. For these reasons, this work focuses on the study of providing a protein feed to Aphytis lingnanensis (Compere) and A. melinus DeBach to improve the egg load before their release. The addition of protein to a honey diet during the first 2 d after the adult parasitoid emergence increased the initial egg load in both species of parasitoids by more than five eggs. Furthermore, the addition of protein increased the total number of eggs laid by A. lingnanensis on oleander scale, Aspidiotus nerii Bouché (Hemiptera: Diaspididae). In contrast, this effect was not observed on A. melinus probably because A. nerii is considered a suboptimal host for this parasitoid. The host-feeding activities of the two Aphytis species were differentially affected by the addition of protein to their diets. These results may have direct implications for augmentative biological control programs, especially during transportation from insectaries to the field, a period of time when parasitoids are deprived of hosts. PMID:25502042

Links between Iron Fertilization and Biological Pump Efficiency in the Bering Sea Over the Last 3.5 Myrs

NASA Astrophysics Data System (ADS)

Bartoli, G. L.; Studer, A. S.; Martinez Garcia, A.; Haug, G. H.

2011-12-01

The Bering Sea is one of the major sink of atmospheric CO2 today, due to the efficiency of its biological pump, despite a limitation by iron. Here we present records of iron fertilization by aeolian dust deposition (n-alkane concentration) and phytoplankton nutrient consumption (diatom-bound δ15N record) over the last 3.5 Myrs in the southwestern Bering Sea at Site U1341 drilled during IODP Expedition 323. During the Pliocene Epoch, when sea surface temperatures were 3-4°C warmer than today and sea-ice cover was reduced, the biological pump efficiency during glacial and interglacial stages was minimal, similar to Quaternary interglacials. Low iron deposition and weaker surface water stratification resulting in higher nutrient inputs contributed to reduce the biological pump efficiency until 1.5 Ma. After the intensification of glacial conditions in the Bering Sea and the increase in sea-ice cover and iron inputs, the biological pump efficiency progressively increased, reaching values similar to Quaternary glacials after the mid-Pleistocene transition.

Reproductive Biology and Functional Response of Dineulophus phtorimaeae, a Natural Enemy of the Tomato Moth, Tuta absoluta

PubMed Central

Savino, Vivina; Coviella, Carlos E.; Luna, María G.

2012-01-01

The tomato moth, Tuta absoluta (Lepidoptera: Gelechiidae), is a major pest in South America and is at present an important invasive species in the Mediterranean Basin. The larval stadium mines leaves, stems, and fruits, and chemical control is the most used control method in both its original range and the invaded distribution regions. Since current T. absoluta control strategies seem limited, biological control is a prominent tool to be applied abroad. The naturally occurring larval ectoparasitoid in Argentina and Chile Dineulophus phtorimaeae (Hymenoptera: Eulophidae) has been reported to have potential biocontrol efficiency. In this study, the ovigeny strategy of D. phtorimaeae was analyzed throughout the adult female lifetime, and the functional response of females offered a range of 2–15 T. absoluta larvae was measured over a 48-hour period. Mean D. phtorimaeae egg load was 4.15 eggs, and egg production resulted in extremely synovigenic behavior. Meanwhile, a decreasing number of eggs, due to resorption, was found. Proportions of attacked (host-fed and/or parasitized) and only host-fed hosts by the ectoparasitoid were density independent for the tested host range, exhibiting a type I functional response to T. absoluta, with an attack rate of 0.20 host larvae. Meanings of this reproductive strategy in evolutionary time as well as the consequences for augmentative biological control programs are discussed. PMID:23464576

Synthetic analog computation in living cells.

PubMed

Daniel, Ramiz; Rubens, Jacob R; Sarpeshkar, Rahul; Lu, Timothy K

2013-05-30

A central goal of synthetic biology is to achieve multi-signal integration and processing in living cells for diagnostic, therapeutic and biotechnology applications. Digital logic has been used to build small-scale circuits, but other frameworks may be needed for efficient computation in the resource-limited environments of cells. Here we demonstrate that synthetic analog gene circuits can be engineered to execute sophisticated computational functions in living cells using just three transcription factors. Such synthetic analog gene circuits exploit feedback to implement logarithmically linear sensing, addition, ratiometric and power-law computations. The circuits exhibit Weber's law behaviour as in natural biological systems, operate over a wide dynamic range of up to four orders of magnitude and can be designed to have tunable transfer functions. Our circuits can be composed to implement higher-order functions that are well described by both intricate biochemical models and simple mathematical functions. By exploiting analog building-block functions that are already naturally present in cells, this approach efficiently implements arithmetic operations and complex functions in the logarithmic domain. Such circuits may lead to new applications for synthetic biology and biotechnology that require complex computations with limited parts, need wide-dynamic-range biosensing or would benefit from the fine control of gene expression.

Iron control on global productivity: an efficient inverse model of the ocean's coupled phosphate and iron cycles.

NASA Astrophysics Data System (ADS)

Pasquier, B.; Holzer, M.; Frants, M.

2016-02-01

We construct a data-constrained mechanistic inverse model of the ocean's coupled phosphorus and iron cycles. The nutrient cycling is embedded in a data-assimilated steady global circulation. Biological nutrient uptake is parameterized in terms of nutrient, light, and temperature limitations on growth for two classes of phytoplankton that are not transported explicitly. A matrix formulation of the discretized nutrient tracer equations allows for efficient numerical solutions, which facilitates the objective optimization of the key biogeochemical parameters. The optimization minimizes the misfit between the modelled and observed nutrient fields of the current climate. We systematically assess the nonlinear response of the biological pump to changes in the aeolian iron supply for a variety of scenarios. Specifically, Green-function techniques are employed to quantify in detail the pathways and timescales with which those perturbations are propagated throughout the world oceans, determining the global teleconnections that mediate the response of the global ocean ecosystem. We confirm previous findings from idealized studies that increased iron fertilization decreases biological production in the subtropical gyres and we quantify the counterintuitive and asymmetric response of global productivity to increases and decreases in the aeolian iron supply.

Linking the rise of atmospheric oxygen to growth in the continental phosphorus inventory

NASA Astrophysics Data System (ADS)

Cox, Grant M.; Lyons, Timothy W.; Mitchell, Ross N.; Hasterok, Derrick; Gard, Matthew

2018-05-01

The concentration of atmospheric oxygen (pO2) is thought to have increased throughout Earth history, punctuated by rapid increases ca. 2.4 and 0.8 billion years ago near the beginning and end of the Proterozoic Eon. As photosynthesis is the largest source of free O2, the reigning paradigm of rising O2 levels centres around biologic metabolism. Here we show that the phosphorus content of igneous rocks correlates, in a first-order sense, with secular increases in O2 through time, suggesting that rising O2 levels are affected by long-term mantle cooling and its effect on the continental phosphorus inventory. Because phosphorus is the limiting nutrient for primary productivity, its availability has fundamental control over the efficiency of oxygenic photosynthesis, pointing to a previously unrecognized role of the solid Earth in biologic and atmospheric evolution. Furthermore, as many bio-essential elements are effectively incompatible in the mantle, this relationship has implications for any terrestrial planet. All planets will cool, and those with efficient plate tectonic convection will cool more rapidly. We are left concluding that the speed of such cooling may affect pattern of biological evolution on any habitable planet.

Effective production of biologically active water-soluble β-1,3-glucan by a coupled system of Agrobacterium sp. and Trichoderma harzianum.

PubMed

Liang, Ying; Zhu, Li; Gao, Minjie; Wu, Jianrong; Zhan, Xiaobei

2018-05-28

Water-soluble β-1,3-glucan (w-glucan) prepared from curdlan is reported to possess various bioactive and medicinal properties. To develop an efficient and cost-effective microbial fermentation method for the direct production of w-glucan, a coupled fermentation system of Agrobacterium sp. and Trichoderma harzianum (CFS-AT) was established. The effects of Tween-80, glucose flow rate, and the use of a dissolved oxygen (DO) control strategy on w-glucan production were assessed. The addition of 10 g L -1 Tween-80 to the CFS-AT enhanced w-glucan production, presumably by loosening the curdlan ultrastructure and increasing the efficiency of curdlan hydrolysis. A two-stage glucose and DO control strategy was optimal for w-glucan production. At the T. harzianum cell growth stage, the optimal glucose flow rate and agitation speed were 2.0 g L -1 hr -1 and 600 rpm, respectively, and at the w-glucan production stage, they were 0.5 g L -1 hr -1 and 400 rpm, respectively. W-glucan production reached 17.31 g L -1 , with a degree of polymerization of 19-25. Furthermore, w-glucan at high concentrations exhibited anti-tumor activity against MCF-7, HepG2, and Hela cancer cells in vitro. This study provides a novel, cost-effective, eco-friendly, and efficient microbial fermentation method for the direct production of biologically active w-glucan.

Cyber-physical experiments on the efficiency of swimming protocols

NASA Astrophysics Data System (ADS)

Wei, Nathaniel; Floryan, Daniel; van Buren, Tyler; Smits, Alexander

2016-11-01

We present results from experiments on a biologically inspired cyber-physical system, composed of a two-dimensional heaving and pitching rigid airfoil attached to a six component load cell, mounted to a traverse that can move along a water channel. A feedback controller, influenced by the apparatus of Mackowski and Williamson, introduces the effects of a fictional drag force specified by a virtual body profile and drives the traverse accordingly. Free-swimming protocols using the force-feedback system are compared with similar motions on a motionless traverse. The propulsive efficiency of burst-and-coast kinematics is also considered. Of particular interest are (1) the implementation of the cyber-physical control system with respect to the accessible experimental parameter space, (2) the impact of force-based streamwise actuation on experimental data, and (3) the effects of burst-and-coast motions on propulsive efficiency. The work was supported by the Office of Naval Research (ONR) under MURI Grant N00014-14-1-0533.

System contemplations for precision irrigation in agriculture

NASA Astrophysics Data System (ADS)

Schubert, Martin J. W.

2017-04-01

This communication contemplates political, biological and technical aspects for efficient and profitable irrigation in sustainable agriculture. A standard for irrigation components is proposed. The need for many, and three-dimensionally distributed, soil measurement points is explained, thus enabling the control of humidity in selected layers of earth. Combined wireless and wired data transmission is proposed. Energy harvesting and storage together with mechanical sensor construction are discussed.

Tanshinones as Effective Therapeutic Agents for Prostate Cancer

DTIC Science & Technology

2011-06-01

BW) and the routes of administration (oral gavaging with corn oil or dietary supplementation ) in inhibiting the growth of PC-3 tumors. We found...activity against PC3 tumors. Although dietary supplementation was labor-efficient, the intake of the active agents could not be controlled because the...basis for most modern pharmaceutical drugs. Herbal medicines usually contain multiple bioactive compo- nents with specific biological activities and

New Method for Producing Significant Amounts of RNA Labeled at Specific Sites | Center for Cancer Research

Cancer.gov

Among biomacromolecules, RNA is the most versatile, and it plays indispensable roles in almost all aspects of biology. For example, in addition to serving as mRNAs coding for proteins, RNAs regulate gene expression, such as controlling where, when, and how efficiently a gene gets expressed, participate in RNA processing, encode the genetic information of some viruses, serve as

Millennial-scale changes in atmospheric CO2 levels linked to the Southern Ocean carbon isotope gradient and dust flux

NASA Astrophysics Data System (ADS)

Ziegler, Martin; Diz, Paula; Hall, Ian R.; Zahn, Rainer

2013-06-01

The rise in atmospheric CO2 concentrations observed at the end of glacial periods has, at least in part, been attributed to the upwelling of carbon-rich deep water in the Southern Ocean. The magnitude of outgassing of dissolved CO2, however, is influenced by the biological fixation of upwelled inorganic carbon and its transfer back to the deep sea as organic carbon. The efficiency of this biological pump is controlled by the extent of nutrient utilization, which can be stimulated by the delivery of iron by atmospheric dust particles. Changes in nutrient utilization should be reflected in the δ13C gradient between intermediate and deep waters. Here we use the δ13C values of intermediate- and bottom-dwelling foraminifera to reconstruct the carbon isotope gradient between thermocline and abyssal water in the subantarctic zone of the South Atlantic Ocean over the past 360,000 years. We find millennial-scale oscillations of the carbon isotope gradient that correspond to changes in dust flux and atmospheric CO2 concentrations as reported from Antarctic ice cores. We interpret this correlation as a relationship between the efficiency of the biological pump and fertilization by dust-borne iron. As the correlation is exponential, we suggest that the sensitivity of the biological pump to dust-borne iron fertilization may be increased when the background dust flux is low.

Multilevel systems biology modeling characterized the atheroprotective efficiencies of modified dairy fats in a hamster model.

PubMed

Martin, Jean-Charles; Berton, Amélie; Ginies, Christian; Bott, Romain; Scheercousse, Pierre; Saddi, Alessandra; Gripois, Daniel; Landrier, Jean-François; Dalemans, Daniel; Alessi, Marie-Christine; Delplanque, Bernadette

2015-09-01

We assessed the atheroprotective efficiency of modified dairy fats in hyperlipidemic hamsters. A systems biology approach was implemented to reveal and quantify the dietary fat-related components of the disease. Three modified dairy fats (40% energy) were prepared from regular butter by mixing with a plant oil mixture, by removing cholesterol alone, or by removing cholesterol in combination with reducing saturated fatty acids. A plant oil mixture and a regular butter were used as control diets. The atherosclerosis severity (aortic cholesteryl-ester level) was higher in the regular butter-fed hamsters than in the other four groups (P < 0.05). Eighty-seven of the 1,666 variables measured from multiplatform analysis were found to be strongly associated with the disease. When aggregated into 10 biological clusters combined into a multivariate predictive equation, these 87 variables explained 81% of the disease variability. The biological cluster "regulation of lipid transport and metabolism" appeared central to atherogenic development relative to diets. The "vitamin E metabolism" cluster was the main driver of atheroprotection with the best performing transformed dairy fat. Under conditions that promote atherosclerosis, the impact of dairy fats on atherogenesis could be greatly ameliorated by technological modifications. Our modeling approach allowed for identifying and quantifying the contribution of complex factors to atherogenic development in each dietary setup. Copyright © 2015 the American Physiological Society.

Efficiently Photocontrollable or not? Biological Activity of Photoisomerizable Diarylethenes.

PubMed

Komarov, Igor V; Afonin, Sergii; Babii, Oleg; Schober, Tim; Ulrich, Anne S

2018-04-06

Diarylethene derivatives, whose biological activity can be reversibly changed by irradiation with light of different wavelengths, have shown promise as scientific tools and as candidates for photocontrollable drugs. However, examples demonstrating efficient photocontrol of their biological activity are still relatively rare. This concept article discusses the possible reasons for this situation and presents a critical analysis of existing data and hypotheses in this field, in order to extract the design principles enabling the construction of efficient photocontrollable diarylethene-based molecules. Papers addressing biologically relevant interactions between diarylethenes and biomolecules are analyzed; however, in most published cases, the efficiency of photocontrol in living systems remains to be demonstrated. We hope that this article will encourage further discussion of design principles, primarily among pharmacologists and synthetic and medicinal chemists. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Flexible Wing Base Micro Aerial Vehicles: Micro Air Vehicles (MAVs) for Surveillance and Remote Sensor Delivery

NASA Technical Reports Server (NTRS)

Ifju, Peter

2002-01-01

Micro Air Vehicles (MAVs) will be developed for tracking individuals, locating terrorist threats, and delivering remote sensors, for surveillance and chemical/biological agent detection. The tasks are: (1) Develop robust MAV platform capable of carrying sensor payload. (2) Develop fully autonomous capabilities for delivery of sensors to remote and distant locations. The current capabilities and accomplishments are: (1) Operational electric (inaudible) 6-inch MAVs with novel flexible wing, providing superior aerodynamic efficiency and control. (2) Vision-based flight stability and control (from on-board cameras).

Optimization of substrate preparation for oyster mushroom (Pleurotus ostreatus) cultivation by studying different raw materials and substrate preparation conditions (composting: phases I and II).

PubMed

Vieira, Fabrício Rocha; de Andrade, Meire Cristina Nogueira

2016-11-01

In recent years, oyster mushroom (Pleurotus ostreatus) has become one of the most cultivated mushrooms in the world, mainly in Brazil. Among many factors involved in a mushroom production, substrate preparation is the most critical step, which can be influenced by composting management techniques. Looking forward to optimizing the substrate preparation process, were tested different composting conditions (7 and 14 days of composting with or without conditioning), potential raw materials (decumbens grass, brizantha grass and sugarcane straw) and nitrogen supplementation (with or without wheat bran) on oyster mushroom yield and biological efficiency (BE). The substrate composted for 7 days with conditioning showed higher yield and biological efficiency of mushroom (24.04 and 100.54 %, respectively). Substrates without conditioning (7 and 14 days of composting) showed smaller mushroom yield and biological efficiency. Among the raw materials tested, brizantha grass showed higher mushroom yield followed by decumbens grass, sugarcane straw and wheat straw (28.5, 24.32, 23.5 and 19.27 %, respectively). Brizantha grass also showed higher biological efficiency followed by sugarcane straw, decumbens grass and wheat straw (123.95, 103.70, 96.90 and 86.44 %, respectively). Supplementation with wheat bran improved yield and biological efficiency in all substrate formulations tested; thus, oyster mushroom yield and biological efficiency were influenced by substrate formulation (raw materials), supplementation and composting conditions.

Integrative systems control approach for reactivating Kaposi's sarcoma-associated herpesvirus (KSHV) with combinatory drugs

PubMed Central

Sun, Chien-Pin; Usui, Takane; Yu, Fuqu; Al-Shyoukh, Ibrahim; Shamma, Jeff; Sun, Ren; Ho, Chih-Ming

2009-01-01

Cells serve as basic units of life and represent intricate biological molecular systems. The vast number of cellular molecules with their signaling and regulatory circuitries forms an intertwined network. In this network, each pathway interacts non-linearly with others through different intermediates. Thus, the challenge of manipulating cellular functions for desired outcomes, such as cancer eradication and controlling viral infection lies within the integrative system of regulatory circuitries. By using a closed-loop system control scheme, we can efficiently analyze biological signaling networks and manipulate their behavior through multiple stimulations on a collection of pathways. Specifically, we aimed to maximize the reactivation of Kaposi's Sarcoma-associated Herpesvirus (KSHV) in a Primary Effusion Lymphoma cell line. The advantage of this approach is that it is well-suited to study complex integrated systems; it circumvents the need for detailed information of individual signaling components; and it investigates the network as a whole by utilizing key systemic outputs as indicators. PMID:19851479

Integrative systems control approach for reactivating Kaposi's sarcoma-associated herpesvirus (KSHV) with combinatory drugs.

PubMed

Sun, Chien-Pin; Usui, Takane; Yu, Fuqu; Al-Shyoukh, Ibrahim; Shamma, Jeff; Sun, Ren; Ho, Chih-Ming

2009-01-01

Cells serve as basic units of life and represent intricate biological molecular systems. The vast number of cellular molecules with their signaling and regulatory circuitries forms an intertwined network. In this network, each pathway interacts non-linearly with others through different intermediates. Thus, the challenge of manipulating cellular functions for desired outcomes, such as cancer eradication and controlling viral infection lies within the integrative system of regulatory circuitries. By using a closed-loop system control scheme, we can efficiently analyze biological signaling networks and manipulate their behavior through multiple stimulations on a collection of pathways. Specifically, we aimed to maximize the reactivation of Kaposi's Sarcoma-associated Herpesvirus (KSHV) in a Primary Effusion Lymphoma cell line. The advantage of this approach is that it is well-suited to study complex integrated systems; it circumvents the need for detailed information of individual signaling components; and it investigates the network as a whole by utilizing key systemic outputs as indicators.

Bioimpedance for the spot measurement of tissue density

NASA Astrophysics Data System (ADS)

Dylke, E. S.; Ward, L. C.; Stannard, C.; Leigh, A.; Kilbreath, S. L.

2013-04-01

Long-standing lymphoedema is characterised by tissues changes which are currently not detectable using bioimpedance spectroscopy. It has been suggested that a combination of bipolar and tetrapolar measurements may be used to detect these tissues changes for a single site in the transverse direction. This was technique was trialled in a group of control participants with no history of lymphoedema or recent upper limb trauma. Repeated spot measurements were done without removal of electrodes to determine biological variability as well as with removal of electrodes to determine technical reproducibility. The inter-limb spot ratio of the controls was then compared to that of a number of women previously diagnosed with secondary lymphoedema in the forearm. Biological variability was not found to greatly influence repeated measures but only moderate technical reliability was found despite excellent co-efficient of variation for the majority of the measurements. A difference was seen between those with more severe swelling and the controls. This novel technique shows promise in detecting tissue changes associated with long-standing lymphoedema.

Conjugated Polymer for Voltage-Controlled Release of Molecules.

PubMed

Liu, Shenghua; Fu, Ying; Li, Guijun; Li, Li; Law, Helen Ka-Wai; Chen, Xianfeng; Yan, Feng

2017-09-01

Conjugated polymers are attractive in numerous biological applications because they are flexible, biocompatible, cost-effective, solution-processable, and electronic/ionic conductive. One interesting application is for controllable drug release, and this has been realized previously using organic electronic ion pumps. However, organic electronic ion pumps show high operating voltages and limited transportation efficiency. Here, the first report of low-voltage-controlled molecular release with a novel organic device based on a conjugated polymer poly(3-hexylthiophene) is presented. The releasing rate of molecules can be accurately controlled by the duration of the voltage applied on the device. The use of a handy mobile phone to remotely control the releasing process and its application in delivering an anticancer drug to treat cancer cells are also successfully demonstrated. The working mechanism of the device is attributed to the unique switchable permeability of poly(3-hexylthiophene) in aqueous solutions under a bias voltage that can tune the wettability of poly(3-hexylthiophene) via oxidation or reduction processes. The organic devices are expected to find many promising applications for controllable drug delivery in biological systems. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Trichoderma harzianum strain SQR-T37 and its bio-organic fertilizer could control Rhizoctonia solani damping-off disease in cucumber seedlings mainly by the mycoparasitism.

PubMed

Huang, Xinqi; Chen, Lihua; Ran, Wei; Shen, Qirong; Yang, Xingming

2011-08-01

Damping-off disease is caused by Rhizoctonia solani and leads to serious loss in many crops. Biological control is an efficient and environmentally friendly way to prevent damping-off disease. Optical micrographs, scanning electron micrographs, and the determination of hydrolytic enzymes were used to investigate the antagonism of Trichoderma harzianum SQR-T37 (SQR-T37) against R. solani. Experiments were performed in pots to assess the in vivo disease-control efficiency of SQR-T37 and bio-organic fertilizer. The results indicate that the mycoparasitism was the main mechanism accounting for the antagonistic activity of SQR-T37. In one experiment, the population of R. solani was decreased from 10(6) internal transcribed spacer (ITS) copies per gram soil to 10(4) ITS copies per gram soil by the presence of the antagonist. In this experiment, 45% of the control efficiency was obtained when 8 g of SQR-T37 hyphae per gram soil was applied. In a second experiment, as much as 81.82% of the control efficiency was obtained when bio-organic fertilizer (SQR-T37 fermented organic fertilizer, BIO) was applied compared to only 27.27% of the control efficiency when only 4 g of SQR-T37 hyphae per gram soil was applied. Twenty days after incubation, the population of T. harzianum was 4.12 × 10(7) ITS copies per gram soil in the BIO treatment, which was much higher than that in the previous treatment (8.77 × 10(5) ITS copies per gram soil), where only SQR-T37 was applied. The results indicated that SQR-T37 was a potent antagonist against R. solani in a mycoparasitic way that decreased the population of the pathogen. Applying BIO was more efficient than SQR-T37 application alone because it stabilized the population of the antagonist.

Quality Leadership and Quality Control

PubMed Central

Badrick, Tony

2003-01-01

Different quality control rules detect different analytical errors with varying levels of efficiency depending on the type of error present, its prevalence and the number of observations. The efficiency of a rule can be gauged by inspection of a power function graph. Control rules are only part of a process and not an end in itself; just as important are the trouble-shooting systems employed when a failure occurs. 'Average of patient normals' may develop as a usual adjunct to conventional quality control serum based programmes. Acceptable error can be based on various criteria; biological variation is probably the most sensible. Once determined, acceptable error can be used as limits in quality control rule systems. A key aspect of an organisation is leadership, which links the various components of the quality system. Leadership is difficult to characterise but its key aspects include trust, setting an example, developing staff and critically setting the vision for the organisation. Organisations also have internal characteristics such as the degree of formalisation, centralisation, and complexity. Medical organisations can have internal tensions because of the dichotomy between the bureaucratic and the shadow medical structures. PMID:18568046

Genetic and Biological Analysis of Colombian Phthorimaea operculella Granulovirus Isolated from Tecia solanivora (Lepidoptera: Gelechiidae)▿

PubMed Central

Espinel-Correal, Carlos; Léry, Xavier; Villamizar, Laura; Gómez, Juliana; Zeddam, Jean Louis; Cotes, Alba Marina; López-Ferber, Miguel

2010-01-01

Tecia solanivora (Lepidoptera: Gelechiidae) is an invasive potato pest of the north of South America that recently colonized zones where Phthorimaea operculella (Lepidoptera: Gelechiidae), a taxonomically related insect, was established. Nowadays, both species can be found in most areas in different proportions. The Phthorimaea operculella granulovirus (PhopGV) was found to efficiently control P. operculella and was used as a biopesticide in storage conditions. However, no appropriate biological control methods exist for T. solanivora, and the use of granulovirus isolates would provide a solution. The Colombian Corporation for Agricultural Research (CORPOICA) carried out several T. solanivora larva samplings in Colombia with the aim of finding potential isolates. Five geographical granulovirus isolates from T. solanivora (VG001, VG002, VG003, VG004, and VG005) were found, and molecular analysis by REN profiles shows three different genotypic variants in Colombia. Analysis of their genomes revealed their relatedness to PhopGV. Two isolates exhibited submolar bands in their REN patterns, suggesting a mixture of viral genotypes. These data were confirmed by PCR amplification and sequencing of particular regions of the viral genomes. Their biological activity was assayed on both hosts, T. solanivora and P. operculella. A significantly higher pathogenicity in both hosts was observed with isolates VG001 and VG005 than with isolate VG003 or a Peruvian isolate (from P. operculella) used as a reference in the bioassay. Based on their molecular and biological activity characteristics, VG001 and VG005 isolates should be selected for further analysis in order to establish their potential as biological control agents. PMID:20870793

Biology and management of two important Conyza weeds: a global review.

PubMed

Bajwa, Ali Ahsan; Sadia, Sehrish; Ali, Hafiz Haider; Jabran, Khawar; Peerzada, Arslan Masood; Chauhan, Bhagirath Singh

2016-12-01

Weed management is one of the prime concerns for sustainable crop production. Conyza bonariensis and Conyza canadensis are two of the most problematic, noxious, invasive and widespread weeds in modern-day agriculture. The biology, ecology and interference of C. bonariensis and C. canadensis have been reviewed here to highlight pragmatic management options. Both these species share a unique set of biological features, which enables them to invade and adapt a wide range of environmental conditions. Distinct reproductive biology and an efficient seed dispersal mechanism help these species to spread rapidly. Ability to interfere strongly and to host crop pests makes these two species worst weeds of cropping systems. These weed species cause 28-68 % yield loss in important field crops such as soybean and cotton every year. These weeds are more prevalent in no-till systems and, thus, becoming a major issue in conservation agriculture. Cultural practices such as crop rotations, seed rate manipulation, mulching, inter-row tillage and narrow row spacing may provide an effective control of these species. However, such methods are not feasible and applicable under all types of conditions. Different herbicides also provide a varying degree of control depending on crop, agronomic practices, herbicide dose, application time and season. However, both these species have evolved resistance against multiple herbicides, including glyphosate and paraquat. The use of alternative herbicides and integrated management strategies may provide better control of herbicide-resistant C. bonariensis and C. canadensis. Management plans based on the eco-biological interactions of these species may prove sustainable in the future.

Bioactivity of Piper hispidinervum (Piperales: Piperaceae) and Syzygium aromaticum (Myrtales: Myrtaceae) oils, with or without formulated Bta on the biology and immunology of Spodoptera frugiperda (Lepidoptera: Noctuidae).

PubMed

Cruz, G S; Wanderley-Teixeira, V; Oliveira, J V; Correia, A A; Breda, M O; Alves, T J S; Cunha, F M; Teixeira, A A C; Dutra, K A; Navarro, D M A F

2014-02-01

The combination of essential oils and Bacillus thuringiensis Berliner may represent an interesting control strategy. Thus, the study tested the following hypothesis: the combination of long pepper oil (Piper hispidinervum L.) and clove (Syzygium aromaticum L.) oils in two concentrations with Xentari WG (Bta) yields a more effective control of Spodoptera frugiperda (JE Smith) (Lepidoptera: Noctuidae) affecting biological and reproductive parameters and leading to changes in the levels of phenoloxidase and nitric oxide in the hemolymph of the pest. The results demonstrate that only long pepper oil, at the highest concentration with Xentari WG (Bta), promotes reduced larval survival. However, both oils with or without the insecticide interfere in the biology and humoral immunity of S.frugiperda. All treatments caused a decrease in the amount of eggs, except for the clove oil at both concentrations without Bta. Therefore, the use of these oils is a promising alternative for the integrated management of S. frugiperda; however, its association with Bta demonstrated no significant increase in their efficiency.

The magnetic graphene-based nanocomposite: An efficient anticancer delivery system

NASA Astrophysics Data System (ADS)

Jafarizad, Abbas; Jaymand, Mehdi; Taghizadehghalehjougi, Ali; Mohammadi-Nasr, Saeed; Jabbari, Amir Mohammad

2018-01-01

The aim of this study is the development of an efficient anticancer drug delivery nanosystem using PEGylated graphene oxide/magnetite nanoparticles (PEG-GO/Fe3O4). The nanosystem was loaded with mitoxantrone (MTX) as a universal anticancer drug. The cytotoxicity effect of the MTX-loaded GO-PEG/Fe3O4 nanocomposite was studied against U87 MG cell line using MTT cell viablity assay. The mechanism of action, the genes contributed in apoptosis (Casp 9, and Casp 3) and survival (BcL-2, BAX) have been investigated using quantitative real time-PCR. As the results of biological assays, controlled drug release behavior of the developed nanosystem as well as the inherent physicochemical and biological characteristics of both magnetit nanoparticles and graphene nanomaterials, we envision that the GO-PEG/Fe3O4 nanocomposite may be applied as enhanced drug delivery system for various cancer therapies (e.g., brain cancer) using both chemo- and photothermal therapy methods.

Efficient 3D kinetic Monte Carlo method for modeling of molecular structure and dynamics.

PubMed

Panshenskov, Mikhail; Solov'yov, Ilia A; Solov'yov, Andrey V

2014-06-30

Self-assembly of molecular systems is an important and general problem that intertwines physics, chemistry, biology, and material sciences. Through understanding of the physical principles of self-organization, it often becomes feasible to control the process and to obtain complex structures with tailored properties, for example, bacteria colonies of cells or nanodevices with desired properties. Theoretical studies and simulations provide an important tool for unraveling the principles of self-organization and, therefore, have recently gained an increasing interest. The present article features an extension of a popular code MBN EXPLORER (MesoBioNano Explorer) aiming to provide a universal approach to study self-assembly phenomena in biology and nanoscience. In particular, this extension involves a highly parallelized module of MBN EXPLORER that allows simulating stochastic processes using the kinetic Monte Carlo approach in a three-dimensional space. We describe the computational side of the developed code, discuss its efficiency, and apply it for studying an exemplary system. Copyright © 2014 Wiley Periodicals, Inc.

Spectral and spatial shaping of a laser-produced ion beam for radiation-biology experiments

NASA Astrophysics Data System (ADS)

Pommarel, L.; Vauzour, B.; Mégnin-Chanet, F.; Bayart, E.; Delmas, O.; Goudjil, F.; Nauraye, C.; Letellier, V.; Pouzoulet, F.; Schillaci, F.; Romano, F.; Scuderi, V.; Cirrone, G. A. P.; Deutsch, E.; Flacco, A.; Malka, V.

2017-03-01

The study of radiation biology on laser-based accelerators is most interesting due to the unique irradiation conditions they can produce, in terms of peak current and duration of the irradiation. In this paper we present the implementation of a beam transport system to transport and shape the proton beam generated by laser-target interaction for in vitro irradiation of biological samples. A set of four permanent magnet quadrupoles is used to transport and focus the beam, efficiently shaping the spectrum and providing a large and relatively uniform irradiation surface. Real time, absolutely calibrated, dosimetry is installed on the beam line, to enable shot-to-shot control of dose deposition in the irradiated volume. Preliminary results of cell sample irradiation are presented to validate the robustness of the full system.

The use of 'Omics technology to rationally improve industrial mammalian cell line performance.

PubMed

Lewis, Amanda M; Abu-Absi, Nicholas R; Borys, Michael C; Li, Zheng Jian

2016-01-01

Biologics represent an increasingly important class of therapeutics, with 7 of the 10 top selling drugs from 2013 being in this class. Furthermore, health authority approval of biologics in the immuno-oncology space is expected to transform treatment of patients with debilitating and deadly diseases. The growing importance of biologics in the healthcare field has also resulted in the recent approvals of several biosimilars. These recent developments, combined with pressure to provide treatments at lower costs to payers, are resulting in increasing need for the industry to quickly and efficiently develop high yielding, robust processes for the manufacture of biologics with the ability to control quality attributes within narrow distributions. Achieving this level of manufacturing efficiency and the ability to design processes capable of regulating growth, death and other cellular pathways through manipulation of media, feeding strategies, and other process parameters will undoubtedly be facilitated through systems biology tools generated in academic and public research communities. Here we discuss the intersection of systems biology, 'Omics technologies, and mammalian bioprocess sciences. Specifically, we address how these methods in conjunction with traditional monitoring techniques represent a unique opportunity to better characterize and understand host cell culture state, shift from an empirical to rational approach to process development and optimization of bioreactor cultivation processes. We summarize the following six key areas: (i) research applied to parental, non-recombinant cell lines; (ii) systems level datasets generated with recombinant cell lines; (iii) datasets linking phenotypic traits to relevant biomarkers; (iv) data depositories and bioinformatics tools; (v) in silico model development, and (vi) examples where these approaches have been used to rationally improve cellular processes. We critically assess relevant and state of the art research being conducted in academic, government and industrial laboratories. Furthermore, we apply our expertise in bioprocess to define a potential model for integration of these systems biology approaches into biologics development. © 2015 Wiley Periodicals, Inc.

Use of maize wastewater for the cultivation of the Pleurotus spp. mushroom and optimization of its biological efficiency.

PubMed

Loss, Edenes; Royer, Andrea Rafaela; Barreto-Rodrigues, Marcio; Barana, Ana Claudia

2009-07-30

This study evaluated the Pleurotus spp. mushroom production process using an effluent from the maize agroindustrial process as a carbon and nitrogen source and as a wetting agent. A complete experimental design based on factorial planning was used to optimize the biological efficiency and evaluate the effect of the concentration of effluent, pH and species of Pleurotus. The results indicated that the effluent affects the biological efficiency for the production of both species of mushrooms at all pH values studied. The maximum biological efficiency predicted by the model (81.36%) corresponded to the point defined by the effluent contents (X(1)=1), pH (X(2)=-1) and fungus species (X(3)=1), specifically 50%, 5.0 and P. floridae, respectively. The results demonstrated that the effluent is a good alternative for the production of Pleurotus mushrooms.

Cell Biology: Control of Partner Lifetime in a Plant-Fungus Relationship.

PubMed

Gutjahr, Caroline; Parniske, Martin

2017-06-05

Arbuscules are tree-shaped fungal structures inside plant root cells that facilitate the exchange of nutrients delivered by the fungus with carbon sources from the host. To maintain symbiotic efficiency, plant cells can trigger degeneration of underperforming arbuscules. A recent study reveals the first transcription factor, which induces genes encoding hydrolytic enzymes, to mediate arbuscule degeneration. Copyright © 2017 Elsevier Ltd. All rights reserved.

Ecological Interactions Affecting the Efficacy of Aphidius colemani in Greenhouse Crops

PubMed Central

Prado, Sara G.; Jandricic, Sarah E.; Frank, Steven D.

2015-01-01

Aphidius colemani Viereck (Hymenoptera: Braconidae) is a solitary endoparasitoid used for biological control of many economically important pest aphids. Given its widespread use, a vast array of literature on this natural enemy exists. Though often highly effective for aphid suppression, the literature reveals that A. colemani efficacy within greenhouse production systems can be reduced by many stressors, both biotic (plants, aphid hosts, other natural enemies) and abiotic (climate and lighting). For example, effects from 3rd and 4th trophic levels (fungal-based control products, hyperparasitoids) can suddenly decimate A. colemani populations. But, the most chronic negative effects (reduced parasitoid foraging efficiency, fitness) seem to be from stressors at the first trophic level. Negative effects from the 1st trophic level are difficult to mediate since growers are usually constrained to particular plant varieties due to market demands. Major research gaps identified by our review include determining how plants, aphid hosts, and A. colemani interact to affect the net aphid population, and how production conditions such as temperature, humidity and lighting affect both the population growth rate of A. colemani and its target pest. Decades of research have made A. colemani an essential part of biological control programs in greenhouse crops. Future gains in A. colemani efficacy and aphid biological control will require an interdisciplinary, systems approach that considers plant production and climate effects at all trophic levels. PMID:26463203

[Biological evaluation of a protein mixture intended for enteral nutrition].

PubMed

Meneses, J Olza; Foulquie, J Porres; Valero, G Urbano; de Victoria, E Martínez; Hernández, A Gil

2008-01-01

Enteral nutrition is the best way to feed or supplement the diet when gastrointestinal tract functions of patients are partially or totally preserved. Whenever total enteral nutrition is needed, it represents the only source of nutrients for patients. Thus, it is mandatory to ensure that high biological value proteins are included in enteral formulae. To assess the biological quality of a protein blend constituted by 50% potassium caseinate, 25% whey protein and 25% pea protein intended to be used in enteral nutrition products. Forty Wistar rats (20 male and 20 female), with initial body weight of 51 g, where divided into four groups and feed for 10 days with: casein (Control), experimental protein blend (Experimental), liophylized normo- and hyperproteic enteral nutrition formulae adapted to the animal nutritional requirements (Normoproteic and Hyperproteic). Protein efficiency ratio (PER), apparent digestibility coefficient (ADC), relationship between retained and absorbed nitrogen (R/A) and relationship between retained and consumed nitrogen (R/I) where calculated. Experimental and control groups had similar values for all analysed indices (PER, ADC, R/A and R/I). These indices where also similar between normo and hyperproteic groups, but lower than experimental and control groups, except in PER, where normoproteic group was either similar to control and hiperproteic group. The quality of the protein blend used in this study is high. It is a good protein source to be used in the development of new enteral nutritional products.

Biological network motif detection and evaluation

PubMed Central

2011-01-01

Background Molecular level of biological data can be constructed into system level of data as biological networks. Network motifs are defined as over-represented small connected subgraphs in networks and they have been used for many biological applications. Since network motif discovery involves computationally challenging processes, previous algorithms have focused on computational efficiency. However, we believe that the biological quality of network motifs is also very important. Results We define biological network motifs as biologically significant subgraphs and traditional network motifs are differentiated as structural network motifs in this paper. We develop five algorithms, namely, EDGEGO-BNM, EDGEBETWEENNESS-BNM, NMF-BNM, NMFGO-BNM and VOLTAGE-BNM, for efficient detection of biological network motifs, and introduce several evaluation measures including motifs included in complex, motifs included in functional module and GO term clustering score in this paper. Experimental results show that EDGEGO-BNM and EDGEBETWEENNESS-BNM perform better than existing algorithms and all of our algorithms are applicable to find structural network motifs as well. Conclusion We provide new approaches to finding network motifs in biological networks. Our algorithms efficiently detect biological network motifs and further improve existing algorithms to find high quality structural network motifs, which would be impossible using existing algorithms. The performances of the algorithms are compared based on our new evaluation measures in biological contexts. We believe that our work gives some guidelines of network motifs research for the biological networks. PMID:22784624

An improved method to quantitate mature plant microRNA in biological matrices using modified periodate treatment and inclusion of internal controls.

PubMed

Huang, Haiqiu; Roh, Jamin; Davis, Cindy D; Wang, Thomas T Y

2017-01-01

MicroRNAs (miRNAs) ubiquitously exist in microorganisms, plants, and animals, and appear to modulate a wide range of critical biological processes. However, no definitive conclusion has been reached regarding the uptake of exogenous dietary small RNAs into mammalian circulation and organs and cross-kingdom regulation. One of the critical issues is our ability to assess and distinguish the origin of miRNAs. Although periodate oxidation has been used to differentiate mammalian and plant miRNAs, validation of treatment efficiency and the inclusion of proper controls for this method were lacking in previous studies. This study aimed to address: 1) the efficiency of periodate treatment in a plant or mammalian RNA matrix, and 2) the necessity of inclusion of internal controls. We designed and tested spike-in synthetic miRNAs in various plant and mammalian matrices and showed that they can be used as a control for the completion of periodate oxidation. We found that overloading the reaction system with high concentration of RNA resulted in incomplete oxidation of unmethylated miRNA. The abundant miRNAs from soy and corn were analyzed in the plasma, liver, and fecal samples of C57BL/6 mice fed a corn and soy-based chow diet using our improved methodology. The improvement resulted in the elimination of the false positive detection in the liver, and we did not detect plant miRNAs in the mouse plasma or liver samples. In summary, an improved methodology was developed for plant miRNA detection that appears to work well in different sample matrices.

The dynamic ocean biological pump: Insights from a global compilation of particulate organic carbon, CaCO3, and opal concentration profiles from the mesopelagic

NASA Astrophysics Data System (ADS)

Lam, Phoebe J.; Doney, Scott C.; Bishop, James K. B.

2011-09-01

We have compiled a global data set of 62 open ocean profiles of particulate organic carbon (POC), CaCO3, and opal concentrations collected by large volume in situ filtration in the upper 1000 m over the last 30 years. We define concentration-based metrics for the strength (POC concentration at depth) and efficiency (attenuation of POC with depth in the mesopelagic) of the biological pump. We show that the strength and efficiency of the biological pump are dynamic and are characterized by a regime of constant and high transfer efficiency at low to moderate surface POC and a bloom regime where the height of the bloom is characterized by a weak deep biological pump and low transfer efficiency. The variability in POC attenuation length scale manifests in a clear decoupling between the strength of the shallow biological pump (e.g., POC at the export depth) and the strength of the deep biological pump (POC at 500 m). We suggest that the paradigm of diatom-driven export production is driven by a too restrictive perspective on upper mesopelagic dynamics. Indeed, our full mesopelagic analysis suggests that large, blooming diatoms have low transfer efficiency and thus may not export substantially to depth; rather, our analysis suggests that ecosystems characterized by smaller cells and moderately high %CaCO3 have a high mesopelagic transfer efficiency and can have higher POC concentrations in the deep mesopelagic even with relatively low surface or near-surface POC. This has negative implications for the carbon sequestration prospects of deliberate iron fertilization.

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

Synthetic predator cues impair immune function and make the biological pesticide Bti more lethal for vector mosquitoes.

PubMed

Op De Beeck, Lin; Janssens, Lizanne; Stoks, Robby

2016-03-01

The control of vector mosquitoes is one of the biggest challenges facing humankind with the use of chemical pesticides often leading to environmental impact and the evolution of resistance. Although to a lesser extent, this also holds for Bacillus thuringiensis israelensis (Bti), the most widely used biological pesticide to control mosquito populations. This raises the need for the development of integrated pest management strategies that allow the reduction of Bti concentrations without loss of the mosquito control efficiency. To this end, we tested in a laboratory experiment the combined effects of larval exposure to a sublethal Bti concentration and predation risk cues on life history and physiology of larval and adult Culex pipiens mosquitoes. Besides natural predator kairomones and prey alarm cues, we also tested synthetic kairomones of Notonecta predators. Neither Bti nor predation risk cues affected mortality, yet when both stressors were combined mortality increased on average by 133% compared to the treatment with only predation risk cues. This synergistic interaction was also present when Bti was combined with synthetic kairomones. This was further reflected in changes of the composite index of population performance, which suggested lowered per capita growth rates in mosquitoes exposed to Bti but only when Bti was combined with synthetic kairomones. Furthermore, predation risk cues shortened larval development time, reduced mass at metamorphosis in males, and had an immunosuppressive effect in larval and adult mosquitoes which may affect the mosquito vector competence. We provide the first demonstration that synthetic kairomones may generate similar effects on prey as natural kairomones. The identified immunosuppressive effect of synthetic kairomones and the novel lethal synergism type between a biological pesticide and synthetic predator kairomones provide an important proof of principle illustrating the potential of this combination for integrated mosquito control and should in a next step be evaluated under more natural conditions. It may guide novel integrated pest management programs with Bti that incorporate synthetic kairomones and thereby can reduce environmental impact and evolution of resistance creating more efficient and sustainable mosquito control.

Applying the Nernst equation to simulate redox potential variations for biological nitrification and denitrification processes.

PubMed

Chang, Cheng-Nan; Cheng, Hong-Bang; Chao, Allen C

2004-03-15

In this paper, various forms of Nernst equations have been developed based on the real stoichiometric relationship of biological nitrification and denitrification reactions. Instead of using the Nernst equation based on a one-to-one stoichiometric relation for the oxidizing and the reducing species, the basic Nernst equation is modified into slightly different forms. Each is suitable for simulating the redox potential (ORP) variation of a specific biological nitrification or denitrification process. Using the data published in the literature, the validity of these developed Nernst equations has been verified by close fits of the measured ORP data with the calculated ORP curve. The simulation results also indicate that if the biological process is simulated using an incorrect form of Nernst equation, the calculated ORP curve will not fit the measured data. Using these Nernst equations, the ORP value that corresponds to a predetermined degree of completion for the biochemical reaction can be calculated. Thus, these Nernst equations will enable a more efficient on-line control of the biological process.

Bioprocess systems engineering: transferring traditional process engineering principles to industrial biotechnology.

PubMed

Koutinas, Michalis; Kiparissides, Alexandros; Pistikopoulos, Efstratios N; Mantalaris, Athanasios

2012-01-01

The complexity of the regulatory network and the interactions that occur in the intracellular environment of microorganisms highlight the importance in developing tractable mechanistic models of cellular functions and systematic approaches for modelling biological systems. To this end, the existing process systems engineering approaches can serve as a vehicle for understanding, integrating and designing biological systems and processes. Here, we review the application of a holistic approach for the development of mathematical models of biological systems, from the initial conception of the model to its final application in model-based control and optimisation. We also discuss the use of mechanistic models that account for gene regulation, in an attempt to advance the empirical expressions traditionally used to describe micro-organism growth kinetics, and we highlight current and future challenges in mathematical biology. The modelling research framework discussed herein could prove beneficial for the design of optimal bioprocesses, employing rational and feasible approaches towards the efficient production of chemicals and pharmaceuticals.

Bioprocess systems engineering: transferring traditional process engineering principles to industrial biotechnology

PubMed Central

Koutinas, Michalis; Kiparissides, Alexandros; Pistikopoulos, Efstratios N.; Mantalaris, Athanasios

2013-01-01

The complexity of the regulatory network and the interactions that occur in the intracellular environment of microorganisms highlight the importance in developing tractable mechanistic models of cellular functions and systematic approaches for modelling biological systems. To this end, the existing process systems engineering approaches can serve as a vehicle for understanding, integrating and designing biological systems and processes. Here, we review the application of a holistic approach for the development of mathematical models of biological systems, from the initial conception of the model to its final application in model-based control and optimisation. We also discuss the use of mechanistic models that account for gene regulation, in an attempt to advance the empirical expressions traditionally used to describe micro-organism growth kinetics, and we highlight current and future challenges in mathematical biology. The modelling research framework discussed herein could prove beneficial for the design of optimal bioprocesses, employing rational and feasible approaches towards the efficient production of chemicals and pharmaceuticals. PMID:24688682

HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing.

PubMed

Wan, Shixiang; Zou, Quan

2017-01-01

Multiple sequence alignment (MSA) plays a key role in biological sequence analyses, especially in phylogenetic tree construction. Extreme increase in next-generation sequencing results in shortage of efficient ultra-large biological sequence alignment approaches for coping with different sequence types. Distributed and parallel computing represents a crucial technique for accelerating ultra-large (e.g. files more than 1 GB) sequence analyses. Based on HAlign and Spark distributed computing system, we implement a highly cost-efficient and time-efficient HAlign-II tool to address ultra-large multiple biological sequence alignment and phylogenetic tree construction. The experiments in the DNA and protein large scale data sets, which are more than 1GB files, showed that HAlign II could save time and space. It outperformed the current software tools. HAlign-II can efficiently carry out MSA and construct phylogenetic trees with ultra-large numbers of biological sequences. HAlign-II shows extremely high memory efficiency and scales well with increases in computing resource. THAlign-II provides a user-friendly web server based on our distributed computing infrastructure. HAlign-II with open-source codes and datasets was established at http://lab.malab.cn/soft/halign.

Response of an invasive liana to simulated herbivory: implications for its biological control

NASA Astrophysics Data System (ADS)

Raghu, S.; Dhileepan, K.; Treviño, M.

2006-05-01

Pre-release evaluation of the efficacy of biological control agents is often not possible in the case of many invasive species targeted for biocontrol. In such circumstances simulating herbivory could yield significant insights into plant response to damage, thereby improving the efficiency of agent prioritisation, increasing the chances of regulating the performance of invasive plants through herbivory and minimising potential risks posed by release of multiple herbivores. We adopted this approach to understand the weaknesses herbivores could exploit, to manage the invasive liana, Macfadyena unguis-cati. We simulated herbivory by damaging the leaves, stem, root and tuber of the plant, in isolation and in combination. We also applied these treatments at multiple frequencies. Plant response in terms of biomass allocation showed that at least two severe defoliation treatments were required to diminish this liana's climbing habit and reduce its allocation to belowground tuber reserves. Belowground damage appears to have negligible effect on the plant's biomass production and tuber damage appears to trigger a compensatory response. Plant response to combinations of different types of damage did not differ significantly to that from leaf damage. This suggests that specialist herbivores in the leaf-feeding guild capable of removing over 50% of the leaf tissue may be desirable in the biological control of this invasive species.

MIMO: an efficient tool for molecular interaction maps overlap

PubMed Central

2013-01-01

Background Molecular pathways represent an ensemble of interactions occurring among molecules within the cell and between cells. The identification of similarities between molecular pathways across organisms and functions has a critical role in understanding complex biological processes. For the inference of such novel information, the comparison of molecular pathways requires to account for imperfect matches (flexibility) and to efficiently handle complex network topologies. To date, these characteristics are only partially available in tools designed to compare molecular interaction maps. Results Our approach MIMO (Molecular Interaction Maps Overlap) addresses the first problem by allowing the introduction of gaps and mismatches between query and template pathways and permits -when necessary- supervised queries incorporating a priori biological information. It then addresses the second issue by relying directly on the rich graph topology described in the Systems Biology Markup Language (SBML) standard, and uses multidigraphs to efficiently handle multiple queries on biological graph databases. The algorithm has been here successfully used to highlight the contact point between various human pathways in the Reactome database. Conclusions MIMO offers a flexible and efficient graph-matching tool for comparing complex biological pathways. PMID:23672344

Automatic control and remote monitoring system for biological nutrient removal on small wastewater treatment plants in Korea.

PubMed

Lee, H; Min, Y M; Park, C H; Park, Y H

2004-01-01

Many small-size wastewater treatment plants in Korea's rural communities are designed to remove organic and suspended matter only, and they generally show a large fluctuation in the influent loading compared to municipal wastewater treatment plants (MWWTPs). They also have no professional engineers stationed for efficient operation against mechanical breakdown. For those reasons, the wastewater treatment plants have low efficiency in treatment of nitrogen and phosphorus as well as organic matter. In order to solve those problems, this study developed an automatic control system and RMS (remote monitoring system), which can keep efficiency stable despite any change in the small plants' loading rates and are capable of removing nutrient materials such as nitrogen or phosphorus. According to the results of the Experimental SBR system of the automatic control program, complete nitrification was made under oxic conditions and denitrification occurred as NO3-N concentration decreased by 0.5 mg/l in anoxic conditions and excellent nitrogen removal efficiency was seen generally. The Experimental SBR system created "phosphate release and uptake" effectively and displayed phosphate-removing efficiency up to more than 80% as the concentration of effluent was kept low by 0.4 mg/l. RMS developed in this study transmits a plant's data and operation states to clients in remote locations in real-time interval through the Internet. Therefore, although you are in a remote location, it allows you to see if a plant is properly operated or there is any breakdown.

Ultra-high enhancement of light focusing through disordered media controlled by mega-pixel modes (Conference Presentation)

NASA Astrophysics Data System (ADS)

Yu, Hyeonseung; Lee, KyeoReh; Park, YongKeun

2017-02-01

Developing an efficient strategy for light focusing through scattering media is an important topic in the study of multiple light scattering. The enhancement factor of the light focusing, defined as the ratio between the optimized intensity and the background intensity is proportional to the number of controlling modes in a spatial light modulator (SLM). The demonstrated enhancement factors in previous studies are typically less than 1,000 due to several limiting factors, such as the slow refresh rate of a LCoS SLM, long optimization time, and lack of an efficient algorithm for high controlling modes. A digital micro-mirror device is an amplitude modulator, which is recently widely used for fast optimization through dynamic biological tissues. The fast frame rate of the DMD up to 16 kHz can also be exploited for increasing the number of controlling modes. However, the manipulation of large pattern data and efficient calculation of the optimized pattern remained as an issue. In this work, we demonstrate the enhancement factor more than 100,000 in focusing through scattering media by using 1 Mega controlling modes of a DMD. Through careful synchronization between a DMD, a photo-detector and an additional computer for parallel optimization, we achieved the unprecedented enhancement factor with 75 mins of the optimization time. We discuss the design principles of the system and the possible applications of the enhanced light focusing.

Maneuvering control and configuration adaptation of a biologically inspired morphing aircraft

NASA Astrophysics Data System (ADS)

Abdulrahim, Mujahid

Natural flight as a source of inspiration for aircraft design was prominent with early aircraft but became marginalized as aircraft became larger and faster. With recent interest in small unmanned air vehicles, biological inspiration is a possible technology to enhance mission performance of aircraft that are dimensionally similar to gliding birds. Serial wing joints, loosely modeling the avian skeletal structure, are used in the current study to allow significant reconfiguration of the wing shape. The wings are reconfigured to optimize aerodynamic performance and maneuvering metrics related to specific mission tasks. Wing shapes for each mission are determined and related to the seagulls, falcons, albatrosses, and non-migratory African swallows on which the aircraft are based. Variable wing geometry changes the vehicle dynamics, affording versatility in flight behavior but also requiring appropriate compensation to maintain stability and controllability. Time-varying compensation is in the form of a baseline controller which adapts to both the variable vehicle dynamics and to the changing mission requirements. Wing shape is adapted in flight to minimize a cost function which represents energy, temporal, and spatial efficiency. An optimal control architecture unifies the control and adaptation tasks.

Equity and adequacy of international donor assistance for global malaria control: an analysis of populations at risk and external funding commitments.

PubMed

Snow, Robert W; Okiro, Emelda A; Gething, Peter W; Atun, Rifat; Hay, Simon I

2010-10-23

Financing for malaria control has increased as part of international commitments to achieve the Millennium Development Goals (MDGs). We aimed to identify the unmet financial needs that would be biologically and economically equitable and would increase the chances of reaching worldwide malaria-control ambitions. Populations at risk of stable Plasmodium falciparum or Plasmodium vivax transmission were calculated for 2007 and 2009 for 93 malaria-endemic countries to measure biological need. National per-person gross domestic product (GDP) was used to define economic need. An analysis of external donor assistance for malaria control was done for the period 2002-09 to compute overall and annualised per-person at-risk-funding commitments. Annualised malaria donor assistance was compared with independent predictions of funding needed to reach international targets of 80% coverage of best practices in case-management and effective disease prevention. Countries were ranked in relation to biological, economic, and unmet needs to examine equity and adequacy of support by 2010. International financing for malaria control has increased by 166% (from $0·73 billion to $1·94 billion) since 2007 and is broadly consistent with biological needs. African countries have become major recipients of external assistance; however, countries where P vivax continues to pose threats to control ambitions are not as well funded. 21 countries have reached adequate assistance to provide a comprehensive suite of interventions by 2009, including 12 countries in Africa. However, this assistance was inadequate for 50 countries representing 61% of the worldwide population at risk of malaria-including ten countries in Africa and five in Asia that coincidentally are some of the poorest countries. Approval of donor funding for malaria control does not correlate with GDP. Funding for malaria control worldwide is 60% lower than the US$4·9 billion needed for comprehensive control in 2010; this includes funding shortfalls for a wide range of countries with different numbers of people at risk and different levels of domestic income. More efficient targeting of financial resources against biological need and national income should create a more equitable investment portfolio that with increased commitments will guarantee sustained financing of control in countries most at risk and least able to support themselves. Wellcome Trust. Copyright © 2010 Elsevier Ltd. All rights reserved.

Equity and adequacy of international donor assistance for global malaria control: an analysis of populations at risk and external funding commitments

PubMed Central

Snow, Robert W; Okiro, Emelda A; Gething, Peter W; Atun, Rifat; Hay, Simon I

2010-01-01

Summary Background Financing for malaria control has increased as part of international commitments to achieve the Millennium Development Goals (MDGs). We aimed to identify the unmet financial needs that would be biologically and economically equitable and would increase the chances of reaching worldwide malaria-control ambitions. Methods Populations at risk of stable Plasmodium falciparum or Plasmodium vivax transmission were calculated for 2007 and 2009 for 93 malaria-endemic countries to measure biological need. National per-person gross domestic product (GDP) was used to define economic need. An analysis of external donor assistance for malaria control was done for the period 2002–09 to compute overall and annualised per-person at-risk-funding commitments. Annualised malaria donor assistance was compared with independent predictions of funding needed to reach international targets of 80% coverage of best practices in case-management and effective disease prevention. Countries were ranked in relation to biological, economic, and unmet needs to examine equity and adequacy of support by 2010. Findings International financing for malaria control has increased by 166% (from $0·73 billion to $1·94 billion) since 2007 and is broadly consistent with biological needs. African countries have become major recipients of external assistance; however, countries where P vivax continues to pose threats to control ambitions are not as well funded. 21 countries have reached adequate assistance to provide a comprehensive suite of interventions by 2009, including 12 countries in Africa. However, this assistance was inadequate for 50 countries representing 61% of the worldwide population at risk of malaria—including ten countries in Africa and five in Asia that coincidentally are some of the poorest countries. Approval of donor funding for malaria control does not correlate with GDP. Interpretation Funding for malaria control worldwide is 60% lower than the US$4·9 billion needed for comprehensive control in 2010; this includes funding shortfalls for a wide range of countries with different numbers of people at risk and different levels of domestic income. More efficient targeting of financial resources against biological need and national income should create a more equitable investment portfolio that with increased commitments will guarantee sustained financing of control in countries most at risk and least able to support themselves. Funding Wellcome Trust. PMID:20889199

Enhanced efficiency of biological excess sludge hydrolysis under anaerobic digestion by additional enzymes.

PubMed

Yang, Qi; Luo, Kun; Li, Xiao-ming; Wang, Dong-bo; Zheng, Wei; Zeng, Guang-ming; Liu, Jing-jin

2010-05-01

In this investigation, the effects of commercial enzyme preparation containing alpha amylase and neutral protease on hydrolysis of excess sludge and the kinetic analysis of hydrolysis process were evaluated. The results indicated that amylase treatment displayed higher hydrolysis efficiency than that of protease. VSS reduction greatly increased to 39.70% for protease and 54.24% for amylase at the enzyme dosage of 6% (w/w), respectively. The hydrolysis rate of sludge improved with temperature increasing from 40 to 50 degrees Celsius, which could be well described by the amended Arrhenius equation. Mixed-enzyme had great impact on sludge solubilisation than single enzyme. The mixture of two enzymes (protease:amylase=1:3) resulted in optimum hydrolysis efficiency, the efficiency of solids hydrolysis increased from 10% (control test) to 68.43% at the temperature of 50 degrees Celsius. Correspondingly, the concentration of reducing sugar and NH(4)(+)-N improved about 377% and 201%, respectively. According to the kinetic analysis of enzymatic hydrolysis process, VSS solubilisation process within prior 4 h followed first-order kinetics. Compared with control test, the hydrolysis rate improved significantly at 50 degrees Celsius when either single enzyme or mixed-enzyme was added. Copyright 2009. Published by Elsevier Ltd.

A controllable molecular sieve for Na+ and K+ ions.

PubMed

Gong, Xiaojing; Li, Jichen; Xu, Ke; Wang, Jianfeng; Yang, Hui

2010-02-17

The selective rate of specific ion transport across nanoporous material is critical to biological and nanofluidic systems. Molecular sieves for ions can be achieved by steric and electrical effects. However, the radii of Na(+) and K(+) are quite similar; they both carry a positive charge, making them difficult to separate. Biological ionic channels contain precisely arranged arrays of amino acids that can efficiently recognize and guide the passage of K(+) or Na(+) across the cell membrane. However, the design of inorganic channels with novel recognition mechanisms that control the ionic selectivity remains a challenge. We present here a design for a controllable ion-selective nanopore (molecular sieve) based on a single-walled carbon nanotube with specially arranged carbonyl oxygen atoms modified inside the nanopore, which was inspired by the structure of potassium channels in membrane spanning proteins (e.g., KcsA). Our molecular dynamics simulations show that the remarkable selectivity is attributed to the hydration structure of Na(+) or K(+) confined in the nanochannels, which can be precisely tuned by different patterns of the carbonyl oxygen atoms. The results also suggest that a confined environment plays a dominant role in the selectivity process. These studies provide a better understanding of the mechanism of ionic selectivity in the KcsA channel and possible technical applications in nanotechnology and biotechnology, including serving as a laboratory-in-nanotube for special chemical interactions and as a high-efficiency nanodevice for purification or desalination of sea and brackish water.

[Research on removal efficiency of Cd (II)-bearing wastewater by sulfate-reducing biological filter].

PubMed

Wu, Xuan; Tan, Ke-Yan; Hu, Xi-Jia; Gu, Yun; Yang, Hong

2014-04-01

At the temperature of 18.0-22.3 degrees C, biological carriers were produce from pure SRB and zeolite by the embedding immobilized method, and a sulfate-reducing biological filter filled with filter carriers was built to treat cadmium-containing wastewater. Experimental research on removal efficiency of Cd2+, COD and SO4(2-) in wastewater by the biological filter was carried out after SRB domestication. Results show that cadmium can be removed satisfactorily from wastewater using SRB by the biological filter filled with sulfate-reducing bacteria. When the filtration rate was 0.4 m x h(-1) and the cadmium concentration in wastewater was not more than 15 mg x L(-1), the processing efficiency was the best. In the formal running period, the removal rates of Cd2+, COD and SO4(2-) by the biological filter were more than 99%, 75% and 50%. The effluent Cd2+ concentration was less than 0.1 mg x L(-1), which could meet the cadmium emission requirements in the wastewater quality standards for discharge to municipal sewers (CJ 343-2010). The removal of Cd2+, COD and SO4(2-) by biological filter mainly occurs in the top 60 cm of the filter bed during stable operation. When the filtration rate was less than 0.6 m x h(-1), Cd(2+) can be removed by the biological filter with high efficiency and stability.

Yeast synthetic biology toolbox and applications for biofuel production.

PubMed

Tsai, Ching-Sung; Kwak, Suryang; Turner, Timothy L; Jin, Yong-Su

2015-02-01

Yeasts are efficient biofuel producers with numerous advantages outcompeting bacterial counterparts. While most synthetic biology tools have been developed and customized for bacteria especially for Escherichia coli, yeast synthetic biological tools have been exploited for improving yeast to produce fuels and chemicals from renewable biomass. Here we review the current status of synthetic biological tools and their applications for biofuel production, focusing on the model strain Saccharomyces cerevisiae We describe assembly techniques that have been developed for constructing genes, pathways, and genomes in yeast. Moreover, we discuss synthetic parts for allowing precise control of gene expression at both transcriptional and translational levels. Applications of these synthetic biological approaches have led to identification of effective gene targets that are responsible for desirable traits, such as cellulosic sugar utilization, advanced biofuel production, and enhanced tolerance against toxic products for biofuel production from renewable biomass. Although an array of synthetic biology tools and devices are available, we observed some gaps existing in tool development to achieve industrial utilization. Looking forward, future tool development should focus on industrial cultivation conditions utilizing industrial strains. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

PubMed Central

Westbrook, John D; Feng, Zukang; Persikova, Irina; Sala, Raul; Sen, Sanchayita; Berrisford, John M; Swaminathan, G Jawahar; Oldfield, Thomas J; Gutmanas, Aleksandras; Igarashi, Reiko; Armstrong, David R; Baskaran, Kumaran; Chen, Li; Chen, Minyu; Clark, Alice R; Di Costanzo, Luigi; Dimitropoulos, Dimitris; Gao, Guanghua; Ghosh, Sutapa; Gore, Swanand; Guranovic, Vladimir; Hendrickx, Pieter M S; Hudson, Brian P; Ikegawa, Yasuyo; Kengaku, Yumiko; Lawson, Catherine L; Liang, Yuhe; Mak, Lora; Mukhopadhyay, Abhik; Narayanan, Buvaneswari; Nishiyama, Kayoko; Patwardhan, Ardan; Sahni, Gaurav; Sanz-García, Eduardo; Sato, Junko; Sekharan, Monica R; Shao, Chenghua; Smart, Oliver S; Tan, Lihua; van Ginkel, Glen; Yang, Huanwang; Zhuravleva, Marina A; Markley, John L; Nakamura, Haruki; Kurisu, Genji; Kleywegt, Gerard J; Velankar, Sameer; Berman, Helen M; Burley, Stephen K

2018-01-01

Abstract The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands. The worldwide PDB (wwPDB) is the international collaboration that manages the PDB archive according to the FAIR principles: Findability, Accessibility, Interoperability and Reusability. The wwPDB recently developed OneDep, a unified tool for deposition, validation and biocuration of structures of biological macromolecules. All data deposited to the PDB undergo critical review by wwPDB Biocurators. This article outlines the importance of biocuration for structural biology data deposited to the PDB and describes wwPDB biocuration processes and the role of expert Biocurators in sustaining a high-quality archive. Structural data submitted to the PDB are examined for self-consistency, standardized using controlled vocabularies, cross-referenced with other biological data resources and validated for scientific/technical accuracy. We illustrate how biocuration is integral to PDB data archiving, as it facilitates accurate, consistent and comprehensive representation of biological structure data, allowing efficient and effective usage by research scientists, educators, students and the curious public worldwide. Database URL: https://www.wwpdb.org/ PMID:29688351

Engineering modular ‘ON’ RNA switches using biological components

PubMed Central

Ceres, Pablo; Trausch, Jeremiah J.; Batey, Robert T.

2013-01-01

Riboswitches are cis-acting regulatory elements broadly distributed in bacterial mRNAs that control a wide range of critical metabolic activities. Expression is governed by two distinct domains within the mRNA leader: a sensory ‘aptamer domain’ and a regulatory ‘expression platform’. Riboswitches have also received considerable attention as important tools in synthetic biology because of their conceptually simple structure and the ability to obtain aptamers that bind almost any conceivable small molecule using in vitro selection (referred to as SELEX). In the design of artificial riboswitches, a significant hurdle has been to couple the two domains enabling their efficient communication. We previously demonstrated that biological transcriptional ‘OFF’ expression platforms are easily coupled to diverse aptamers, both biological and SELEX-derived, using simple design rules. Here, we present two modular transcriptional ‘ON’ riboswitch expression platforms that are also capable of hosting foreign aptamers. We demonstrate that these biological parts can be used to facilely generate artificial chimeric riboswitches capable of robustly regulating transcription both in vitro and in vivo. We expect that these modular expression platforms will be of great utility for various synthetic biological applications that use RNA-based biosensors. PMID:23999097

Velocity-curvature patterns limit human-robot physical interaction

PubMed Central

Maurice, Pauline; Huber, Meghan E.; Hogan, Neville; Sternad, Dagmar

2018-01-01

Physical human-robot collaboration is becoming more common, both in industrial and service robotics. Cooperative execution of a task requires intuitive and efficient interaction between both actors. For humans, this means being able to predict and adapt to robot movements. Given that natural human movement exhibits several robust features, we examined whether human-robot physical interaction is facilitated when these features are considered in robot control. The present study investigated how humans adapt to biological and non-biological velocity patterns in robot movements. Participants held the end-effector of a robot that traced an elliptic path with either biological (two-thirds power law) or non-biological velocity profiles. Participants were instructed to minimize the force applied on the robot end-effector. Results showed that the applied force was significantly lower when the robot moved with a biological velocity pattern. With extensive practice and enhanced feedback, participants were able to decrease their force when following a non-biological velocity pattern, but never reached forces below those obtained with the 2/3 power law profile. These results suggest that some robust features observed in natural human movements are also a strong preference in guided movements. Therefore, such features should be considered in human-robot physical collaboration. PMID:29744380

Velocity-curvature patterns limit human-robot physical interaction.

PubMed

Maurice, Pauline; Huber, Meghan E; Hogan, Neville; Sternad, Dagmar

2018-01-01

Physical human-robot collaboration is becoming more common, both in industrial and service robotics. Cooperative execution of a task requires intuitive and efficient interaction between both actors. For humans, this means being able to predict and adapt to robot movements. Given that natural human movement exhibits several robust features, we examined whether human-robot physical interaction is facilitated when these features are considered in robot control. The present study investigated how humans adapt to biological and non-biological velocity patterns in robot movements. Participants held the end-effector of a robot that traced an elliptic path with either biological (two-thirds power law) or non-biological velocity profiles. Participants were instructed to minimize the force applied on the robot end-effector. Results showed that the applied force was significantly lower when the robot moved with a biological velocity pattern. With extensive practice and enhanced feedback, participants were able to decrease their force when following a non-biological velocity pattern, but never reached forces below those obtained with the 2/3 power law profile. These results suggest that some robust features observed in natural human movements are also a strong preference in guided movements. Therefore, such features should be considered in human-robot physical collaboration.

Zirconium, calcium, and strontium contents in magnesium based biodegradable alloys modulate the efficiency of implant-induced osseointegration

PubMed Central

Mushahary, Dolly; Sravanthi, Ragamouni; Li, Yuncang; Kumar, Mahesh J; Harishankar, Nemani; Hodgson, Peter D; Wen, Cuie; Pande, Gopal

2013-01-01

Development of new biodegradable implants and devices is necessary to meet the increasing needs of regenerative orthopedic procedures. An important consideration while formulating new implant materials is that they should physicochemically and biologically mimic bone-like properties. In earlier studies, we have developed and characterized magnesium based biodegradable alloys, in particular magnesium-zirconium (Mg-Zr) alloys. Here we have reported the biological properties of four Mg-Zr alloys containing different quantities of strontium or calcium. The alloys were implanted in small cavities made in femur bones of New Zealand White rabbits, and the quantitative and qualitative assessments of newly induced bone tissue were carried out. A total of 30 experimental animals, three for each implant type, were studied, and bone induction was assessed by histological, immunohistochemical and radiological methods; cavities in the femurs with no implants and observed for the same period of time were kept as controls. Our results showed that Mg-Zr alloys containing appropriate quantities of strontium were more efficient in inducing good quality mineralized bone than other alloys. Our results have been discussed in the context of physicochemical and biological properties of the alloys, and they could be very useful in determining the nature of future generations of biodegradable orthopedic implants. PMID:23976848

Zn (II) Removal from River Water Samples of Sembrong, Johor State, Malaysia by Electrokinetic Remediation

NASA Astrophysics Data System (ADS)

Zaidi, E.; Husna, MNF; Shakila, A.; Azhar, ATS; Arif, AM; Norshuhaila, MS

2017-08-01

Heavy metals pollution has become one of the most serious environmental problems today. The treatment of heavy metals is of special concern due to their recalcitrance and persistence in the environment. Even many physical, chemical and biological treatment processes have been proposed to remove heavy metals from river water, the use of these treatment processes are not efficient and relatively costly. This study focused on the potential application of electrokinetic (EK) remediation in Sembrong River water to remove zinc (Zn2+). The physicochemical and biological parameters and water quality index (WQI) of Sembrong River water was characterized. The electrokinetic remediation experiments were performed by controlling pH, and electric density on voltage were observed and investigated. The results indicated that all physicochemical and biological parameters of Sembrong River complied with the standard discharged limit set by the Department of Environment (DOE). However, suspended solids (SS) and pH can be categorized as Class III according to INWQS. The best performance of 88% efficiency of zinc can be achieved EK experiment run at a fixed voltage of 30 V at pH 5.14 after 60 min of the process operate. This technology may be proposed for faster and eco-friendly removal of heavy metals in the environment.

Design control considerations for biologic-device combination products.

PubMed

Anderson, Dave; Liu, Roger; Anand Subramony, J; Cammack, Jon

2017-03-01

Combination products are therapeutic and diagnostic medical products that combine drugs, devices, and/or biological products with one another. Historically, biologics development involved identifying efficacious doses administered to patients intravenously or perhaps by a syringe. Until fairly recently, there has been limited focus on developing an accompanying medical device, such as a prefilled syringe or auto-injector, to enable easy and more efficient delivery. For the last several years, and looking forward, where there may be little to distinguish biologics medicines with relatively similar efficacy profiles, the biotechnology market is beginning to differentiate products by patient-focused, biologic-device based combination products. As innovative as biologic-device combination products are, they can pose considerable development, regulatory, and commercialization challenges due to unique physicochemical properties and special clinical considerations (e.g., dosing volumes, frequency, co-medications, etc.) of the biologic medicine. A biologic-device combination product is a marriage between two partners with "cultural differences," so to speak. There are clear differences in the development, review, and commercialization processes of the biologic and the device. When these two cultures come together in a combination product, developers and reviewers must find ways to address the design controls and risk management processes of both the biologic and device, and knit them into a single entity with supporting product approval documentation. Moreover, digital medicine and connected health trends are pushing the boundaries of combination product development and regulations even further. Despite an admirable cooperation between industry and FDA in recent years, unique product configurations and design features have resulted in review challenges. These challenges have prompted agency reviewers to modernize consultation processes, while at the same time, promoting development of innovative, safe and effective combination products. It remains the manufacturer's responsibility to comply with the relevant requirements and regulations, and develop good business practices that clearly describe how these practices comply with FDA's final rule (21 CFR Part 4) and aligns with the company's already established quality system. Copyright © 2017 Elsevier B.V. All rights reserved.

Biotreatment of ammonia- and butanal-containing waste gases.

PubMed

Weckhuysen, B; Vriens, L; Verachtert, H

1994-10-01

The biological removal of ammonia and butanal in contaminated air was investigated by using, respectively, a laboratory-scale filter and a scrubber-filter combination. It was shown that ammonia can be removed with an elimination efficiency of 83% at a volumetric load of 100 m3.m-2.h-1 with 4-16 ppm of ammonia. During the experiment percolates were analysed for nitrate, nitrite, ammonium and pH. It was found that the nitrification in the biofilter could deteriorate due to an inhibition of Nitrobacter species, when the free ammonia concentration was rising in the percolate. It should be easy to control such inhibition through periodic analysis of the liquid phase by using a filter-scrubber combination. Such a combination was studied for butanal removal. Butanal was removed with an elimination efficiency of 80% by a scrubber-filter combination at a volumetric load of 100 m3.m-2.h-1 and a high butanal input concentration. Mixing the filter material with CaCO3 and pH control of the liquid in the scrubber resulted in an increase of the elimination efficiency. These results, combined with previous results on the biofiltration of butanal and butyric acid, allow us to discuss the influence of odour compounds on the removal efficiency of such systems and methods for control. The results were used to construct a full-size system, which is described.

Tantalum Sulfide Nanosheets as a Theranostic Nanoplatform for Computed Tomography Imaging-Guided Combinatorial Chemo-Photothermal Therapy.

PubMed

Liu, Yanlan; Ji, Xiaoyuan; Liu, Jianhua; Tong, Winnie W L; Askhatova, Diana; Shi, Jinjun

2017-10-19

Near-infrared (NIR)-absorbing metal-based nanomaterials have shown tremendous potential for cancer therapy, given their facile and controllable synthesis, efficient photothermal conversion, capability of spatiotemporal-controlled drug delivery, and intrinsic imaging function. Tantalum (Ta) is among the most biocompatible metals and arouses negligible adverse biological responses in either oxidized or reduced forms, and thus Ta-derived nanomaterials represent promising candidates for biomedical applications. However, Ta-based nanomaterials by themselves have not been explored for NIR-mediated photothermal ablation therapy. In this work, we report an innovative Ta-based multifunctional nanoplatform composed of biocompatible tantalum sulfide (TaS 2 ) nanosheets (NSs) for simultaneous NIR hyperthermia, drug delivery, and computed tomography (CT) imaging. The TaS 2 NSs exhibit multiple unique features including (i) efficient NIR light-to-heat conversion with a high photothermal conversion efficiency of 39%. (ii) high drug loading (177% by weight), (iii) controlled drug release triggered by NIR light and moderate acidic pH, (iv) high tumor accumulation via heat-enhanced tumor vascular permeability, (v) complete tumor ablation and negligible side effects, and (vi) comparable CT imaging contrast efficiency to the widely clinically used agent iobitridol. We expect that this multifunctional NS platform can serve as a promising candidate for imaging-guided cancer therapy and selection of cancer patients with high tumor accumulation.

Click Chemistry Mediated Functionalization of Vertical Nanowires for Biological Applications.

PubMed

Vutti, Surendra; Schoffelen, Sanne; Bolinsson, Jessica; Buch-Månson, Nina; Bovet, Nicolas; Nygård, Jesper; Martinez, Karen L; Meldal, Morten

2016-01-11

Semiconductor nanowires (NWs) are gaining significant importance in various biological applications, such as biosensing and drug delivery. Efficient and controlled immobilization of biomolecules on the NW surface is crucial for many of these applications. Here, we present for the first time the use of the Cu(I) -catalyzed alkyne-azide cycloaddition and its strain-promoted variant for the covalent functionalization of vertical NWs with peptides and proteins. The potential of the approach was demonstrated in two complementary applications of measuring enzyme activity and protein binding, which is of general interest for biological studies. The attachment of a peptide substrate provided NW arrays for the detection of protease activity. In addition, green fluorescent protein was immobilized in a site-specific manner and recognized by antibody binding to demonstrate the proof-of-concept for the use of covalently modified NWs for diagnostic purposes using minute amounts of material. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Computer-aided design of biological circuits using TinkerCell

PubMed Central

Bergmann, Frank T; Sauro, Herbert M

2010-01-01

Synthetic biology is an engineering discipline that builds on modeling practices from systems biology and wet-lab techniques from genetic engineering. As synthetic biology advances, efficient procedures will be developed that will allow a synthetic biologist to design, analyze and build biological networks. In this idealized pipeline, computer-aided design (CAD) is a necessary component. The role of a CAD application would be to allow efficient transition from a general design to a final product. TinkerCell is a design tool for serving this purpose in synthetic biology. In TinkerCell, users build biological networks using biological parts and modules. The network can be analyzed using one of several functions provided by TinkerCell or custom programs from third-party sources. Since best practices for modeling and constructing synthetic biology networks have not yet been established, TinkerCell is designed as a flexible and extensible application that can adjust itself to changes in the field. PMID:21327060

Occurrence of cyclophosphamide and ifosfamide in aqueous environment and their removal by biological and abiotic wastewater treatment processes.

PubMed

Česen, Marjeta; Kosjek, Tina; Laimou-Geraniou, Maria; Kompare, Boris; Širok, Brane; Lambropolou, Dimitra; Heath, Ester

2015-09-15

Cytostatic drug residues in the aqueous environment are of concern due to their possible adverse effects on non-target organisms. Here we report the occurrence and removal efficiency of cyclophosphamide (CP) and ifosfamide (IF) by biological and abiotic treatments including advanced oxidation processes (AOPs). Cyclophosphamide was detected in hospital wastewaters (14-22,000 ng L(-1)), wastewater treatment plant influents (19-27 ng L(-1)) and effluent (17 ng L(-1)), whereas IF was detected only in hospital wastewaters (48-6800 ng L(-1)). The highest removal efficiency during biological treatment (attached growth biomass in a flow through bioreactor) was 59 ± 15% and 35 ± 9.3% for CP and IF, respectively. Also reported are the removal efficiencies of both compounds from wastewater using hydrodynamic cavitation (HC), ozonation (O3) and/or UV, either individually or in combination with hydrogen peroxide (H2O2). Hydrodynamic cavitation did not remove CP and IF to any significant degree. The highest removal efficiencies: 99 ± 0.71% for CP and 94 ± 2.4% for IF, were achieved using UV/O3/H2O2 at 5 g L(-1) for 120 min. When combined with biological treatment, removal efficiencies were >99% for both compounds. This is the first report of combined biological and AOP treatment of CP and IF from wastewater with a removal efficiency >99%. Copyright © 2015 Elsevier B.V. All rights reserved.

A retrospective likelihood approach for efficient integration of multiple omics factors in case-control association studies.

PubMed

Balliu, Brunilda; Tsonaka, Roula; Boehringer, Stefan; Houwing-Duistermaat, Jeanine

2015-03-01

Integrative omics, the joint analysis of outcome and multiple types of omics data, such as genomics, epigenomics, and transcriptomics data, constitute a promising approach for powerful and biologically relevant association studies. These studies often employ a case-control design, and often include nonomics covariates, such as age and gender, that may modify the underlying omics risk factors. An open question is how to best integrate multiple omics and nonomics information to maximize statistical power in case-control studies that ascertain individuals based on the phenotype. Recent work on integrative omics have used prospective approaches, modeling case-control status conditional on omics, and nonomics risk factors. Compared to univariate approaches, jointly analyzing multiple risk factors with a prospective approach increases power in nonascertained cohorts. However, these prospective approaches often lose power in case-control studies. In this article, we propose a novel statistical method for integrating multiple omics and nonomics factors in case-control association studies. Our method is based on a retrospective likelihood function that models the joint distribution of omics and nonomics factors conditional on case-control status. The new method provides accurate control of Type I error rate and has increased efficiency over prospective approaches in both simulated and real data. © 2015 Wiley Periodicals, Inc.

Solution Exchange Lithography: A Versatile Tool for Sequential Surface Engineering

NASA Astrophysics Data System (ADS)

Pester, Christian; Mattson, Kaila; Bothman, David; Klinger, Daniel; Lee, Kenneth; Discekici, Emre; Narupai, Benjaporn; Hawker, Craig

The covalent attachment of polymers has emerged as a viable strategy for the preparation of multi-functional surfaces. Patterned, surface-grafted polymer brushes provide spatial control over wetting, mechanical, biological or electronic properties, and allow fabrication of `intelligent' substrates which selectively adapt to their environment. However, the route towards patterned polymer brush surfaces often remains challenging, creating a demand for more efficient and less complicated fabrication strategies. We describe the design and application of a novel experimental setup to combine light-mediated and flow chemistry for the fabrication of hierarchical surface-grafted polymer brushes. Using light-mediated, surface initiated controlled radical polymerization and post-functionalization via well-established, and highly efficient chemistries, polymer brush films of previously unimaginable complexity are now shown to be accessible. This methodology allows full flexibility to exchange both lithographic photomasks and chemical environments in-situ, readily affording multidimensional thin film architectures, all from uniformly functionalized substrates.

An efficient variational method to study the denaturation of DNA induced by superhelical stress

NASA Astrophysics Data System (ADS)

Jost, Daniel; Everaers, Ralf

2010-03-01

Many fundamental biological processes, like transcription or replication, need the opening of the double-stranded DNA. One common way to control the local denaturation is to impose superhelical stress to the DNA using protein machineries. To describe superhelical effect for circular molecules, Benham introduced a model where the standard thermodynamic description of base-pairing is coupled with torsional stress energetics. Here, we introduce an efficient mean-field approximation of the Benham model. Our self-consistent solution is confident and computationally-fast, compared to the full treatment of the model. In particular, our formulation allows to compute the probability of bubble formation for given length and position along the sequence. Evolution of this probability as a function of the superhelical stress could inform us on the ability for organisms to control the strength of superhelicity acting on their genomes.

Emergence and Utility of Nonspherical Particles in Biomedicine

PubMed Central

Fish, Margaret B.; Thompson, Alex J.; Fromen, Catherine A.; Eniola-Adefeso, Omolola

2016-01-01

The importance of the size of targeted, spherical drug carriers has been previously explored and reviewed. Particle shape has emerged as an equally important parameter in determining the in vivo journey and efficiency of drug carrier systems. Researchers have invented techniques to better control the geometry of particles of many different materials, which have allowed for exploration of the role of particle geometry in the phases of drug delivery. The important biological processes include clearance by the immune system, trafficking to the target tissue, margination to the endothelial surface, interaction with the target cell, and controlled release of a payload. The review of current literature herein supports that particle shape can be altered to improve a system’s targeting efficiency. Non-spherical particles can harness the potential of targeted drug carriers by enhancing targeted site accumulation while simultaneously decreasing side effects and mitigating some limitations faced by spherical carriers. PMID:27182109

Enhanced analysis of real-time PCR data by using a variable efficiency model: FPK-PCR

PubMed Central

Lievens, Antoon; Van Aelst, S.; Van den Bulcke, M.; Goetghebeur, E.

2012-01-01

Current methodology in real-time Polymerase chain reaction (PCR) analysis performs well provided PCR efficiency remains constant over reactions. Yet, small changes in efficiency can lead to large quantification errors. Particularly in biological samples, the possible presence of inhibitors forms a challenge. We present a new approach to single reaction efficiency calculation, called Full Process Kinetics-PCR (FPK-PCR). It combines a kinetically more realistic model with flexible adaptation to the full range of data. By reconstructing the entire chain of cycle efficiencies, rather than restricting the focus on a ‘window of application’, one extracts additional information and loses a level of arbitrariness. The maximal efficiency estimates returned by the model are comparable in accuracy and precision to both the golden standard of serial dilution and other single reaction efficiency methods. The cycle-to-cycle changes in efficiency, as described by the FPK-PCR procedure, stay considerably closer to the data than those from other S-shaped models. The assessment of individual cycle efficiencies returns more information than other single efficiency methods. It allows in-depth interpretation of real-time PCR data and reconstruction of the fluorescence data, providing quality control. Finally, by implementing a global efficiency model, reproducibility is improved as the selection of a window of application is avoided. PMID:22102586

Small-angle neutron scattering reveals the assembly mode and oligomeric architecture of TET, a large, dodecameric aminopeptidase

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

Appolaire, Alexandre; Girard, Eric; Colombo, Matteo

2014-11-01

The present work illustrates that small-angle neutron scattering, deuteration and contrast variation, combined with in vitro particle reconstruction, constitutes a very efficient approach to determine subunit architectures in large, symmetric protein complexes. In the case of the 468 kDa heterododecameric TET peptidase machine, it was demonstrated that the assembly of the 12 subunits is a highly controlled process and represents a way to optimize the catalytic efficiency of the enzyme. The specific self-association of proteins into oligomeric complexes is a common phenomenon in biological systems to optimize and regulate their function. However, de novo structure determination of these important complexesmore » is often very challenging for atomic-resolution techniques. Furthermore, in the case of homo-oligomeric complexes, or complexes with very similar building blocks, the respective positions of subunits and their assembly pathways are difficult to determine using many structural biology techniques. Here, an elegant and powerful approach based on small-angle neutron scattering is applied, in combination with deuterium labelling and contrast variation, to elucidate the oligomeric organization of the quaternary structure and the assembly pathways of 468 kDa, hetero-oligomeric and symmetric Pyrococcus horikoshii TET2–TET3 aminopeptidase complexes. The results reveal that the topology of the PhTET2 and PhTET3 dimeric building blocks within the complexes is not casual but rather suggests that their quaternary arrangement optimizes the catalytic efficiency towards peptide substrates. This approach bears important potential for the determination of quaternary structures and assembly pathways of large oligomeric and symmetric complexes in biological systems.« less

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Design of high efficiency and energy saving aeration device for aquaculture

NASA Astrophysics Data System (ADS)

Liu, Sibo

2017-03-01

Energy efficient aeration device for aquaculture, in line with "by more than a generation, dynamic aeration" train of thought for technical design and improvement. Removable aeration terminal as the core, multi-level water to improve the method, the mobile fading pore aeration, intelligent mobile and open and close as the main function, aimed at solving the existing pond aeration efficiency, low energy consumption is high, the function of a single problem. From energy saving, efficiency, biological bacteria on the three directions, the aquaculture industry of energy conservation and emissions reduction. Device of the main advantages are: 1, original mobile fading aerator on the one hand, to expand the scope of work, playing a micro porous aeration of dissolved oxygen with high efficiency and to achieve "by more than a generation", on the other hand, through the sports equipment, stir the mixture of water, the water surface of photosynthesis of plants rich in dissolved oxygen input parts of the tank, compared to the stillness of the aerator can be more fully dissolved oxygen.2, through the opening of the pressure sensor indirect control device, can make the equipment timely and stop operation, convenient in use at the same time avoid the waste of energy.3, the biofilm suspension in aeration terminal, can be accomplished by nitration of microbial multi-level water improvement, still can make biofilm increase rate of netting in the movement process, the biological and mechanical aerobic promote each other, improve the efficiency of both. In addition, the device has small power consumption, low cost of characteristics. And have a certain degree of technical barriers, have their own intellectual property rights, and high degree of product market demand, easily accepted by customers, has a very high popularization value.

Scaling and biomechanics of surface attachment in climbing animals

PubMed Central

Labonte, David; Federle, Walter

2015-01-01

Attachment devices are essential adaptations for climbing animals and valuable models for synthetic adhesives. A major unresolved question for both natural and bioinspired attachment systems is how attachment performance depends on size. Here, we discuss how contact geometry and mode of detachment influence the scaling of attachment forces for claws and adhesive pads, and how allometric data on biological systems can yield insights into their mechanism of attachment. Larger animals are expected to attach less well to surfaces, due to their smaller surface-to-volume ratio, and because it becomes increasingly difficult to distribute load uniformly across large contact areas. In order to compensate for this decrease of weight-specific adhesion, large animals could evolve overproportionally large pads, or adaptations that increase attachment efficiency (adhesion or friction per unit contact area). Available data suggest that attachment pad area scales close to isometry within clades, but pad efficiency in some animals increases with size so that attachment performance is approximately size-independent. The mechanisms underlying this biologically important variation in pad efficiency are still unclear. We suggest that switching between stress concentration (easy detachment) and uniform load distribution (strong attachment) via shear forces is one of the key mechanisms enabling the dynamic control of adhesion during locomotion. PMID:25533088

Thrust performance of unsteady propulsors using a novel measurement system, and corresponding wake patterns

PubMed Central

Clark, Richard P.; Smits, Alexander J.

2009-01-01

An apparatus is described for the measurement of unsteady thrust and propulsive efficiency produced by biologically inspired oscillating hydrodynamic propulsors. Force measurement is achieved using a strain-gauge-based force transducer, augmented with a lever to amplify or attenuate the applied force and control the measurement sensitivity and natural frequency of vibration. The lever can be used to tune the system to a specific application and it is shown that, using the lever, the stiffness can be made to increase more rapidly than the measurement sensitivity decreases. Efficiency is computed from measurements of the time-averaged power imparted to the fluid. The apparatus is applied to two different propulsors, demonstrating the versatility of the system; wake visualizations are examined, which provide insight into the physical mechanisms of efficient propulsion. PMID:19946574

Biomimetic structural engineering of P22 virus-like particles for catalysis and immune modulation

NASA Astrophysics Data System (ADS)

Schwarz, Benjamin

Within biology molecules are arranged in hierarchical structures that coordinate and control the many processes that allow for complex organisms to exist. Proteins and other functional macromolecules are often studied outside their natural nanostructural context because it remains difficult to create controlled arrangements of proteins at this size scale. Viruses are elegantly simple nano-systems that exist at the interface of living organisms and non-living biological machines. Studied and viewed primarily as pathogens to be combatted, viruses have emerged as models of structural efficiency at the nanoscale and have spurred the development of biomimetic nanoparticle systems. Virus-like particles (VLPs) are noninfectious protein cages derived from viruses or other cage-forming systems. VLPs provide incredibly regular scaffolds for building at the nanoscale. In this work I have utilized the VLP derived from the bacteriophage P22 as a platform for the organization of enzymes, antigens, and immune-stimulating proteins inside and outside the capsid through purely genetic means. In the case of enzymes, encapsulation of a two-enzyme pathway has led to the development of metabolic nanoparticle catalysts and an expanded understanding of the control that structure exerts on metabolic flux. These same structural elements applied to the delivery of protein subunit antigens directed at cytotoxic T cell immunity result in drastically enhanced antigen processing and lasting immunological memory. Lastly, presentation of immune-stimulating proteins from the Tumor Necrosis Factor Super Family on the surface of the P22 VLP enhances the cell signaling efficiency of these compounds 50-fold and provides strategies for the application of these proteins as immune modulatory oncology therapeutics. In all of these cases, the reintroduction of nanostructure to these protein systems, reminiscent of their natural environment, has led to both new technologies and a better understanding of the role of structure in biological processes.

Efficient computation of co-transcriptional RNA-ligand interaction dynamics.

PubMed

Wolfinger, Michael T; Flamm, Christoph; Hofacker, Ivo L

2018-05-04

Riboswitches form an abundant class of cis-regulatory RNA elements that mediate gene expression by binding a small metabolite. For synthetic biology applications, they are becoming cheap and accessible systems for selectively triggering transcription or translation of downstream genes. Many riboswitches are kinetically controlled, hence knowledge of their co-transcriptional mechanisms is essential. We present here an efficient implementation for analyzing co-transcriptional RNA-ligand interaction dynamics. This approach allows for the first time to model concentration-dependent metabolite binding/unbinding kinetics. We exemplify this novel approach by means of the recently studied I-A 2 ' -deoxyguanosine (2 ' dG)-sensing riboswitch from Mesoplasma florum. Copyright © 2018 Elsevier Inc. All rights reserved.

Biofiltration: Fundamentals, design and operations principles and applications

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

Swanson, W.J.; Loehr, R.C.

1997-06-01

Biofiltration is a biological air pollution control technology for volatile organic compounds (VOCs). This paper summarizes the fundamentals, design and operation, and application of the process. Biofiltration has been demonstrated to be an effective technology for VOCs from many industries. Large and full-scale systems are in use in Europe and the US. With proper design and operation, VOC removal efficiencies of 95--99% have been achieved. Important parameters for design and performance are empty-bed contact time, gas surface loading, mass loading, elimination capacity, and removal efficiency. Key design and operation factors include chemical and media properties, moisture, pH, temperature, nutrient availability,more » gas pretreatment, and variations in loading.« less

Membrane processes for alcohol-water separation: Improving the energy efficiency of biofuel production

EPA Science Inventory

The economics and environmental impact of producing fuels and chemicals biologically can be a strong function of the efficiency with which the fermentation products are removed from the biological media. Due to growth inhibition by some fermentation products, including ethanol an...

FPGA implementation of a configurable neuromorphic CPG-based locomotion controller.

PubMed

Barron-Zambrano, Jose Hugo; Torres-Huitzil, Cesar

2013-09-01

Neuromorphic engineering is a discipline devoted to the design and development of computational hardware that mimics the characteristics and capabilities of neuro-biological systems. In recent years, neuromorphic hardware systems have been implemented using a hybrid approach incorporating digital hardware so as to provide flexibility and scalability at the cost of power efficiency and some biological realism. This paper proposes an FPGA-based neuromorphic-like embedded system on a chip to generate locomotion patterns of periodic rhythmic movements inspired by Central Pattern Generators (CPGs). The proposed implementation follows a top-down approach where modularity and hierarchy are two desirable features. The locomotion controller is based on CPG models to produce rhythmic locomotion patterns or gaits for legged robots such as quadrupeds and hexapods. The architecture is configurable and scalable for robots with either different morphologies or different degrees of freedom (DOFs). Experiments performed on a real robot are presented and discussed. The obtained results demonstrate that the CPG-based controller provides the necessary flexibility to generate different rhythmic patterns at run-time suitable for adaptable locomotion. Copyright © 2013 Elsevier Ltd. All rights reserved.

Relationship between mycoparasites lifestyles and biocontrol behaviors against Fusarium spp. and mycotoxins production.

PubMed

Kim, Seon Hwa; Vujanovic, Vladimir

2016-06-01

Global food security research is seeking eco-friendly solutions to control mycotoxins in grain infected by fungi (molds). In particular, mycotoxigenic Fusarium spp. outbreak is a chronic threat for cereal grain production, human, and animal health. In this review paper, we discuss up-to-date biological control strategies in applying mycoparasites as biological control agents (BCA) to prevent plant diseases in crops and mycotoxins in grain, food, and feed. The aim is to increase food safety and to minimize economic losses due to the reduced grain yield and quality. However, recent papers indicate that the study of the BCA specialists with biotrophic lifestyle lags behind our understanding of the BCA generalists with necrotrophic lifestyle. We examine critical behavioral traits of the two BCA groups of mycoparasites. The goal is to highlight their major characteristics in the context of future research towards an efficient biocontrol strategy against mycotoxin-producing Fusarium species. The emphasis is put on biocontrol of Fusarium graminearum, F. avenaceum, and F. culmorum causing Fusarium head blight (FHB) in cereals and their mycotoxins.

Cobalamin-fluorophores' photochemistry and biomedical applications

NASA Astrophysics Data System (ADS)

Rodgers, Zachary Lewis

As science focuses on the finer details of complex processes occurring in biology, the need for tools responsive to researcher control have become critical to communicate with cellular functions in both a spatial and temporal manner. To this end, light responsive "caging groups" have been used to generate molecular constructs with which researchers can activate using directed irradiation to elicit biological responses where and when they want. This advancement in molecular control has greatly improved our ability to study biological systems in their dynamically intricate form. Most of these photoresponsive moieties perform well within a petri dish, but their application is limited in vivo. Current photochemical tools require high energy light for their activation. Dermal tissue contains bio chromophores that absorb this light and prevents its penetration to less than a few millimeters making photoactivation impossible. However, tissue has an "optical window" in the red and near infrared (600 -- 1000 nm) where light penetrates efficiently to clinically relevant depths. Therefore, researchers have sought long wavelength responsive caging groups but have had little success to date. Herein, I report the development of an entire class of red and near infrared responsive (600 -- 800 nm) caging groups based on Vitamin B12 or cobalamin. Upon modification with a fluorophore antenna, these metal complexes can capture long wavelength light to perform photochemical work in the form of bond scission reactions. The effect is compatible with a range of fluorophores covering the entire near infrared spectrum, and bond scission proceeds rapidly with extremely high efficiencies. In this work, the initial development and characterization of these molecules as photoactivateable groups will be discussed. Furthermore, I will demonstrate how these molecules can be applied for clinical applications, such as drug delivery and tissue scaffold formation, to provide safer and less invasive treatments.

An improved method to quantitate mature plant microRNA in biological matrices using modified periodate treatment and inclusion of internal controls

PubMed Central

Roh, Jamin; Davis, Cindy D.; Wang, Thomas T. Y.

2017-01-01

MicroRNAs (miRNAs) ubiquitously exist in microorganisms, plants, and animals, and appear to modulate a wide range of critical biological processes. However, no definitive conclusion has been reached regarding the uptake of exogenous dietary small RNAs into mammalian circulation and organs and cross-kingdom regulation. One of the critical issues is our ability to assess and distinguish the origin of miRNAs. Although periodate oxidation has been used to differentiate mammalian and plant miRNAs, validation of treatment efficiency and the inclusion of proper controls for this method were lacking in previous studies. This study aimed to address: 1) the efficiency of periodate treatment in a plant or mammalian RNA matrix, and 2) the necessity of inclusion of internal controls. We designed and tested spike-in synthetic miRNAs in various plant and mammalian matrices and showed that they can be used as a control for the completion of periodate oxidation. We found that overloading the reaction system with high concentration of RNA resulted in incomplete oxidation of unmethylated miRNA. The abundant miRNAs from soy and corn were analyzed in the plasma, liver, and fecal samples of C57BL/6 mice fed a corn and soy-based chow diet using our improved methodology. The improvement resulted in the elimination of the false positive detection in the liver, and we did not detect plant miRNAs in the mouse plasma or liver samples. In summary, an improved methodology was developed for plant miRNA detection that appears to work well in different sample matrices. PMID:28399134

Bioinformatics-based tools in drug discovery: the cartography from single gene to integrative biological networks.

PubMed

Ramharack, Pritika; Soliman, Mahmoud E S

2018-06-01

Originally developed for the analysis of biological sequences, bioinformatics has advanced into one of the most widely recognized domains in the scientific community. Despite this technological evolution, there is still an urgent need for nontoxic and efficient drugs. The onus now falls on the 'omics domain to meet this need by implementing bioinformatics techniques that will allow for the introduction of pioneering approaches in the rational drug design process. Here, we categorize an updated list of informatics tools and explore the capabilities of integrative bioinformatics in disease control. We believe that our review will serve as a comprehensive guide toward bioinformatics-oriented disease and drug discovery research. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

PubMed

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

2016-03-23

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

Controlled-release Hydrogen Peroxide for On-site Treatment of Organic Pollutants in Urban Storm Runoff

NASA Astrophysics Data System (ADS)

Lee, E.; Sun, S.; Kim, Y.

2011-12-01

Nonpoint source (NPS) pollutants are the remaining cause of the environment problems, significantly impairing the hydrologic and biologic function of urban water systems and human health. Managing the NPS loads to urban aquatic systems remains a challenge because of ubiquitous contaminant sources and large pollutants loads in the first flush. Best management practices (BMPs) exist for reducing the NPS pollutants in urban storm waters, but the remedial efficiencies of these passive schemes are unpredictable. This study aims to develop a controlled-release system as part of an in situ chemical oxidation scheme designed for on-site treatment of organic pollutants in urban runoff. Controlled-release hydrogen peroxide (CR-HP) solids were manufactured by dispersing fine sodium percarbonate granules in paraffin wax matrices. Release kinetics and treatment efficiencies of CR-HP for BTEX and MTBE were investigated through a series of column tests. Release data indicated that the CR-HP could continually release hydrogen peroxide (H2O2) in flowing water at controlled rates over 276-1756 days, and the release rates could be adjusted by changing the mixing ratios of sodium percarbonate and wax matrices. Additional column tests and model calculations demonstrated that CR-HP/UV systems can provide low-cost, target-specific, and persistent source of oxidants for efficient treatment of organic compounds in urban storm runoff.

Environmental Engineering Approaches toward Sustainable Management of Spider Mites.

PubMed

Suzuki, Takeshi

2012-10-26

Integrated pest management (IPM), which combines physical, biological, and chemical control measures to complementary effect, is one of the most important approaches to environmentally friendly sustainable agriculture. To expand IPM, we need to develop new pest control measures, reinforce existing measures, and investigate interactions between measures. Continued progress in the development of environmental control technologies and consequent price drops have facilitated their integration into plant production and pest control. Here I describe environmental control technologies for the IPM of spider mites through: (1) the disturbance of photoperiod-dependent diapause by artificial light, which may lead to death in seasonal environments; (2) the use of ultraviolet radiation to kill or repel mites; and (3) the use of water vapor control for the long-term cold storage of commercially available natural enemies. Such environmental control technologies have great potential for the efficient control of spider mites through direct physical effects and indirect effects via natural enemies.

Environmental Engineering Approaches toward Sustainable Management of Spider Mites

PubMed Central

Suzuki, Takeshi

2012-01-01

Integrated pest management (IPM), which combines physical, biological, and chemical control measures to complementary effect, is one of the most important approaches to environmentally friendly sustainable agriculture. To expand IPM, we need to develop new pest control measures, reinforce existing measures, and investigate interactions between measures. Continued progress in the development of environmental control technologies and consequent price drops have facilitated their integration into plant production and pest control. Here I describe environmental control technologies for the IPM of spider mites through: (1) the disturbance of photoperiod-dependent diapause by artificial light, which may lead to death in seasonal environments; (2) the use of ultraviolet radiation to kill or repel mites; and (3) the use of water vapor control for the long-term cold storage of commercially available natural enemies. Such environmental control technologies have great potential for the efficient control of spider mites through direct physical effects and indirect effects via natural enemies. PMID:26466730

Function-Based Algorithms for Biological Sequences

ERIC Educational Resources Information Center

Mohanty, Pragyan Sheela P.

2015-01-01

Two problems at two different abstraction levels of computational biology are studied. At the molecular level, efficient pattern matching algorithms in DNA sequences are presented. For gene order data, an efficient data structure is presented capable of storing all gene re-orderings in a systematic manner. A common characteristic of presented…

Efficient Mining of Interesting Patterns in Large Biological Sequences

PubMed Central

Rashid, Md. Mamunur; Karim, Md. Rezaul; Jeong, Byeong-Soo

2012-01-01

Pattern discovery in biological sequences (e.g., DNA sequences) is one of the most challenging tasks in computational biology and bioinformatics. So far, in most approaches, the number of occurrences is a major measure of determining whether a pattern is interesting or not. In computational biology, however, a pattern that is not frequent may still be considered very informative if its actual support frequency exceeds the prior expectation by a large margin. In this paper, we propose a new interesting measure that can provide meaningful biological information. We also propose an efficient index-based method for mining such interesting patterns. Experimental results show that our approach can find interesting patterns within an acceptable computation time. PMID:23105928

Efficient mining of interesting patterns in large biological sequences.

PubMed

Rashid, Md Mamunur; Karim, Md Rezaul; Jeong, Byeong-Soo; Choi, Ho-Jin

2012-03-01

Pattern discovery in biological sequences (e.g., DNA sequences) is one of the most challenging tasks in computational biology and bioinformatics. So far, in most approaches, the number of occurrences is a major measure of determining whether a pattern is interesting or not. In computational biology, however, a pattern that is not frequent may still be considered very informative if its actual support frequency exceeds the prior expectation by a large margin. In this paper, we propose a new interesting measure that can provide meaningful biological information. We also propose an efficient index-based method for mining such interesting patterns. Experimental results show that our approach can find interesting patterns within an acceptable computation time.

User-centered evaluation of Arizona BioPathway: an information extraction, integration, and visualization system.

PubMed

Quiñones, Karin D; Su, Hua; Marshall, Byron; Eggers, Shauna; Chen, Hsinchun

2007-09-01

Explosive growth in biomedical research has made automated information extraction, knowledge integration, and visualization increasingly important and critically needed. The Arizona BioPathway (ABP) system extracts and displays biological regulatory pathway information from the abstracts of journal articles. This study uses relations extracted from more than 200 PubMed abstracts presented in a tabular and graphical user interface with built-in search and aggregation functionality. This paper presents a task-centered assessment of the usefulness and usability of the ABP system focusing on its relation aggregation and visualization functionalities. Results suggest that our graph-based visualization is more efficient in supporting pathway analysis tasks and is perceived as more useful and easier to use as compared to a text-based literature-viewing method. Relation aggregation significantly contributes to knowledge-acquisition efficiency. Together, the graphic and tabular views in the ABP Visualizer provide a flexible and effective interface for pathway relation browsing and analysis. Our study contributes to pathway-related research and biological information extraction by assessing the value of a multiview, relation-based interface that supports user-controlled exploration of pathway information across multiple granularities.

A review of recent activities in the NASA CELSS program

NASA Technical Reports Server (NTRS)

Macelroy, R. D.; Tremor, J.; Smernoff, D. T.; Knott, W.; Prince, R. P.

1987-01-01

A CELSS (Controlled Ecological Life Support System) is a device that utilizes photosynthetic organisms and light energy to regenerate waste materials into oxygen and food for a crew in space. The results of studies with the CELSS program suggest that a bioregenerative life support system is a useful and effective method of regenerating consumable materials for crew sustenance. The data suggests that the operation of a CELSS in space is practical if plants can be made to behave predictably in the space environment. Much of the work centers on the biological components of the CELSS system. Ways of achieving high efficiency and long term stability of all components of the system are examined. Included are explorations of the conversion of nonedible cellulose to edible materials, nitrogen fixation by biological and chemical methods, and methods of waste processing. A description is provided of the extent to which a bioregenerative life support system can meet the constraints of the space environment, and the degree is assessed to which system efficiency and stability can be increased during the next decade.

Optogenetics-enabled assessment of viral gene and cell therapy for restoration of cardiac excitability

PubMed Central

Ambrosi, Christina M.; Boyle, Patrick M.; Chen, Kay; Trayanova, Natalia A.; Entcheva, Emilia

2015-01-01

Multiple cardiac pathologies are accompanied by loss of tissue excitability, which leads to a range of heart rhythm disorders (arrhythmias). In addition to electronic device therapy (i.e. implantable pacemakers and cardioverter/defibrillators), biological approaches have recently been explored to restore pacemaking ability and to correct conduction slowing in the heart by delivering excitatory ion channels or ion channel agonists. Using optogenetics as a tool to selectively interrogate only cells transduced to produce an exogenous excitatory ion current, we experimentally and computationally quantify the efficiency of such biological approaches in rescuing cardiac excitability as a function of the mode of application (viral gene delivery or cell delivery) and the geometry of the transduced region (focal or spatially-distributed). We demonstrate that for each configuration (delivery mode and spatial pattern), the optical energy needed to excite can be used to predict therapeutic efficiency of excitability restoration. Taken directly, these results can help guide optogenetic interventions for light-based control of cardiac excitation. More generally, our findings can help optimize gene therapy for restoration of cardiac excitability. PMID:26621212

A functionalizable polyester with free hydroxyl groups and tunable physiochemical and biological properties

PubMed Central

You, Zhengwei; Cao, Haiping; Gao, Jin; Shin, Paul H.; Day, Billy W.; Wang, Yadong

2010-01-01

Polyesters with free functional groups allow facile modifications with biomolecules, which can lead to versatile biomaterials that afford controlled interactions with cells and tissues. Efficient synthesis of functionalizable polyesters is still a challenge that greatly limits the availability and widespread applications of biofunctionalized synthetic polymers. Here we report a simple route to prepare a functionalizable polyester, poly(sebacoyl diglyceride) (PSeD) bearing free hydroxyl groups. The key synthetic step is an epoxide ring-opening polymerization, instead of the traditional polycondensation, that produces poly(glycerol sebacate) (PGS) [1]. PSeD has a more defined structure with mostly linear backbone, more free hydroxyl groups, higher molecular weight, and lower polydispersity than PGS. Crosslinking PSeD with sebacic acid yields a polymer five times tougher and more elastic than cured PGS. PSeD exhibits good cytocompatibility in vitro. Furthermore, functionalization by glycine proceeds with high efficiency. This versatile synthetic platform can offer a large family of biodegradable, functionalized polymers with tunable physiochemical and biological properties useful for a wide range of biomedical applications. PMID:20149441

Bioaccumulation of (63)Ni in the scleractinian coral Stylophora pistillata and isolated Symbiodinium using radiotracer techniques.

PubMed

Hédouin, Laetitia; Metian, Marc; Teyssié, Jean-Louis; Oberhänsli, François; Ferrier-Pagès, Christine; Warnau, Michel

2016-08-01

Development of nickel mining activities along the New Caledonia coasts threatens the biodiversity of coral reefs. Although the validation of tropical marine organisms as bioindicators of metal mining contamination has received much attention in the literature over the last decade, few studies have examined the potential of corals, the fundamental organisms of coral reefs, to monitor nickel (Ni) contamination in tropical marine ecosystems. In an effort to bridge this gap, the present work investigated the bioaccumulation of (63)Ni in the scleractinian coral Stylophora pistillata and in its isolated zooxanthellae Symbiodinium, using radiotracer techniques. Results highlight the high capacities of coral tissues (zooxanthellae and host tissues) to efficiently bioconcentrate (63)Ni compared to skeleton (Concentration Factors CF at 14 days of exposure are 3 orders of magnitude higher in tissues than in skeleton). When non-contaminated conditions were restored, (63)Ni was more efficiently retained in skeleton than in coral tissues, with biological half-lives (Tb½) of 44.3 and 6.5 days, respectively. In addition, our work showed that Symbiodinium bioconcentrated (63)Ni exponentially, with a vol/vol concentration factor at steady state (VCFSS) reaching 14,056. However, compilation of our results highlighted that despite efficient bioconcentration of (63)Ni in Symbiodinium, their contribution to the whole (63)Ni accumulation in coral nubbins represents less than 7%, suggesting that other biologically controlled processes occur in coral host allowing such efficient bioconcentration in coral tissues. Copyright © 2016 Elsevier Ltd. All rights reserved.

Applications of Fluorescence Spectroscopy for dissolved organic matter characterization in wastewater treatment plants

NASA Astrophysics Data System (ADS)

Goffin, Angélique; Guérin, Sabrina; Rocher, Vincent; Varrault, Gilles

2016-04-01

Dissolved organic matter (DOM) influences wastewater treatment plants efficiency (WTTP): variations in its quality and quantity can induce a foaming phenomenon and a fouling event inside biofiltration processes. Moreover, in order to manage denitrification step (control and optimization of the nitrate recirculation), it is important to be able to estimate biodegradable organic matter quantity before biological treatment. But the current methods used to characterize organic matter quality, like biological oxygen demand are laborious, time consuming and sometimes not applicable to directly monitor organic matter in situ. In the context of MOCOPEE research program (www.mocopee.com), this study aims to assess the use of optical techniques, such as UV-Visible absorbance and more specifically fluorescence spectroscopy in order to monitor and to optimize process efficiency in WWTP. Fluorescence excitation-emission matrix (EEM) spectroscopy was employed to prospect the possibility of using this technology online and in real time to characterize dissolved organic matter in different effluents of the WWTP Seine Centre (240,000 m3/day) in Paris, France. 35 sewage water influent samples were collected on 10 days at different hours. Data treatment were performed by two methods: peak picking and parallel factor analysis (PARAFAC). An evolution of DOM quality (position of excitation - emission peaks) and quantity (intensity of fluorescence) was observed between the different treatment steps (influent, primary treatment, biological treatment, effluent). Correlations were found between fluorescence indicators and different water quality key parameters in the sewage influents. We developed different multivariate linear regression models in order to predict a variety of water quality parameters by fluorescence intensity at specific excitation-emission wavelengths. For example dissolved biological oxygen demand (r2=0,900; p<0,0001) and ammonium concentration (r2=0,898; p<0,0001) present good correlation with specific fluorescence peaks and indicators. These indicators derived from 3D spectrofluorescence could be used in order to characterize DOM online and thus to optimize process efficiency in WWTP.

Organic Matter Composition, Recycling Susceptibility, and the Effectiveness of the Biological Pump – An Evaluation Using NMR Spectra of Marine Plankton

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

Paytan, Adina

Carbon (C) sequestration through fertilization of phytoplankton with micronutrients and enhancement of the absorption and retention of atmospheric C by ocean biota heavily depends on the efficiency of the “biological pump”. The long-term effectiveness of this strategy depends on a net transfer of C from the upper ocean-atmosphere system to the deep ocean where the C is removed from contact with the atmosphere for an extended period of time. This C removal can be equated to the amount of C fixation by phytoplankton minus the C cycling and regeneration in the euphotic zone. If the regeneration efficiency is increased, thenmore » despite increased C fixation, no net loss (sequestration) of C will result. A reduction in cycling efficiency in the euphotic zone, on the other hand, will increase the effectiveness of the “biological pump” and thus C sequestration. The degree of organic matter biodegradation and recycling depends on the “reactivity” of compounds synthesized by the biota, which in turn, is controlled by the structural characteristic of these compounds. There is considerable evidence that different phytoplankton taxa differ substantially in their biogeochemical characteristics and it is likely that the relative abundance of different compounds synthesized by these distinct taxa, and even within each group at different growth conditions, will differ too. This variability in biosynthesis and thus abundance of a wide range of organic compounds in the water column would lend itself to different susceptibility for biodegradation and regeneration. Knowledge of the distribution of various organic matter structural groups synthesized by distinct taxa, the dependence of the organic matter compound classes on different growth conditions (temperature, light, nutrients) and the selective susceptibility of these compound to regeneration is crucial for estimating the potential for rapid regeneration in the euphotic zone, and thus the effectiveness of the “biological pump”.« less

Regular dislocation networks in silicon as a tool for nanostructure devices used in optics, biology, and electronics.

PubMed

Kittler, M; Yu, X; Mchedlidze, T; Arguirov, T; Vyvenko, O F; Seifert, W; Reiche, M; Wilhelm, T; Seibt, M; Voss, O; Wolff, A; Fritzsche, W

2007-06-01

Well-controlled fabrication of dislocation networks in Si using direct wafer bonding opens broad possibilities for nanotechnology applications. Concepts of dislocation-network-based light emitters, manipulators of biomolecules, gettering and insulating layers, and three-dimensional buried conductive channels are presented and discussed. A prototype of a Si-based light emitter working at a wavelength of about 1.5 microm with an efficiency potential estimated at 1% is demonstrated.

Circular RNA profile in gliomas revealed by identification tool UROBORUS.

PubMed

Song, Xiaofeng; Zhang, Naibo; Han, Ping; Moon, Byoung-San; Lai, Rose K; Wang, Kai; Lu, Wange

2016-05-19

Recent evidence suggests that many endogenous circular RNAs (circRNAs) may play roles in biological processes. However, the expression patterns and functions of circRNAs in human diseases are not well understood. Computationally identifying circRNAs from total RNA-seq data is a primary step in studying their expression pattern and biological roles. In this work, we have developed a computational pipeline named UROBORUS to detect circRNAs in total RNA-seq data. By applying UROBORUS to RNA-seq data from 46 gliomas and normal brain samples, we detected thousands of circRNAs supported by at least two read counts, followed by successful experimental validation on 24 circRNAs from the randomly selected 27 circRNAs. UROBORUS is an efficient tool that can detect circRNAs with low expression levels in total RNA-seq without RNase R treatment. The circRNAs expression profiling revealed more than 476 circular RNAs differentially expressed in control brain tissues and gliomas. Together with parental gene expression, we found that circRNA and its parental gene have diversified expression patterns in gliomas and control brain tissues. This study establishes an efficient and sensitive approach for predicting circRNAs using total RNA-seq data. The UROBORUS pipeline can be accessed freely for non-commercial purposes at http://uroborus.openbioinformatics.org/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Advancing vector biology research: a community survey for future directions, research applications and infrastructure requirements

PubMed Central

Kohl, Alain; Pondeville, Emilie; Schnettler, Esther; Crisanti, Andrea; Supparo, Clelia; Christophides, George K.; Kersey, Paul J.; Maslen, Gareth L.; Takken, Willem; Koenraadt, Constantianus J. M.; Oliva, Clelia F.; Busquets, Núria; Abad, F. Xavier; Failloux, Anna-Bella; Levashina, Elena A.; Wilson, Anthony J.; Veronesi, Eva; Pichard, Maëlle; Arnaud Marsh, Sarah; Simard, Frédéric; Vernick, Kenneth D.

2016-01-01

Vector-borne pathogens impact public health, animal production, and animal welfare. Research on arthropod vectors such as mosquitoes, ticks, sandflies, and midges which transmit pathogens to humans and economically important animals is crucial for development of new control measures that target transmission by the vector. While insecticides are an important part of this arsenal, appearance of resistance mechanisms is increasingly common. Novel tools for genetic manipulation of vectors, use of Wolbachia endosymbiotic bacteria, and other biological control mechanisms to prevent pathogen transmission have led to promising new intervention strategies, adding to strong interest in vector biology and genetics as well as vector–pathogen interactions. Vector research is therefore at a crucial juncture, and strategic decisions on future research directions and research infrastructure investment should be informed by the research community. A survey initiated by the European Horizon 2020 INFRAVEC-2 consortium set out to canvass priorities in the vector biology research community and to determine key activities that are needed for researchers to efficiently study vectors, vector-pathogen interactions, as well as access the structures and services that allow such activities to be carried out. We summarize the most important findings of the survey which in particular reflect the priorities of researchers in European countries, and which will be of use to stakeholders that include researchers, government, and research organizations. PMID:27677378

Controlling chitosan-based encapsulation for protein and vaccine delivery

PubMed Central

Koppolu, Bhanu prasanth; Smith, Sean G.; Ravindranathan, Sruthi; Jayanthi, Srinivas; Kumar, Thallapuranam K.S.; Zaharoff, David A.

2014-01-01

Chitosan-based nano/microencapsulation is under increasing investigation for the delivery of drugs, biologics and vaccines. Despite widespread interest, the literature lacks a defined methodology to control chitosan particle size and drug/protein release kinetics. In this study, the effects of precipitation-coacervation formulation parameters on chitosan particle size, protein encapsulation efficiency and protein release were investigated. Chitosan particle sizes, which ranged from 300 nm to 3 μm, were influenced by chitosan concentration, chitosan molecular weight and addition rate of precipitant salt. The composition of precipitant salt played a significant role in particle formation with upper Hofmeister series salts containing strongly hydrated anions yielding particles with a low polydispersity index (PDI) while weaker anions resulted in aggregated particles with high PDIs. Sonication power had minimal effect on mean particle size, however, it significantly reduced polydispersity. Protein loading efficiencies in chitosan nano/microparticles, which ranged from 14.3% to 99.2%, was inversely related to the hydration strength of precipitant salts, protein molecular weight and directly related to the concentration and molecular weight of chitosan. Protein release rates increased with particle size and were generally inversely related to protein molecular weight. This study demonstrates that chitosan nano/microparticles with high protein loading efficiencies can be engineered with well-defined sizes and controllable release kinetics through manipulation of specific formulation parameters. PMID:24560459

Granular formulation of Fusarium oxysporum for biological control of faba bean and tomato Orobanche.

PubMed

Nemat Alla, Mamdouh M; Shabana, Yasser M; Serag, Mamdouh M; Hassan, Nemat M; El-Hawary, Mohamed M

2008-12-01

Orobanche spp. represent a serious threat to a wide range of crops. They are difficult targets for herbicides, and biological control could provide a possible solution. This work therefore aimed to formulate mycoherbicides of Fusarium with adequate shelf life and virulence against Orobanche but safe to faba bean and tomato. Only two isolates of Fusarium oxysporum Schlecht. (Foxy I and Foxy II) obtained from diseased Orobanche shoots were found to be pathogenic to Orobanche crenata Forsk. and Orobanche ramosa L. Conidial suspension of both isolates significantly decreased germination, attachments and tubercles of Orobanche. Microconidia and chlamydospores of both isolates were formulated as mycoherbicides encapsulated in a wheat flour-kaolin matrix (four different formulations). All formulations greatly diminished Orobanche emerged shoots, total shoot number, shoot height, attachment of emerged shoots, the germinated seeds that succeeded in emerging above the soil surface and dry weight. Meanwhile, disease incidence and disease severity of emerged shoots were enhanced. The shelf life was adequate, particularly for coarse, freshly prepared, low-temperature-stored, microconidia-rich formulations. The induced growth reduction of Orobanche-infected host plants seemed to be nullified by formulations, particularly at the highest dose. These formulations seemed to destroy Orobanche but appeared harmless to host plants. Hence, they could be efficiently used as mycoherbicides for biological control of Orobanche in faba bean and tomato.

Toward Contactless Biology: Acoustophoretic DNA Transfection

NASA Astrophysics Data System (ADS)

Vasileiou, Thomas; Foresti, Daniele; Bayram, Adem; Poulikakos, Dimos; Ferrari, Aldo

2016-02-01

Acoustophoresis revolutionized the field of container-less manipulation of liquids and solids by enabling mixing procedures which avoid contamination and loss of reagents due to the contact with the support. While its applications to chemistry and engineering are straightforward, additional developments are needed to obtain reliable biological protocols in a contactless environment. Here, we provide a first, fundamental step towards biological reactions in air by demonstrating the acoustophoretic DNA transfection of mammalian cells. We developed an original acoustophoretic design capable of levitating, moving and mixing biological suspensions of living mammalians cells and of DNA plasmids. The precise and sequential delivery of the mixed solutions into tissue culture plates is actuated by a novel mechanism based on the controlled actuation of the acoustophoretic force. The viability of the contactless procedure is tested using a cellular model sensitive to small perturbation of neuronal differentiation pathways. Additionally, the efficiency of the transfection procedure is compared to standard, container-based methods for both single and double DNA transfection and for different cell types including adherent growing HeLa cancer cells, and low adhesion neuron-like PC12 cells. In all, this work provides a proof of principle which paves the way to the development of high-throughput acoustophoretic biological reactors.

Toward Contactless Biology: Acoustophoretic DNA Transfection.

PubMed

Vasileiou, Thomas; Foresti, Daniele; Bayram, Adem; Poulikakos, Dimos; Ferrari, Aldo

2016-02-01

Acoustophoresis revolutionized the field of container-less manipulation of liquids and solids by enabling mixing procedures which avoid contamination and loss of reagents due to the contact with the support. While its applications to chemistry and engineering are straightforward, additional developments are needed to obtain reliable biological protocols in a contactless environment. Here, we provide a first, fundamental step towards biological reactions in air by demonstrating the acoustophoretic DNA transfection of mammalian cells. We developed an original acoustophoretic design capable of levitating, moving and mixing biological suspensions of living mammalians cells and of DNA plasmids. The precise and sequential delivery of the mixed solutions into tissue culture plates is actuated by a novel mechanism based on the controlled actuation of the acoustophoretic force. The viability of the contactless procedure is tested using a cellular model sensitive to small perturbation of neuronal differentiation pathways. Additionally, the efficiency of the transfection procedure is compared to standard, container-based methods for both single and double DNA transfection and for different cell types including adherent growing HeLa cancer cells, and low adhesion neuron-like PC12 cells. In all, this work provides a proof of principle which paves the way to the development of high-throughput acoustophoretic biological reactors.

Using Collision Cones to Asses Biological Deconiction Methods

NASA Astrophysics Data System (ADS)

Brace, Natalie

For autonomous vehicles to navigate the world as efficiently and effectively as biological species, improvements are needed in terms of control strategies and estimation algorithms. Reactive collision avoidance is one specific area where biological systems outperform engineered algorithms. To better understand the discrepancy between engineered and biological systems, a collision avoidance algorithm was applied to frames of trajectory data from three biological species (Myotis velifer, Hirundo rustica, and Danio aequipinnatus). The algorithm uses information that can be sensed through visual cues (relative position and velocity) to define collision cones which are used to determine if agents are on a collision course and if so, to find a safe velocity that requires minimal deviation from the original velocity for each individual agent. Two- and three-dimensional versions of the algorithm with constant speed and maximum speed velocity requirements were considered. The obstacles provided to the algorithm were determined by the sensing range in terms of either metric or topological distance. The calculated velocities showed good correlation with observed velocities over the range of sensing parameters, indicating that the algorithm is a good basis for comparison and could potentially be improved with further study.

Toward Contactless Biology: Acoustophoretic DNA Transfection

PubMed Central

Vasileiou, Thomas; Foresti, Daniele; Bayram, Adem; Poulikakos, Dimos; Ferrari, Aldo

2016-01-01

Acoustophoresis revolutionized the field of container-less manipulation of liquids and solids by enabling mixing procedures which avoid contamination and loss of reagents due to the contact with the support. While its applications to chemistry and engineering are straightforward, additional developments are needed to obtain reliable biological protocols in a contactless environment. Here, we provide a first, fundamental step towards biological reactions in air by demonstrating the acoustophoretic DNA transfection of mammalian cells. We developed an original acoustophoretic design capable of levitating, moving and mixing biological suspensions of living mammalians cells and of DNA plasmids. The precise and sequential delivery of the mixed solutions into tissue culture plates is actuated by a novel mechanism based on the controlled actuation of the acoustophoretic force. The viability of the contactless procedure is tested using a cellular model sensitive to small perturbation of neuronal differentiation pathways. Additionally, the efficiency of the transfection procedure is compared to standard, container-based methods for both single and double DNA transfection and for different cell types including adherent growing HeLa cancer cells, and low adhesion neuron-like PC12 cells. In all, this work provides a proof of principle which paves the way to the development of high-throughput acoustophoretic biological reactors. PMID:26828312

Computer-aided design of biological circuits using TinkerCell.

PubMed

Chandran, Deepak; Bergmann, Frank T; Sauro, Herbert M

2010-01-01

Synthetic biology is an engineering discipline that builds on modeling practices from systems biology and wet-lab techniques from genetic engineering. As synthetic biology advances, efficient procedures will be developed that will allow a synthetic biologist to design, analyze, and build biological networks. In this idealized pipeline, computer-aided design (CAD) is a necessary component. The role of a CAD application would be to allow efficient transition from a general design to a final product. TinkerCell is a design tool for serving this purpose in synthetic biology. In TinkerCell, users build biological networks using biological parts and modules. The network can be analyzed using one of several functions provided by TinkerCell or custom programs from third-party sources. Since best practices for modeling and constructing synthetic biology networks have not yet been established, TinkerCell is designed as a flexible and extensible application that can adjust itself to changes in the field. © 2010 Landes Bioscience

A RNA nanotechnology platform for a simultaneous two-in-one siRNA delivery and its application in synergistic RNAi therapy

PubMed Central

Jang, Mihue; Han, Hee Dong; Ahn, Hyung Jun

2016-01-01

Incorporating multiple copies of two RNAi molecules into a single nanostructure in a precisely controlled manner can provide an efficient delivery tool to regulate multiple gene pathways in the relation of mutual dependence. Here, we show a RNA nanotechnology platform for a two-in-one RNAi delivery system to contain polymeric two RNAi molecules within the same RNA nanoparticles, without the aid of polyelectrolyte condensation reagents. As our RNA nanoparticles lead to the simultaneous silencing of two targeted mRNAs, of which biological functions are highly interdependent, combination therapy for multi-drug resistance cancer cells, which was studied as a specific application of our two-in-one RNAi delivery system, demonstrates the efficient synergistic effects for cancer therapy. Therefore, this RNA nanoparticles approach has an efficient tool for a simultaneous co-delivery of RNAi molecules in the RNAi-based biomedical applications, and our current studies present an efficient strategy to overcome multi-drug resistance caused by malfunction of genes in chemotherapy. PMID:27562435

Models for integrated pest control and their biological implications.

PubMed

Tang, Sanyi; Cheke, Robert A

2008-09-01

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

A light-controlled cell lysis system in bacteria.

PubMed

Wang, Geyi; Lu, Xin; Zhu, Yisha; Zhang, Wei; Liu, Jiahui; Wu, Yankang; Yu, Liyang; Sun, Dongchang; Cheng, Feng

2018-05-08

Intracellular products (e.g., insulin), which are obtained through cell lysis, take up a big share of the biotech industry. It is often time-consuming, laborious, and environment-unfriendly to disrupt bacterial cells with traditional methods. In this study, we developed a molecular device for controlling cell lysis with light. We showed that intracellular expression of a single lysin protein was sufficient for efficient bacterial cell lysis. By placing the lysin-encoding gene under the control of an improved light-controlled system, we successfully controlled cell lysis by switching on/off light: OD 600 of the Escherichia coli cell culture was decreased by twofold when the light-controlled system was activated under dark condition. We anticipate that our work would not only pave the way for cell lysis through a convenient biological way in fermentation industry, but also provide a paradigm for applying the light-controlled system in other fields of biotech industry.

Tapping bioremediation's potential -- A matter of sweat and tiers

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

Merski, A.T.; Griffin, W.M.

Bioremediation's potential for treating environmental contamination is gaining greater recognition among regulators and the regulated community. For example, biological treatment is routinely applied to municipal wastewater, which typically contains readily biodegradable materials. Industrial wastewaters, by contrast, often contain higher concentrations of materials that present unique challenges to biological treatment. In both areas, biological treatment has succeeded by using contained, relatively controlled systems engineered to optimize performance of the biological component. Uncontrolled releases into such matrices as soil, and fresh and marine waters increase the complexity of the biological challenge, requiring development of novel products and procedures for efficient biological treatmentmore » and monitoring. One of the goals of the National Environmental Technology Applications Corporation (NETAC; Pittsburgh) is to support scientific development of bioremediation technology. NETAC is a non-profit corporation formed in 1988 through a cooperative agreement between EPA and the University of Pittsburgh Trust. Its overall mission is to accelerate development, application and commercialization of priority environmental technologies for national and international markets. NETAC provides technical and business expertise to assist in evaluating, commercializing and publicizing new environmental technologies. The organization assumes no financial interest in any technology but provides independent third-party support and analysis on a fee-for-service basis to technology users and developers.« less

Designing interfaces of hydrogenase-nanomaterial hybrids for efficient solar conversion.

PubMed

King, Paul W

2013-01-01

The direct conversion of sunlight into biofuels is an intriguing alternative to a continued reliance on fossil fuels. Natural photosynthesis has long been investigated both as a potential solution, and as a model for utilizing solar energy to drive a water-to-fuel cycle. The molecules and organizational structure provide a template to inspire the design of efficient molecular systems for photocatalysis. A clear design strategy is the coordination of molecular interactions that match kinetic rates and energetic levels to control the direction and flow of energy from light harvesting to catalysis. Energy transduction and electron-transfer reactions occur through interfaces formed between complexes of donor-acceptor molecules. Although the structures of several of the key biological complexes have been solved, detailed descriptions of many electron-transfer complexes are lacking, which presents a challenge to designing and engineering biomolecular systems for solar conversion. Alternatively, it is possible to couple the catalytic power of biological enzymes to light harvesting by semiconductor nanomaterials. In these molecules, surface chemistry and structure can be designed using ligands. The passivation effect of the ligand can also dramatically affect the photophysical properties of the semiconductor, and energetics of external charge-transfer. The length, degree of bond saturation (aromaticity), and solvent exposed functional groups of ligands can be manipulated to further tune the interface to control molecular assembly, and complex stability in photocatalytic hybrids. The results of this research show how ligand selection is critical to designing molecular interfaces that promote efficient self-assembly, charge-transfer and photocatalysis. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems. Copyright © 2013 Elsevier B.V. All rights reserved.

FERN - a Java framework for stochastic simulation and evaluation of reaction networks.

PubMed

Erhard, Florian; Friedel, Caroline C; Zimmer, Ralf

2008-08-29

Stochastic simulation can be used to illustrate the development of biological systems over time and the stochastic nature of these processes. Currently available programs for stochastic simulation, however, are limited in that they either a) do not provide the most efficient simulation algorithms and are difficult to extend, b) cannot be easily integrated into other applications or c) do not allow to monitor and intervene during the simulation process in an easy and intuitive way. Thus, in order to use stochastic simulation in innovative high-level modeling and analysis approaches more flexible tools are necessary. In this article, we present FERN (Framework for Evaluation of Reaction Networks), a Java framework for the efficient simulation of chemical reaction networks. FERN is subdivided into three layers for network representation, simulation and visualization of the simulation results each of which can be easily extended. It provides efficient and accurate state-of-the-art stochastic simulation algorithms for well-mixed chemical systems and a powerful observer system, which makes it possible to track and control the simulation progress on every level. To illustrate how FERN can be easily integrated into other systems biology applications, plugins to Cytoscape and CellDesigner are included. These plugins make it possible to run simulations and to observe the simulation progress in a reaction network in real-time from within the Cytoscape or CellDesigner environment. FERN addresses shortcomings of currently available stochastic simulation programs in several ways. First, it provides a broad range of efficient and accurate algorithms both for exact and approximate stochastic simulation and a simple interface for extending to new algorithms. FERN's implementations are considerably faster than the C implementations of gillespie2 or the Java implementations of ISBJava. Second, it can be used in a straightforward way both as a stand-alone program and within new systems biology applications. Finally, complex scenarios requiring intervention during the simulation progress can be modelled easily with FERN.

Bio-Fluid Dynamics in a Centimeter-Scale Diagnostics Incubator with Integrated Perfusion

NASA Astrophysics Data System (ADS)

Vukasinovic, J.; Cullen, D. K.; Glezer, A.; Laplaca, M. C.

2006-11-01

Growing demands for long-term incubation of biologically faithful, three-dimensional neuronal and other cultures during extended physiological studies require efficient perfusion platforms with functional vasculatures that mimic the in vivo condition in a thermally regulated environment. While thermostatically controlled incubation baths with capillary action perfusion are available, their use is confined to specific experimental conditions. The interstitial nutrient and gas delivery remains diffusion limited over the long term and cultures decay metabolically. To overcome these problems, we describe simple fabrication and experimental characterization of a compact, diagnostics incubator that allows in situ monitoring of culture activity with a superior control of critical biological functions using convectively enhanced heat and mass transport. To overcome intercellular diffusion barriers culture is exposed to a direct flow of media issuing from an array of micro-nozzles that are directed normal to the substrate upholding the culture, and further improved by 3-D convection induced by jet interactions and biased, peripheral perfusate extraction through an array of microchannels as demonstrated by microPIV measurements.

The genetic and biological basis of feed efficiency in mid-lactation Holstein dairy cows

USDA-ARS?s Scientific Manuscript database

The objective of this study was to characterize the genetic architecture and biological basis of feed efficiency in lactating Holstein cows. In total, 4,916 cows with actual or imputed genotypes for 60,671 SNP had individual feed intake, milk yield, milk composition, and body weight records. Cows we...

Efficient biological conversion of carbon monoxide (CO) to carbon dioxide (CO2) and for utilization in bioplastic production by Ralstonia eutropha through the display of an enzyme complex on the cell surface.

PubMed

Hyeon, Jeong Eun; Kim, Seung Wook; Park, Chulhwan; Han, Sung Ok

2015-06-25

An enzyme complex for biological conversion of CO to CO2 was anchored on the cell surface of the CO2-utilizing Ralstonia eutropha and successfully resulted in a 3.3-fold increase in conversion efficiency. These results suggest that this complexed system may be a promising strategy for CO2 utilization as a biological tool for the production of bioplastics.

Neural control and adaptive neural forward models for insect-like, energy-efficient, and adaptable locomotion of walking machines

PubMed Central

Manoonpong, Poramate; Parlitz, Ulrich; Wörgötter, Florentin

2013-01-01

Living creatures, like walking animals, have found fascinating solutions for the problem of locomotion control. Their movements show the impression of elegance including versatile, energy-efficient, and adaptable locomotion. During the last few decades, roboticists have tried to imitate such natural properties with artificial legged locomotion systems by using different approaches including machine learning algorithms, classical engineering control techniques, and biologically-inspired control mechanisms. However, their levels of performance are still far from the natural ones. By contrast, animal locomotion mechanisms seem to largely depend not only on central mechanisms (central pattern generators, CPGs) and sensory feedback (afferent-based control) but also on internal forward models (efference copies). They are used to a different degree in different animals. Generally, CPGs organize basic rhythmic motions which are shaped by sensory feedback while internal models are used for sensory prediction and state estimations. According to this concept, we present here adaptive neural locomotion control consisting of a CPG mechanism with neuromodulation and local leg control mechanisms based on sensory feedback and adaptive neural forward models with efference copies. This neural closed-loop controller enables a walking machine to perform a multitude of different walking patterns including insect-like leg movements and gaits as well as energy-efficient locomotion. In addition, the forward models allow the machine to autonomously adapt its locomotion to deal with a change of terrain, losing of ground contact during stance phase, stepping on or hitting an obstacle during swing phase, leg damage, and even to promote cockroach-like climbing behavior. Thus, the results presented here show that the employed embodied neural closed-loop system can be a powerful way for developing robust and adaptable machines. PMID:23408775

Development of Quenching-qPCR (Q-Q) assay for measuring absolute intracellular cleavage efficiency of ribozyme.

PubMed

Kim, Min Woo; Sun, Gwanggyu; Lee, Jung Hyuk; Kim, Byung-Gee

2018-06-01

Ribozyme (Rz) is a very attractive RNA molecule in metabolic engineering and synthetic biology fields where RNA processing is required as a control unit or ON/OFF signal for its cleavage reaction. In order to use Rz for such RNA processing, Rz must have highly active and specific catalytic activity. However, current methods for assessing the intracellular activity of Rz have limitations such as difficulty in handling and inaccuracies in the evaluation of correct cleavage activity. In this paper, we proposed a simple method to accurately measure the "intracellular cleavage efficiency" of Rz. This method deactivates unwanted activity of Rz which may consistently occur after cell lysis using DNA quenching method, and calculates the cleavage efficiency by analyzing the cleaved fraction of mRNA by Rz from the total amount of mRNA containing Rz via quantitative real-time PCR (qPCR). The proposed method was applied to measure "intracellular cleavage efficiency" of sTRSV, a representative Rz, and its mutant, and their intracellular cleavage efficiencies were calculated as 89% and 93%, respectively. Copyright © 2018 Elsevier Inc. All rights reserved.

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

Jawdy, Sara S.; Gunter, Lee E.; Engle, Nancy L.

Here, the biological function of the plant-microbiome system is the result of contributions from the host plant and microbiome members. In this work we study the function of a simplified community consisting of Pseudomonas and Burkholderia bacterial strains isolated from Populus hosts and inoculated on axenic Populus cutting in controlled laboratory conditions. Inoculation individually with either bacterial isolate increased root growth relative to uninoculated controls. Root area, photosynthetic efficiency, gene expression and metabolite expression data in individual and dual inoculated treatments indicate that the effects of these bacteria are unique and additive, suggesting that the function of a microbiome communitymore » may be predicted from the additive functions of the individual members.« less

OWL reasoning framework over big biological knowledge network.

PubMed

Chen, Huajun; Chen, Xi; Gu, Peiqin; Wu, Zhaohui; Yu, Tong

2014-01-01

Recently, huge amounts of data are generated in the domain of biology. Embedded with domain knowledge from different disciplines, the isolated biological resources are implicitly connected. Thus it has shaped a big network of versatile biological knowledge. Faced with such massive, disparate, and interlinked biological data, providing an efficient way to model, integrate, and analyze the big biological network becomes a challenge. In this paper, we present a general OWL (web ontology language) reasoning framework to study the implicit relationships among biological entities. A comprehensive biological ontology across traditional Chinese medicine (TCM) and western medicine (WM) is used to create a conceptual model for the biological network. Then corresponding biological data is integrated into a biological knowledge network as the data model. Based on the conceptual model and data model, a scalable OWL reasoning method is utilized to infer the potential associations between biological entities from the biological network. In our experiment, we focus on the association discovery between TCM and WM. The derived associations are quite useful for biologists to promote the development of novel drugs and TCM modernization. The experimental results show that the system achieves high efficiency, accuracy, scalability, and effectivity.

OWL Reasoning Framework over Big Biological Knowledge Network

PubMed Central

Chen, Huajun; Chen, Xi; Gu, Peiqin; Wu, Zhaohui; Yu, Tong

2014-01-01

Recently, huge amounts of data are generated in the domain of biology. Embedded with domain knowledge from different disciplines, the isolated biological resources are implicitly connected. Thus it has shaped a big network of versatile biological knowledge. Faced with such massive, disparate, and interlinked biological data, providing an efficient way to model, integrate, and analyze the big biological network becomes a challenge. In this paper, we present a general OWL (web ontology language) reasoning framework to study the implicit relationships among biological entities. A comprehensive biological ontology across traditional Chinese medicine (TCM) and western medicine (WM) is used to create a conceptual model for the biological network. Then corresponding biological data is integrated into a biological knowledge network as the data model. Based on the conceptual model and data model, a scalable OWL reasoning method is utilized to infer the potential associations between biological entities from the biological network. In our experiment, we focus on the association discovery between TCM and WM. The derived associations are quite useful for biologists to promote the development of novel drugs and TCM modernization. The experimental results show that the system achieves high efficiency, accuracy, scalability, and effectivity. PMID:24877076

Supramolecularly Engineered Circular Bivalent Aptamer for Enhanced Functional Protein Delivery.

PubMed

Jiang, Ying; Pan, Xiaoshu; Chang, Jin; Niu, Weijia; Hou, Weijia; Kuai, Hailan; Zhao, Zilong; Liu, Ji; Wang, Ming; Tan, Weihong

2018-06-06

Circular bivalent aptamers (cb-apt) comprise an emerging class of chemically engineered aptamers with substantially improved stability and molecular recognition ability. Its therapeutic application, however, is challenged by the lack of functional modules to control the interactions of cb-apt with therapeutics. We present the design of a β-cyclodextrin-modified cb-apt (cb-apt-βCD) and its supramolecular interaction with molecular therapeutics via host-guest chemistry for targeted intracellular delivery. The supramolecular ensemble exhibits high serum stability and enhanced intracellular delivery efficiency compared to a monomeric aptamer. The cb-apt-βCD ensemble delivers green fluorescent protein into targeted cells with efficiency as high as 80%, or cytotoxic saporin to efficiently inhibit tumor cell growth. The strategy of conjugating βCD to cb-apt, and subsequently modulating the supramolecular chemistry of cb-apt-βCD, provides a general platform to expand and diversify the function of aptamers, enabling new biological and therapeutic applications.

Harvesting and contamination control of microalgae Chlorella ellipsoidea using the bio-polymeric flocculant α-poly-l-lysine.

PubMed

Noh, Won; Kim, Jungmin; Lee, Sang-Jun; Ryu, Byung-Gon; Kang, Chang-Min

2018-02-01

Microalgae have been extensively studied for the production of various products. However, to date, microalgal biomass has not become economically feasible, mainly due to different issues such as contamination from various sources that occurs during downstream processes, and which leads to low quality biomass with limited application. In this study, to overcome contamination by flocculants and other microorganisms, the cationic biopolymer α-Poly-l-lysine (α-PLL) was applied. The cationic amine moiety and polymeric chain of α-PLL rendered microalgal harvesting efficient. With increasing α-PLL chain length, efficient dose- and time-dependent harvesting was achieved. In addition to efficient flocculation performance, biomass harvested using α-PLL showed suppressed biological contamination through the inherent antimicrobial activity of α-PLL. Thus, it is possible to upgrade the quality and storability of produced microalgal biomass using α-PLL-induced flocculation. Copyright © 2017 Elsevier Ltd. All rights reserved.

A benchtop biorobotic platform for in vitro observation of muscle-tendon dynamics with parallel mechanical assistance from an elastic exoskeleton.

PubMed

Robertson, Benjamin D; Vadakkeveedu, Siddarth; Sawicki, Gregory S

2017-05-24

We present a novel biorobotic framework comprised of a biological muscle-tendon unit (MTU) mechanically coupled to a feedback controlled robotic environment simulation that mimics in vivo inertial/gravitational loading and mechanical assistance from a parallel elastic exoskeleton. Using this system, we applied select combinations of biological muscle activation (modulated with rate-coded direct neural stimulation) and parallel elastic assistance (applied via closed-loop mechanical environment simulation) hypothesized to mimic human behavior based on previously published modeling studies. These conditions resulted in constant system-level force-length dynamics (i.e., stiffness), reduced biological loads, increased muscle excursion, and constant muscle average positive power output-all consistent with laboratory experiments on intact humans during exoskeleton assisted hopping. Mechanical assistance led to reduced estimated metabolic cost and MTU apparent efficiency, but increased apparent efficiency for the MTU+Exo system as a whole. Findings from this study suggest that the increased natural resonant frequency of the artificially stiffened MTU+Exo system, along with invariant movement frequencies, may underlie observed limits on the benefits of exoskeleton assistance. Our novel approach demonstrates that it is possible to capture the salient features of human locomotion with exoskeleton assistance in an isolated muscle-tendon preparation, and introduces a powerful new tool for detailed, direct examination of how assistive devices affect muscle-level neuromechanics and energetics. Copyright © 2017 Elsevier Ltd. All rights reserved.

Degradation of triclosan and its main intermediates during the combined irradiation and biological treatment.

PubMed

Wang, Shizong; Wang, Jianlong

2018-05-01

Triclosan is an extensively applied antimicrobial agent which has been frequently detected in the environment. In this paper, the degradation of triclosan and its main intermediates was investigated during the combined irradiation and biological treatment. The results showed that triclosan degradation increased with increase of absorbed dose, the removal efficiency of triclosan was 62%, 77%, 87%, 91% and 94%, respectively at 1, 2, 3, 4 and 5 kGy. The final removal efficiency of triclosan after the combined irradiation and biological process was 81%, 86%, 90%, 92% and 95%, respectively. During the irradiation process, two main intermediates, that is, 4,4'-2'-phenoxyphenol (Intermediate 1) and 4-chloro-2'-phenoxyphenol (Intermediate 2) were detected, in which Intermediate 1 dominated during the irradiation process. In the following biological treatment process, Intermediates 1 and 2 could be further degraded. In single biological treatment process, the final removal efficiency of triclosan was 54%, and Intermediates 1 and 2 were detected. Intermediate 1 could be biodegraded while Intermediate 2 could not. The concentration of Intermediate 2 increased during biological treatment process. In conclusion, irradiation as pre-treatment process can enhance the degradation of triclosan and improve the biodegradability of Intermediate 2. Combined irradiation and biological process can be promising for treating antibiotic-containing wastewater.

A conceptual review on systems biology in health and diseases: from biological networks to modern therapeutics.

PubMed

Somvanshi, Pramod Rajaram; Venkatesh, K V

2014-03-01

Human physiology is an ensemble of various biological processes spanning from intracellular molecular interactions to the whole body phenotypic response. Systems biology endures to decipher these multi-scale biological networks and bridge the link between genotype to phenotype. The structure and dynamic properties of these networks are responsible for controlling and deciding the phenotypic state of a cell. Several cells and various tissues coordinate together to generate an organ level response which further regulates the ultimate physiological state. The overall network embeds a hierarchical regulatory structure, which when unusually perturbed can lead to undesirable physiological state termed as disease. Here, we treat a disease diagnosis problem analogous to a fault diagnosis problem in engineering systems. Accordingly we review the application of engineering methodologies to address human diseases from systems biological perspective. The review highlights potential networks and modeling approaches used for analyzing human diseases. The application of such analysis is illustrated in the case of cancer and diabetes. We put forth a concept of cell-to-human framework comprising of five modules (data mining, networking, modeling, experimental and validation) for addressing human physiology and diseases based on a paradigm of system level analysis. The review overtly emphasizes on the importance of multi-scale biological networks and subsequent modeling and analysis for drug target identification and designing efficient therapies.

Assaying effector function in planta using double-barreled particle bombardment.

PubMed

Kale, Shiv D; Tyler, Brett M

2011-01-01

The biolistic transient gene expression assay is a beneficial tool for studying gene function in vivo. However, biolistic transient assay systems have inherent pitfalls that often cause experimental inaccuracies such as poor transformation efficiency, which can be confused with biological phenomena. The double-barreled gene gun device is an inexpensive and highly effective attachment that enables statistically significant data to be obtained with one-tenth the number of experimental replicates compared to conventional biolistic assays. The principle behind the attachment is to perform two simultaneous bombardments with control and test DNA preparations onto the same leaf. The control bombardment measures the efficiency of the transformation while the ratio of the test bombardment to the control bombardment measures the activity of the gene of interest. With care, the ratio between the pair of bombardments can be highly reproducible from bombardment to bombardment. The double-barreled attachment has been used to study plant resistance (R) gene-mediated responses to effectors, induction and suppression of cell death by a wide variety of pathogen and host molecules, and the role of oömycete effector RXLR motifs in cell reentry.

Engineered Ferritin for Magnetogenetic Manipulation of Proteins and Organelles Inside Living Cells.

PubMed

Liße, Domenik; Monzel, Cornelia; Vicario, Chiara; Manzi, John; Maurin, Isabelle; Coppey, Mathieu; Piehler, Jacob; Dahan, Maxime

2017-11-01

Magnetogenetics is emerging as a novel approach for remote-controlled manipulation of cellular functions in tissues and organisms with high spatial and temporal resolution. A critical, still challenging issue for these techniques is to conjugate target proteins with magnetic probes that can satisfy multiple colloidal and biofunctional constraints. Here, semisynthetic magnetic nanoparticles are tailored based on human ferritin coupled to monomeric enhanced green fluorescent protein (mEGFP) for magnetic manipulation of proteins inside living cells. This study demonstrates efficient delivery, intracellular stealth properties, and rapid subcellular targeting of those magnetic nanoparticles via GFP-nanobody interactions. By means of magnetic field gradients, rapid spatial reorganization in the cytosol of proteins captured to the nanoparticle surface is achieved. Moreover, exploiting efficient nanoparticle targeting to intracellular membranes, remote-controlled arrest of mitochondrial dynamics using magnetic fields is demonstrated. The studies establish subcellular control of proteins and organelles with unprecedented spatial and temporal resolution, thus opening new prospects for magnetogenetic applications in fundamental cell biology and nanomedicine. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Characteristics of microbial community and operation efficiency in biofilter process for drinking water purification].

PubMed

Xiang, Hong; Lü, Xi-Wu; Yang, Fei; Yin, Li-Hong; Zhu, Guang-Can

2011-04-01

In order to explore characteristics of microbial community and operation efficiency in biofilter (biologically-enhanced active filter and biological activated carbon filter) process for drinking water purification, Biolog and polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) techniques were applied to analyze the metabolic function and structure of microbial community developing in biofilters. Water quality parameters, such as NH; -N, NO; -N, permanganate index, UV254 and BDOC etc, were determined in inflow and outflow of biofilters for investigation of operation efficiency of the biofilters. The results show that metabolic capacity of microbial community of the raw water is reduced after the biofilters, which reflect that metabolically active microbial communities in the raw water can be intercepted by biofilters. After 6 months operation of biofilters, the metabolic profiles of microbial communities are similar between two kinds of biologically-enhanced active filters, and utilization of carbon sources of microbial communities in the two filters are 73.4% and 75.5%, respectively. The metabolic profiles of microbial communities in two biological activated carbon filters showed significant difference. The carbon source utilization rate of microbial community in granule-activated carbon filter is 79.6%, which is obviously higher than 53.8% of the rate in the columnar activated carbon filter (p < 0.01). The analysis results of PCR-SSCP indicate that microbial communities in each biofilter are variety, but the structure of dominant microorganisms is similar among different biofilters. The results also show that the packing materials had little effect on the structure and metabolic function of microbial community in biologically-enhanced active filters, and the difference between two biofilters for the water purification efficiency was not significant (p > 0.05). However, in biological activated carbon filters, granule-activated carbon is conducive to microbial growth and reproduction, and the microbial communities in the biofilter present high metabolic activities, and the removal efficiency for NH4(+)-N, permanganate index and BDOC is better than the columnar activated carbon filter(p < 0.05). The results also suggest that operation efficiency of biofilter is related to the metabolic capacity of microbial community in biofilter.

A Control System and Streaming DAQ Platform with Image-Based Trigger for X-ray Imaging

NASA Astrophysics Data System (ADS)

Stevanovic, Uros; Caselle, Michele; Cecilia, Angelica; Chilingaryan, Suren; Farago, Tomas; Gasilov, Sergey; Herth, Armin; Kopmann, Andreas; Vogelgesang, Matthias; Balzer, Matthias; Baumbach, Tilo; Weber, Marc

2015-06-01

High-speed X-ray imaging applications play a crucial role for non-destructive investigations of the dynamics in material science and biology. On-line data analysis is necessary for quality assurance and data-driven feedback, leading to a more efficient use of a beam time and increased data quality. In this article we present a smart camera platform with embedded Field Programmable Gate Array (FPGA) processing that is able to stream and process data continuously in real-time. The setup consists of a Complementary Metal-Oxide-Semiconductor (CMOS) sensor, an FPGA readout card, and a readout computer. It is seamlessly integrated in a new custom experiment control system called Concert that provides a more efficient way of operating a beamline by integrating device control, experiment process control, and data analysis. The potential of the embedded processing is demonstrated by implementing an image-based trigger. It records the temporal evolution of physical events with increased speed while maintaining the full field of view. The complete data acquisition system, with Concert and the smart camera platform was successfully integrated and used for fast X-ray imaging experiments at KIT's synchrotron radiation facility ANKA.

Modelling and simulation of passive Lab-on-a-Chip (LoC) based micromixer for clinical application

NASA Astrophysics Data System (ADS)

Saikat, Chakraborty; Sharath, M.; Srujana, M.; Narayan, K.; Pattnaik, Prasant Kumar

2016-03-01

In biomedical application, micromixer is an important component because of many processes requires rapid and efficient mixing. At micro scale, the flow is Laminar due to small channel size which enables controlled rapid mixing. The reduction in analysis time along with high throughput can be achieved with the help of rapid mixing. In LoC application, micromixer is used for mixing of fluids especially for the devices which requires efficient mixing. Micromixer of this type of microfluidic devices with a rapid mixing is useful in application such as DNA/RNA synthesis, drug delivery system & biological agent detection. In this work, we design and simulate a microfluidic based passive rapid micromixer for lab-on-a-chip application.

Algal culture studies related to a Closed Ecological Life Support System (CELSS)

NASA Technical Reports Server (NTRS)

Radmer, R.; Behrens, P.; Fernandez, E.; Ollinger, O.; Howell, C.; Venables, A.; Huggins, D.; Gladue, R.

1984-01-01

In many respects, algae would be the ideal plant component for a biologically based controlled life support system, since they are eminently suited to the closely coupled functions of atmosphere regeneration and food production. Scenedesmus obliquus and Spirulina platensis were grown in three continuous culture apparatuses. Culture vessels their operation and relative merits are described. Both light and nitrogen utilization efficiency are examined. Long term culture issues are detailed and a discussion of a plasmid search in Spirulina is included.

RNA interference in the clinic: challenges and future directions

PubMed Central

Pecot, Chad V.; Calin, George A.; Coleman, Robert L.; Lopez-Berestein, Gabriel; Sood, Anil K.

2011-01-01

Inherent difficulties with blocking many desirable targets using conventional approaches have prompted many to consider using RNA interference (RNAi) as a therapeutic approach. Although exploitation of RNAi has immense potential as a cancer therapeutic, many physiological obstacles stand in the way of successful and efficient delivery. This Review explores current challenges to the development of synthetic RNAi-based therapies and considers new approaches to circumvent biological barriers, to avoid intolerable side effects and to achieve controlled and sustained release. PMID:21160526

Analysis of a predator-prey model with Holling II functional response concerning impulsive control strategy

NASA Astrophysics Data System (ADS)

Liu, Bing; Teng, Zhidong; Chen, Lansun

2006-08-01

According to biological and chemical control strategy for pest control, we investigate the dynamic behavior of a Holling II functional response predator-prey system concerning impulsive control strategy-periodic releasing natural enemies and spraying pesticide at different fixed times. By using Floquet theorem and small amplitude perturbation method, we prove that there exists a stable pest-eradication periodic solution when the impulsive period is less than some critical value. Further, the condition for the permanence of the system is also given. Numerical results show that the system we consider can take on various kinds of periodic fluctuations and several types of attractor coexistence and is dominated by periodic, quasiperiodic and chaotic solutions, which implies that the presence of pulses makes the dynamic behavior more complex. Finally, we conclude that our impulsive control strategy is more effective than the classical one if we take chemical control efficiently.

Time Efficiency, Written Feedback, and Student Achievement in Inquiry-Oriented Biology Labs

ERIC Educational Resources Information Center

Basey, John M.; Maines, Anastasia P.; Francis, Clinton D.

2014-01-01

We examined how different styles of written feedback by graduate-student teaching assistants (GTAs) in college intro biology lab (USA) influenced student achievement and related the different styles to time efficiency. We quantified GTA feedback on formative lab reports and student achievement on two different types of assessments, a quiz in 2010…

THE INFLUENCE OF VARIABLE TEMPERATURE AND HUMIDITY ON THE PREDATION EFFICIENCY OF P. PERSIMILIS, N. CALIFORNICUS AND N. FALLACIS.

PubMed

Audenaert, J; Vangansbeke, D; Verhoeven, R; De Clercq, P; Tirry, L; Gobin, B

2014-01-01

Predatory mites like Phytoseiulus persimilis Athias-Henriot, Neoseiulus californicus McGregor and N. fallacis (Garman) (Acari: Phytoseiidae) are essential in sustainable control strategies of the two-spotted spider mite Tetranychus urticae Koch (Acari: Tetranychidae) in warm greenhouse cultures to complement imited available pesticides and to tackle emerging resistance. However, in response to high energy prices, greenhouse plant breeders have recently changed their greenhouse steering strategies, allowing more variation in temperature and humidity. The impact of these variations on biological control agents is poorly understood. Therefore, we constructed functional response models to demonstrate the impact of realistic climate variations on predation efficiency. First, two temperature regimes were compared at constant humidity (70%) and photoperiod (16L:8D): DIF0 (constant temperature) and DIF15 (variable temperature with day-night difference of 15°C). At mean temperatures of 25°C, DIF15 had a negative influence on the predation efficiency of P. persimilis and N. californicus, as compared to DIF0. At low mean temperatures of 15°C, however, DIF15 showed a higher predation efficiency for P. persimilis and N. californicus. For N. fallacis no difference was observed at both 15°C and 25°C. Secondly, two humidity regimes were compared, at a mean temperature of 25°C (DIFO) and constant photoperiod (16L:8D): RHCTE (constant 70% humidity) and RHALT (alternating 40% L:70%D humidity). For P. persimilis and N. fallacis RHCTE resulted in a higher predation efficiency than RHALT, for N. californicus this effect was opposite. This shows that N. californicus is more adapted to dry climates as compared to the other predatory mites. We conclude that variable greenhouse climates clearly affect predation efficiency of P. persimilis, N. californicus and N. fallacis. To obtain optimal control efficiency, the choice of predatory mites (including dose and application frequency) should be adapted to the actual greenhouse climate.

Chemical and biological extraction of metals present in E waste: A hybrid technology

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

Pant, Deepak, E-mail: deepakpant1@rediffmail.com; Joshi, Deepika; Upreti, Manoj K.

2012-05-15

Highlights: Black-Right-Pointing-Pointer Hybrid methodology for E waste management. Black-Right-Pointing-Pointer Efficient extraction of metals. Black-Right-Pointing-Pointer Trace metal extraction is possible. - Abstract: Management of metal pollution associated with E-waste is widespread across the globe. Currently used techniques for the extraction of metals from E-waste by using either chemical or biological leaching have their own limitations. Chemical leaching is much rapid and efficient but has its own environmental consequences, even the future prospects of associated nanoremediation are also uncertain. Biological leaching on the other hand is comparatively a cost effective technique but at the same moment it is time consuming and themore » complete recovery of the metal, alone by biological leaching is not possible in most of the cases. The current review addresses the individual issues related to chemical and biological extraction techniques and proposes a hybrid-methodology which incorporates both, along with safer chemicals and compatible microbes for better and efficient extraction of metals from the E-waste.« less

Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems

PubMed Central

Cilfone, Nicholas A.; Kirschner, Denise E.; Linderman, Jennifer J.

2015-01-01

Biologically related processes operate across multiple spatiotemporal scales. For computational modeling methodologies to mimic this biological complexity, individual scale models must be linked in ways that allow for dynamic exchange of information across scales. A powerful methodology is to combine a discrete modeling approach, agent-based models (ABMs), with continuum models to form hybrid models. Hybrid multi-scale ABMs have been used to simulate emergent responses of biological systems. Here, we review two aspects of hybrid multi-scale ABMs: linking individual scale models and efficiently solving the resulting model. We discuss the computational choices associated with aspects of linking individual scale models while simultaneously maintaining model tractability. We demonstrate implementations of existing numerical methods in the context of hybrid multi-scale ABMs. Using an example model describing Mycobacterium tuberculosis infection, we show relative computational speeds of various combinations of numerical methods. Efficient linking and solution of hybrid multi-scale ABMs is key to model portability, modularity, and their use in understanding biological phenomena at a systems level. PMID:26366228

The drivers of corporate environment inputs: Based on neo-institution theory evidence from Chinese listed biological and other companies.

PubMed

Guo, Rui; Tao, Lan; Yan, Liang; Chen, Lianfang; Wang, Haijun

2014-09-01

From corporate internal governance structure and external institutional environment, this study uses a legitimacy perspective of intuitional theory to analyze the main influence factors on corporate environmental protection inputs and propose some hypotheses. With the establishment of empirical models, it analyzes the data of 2004-2009 listed biological and other companies in China to test the hypotheses. The findings are concluded that in internal institutional environment, the nature of the controlling shareholder, the proportion of the first shareholder in the ownership structure, the combination of chairman and general manager in board efficiency and the intensity of environmental laws and regulations of the industry in external institutional environment have an significant impact on the behaviors of corporate environmental protection inputs.

X-ray microscopy as an approach to increasing accuracy and efficiency of serial block-face imaging for correlated light and electron microscopy of biological specimens.

PubMed

Bushong, Eric A; Johnson, Donald D; Kim, Keun-Young; Terada, Masako; Hatori, Megumi; Peltier, Steven T; Panda, Satchidananda; Merkle, Arno; Ellisman, Mark H

2015-02-01

The recently developed three-dimensional electron microscopic (EM) method of serial block-face scanning electron microscopy (SBEM) has rapidly established itself as a powerful imaging approach. Volume EM imaging with this scanning electron microscopy (SEM) method requires intense staining of biological specimens with heavy metals to allow sufficient back-scatter electron signal and also to render specimens sufficiently conductive to control charging artifacts. These more extreme heavy metal staining protocols render specimens light opaque and make it much more difficult to track and identify regions of interest (ROIs) for the SBEM imaging process than for a typical thin section transmission electron microscopy correlative light and electron microscopy study. We present a strategy employing X-ray microscopy (XRM) both for tracking ROIs and for increasing the efficiency of the workflow used for typical projects undertaken with SBEM. XRM was found to reveal an impressive level of detail in tissue heavily stained for SBEM imaging, allowing for the identification of tissue landmarks that can be subsequently used to guide data collection in the SEM. Furthermore, specific labeling of individual cells using diaminobenzidine is detectable in XRM volumes. We demonstrate that tungsten carbide particles or upconverting nanophosphor particles can be used as fiducial markers to further increase the precision and efficiency of SBEM imaging.

X-ray Microscopy as an Approach to Increasing Accuracy and Efficiency of Serial Block-face Imaging for Correlated Light and Electron Microscopy of Biological Specimens

PubMed Central

Bushong, Eric A.; Johnson, Donald D.; Kim, Keun-Young; Terada, Masako; Hatori, Megumi; Peltier, Steven T.; Panda, Satchidananda; Merkle, Arno; Ellisman, Mark H.

2015-01-01

The recently developed three-dimensional electron microscopic (EM) method of serial block-face scanning electron microscopy (SBEM) has rapidly established itself as a powerful imaging approach. Volume EM imaging with this scanning electron microscopy (SEM) method requires intense staining of biological specimens with heavy metals to allow sufficient back-scatter electron signal and also to render specimens sufficiently conductive to control charging artifacts. These more extreme heavy metal staining protocols render specimens light opaque and make it much more difficult to track and identify regions of interest (ROIs) for the SBEM imaging process than for a typical thin section transmission electron microscopy correlative light and electron microscopy study. We present a strategy employing X-ray microscopy (XRM) both for tracking ROIs and for increasing the efficiency of the workflow used for typical projects undertaken with SBEM. XRM was found to reveal an impressive level of detail in tissue heavily stained for SBEM imaging, allowing for the identification of tissue landmarks that can be subsequently used to guide data collection in the SEM. Furthermore, specific labeling of individual cells using diaminobenzidine is detectable in XRM volumes. We demonstrate that tungsten carbide particles or upconverting nanophosphor particles can be used as fiducial markers to further increase the precision and efficiency of SBEM imaging. PMID:25392009

Development of an efficient pheromone-based trapping method for the banana root borer Cosmopolites sordidus.

PubMed

Reddy, G V P; Cruz, Z T; Guerrero, A

2009-01-01

The banana root borer Cosmopolites sordidus (Germar) (Coleoptera: Curculionidae) is a major pest of bananas throughout the world. Chemical control is both undesirable and expensive, where biological control alternatives are limited, and pheromone-based trapping results in low captures. In this study, several important factors that affect pheromone-based catches, such as trap type, trap dimensions, and color and position of the traps, were optimized. Ground traps were found to be superior to ramp and pitfall traps, and larger traps (40 x 25 cm and above) were more efficient than smaller ones (30 x 15 cm). In a color-choice test, the banana weevil clearly preferred brown traps over yellow, red, gray, blue, black, white, and green, with mahogany being more attractive than other shades of brown. In addition, pheromone baited ground traps positioned in the shade of the canopy caught significantly more adults than those placed in sunlight. Therefore, mahogany-brown ground traps 40 x 25 cm appear to be the most efficient at catching C. sordidus adults and have the greatest potential for use in mass trapping and programs for eradication of this pest.

Structure and formation of ant transportation networks

PubMed Central

Latty, Tanya; Ramsch, Kai; Ito, Kentaro; Nakagaki, Toshiyuki; Sumpter, David J. T.; Middendorf, Martin; Beekman, Madeleine

2011-01-01

Many biological systems use extensive networks for the transport of resources and information. Ants are no exception. How do biological systems achieve efficient transportation networks in the absence of centralized control and without global knowledge of the environment? Here, we address this question by studying the formation and properties of inter-nest transportation networks in the Argentine ant (Linepithema humile). We find that the formation of inter-nest networks depends on the number of ants involved in the construction process. When the number of ants is sufficient and networks do form, they tend to have short total length but a low level of robustness. These networks are topologically similar to either minimum spanning trees or Steiner networks. The process of network formation involves an initial construction of multiple links followed by a pruning process that reduces the number of trails. Our study thus illuminates the conditions under and the process by which minimal biological transport networks can be constructed. PMID:21288958

Surface modification of biomaterials using plasma immersion ion implantation and deposition

PubMed Central

Lu, Tao; Qiao, Yuqin; Liu, Xuanyong

2012-01-01

Although remarkable progress has been made on biomaterial research, the ideal biomaterial that satisfies all the technical requirements and biological functions is not available up to now. Surface modification seems to be a more economic and efficient way to adjust existing conventional biomaterials to meet the current and ever-evolving clinical needs. From an industrial perspective, plasma immersion ion implantation and deposition (PIII&D) is an attractive method for biomaterials owing to its capability of treating objects with irregular shapes, as well as the control of coating composition. It is well acknowledged that the physico-chemical characteristics of biomaterials are the decisive factors greatly affecting the biological responses of biomaterials including bioactivity, haemocompatibility and antibacterial activity. Here, we mainly review the recent advances in surface modification of biomaterials via PIII&D technology, especially titanium alloys and polymers used for orthopaedic, dental and cardiovascular implants. Moreover, the variations of biological performances depending on the physico-chemical properties of modified biomaterials will be discussed. PMID:23741609

Recent advances and industrial viewpoint for biological treatment of wastewaters by oleaginous microorganisms.

PubMed

Huang, Chao; Luo, Mu-Tan; Chen, Xue-Fang; Xiong, Lian; Li, Xiao-Mei; Chen, Xin-De

2017-05-01

Recently, technology of using oleaginous microorganisms for biological treatment of wastewaters has become one hot topic in biochemical and environmental engineering for its advantages such as easy for operation in basic bioreactor, having potential to produce valuable bio-products, efficient wastewaters treatment in short period, etc. To promote its industrialization, this article provides some comprehensive analysis of this technology such as its advances, issues, and outlook especially from industrial viewpoint. In detail, the types of wastewaters can be treated and the kinds of oleaginous microorganisms used for biological treatment are introduced, the potential of industrial application and issues (relatively low COD removal, low lipid yield, cost of operation, and lack of scale up application) of this technology are presented, and some critical outlook mainly on co-culture method, combination with other treatments, process controlling and adjusting are discussed systematically. By this article, some important information to develop this technology can be obtained. Copyright © 2017 Elsevier Ltd. All rights reserved.

Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

PubMed Central

Kim, Lavane; Pagaling, Eulyn; Zuo, Yi Y.

2014-01-01

The impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected, Burkholderiales and Rhodocyclales of the Betaproteobacteria class were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes. PMID:24141134

Advancing metabolic engineering through systems biology of industrial microorganisms.

PubMed

Dai, Zongjie; Nielsen, Jens

2015-12-01

Development of sustainable processes to produce bio-based compounds is necessary due to the severe environmental problems caused by the use of fossil resources. Metabolic engineering can facilitate the development of highly efficient cell factories to produce these compounds from renewable resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further. Copyright © 2015 Elsevier Ltd. All rights reserved.

Powerful inner/outer controlled multi-target magnetic nanoparticle drug carrier prepared by liquid photo-immobilization

NASA Astrophysics Data System (ADS)

Guan, Yan-Qing; Zheng, Zhe; Huang, Zheng; Li, Zhibin; Niu, Shuiqin; Liu, Jun-Ming

2014-05-01

Nanomagnetic materials offer exciting avenues for advancing cancer therapies. Most researches have focused on efficient delivery of drugs in the body by incorporating various drug molecules onto the surface of nanomagnetic particles. The challenge is how to synthesize low toxic nanocarriers with multi-target drug loading. The cancer cell death mechanisms associated with those nanocarriers remain unclear either. Following the cell biology mechanisms, we develop a liquid photo-immobilization approach to attach doxorubicin, folic acid, tumor necrosis factor-α, and interferon-γ onto the oleic acid molecules coated Fe3O4 magnetic nanoparticles to prepare a kind of novel inner/outer controlled multi-target magnetic nanoparticle drug carrier. In this work, this approach is demonstrated by a variety of structural and biomedical characterizations, addressing the anti-cancer effects in vivo and in vitro on the HeLa, and it is highly efficient and powerful in treating cancer cells in a valuable programmed cell death mechanism for overcoming drug resistance.

Human cell culture in a space bioreactor

NASA Technical Reports Server (NTRS)

Morrison, Dennis R.

1988-01-01

Microgravity offers new ways of handling fluids, gases, and growing mammalian cells in efficient suspension cultures. In 1976 bioreactor engineers designed a system using a cylindrical reactor vessel in which the cells and medium are slowly mixed. The reaction chamber is interchangeable and can be used for several types of cell cultures. NASA has methodically developed unique suspension type cell and recovery apparatus culture systems for bioprocess technology experiments and production of biological products in microgravity. The first Space Bioreactor was designed for microprocessor control, no gaseous headspace, circulation and resupply of culture medium, and slow mixing in very low shear regimes. Various ground based bioreactors are being used to test reactor vessel design, on-line sensors, effects of shear, nutrient supply, and waste removal from continuous culture of human cells attached to microcarriers. The small Bioreactor is being constructed for flight experiments in the Shuttle Middeck to verify systems operation under microgravity conditions and to measure the efficiencies of mass transport, gas transfer, oxygen consumption and control of low shear stress on cells.

Toward scalable parts families for predictable design of biological circuits.

PubMed

Lucks, Julius B; Qi, Lei; Whitaker, Weston R; Arkin, Adam P

2008-12-01

Our current ability to engineer biological circuits is hindered by design cycles that are costly in terms of time and money, with constructs failing to operate as desired, or evolving away from the desired function once deployed. Synthetic biologists seek to understand biological design principles and use them to create technologies that increase the efficiency of the genetic engineering design cycle. Central to the approach is the creation of biological parts--encapsulated functions that can be composited together to create new pathways with predictable behaviors. We define five desirable characteristics of biological parts--independence, reliability, tunability, orthogonality and composability, and review studies of small natural and synthetic biological circuits that provide insights into each of these characteristics. We propose that the creation of appropriate sets of families of parts with these properties is a prerequisite for efficient, predictable engineering of new function in cells and will enable a large increase in the sophistication of genetic engineering applications.

Altered resting-state functional connectivity in women with chronic fatigue syndrome.

PubMed

Kim, Byung-Hoon; Namkoong, Kee; Kim, Jae-Jin; Lee, Seojung; Yoon, Kang Joon; Choi, Moonjong; Jung, Young-Chul

2015-12-30

The biological underpinnings of the psychological factors characterizing chronic fatigue syndrome (CFS) have not been extensively studied. Our aim was to evaluate alterations of resting-state functional connectivity in CFS patients. Participants comprised 18 women with CFS and 18 age-matched female healthy controls who were recruited from the local community. Structural and functional magnetic resonance images were acquired during a 6-min passive-viewing block scan. Posterior cingulate cortex seeded resting-state functional connectivity was evaluated, and correlation analyses of connectivity strength were performed. Graph theory analysis of 90 nodes of the brain was conducted to compare the global and local efficiency of connectivity networks in CFS patients with that in healthy controls. The posterior cingulate cortex in CFS patients showed increased resting-state functional connectivity with the dorsal and rostral anterior cingulate cortex. Connectivity strength of the posterior cingulate cortex to the dorsal anterior cingulate cortex significantly correlated with the Chalder Fatigue Scale score, while the Beck Depression Inventory (BDI) score was controlled. Connectivity strength to the rostral anterior cingulate cortex significantly correlated with the Chalder Fatigue Scale score. Global efficiency of the posterior cingulate cortex was significantly lower in CFS patients, while local efficiency showed no difference from findings in healthy controls. The findings suggest that CFS patients show inefficient increments in resting-state functional connectivity that are linked to the psychological factors observed in the syndrome. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Large-scale self-assembly of uniform submicron silver sulfide material driven by precise pressure control

NASA Astrophysics Data System (ADS)

Qi, Juanjuan; Chen, Ke; Zhang, Shuhao; Yang, Yun; Guo, Lin; Yang, Shihe

2017-03-01

The controllable self-assembly of nanosized building blocks into larger specific structures can provide an efficient method of synthesizing novel materials with excellent properties. The self-assembly of nanocrystals by assisted means is becoming an extremely active area of research, because it provides a method of producing large-scale advanced functional materials with potential applications in the areas of energy, electronics, optics, and biologics. In this study, we applied an efficient strategy, namely, the use of ‘pressure control’ to the assembly of silver sulfide (Ag2S) nanospheres with a diameter of approximately 33 nm into large-scale, uniform Ag2S sub-microspheres with a size of about 0.33 μm. More importantly, this strategy realizes the online control of the overall reaction system, including the pressure, reaction time, and temperature, and could also be used to easily fabricate other functional materials on an industrial scale. Moreover, the thermodynamics and kinetics parameters for the thermal decomposition of silver diethyldithiocarbamate (Ag(DDTC)) are also investigated to explore the formation mechanism of the Ag2S nanosized building blocks which can be assembled into uniform sub-micron scale architecture. As a method of producing sub-micron Ag2S particles by means of the pressure-controlled self-assembly of nanoparticles, we foresee this strategy being an efficient and universally applicable option for constructing other new building blocks and assembling novel and large functional micromaterials on an industrial scale.

Crapemyrtle Bark Scale: A New Threat for Crapemyrtles, a Popular Landscape Plant in the U.S.

PubMed Central

Wang, Zinan; Chen, Yan; Gu, Mengmeng; Vafaie, Erfan; Merchant, Michael; Diaz, Rodrigo

2016-01-01

Crapemyrtle bark scale, Acanthococcus (=Eriococcus) lagerstroemiae (Kuwana) (Hemiptera: Eriococcidae), is a newly introduced insect pest on crapemyrtles, Lagerstroemia spp. (Myrtales: Lythraceae), one of the most popular flowering shrubs in the U.S. Since first detected in Texas in 2004, this pest has spread to twelve states causing losses to stakeholders. To develop a management plan, we reviewed current knowledge about the pest’s biology and ecology, and suggested research approaches including studying its thermal tolerance, host range, plant resistance and biological control. Parasitoids and predators have been reared from A. lagerstroemiae in the U.S. and China. However, new surveys of natural enemies should be conducted in China, and studies on the host range and impacts of natural enemies on A. lagerstroemiae may help determine the potential for classical biological control. The life history, preying efficiency and rearing methods are important for coccinellid predators found in the U.S. including Chilocorus cacti L. and Hyperaspis spp. To enhance natural enemy performance, it is important to evaluate a sustainable insecticide program that considers efficacy, timing, rate and impact on pollinator health. Finally, an integrated management program of A. lagerstroemiae is discussed including planting resistant cultivars, using host specific natural enemies, and prudent use of insecticides. PMID:27999262

The effect of temperature on the functional response of Phytoseiulus persimilis (Acari: Phytoseiidae).

PubMed

Skirvin, David J; Fenlon, John S

2003-01-01

Environmental variables, such as temperature, are important in determining the efficiency of biological control in ornamental crops. This paper examines the effect of temperature on the functional response of adult female Phytoseiulus persimilis to eggs of the spider mite, Tetranychus urticae. The functional response was determined using a new functional response assay technique with plant stems as an arena, rather than leaf discs. The use of plant stems allows the influence that plant structure has on predation to be incorporated into the assay. Control assays were also used (without predators) to estimate natural losses of prey. The data were analysed using a binomial model, with the use of Abbot's formula to correct for the losses in the controls. A combined equation to describe the effect of temperature and prey density on the predation rate of Phytoseiulus persimilis was derived. The results showed that more prey are eaten as the temperature increases from 15 degrees C to 25 degrees C, but the number of prey eaten then declines at 30 degrees C, although not to the levels seen at 20 degrees C. The implication of these results for biological control in ornamental crops, where the temperature can often exceed 30 degrees C, is discussed.

CELSS research and development program

NASA Technical Reports Server (NTRS)

Bubenheim, David

1990-01-01

Research in Controlled Ecological Life Support Systems (CELSS) conducted by NASA indicate that plant based systems are feasible candidates for human support in space. Ames has responsibility for research and development, systems integration and control, and space flight experiment portions of the CELSS program. Important areas for development of new methods and technologies are biomass production, waste processing, water purification, air revitalization, and food processing. For the plant system, the approach was to identify the flexibility and response time for the food, water, and oxygen production, and carbon dioxide consumption processes. Tremendous increases in productivity, compared with terrestrial agriculture, were realized. Waste processing research emphasizes recycle (transformation) of human wastes, trash, and inedible biomass to forms usable as inputs to the plant production system. Efforts to improve efficiency of the plant system, select new CELSS crops for a balanced diet, and initiate closed system research with the Crop Growth Research Chambers continue. The System Control and Integration program goal is to insure orchestrated system operation of the biological, physical, and chemical operation of the biological, physical, and chemical component processors of the CELSS. Space flight studies are planned to verify adequate operation of the system in reduced gravity or microgravity environments.

Screening of bacterial antagonists for biological control of Phytophthora blight of pepper.

PubMed

Rajkumar, M; Lee, Wang Hyu; Lee, Kui Jae

2005-01-01

The aim of this study was to assess the potential of bacterial antagonists to control Phytophthora blight of pepper caused by P. capsici using different screening methods. Among a collection of fluorescent pseudomonas isolated from the rhizosphere of pepper, twelve isolates were initially selected based on dual culture assay on potato dextrose agar and corn meal agar. Further, these twelve isolates were screened for the reduction of disease severity caused by P. capsici using detached leaves and seedling assay. Most of the antagonists showed varying levels of antagonism against P. capsici in both detached leaves and seedlings assay. In addition, few isolates increased shoot and root length of pepper in seedling assays. Among them, isolate PS119 showing highest ability to reduce the disease severity in the in vitro seedling assay was found to be the most efficient antagonists against P. capsici in the in vivo biological control tests. These results indicate that the in vitro seedling assay can be used as a rapid and more accurate technique for the selection of promising biocontrol agents against P. capsici. ((c) 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim).

Biomedical and Catalytic Opportunities of Virus-Like Particles in Nanotechnology

PubMed Central

Schwarz, B.; Uchida, M.; Douglas, T.

2016-01-01

Within biology, molecules are arranged in hierarchical structures that coordinate and control the many processes that allow for complex organisms to exist. Proteins and other functional macromolecules are often studied outside their natural nanostructural context because it remains difficult to create controlled arrangements of proteins at this size scale. Viruses are elegantly simple nanosystems that exist at the interface of living organisms and nonliving biological machines. Studied and viewed primarily as pathogens to be combatted, viruses have emerged as models of structural efficiency at the nanoscale and have spurred the development of biomimetic nanoparticle systems. Virus-like particles (VLPs) are noninfectious protein cages derived from viruses or other cage-forming systems. VLPs provide incredibly regular scaffolds for building at the nanoscale. Composed of self-assembling protein subunits, VLPs provide both a model for studying materials’ assembly at the nanoscale and useful building blocks for materials design. The robustness and degree of understanding of many VLP structures allow for the ready use of these systems as versatile nanoparticle platforms for the conjugation of active molecules or as scaffolds for the structural organization of chemical processes. Lastly the prevalence of viruses in all domains of life has led to unique activities of VLPs in biological systems most notably the immune system. Here we discuss recent efforts to apply VLPs in a wide variety of applications with the aim of highlighting how the common structural elements of VLPs have led to their emergence as paradigms for the understanding and design of biological nanomaterials. PMID:28057256

Advances in Targeted Pesticides with Environmentally Responsive Controlled Release by Nanotechnology

PubMed Central

Huang, Bingna; Chen, Feifei; Shen, Yue; Wang, Yan; Sun, Changjiao; Zhao, Xiang; Cui, Bo; Gao, Fei; Zeng, Zhanghua; Cui, Haixin

2018-01-01

Pesticides are the basis for defending against major biological disasters and important for ensuring national food security. Biocompatible, biodegradable, intelligent, and responsive materials are currently an emerging area of interest in the field of efficient, safe, and green pesticide formulation. Using nanotechnology to design and prepare targeted pesticides with environmentally responsive controlled release via compound and chemical modifications has also shown great potential in creating novel formulations. In this review, special attention has been paid to intelligent pesticides with precise controlled release modes that can respond to micro-ecological environment changes such as light-sensitivity, thermo-sensitivity, humidity sensitivity, soil pH, and enzyme activity. Moreover, establishing intelligent and controlled pesticide release technologies using nanomaterials are reported. These technologies could increase pesticide-loading, improve the dispersibility and stability of active ingredients, and promote target ability. PMID:29439498

Biologically-Inspired Control for a Planetary Exploration Tensegrity Robot

NASA Technical Reports Server (NTRS)

Leroy, Marc

2017-01-01

Tensegrity structures are becoming increasingly popular as mechanical structures for robots. Their inherent compliance makes them extremely robust to environmental disturbances, and their design allows them to have a high strength-to-weight ratio whilst being lightweight compared to traditional robots. For these reasons they would be of interest to the aerospace industry, particularly for planetary exploration. However, being such compliant structures thanks to their network of elastic elements also means that their control is not an easy task. Relying solely on traditional control strategies to generate efficient locomotion would surely be near impossible due to the complex oscillatory motions and nonlinear interactions of its members. The goal of this project was to use bio-inspired control techniques to generate locomotion for a tensegrity icosahedron, namely the SUPERball project of the Intelligent Robotics Group of NASA Ames Research Center.

Cardiac Muscle-cell Based Actuator and Self-stabilizing Biorobot - PART 1.

PubMed

Holley, Merrel T; Nagarajan, Neerajha; Danielson, Christian; Zorlutuna, Pinar; Park, Kidong

2017-07-11

Biological machines often referred to as biorobots, are living cell- or tissue-based devices that are powered solely by the contractile activity of living components. Due to their inherent advantages, biorobots are gaining interest as alternatives to traditional fully artificial robots. Various studies have focused on harnessing the power of biological actuators, but only recently studies have quantitatively characterized the performance of biorobots and studied their geometry to enhance functionality and efficiency. Here, we demonstrate the development of a self-stabilizing swimming biorobot that can maintain its pitch, depth, and roll without external intervention. The design and fabrication of the PDMS scaffold for the biological actuator and biorobot followed by the functionalization with fibronectin is described in this first part. In the second part of this two-part article, we detail the incorporation of cardiomyocytes and characterize the biological actuator and biorobot function. Both incorporate a base and tail (cantilever) which produce fin-based propulsion. The tail is constructed with soft lithography techniques using PDMS and laser engraving. After incorporating the tail with the device base, it is functionalized with a cell adhesive protein and seeded confluently with cardiomyocytes. The base of the biological actuator consists of a solid PDMS block with a central glass bead (acts as a weight). The base of the biorobot consists of two composite PDMS materials, Ni-PDMS and microballoon-PDMS (MB-PDMS). The nickel powder (in Ni-PDMS) allows magnetic control of the biorobot during cells seeding and stability during locomotion. Microballoons (in MB-PDMS) decrease the density of MB-PDMS, and enable the biorobot to float and swim steadily. The use of these two materials with different mass densities, enabled precise control over the weight distribution to ensure a positive restoration force at any angle of the biorobot. This technique produces a magnetically controlled self-stabilizing swimming biorobot.

Uncertainty, learning, and the optimal management of wildlife

USGS Publications Warehouse

Williams, B.K.

2001-01-01

Wildlife management is limited by uncontrolled and often unrecognized environmental variation, by limited capabilities to observe and control animal populations, and by a lack of understanding about the biological processes driving population dynamics. In this paper I describe a comprehensive framework for management that includes multiple models and likelihood values to account for structural uncertainty, along with stochastic factors to account for environmental variation, random sampling, and partial controllability. Adaptive optimization is developed in terms of the optimal control of incompletely understood populations, with the expected value of perfect information measuring the potential for improving control through learning. The framework for optimal adaptive control is generalized by including partial observability and non-adaptive, sample-based updating of model likelihoods. Passive adaptive management is derived as a special case of constrained adaptive optimization, representing a potentially efficient suboptimal alternative that nonetheless accounts for structural uncertainty.

Control of fluxes in metabolic networks

PubMed Central

Basler, Georg; Nikoloski, Zoran; Larhlimi, Abdelhalim; Barabási, Albert-László; Liu, Yang-Yu

2016-01-01

Understanding the control of large-scale metabolic networks is central to biology and medicine. However, existing approaches either require specifying a cellular objective or can only be used for small networks. We introduce new coupling types describing the relations between reaction activities, and develop an efficient computational framework, which does not require any cellular objective for systematic studies of large-scale metabolism. We identify the driver reactions facilitating control of 23 metabolic networks from all kingdoms of life. We find that unicellular organisms require a smaller degree of control than multicellular organisms. Driver reactions are under complex cellular regulation in Escherichia coli, indicating their preeminent role in facilitating cellular control. In human cancer cells, driver reactions play pivotal roles in malignancy and represent potential therapeutic targets. The developed framework helps us gain insights into regulatory principles of diseases and facilitates design of engineering strategies at the interface of gene regulation, signaling, and metabolism. PMID:27197218

Removal of pharmaceuticals from wastewater by biological processes, hydrodynamic cavitation and UV treatment.

PubMed

Zupanc, Mojca; Kosjek, Tina; Petkovšek, Martin; Dular, Matevž; Kompare, Boris; Širok, Brane; Blažeka, Željko; Heath, Ester

2013-07-01

To augment the removal of pharmaceuticals different conventional and alternative wastewater treatment processes and their combinations were investigated. We tested the efficiency of (1) two distinct laboratory scale biological processes: suspended activated sludge and attached-growth biomass, (2) a combined hydrodynamic cavitation-hydrogen peroxide process and (3) UV treatment. Five pharmaceuticals were chosen including ibuprofen, naproxen, ketoprofen, carbamazepine and diclofenac, and an active metabolite of the lipid regulating agent clofibric acid. Biological treatment efficiency was evaluated using lab-scale suspended activated sludge and moving bed biofilm flow-through reactors, which were operated under identical conditions in respect to hydraulic retention time, working volume, concentration of added pharmaceuticals and synthetic wastewater composition. The suspended activated sludge process showed poor and inconsistent removal of clofibric acid, carbamazepine and diclofenac, while ibuprofen, naproxen and ketoprofen yielded over 74% removal. Moving bed biofilm reactors were filled with two different types of carriers i.e. Kaldnes K1 and Mutag BioChip™ and resulted in higher removal efficiencies for ibuprofen and diclofenac. Augmentation and consistency in the removal of diclofenac were observed in reactors using Mutag BioChip™ carriers (85%±10%) compared to reactors using Kaldnes carriers and suspended activated sludge (74%±22% and 48%±19%, respectively). To enhance the removal of pharmaceuticals hydrodynamic cavitation with hydrogen peroxide process was evaluated and optimal conditions for removal were established regarding the duration of cavitation, amount of added hydrogen peroxide and initial pressure, all of which influence the efficiency of the process. Optimal parameters resulted in removal efficiencies between 3-70%. Coupling the attached-growth biomass biological treatment, hydrodynamic cavitation/hydrogen peroxide process and UV treatment resulted in removal efficiencies of >90% for clofibric acid and >98% for carbamazepine and diclofenac, while the remaining compounds were reduced to levels below the LOD. For ibuprofen, naproxen, ketoprofen and diclofenac the highest contribution to overall removal was attributed to biological treatment, for clofibric acid UV treatment was the most efficient, while for carbamazepine hydrodynamic cavitation/hydrogen peroxide process and UV treatment were equally efficient. Copyright © 2012 Elsevier B.V. All rights reserved.

Dynamic sensitivity analysis of biological systems

PubMed Central

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

2008-01-01

Background A mathematical model to understand, predict, control, or even design a real biological system is a central theme in systems biology. A dynamic biological system is always modeled as a nonlinear ordinary differential equation (ODE) system. How to simulate the dynamic behavior and dynamic parameter sensitivities of systems described by ODEs efficiently and accurately is a critical job. In many practical applications, e.g., the fed-batch fermentation systems, the system admissible input (corresponding to independent variables of the system) can be time-dependent. The main difficulty for investigating the dynamic log gains of these systems is the infinite dimension due to the time-dependent input. The classical dynamic sensitivity analysis does not take into account this case for the dynamic log gains. Results We present an algorithm with an adaptive step size control that can be used for computing the solution and dynamic sensitivities of an autonomous ODE system simultaneously. Although our algorithm is one of the decouple direct methods in computing dynamic sensitivities of an ODE system, the step size determined by model equations can be used on the computations of the time profile and dynamic sensitivities with moderate accuracy even when sensitivity equations are more stiff than model equations. To show this algorithm can perform the dynamic sensitivity analysis on very stiff ODE systems with moderate accuracy, it is implemented and applied to two sets of chemical reactions: pyrolysis of ethane and oxidation of formaldehyde. The accuracy of this algorithm is demonstrated by comparing the dynamic parameter sensitivities obtained from this new algorithm and from the direct method with Rosenbrock stiff integrator based on the indirect method. The same dynamic sensitivity analysis was performed on an ethanol fed-batch fermentation system with a time-varying feed rate to evaluate the applicability of the algorithm to realistic models with time-dependent admissible input. Conclusion By combining the accuracy we show with the efficiency of being a decouple direct method, our algorithm is an excellent method for computing dynamic parameter sensitivities in stiff problems. We extend the scope of classical dynamic sensitivity analysis to the investigation of dynamic log gains of models with time-dependent admissible input. PMID:19091016

Complementary Constraints from Carbon (13C) and Nitrogen (15N) Isotopes on the Efficiency of the Glacial Ocean's Soft-Tissue Biological Pump

NASA Astrophysics Data System (ADS)

Schmittner, A.; Somes, C. J.

2016-12-01

A three-dimensional, process-based model of the ocean's carbon and nitrogen cycles, including 13C and 15N isotopes, is used to explore effects of idealized changes in the soft-tissue biological pump. Results are presented from one preindustrial control run and six simulations of the Last Glacial Maximum (LGM) with increasing values of the spatially constant maximum phytoplankton growth rate μmax, which mimicks iron fertilization. The default LGM simulation, without increasing μmax and with a shallower and weaker Atlantic Meridional Overturning Circulation and increased sea ice cover, leads to 280 Pg more respired organic carbon (Corg) than the pre-industrial control. Dissolved oxygen in the thermocline increase, which reduces water column denitrification and nitrogen fixation, thus increasing the ocean's fixed nitrogen inventory and decreasing δ15NNO3. This simulation already fits observed carbon and nitrogen isotopes relatively well, but it overestimates deep ocean δ13CDIC and underestimates δ15NNO3 at high latitudes. Increasing μmax enhances Corg and lowers deep ocean δ13CDIC, improving the fit. Modest increases in μmax result in higher subpolar δ15NNO3 due to enhanced local nutrient utilization, and better agreement with reconstructions. Large increases in nutrient utilization are inconsistent with nitrogen isotopes although they still fit the carbon isotopes reasonably well. The best fitting models with modest increases in μmax reproduce major features of the glacial δ13CDIC, δ15N, and oxygen reconstructions while simulating increased Corg by 510-670 Pg. These results are consistent with the idea that the soft-tissue pump was more efficient during the LGM. Both circulation and biological nutrient utilization contribute. However, these conclusions are preliminary given our idealized experiments, which do not consider changes in benthic denitrification and spatially inhomogenous changes in aeolian iron fluxes. The analysis illustrates interactions between the carbon and nitrogen cycles as well as the complementary constraints provided by their isotopes. Whereas carbon isotopes are sensitive to circulation changes and indicate well the three-dimensional Corg distribution, nitrogen isotopes are more sensitive to biological nutrient utilization.

[Survival strategy of photosynthetic organisms. 1. Variability of the extent of light-harvesting pigment aggregation as a structural factor optimizing the function of oligomeric photosynthetic antenna. Model calculations].

PubMed

Fetisova, Z G

2004-01-01

In accordance with our concept of rigorous optimization of photosynthetic machinery by a functional criterion, this series of papers continues purposeful search in natural photosynthetic units (PSU) for the basic principles of their organization that we predicted theoretically for optimal model light-harvesting systems. This approach allowed us to determine the basic principles for the organization of a PSU of any fixed size. This series of papers deals with the problem of structural optimization of light-harvesting antenna of variable size controlled in vivo by the light intensity during the growth of organisms, which accentuates the problem of antenna structure optimization because optimization requirements become more stringent as the PSU increases in size. In this work, using mathematical modeling for the functioning of natural PSUs, we have shown that the aggregation of pigments of model light-harvesting antenna, being one of universal optimizing factors, furthermore allows controlling the antenna efficiency if the extent of pigment aggregation is a variable parameter. In this case, the efficiency of antenna increases with the size of the elementary antenna aggregate, thus ensuring the high efficiency of the PSU irrespective of its size; i.e., variation in the extent of pigment aggregation controlled by the size of light-harvesting antenna is biologically expedient.

Synthetic Biology of Polyhydroxyalkanoates (PHA).

PubMed

Meng, De-Chuan; Chen, Guo-Qiang

Microbial polyhydroxyalkanoates (PHA) are a family of biodegradable and biocompatible polyesters which have been extensively studied using synthetic biology and metabolic engineering methods for improving production and for widening its diversity. Synthetic biology has allowed PHA to become composition controllable random copolymers, homopolymers, and block copolymers. Recent developments showed that it is possible to establish a microbial platform for producing not only random copolymers with controllable monomers and their ratios but also structurally defined homopolymers and block copolymers. This was achieved by engineering the genome of Pseudomonas putida or Pseudomonas entomophiles to weaken the β-oxidation and in situ fatty acid synthesis pathways, so that a fatty acid fed to the bacteria maintains its original chain length and structures when incorporated into the PHA chains. The engineered bacterium allows functional groups in a fatty acid to be introduced into PHA, forming functional PHA, which, upon grafting, generates endless PHA variety. Recombinant Escherichia coli also succeeded in producing efficiently poly(3-hydroxypropionate) or P3HP, the strongest member of PHA. Synthesis pathways of P3HP and its copolymer P3HB3HP of 3-hydroxybutyrate and 3-hydroxypropionate were assembled respectively to allow their synthesis from glucose. CRISPRi was also successfully used to manipulate simultaneously multiple genes and control metabolic flux in E. coli to obtain a series of copolymer P3HB4HB of 3-hydroxybutyrate (3HB) and 4-hydroxybutyrate (4HB). The bacterial shapes were successfully engineered for enhanced PHA accumulation.

A novel self-catalyzed photoATRP strategy for preparation of fluorescent hydroxyapatite nanoparticles and their biological imaging

NASA Astrophysics Data System (ADS)

Jiang, Ruming; Liu, Meiying; Huang, Hongye; Huang, Long; Huang, Qiang; Wen, Yuanqing; Cao, Qian-yong; Tian, Jianwen; Zhang, Xiaoyong; Wei, Yen

2018-03-01

Hydroxyapatite (HAp), as an important biomaterial for the regeneration and reconstruction of bone tissue, has attracted more and more attention of researchers and scientists due to its unique structure and compositions. However, the preparation of fluorescent HAp with controllable morphology has achieved only limited success. In this work, we reported a novel strategy to construct the water dispersible fluorescent HAp nanorods via the combination of ligand exchange and metal-free atom transfer radical polymerization (ATRP). The Br-containing fluorescent HAp nanorods with controllable size and morphology were first prepared through hydrothermal treatment. A multifunctional organic molecule (named as PTH-Br) with aggregation-induced emission feature was immobilized on the surface of hydrophobic HAp nanorods through ligand exchange reaction. The PTH-Br could be used as the initiator and catalyst for surface-initiated metal-free ATRP using poly(ethylene glycol) methacrylate as monomer to obtain hydrophilic fluorescent HAp polymer nanoparticles. This strategy successfully endowed HAp nanorods excellent fluorescence properties and favorable water dispersibility but well preserved their regular morphology. Biological assays demonstrated that the HAp-PTH-poly(PEGMA) nanoparticles exhibited good biocompatibility and efficient cell uptake performance. Taken together, we have developed a rather facile strategy based on the surface ligand exchange reaction and metal-free photoATRP to fabricate fluorescent HAp with controllable size and morphology, high water dispersibility and biological properties. These HAp-PTH-poly(PEGMA) nanoparticles should be novel and promising candidates for biomedical applications.

Developmental biology and tissue engineering.

PubMed

Marga, Francoise; Neagu, Adrian; Kosztin, Ioan; Forgacs, Gabor

2007-12-01

Morphogenesis implies the controlled spatial organization of cells that gives rise to tissues and organs in early embryonic development. While morphogenesis is under strict genetic control, the formation of specialized biological structures of specific shape hinges on physical processes. Tissue engineering (TE) aims at reproducing morphogenesis in the laboratory, i.e., in vitro, to fabricate replacement organs for regenerative medicine. The classical approach to generate tissues/organs is by seeding and expanding cells in appropriately shaped biocompatible scaffolds, in the hope that the maturation process will result in the desired structure. To accomplish this goal more naturally and efficiently, we set up and implemented a novel TE method that is based on principles of developmental biology and employs bioprinting, the automated delivery of cellular composites into a three-dimensional (3D) biocompatible environment. The novel technology relies on the concept of tissue liquidity according to which multicellular aggregates composed of adhesive and motile cells behave in analogy with liquids: in particular, they fuse. We emphasize the major role played by tissue fusion in the embryo and explain how the parameters (surface tension, viscosity) that govern tissue fusion can be used both experimentally and theoretically to control and simulate the self-assembly of cellular spheroids into 3D living structures. The experimentally observed postprinting shape evolution of tube- and sheet-like constructs is presented. Computer simulations, based on a liquid model, support the idea that tissue liquidity may provide a mechanism for in vitro organ building. Copyright 2008 Wiley-Liss, Inc.

The biological carbon pump in the ocean: Reviewing model representations and its feedbacks on climate perturbations.

NASA Astrophysics Data System (ADS)

Hülse, Dominik; Arndt, Sandra; Ridgwell, Andy; Wilson, Jamie

2016-04-01

The ocean-sediment system, as the biggest carbon reservoir in the Earth's carbon cycle, plays a crucial role in regulating atmospheric carbon dioxide concentrations and climate. Therefore, it is essential to constrain the importance of marine carbon cycle feedbacks on global warming and ocean acidification. Arguably, the most important single component of the ocean's carbon cycle is the so-called "biological carbon pump". It transports carbon that is fixed in the light-flooded surface layer of the ocean to the deep ocean and the surface sediment, where it is degraded/dissolved or finally buried in the deep sediments. Over the past decade, progress has been made in understanding different factors that control the efficiency of the biological carbon pump and their feedbacks on the global carbon cycle and climate (i.e. ballasting = ocean acidification feedback; temperature dependant organic matter degradation = global warming feedback; organic matter sulphurisation = anoxia/euxinia feedback). Nevertheless, many uncertainties concerning the interplay of these processes and/or their relative significance remain. In addition, current Earth System Models tend to employ empirical and static parameterisations of the biological pump. As these parametric representations are derived from a limited set of present-day observations, their ability to represent carbon cycle feedbacks under changing climate conditions is limited. The aim of my research is to combine past carbon cycling information with a spatially resolved global biogeochemical model to constrain the functioning of the biological pump and to base its mathematical representation on a more mechanistic approach. Here, I will discuss important aspects that control the efficiency of the ocean's biological carbon pump, review how these processes of first order importance are mathematically represented in existing Earth system Models of Intermediate Complexity (EMIC) and distinguish different approaches to approximate biogeochemical processes in the sediments. The performance of the respective mathematical representations in constraining the importance of carbon pump feedbacks on marine biogeochemical dynamics is then compared and evaluated under different extreme climate scenarios (e.g. OAE2, Eocene) using the Earth system model 'GENIE' and proxy records. The compiled mathematical descriptions and the model results underline the lack of a complete and mechanistic framework to represent the short-term carbon cycle in most EMICs which seriously limits the ability of these models to constrain the response of the ocean's carbon cycle to past and in particular future climate change. In conclusion, this presentation will critically evaluate the approaches currently used in marine biogeochemical modelling and outline key research directions concerning model development in the future.

Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges.

PubMed

Yin, Zekun; Lan, Haidong; Tan, Guangming; Lu, Mian; Vasilakos, Athanasios V; Liu, Weiguo

2017-01-01

The last decade has witnessed an explosion in the amount of available biological sequence data, due to the rapid progress of high-throughput sequencing projects. However, the biological data amount is becoming so great that traditional data analysis platforms and methods can no longer meet the need to rapidly perform data analysis tasks in life sciences. As a result, both biologists and computer scientists are facing the challenge of gaining a profound insight into the deepest biological functions from big biological data. This in turn requires massive computational resources. Therefore, high performance computing (HPC) platforms are highly needed as well as efficient and scalable algorithms that can take advantage of these platforms. In this paper, we survey the state-of-the-art HPC platforms for big biological data analytics. We first list the characteristics of big biological data and popular computing platforms. Then we provide a taxonomy of different biological data analysis applications and a survey of the way they have been mapped onto various computing platforms. After that, we present a case study to compare the efficiency of different computing platforms for handling the classical biological sequence alignment problem. At last we discuss the open issues in big biological data analytics.

An energy-efficient communication method based on the relationships between biological signals for ubiquitous health monitoring.

PubMed

Kwon, Hyok Chon; Na, Doosu; Ko, Byung Geun; Lee, Songjun

2008-01-01

Wireless sensor networks have been studied in the area of intelligent transportation systems, disaster perception, environment monitoring, ubiquitous healthcare, home network, and so on. For the ubiquitous healthcare, the previous systems collect the sensed health related data at portable devices without regard to correlations of various biological signals to determine the health conditions. It is not the energy-efficient method to gather a lot of information into a specific node to decide the health condition. Since the biological signals are related with each other to estimate certain body condition, it is necessary to be collected selectively by their relationship for energy efficiency of the networked nodes. One of researches about low power consumption is the reduction of the amount of packet transmission. In this paper, a health monitoring system, which allows the transmission of the reduced number of packets by means of setting the routing path considered the relations of biological signals, is proposed.

A novel approach to enhance biological nutrient removal using a culture supernatant from Micrococcus luteus containing resuscitation-promoting factor (Rpf) in SBR process.

PubMed

Liu, Yindong; Su, Xiaomei; Lu, Lian; Ding, Linxian; Shen, Chaofeng

2016-03-01

A culture supernatant from Micrococcus luteus containing resuscitation-promoting factor (SRpf) was used to enhance the biological nutrient removal of potentially functional bacteria. The obtained results suggest that SRpf accelerated the start-up process and significantly enhanced the biological nutrient removal in sequencing batch reactor (SBR). PO4 (3-)-P removal efficiency increased by over 12 % and total nitrogen removal efficiency increased by over 8 % in treatment reactor acclimated by SRpf compared with those without SRpf addition. The Illumina high-throughput sequencing analysis showed that SRpf played an essential role in shifts in the composition and diversity of bacterial community. The phyla of Proteobacteria and Actinobacteria, which were closely related to biological nutrient removal, were greatly abundant after SRpf addition. This study demonstrates that SRpf acclimation or addition might hold great potential as an efficient and cost-effective alternative for wastewater treatment plants (WWTPs) to meet more stringent operation conditions and legislations.

Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities.

PubMed

Narayanasamy, Shaman; Muller, Emilie E L; Sheik, Abdul R; Wilmes, Paul

2015-05-01

Biological wastewater treatment plants harbour diverse and complex microbial communities which prominently serve as models for microbial ecology and mixed culture biotechnological processes. Integrated omic analyses (combined metagenomics, metatranscriptomics, metaproteomics and metabolomics) are currently gaining momentum towards providing enhanced understanding of community structure, function and dynamics in situ as well as offering the potential to discover novel biological functionalities within the framework of Eco-Systems Biology. The integration of information from genome to metabolome allows the establishment of associations between genetic potential and final phenotype, a feature not realizable by only considering single 'omes'. Therefore, in our opinion, integrated omics will become the future standard for large-scale characterization of microbial consortia including those underpinning biological wastewater treatment processes. Systematically obtained time and space-resolved omic datasets will allow deconvolution of structure-function relationships by identifying key members and functions. Such knowledge will form the foundation for discovering novel genes on a much larger scale compared with previous efforts. In general, these insights will allow us to optimize microbial biotechnological processes either through better control of mixed culture processes or by use of more efficient enzymes in bioengineering applications. © 2015 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Robust synthetic biology design: stochastic game theory approach.

PubMed

Chen, Bor-Sen; Chang, Chia-Hung; Lee, Hsiao-Ching

2009-07-15

Synthetic biology is to engineer artificial biological systems to investigate natural biological phenomena and for a variety of applications. However, the development of synthetic gene networks is still difficult and most newly created gene networks are non-functioning due to uncertain initial conditions and disturbances of extra-cellular environments on the host cell. At present, how to design a robust synthetic gene network to work properly under these uncertain factors is the most important topic of synthetic biology. A robust regulation design is proposed for a stochastic synthetic gene network to achieve the prescribed steady states under these uncertain factors from the minimax regulation perspective. This minimax regulation design problem can be transformed to an equivalent stochastic game problem. Since it is not easy to solve the robust regulation design problem of synthetic gene networks by non-linear stochastic game method directly, the Takagi-Sugeno (T-S) fuzzy model is proposed to approximate the non-linear synthetic gene network via the linear matrix inequality (LMI) technique through the Robust Control Toolbox in Matlab. Finally, an in silico example is given to illustrate the design procedure and to confirm the efficiency and efficacy of the proposed robust gene design method. http://www.ee.nthu.edu.tw/bschen/SyntheticBioDesign_supplement.pdf.

Nature as an engineer: one simple concept of a bio-inspired functional artificial muscle.

PubMed

Schmitt, S; Haeufle, D F B; Blickhan, R; Günther, M

2012-09-01

The biological muscle is a powerful, flexible and versatile actuator. Its intrinsic characteristics determine the way how movements are generated and controlled. Robotic and prosthetic applications expect to profit from relying on bio-inspired actuators which exhibit natural (muscle-like) characteristics. As of today, when constructing a technical actuator, it is not possible to copy the exact molecular structure of a biological muscle. Alternatively, the question may be put how its characteristics can be realized with known mechanical components. Recently, a mechanical construct for an artificial muscle was proposed, which exhibits hyperbolic force-velocity characteristics. In this paper, we promote the constructing concept which is made by substantiating the mechanical design of biological muscle by a simple model, proving the feasibility of its real-world implementation, and checking their output both for mutual consistency and agreement with biological measurements. In particular, the relations of force, enthalpy rate and mechanical efficiency versus contraction velocity of both the construct's technical implementation and its numerical model were determined in quick-release experiments. All model predictions for these relations and the hardware results are now in good agreement with the biological literature. We conclude that the construct represents a mechanical concept of natural actuation, which is suitable for laying down some useful suggestions when designing bio-inspired actuators.

Doctoral conceptual thresholds in cellular and molecular biology

NASA Astrophysics Data System (ADS)

Feldon, David F.; Rates, Christopher; Sun, Chongning

2017-12-01

In the biological sciences, very little is known about the mechanisms by which doctoral students acquire the skills they need to become independent scientists. In the postsecondary biology education literature, identification of specific skills and effective methods for helping students to acquire them are limited to undergraduate education. To establish a foundation from which to investigate the developmental trajectory of biologists' research skills, it is necessary to identify those skills which are integral to doctoral study and distinct from skills acquired earlier in students' educational pathways. In this context, the current study engages the framework of threshold concepts to identify candidate skills that are both obstacles and significant opportunities for developing proficiency in conducting research. Such threshold concepts are typically characterised as transformative, integrative, irreversible, and challenging. The results from interviews and focus groups with current and former doctoral students in cellular and molecular biology suggest two such threshold concepts relevant to their subfield: the first is an ability to effectively engage primary research literature from the biological sciences in a way that is critical without dismissing the value of its contributions. The second is the ability to conceptualise appropriate control conditions necessary to design and interpret the results of experiments in an efficient and effective manner for research in the biological sciences as a discipline. Implications for prioritising and sequencing graduate training experiences are discussed on the basis of the identified thresholds.

Separating biological cells

NASA Technical Reports Server (NTRS)

Brooks, D. E.

1979-01-01

Technique utilizing electric field to promote biological cell separation from suspending medium in zero gravity increases speed, reduces sedimentation, and improves efficiency of separation in normal gravity.

Curcumin conjugated with PLGA potentiates sustainability, anti-proliferative activity and apoptosis in human colon carcinoma cells.

PubMed

Waghela, Bhargav N; Sharma, Anupama; Dhumale, Suhashini; Pandey, Shashibahl M; Pathak, Chandramani

2015-01-01

Curcumin, an ingredient of turmeric, exhibits a variety of biological activities such as anti-inflammatory, anti-atherosclerotic, anti-proliferative, anti-oxidant, anti-cancer and anti-metastatic. It is a highly pleiotropic molecule that inhibits cell proliferation and induces apoptosis in cancer cells. Despite its imperative biological activities, chemical instability, photo-instability and poor bioavailability limits its utilization as an effective therapeutic agent. Therefore, enhancing the bioavailability of curcumin may improve its therapeutic index for clinical setting. In the present study, we have conjugated curcumin with a biodegradable polymer Poly (D, L-lactic-co-glycolic acid) and evaluated its apoptotic potential in human colon carcinoma cells (HCT 116). The results show that curcumin-PLGA conjugate efficiently inhibits cell proliferation and cell survival in human colon carcinoma cells as compared to native curcumin. Additionally, curcumin conjugated with PLGA shows improved cellular uptake and exhibits controlled release at physiological pH as compared to native curcumin. The curcumin-PLGA conjugate efficiently activates the cascade of caspases and promotes intrinsic apoptotic signaling. Thus, the results suggest that conjugation potentiates the sustainability, anti-proliferative and apoptotic activity of curcumin. This approach could be a promising strategy to improve the therapeutic index of cancer therapy.

A review of recent activities in the NASA CELSS program

NASA Technical Reports Server (NTRS)

Macelroy, R. D.; Tremor, J.; Smernoff, D. T.; Knott, W.; Prince, R. P.

1987-01-01

A CELSS (Controlled Ecological Life Support System) is a device that utilizes photosynthetic organisms and light energy to regenerate waste materials into oxygen and food for a crew in space. The results of theoretical and practical studies conducted by investigators within the CELSS program suggest that a bioregenerative life support system can be a useful and effective method of regenerating consumable materials for crew sustenance. Experimental data suggests that the operation of a CELSS in space will be practical if plants can be made to behave predictably in the space environment. Much of the work currently conducted within the CELSS program centers on the biological components of the CELSS system. The work is particularly directed at ways of achieving high efficiency and long term stability of all components of the system. Included are explorations of the conversion of nonedible cellulose to edible materials, nitrogen fixation by biological and chemical methods, and methods of waste processing. It is the intent of the presentation to provide a description of the extent to which a bioregenerative life support system can meet the constraints of the space environment, and to assess the degree to which system efficiency and stability can be increased during the next decade.

Competition between Methanogens and Acetogens in Biocathodes: A Comparison between Potentiostatic and Galvanostatic Control

PubMed Central

Molenaar, Sam D.; Saha, Pradip; Mol, Annemerel R.; Sleutels, Tom H. J. A.; ter Heijne, Annemiek; Buisman, Cees J. N.

2017-01-01

Microbial electrosynthesis is a useful form of technology for the renewable production of organic commodities from biologically catalyzed reduction of CO2. However, for the technology to become applicable, process selectivity, stability and efficiency need strong improvement. Here we report on the effect of different electrochemical control modes (potentiostatic/galvanostatic) on both the start-up characteristics and steady-state performance of biocathodes using a non-enriched mixed-culture inoculum. Based on our results, it seems that kinetic differences exist between the two dominant functional microbial groups (i.e., homoacetogens and methanogens) and that by applying different current densities, these differences may be exploited to steer product selectivity and reactor performance. PMID:28106846

Competition between Methanogens and Acetogens in Biocathodes: A Comparison between Potentiostatic and Galvanostatic Control.

PubMed

Molenaar, Sam D; Saha, Pradip; Mol, Annemerel R; Sleutels, Tom H J A; Ter Heijne, Annemiek; Buisman, Cees J N

2017-01-19

Microbial electrosynthesis is a useful form of technology for the renewable production of organic commodities from biologically catalyzed reduction of CO₂. However, for the technology to become applicable, process selectivity, stability and efficiency need strong improvement. Here we report on the effect of different electrochemical control modes (potentiostatic/galvanostatic) on both the start-up characteristics and steady-state performance of biocathodes using a non-enriched mixed-culture inoculum. Based on our results, it seems that kinetic differences exist between the two dominant functional microbial groups (i.e., homoacetogens and methanogens) and that by applying different current densities, these differences may be exploited to steer product selectivity and reactor performance.

The plumbing of the global biological pump: Efficiency control through leaks, pathways, and time scales

NASA Astrophysics Data System (ADS)

Pasquier, Benoît; Holzer, Mark

2016-08-01

We systematically quantify the pathways and time scales that set the efficiency, Ebio, of the global biological pump by applying Green-function-based diagnostics to a data-assimilated phosphorus cycle embedded in a jointly assimilated ocean circulation. We consider "bio pipes" that consist of phosphorus paths that connect specified regions of last biological utilization with regions where regenerated phosphate first reemerges into the euphotic zone. The bio pipes that contribute most to Ebio connect the Eastern Equatorial Pacific (EEqP) and Equatorial Atlantic to the Southern Ocean ((21 ± 3)% of Ebio), as well as the Southern Ocean to itself ((15 ± 3)% of Ebio). The bio pipes with the largest phosphorus flow rates connect the EEqP to itself and the subantarctic Southern Ocean to itself. The global mean sequestration time of the biological pump is 130 ± 70 years, while the sequestration time of the bio pipe from anywhere to the Antarctic region of the Southern Ocean is 430 ± 30 years. The distribution of phosphorus flowing within a given bio pipe is quantified by its transit-time partitioned path density. For the largest bio pipes, ˜1/7 of their phosphorus is carried by thermocline paths with transit times less than ˜300-400 years, while ˜4/7 of their phosphorus is carried by abyssal paths with transit times exceeding ˜700 years. The path density reveals that Antarctic Intermediate Water carries about a third of the regenerated phosphate last utilized in the EEqP that is destined for the Southern Ocean euphotic zone. The Southern Ocean is where (62 ± 2)% of the regenerated inventory and (69 ± 1)% of the preformed inventory first reemerge into the euphotic zone.

Controlled flight of a biologically inspired, insect-scale robot.

PubMed

Ma, Kevin Y; Chirarattananon, Pakpong; Fuller, Sawyer B; Wood, Robert J

2013-05-03

Flies are among the most agile flying creatures on Earth. To mimic this aerial prowess in a similarly sized robot requires tiny, high-efficiency mechanical components that pose miniaturization challenges governed by force-scaling laws, suggesting unconventional solutions for propulsion, actuation, and manufacturing. To this end, we developed high-power-density piezoelectric flight muscles and a manufacturing methodology capable of rapidly prototyping articulated, flexure-based sub-millimeter mechanisms. We built an 80-milligram, insect-scale, flapping-wing robot modeled loosely on the morphology of flies. Using a modular approach to flight control that relies on limited information about the robot's dynamics, we demonstrated tethered but unconstrained stable hovering and basic controlled flight maneuvers. The result validates a sufficient suite of innovations for achieving artificial, insect-like flight.

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

Treesearch

Dean E. Pearson; Ragan M. Callaway

2005-01-01

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

Rapid and efficient gene delivery into the adult mouse brain via focal electroporation

PubMed Central

Nomura, Tadashi; Nishimura, Yusuke; Gotoh, Hitoshi; Ono, Katsuhiko

2016-01-01

In vivo gene delivery is required for studying the cellular and molecular mechanisms of various biological events. Virus-mediated gene transfer or generation of transgenic animals is widely used; however, these methods are time-consuming and expensive. Here we show an improved electroporation technique for acute gene delivery into the adult mouse brain. Using a syringe-based microelectrode, local DNA injection and the application of electric current can be performed simultaneously; this allows rapid and efficient gene transduction of adult non-neuronal cells. Combining this technique with various expression vectors that carry specific promoters resulted in targeted gene expression in astrocytic cells. Our results constitute a powerful strategy for the genetic manipulation of adult brains in a spatio-temporally controlled manner. PMID:27430903

Systems Biology for Smart Crops and Agricultural Innovation: Filling the Gaps between Genotype and Phenotype for Complex Traits Linked with Robust Agricultural Productivity and Sustainability

PubMed Central

Pathak, Rajesh Kumar; Gupta, Sanjay Mohan; Gaur, Vikram Singh; Pandey, Dinesh

2015-01-01

Abstract In recent years, rapid developments in several omics platforms and next generation sequencing technology have generated a huge amount of biological data about plants. Systems biology aims to develop and use well-organized and efficient algorithms, data structure, visualization, and communication tools for the integration of these biological data with the goal of computational modeling and simulation. It studies crop plant systems by systematically perturbing them, checking the gene, protein, and informational pathway responses; integrating these data; and finally, formulating mathematical models that describe the structure of system and its response to individual perturbations. Consequently, systems biology approaches, such as integrative and predictive ones, hold immense potential in understanding of molecular mechanism of agriculturally important complex traits linked to agricultural productivity. This has led to identification of some key genes and proteins involved in networks of pathways involved in input use efficiency, biotic and abiotic stress resistance, photosynthesis efficiency, root, stem and leaf architecture, and nutrient mobilization. The developments in the above fields have made it possible to design smart crops with superior agronomic traits through genetic manipulation of key candidate genes. PMID:26484978

Enhanced Removal of Lead by Chemically and Biologically Treated Carbonaceous Materials

PubMed Central

Mahmoud, Mohamed E.; Osman, Maher M.; Ahmed, Somia B.; Abdel-Fattah, Tarek M.

2012-01-01

Hybrid sorbents and biosorbents were synthesized via chemical and biological treatment of active carbon by simple and direct redox reaction followed by surface loading of baker's yeast. Surface functionality and morphology of chemically and biologically modified sorbents and biosorbents were studied by Fourier Transform Infrared analysis and scanning electron microscope imaging. Hybrid carbonaceous sorbents and biosorbents were characterized by excellent efficiency and superiority toward lead(II) sorption compared to blank active carbon providing a maximum sorption capacity of lead(II) ion as 500 μmol g−1. Sorption processes of lead(II) by these hybrid materials were investigated under the influence of several controlling parameters such as pH, contact time, mass of sorbent and biosorbent, lead(II) concentration, and foreign ions. Lead(II) sorption mechanisms were found to obey the Langmuir and BET isotherm models. The potential applications of chemically and biologically modified-active carbonaceous materials for removal and extraction of lead from real water matrices were also studied via a double-stage microcolumn technique. The results of this study were found to denote to superior recovery values of lead (95.0–99.0 ± 3.0–5.0%) by various carbonaceous-modified-bakers yeast biosorbents. PMID:22629157

"Shoot and Sense" Janus Micromotors-Based Strategy for the Simultaneous Degradation and Detection of Persistent Organic Pollutants in Food and Biological Samples.

PubMed

Rojas, D; Jurado-Sánchez, B; Escarpa, A

2016-04-05

A novel Janus micromotor-based strategy for the direct determination of diphenyl phthalate (DPP) in food and biological samples is presented. Mg/Au Janus micromotors are employed as novel analytical platforms for the degradation of the non-electroactive DPP into phenol, which is directly measured by difference pulse voltammetry on disposable screen-printed electrodes. The self-movement of the micromotors along the samples result in the generation of hydrogen microbubbles and hydroxyl ions for DPP degradation. The increased fluid transport improves dramatically the analytical signal, increasing the sensitivity while lowering the detection potential. The method has been successfully applied to the direct analysis of DPP in selected food and biological samples, without any sample treatment and avoiding any potential contamination from laboratory equipment. The developed approach is fast (∼5 min) and accurate with recoveries of ∼100%. In addition, efficient propulsion of multiple Mg/Au micromotors in complex samples has also been demonstrated. The advantages of the micromotors-assisted technology, i.e., disposability, portability, and the possibility to carry out multiple analysis simultaneously, hold considerable promise for its application in food and biological control in analytical applications with high significance.

Next-generation mammalian genetics toward organism-level systems biology.

PubMed

Susaki, Etsuo A; Ukai, Hideki; Ueda, Hiroki R

2017-01-01

Organism-level systems biology in mammals aims to identify, analyze, control, and design molecular and cellular networks executing various biological functions in mammals. In particular, system-level identification and analysis of molecular and cellular networks can be accelerated by next-generation mammalian genetics. Mammalian genetics without crossing, where all production and phenotyping studies of genome-edited animals are completed within a single generation drastically reduce the time, space, and effort of conducting the systems research. Next-generation mammalian genetics is based on recent technological advancements in genome editing and developmental engineering. The process begins with introduction of double-strand breaks into genomic DNA by using site-specific endonucleases, which results in highly efficient genome editing in mammalian zygotes or embryonic stem cells. By using nuclease-mediated genome editing in zygotes, or ~100% embryonic stem cell-derived mouse technology, whole-body knock-out and knock-in mice can be produced within a single generation. These emerging technologies allow us to produce multiple knock-out or knock-in strains in high-throughput manner. In this review, we discuss the basic concepts and related technologies as well as current challenges and future opportunities for next-generation mammalian genetics in organism-level systems biology.

Sequential chemical-biological processes for the treatment of industrial wastewaters: review of recent progresses and critical assessment.

PubMed

Guieysse, Benoit; Norvill, Zane N

2014-02-28

When direct wastewater biological treatment is unfeasible, a cost- and resource-efficient alternative to direct chemical treatment consists of combining biological treatment with a chemical pre-treatment aiming to convert the hazardous pollutants into more biodegradable compounds. Whereas the principles and advantages of sequential treatment have been demonstrated for a broad range of pollutants and process configurations, recent progresses (2011-present) in the field provide the basis for refining assessment of feasibility, costs, and environmental impacts. This paper thus reviews recent real wastewater demonstrations at pilot and full scale as well as new process configurations. It also discusses new insights on the potential impacts of microbial community dynamics on process feasibility, design and operation. Finally, it sheds light on a critical issue that has not yet been properly addressed in the field: integration requires complex and tailored optimization and, of paramount importance to full-scale application, is sensitive to uncertainty and variability in the inputs used for process design and operation. Future research is therefore critically needed to improve process control and better assess the real potential of sequential chemical-biological processes for industrial wastewater treatment. Copyright © 2013 Elsevier B.V. All rights reserved.

Treatment of laundry wastewater by biological and electrocoagulation methods.

PubMed

Ramcharan, Terelle; Bissessur, Ajay

2017-01-01

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

Real-Time PCR Quantification Using A Variable Reaction Efficiency Model

PubMed Central

Platts, Adrian E.; Johnson, Graham D.; Linnemann, Amelia K.; Krawetz, Stephen A.

2008-01-01

Quantitative real-time PCR remains a cornerstone technique in gene expression analysis and sequence characterization. Despite the importance of the approach to experimental biology the confident assignment of reaction efficiency to the early cycles of real-time PCR reactions remains problematic. Considerable noise may be generated where few cycles in the amplification are available to estimate peak efficiency. An alternate approach that uses data from beyond the log-linear amplification phase is explored with the aim of reducing noise and adding confidence to efficiency estimates. PCR reaction efficiency is regressed to estimate the per-cycle profile of an asymptotically departed peak efficiency, even when this is not closely approximated in the measurable cycles. The process can be repeated over replicates to develop a robust estimate of peak reaction efficiency. This leads to an estimate of the maximum reaction efficiency that may be considered primer-design specific. Using a series of biological scenarios we demonstrate that this approach can provide an accurate estimate of initial template concentration. PMID:18570886

Nitrogen removal via nitrite from seawater contained sewage.

PubMed

Peng, Yongzhen; Yu, De-Shuang; Liang, Dawei; Zhu, Guibing

2004-01-01

Under the control of both pH and the concentration of free ammonia (FA), the nitrification-denitrification via nitrite pathway was accomplished in SBR to achieve enhanced biological nitrogen removal from seawater contained wastewater, which is used to flush toilet, under relatively high salinity. Several parameters including salinity, temperature, pH, and NH4+-N loading rate were studied to evaluate their effects. The results indicate that at different salinity the nitrogen removal efficiency is relative to ammonia-nitrogen loading rate. The nitrogen removal efficiency reaches above 90% when the NH4+-N loading does not exceed 0.15 kg NH4+-N/kg MLSS d. With the salinity increasing, the ammonia-nitrogen loading rate should be lowered to obtain high removal efficiency. The evaluation of temperature effect shows that nitrogen removal efficiency is promoted twice when reaction temperature is elevated from 20 to 30 degrees C. Moderately high pH in the range of 7.5-8.5 has advantage to achieve effective nitrification-denitrification via nitrite, the process of which is caused by the selective inhibition of free ammonia (FA).

A high-performance protocol for extraction of microplastics in fish.

PubMed

Karami, Ali; Golieskardi, Abolfazl; Choo, Cheng Keong; Romano, Nicholas; Ho, Yu Bin; Salamatinia, Babak

2017-02-01

So far, several classes of digesting solutions have been employed to extract microplastics (MPs) from biological matrices. However, the performance of digesting solutions across different temperatures has never been systematically investigated. In the first phase of the present study, we measured the efficiency of different oxidative agents (NaClO or H 2 O 2 ), bases (NaOH or KOH), and acids [HCl or HNO 3 ; concentrated and diluted (5%)] in digesting fish tissues at room temperature (RT, 25°C), 40, 50, or 60°C. In the second phase, the treatments that were efficient in digesting the biological materials (>95%) were evaluated for their compatibility with eight major plastic polymers (assessed through recovery rate, Raman spectroscopy analysis, and morphological changes). Among the tested solutions, NaClO, NaOH, and diluted acids did not result in a satisfactory digestion efficiency at any of the temperatures. The H 2 O 2 treatment at 50°C efficiently digested the biological materials, although it decreased the recovery rate of nylon-6 (NY6) and nylon-66 (NY66) and altered the colour of polyethylene terephthalate (PET) fragments. Similarly, concentrated HCl and HNO 3 treatments at RT fully digested the fish tissues, but also fully dissolved NY6 and NY66, and reduced the recovery rate of most or all of the polymers, respectively. Potassium hydroxide solution fully eliminated the biological matrices at all temperatures. However, at 50 and 60°C, it degraded PET, reduced the recovery rate of PET and polyvinyl chloride (PVC), and changed the colour of NY66. According to our results, treating biological materials with a 10% KOH solution and incubating at 40°C was both time and cost-effective, efficient in digesting biological materials, and had no impact on the integrity of the plastic polymers. Furthermore, coupling this treatment with NaI extraction created a promising protocol to isolate MPs from whole fish samples. Copyright © 2016 Elsevier B.V. All rights reserved.

A network-based multi-target computational estimation scheme for anticoagulant activities of compounds.

PubMed

Li, Qian; Li, Xudong; Li, Canghai; Chen, Lirong; Song, Jun; Tang, Yalin; Xu, Xiaojie

2011-03-22

Traditional virtual screening method pays more attention on predicted binding affinity between drug molecule and target related to a certain disease instead of phenotypic data of drug molecule against disease system, as is often less effective on discovery of the drug which is used to treat many types of complex diseases. Virtual screening against a complex disease by general network estimation has become feasible with the development of network biology and system biology. More effective methods of computational estimation for the whole efficacy of a compound in a complex disease system are needed, given the distinct weightiness of the different target in a biological process and the standpoint that partial inhibition of several targets can be more efficient than the complete inhibition of a single target. We developed a novel approach by integrating the affinity predictions from multi-target docking studies with biological network efficiency analysis to estimate the anticoagulant activities of compounds. From results of network efficiency calculation for human clotting cascade, factor Xa and thrombin were identified as the two most fragile enzymes, while the catalytic reaction mediated by complex IXa:VIIIa and the formation of the complex VIIIa:IXa were recognized as the two most fragile biological matter in the human clotting cascade system. Furthermore, the method which combined network efficiency with molecular docking scores was applied to estimate the anticoagulant activities of a serial of argatroban intermediates and eight natural products respectively. The better correlation (r = 0.671) between the experimental data and the decrease of the network deficiency suggests that the approach could be a promising computational systems biology tool to aid identification of anticoagulant activities of compounds in drug discovery. This article proposes a network-based multi-target computational estimation method for anticoagulant activities of compounds by combining network efficiency analysis with scoring function from molecular docking.

A Network-Based Multi-Target Computational Estimation Scheme for Anticoagulant Activities of Compounds

PubMed Central

Li, Canghai; Chen, Lirong; Song, Jun; Tang, Yalin; Xu, Xiaojie

2011-01-01

Background Traditional virtual screening method pays more attention on predicted binding affinity between drug molecule and target related to a certain disease instead of phenotypic data of drug molecule against disease system, as is often less effective on discovery of the drug which is used to treat many types of complex diseases. Virtual screening against a complex disease by general network estimation has become feasible with the development of network biology and system biology. More effective methods of computational estimation for the whole efficacy of a compound in a complex disease system are needed, given the distinct weightiness of the different target in a biological process and the standpoint that partial inhibition of several targets can be more efficient than the complete inhibition of a single target. Methodology We developed a novel approach by integrating the affinity predictions from multi-target docking studies with biological network efficiency analysis to estimate the anticoagulant activities of compounds. From results of network efficiency calculation for human clotting cascade, factor Xa and thrombin were identified as the two most fragile enzymes, while the catalytic reaction mediated by complex IXa:VIIIa and the formation of the complex VIIIa:IXa were recognized as the two most fragile biological matter in the human clotting cascade system. Furthermore, the method which combined network efficiency with molecular docking scores was applied to estimate the anticoagulant activities of a serial of argatroban intermediates and eight natural products respectively. The better correlation (r = 0.671) between the experimental data and the decrease of the network deficiency suggests that the approach could be a promising computational systems biology tool to aid identification of anticoagulant activities of compounds in drug discovery. Conclusions This article proposes a network-based multi-target computational estimation method for anticoagulant activities of compounds by combining network efficiency analysis with scoring function from molecular docking. PMID:21445339

Synthetic Biology and Microbial Fuel Cells: Towards Self-Sustaining Life Support Systems

NASA Technical Reports Server (NTRS)

Hogan, John Andrew

2014-01-01

NASA ARC and the J. Craig Venter Institute (JCVI) collaborated to investigate the development of advanced microbial fuels cells (MFCs) for biological wastewater treatment and electricity production (electrogenesis). Synthetic biology techniques and integrated hardware advances were investigated to increase system efficiency and robustness, with the intent of increasing power self-sufficiency and potential product formation from carbon dioxide. MFCs possess numerous advantages for space missions, including rapid processing, reduced biomass and effective removal of organics, nitrogen and phosphorus. Project efforts include developing space-based MFC concepts, integration analyses, increasing energy efficiency, and investigating novel bioelectrochemical system applications

Ice Nucleation Efficiency of Hydroxylated Organic Surfaces Is Controlled by Their Structural Fluctuations and Mismatch to Ice.

PubMed

Qiu, Yuqing; Odendahl, Nathan; Hudait, Arpa; Mason, Ryan; Bertram, Allan K; Paesani, Francesco; DeMott, Paul J; Molinero, Valeria

2017-03-01

Heterogeneous nucleation of ice induced by organic materials is of fundamental importance for climate, biology, and industry. Among organic ice-nucleating surfaces, monolayers of long chain alcohols are particularly effective, while monolayers of fatty acids are significantly less so. As these monolayers expose to water hydroxyl groups with an order that resembles the one in the basal plane of ice, it was proposed that lattice matching between ice and the surface controls their ice-nucleating efficiency. Organic monolayers are soft materials and display significant fluctuations. It has been conjectured that these fluctuations assist in the nucleation of ice. Here we use molecular dynamic simulations and laboratory experiments to investigate the relationship between the structure and fluctuations of hydroxylated organic surfaces and the temperature at which they nucleate ice. We find that these surfaces order interfacial water to form domains with ice-like order that are the birthplace of ice. Both mismatch and fluctuations decrease the size of the preordered domains and monotonously decrease the ice freezing temperature. The simulations indicate that fluctuations depress the freezing efficiency of monolayers of alcohols or acids to half the value predicted from lattice mismatch alone. The model captures the experimental trend in freezing efficiencies as a function of chain length and predicts that alcohols have higher freezing efficiency than acids of the same chain length. These trends are mostly controlled by the modulation of the structural mismatch to ice. We use classical nucleation theory to show that the freezing efficiencies of the monolayers are directly related to their free energy of binding to ice. This study provides a general framework to relate the equilibrium thermodynamics of ice binding to a surface and the nonequilibrium ice freezing temperature and suggests that these could be predicted from the structure of interfacial water.

70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence.

PubMed

Schneider, Thomas D

2010-10-01

The relationship between information and energy is key to understanding biological systems. We can display the information in DNA sequences specifically bound by proteins by using sequence logos, and we can measure the corresponding binding energy. These can be compared by noting that one of the forms of the second law of thermodynamics defines the minimum energy dissipation required to gain one bit of information. Under the isothermal conditions that molecular machines function this is [Formula in text] joules per bit (kB is Boltzmann's constant and T is the absolute temperature). Then an efficiency of binding can be computed by dividing the information in a logo by the free energy of binding after it has been converted to bits. The isothermal efficiencies of not only genetic control systems, but also visual pigments are near 70%. From information and coding theory, the theoretical efficiency limit for bistate molecular machines is ln 2=0.6931. Evolutionary convergence to maximum efficiency is limited by the constraint that molecular states must be distinct from each other. The result indicates that natural molecular machines operate close to their information processing maximum (the channel capacity), and implies that nanotechnology can attain this goal.

70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence

PubMed Central

Schneider, Thomas D.

2010-01-01

The relationship between information and energy is key to understanding biological systems. We can display the information in DNA sequences specifically bound by proteins by using sequence logos, and we can measure the corresponding binding energy. These can be compared by noting that one of the forms of the second law of thermodynamics defines the minimum energy dissipation required to gain one bit of information. Under the isothermal conditions that molecular machines function this is joules per bit ( is Boltzmann's constant and T is the absolute temperature). Then an efficiency of binding can be computed by dividing the information in a logo by the free energy of binding after it has been converted to bits. The isothermal efficiencies of not only genetic control systems, but also visual pigments are near 70%. From information and coding theory, the theoretical efficiency limit for bistate molecular machines is ln 2 = 0.6931. Evolutionary convergence to maximum efficiency is limited by the constraint that molecular states must be distinct from each other. The result indicates that natural molecular machines operate close to their information processing maximum (the channel capacity), and implies that nanotechnology can attain this goal. PMID:20562221

Methods for producing hydrogen (BI) sulfide and/or removing metals

DOEpatents

Truex, Michael J [Richland, WA; Peyton, Brent M [Pullman, WA; Toth, James J [Kennewick, WA

2002-05-14

The present invention is a process wherein sulfide production by bacteria is efficiently turned on and off, using pH adjustment. The adjustment of pH impacts sulfide production by bacteria by altering the relative amounts of H.sub.2 S and HS-- in solution and thereby control the inhibition of the bacterial metabolism that produces sulfide. This process can be used to make a bioreactor produce sulfide "on-demand" so that the production of sulfide can be matched to its use as a metal precipitation reagent. The present invention is of significance because it enables the use of a biological reactor, a cost effective sulfide production system, by making the biological reactor produce hydrogen sulfide "on demand", and therefore responsive to production schedules, waste stream generation rate, and health and safety requirements/goals.

Comparative reproductive biology of the social parasite Acromyrmex ameliae de Souza, Soares & Della Lucia and of its host Acromyrmex subterraneus subterraneus Forel (Hymenoptera: Formicidae).

PubMed

Soares, Ilka M F; Della Lucia, Terezinha M C; Pereira, Alice S; Serrão, José E; Ribeiro, Myriam M R; De Souza, Danival J

2010-01-01

Social parasites exhibit several characteristics that allow them to exploit their host species efficiently. The smaller size of parasite species is a trait commonly found in ants. In this work, we investigated several aspects of the reproductive biology of Acromyrmex ameliae De Souza, Soares & Della Lucia, a recently discovered parasite of Acromyrmex subterraneus subterraneus Forel. Sexuals of A. ameliae are substantially smaller than those from host species. Parasite queens laid significantly less worker eggs than host queens and inhibit sexual production of the host. The sex ratio of parasite species is highly female biased. Interestingly, we have observed parasite coupling on the laboratory, inside the nests and in the ground, opening the possibility to use controlled mating to study genetic approaches of parasitism in the ants.

[Methods of high-throughput plant phenotyping for large-scale breeding and genetic experiments].

PubMed

Afonnikov, D A; Genaev, M A; Doroshkov, A V; Komyshev, E G; Pshenichnikova, T A

2016-07-01

Phenomics is a field of science at the junction of biology and informatics which solves the problems of rapid, accurate estimation of the plant phenotype; it was rapidly developed because of the need to analyze phenotypic characteristics in large scale genetic and breeding experiments in plants. It is based on using the methods of computer image analysis and integration of biological data. Owing to automation, new approaches make it possible to considerably accelerate the process of estimating the characteristics of a phenotype, to increase its accuracy, and to remove a subjectivism (inherent to humans). The main technologies of high-throughput plant phenotyping in both controlled and field conditions, their advantages and disadvantages, and also the prospects of their use for the efficient solution of problems of plant genetics and breeding are presented in the review.

Biocontrol of Rhizoctonia solani damping-off disease in cucumber with Bacillus pumilus SQR-N43.

PubMed

Huang, Xinqi; Zhang, Nan; Yong, Xiaoyu; Yang, Xingming; Shen, Qirong

2012-03-20

Biological control is an efficient and environmentally friendly way to prevent damping-off disease. Micrographs were used to investigate the ability of Bacillus pumilus (B. pumilus) SQR-N43 to control Rhizoctonia solani (R. solani) Q1 in cucumbers. The root colonization ability of B. pumilus SQR-N43 was analyzed in vivo with a green fluorescent protein (GFP) tag. A pot experiment was performed to assess the in vivo disease-control efficiency of B. pumilus SQR-N43 and its bio-organic fertilizer. Results indicate that B. pumilus SQR-N43 induced hyphal deformation, enlargement of cytoplasmic vacuoles and cytoplasmic leakage in R. solani Q1 mycelia. A biofilm on the root surface was formed when the roots were inoculated with 10(7)-10(8)cells g(-1) of soil of GFP-tagged B. pumilus SQR-N43. In the pot experiment, the biocontrol reduced the concentration of R. solani. In contrast to applications of only B. pumilus SQR-N43 (N treatment), which produced control efficiencies of 23%, control efficiencies of 68% were obtained with applications of a fermented organic fertilizer inoculated with B. pumilus SQR-N43 (BIO treatment). After twenty days of incubation, significant differences in the number of CFUs and the percentage of spores of B. pumilus SQR-N43 were recorded between the N treatment (2.20×10(7)CFU g(-1) of soil and 79%, respectively) and the BIO treatment (1.67×10(8)CFU g(-1) of soil and 52%, respectively). The results indicate that B. pumilus SQR-N43 is a potent antagonist against R. solani Q1. The BIO treatment was more effective than the N treatment because it stabilized the population and increased the active form of the antagonist. Copyright © 2011 Elsevier GmbH. All rights reserved.

Potential of Biological Agents in Decontamination of Agricultural Soil

PubMed Central

Javaid, Muhammad Kashif; Ashiq, Mehrban; Tahir, Muhammad

2016-01-01

Pesticides are widely used for the control of weeds, diseases, and pests of cultivated plants all over the world, mainly since the period after the Second World War. The use of pesticides is very extensive to control harm of pests all over the globe. Persistent nature of most of the synthetic pesticides causes serious environmental concerns. Decontamination of these hazardous chemicals is very essential. This review paper elaborates the potential of various biological agents in decontamination of agricultural soils. The agricultural crop fields are contaminated by the periodic applications of pesticides. Biodegradation is an ecofriendly, cost-effective, highly efficient approach compared to the physical and chemical methods which are expensive as well as unfriendly towards environment. Biodegradation is sensitive to the concentration levels of hydrogen peroxide and nitrogen along with microbial community, temperature, and pH changes. Experimental work for optimum conditions at lab scale can provide very fruitful results about specific bacterial, fungal strains. This study revealed an upper hand of bioremediation over physicochemical approaches. Further studies should be carried out to understand mechanisms of biotransformation. PMID:27293964

Potential of Biological Agents in Decontamination of Agricultural Soil.

PubMed

Javaid, Muhammad Kashif; Ashiq, Mehrban; Tahir, Muhammad

2016-01-01

Pesticides are widely used for the control of weeds, diseases, and pests of cultivated plants all over the world, mainly since the period after the Second World War. The use of pesticides is very extensive to control harm of pests all over the globe. Persistent nature of most of the synthetic pesticides causes serious environmental concerns. Decontamination of these hazardous chemicals is very essential. This review paper elaborates the potential of various biological agents in decontamination of agricultural soils. The agricultural crop fields are contaminated by the periodic applications of pesticides. Biodegradation is an ecofriendly, cost-effective, highly efficient approach compared to the physical and chemical methods which are expensive as well as unfriendly towards environment. Biodegradation is sensitive to the concentration levels of hydrogen peroxide and nitrogen along with microbial community, temperature, and pH changes. Experimental work for optimum conditions at lab scale can provide very fruitful results about specific bacterial, fungal strains. This study revealed an upper hand of bioremediation over physicochemical approaches. Further studies should be carried out to understand mechanisms of biotransformation.

Peripersonal Space and Margin of Safety around the Body: Learning Visuo-Tactile Associations in a Humanoid Robot with Artificial Skin.

PubMed

Roncone, Alessandro; Hoffmann, Matej; Pattacini, Ugo; Fadiga, Luciano; Metta, Giorgio

2016-01-01

This paper investigates a biologically motivated model of peripersonal space through its implementation on a humanoid robot. Guided by the present understanding of the neurophysiology of the fronto-parietal system, we developed a computational model inspired by the receptive fields of polymodal neurons identified, for example, in brain areas F4 and VIP. The experiments on the iCub humanoid robot show that the peripersonal space representation i) can be learned efficiently and in real-time via a simple interaction with the robot, ii) can lead to the generation of behaviors like avoidance and reaching, and iii) can contribute to the understanding the biological principle of motor equivalence. More specifically, with respect to i) the present model contributes to hypothesizing a learning mechanisms for peripersonal space. In relation to point ii) we show how a relatively simple controller can exploit the learned receptive fields to generate either avoidance or reaching of an incoming stimulus and for iii) we show how the robot can select arbitrary body parts as the controlled end-point of an avoidance or reaching movement.

Surface grafting of Eu3+ doped luminescent hydroxyapatite nanomaterials through metal free light initiated atom transfer radical polymerization for theranostic applications.

PubMed

Zeng, Guangjian; Liu, Meiying; Jiang, Ruming; Heng, Chunning; Huang, Qiang; Mao, Liucheng; Hui, Junfeng; Deng, Fengjie; Zhang, Xiaoyong; Wei, Yen

2017-08-01

We reported a simple and efficient method to prepare the hydrophilic luminescent HAp polymer nanocomposites through the combination of ligand exchange and metal free light initiated surface-initiated atom transfer radical polymerization (SI-ATRP) using 10-phenylphenothiazine (PTH) as organic catalyst and 2-methacryloyloxyethyl phosphorylcholine (MPC) and itaconic acid (IA) as monomers. The biological imaging and drug delivery performance of HAp-poly(MPC-IA) nanorods were examined to evaluate their potential for biomedical applications. Results suggested that hydrophilic HAp-poly(MPC-IA) nanorods can be successfully prepared. More importantly, the HAp-poly(MPC-IA) exhibited excellent water dispersibility, desirable biocompatibility and good performance for biological imaging and controlled drug delivery applications. As compared with other controlled living polymerization reactions, the metal free light initiated SI-ATRP displayed many advantages such as easy for handle, mild reaction conditions, toxicity and fluorescence quenching from metal catalysts. Therefore, we believe that this strategy should be a useful and effective strategy for preparation of HAp nanomaterials for biomedical applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Natural photosystems from an engineer's perspective: length, time, and energy scales of charge and energy transfer.

PubMed

Noy, Dror

2008-01-01

The vast structural and functional information database of photosynthetic enzymes includes, in addition to detailed kinetic records from decades of research on physical processes and chemical reaction-pathways, a variety of high and medium resolution crystal structures of key photosynthetic enzymes. Here, it is examined from an engineer's point of view with the long-term goal of reproducing the key features of natural photosystems in novel biological and non-biological solar-energy conversion systems. This survey reveals that the basic physics of the transfer processes, namely, the time constraints imposed by the rates of incoming photon flux and the various decay processes allow for a large degree of tolerance in the engineering parameters. Furthermore, the requirements to guarantee energy and electron transfer rates that yield high efficiency in natural photosystems are largely met by control of distance between chromophores and redox cofactors. This underlines a critical challenge for projected de novo designed constructions, that is, the control of spatial organization of cofactor molecules within dense array of different cofactors, some well within 1 nm from each other.

Economic value of biological control in integrated pest management of managed plant systems.

PubMed

Naranjo, Steven E; Ellsworth, Peter C; Frisvold, George B

2015-01-07

Biological control is an underlying pillar of integrated pest management, yet little focus has been placed on assigning economic value to this key ecosystem service. Setting biological control on a firm economic foundation would help to broaden its utility and adoption for sustainable crop protection. Here we discuss approaches and methods available for valuation of biological control of arthropod pests by arthropod natural enemies and summarize economic evaluations in classical, augmentative, and conservation biological control. Emphasis is placed on valuation of conservation biological control, which has received little attention. We identify some of the challenges of and opportunities for applying economics to biological control to advance integrated pest management. Interaction among diverse scientists and stakeholders will be required to measure the direct and indirect costs and benefits of biological control that will allow farmers and others to internalize the benefits that incentivize and accelerate adoption for private and public good.

Methods and Apparatus for Autonomous Robotic Control

NASA Technical Reports Server (NTRS)

Gorshechnikov, Anatoly (Inventor); Livitz, Gennady (Inventor); Versace, Massimiliano (Inventor); Palma, Jesse (Inventor)

2017-01-01

Sensory processing of visual, auditory, and other sensor information (e.g., visual imagery, LIDAR, RADAR) is conventionally based on "stovepiped," or isolated processing, with little interactions between modules. Biological systems, on the other hand, fuse multi-sensory information to identify nearby objects of interest more quickly, more efficiently, and with higher signal-to-noise ratios. Similarly, examples of the OpenSense technology disclosed herein use neurally inspired processing to identify and locate objects in a robot's environment. This enables the robot to navigate its environment more quickly and with lower computational and power requirements.

LaF3 core/shell nanoparticles for subcutaneous heating and thermal sensing in the second biological-window

NASA Astrophysics Data System (ADS)

Ximendes, Erving Clayton; Rocha, Uéslen; Kumar, Kagola Upendra; Jacinto, Carlos; Jaque, Daniel

2016-06-01

We report on Ytterbium and Neodymium codoped LaF3 core/shell nanoparticles capable of simultaneous heating and thermal sensing under single beam infrared laser excitation. Efficient light-to-heat conversion is produced at the Neodymium highly doped shell due to non-radiative de-excitations. Thermal sensing is provided by the temperature dependent Nd3+ → Yb3+ energy transfer processes taking place at the core/shell interface. The potential application of these core/shell multifunctional nanoparticles for controlled photothermal subcutaneous treatments is also demonstrated.

Enantioselective cellular uptake of chiral semiconductor nanocrystals

NASA Astrophysics Data System (ADS)

Martynenko, I. V.; Kuznetsova, V. A.; Litvinov, I. K.; Orlova, A. O.; Maslov, V. G.; Fedorov, A. V.; Dubavik, A.; Purcell-Milton, F.; Gun'ko, Yu K.; Baranov, A. V.

2016-02-01

The influence of the chirality of semiconductor nanocrystals, CdSe/ZnS quantum dots (QDs) capped with L- and D-cysteine, on the efficiency of their uptake by living Ehrlich Ascite carcinoma cells is studied by spectral- and time-resolved fluorescence microspectroscopy. We report an evident enantioselective process where cellular uptake of the L-Cys QDs is almost twice as effective as that of the D-Cys QDs. This finding paves the way for the creation of novel approaches to control the biological properties and behavior of nanomaterials in living cells.

Removal of nitrogen oxides from gas streams by biofiltration

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

Barrett, K.B.; Barnes, J.M.; Apel, W.A.

1994-12-31

Nitrogen oxides (NO{sub x}) are primary air pollutants and, as such, there is considerable interest in the development of efficient, cost effective technologies to remediate NO{sub x} containing emissions. Biofiltration involves the venting of contaminated gas streams through biologically active material such as soil or compost. This technology has been used successfully to control odors as well as volatile organic compounds from a variety of industrial and public sources. The purpose of this study was to evaluate the feasibility of using biofiltration to convert NO{sub x} to nitrogen gas.

Biological control of wilt disease complex on tomato crop caused by Meloidogyne javanica and Fusarium oxysporum f.sp. lycopersici by Verticillium leptobactrum.

PubMed

Hajji-Hedfi, Lobna; Regaieg, Hajer; Larayedh, Asma; Chihani, Noura; Horrigue-Raouani, Najet

2017-09-23

The efficacy of Verticillium leptobactrum isolate (HR1) was evaluated in the control of root-knot nematode and Fusarium wilt fungus under laboratory and greenhouse conditions. Five concentrations of V. leptobactrum (HR1) isolate were tested for their nematicidal and fungicidal activities against Meloidogyne javanica and Fusarium oxysporum f.sp. lycopersici in vitro. Laboratory trials showed that mycelium growth inhibition of Fusarium wilt fungus was correlated to the increase of the concentration of culture filtrate. All dilutions showed efficiency in reducing the growth of Fusarium oxysporum f.sp. lycopersici. The greatest nematicidal activity was observed at 50, 75, and 100% filtrate dilutions. The egg hatching percentage reached 42%, and the juvenile's corrected mortality registered 90% for the above treatments. In greenhouse experiment, the biocontrol agent fungus enhanced significantly tomato growth components (height and weight of plant and root). The multiplication rate of root-knot nematode and the Fusarium wilt disease incidence declined significantly with soil application of V. leptobactrum as with chemical treatments. The isolate HR1 was efficient to control wilt disease complex caused by M. javanica and Fusarium oxysporum f.sp. lycopersici.

Efficient experimental design of high-fidelity three-qubit quantum gates via genetic programming

NASA Astrophysics Data System (ADS)

Devra, Amit; Prabhu, Prithviraj; Singh, Harpreet; Arvind; Dorai, Kavita

2018-03-01

We have designed efficient quantum circuits for the three-qubit Toffoli (controlled-controlled-NOT) and the Fredkin (controlled-SWAP) gate, optimized via genetic programming methods. The gates thus obtained were experimentally implemented on a three-qubit NMR quantum information processor, with a high fidelity. Toffoli and Fredkin gates in conjunction with the single-qubit Hadamard gates form a universal gate set for quantum computing and are an essential component of several quantum algorithms. Genetic algorithms are stochastic search algorithms based on the logic of natural selection and biological genetics and have been widely used for quantum information processing applications. We devised a new selection mechanism within the genetic algorithm framework to select individuals from a population. We call this mechanism the "Luck-Choose" mechanism and were able to achieve faster convergence to a solution using this mechanism, as compared to existing selection mechanisms. The optimization was performed under the constraint that the experimentally implemented pulses are of short duration and can be implemented with high fidelity. We demonstrate the advantage of our pulse sequences by comparing our results with existing experimental schemes and other numerical optimization methods.

Brain Anatomical Network and Intelligence

PubMed Central

Li, Jun; Qin, Wen; Li, Kuncheng; Yu, Chunshui; Jiang, Tianzi

2009-01-01

Intuitively, higher intelligence might be assumed to correspond to more efficient information transfer in the brain, but no direct evidence has been reported from the perspective of brain networks. In this study, we performed extensive analyses to test the hypothesis that individual differences in intelligence are associated with brain structural organization, and in particular that higher scores on intelligence tests are related to greater global efficiency of the brain anatomical network. We constructed binary and weighted brain anatomical networks in each of 79 healthy young adults utilizing diffusion tensor tractography and calculated topological properties of the networks using a graph theoretical method. Based on their IQ test scores, all subjects were divided into general and high intelligence groups and significantly higher global efficiencies were found in the networks of the latter group. Moreover, we showed significant correlations between IQ scores and network properties across all subjects while controlling for age and gender. Specifically, higher intelligence scores corresponded to a shorter characteristic path length and a higher global efficiency of the networks, indicating a more efficient parallel information transfer in the brain. The results were consistently observed not only in the binary but also in the weighted networks, which together provide convergent evidence for our hypothesis. Our findings suggest that the efficiency of brain structural organization may be an important biological basis for intelligence. PMID:19492086

Investigation of innovative synthesis of biologically active compounds on the basis of newly developed reactions.

PubMed

Honda, Toshio

2012-01-01

Synthesis of biologically active compounds, including natural products and pharmaceutical agents, is an important and interesting research area since the large structural diversity and complexity of bioactive compounds make them an important source of leads and scaffolds in drug discovery and development. Many structurally and also biologically interesting compounds, including marine natural products, have been isolated from nature and have also been prepared on the basis of a computational design for the purpose of developing medicinal chemistry. In order to obtain a wide variety of derivatives of biologically active compounds from the viewpoint of medicinal chemistry, it is essential to establish efficient synthetic procedures for desired targets. Newly developed reactions should also be used for efficient synthesis of desired compounds. Thus, recent progress in the synthesis of biologically active compounds by focusing on the development of new reactions is summarized in this review article.

Advanced treatment of biologically pretreated coal gasification wastewater by a novel integration of heterogeneous catalytic ozonation and biological process.

PubMed

Zhuang, Haifeng; Han, Hongjun; Jia, Shengyong; Hou, Baolin; Zhao, Qian

2014-08-01

Advanced treatment of biologically pretreated coal gasification wastewater (CGW) was investigated employing heterogeneous catalytic ozonation integrated with anoxic moving bed biofilm reactor (ANMBBR) and biological aerated filter (BAF) process. The results indicated that catalytic ozonation with the prepared catalyst (i.e. MnOx/SBAC, sewage sludge was converted into sludge based activated carbon (SBAC) which loaded manganese oxides) significantly enhanced performance of pollutants removal by generated hydroxyl radicals. The effluent of catalytic ozonation process was more biodegradable and less toxic than that in ozonation alone. Meanwhile, ANMBBR-BAF showed efficient capacity of pollutants removal in treatment of the effluent of catalytic ozonation at a shorter reaction time, allowing the discharge limits to be met. Therefore, the integrated process with efficient, economical and sustainable advantages was suitable for advanced treatment of real biologically pretreated CGW. Copyright © 2014 Elsevier Ltd. All rights reserved.

Chemical and biological extraction of metals present in E waste: A hybrid technology.

PubMed

Pant, Deepak; Joshi, Deepika; Upreti, Manoj K; Kotnala, Ravindra K

2012-05-01

Management of metal pollution associated with E-waste is widespread across the globe. Currently used techniques for the extraction of metals from E-waste by using either chemical or biological leaching have their own limitations. Chemical leaching is much rapid and efficient but has its own environmental consequences, even the future prospects of associated nanoremediation are also uncertain. Biological leaching on the other hand is comparatively a cost effective technique but at the same moment it is time consuming and the complete recovery of the metal, alone by biological leaching is not possible in most of the cases. The current review addresses the individual issues related to chemical and biological extraction techniques and proposes a hybrid-methodology which incorporates both, along with safer chemicals and compatible microbes for better and efficient extraction of metals from the E-waste. Copyright © 2011 Elsevier Ltd. All rights reserved.

Synthetic biology as it relates to CAM photosynthesis: challenges and opportunities.

PubMed

DePaoli, Henrique C; Borland, Anne M; Tuskan, Gerald A; Cushman, John C; Yang, Xiaohan

2014-07-01

To meet future food and energy security needs, which are amplified by increasing population growth and reduced natural resource availability, metabolic engineering efforts have moved from manipulating single genes/proteins to introducing multiple genes and novel pathways to improve photosynthetic efficiency in a more comprehensive manner. Biochemical carbon-concentrating mechanisms such as crassulacean acid metabolism (CAM), which improves photosynthetic, water-use, and possibly nutrient-use efficiency, represent a strategic target for synthetic biology to engineer more productive C3 crops for a warmer and drier world. One key challenge for introducing multigene traits like CAM onto a background of C3 photosynthesis is to gain a better understanding of the dynamic spatial and temporal regulatory events that underpin photosynthetic metabolism. With the aid of systems and computational biology, vast amounts of experimental data encompassing transcriptomics, proteomics, and metabolomics can be related in a network to create dynamic models. Such models can undergo simulations to discover key regulatory elements in metabolism and suggest strategic substitution or augmentation by synthetic components to improve photosynthetic performance and water-use efficiency in C3 crops. Another key challenge in the application of synthetic biology to photosynthesis research is to develop efficient systems for multigene assembly and stacking. Here, we review recent progress in computational modelling as applied to plant photosynthesis, with attention to the requirements for CAM, and recent advances in synthetic biology tool development. Lastly, we discuss possible options for multigene pathway construction in plants with an emphasis on CAM-into-C3 engineering. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Novel statistical framework to identify differentially expressed genes allowing transcriptomic background differences.

PubMed

Ling, Zhi-Qiang; Wang, Yi; Mukaisho, Kenichi; Hattori, Takanori; Tatsuta, Takeshi; Ge, Ming-Hua; Jin, Li; Mao, Wei-Min; Sugihara, Hiroyuki

2010-06-01

Tests of differentially expressed genes (DEGs) from microarray experiments are based on the null hypothesis that genes that are irrelevant to the phenotype/stimulus are expressed equally in the target and control samples. However, this strict hypothesis is not always true, as there can be several transcriptomic background differences between target and control samples, including different cell/tissue types, different cell cycle stages and different biological donors. These differences lead to increased false positives, which have little biological/medical significance. In this article, we propose a statistical framework to identify DEGs between target and control samples from expression microarray data allowing transcriptomic background differences between these samples by introducing a modified null hypothesis that the gene expression background difference is normally distributed. We use an iterative procedure to perform robust estimation of the null hypothesis and identify DEGs as outliers. We evaluated our method using our own triplicate microarray experiment, followed by validations with reverse transcription-polymerase chain reaction (RT-PCR) and on the MicroArray Quality Control dataset. The evaluations suggest that our technique (i) results in less false positive and false negative results, as measured by the degree of agreement with RT-PCR of the same samples, (ii) can be applied to different microarray platforms and results in better reproducibility as measured by the degree of DEG identification concordance both intra- and inter-platforms and (iii) can be applied efficiently with only a few microarray replicates. Based on these evaluations, we propose that this method not only identifies more reliable and biologically/medically significant DEG, but also reduces the power-cost tradeoff problem in the microarray field. Source code and binaries freely available for download at http://comonca.org.cn/fdca/resources/softwares/deg.zip.

Species Diversity in the Parasitoid Genus Asobara (Hymenoptera: Braconidae) from the Native Area of the Fruit Fly Pest Drosophila suzukii (Diptera: Drosophilidae).

PubMed

Guerrieri, Emilio; Giorgini, Massimo; Cascone, Pasquale; Carpenito, Simona; van Achterberg, Cees

2016-01-01

Drosophila suzukii (Matsumura), commonly known as Spotted Wing Drosophila (SWD), is a worldwide serious economic threat to the production of berries and stone fruits. The chemical control widely used against this pest is often not able to preventing yield losses because wild flora offers an abundance of fruits to D. suzukii where the pest is able to reproduce and from where it recolonizes neighbouring cultivated fields. Alternatively, within Integrated Pest Management protocols for D. suzukii, biological control could play a key role by reducing its populations particularly in non-cultivated habitats, thus increasing the effectiveness and reducing the side negative effects of other management strategies. Because of the scarcity and of the low efficiency of autochthonous parasitoids in the new invaded territories, in the last few years, a number of surveys started in the native area of D. suzukii to find parasitoid species to be evaluated in quarantine structures and eventually released in the field, following a classical biological control approach. This paper reports the results of these surveys carried out in South Korea and for the first time in China. Among the parasitoids collected, those belonging to the genus Asobara Foerster resulted dominant both by number and species diversity. By combining morphological characters and the mitochondrial COI gene as a molecular marker, we identified seven species of Asobara, of which two associated with D. suzukii, namely A. japonica and A leveri, and five new to science, namely Asobara brevicauda, A. elongata, A mesocauda, A unicolorata, A. triangulata. Our findings offer new opportunity to find effective parasitoids to be introduced in classical biological control programmes in the territories recently invaded by D. suzukii.

Geometric effects in microfluidics on heterogeneous cell stress using an Eulerian-Lagrangian approach.

PubMed

Warren, K M; Mpagazehe, J N; LeDuc, P R; Higgs, C F

2016-02-07

The response of individual cells at the micro-scale in cell mechanics is important in understanding how they are affected by changing environments. To control cell stresses, microfluidics can be implemented since there is tremendous control over the geometry of the devices. Designing microfluidic devices to induce and manipulate stress levels on biological cells can be aided by computational modeling approaches. Such approaches serve as an efficient precursor to fabricating various microfluidic geometries that induce predictable levels of stress on biological cells, based on their mechanical properties. Here, a three-dimensional, multiphase computational fluid dynamics (CFD) modeling approach was implemented for soft biological materials. The computational model incorporates the physics of the particle dynamics, fluid dynamics and solid mechanics, which allows us to study how stresses affect the cells. By using an Eulerian-Lagrangian approach to treat the fluid domain as a continuum in the microfluidics, we are conducting studies of the cells' movement and the stresses applied to the cell. As a result of our studies, we were able to determine that a channel with periodically alternating columns of obstacles was capable of stressing cells at the highest rate, and that microfluidic systems can be engineered to impose heterogenous cell stresses through geometric configuring. We found that when using controlled geometries of the microfluidics channels with staggered obstructions, we could increase the maximum cell stress by nearly 200 times over cells flowing through microfluidic channels with no obstructions. Incorporating computational modeling in the design of microfluidic configurations for controllable cell stressing could help in the design of microfludic devices for stressing cells such as cell homogenizers.

Distributed power and control actuation in the thoracic mechanics of a robotic insect.

PubMed

Finio, Benjamin M; Wood, Robert J

2010-12-01

Recent advances in the understanding of biological flight have inspired roboticists to create flapping-wing vehicles on the scale of insects and small birds. While our understanding of the wing kinematics, flight musculature and neuromotor control systems of insects has expanded, in practice it has proven quite difficult to construct an at-scale mechanical device capable of similar flight performance. One of the key challenges is the development of an effective and efficient transmission mechanism to control wing motions. Here we present multiple insect-scale robotic thorax designs capable of producing asymmetric wing kinematics similar to those observed in nature and utilized by dipteran insects to maneuver. Inspired by the thoracic mechanics of dipteran insects, which entail a morphological separation of power and control muscles, these designs show that such distributed actuation can also modulate wing motion in a robotic design.

Biofiltration: an innovative air pollution control technology for VOC emissions.

PubMed

Leson, G; Winer, A M

1991-08-01

Biofiltration is a relatively recent air pollution control (APC) technology in which off-gases containing biodegradable volatile organic compounds (VOC) or inorganic air toxics are vented through a biologically active material. This technology has been successfully applied in Germany and The Netherlands in many full-scale applications to control odors, VOC and air toxic emissions from a wide range of industrial and public sector sources. Control efficiencies of more than 90 percent have been achieved for many common air pollutants. Due to lower operating costs, biofiltration can provide significant economic advantages over other APC technologies if applied to off-gases that contain readily biodegradable pollutants in low concentrations. Environmental benefits include low energy requirements and the avoidance of cross media transfer of pollutants. This paper reviews the history and current status of biofiltration, outlines its underlying scientific and engineering principles, and discusses the applicability of biofilters for a wide range of specific emission sources.

A "ship in a bottle" strategy to load a hydrophilic anticancer drug in porous metal organic framework nanoparticles: efficient encapsulation, matrix stabilization, and photodelivery.

PubMed

di Nunzio, Maria Rosaria; Agostoni, Valentina; Cohen, Boiko; Gref, Ruxandra; Douhal, Abderrazzak

2014-01-23

An essential challenge in the development of nanosized metal organic framework (nanoMOF) materials in biomedicine is to develop a strategy to stabilize their supramolecular structure in biological media while being able to control drug encapsulation and release. We have developed a method to efficiently encapsulate topotecan (TPT, 1), an important cytotoxic drug, in biodegradable nanoMOFs. Once inside the pores, 1 monomers aggregate in a "ship in a bottle" fashion, thus filling practically all of the nanoMOFs' available free volume and stabilizing their crystalline supramolecular structures. Highly efficient results have been found with the human pancreatic cell line PANC1, in contrast with free 1. We also demonstrate that one- and two-photon light irradiation emerges as a highly promising strategy to promote stimuli-dependent 1 release from the nanoMOFs, hence opening new standpoints for further developments in triggered drug delivery.

Deep Learning for Flow Sculpting: Insights into Efficient Learning using Scientific Simulation Data

NASA Astrophysics Data System (ADS)

Stoecklein, Daniel; Lore, Kin Gwn; Davies, Michael; Sarkar, Soumik; Ganapathysubramanian, Baskar

2017-04-01

A new technique for shaping microfluid flow, known as flow sculpting, offers an unprecedented level of passive fluid flow control, with potential breakthrough applications in advancing manufacturing, biology, and chemistry research at the microscale. However, efficiently solving the inverse problem of designing a flow sculpting device for a desired fluid flow shape remains a challenge. Current approaches struggle with the many-to-one design space, requiring substantial user interaction and the necessity of building intuition, all of which are time and resource intensive. Deep learning has emerged as an efficient function approximation technique for high-dimensional spaces, and presents a fast solution to the inverse problem, yet the science of its implementation in similarly defined problems remains largely unexplored. We propose that deep learning methods can completely outpace current approaches for scientific inverse problems while delivering comparable designs. To this end, we show how intelligent sampling of the design space inputs can make deep learning methods more competitive in accuracy, while illustrating their generalization capability to out-of-sample predictions.

XML-based data model and architecture for a knowledge-based grid-enabled problem-solving environment for high-throughput biological imaging.

PubMed

Ahmed, Wamiq M; Lenz, Dominik; Liu, Jia; Paul Robinson, J; Ghafoor, Arif

2008-03-01

High-throughput biological imaging uses automated imaging devices to collect a large number of microscopic images for analysis of biological systems and validation of scientific hypotheses. Efficient manipulation of these datasets for knowledge discovery requires high-performance computational resources, efficient storage, and automated tools for extracting and sharing such knowledge among different research sites. Newly emerging grid technologies provide powerful means for exploiting the full potential of these imaging techniques. Efficient utilization of grid resources requires the development of knowledge-based tools and services that combine domain knowledge with analysis algorithms. In this paper, we first investigate how grid infrastructure can facilitate high-throughput biological imaging research, and present an architecture for providing knowledge-based grid services for this field. We identify two levels of knowledge-based services. The first level provides tools for extracting spatiotemporal knowledge from image sets and the second level provides high-level knowledge management and reasoning services. We then present cellular imaging markup language, an extensible markup language-based language for modeling of biological images and representation of spatiotemporal knowledge. This scheme can be used for spatiotemporal event composition, matching, and automated knowledge extraction and representation for large biological imaging datasets. We demonstrate the expressive power of this formalism by means of different examples and extensive experimental results.

Node fingerprinting: an efficient heuristic for aligning biological networks.

PubMed

Radu, Alex; Charleston, Michael

2014-10-01

With the continuing increase in availability of biological data and improvements to biological models, biological network analysis has become a promising area of research. An emerging technique for the analysis of biological networks is through network alignment. Network alignment has been used to calculate genetic distance, similarities between regulatory structures, and the effect of external forces on gene expression, and to depict conditional activity of expression modules in cancer. Network alignment is algorithmically complex, and therefore we must rely on heuristics, ideally as efficient and accurate as possible. The majority of current techniques for network alignment rely on precomputed information, such as with protein sequence alignment, or on tunable network alignment parameters, which may introduce an increased computational overhead. Our presented algorithm, which we call Node Fingerprinting (NF), is appropriate for performing global pairwise network alignment without precomputation or tuning, can be fully parallelized, and is able to quickly compute an accurate alignment between two biological networks. It has performed as well as or better than existing algorithms on biological and simulated data, and with fewer computational resources. The algorithmic validation performed demonstrates the low computational resource requirements of NF.

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Science.gov Websites

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Optimizing nitrogen application rate and plant density for improving cotton yield and nitrogen use efficiency in the North China Plain

PubMed Central

Dong, Helin; Zheng, Cangsong; Sun, Miao; Liu, Aizhong; Wang, Guoping; Liu, Shaodong; Zhang, Siping; Chen, Jing; Li, Yabing; Pang, Chaoyou; Zhao, Xinhua

2017-01-01

Plant population density (PPD) and nitrogen (N) application rate (NAR) are two controllable factors in cotton production. We conducted field experiments to investigate the effects of PPD, NAR and their interaction (PPD × NAR) on yield, N uptake and N use efficiency (NUE) of cotton using a split-plot design in the North China Plain during 2013 and 2014. The main plots were PPDs (plants m−2) of 3.00 (low), 5.25 (medium) and 7.50 (high) and the subplots were NARs of 0 (N-free), 112.5 (low), 225.0 (moderate) and 337.5 (high). During both 2013 and 2014, biological yield and N uptake of cotton increased significantly, but harvesting index decreased significantly with NAR and PPD increasing. With NAR increasing, internal nitrogen use efficiency(NUE) decreased significantly under three PPDs and agronomical NUE, physiologilal NUE, nitrogen recovery efficiency(NRE) and partial factor productivity from applied nitrogen (PFPN) also decreased significantly under high PPD between two years. Lint yield increment varied during different PPDs and years, but NAR enhancement showed less function under higher PPD than lower PPD in general. Taken together, moderate NAR under medium PPD combined higher lint yield with higher agronomic NUE, physiological NUE, and NRE, while low NAR with high PPD would achieve a comparable yield with superior NRE and PFPN and high NAR under high PPD and medium PPD produced higher biological yield but lower harvest index, lint yield and NUE compared to moderate NAR with medium PPD. Our overall results indicated that, in this region, increasing PPD and decreasing NAR properly would enhance both lint yield and NUE of cotton. PMID:28981538

Durably controlling bovine hypodermosis.

PubMed

Boulard, Chantal

2002-01-01

Cattle hypodermosis, due to insect larvae, is widely spread over the northern hemisphere. Very efficient insecticides are available and their use in most countries are done on an individual level but never cover the whole cattle population of a country. Untreated animals remain the reservoir of the disease and annually re-infest the cattle population. The economic effects of this disease on animal production (meat, milk and the leather industry) but also on the general cattle health status, have led many European countries to launch organised control programs. The first example of definitive hypodermosis control goes back one hundred years ago when Danish farmers eradicated hypodermosis from the Danish islands by manual elimination of the warbles. Since then, more and more European countries have considered the feasibility and economic returns of such programs. The various factors which foster these programs are related to (i) biological factors, (parasite cattle specificity, synchronous biological cycles of both species of insects involved), (ii) the development of more and more efficient insecticides used only once a year by systemic application, with high efficiency at very low dosages against the first larval stage of Hypoderma spp., (iii) the development of acute techniques of detection of the disease for the monitoring of hypodermosis free countries and (iv) the durable successful results obtained in more and more European countries. Although the programs were imposed by different partners of the livestock channel production (farmers, dairy industry, leather industry) and have been engaged within the last 50 years in many European countries (Denmark, The Netherlands, Ireland, the United Kingdom, the Czech Republic, Germany, France and Switzerland) common features have emerged among these different eradication programs. They all need a preliminary statement of the economic impact of this pest and the farmers' awareness of the economic returns of such programs. The programs' efficacy depends: (i) on a good knowledge ofthe epidemiology of the parasites, (ii) on the simultaneous implementation of the control program on the whole national cattle population whatever the structure monitoring the treatments (veterinary services, farmers association), (iii) on a national Warble fly legislation making the treatments compulsory and (iv) on an acute epidemiological survey as soon as the status of a hypodermosis free country is reached and the treatments are suspended. The sanitary and financial returns of such programs are a benefit to all the partners of livestock production, to the quality of the environment and to the consumers.

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

PubMed Central

Crowder, David W.

2007-01-01

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

Molecular biomimetics: GEPI-based biological routes to technology.

PubMed

Tamerler, Candan; Khatayevich, Dmitriy; Gungormus, Mustafa; Kacar, Turgay; Oren, E Emre; Hnilova, Marketa; Sarikaya, Mehmet

2010-01-01

In nature, the viability of biological systems is sustained via specific interactions among the tens of thousands of proteins, the major building blocks of organisms from the simplest single-celled to the most complex multicellular species. Biomolecule-material interaction is accomplished with molecular specificity and efficiency leading to the formation of controlled structures and functions at all scales of dimensional hierarchy. Through evolution, Mother Nature developed molecular recognition by successive cycles of mutation and selection. Molecular specificity of probe-target interactions, e.g., ligand-receptor, antigen-antibody, is always based on specific peptide molecular recognition. Using biology as a guide, we can now understand, engineer, and control peptide-material interactions and exploit them as a new design tool for novel materials and systems. We adapted the protocols of combinatorially designed peptide libraries, via both cell surface or phage display methods; using these we select short peptides with specificity to a variety of practical materials. These genetically engineered peptides for inorganics (GEPI) are then studied experimentally to establish their binding kinetics and surface stability. The bound peptide structure and conformations are interrogated both experimentally and via modeling, and self-assembly characteristics are tested via atomic force microscopy. We further engineer the peptide binding and assembly characteristics using a computational biomimetics approach where bioinformatics based peptide-sequence similarity analysis is developed to design higher generation function-specific peptides. The molecular biomimetic approach opens up new avenues for the design and utilization of multifunctional molecular systems in a wide-range of applications from tissue engineering, disease diagnostics, and therapeutics to various areas of nanotechnology where integration is required among inorganic, organic and biological materials. Here, we describe lessons from biology with examples of protein-mediated functional biological materials, explain how novel peptides can be designed with specific affinity to inorganic solids using evolutionary engineering approaches, give examples of their potential utilizations in technology and medicine, and, finally, provide a summary of challenges and future prospects. (c) 2010 Wiley Periodicals, Inc.

Life Sciences Research in the Centrifuge Accommodation Module of the International Space Station

NASA Technical Reports Server (NTRS)

Dalton, Bonnie P.; Plaut, Karen; Meeker, Gabrielle B.; Sun, Sid (Technical Monitor)

2000-01-01

The Centrifuge Accommodation Module (CAM) will be the home of the fundamental biology research facilities on the International Space Station (ISS). These facilities are being built by the Biological Research Project (BRP), whose goal is to oversee development of a wide variety of habitats and host systems to support life sciences research on the ISS. The habitats and host systems are designed to provide life support for a variety of specimens including cells, bacteria, yeast, plants, fish, rodents, eggs (e.g., quail), and insects. Each habitat contains specimen chambers that allow for easy manipulation of specimens and alteration of sample numbers. All habitats are capable of sustaining life support for 90 days and have automated as well as full telescience capabilities for sending habitat parameters data to investigator homesite laboratories. The habitats provide all basic life support capabilities including temperature control, humidity monitoring and control, waste management, food, media and water delivery as well as adjustable lighting. All habitats will have either an internal centrifuge or are fitted to the 2.5-meter diameter centrifuge allowing for variable centrifugation up to 2 g. Specimen chambers are removable so that the specimens can be handled in the life sciences glovebox. Laboratory support equipment is provided for handling the specimens. This includes a compound and dissecting microscope with advanced video imaging, mass measuring devices, refrigerated centrifuge for processing biological samples, pH meter, fixation and complete cryogenic storage capabilities. The research capabilities provided by the fundamental biology facilities will allow for flexibility and efficiency for long term research on the International Space Station.

Biomedical and Catalytic Opportunities of Virus-Like Particles in Nanotechnology.

PubMed

Schwarz, B; Uchida, M; Douglas, T

2017-01-01

Within biology, molecules are arranged in hierarchical structures that coordinate and control the many processes that allow for complex organisms to exist. Proteins and other functional macromolecules are often studied outside their natural nanostructural context because it remains difficult to create controlled arrangements of proteins at this size scale. Viruses are elegantly simple nanosystems that exist at the interface of living organisms and nonliving biological machines. Studied and viewed primarily as pathogens to be combatted, viruses have emerged as models of structural efficiency at the nanoscale and have spurred the development of biomimetic nanoparticle systems. Virus-like particles (VLPs) are noninfectious protein cages derived from viruses or other cage-forming systems. VLPs provide incredibly regular scaffolds for building at the nanoscale. Composed of self-assembling protein subunits, VLPs provide both a model for studying materials' assembly at the nanoscale and useful building blocks for materials design. The robustness and degree of understanding of many VLP structures allow for the ready use of these systems as versatile nanoparticle platforms for the conjugation of active molecules or as scaffolds for the structural organization of chemical processes. Lastly the prevalence of viruses in all domains of life has led to unique activities of VLPs in biological systems most notably the immune system. Here we discuss recent efforts to apply VLPs in a wide variety of applications with the aim of highlighting how the common structural elements of VLPs have led to their emergence as paradigms for the understanding and design of biological nanomaterials. © 2017 Elsevier Inc. All rights reserved.

MIDAS: A Modular DNA Assembly System for Synthetic Biology.

PubMed

van Dolleweerd, Craig J; Kessans, Sarah A; Van de Bittner, Kyle C; Bustamante, Leyla Y; Bundela, Rudranuj; Scott, Barry; Nicholson, Matthew J; Parker, Emily J

2018-04-20

A modular and hierarchical DNA assembly platform for synthetic biology based on Golden Gate (Type IIS restriction enzyme) cloning is described. This enabling technology, termed MIDAS (for Modular Idempotent DNA Assembly System), can be used to precisely assemble multiple DNA fragments in a single reaction using a standardized assembly design. It can be used to build genes from libraries of sequence-verified, reusable parts and to assemble multiple genes in a single vector, with full user control over gene order and orientation, as well as control of the direction of growth (polarity) of the multigene assembly, a feature that allows genes to be nested between other genes or genetic elements. We describe the detailed design and use of MIDAS, exemplified by the reconstruction, in the filamentous fungus Penicillium paxilli, of the metabolic pathway for production of paspaline and paxilline, key intermediates in the biosynthesis of a range of indole diterpenes-a class of secondary metabolites produced by several species of filamentous fungi. MIDAS was used to efficiently assemble a 25.2 kb plasmid from 21 different modules (seven genes, each composed of three basic parts). By using a parts library-based system for construction of complex assemblies, and a unique set of vectors, MIDAS can provide a flexible route to assembling tailored combinations of genes and other genetic elements, thereby supporting synthetic biology applications in a wide range of expression hosts.

Nonlinear Time Series Analysis of Nodulation Factor Induced Calcium Oscillations: Evidence for Deterministic Chaos?

PubMed Central

Hazledine, Saul; Sun, Jongho; Wysham, Derin; Downie, J. Allan; Oldroyd, Giles E. D.; Morris, Richard J.

2009-01-01

Legume plants form beneficial symbiotic interactions with nitrogen fixing bacteria (called rhizobia), with the rhizobia being accommodated in unique structures on the roots of the host plant. The legume/rhizobial symbiosis is responsible for a significant proportion of the global biologically available nitrogen. The initiation of this symbiosis is governed by a characteristic calcium oscillation within the plant root hair cells and this signal is activated by the rhizobia. Recent analyses on calcium time series data have suggested that stochastic effects have a large role to play in defining the nature of the oscillations. The use of multiple nonlinear time series techniques, however, suggests an alternative interpretation, namely deterministic chaos. We provide an extensive, nonlinear time series analysis on the nature of this calcium oscillation response. We build up evidence through a series of techniques that test for determinism, quantify linear and nonlinear components, and measure the local divergence of the system. Chaos is common in nature and it seems plausible that properties of chaotic dynamics might be exploited by biological systems to control processes within the cell. Systems possessing chaotic control mechanisms are more robust in the sense that the enhanced flexibility allows more rapid response to environmental changes with less energetic costs. The desired behaviour could be most efficiently targeted in this manner, supporting some intriguing speculations about nonlinear mechanisms in biological signaling. PMID:19675679

Combining epidemiology with basic biology of sand flies, parasites, and hosts to inform leishmaniasis transmission dynamics and control.

PubMed

Courtenay, Orin; Peters, Nathan C; Rogers, Matthew E; Bern, Caryn

2017-10-01

Quantitation of the nonlinear heterogeneities in Leishmania parasites, sand fly vectors, and mammalian host relationships provides insights to better understand leishmanial transmission epidemiology towards improving its control. The parasite manipulates the sand fly via production of promastigote secretory gel (PSG), leading to the "blocked sand fly" phenotype, persistent feeding attempts, and feeding on multiple hosts. PSG is injected into the mammalian host with the parasite and promotes the establishment of infection. Animal models demonstrate that sand flies with the highest parasite loads and percent metacyclic promastigotes transmit more parasites with greater frequency, resulting in higher load infections that are more likely to be both symptomatic and efficient reservoirs. The existence of mammalian and sand fly "super-spreaders" provides a biological basis for the spatial and temporal clustering of clinical leishmanial disease. Sand fly blood-feeding behavior will determine the efficacies of indoor residual spraying, topical insecticides, and bed nets. Interventions need to have sufficient coverage to include transmission hot spots, especially in the absence of field tools to assess infectiousness. Interventions that reduce sand fly densities in the absence of elimination could have negative consequences, for example, by interfering with partial immunity conferred by exposure to sand fly saliva. A deeper understanding of both sand fly and host biology and behavior is essential to ensuring effectiveness of vector interventions.

Construction of a cost effective optical tweezers for manipulation of birefringent materials using circularly polarized light

NASA Astrophysics Data System (ADS)

McMahon, Allison; Sauncy, Toni

2008-10-01

Light manipulation is a very powerful tool in physics, biology, and chemistry. There are several physical principles underlying the apparatus known as the ``optical tweezers,'' the term given to using focused light to manipulate and control small objects. By carefully controlling the orientation and position of a focused laser beam, dielectric particles can be effectively trapped and manipulated. We have designed a cost efficient and effective undergraduate optical tweezers apparatus by using standard ``off the shelf'' components and starting with a standard undergraduate laboratory microscope. Images are recorded using a small CCD camera interfaced to a computer and controlled by LabVIEW^TM software. By using wave plates to produce circular polarized light, rotational motion can be induced in small particles of birefringent materials such as calcite and mica.

SU-F-J-193: Efficient Dose Extinction Method for Water Equivalent Path Length (WEPL) of Real Tissue Samples for Validation of CT HU to Stopping Power Conversion

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

Zhang, R; Baer, E; Jee, K

Purpose: For proton therapy, an accurate model of CT HU to relative stopping power (RSP) conversion is essential. In current practice, validation of these models relies solely on measurements of tissue substitutes with standard compositions. Validation based on real tissue samples would be much more direct and can address variations between patients. This study intends to develop an efficient and accurate system based on the concept of dose extinction to measure WEPL and retrieve RSP in biological tissue in large number of types. Methods: A broad AP proton beam delivering a spread out Bragg peak (SOBP) is used to irradiatemore » the samples with a Matrixx detector positioned immediately below. A water tank was placed on top of the samples, with the water level controllable in sub-millimeter by a remotely controlled dosing pump. While gradually lowering the water level with beam on, the transmission dose was recorded at 1 frame/sec. The WEPL were determined as the difference between the known beam range of the delivered SOBP (80%) and the water level corresponding to 80% of measured dose profiles in time. A Gammex 467 phantom was used to test the system and various types of biological tissue was measured. Results: RSP for all Gammex inserts, expect the one made with lung-450 material (<2% error), were determined within ±0.5% error. Depends on the WEPL of investigated phantom, a measurement takes around 10 min, which can be accelerated by a faster pump. Conclusion: Based on the concept of dose extinction, a system was explored to measure WEPL efficiently and accurately for a large number of samples. This allows the validation of CT HU to stopping power conversions based on large number of samples and real tissues. It also allows the assessment of beam uncertainties due to variations over patients, which issue has never been sufficiently studied before.« less

Systematic design of membership functions for fuzzy-logic control: A case study on one-stage partial nitritation/anammox treatment systems.

PubMed

Boiocchi, Riccardo; Gernaey, Krist V; Sin, Gürkan

2016-10-01

A methodology is developed to systematically design the membership functions of fuzzy-logic controllers for multivariable systems. The methodology consists of a systematic derivation of the critical points of the membership functions as a function of predefined control objectives. Several constrained optimization problems corresponding to different qualitative operation states of the system are defined and solved to identify, in a consistent manner, the critical points of the membership functions for the input variables. The consistently identified critical points, together with the linguistic rules, determine the long term reachability of the control objectives by the fuzzy logic controller. The methodology is highlighted using a single-stage side-stream partial nitritation/Anammox reactor as a case study. As a result, a new fuzzy-logic controller for high and stable total nitrogen removal efficiency is designed. Rigorous simulations are carried out to evaluate and benchmark the performance of the controller. The results demonstrate that the novel control strategy is capable of rejecting the long-term influent disturbances, and can achieve a stable and high TN removal efficiency. Additionally, the controller was tested, and showed robustness, against measurement noise levels typical for wastewater sensors. A feedforward-feedback configuration using the present controller would give even better performance. In comparison, a previously developed fuzzy-logic controller using merely expert and intuitive knowledge performed worse. This proved the importance of using a systematic methodology for the derivation of the membership functions for multivariable systems. These results are promising for future applications of the controller in real full-scale plants. Furthermore, the methodology can be used as a tool to help systematically design fuzzy logic control applications for other biological processes. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

USDA-ARS?s Scientific Manuscript database

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

Anti-Sigma Factors in E. coli: Common Regulatory Mechanisms Controlling Sigma Factors Availability

PubMed Central

Treviño-Quintanilla, Luis Gerardo; Freyre-González, Julio Augusto; Martínez-Flores, Irma

2013-01-01

In bacteria, transcriptional regulation is a key step in cellular gene expression. All bacteria contain a core RNA polymerase that is catalytically competent but requires an additional σ factor for specific promoter recognition and correct transcriptional initiation. The RNAP core is not able to selectively bind to a given σ factor. In contrast, different σ factors have different affinities for the RNAP core. As a consequence, the concentration of alternate σ factors requires strict regulation in order to properly control the delicate interplay among them, which favors the competence for the RNAP core. This control is archived by different σ/anti-σ controlling mechanisms that shape complex regulatory networks and cascades, and enable the response to sudden environmental cues, whose global understanding is a current challenge for systems biology. Although there have been a number of excellent studies on each of these σ/anti-σ post-transcriptional regulatory systems, no comprehensive comparison of these mechanisms in a single model organism has been conducted. Here, we survey all these systems in E. coli dissecting and analyzing their inner workings and highlightin their differences. Then, following an integral approach, we identify their commonalities and outline some of the principles exploited by the cell to effectively and globally reprogram the transcriptional machinery. These principles provide guidelines for developing biological synthetic circuits enabling an efficient and robust response to sudden stimuli. PMID:24396271

Live Imaging Followed by Single Cell Tracking to Monitor Cell Biology and the Lineage Progression of Multiple Neural Populations.

PubMed

Gómez-Villafuertes, Rosa; Paniagua-Herranz, Lucía; Gascon, Sergio; de Agustín-Durán, David; Ferreras, María de la O; Gil-Redondo, Juan Carlos; Queipo, María José; Menendez-Mendez, Aida; Pérez-Sen, Ráquel; Delicado, Esmerilda G; Gualix, Javier; Costa, Marcos R; Schroeder, Timm; Miras-Portugal, María Teresa; Ortega, Felipe

2017-12-16

Understanding the mechanisms that control critical biological events of neural cell populations, such as proliferation, differentiation, or cell fate decisions, will be crucial to design therapeutic strategies for many diseases affecting the nervous system. Current methods to track cell populations rely on their final outcomes in still images and they generally fail to provide sufficient temporal resolution to identify behavioral features in single cells. Moreover, variations in cell death, behavioral heterogeneity within a cell population, dilution, spreading, or the low efficiency of the markers used to analyze cells are all important handicaps that will lead to incomplete or incorrect read-outs of the results. Conversely, performing live imaging and single cell tracking under appropriate conditions represents a powerful tool to monitor each of these events. Here, a time-lapse video-microscopy protocol, followed by post-processing, is described to track neural populations with single cell resolution, employing specific software. The methods described enable researchers to address essential questions regarding the cell biology and lineage progression of distinct neural populations.

Chromatin Computation

PubMed Central

Bryant, Barbara

2012-01-01

In living cells, DNA is packaged along with protein and RNA into chromatin. Chemical modifications to nucleotides and histone proteins are added, removed and recognized by multi-functional molecular complexes. Here I define a new computational model, in which chromatin modifications are information units that can be written onto a one-dimensional string of nucleosomes, analogous to the symbols written onto cells of a Turing machine tape, and chromatin-modifying complexes are modeled as read-write rules that operate on a finite set of adjacent nucleosomes. I illustrate the use of this “chromatin computer” to solve an instance of the Hamiltonian path problem. I prove that chromatin computers are computationally universal – and therefore more powerful than the logic circuits often used to model transcription factor control of gene expression. Features of biological chromatin provide a rich instruction set for efficient computation of nontrivial algorithms in biological time scales. Modeling chromatin as a computer shifts how we think about chromatin function, suggests new approaches to medical intervention, and lays the groundwork for the engineering of a new class of biological computing machines. PMID:22567109

[Feasibility of treatment of micro-pollutant water polluted by nitrobenzene with IBAC-process].

PubMed

Wang, Chen; Ma, Fang; Shan, Dan; Yang, Ji-xian; Lan, Yuan-dong; Gao, Guo-wei

2007-07-01

The performance and feasibility of immobilization biological activated carbon (IBAC) were investigated to treat micro-pollutant water containing nitrobenzene. IBAC has been developed on the granular activated carbon by immobilization of selected and acclimated species of engineering bacteria to treat the micro-pollutant water containing nitrobenzene. The IBAC removal efficiencies for nitrobenzene, permanganate index, turbidity, UV, ammonia and nitrite were compared with granular activated carbon (GAC) process. Biological toxicity of influent and effluent of filter were determined. Amount of bacteria in carbon was measured when carbon filter was inoculated and circulated stably. The results showed that compared with GAC, it took short time for IABC to startup and recover to normal after impact burden. In addition, IBAC was more effective to treat micro-pollutants. In order to ensure security of drinking water, the influent nitrobenzene should be controlled below 26 microg/L. Effluent biological toxicity treated with IBAC was less than that with GAC. The performance of IBAC was much better than that of GAC. Amount of bacteria in both activated carbon filter increased first and then declined from inlet to outlet.

Simultaneous chemical oxygen demand removal, methane production and heavy metal precipitation in the biological treatment of landfill leachate using acid mine drainage as sulfate resource.

PubMed

Li, Yu-Long; Wang, Jin; Yue, Zheng-Bo; Tao, Wei; Yang, Hai-Bin; Zhou, Yue-Fei; Chen, Tian-Hu

2017-07-01

Biological treatment played an important role in the treatment of landfill leachate. In the current study, acid mine drainage (AMD) was used as a source of sulfate to strengthen the anaerobic treatment of landfill leachate. Effects of chemical oxygen demand (COD) and SO 4 2- mass concentration ratio on the decomposition of organic matter, methane production and sulfate reduction were investigated and the microbial community was analyzed using the high throughout methods. Results showed that high removal efficiency of COD, methane production and heavy metal removal was achieved when the initial COD/SO 4 2- ratio (based on mass) was set at 3.0. The relative abundance of anaerobic hydrogen-producing bacteria (Candidatus Cloacamonas) in the experimental group with the addition of AMD was significantly increased compared to the control. Abundance of hydrogenotrophic methanogens of Methanosarcina and Methanomassiliicoccus was increased. Results confirmed that AMD could be used as sulfate resource to strengthen the biological treatment of landfill leachate. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Practical applications of insects' sexual development for pest control.

PubMed

Koukidou, M; Alphey, L

2014-01-01

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

Two poplar-associated bacterial isolates induce additive favorable responses in a constructed plant-microbiome system

DOE PAGES

Jawdy, Sara S.; Gunter, Lee E.; Engle, Nancy L.; ...

2016-04-26

Here, the biological function of the plant-microbiome system is the result of contributions from the host plant and microbiome members. In this work we study the function of a simplified community consisting of Pseudomonas and Burkholderia bacterial strains isolated from Populus hosts and inoculated on axenic Populus cutting in controlled laboratory conditions. Inoculation individually with either bacterial isolate increased root growth relative to uninoculated controls. Root area, photosynthetic efficiency, gene expression and metabolite expression data in individual and dual inoculated treatments indicate that the effects of these bacteria are unique and additive, suggesting that the function of a microbiome communitymore » may be predicted from the additive functions of the individual members.« less

Control system for the 2nd generation Berkeley AutoMounters (BAM2) at GM/CA CAT macromolecular crystallography beamlines

PubMed Central

Makarov, O.; Hilgart, M.; Ogata, C.; Pothineni, S.; Cork, C.

2011-01-01

GM/CA CAT at Sector 23 of the Advanced Photon Source (APS) is an NIH funded facility for crystallographic structure determination of biological macromolecules by X-ray diffraction. A second generation Berkeley automounter is being integrated into the beamline control system at the 23-BM experimental station. This new device replaces the previous all-pneumatic gripper motions with a combination of pneumatics and XYZ motorized linear stages. The latter adds a higher degree of flexibility to the robot including auto-alignment capability, accommodation of a larger capacity sample Dewar of arbitrary shape, and support for advanced operations such as crystal washing, while preserving the overall simplicity and efficiency of the Berkeley automounter design. PMID:21822343

Wars between microbes on roots and fruits

PubMed Central

Lugtenberg, Ben; Rozen, Daniel E.; Kamilova, Faina

2017-01-01

Microbes in nature often live in unfavorable conditions. To survive, they have to occupy niches close to food sources and efficiently utilize nutrients that are often present in very low concentrations. Moreover, they have to possess an arsenal of attack and defense mechanisms against competing bacteria. In this review, we will discuss strategies used by microbes to compete with each other in the rhizosphere and on fruits, with a focus on mechanisms of inter- and intra-species antagonism. Special attention will be paid to the recently discovered roles of volatile organic compounds. Several microbes with proven capabilities in the art of warfare are being applied in products used for the biological control of plant diseases, including post-harvest control of fruits and vegetables. PMID:28408980

Removal of arsenic and iron removal from drinking water using coagulation and biological treatment.

PubMed

Pramanik, Biplob Kumar; Pramanik, Sagor Kumar; Suja, Fatihah

2016-02-01

Effects of biological activated carbon (BAC), biological aerated filter (BAF), alum coagulation and Moringa oleifera coagulation were investigated to remove iron and arsenic contaminants from drinking water. At an initial dose of 5 mg/L, the removal efficiency for arsenic and iron was 63% and 58% respectively using alum, and 47% and 41% respectively using Moringa oleifera. The removal of both contaminants increased with the increase in coagulant dose and decrease in pH. Biological processes were more effective in removing these contaminants than coagulation. Compared to BAF, BAC gave greater removal of both arsenic and iron, removing 85% and 74%, respectively. Longer contact time for both processes could reduce the greater concentration of arsenic and iron contaminants. The addition of coagulation (at 5 mg/L dosage) and a biological process (with 15 or 60 min contact time) could significantly increase removal efficiency, and the maximum removal was observed for the combination of alum and BAC treatment (60 min contact time), with 100% and 98.56% for arsenic and iron respectively. The reduction efficiency of arsenic and iron reduced with the increase in the concentration of dissolved organics in the feedwater due to the adsorption competition between organic molecules and heavy metals.

Artificial muscles on heat

NASA Astrophysics Data System (ADS)

McKay, Thomas G.; Shin, Dong Ki; Percy, Steven; Knight, Chris; McGarry, Scott; Anderson, Iain A.

2014-03-01

Many devices and processes produce low grade waste heat. Some of these include combustion engines, electrical circuits, biological processes and industrial processes. To harvest this heat energy thermoelectric devices, using the Seebeck effect, are commonly used. However, these devices have limitations in efficiency, and usable voltage. This paper investigates the viability of a Stirling engine coupled to an artificial muscle energy harvester to efficiently convert heat energy into electrical energy. The results present the testing of the prototype generator which produced 200 μW when operating at 75°C. Pathways for improved performance are discussed which include optimising the electronic control of the artificial muscle, adjusting the mechanical properties of the artificial muscle to work optimally with the remainder of the system, good sealing, and tuning the resonance of the displacer to minimise the power required to drive it.

An efficient process for wastewater treatment to mitigate free nitrous acid generation and its inhibition on biological phosphorus removal

PubMed Central

Zhao, Jianwei; Wang, Dongbo; Li, Xiaoming; Yang, Qi; Chen, Hongbo; Zhong, Yu; An, Hongxue; Zeng, Guangming

2015-01-01

Free nitrous acid (FNA), which is the protonated form of nitrite and inevitably produced during biological nitrogen removal, has been demonstrated to strongly inhibit the activity of polyphosphate accumulating organisms (PAOs). Herein we reported an efficient process for wastewater treatment, i.e., the oxic/anoxic/oxic/extended-idle process to mitigate the generation of FNA and its inhibition on PAOs. The results showed that this new process enriched more PAOs which thereby achieved higher phosphorus removal efficiency than the conventional four-step (i.e., anaerobic/oxic/anoxic/oxic) biological nutrient removal process (41 ± 7% versus 30 ± 5% in abundance of PAOs and 97 ± 0.73% versus 82 ± 1.2% in efficiency of phosphorus removal). It was found that this new process increased pH value but decreased nitrite accumulation, resulting in the decreased FNA generation. Further experiments showed that the new process could alleviate the inhibition of FNA on the metabolisms of PAOs even under the same FNA concentration. PMID:25721019

Biological nitrification/denitrification of high sodium nitrite (navy shipyard) wastewater.

PubMed

Kamath, S; Sabatini, D A; Canter, L W

1991-01-01

In the hydroblasting of ships' boiler tubes, a wastewater high in nitrite (as high as 1200 mg litre(-1)) is produced by the US Navy. This research has evaluated the use of a suspended-growth biological system to treat this wastewater by denitrification. Two biological treatment configurations were evaluated (direct denitrification versus nitrification/denitrification) with nitrification/denitrification producing better nitrite removal efficiencies (54 to 62% versus 40%, respectively). The introduction of metals (cadmium, chromium, lead, copper and iron) in concentrations typical for this wastewater did not inhibit the nitrite removal efficiencies. The influent metal concentrations ranged from 0.02 mg litre(-1) for cadmium to 22 mg litre(-1) for iron and the metal removal efficiencies ranged from 4.8% for cadmium to 50% for copper. Increasing sludge age resulted in improved nitrite removal efficiencies (52%, 57% and 74% for sludge ages of 4, 6 and 8 days, respectively). The resulting biokinetic constants were similar to those reported by others for lower influent concentrations of nitrite or nitrate (Ygs=0.02 mg/mg; Ygn=0.16 mg/mg; Yb=0.8 mg/mg; and b=0.006 h(-1)).

Comparison of UHPLC and HPLC in benzodiazepines analysis of postmortem samples: a case-control study.

PubMed

Behnoush, Behnam; Sheikhazadi, Ardeshir; Bazmi, Elham; Fattahi, Akbar; Sheikhazadi, Elham; Saberi Anary, Seyed Hossein

2015-04-01

The aim of this study was to compare system efficiency and analysis duration regarding the solvent consumption and system maintenance in high-pressure liquid chromatography (HPLC) and ultra high-pressure liquid chromatography (UHPLC). In a case-control study, standard solutions of 7 benzodiazepines (BZs) and 73 biological samples such as urine, tissue, stomach content, and bile that screened positive for BZs were analyzed by HPLC and UHPLC in laboratory of forensic toxicology during 2012 to 2013. HPLC analysis was performed using a Knauer by 100-5 C-18 column (250 mm × 4.6 mm) and Knauer photodiode array detector (PAD). UHPLC analysis was performed using Knauer PAD detector with cooling autosampler and Eurospher II 100-3 C-18 column (100 mm × 3 mm) and also 2 pumps. The mean retention time, standard deviation, flow rate, and repeatability of analytical results were compared by using 2 methods. Routine runtimes in HPLC and UHPLC took 40 and 15 minutes, respectively. Changes in mobile phase composition of the 2 methods were not required. Flow rate and solvent consumption in UHPLC decreased. Diazepam and flurazepam were detected more frequently in biological samples. In UHPLC, small particle size and short length of column cause effective separation of BZs in a very short time. Reduced flow rate, solvent consumption, and injection volume cause more efficiency and less analysis costs. Thus, in the detection of BZs, UHPLC is an accurate, sensitive, and fast method with less cost of analysis.

Asymmetric Brownian motor driven by bubble formation in a hydrophobic channel.

PubMed

Arai, Noriyoshi; Yasuoka, Kenji; Koishi, Takahiro; Ebisuzaki, Toshikazu

2010-10-26

The "asymmetric brownian ratchet model" is a variation of Feynman's ratchet and pawl system proposed. In this model, a system consisting of a motor and a rail has two binding states. One is the random brownian state, and the other is the asymmetric potential state. When the system is alternatively switched between these states, the motor can be driven in one direction. This model is believed to explain nanomotor behavior in biological systems. The feasibility of the model has been demonstrated using electrical and magnetic forces; however, switching of these forces is unlikely to be found in biological systems. In this paper, we propose an original mechanism of transition between states by bubble formation in a nanosized channel surrounded by hydrophobic atoms. This amounts to a nanoscale motor system using bubble propulsion. The motor system consists of a hydrophobic motor and a rail on which hydrophobic patterns are printed. Potential asymmetry can be produced by using a left-right asymmetric pattern shape. Hydrophobic interactions are believed to play an important role in the binding of biomolecules and molecular recognition. The bubble formation is controlled by changing the width of the channel by an atomic distance (∼0.1 nm). Therefore, the motor is potentially more efficient than systems controlled by other forces, in which a much larger change in the motor position is necessary. We have simulated the bubble-powered motor using dissipative particle dynamics and found behavior in good agreement with that of motor proteins. Energy efficiency is as high as 60%.

Development of a dose-controlled multiculture cell exposure chamber for efficient delivery of airborne and engineered nanoparticles

NASA Astrophysics Data System (ADS)

Asimakopoulou, Akrivi; Daskalos, Emmanouil; Lewinski, Nastassja; Riediker, Michael; Papaioannou, Eleni; Konstandopoulos, Athanasios G.

2013-04-01

In order to study the various health influencing parameters related to engineered nanoparticles as well as to soot emitted by Diesel engines, there is an urgent need for appropriate sampling devices and methods for cell exposure studies that simulate the respiratory system and facilitate associated biological and toxicological tests. The objective of the present work was the further advancement of a Multiculture Exposure Chamber (MEC) into a dose-controlled system for efficient delivery of nanoparticles to cells. It was validated with various types of nanoparticles (Diesel engine soot aggregates, engineered nanoparticles for various applications) and with state-of-the-art nanoparticle measurement instrumentation to assess the local deposition of nanoparticles on the cell cultures. The dose of nanoparticles to which cell cultures are being exposed was evaluated in the normal operation of the in vitro cell culture exposure chamber based on measurements of the size specific nanoparticle collection efficiency of a cell free device. The average efficiency in delivering nanoparticles in the MEC was approximately 82%. The nanoparticle deposition was demonstrated by Transmission Electron Microscopy (TEM). Analysis and design of the MEC employs Computational Fluid Dynamics (CFD) and true to geometry representations of nanoparticles with the aim to assess the uniformity of nanoparticle deposition among the culture wells. Final testing of the dose-controlled cell exposure system was performed by exposing A549 lung cell cultures to fluorescently labeled nanoparticles. Delivery of aerosolized nanoparticles was demonstrated by visualization of the nanoparticle fluorescence in the cell cultures following exposure. Also monitored was the potential of the aerosolized nanoparticles to generate reactive oxygen species (ROS) (e.g. free radicals and peroxides generation), thus expressing the oxidative stress of the cells which can cause extensive cellular damage or damage on DNA.

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

USDA-ARS?s Scientific Manuscript database

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

Fabrication of elastomeric silk fibers.

PubMed

Bradner, Sarah A; Partlow, Benjamin P; Cebe, Peggy; Omenetto, Fiorenzo G; Kaplan, David L

2017-09-01

Methods to generate fibers from hydrogels, with control over mechanical properties, fiber diameter, and crystallinity, while retaining cytocompatibility and degradability, would expand options for biomaterials. Here, we exploited features of silk fibroin protein for the formation of tunable silk hydrogel fibers. The biological, chemical, and morphological features inherent to silk were combined with elastomeric properties gained through enzymatic crosslinking of the protein. Postprocessing via methanol and autoclaving provided tunable control of fiber features. Mechanical, optical, and chemical analyses demonstrated control of fiber properties by exploiting the physical cross-links, and generating double network hydrogels consisting of chemical and physical cross-links. Structure and chemical analyses revealed crystallinity from 30 to 50%, modulus from 0.5 to 4 MPa, and ultimate strength 1-5 MPa depending on the processing method. Fabrication and postprocessing combined provided fibers with extensibility from 100 to 400% ultimate strain. Fibers strained to 100% exhibited fourth order birefringence, revealing macroscopic orientation driven by chain mobility. The physical cross-links were influenced in part by the drying rate of fabricated materials, where bound water, packing density, and microstructural homogeneity influenced cross-linking efficiency. The ability to generate robust and versatile hydrogel microfibers is desirable for bottom-up assembly of biological tissues and for broader biomaterial applications. © 2017 Wiley Periodicals, Inc.

The 'Biologically-Inspired Computing' Column

NASA Technical Reports Server (NTRS)

Hinchey, Mike

2006-01-01

The field of Biology changed dramatically in 1953, with the determination by Francis Crick and James Dewey Watson of the double helix structure of DNA. This discovery changed Biology for ever, allowing the sequencing of the human genome, and the emergence of a "new Biology" focused on DNA, genes, proteins, data, and search. Computational Biology and Bioinformatics heavily rely on computing to facilitate research into life and development. Simultaneously, an understanding of the biology of living organisms indicates a parallel with computing systems: molecules in living cells interact, grow, and transform according to the "program" dictated by DNA. Moreover, paradigms of Computing are emerging based on modelling and developing computer-based systems exploiting ideas that are observed in nature. This includes building into computer systems self-management and self-governance mechanisms that are inspired by the human body's autonomic nervous system, modelling evolutionary systems analogous to colonies of ants or other insects, and developing highly-efficient and highly-complex distributed systems from large numbers of (often quite simple) largely homogeneous components to reflect the behaviour of flocks of birds, swarms of bees, herds of animals, or schools of fish. This new field of "Biologically-Inspired Computing", often known in other incarnations by other names, such as: Autonomic Computing, Pervasive Computing, Organic Computing, Biomimetics, and Artificial Life, amongst others, is poised at the intersection of Computer Science, Engineering, Mathematics, and the Life Sciences. Successes have been reported in the fields of drug discovery, data communications, computer animation, control and command, exploration systems for space, undersea, and harsh environments, to name but a few, and augur much promise for future progress.

Protein Delivery into Plant Cells: Toward In vivo Structural Biology

PubMed Central

Cedeño, Cesyen; Pauwels, Kris; Tompa, Peter

2017-01-01

Understanding the biologically relevant structural and functional behavior of proteins inside living plant cells is only possible through the combination of structural biology and cell biology. The state-of-the-art structural biology techniques are typically applied to molecules that are isolated from their native context. Although most experimental conditions can be easily controlled while dealing with an isolated, purified protein, a serious shortcoming of such in vitro work is that we cannot mimic the extremely complex intracellular environment in which the protein exists and functions. Therefore, it is highly desirable to investigate proteins in their natural habitat, i.e., within live cells. This is the major ambition of in-cell NMR, which aims to approach structure-function relationship under true in vivo conditions following delivery of labeled proteins into cells under physiological conditions. With a multidisciplinary approach that includes recombinant protein production, confocal fluorescence microscopy, nuclear magnetic resonance (NMR) spectroscopy and different intracellular protein delivery strategies, we explore the possibility to develop in-cell NMR studies in living plant cells. While we provide a comprehensive framework to set-up in-cell NMR, we identified the efficient intracellular introduction of isotope-labeled proteins as the major bottleneck. Based on experiments with the paradigmatic intrinsically disordered proteins (IDPs) Early Response to Dehydration protein 10 and 14, we also established the subcellular localization of ERD14 under abiotic stress. PMID:28469623

Fluorescence turn-on detection of alkaline phosphatase activity based on controlled release of PEI-capped Cu nanoclusters from MnO2 nanosheets.

PubMed

Zhang, Yunyi; Li, Yongxin; Zhang, Cuiyun; Zhang, Qingfeng; Huang, Xinan; Yang, Meiding; Shahzad, Sohail Anjum; Lo, Kenneth Kam-Wing; Yu, Cong; Jiang, Shichun

2017-08-01

A fluorescence turn-on assay for alkaline phosphatase (ALP) activity is developed through the controlled release of polyethyleneimine-capped copper nanoclusters (PEI-capped CuNCs) from the MnO 2 nanosheets. In an aqueous solution, the positively charged PEI-capped CuNCs could be adsorbed onto the surface of the negatively charged MnO 2 nanosheets. Such adsorption through favorable electrostatic interactions could efficiently quench the nanocluster fluorescence emission via resonance energy transfer from the PEI-capped CuNCs to the MnO 2 nanosheets. 2-Phospho-L-ascorbic acid (AAP) could be hydrolyzed to L-ascorbic acid (AA) in the presence of ALP. AA could reduce MnO 2 into Mn 2+ and trigger the disintegration of the MnO 2 nanosheets. As a result, the CuNCs were released and the quenched fluorescence was recovered efficiently. The detection strategy is simple, inexpensive, sensitive, selective, with low toxicity, and has better biocompatibility. The newly fabricated biosensor for ALP activity will potentially make it a robust candidate for numerous biological and biomedical applications.

New approaches to design HIV-1 T-cell vaccines.

PubMed

Perrin, Hélène; Canderan, Glenda; Sékaly, Rafick-Pierre; Trautmann, Lydie

2010-09-01

Following the evidence that T-cell responses are crucial in the control of HIV-1 infection, vaccines targeting T-cell responses were tested in recent clinical trials. However, these vaccines showed a lack of efficacy. This review attempts to define the qualitative and quantitative features that are desirable for T-cell-induced responses by vaccines. We also describe strategies that could lead to achievement of this goal. Using the yellow fever vaccine as a benchmark of an efficient vaccine, recent studies identified factors of immune protection and more importantly innate immune pathways needed for the establishment of long-term protective adaptive immunity. To prevent or control HIV-1 infection, a vaccine must induce efficient and persistent antigen-specific T cells endowed with mucosal homing capacity. Such cells should have the capability to counteract HIV-1 diversity and its rapid spread from the initial site of infection. To achieve this goal, the activation of a diversified innate immune response is critical. New systems biology approaches will provide more precise correlates of immune protection that will pave the way for new approaches in T-cell-based vaccines.

Biological Potential of Bioorganic Fertilizer Fortified with Bacterial Antagonist for the Control of Tomato Bacterial Wilt and the Promotion of Crop Yields.

PubMed

Wu, Kai; Fang, Zhiying; Wang, Lili; Yuan, Saifei; Guo, Rong; Shen, Biao; Shen, Qirong

2016-10-28

The application of Bacillus sp. in the biological control of plant soilborne diseases has been shown to be an environmentally friendly alternative to the use of chemical fungicides. In this study, the effects of bioorganic fertilizer (BOF) fortified with Bacillus amyloliquefaciens SQY 162 on the suppression of tomato bacterial wilt were investigated in pot experiments. The disease incidence of tomato wilt after the application of BOF was 65.18% and 41.62% lower at 10 and 20 days after transplantation, respectively, than in the control condition. BOF also promoted the plant growth. The SQY 162 populations efficiently colonized the tomato rhizosphere, which directly suppressed the number of Ralstonia solanacearum in the tomato rhizosphere soil. In the presence of BOF, the activities of defense-related enzymes in tomato were lower than in the presence of the control treatment, but the expression levels of the defense-related genes of the plants in the salicylic acid and jasmonic acid pathways were enhanced. It was also found that strain SQY 162 could secrete antibiotic surfactin, but not volatile organic compounds, to suppress Ralstonia . The strain could also produce plant growth promotion compounds such as siderophores and indole-3-acetic acid. Thus, owing to its innate multiple-functional traits and its broad biocontrol activities, we found that this antagonistic strain isolated from the tobacco rhizosphere could establish itself successfully in the tomato rhizosphere to control soilborne diseases.

Nanoparticles that Communicate In Vivo to Amplify Tumour Targeting

PubMed Central

von Maltzahn, Geoffrey; Park, Ji-Ho; Lin, Kevin Y.; Singh, Neetu; Schwöppe, Christian; Mesters, Rolf; Berdel, Wolfgang E.; Ruoslahti, Erkki; Sailor, Michael J.; Bhatia, Sangeeta N.

2012-01-01

Nanomedicines have enormous potential to improve the precision of cancer therapy, yet our ability to efficiently home these materials to regions of disease in vivo remains very limited. Inspired by the ability for communication to improve targeting in biological systems, such inflammatory cell recruitment to sites of disease, we construct systems where synthetic biological and nanotechnological components communicate to amplify disease targeting in vivo. These systems are composed of ‘Signalling’ modules (nanoparticles or engineered proteins) that target tumours and then locally active the coagulation cascade to broadcast tumour location to clot-targeted ‘Receiving’ nanoparticles in circulation that carry a diagnostic or therapeutic cargo, thereby amplifying their delivery. We show that communicating nanoparticle systems can be composed from multiple types of Signalling and Receiving modules, can transmit information via multiple molecular pathways in coagulation, can operate autonomously, and can target over 40-fold higher doses of chemotherapeutics to tumours than non-communicating controls. PMID:21685903

Recent Advances in Marine Algae Polysaccharides: Isolation, Structure, and Activities.

PubMed

Xu, Shu-Ying; Huang, Xuesong; Cheong, Kit-Leong

2017-12-13

Marine algae have attracted a great deal of interest as excellent sources of nutrients. Polysaccharides are the main components in marine algae, hence a great deal of attention has been directed at isolation and characterization of marine algae polysaccharides because of their numerous health benefits. In this review, extraction and purification approaches and chemico-physical properties of marine algae polysaccharides (MAPs) are summarized. The biological activities, which include immunomodulatory, antitumor, antiviral, antioxidant, and hypolipidemic, are also discussed. Additionally, structure-function relationships are analyzed and summarized. MAPs' biological activities are closely correlated with their monosaccharide composition, molecular weights, linkage types, and chain conformation. In order to promote further exploitation and utilization of polysaccharides from marine algae for functional food and pharmaceutical areas, high efficiency, and low-cost polysaccharide extraction and purification methods, quality control, structure-function activity relationships, and specific mechanisms of MAPs activation need to be extensively investigated.

Biology of the BKPyV: An Update.

PubMed

Helle, Francois; Brochot, Etienne; Handala, Lynda; Martin, Elodie; Castelain, Sandrine; Francois, Catherine; Duverlie, Gilles

2017-11-03

The BK virus (BKPyV) is a member of the Polyomaviridae family first isolated in 1971. BKPyV causes frequent infections during childhood and establishes persistent infections with minimal clinical implications within renal tubular cells and the urothelium. However, reactivation of BKPyV in immunocompromised individuals may cause serious complications. In particular, with the implementation of more potent immunosuppressive drugs in the last decade, BKPyV has become an emerging pathogen in kidney and bone marrow transplant recipients where it often causes associated nephropathy and haemorrhagic cystitis, respectively. Unfortunately, no specific antiviral against BKPyV has been approved yet and the only therapeutic option is a modulation of the immunosuppressive drug regimen to improve immune control though it may increase the risk of rejection. A better understanding of the BKPyV life cycle is thus needed to develop efficient treatment against this virus. In this review, we provide an update on recent advances in understanding the biology of BKPyV.

Model-based design of experiments for cellular processes.

PubMed

Chakrabarty, Ankush; Buzzard, Gregery T; Rundell, Ann E

2013-01-01

Model-based design of experiments (MBDOE) assists in the planning of highly effective and efficient experiments. Although the foundations of this field are well-established, the application of these techniques to understand cellular processes is a fertile and rapidly advancing area as the community seeks to understand ever more complex cellular processes and systems. This review discusses the MBDOE paradigm along with applications and challenges within the context of cellular processes and systems. It also provides a brief tutorial on Fisher information matrix (FIM)-based and Bayesian experiment design methods along with an overview of existing software packages and computational advances that support MBDOE application and adoption within the Systems Biology community. As cell-based products and biologics progress into the commercial sector, it is anticipated that MBDOE will become an essential practice for design, quality control, and production. Copyright © 2013 Wiley Periodicals, Inc.

New Method for Producing Significant Amounts of RNA Labeled at Specific Sites | Center for Cancer Research

Cancer.gov

Among biomacromolecules, RNA is the most versatile, and it plays indispensable roles in almost all aspects of biology. For example, in addition to serving as mRNAs coding for proteins, RNAs regulate gene expression, such as controlling where, when, and how efficiently a gene gets expressed, participate in RNA processing, encode the genetic information of some viruses, serve as scaffolds, and even possess enzymatic activity. To study these RNAs and their biological functions and to make use of those RNA activities for biomedical applications, researchers first need to make various types of RNA. For structural biologists incorporating modified or labeled nucleotides at specific sites in RNA molecules of interest is critical to gain structural insight into RNA functions. However, placing labeled or modified residue(s) in desired positions in a large RNA has not been possible until now.

Application of biomaterials to advance induced pluripotent stem cell research and therapy

PubMed Central

Tong, Zhixiang; Solanki, Aniruddh; Hamilos, Allison; Levy, Oren; Wen, Kendall; Yin, Xiaolei; Karp, Jeffrey M

2015-01-01

Derived from any somatic cell type and possessing unlimited self-renewal and differentiation potential, induced pluripotent stem cells (iPSCs) are poised to revolutionize stem cell biology and regenerative medicine research, bringing unprecedented opportunities for treating debilitating human diseases. To overcome the limitations associated with safety, efficiency, and scalability of traditional iPSC derivation, expansion, and differentiation protocols, biomaterials have recently been considered. Beyond addressing these limitations, the integration of biomaterials with existing iPSC culture platforms could offer additional opportunities to better probe the biology and control the behavior of iPSCs or their progeny in vitro and in vivo. Herein, we discuss the impact of biomaterials on the iPSC field, from derivation to tissue regeneration and modeling. Although still exploratory, we envision the emerging combination of biomaterials and iPSCs will be critical in the successful application of iPSCs and their progeny for research and clinical translation. PMID:25766254

Ferromagnetic resonance for the quantification of superparamagnetic iron oxide nanoparticles in biological materials

PubMed Central

Gamarra, Lionel F; daCosta-Filho, Antonio J; Mamani, Javier B; de Cassia Ruiz, Rita; Pavon, Lorena F; Sibov, Tatiana T; Vieira, Ernanni D; Silva, André C; Pontuschka, Walter M; Amaro, Edson

2010-01-01

The aim of the present work is the presentation of a quantification methodology for the control of the amount of superparamagnetic iron oxide nanoparticles (SPIONs) administered in biological materials by means of the ferromagnetic resonance technique (FMR) applied to studies both in vivo and in vitro. The in vivo study consisted in the analysis of the elimination and biodistribution kinetics of SPIONs after intravenous administration in Wistar rats. The results were corroborated by X-ray fluorescence. For the in vitro study, a quantitative analysis of the concentration of SPIONs bound to the specific AC133 monoclonal antibodies was carried out in order to detect the expression of the antigenic epitopes (CD133) in stem cells from human umbilical cord blood. In both studies FMR has proven to be an efficient technique for the SPIONs quantification per volume unit (in vivo) or per labeled cell (in vitro). PMID:20463936

Biosafety and biosecurity measures: management of biosafety level 3 facilities.

PubMed

Zaki, Adel N

2010-11-01

With the increasing biological threat from emerging infectious diseases and bioterrorism, it has become essential for governments around the globe to increase awareness and preparedness for identifying and containing those agents. This article introduces the basic concepts of laboratory management, laboratory biosafety and laboratory biosecurity. Assessment criteria for laboratories' biorisk should include both biosafety and biosecurity measures. The assessment requires setting specific goals and selecting management approaches. In order to implement technologies at the laboratory working level, a management team should be created whose role is to implement biorisk policies, rules and regulations appropriate for that facility. Rules and regulations required by government authorities are presented, with special emphasis on methods for air control, and liquid and solid waste management. Management and biorisk measures and appropriate physical facilities must keep pace, ensuring efficient facilities that protect workers, the environment, the product (research, diagnostic and/or vaccine) and the biological pathogen. Published by Elsevier B.V.

Synthetic Biology Platform for Sensing and Integrating Endogenous Transcriptional Inputs in Mammalian Cells.

PubMed

Angelici, Bartolomeo; Mailand, Erik; Haefliger, Benjamin; Benenson, Yaakov

2016-08-30

One of the goals of synthetic biology is to develop programmable artificial gene networks that can transduce multiple endogenous molecular cues to precisely control cell behavior. Realizing this vision requires interfacing natural molecular inputs with synthetic components that generate functional molecular outputs. Interfacing synthetic circuits with endogenous mammalian transcription factors has been particularly difficult. Here, we describe a systematic approach that enables integration and transduction of multiple mammalian transcription factor inputs by a synthetic network. The approach is facilitated by a proportional amplifier sensor based on synergistic positive autoregulation. The circuits efficiently transduce endogenous transcription factor levels into RNAi, transcriptional transactivation, and site-specific recombination. They also enable AND logic between pairs of arbitrary transcription factors. The results establish a framework for developing synthetic gene networks that interface with cellular processes through transcriptional regulators. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Direct contribution of the seagrass Thalassia testudinum to lime mud production.

PubMed

Enríquez, Susana; Schubert, Nadine

2014-05-22

Seagrass beds contribute to oceanic carbonate lime mud production by providing a habitat for a wide variety of calcifying organisms and acting as efficient sediment traps. Here we provide evidence for the direct implication of Thalassia testudinum in the precipitation of aragonite needles. The crystals are located internally in the cell walls, and as external deposits on the blade, and are similar in size and shape to the aragonite needles reported for modern tropical carbonate factories. Seagrass calcification is a biological, light-enhanced process controlled by the leaf, and estimates of seagrass annual carbonate production in a Caribbean reef lagoon are as significant as values reported for Halimeda incrassata. Thus, we conclude that seagrass calcification is another biological source for the aragonite lime mud deposits found in tropical banks, and that tropical seagrass habitats may play a more important role in the oceanic carbon cycle than previously considered.

Direct contribution of the seagrass Thalassia testudinum to lime mud production

NASA Astrophysics Data System (ADS)

Enríquez, Susana; Schubert, Nadine

2014-05-01

Seagrass beds contribute to oceanic carbonate lime mud production by providing a habitat for a wide variety of calcifying organisms and acting as efficient sediment traps. Here we provide evidence for the direct implication of Thalassia testudinum in the precipitation of aragonite needles. The crystals are located internally in the cell walls, and as external deposits on the blade, and are similar in size and shape to the aragonite needles reported for modern tropical carbonate factories. Seagrass calcification is a biological, light-enhanced process controlled by the leaf, and estimates of seagrass annual carbonate production in a Caribbean reef lagoon are as significant as values reported for Halimeda incrassata. Thus, we conclude that seagrass calcification is another biological source for the aragonite lime mud deposits found in tropical banks, and that tropical seagrass habitats may play a more important role in the oceanic carbon cycle than previously considered.

Direct contribution of the seagrass Thalassia testudinum to lime mud production

PubMed Central

Enríquez, Susana; Schubert, Nadine

2014-01-01

Seagrass beds contribute to oceanic carbonate lime mud production by providing a habitat for a wide variety of calcifying organisms and acting as efficient sediment traps. Here we provide evidence for the direct implication of Thalassia testudinum in the precipitation of aragonite needles. The crystals are located internally in the cell walls, and as external deposits on the blade, and are similar in size and shape to the aragonite needles reported for modern tropical carbonate factories. Seagrass calcification is a biological, light-enhanced process controlled by the leaf, and estimates of seagrass annual carbonate production in a Caribbean reef lagoon are as significant as values reported for Halimeda incrassata. Thus, we conclude that seagrass calcification is another biological source for the aragonite lime mud deposits found in tropical banks, and that tropical seagrass habitats may play a more important role in the oceanic carbon cycle than previously considered. PMID:24848374

Germline Modification and Engineering in Avian Species

PubMed Central

Lee, Hong Jo; Lee, Hyung Chul; Han, Jae Yong

2015-01-01

Production of genome-edited animals using germline-competent cells and genetic modification tools has provided opportunities for investigation of biological mechanisms in various organisms. The recently reported programmed genome editing technology that can induce gene modification at a target locus in an efficient and precise manner facilitates establishment of animal models. In this regard, the demand for genome-edited avian species, which are some of the most suitable model animals due to their unique embryonic development, has also increased. Furthermore, germline chimera production through long-term culture of chicken primordial germ cells (PGCs) has facilitated research on production of genome-edited chickens. Thus, use of avian germline modification is promising for development of novel avian models for research of disease control and various biological mechanisms. Here, we discuss recent progress in genome modification technology in avian species and its applications and future strategies. PMID:26333275

Nanoparticles that communicate in vivo to amplify tumour targeting

NASA Astrophysics Data System (ADS)

von Maltzahn, Geoffrey; Park, Ji-Ho; Lin, Kevin Y.; Singh, Neetu; Schwöppe, Christian; Mesters, Rolf; Berdel, Wolfgang E.; Ruoslahti, Erkki; Sailor, Michael J.; Bhatia, Sangeeta N.

2011-07-01

Nanomedicines have enormous potential to improve the precision of cancer therapy, yet our ability to efficiently home these materials to regions of disease in vivo remains very limited. Inspired by the ability of communication to improve targeting in biological systems, such as inflammatory-cell recruitment to sites of disease, we construct systems where synthetic biological and nanotechnological components communicate to amplify disease targeting in vivo. These systems are composed of ‘signalling’ modules (nanoparticles or engineered proteins) that target tumours and then locally activate the coagulation cascade to broadcast tumour location to clot-targeted ‘receiving’ nanoparticles in circulation that carry a diagnostic or therapeutic cargo, thereby amplifying their delivery. We show that communicating nanoparticle systems can be composed of multiple types of signalling and receiving modules, can transmit information through multiple molecular pathways in coagulation, can operate autonomously and can target over 40 times higher doses of chemotherapeutics to tumours than non-communicating controls.

Gold-Based Magneto/Optical Nanostructures: Challenges for In Vivo Applications in Cancer Diagnostics and Therapy.

PubMed

Melancon, Marites; Lu, Wei; Li, Chun

2009-06-01

Nanoparticles with gold shell and iron core have unique optical and magnetic properties which can be utilized for simultaneous detection and treatment strategies. Several nanoparticles have been synthesized and shown to mediate a variety of potential applications in biomedicine, including cancer molecular optical and magnetic resonance imaging, controlled drug delivery, and photothermal ablation therapy. However, to be effective, these nanoparticles must be delivered efficiently into their targets. In this review, we will provide an updated summary of the gold-shelled magnetic nanoparticles that have been synthesized, methods for characterization, and their potential for cancer diagnosis and treatment. We will also discuss the biological barriers that need to be overcome for the effective delivery of these nanoparticles. The desired nanoparticle characteristics needed to evade these biological barriers were also explained. Hopefully, this review will help researchers in designing nanoparticles by carefully choosing the optimum size, shape, surface charge, and surface coating.

40 CFR 63.683 - Standards: General.

Code of Federal Regulations, 2011 CFR

2011-07-01

... HAP biodegradation efficiency (Rbio) for the biological treatment process is equal to or greater than 95 percent. The HAP biodegradation efficiency (Rbio) shall be determined in accordance with the...

40 CFR 63.683 - Standards: General.

Code of Federal Regulations, 2014 CFR

2014-07-01

... HAP biodegradation efficiency (Rbio) for the biological treatment process is equal to or greater than 95 percent. The HAP biodegradation efficiency (Rbio) shall be determined in accordance with the...

40 CFR 63.683 - Standards: General.

Code of Federal Regulations, 2012 CFR

2012-07-01

... HAP biodegradation efficiency (Rbio) for the biological treatment process is equal to or greater than 95 percent. The HAP biodegradation efficiency (Rbio) shall be determined in accordance with the...

40 CFR 63.683 - Standards: General.

Code of Federal Regulations, 2013 CFR

2013-07-01

... HAP biodegradation efficiency (Rbio) for the biological treatment process is equal to or greater than 95 percent. The HAP biodegradation efficiency (Rbio) shall be determined in accordance with the...

40 CFR 63.683 - Standards: General.

Code of Federal Regulations, 2010 CFR

2010-07-01

... HAP biodegradation efficiency (Rbio) for the biological treatment process is equal to or greater than 95 percent. The HAP biodegradation efficiency (Rbio) shall be determined in accordance with the...

Non-target effects of an introduced biological control agent on deer mouse ecology

Treesearch

Dean E. Pearson; Kevin S. McKelvey; Leonard F. Ruggiero

2000-01-01

Release of exotic insects as biological control agents is a common approach to controlling exotic plants. Though controversy has ensued regarding the deleterious direct effects of biological control agents to non-target species, few have examined the indirect effects of a "well-behaved" biological control agent on native fauna. We studied a grassland in west-...

Bt maize and integrated pest management--a European perspective.

PubMed

Meissle, Michael; Romeis, Jörg; Bigler, Franz

2011-09-01

The European corn borer (Ostrinia nubilalis), the Mediterranean corn borer (Sesamia nonagrioides) and the western corn rootworm (Diabrotica virgifera virgifera) are the main arthropod pests in European maize production. Practised pest control includes chemical control, biological control and cultural control such as ploughing and crop rotation. A pest control option that is available since 1996 is maize varieties that are genetically engineered (GE) to produce insecticidal compounds. GE maize varieties available today express one or several genes from Bacillus thuringiensis (Bt) that target corn borers or corn rootworms. Incentives to growing Bt maize are simplified farm operations, high pest control efficiency, improved grain quality and ecological benefits. Limitations include the risk of resistance evolution in target pest populations, risk of secondary pest outbreaks and increased administration to comply with licence agreements. Growers willing to plant Bt maize in the European Union (EU) often face the problem that authorisation is denied. Only one Bt maize transformation event (MON810) is currently authorised for commercial cultivation, and some national authorities have banned cultivation. Spain is the only EU member state where Bt maize adoption levels are currently delivering farm income gains near full potential levels. In an integrated pest management (IPM) context, Bt maize can be regarded as a preventive (host plant resistance) or a responsive pest control measure. In any case, Bt maize is a highly specific tool that efficiently controls the main pests and allows combination with other preventive or responsive measures to solve other agricultural problems including those with secondary pests. Copyright © 2011 Society of Chemical Industry.

Fenton-like reaction: a possible way to efficiently remove illicit drugs and pharmaceuticals from wastewater.

PubMed

Mackuľak, Tomáš; Mosný, Michal; Grabic, Roman; Golovko, Oksana; Koba, Olga; Birošová, Lucia

2015-03-01

We analyzed 13 psychoactive pharmaceuticals, illicit drugs and their metabolites in wastewater treatment plant influent and effluent and the possibility of their degradation by biological and chemical processes. Tramadol (413-853 ng/L) and methamphetamine (460-682 ng/L) were the most concentrated compounds in the wastewater in winter and summer, respectively. A significant decrease in the concentration of tramadol in wastewater was measured during the summer. The lowest efficiency was observed for tramadol, venlafaxine, citalopram and oxazepam (∼ 10%) and the highest efficiency was observed for amphetamine and THC-COOH (∼ 80%). The efficiency of compound degradation via the Fenton reaction, a modified Fenton reaction and different degradation (by algae, wood-rotting fungi and enzymes at influent versus effluent) was determined. The Fenton reaction and its modification were efficient at eliminating these substances in comparison with the tested biological processes. Copyright © 2015 Elsevier B.V. All rights reserved.

Microbiological evaluation of the mobile biological isolator system

NASA Technical Reports Server (NTRS)

Taylor, D. M.; Morelli, F.; Neiderheiser, W.; Tratz, W. M.

1979-01-01

Evaluations on critical components of the mobile biological isolation system were performed. High efficiency particulate air filter efficiency and suit integrity were found to withstand repeated ethylene oxide (ETO) sterilizations. The minimum ETO sterilization time required to inactivate all contaminant organisms was established at four hours. Two days of aerating at 120 F was found to dissipate all harmful ETO residuals from the suit. Donning and doffing procedures were clarified and written specifically for isolation rooms.

Morphological constraints on changing avian migration phenology.

PubMed

Møller, A P; Rubolini, D; Saino, N

2017-06-01

Many organisms at northern latitudes have responded to climate warming by advancing their spring phenology. Birds are known to show earlier timing of spring migration and reproduction in response to warmer springs. However, species show heterogeneous phenological responses to climate warming, with those that have not advanced or have delayed migration phenology experiencing population declines. Although some traits (such as migration distance) partly explain heterogeneity in phenological responses, the factors affecting interspecies differences in the responsiveness to climate warming have yet to be fully explored. In this comparative study, we investigate whether variation in wing aspect ratio (reflecting relative wing narrowness), an ecomorphological trait that is strongly associated with flight efficiency and migratory behaviour, affects the ability to advance timing of spring migration during 1960-2006 in a set of 80 European migratory bird species. Species with larger aspect ratio (longer and narrower wings) showed smaller advancement of timing of spring migration compared to species with smaller aspect ratio (shorter and wider wings) while controlling for phylogeny, migration distance and other life-history traits. In turn, migration distance positively predicted aspect ratio across species. Hence, species that are better adapted to migration appear to be more constrained in responding phenologically to rapid climate warming by advancing timing of spring migration. Our findings corroborate the idea that aspect ratio is a major evolutionary correlate of migration, and suggest that selection for energetically efficient flights, as reflected by high aspect ratio, may hinder phenotypically plastic/microevolutionary adjustments of migration phenology to ongoing climatic changes. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Climate matching: implications for the biological control of hemlock woolly adelgid

Treesearch

R. Talbot III Trotter

2008-01-01

Classical biological control programs are faced with a daunting challenge: inserting a new species into an existing ecological system. In order for the newly introduced biological control species to survive and reproduce, the recipient ecosystem must provide the required biotic and abiotic requirements. The Adelgid Biological Control simulator (ABCs), a simulation...

40 CFR 152.20 - Exemptions for pesticides adequately regulated by another Federal agency.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Federal agency. (a) Certain biological control agents. (1) Except as provided by paragraphs (a)(3) and (a)(4) of this section, all biological control agents are exempt from FIFRA requirements. (2) If the Agency determines that an individual biological control agent or class of biological control agents is no...

40 CFR 152.20 - Exemptions for pesticides adequately regulated by another Federal agency.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Federal agency. (a) Certain biological control agents. (1) Except as provided by paragraphs (a)(3) and (a)(4) of this section, all biological control agents are exempt from FIFRA requirements. (2) If the Agency determines that an individual biological control agent or class of biological control agents is no...

Biological control agents elevate hantavirus by subsidizing deer mouse populations

Treesearch

Dean E. Pearson; Ragan M. Callaway

2006-01-01

Biological control of exotic invasive plants using exotic insects is practiced under the assumption that biological control agents are safe if they do not directly attack non-target species. We tested this assumption by evaluating the potential for two host-specific biological control agents (Urophora spp.), widely established in North America for spotted...

Purification of complex samples: Implementation of a modular and reconfigurable droplet-based microfluidic platform with cascaded deterministic lateral displacement separation modules

PubMed Central

Pudda, Catherine; Boizot, François; Verplanck, Nicolas; Revol-Cavalier, Frédéric; Berthier, Jean; Thuaire, Aurélie

2018-01-01

Particle separation in microfluidic devices is a common problematic for sample preparation in biology. Deterministic lateral displacement (DLD) is efficiently implemented as a size-based fractionation technique to separate two populations of particles around a specific size. However, real biological samples contain components of many different sizes and a single DLD separation step is not sufficient to purify these complex samples. When connecting several DLD modules in series, pressure balancing at the DLD outlets of each step becomes critical to ensure an optimal separation efficiency. A generic microfluidic platform is presented in this paper to optimize pressure balancing, when DLD separation is connected either to another DLD module or to a different microfluidic function. This is made possible by generating droplets at T-junctions connected to the DLD outlets. Droplets act as pressure controllers, which perform at the same time the encapsulation of DLD sorted particles and the balance of output pressures. The optimized pressures to apply on DLD modules and on T-junctions are determined by a general model that ensures the equilibrium of the entire platform. The proposed separation platform is completely modular and reconfigurable since the same predictive model applies to any cascaded DLD modules of the droplet-based cartridge. PMID:29768490

Darbishire expands his vision of heredity from Mendelian genetics to inherited memory.

PubMed

Wood, Roger J

2015-10-01

The British biologist A.D. Darbishire (1879-1915) responded to the rediscovery in 1900 of Mendel's theory of heredity by testing it experimentally, first in Oxford, then in Manchester and London. He summarised his conclusions in a textbook 'Breeding and the Mendelian Discovery' (1911), in which he questioned whether Mendelism alone could explain all aspects of practical breeding experience. Already he had begun to think about an alternative theory to give greater emphasis to the widely held conviction among breeders regarding the inheritance of characteristics acquired during an individual's life. Redefining heredity in terms of a germ-plasm based biological memory, he used vocabulary drawn partly from sources outside conventional science, including the metaphysical/vitalistic writings of Samuel Butler and Henri Bergson. An evolving hereditary memory fitted well with the conception of breeding as a creative art aimed at greater economic efficiency. For evolution beyond human control he proposed a self-modifying process, claiming it to surpass in efficiency the chancy mechanism of natural selection proposed by Darwin. From his writings, including early chapters of an unfinished book entitled 'An Introduction to a Biology', we consider how he reached these concepts and how they relate to later advances in understanding the genome and the genetic programme. Copyright © 2015 Elsevier Ltd. All rights reserved.

Total petroleum hydrocarbon degradation by hybrid electrobiochemical reactor in oilfield produced water.

PubMed

Mousa, Ibrahim E

2016-08-15

The crude oil drilling and extraction operations are aimed to maximize the production may be counterbalanced by the huge production of contaminated produced water (PW). PW is conventionally treated through different physical, chemical, and biological technologies. The efficiency of suggested hybrid electrobiochemical (EBC) methods for the simultaneous removal of total petroleum hydrocarbon (TPH) and sulfate from PW generated by petroleum industry is studied. Also, the factors that affect the stability of PW quality are investigated. The results indicated that the effect of biological treatment is very important to keep control of the electrochemical by-products and more TPH removal in the EBC system. The maximum TPH and sulfate removal efficiency was achieved 75% and 25.3%, respectively when the detention time was about 5.1min and the energy consumption was 32.6mA/cm(2). However, a slight increasing in total bacterial count was observed when the EBC compact unit worked at a flow rate of average 20L/h. Pseudo steady state was achieved after 30min of current application in the solution. Also, the results of the study indicate that when the current intensity was increased above optimum level, no significant results occurred due to the release of gases. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular epidemiology biomarkers-Sample collection and processing considerations

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

Holland, Nina T.; Pfleger, Laura; Berger, Eileen

2005-08-07

Biomarker studies require processing and storage of numerous biological samples with the goals of obtaining a large amount of information and minimizing future research costs. An efficient study design includes provisions for processing of the original samples, such as cryopreservation, DNA isolation, and preparation of specimens for exposure assessment. Use of standard, two-dimensional and nanobarcodes and customized electronic databases assure efficient management of large sample collections and tracking results of data analyses. Standard operating procedures and quality control plans help to protect sample quality and to assure validity of the biomarker data. Specific state, federal and international regulations are inmore » place regarding research with human samples, governing areas including custody, safety of handling, and transport of human samples. Appropriate informed consent must be obtained from the study subjects prior to sample collection and confidentiality of results maintained. Finally, examples of three biorepositories of different scale (European Cancer Study, National Cancer Institute and School of Public Health Biorepository, University of California, Berkeley) are used to illustrate challenges faced by investigators and the ways to overcome them. New software and biorepository technologies are being developed by many companies that will help to bring biological banking to a new level required by molecular epidemiology of the 21st century.« less

Curcumin Conjugated with PLGA Potentiates Sustainability, Anti-Proliferative Activity and Apoptosis in Human Colon Carcinoma Cells

PubMed Central

Waghela, Bhargav N.; Sharma, Anupama; Dhumale, Suhashini; Pandey, Shashibahl M.; Pathak, Chandramani

2015-01-01

Curcumin, an ingredient of turmeric, exhibits a variety of biological activities such as anti-inflammatory, anti-atherosclerotic, anti-proliferative, anti-oxidant, anti-cancer and anti-metastatic. It is a highly pleiotropic molecule that inhibits cell proliferation and induces apoptosis in cancer cells. Despite its imperative biological activities, chemical instability, photo-instability and poor bioavailability limits its utilization as an effective therapeutic agent. Therefore, enhancing the bioavailability of curcumin may improve its therapeutic index for clinical setting. In the present study, we have conjugated curcumin with a biodegradable polymer Poly (D, L-lactic-co-glycolic acid) and evaluated its apoptotic potential in human colon carcinoma cells (HCT 116). The results show that curcumin-PLGA conjugate efficiently inhibits cell proliferation and cell survival in human colon carcinoma cells as compared to native curcumin. Additionally, curcumin conjugated with PLGA shows improved cellular uptake and exhibits controlled release at physiological pH as compared to native curcumin. The curcumin-PLGA conjugate efficiently activates the cascade of caspases and promotes intrinsic apoptotic signaling. Thus, the results suggest that conjugation potentiates the sustainability, anti-proliferative and apoptotic activity of curcumin. This approach could be a promising strategy to improve the therapeutic index of cancer therapy. PMID:25692854

Development of a morphing structure with the incorporation of central pattern generators

NASA Astrophysics Data System (ADS)

Bliss, Thomas K.; Bart-Smith, Hilary; Iwasaki, Tetsuya

2006-03-01

The Manta Ray, Manta birostris, is an amazing creature, propelling itself through the water with the elegant and complex flapping of its wings. Achieving outstanding efficiencies, engineers are looking for ways to mimic its flight through the water and harness its propulsive techniques. This study combines two biologically inspired aspects to achieve this goal: morphing structures actuated with a biomimetic neural network control system. It is believed that this combination will prove capable of producing the oscillatory motions necessary for locomotion. In this paper, a four-truss structure with three actuators is chosen and its performance capabilities are analyzed. A synthetic central pattern generator, which provides the fundamental control mechanisms for rhythmic motion in animals, is designed to realize an oscillatory control of the three actuators. The control system is simulated using Matlab, then combined with LabVIEW to control the four-truss structure. The system's performance is analyzed, with specific attention to both transient and steady-state behavior.

Modeling and Advanced Control for Sustainable Process ...

EPA Pesticide Factsheets

This book chapter introduces a novel process systems engineering framework that integrates process control with sustainability assessment tools for the simultaneous evaluation and optimization of process operations. The implemented control strategy consists of a biologically-inspired, multi-agent-based method. The sustainability and performance assessment of process operating points is carried out using the U.S. E.P.A.’s GREENSCOPE assessment tool that provides scores for the selected economic, material management, environmental and energy indicators. The indicator results supply information on whether the implementation of the controller is moving the process towards a more sustainable operation. The effectiveness of the proposed framework is illustrated through a case study of a continuous bioethanol fermentation process whose dynamics are characterized by steady-state multiplicity and oscillatory behavior. This book chapter contribution demonstrates the application of novel process control strategies for sustainability by increasing material management, energy efficiency, and pollution prevention, as needed for SHC Sustainable Uses of Wastes and Materials Management.

Control of fluxes in metabolic networks.

PubMed

Basler, Georg; Nikoloski, Zoran; Larhlimi, Abdelhalim; Barabási, Albert-László; Liu, Yang-Yu

2016-07-01

Understanding the control of large-scale metabolic networks is central to biology and medicine. However, existing approaches either require specifying a cellular objective or can only be used for small networks. We introduce new coupling types describing the relations between reaction activities, and develop an efficient computational framework, which does not require any cellular objective for systematic studies of large-scale metabolism. We identify the driver reactions facilitating control of 23 metabolic networks from all kingdoms of life. We find that unicellular organisms require a smaller degree of control than multicellular organisms. Driver reactions are under complex cellular regulation in Escherichia coli, indicating their preeminent role in facilitating cellular control. In human cancer cells, driver reactions play pivotal roles in malignancy and represent potential therapeutic targets. The developed framework helps us gain insights into regulatory principles of diseases and facilitates design of engineering strategies at the interface of gene regulation, signaling, and metabolism. © 2016 Basler et al.; Published by Cold Spring Harbor Laboratory Press.

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

JOHNSON, A.R.

Biological control is any activity taken to prevent, limit, clean up, or remediate potential environmental, health and safety, or workplace quality impacts from plants, animals, or microorganisms. At Hanford the principal emphasis of biological control is to prevent the transport of radioactive contamination by biological vectors (plants, animals, or microorganisms), and where necessary, control and clean up resulting contamination. Other aspects of biological control at Hanford include industrial weed control (e.g.; tumbleweeds), noxious weed control (invasive, non-native plant species), and pest control (undesirable animals such as rodents and stinging insects; and microorganisms such as molds that adversely affect the qualitymore » of the workplace environment). Biological control activities may be either preventive (apriori) or in response to existing contamination spread (aposteriori). Surveillance activities, including ground, vegetation, flying insect, and other surveys, and apriori control actions, such as herbicide spraying and placing biological barriers, are important in preventing radioactive contamination spread. If surveillance discovers that biological vectors have spread radioactive contamination, aposteriori control measures, such as fixing contamination, followed by cleanup and removal of the contamination to an approved disposal location are typical response functions. In some cases remediation following the contamination cleanup and removal is necessary. Biological control activities for industrial weeds, noxious weeds and pests have similar modes of prevention and response.« less

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

JOHNSON, A.R.

Biological control is any activity taken to prevent, limit, clean up, or remediate potential environmental, health and safety, or workplace quality impacts from plants, animals, or microorganisms. At Hanford the principal emphasis of biological control is to prevent the transport of radioactive contamination by biological vectors (plants, animals, or microorganisms), and where necessary, control and clean up resulting contamination. Other aspects of biological control at Hanford include industrial weed control (e.g.; tumbleweeds), noxious weed control (invasive, non-native plant species), and pest control (undesirable animals such as rodents and stinging insects, and microorganisms such as molds that adversely affect the qualitymore » of the workplace environment). Biological control activities may be either preventive (a priori) or in response to existing contamination spread (a posteriori). Surveillance activities, including ground, vegetation, flying insect, and other surveys, and a priori control actions, such as herbicide spraying and placing biological barriers, are important in preventing radioactive contamination spread. If surveillance discovers that biological vectors have spread radioactive contamination, a posteriori control measures, such as fixing contamination, followed by cleanup and removal of the contamination to an approved disposal location are typical response functions. In some cases remediation following the contamination cleanup and removal is necessary. Biological control activities for industrial weeds, noxious weeds and pests have similar modes of prevention and response.« less

Development of a Biological Control Program for Eurasian Watermilfoil (Myriophyllum spicatum)

DTIC Science & Technology

2008-08-01

spicatum). Rawalpindi: Pakistan Station Commonwealth Institute of Biological Control. Gleason, H. A ., and A . Cronquist . 1991. Manual of vascular plants...ER D C/ EL T R- 08 -2 2 Aquatic Plant Control Research Program Development of a Biological Control Program for Eurasian Watermilfoil... a Biological Control Program for Eurasian Watermilfoil (Myriophyllum spicatum) Matthew J. W. Cock, Hariet L. Hinz, Gitta Grosskopf, and Patrick

What Combined Measurements From Structures and Imaging Tell Us About DNA Damage Responses

PubMed Central

Brosey, Chris A.; Ahmed, Zamal; Lees-Miller, Susan P.; Tainer, John A.

2017-01-01

DNA damage outcomes depend upon the efficiency and fidelity of DNA damage responses (DDRs) for different cells and damage. As such, DDRs represent tightly regulated prototypical systems for linking nanoscale biomolecular structure and assembly to the biology of genomic regulation and cell signaling. However, the dynamic and multifunctional nature of DDR assemblies can render elusive the correlation between the structures of DDR factors and specific biological disruptions to the DDR when these structures are altered. In this chapter, we discuss concepts and strategies for combining structural, biophysical, and imaging techniques to investigate DDR recognition and regulation, and thus bridge sequence-level structural biochemistry to quantitative biological outcomes visualized in cells. We focus on representative DDR responses from PARP/PARG/AIF damage signaling in DNA single-strand break repair and nonhomologous end joining complexes in double-strand break repair. Methods with exemplary experimental results are considered with a focus on strategies for probing flexibility, conformational changes, and assembly processes that shape a predictive understanding of DDR mechanisms in a cellular context. Integration of structural and imaging measurements promises to provide foundational knowledge to rationally control and optimize DNA damage outcomes for synthetic lethality and for immune activation with resulting insights for biology and cancer interventions. PMID:28668129

Hierarchical Surface Architecture of Plants as an Inspiration for Biomimetic Fog Collectors.

PubMed

Azad, M A K; Barthlott, W; Koch, K

2015-12-08

Fog collectors can enable us to alleviate the water crisis in certain arid regions of the world. A continuous fog-collection cycle consisting of a persistent capture of fog droplets and their fast transport to the target is a prerequisite for developing an efficient fog collector. In regard to this topic, a biological superior design has been found in the hierarchical surface architecture of barley (Hordeum vulgare) awns. We demonstrate here the highly wettable (advancing contact angle 16° ± 2.7 and receding contact angle 9° ± 2.6) barbed (barb = conical structure) awn as a model to develop optimized fog collectors with a high fog-capturing capability, an effective water transport, and above all an efficient fog collection. We compare the fog-collection efficiency of the model sample with other plant samples naturally grown in foggy habitats that are supposed to be very efficient fog collectors. The model sample, consisting of dry hydrophilized awns (DH awns), is found to be about twice as efficient (fog-collection rate 563.7 ± 23.2 μg/cm(2) over 10 min) as any other samples investigated under controlled experimental conditions. Finally, a design based on the hierarchical surface architecture of the model sample is proposed for the development of optimized biomimetic fog collectors.

Commercial formulation of Metarhizium anisopliae for the control of Rhipicephalus microplus in a pen study.

PubMed

Camargo, Mariana G; Marciano, Allan F; Sá, Fillipe A; Perinotto, Wendell M S; Quinelato, Simone; Gôlo, Patrícia S; Angelo, Isabele C; Prata, Márcia C A; Bittencourt, Vânia R E P

2014-09-15

The present study evaluated, for the first time, the effect of the commercial formulation Metarril(®) SP Organic of Metarhizium anisopliae plus 10% mineral oil to control Rhipicephalus microplus in a pen study. Three groups were formed with six animals each: the first group was exposed to Metarril(®) plus 10% mineral oil and 1% Tween 80; the second group was exposed to sterile distilled water, mineral oil and Tween 80 (oil control group); and the third group received no treatment (control group). The fungal formulation contained 1 × 10(8)conidiaml(-1). Each animal was sprayed with 3L of formulation. Fallen ticks were counted daily and a sample of 20 engorged females per day was incubated for assessment of biological parameters. Throughout the study period, Metarril(®) oil-based formulation showed an efficacy ranging from 19.20% to 67.39% in comparison with the control group; and from 8.18% to 61.38% in comparison with the oil control group. The average efficacy of Metarril(®) oil-based formulation was 47.74% and 40.89% in comparison with control and oil control groups, respectively. Changes in the biological parameters of engorged R. microplus females were observed in the first three days after treatment, with a significant reduction in hatching percentage and egg production index. We concluded that Metarril(®) SP Organic plus 10% mineral oil was efficient against R. microplus in pen studies. However, further in vivo studies are required to increase the efficacy and to establish a protocol for the use of this product in the field against the cattle tick. Copyright © 2014 Elsevier B.V. All rights reserved.

A review of selected pumping systems in nature and engineering--potential biomimetic concepts for improving displacement pumps and pulsation damping.

PubMed

Bach, D; Schmich, F; Masselter, T; Speck, T

2015-09-03

The active transport of fluids by pumps plays an essential role in engineering and biology. Due to increasing energy costs and environmental issues, topics like noise reduction, increase of efficiency and enhanced robustness are of high importance in the development of pumps in engineering. The study compares pumps in biology and engineering and assesses biomimetic potentials for improving man-made pumping systems. To this aim, examples of common challenges, applications and current biomimetic research for state-of-the art pumps are presented. The biomimetic research is helped by the similar configuration of many positive displacement pumping systems in biology and engineering. In contrast, the configuration and underlying pumping principles for fluid dynamic pumps (FDPs) differ to a greater extent in biology and engineering. However, progress has been made for positive displacement as well as for FDPs by developing biomimetic devices with artificial muscles and cilia that improve energetic efficiency and fail-safe operation or reduce noise. The circulatory system of vertebrates holds a high biomimetic potential for the damping of pressure pulsations, a common challenge in engineering. Damping of blood pressure pulsation results from a nonlinear viscoelastic behavior of the artery walls which represent a complex composite material. The transfer of the underlying functional principle could lead to an improvement of existing technical solutions and be used to develop novel biomimetic damping solutions. To enhance efficiency or thrust of man-made fluid transportation systems, research on jet propulsion in biology has shown that a pulsed jet can be tuned to either maximize thrust or efficiency. The underlying principle has already been transferred into biomimetic applications in open channel water systems. Overall there is a high potential to learn from nature in order to improve pumping systems for challenges like the reduction of pressure pulsations, increase of jet propulsion efficiency or the reduction of wear.

Ex Vivo Application of Secreted Metabolites Produced by Soil-Inhabiting Bacillus spp. Efficiently Controls Foliar Diseases Caused by Alternaria spp.

PubMed Central

El-Sayed, Ashraf S. A.; Patel, Jaimin S.; Green, Kari B.; Ali, Mohammad; Brennan, Mary; Norman, David

2015-01-01

Bacterial biological control agents (BCAs) are largely used as live products to control plant pathogens. However, due to variable environmental and ecological factors, live BCAs usually fail to produce desirable results against foliar pathogens. In this study, we investigated the potential of cell-free culture filtrates of 12 different bacterial BCAs isolated from flower beds for controlling foliar diseases caused by Alternaria spp. In vitro studies showed that culture filtrates from two isolates belonging to Bacillus subtilis and Bacillus amyloliquefaciens displayed strong efficacy and potencies against Alternaria spp. The antimicrobial activity of the culture filtrate of these two biological control agents was effective over a wider range of pH (3.0 to 9.0) and was not affected by autoclaving or proteolysis. Comparative liquid chromatography-mass spectrometry (LC-MS) analyses showed that a complex mixture of cyclic lipopeptides, primarily of the fengycin A and fengycin B families, was significantly higher in these two BCAs than inactive Bacillus spp. Interaction studies with mixtures of culture filtrates of these two species revealed additive activity, suggesting that they produce similar products, which was confirmed by LC-tandem MS analyses. In in planta pre- and postinoculation trials, foliar application of culture filtrates of B. subtilis reduced lesion sizes and lesion frequencies caused by Alternaria alternata by 68 to 81%. Taken together, our studies suggest that instead of live bacteria, culture filtrates of B. subtilis and B. amyloliquefaciens can be applied either individually or in combination for controlling foliar diseases caused by Alternaria species. PMID:26519395

77 FR 46373 - Field Release of Aphelinus glycinis for the Biological Control of the Soybean Aphid in the...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-03

... Inspection Service [Docket No APHIS-2012-0061] Field Release of Aphelinus glycinis for the Biological Control... for the biological control of the soybean aphid, Aphis glycines, in the continental United States. We... glycinis for the Biological Control of the Soybean Aphid in the Continental United States'' (March 2012...

The Brain as an Efficient and Robust Adaptive Learner.

PubMed

Denève, Sophie; Alemi, Alireza; Bourdoukan, Ralph

2017-06-07

Understanding how the brain learns to compute functions reliably, efficiently, and robustly with noisy spiking activity is a fundamental challenge in neuroscience. Most sensory and motor tasks can be described as dynamical systems and could presumably be learned by adjusting connection weights in a recurrent biological neural network. However, this is greatly complicated by the credit assignment problem for learning in recurrent networks, e.g., the contribution of each connection to the global output error cannot be determined based only on locally accessible quantities to the synapse. Combining tools from adaptive control theory and efficient coding theories, we propose that neural circuits can indeed learn complex dynamic tasks with local synaptic plasticity rules as long as they associate two experimentally established neural mechanisms. First, they should receive top-down feedbacks driving both their activity and their synaptic plasticity. Second, inhibitory interneurons should maintain a tight balance between excitation and inhibition in the circuit. The resulting networks could learn arbitrary dynamical systems and produce irregular spike trains as variable as those observed experimentally. Yet, this variability in single neurons may hide an extremely efficient and robust computation at the population level. Copyright © 2017 Elsevier Inc. All rights reserved.

mz5: space- and time-efficient storage of mass spectrometry data sets.

PubMed

Wilhelm, Mathias; Kirchner, Marc; Steen, Judith A J; Steen, Hanno

2012-01-01

Across a host of MS-driven-omics fields, researchers witness the acquisition of ever increasing amounts of high throughput MS data and face the need for their compact yet efficiently accessible storage. Addressing the need for an open data exchange format, the Proteomics Standards Initiative and the Seattle Proteome Center at the Institute for Systems Biology independently developed the mzData and mzXML formats, respectively. In a subsequent joint effort, they defined an ontology and associated controlled vocabulary that specifies the contents of MS data files, implemented as the newer mzML format. All three formats are based on XML and are thus not particularly efficient in either storage space requirements or read/write speed. This contribution introduces mz5, a complete reimplementation of the mzML ontology that is based on the efficient, industrial strength storage backend HDF5. Compared with the current mzML standard, this strategy yields an average file size reduction to ∼54% and increases linear read and write speeds ∼3-4-fold. The format is implemented as part of the ProteoWizard project and is available under a permissive Apache license. Additional information and download links are available from http://software.steenlab.org/mz5.

A study on using fireclay as a biomass carrier in an activated sludge system.

PubMed

Tilaki, Ramazan Ali Dianati

2011-01-01

By adding a biomass carrier to an activated sludge system, the biomass concentration will increase, and subsequently the organic removal efficiency will be enhanced. In this study, the possibility of using excess sludge from ceramic and tile manufacturing plants as a biomass carrier was investigated. The aim of this study was to determine the effect of using fireclay as a biomass carrier on biomass concentration, organic removal and nitrification efficiency in an activated sludge system. Experiments were conducted by using a bench scale activated sludge system operating in batch and continuous modes. Artificial simulated wastewater was made by using recirculated water in a ceramic manufacturing plant. In the continuous mode, hydraulic detention time in the aeration reactor was 8 and 22 h. In the batch mode, aeration time was 8 and 16 h. Fireclay doses were 500, 1,400 and 2,250 mg l(-1), and were added to the reactors in each experiment separately. The reactor with added fireclay was called a Hybrid Biological Reactor (HBR). A reactor without added fireclay was used as a control. Efficiency parameters such as COD, MLVSS and nitrate were measured in the control and HBR reactors according to standard methods. The average concentration of biomass in the HBR reactor was greater than in the control reactor. The total biomass concentration in the HBR reactor (2.25 g l(-1) fireclay) in the continuous mode was 3,000 mg l(-1) and in the batch mode was 2,400 mg l(-1). The attached biomass concentration in the HBR reactor (2.25 g l(-1) fireclay) in the continuous mode was 1,500 mg l(-1) and in the batch mode was 980 mg l(-1). Efficiency for COD removal in the HBR and control reactor was 95 and 55%, respectively. In the HBR reactor, nitrification was enhanced, and the concentration of nitrate was increased by 80%. By increasing the fireclay dose, total and attached biomass was increased. By adding fireclay as a biomass carrier, the efficiency of an activated sludge system to treat wastewater from ceramic manufacturing plants was increased.

Dynamic belief state representations.

PubMed

Lee, Daniel D; Ortega, Pedro A; Stocker, Alan A

2014-04-01

Perceptual and control systems are tasked with the challenge of accurately and efficiently estimating the dynamic states of objects in the environment. To properly account for uncertainty, it is necessary to maintain a dynamical belief state representation rather than a single state vector. In this review, canonical algorithms for computing and updating belief states in robotic applications are delineated, and connections to biological systems are highlighted. A navigation example is used to illustrate the importance of properly accounting for correlations between belief state components, and to motivate the need for further investigations in psychophysics and neurobiology. Copyright © 2014 Elsevier Ltd. All rights reserved.

Morphogenesis of early stage melanoma

NASA Astrophysics Data System (ADS)

Chatelain, Clément; Amar, Martine Ben

2015-08-01

Melanoma early detection is possible by simple skin examination and can insure a high survival probability when successful. However it requires efficient methods for identifying malignant lesions from common moles. This paper provides an overview first of the biological and physical mechanisms controlling melanoma early evolution, and then of the clinical tools available today for detecting melanoma in vivo at an early stage. It highlights the lack of diagnosis methods rationally linking macroscopic observables to the microscopic properties of the tissue, which define the malignancy of the tumor. The possible inputs of multiscale models for improving these methods are shortly discussed.

Development and investigation of a selective latex flocculant

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

Nikitin, I.N.; Preobrazhenskii, B.P.; Tsyrlov, M.Ya.

1982-01-01

Investigations were made on the use of two synthetic latexes as selective flocculants in the flotation cleaning of coal. The most commonly used latex in the industry contained sodium dibutylnaphthalenesulfonate, which is a biologically ''hard'' emulsifier. It was determined that butadiene-styrene latexes may successfully be used as selective coal sludge flocculants. The most efficient was a latex synthesized using biodegradable emulsifiers--potassium soaps of disproportionated rosin with a small quantity of synthetic fatty acids. Also, it was concluded that the values of the ash level in the flotation concentrate and tailings could be controlled by regulating the latex consumption.

Enhanced energy transport in genetically engineered excitonic networks.

PubMed

Park, Heechul; Heldman, Nimrod; Rebentrost, Patrick; Abbondanza, Luigi; Iagatti, Alessandro; Alessi, Andrea; Patrizi, Barbara; Salvalaggio, Mario; Bussotti, Laura; Mohseni, Masoud; Caruso, Filippo; Johnsen, Hannah C; Fusco, Roberto; Foggi, Paolo; Scudo, Petra F; Lloyd, Seth; Belcher, Angela M

2016-02-01

One of the challenges for achieving efficient exciton transport in solar energy conversion systems is precise structural control of the light-harvesting building blocks. Here, we create a tunable material consisting of a connected chromophore network on an ordered biological virus template. Using genetic engineering, we establish a link between the inter-chromophoric distances and emerging transport properties. The combination of spectroscopy measurements and dynamic modelling enables us to elucidate quantum coherent and classical incoherent energy transport at room temperature. Through genetic modifications, we obtain a significant enhancement of exciton diffusion length of about 68% in an intermediate quantum-classical regime.

The influence of the ocean circulation state on ocean carbon storage and CO2 drawdown potential in an Earth system model

NASA Astrophysics Data System (ADS)

Ödalen, Malin; Nycander, Jonas; Oliver, Kevin I. C.; Brodeau, Laurent; Ridgwell, Andy

2018-03-01

During the four most recent glacial cycles, atmospheric CO2 during glacial maxima has been lowered by about 90-100 ppm with respect to interglacials. There is widespread consensus that most of this carbon was partitioned in the ocean. It is, however, still debated which processes were dominant in achieving this increased carbon storage. In this paper, we use an Earth system model of intermediate complexity to explore the sensitivity of ocean carbon storage to ocean circulation state. We carry out a set of simulations in which we run the model to pre-industrial equilibrium, but in which we achieve different states of ocean circulation by changing forcing parameters such as wind stress, ocean diffusivity and atmospheric heat diffusivity. As a consequence, the ensemble members also have different ocean carbon reservoirs, global ocean average temperatures, biological pump efficiencies and conditions for air-sea CO2 disequilibrium. We analyse changes in total ocean carbon storage and separate it into contributions by the solubility pump, the biological pump and the CO2 disequilibrium component. We also relate these contributions to differences in the strength of the ocean overturning circulation. Depending on which ocean forcing parameter is tuned, the origin of the change in carbon storage is different. When wind stress or ocean diapycnal diffusivity is changed, the response of the biological pump gives the most important effect on ocean carbon storage, whereas when atmospheric heat diffusivity or ocean isopycnal diffusivity is changed, the solubility pump and the disequilibrium component are also important and sometimes dominant. Despite this complexity, we obtain a negative linear relationship between total ocean carbon and the combined strength of the northern and southern overturning cells. This relationship is robust to different reservoirs dominating the response to different forcing mechanisms. Finally, we conduct a drawdown experiment in which we investigate the capacity for increased carbon storage by artificially maximising the efficiency of the biological pump in our ensemble members. We conclude that different initial states for an ocean model result in different capacities for ocean carbon storage due to differences in the ocean circulation state and the origin of the carbon in the initial ocean carbon reservoir. This could explain why it is difficult to achieve comparable responses of the ocean carbon pumps in model inter-comparison studies in which the initial states vary between models. We show that this effect of the initial state is quantifiable. The drawdown experiment highlights the importance of the strength of the biological pump in the control state for model studies of increased biological efficiency.

A novel integration of three-dimensional electro-Fenton and biological activated carbon and its application in the advanced treatment of biologically pretreated Lurgi coal gasification wastewater.

PubMed

Hou, Baolin; Han, Hongjun; Zhuang, Haifeng; Xu, Peng; Jia, Shengyong; Li, Kun

2015-11-01

A novel integrated process with three-dimensional electro-Fenton (3D EF) and biological activated carbon (BAC) was employed in advanced treatment of biologically pretreated Lurgi coal gasification wastewater. SAC-Fe (sludge deserved activated carbon from sewage and iron sludge) and SAC (sludge deserved activated carbon) were used in 3D EF as catalytic particle electrodes (CPEs) and in BAC as carriers respectively. Results indicated that 3D EF with SAC-Fe as CPEs represented excellent pollutants and COLOR removals as well as biodegradability improvement. The efficiency enhancement attributed to generating more H2O2 and OH. The integrated process exhibited efficient performance of COD, BOD5, total phenols, TOC, TN and COLOR removals at a much shorter retention time, with the corresponding concentrations in effluent of 31.18, 6.69, 4.29, 17.82, 13.88mg/L and <20 times, allowing discharge criteria to be met. The integrated system was efficient, cost-effective and ecological sustainable and could be a promising technology for engineering applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

Biologically inspired LED lens from cuticular nanostructures of firefly lantern

PubMed Central

Kim, Jae-Jun; Lee, Youngseop; Kim, Ha Gon; Choi, Ki-Ju; Kweon, Hee-Seok; Park, Seongchong; Jeong, Ki-Hun

2012-01-01

Cuticular nanostructures found in insects effectively manage light for light polarization, structural color, or optical index matching within an ultrathin natural scale. These nanostructures are mainly dedicated to manage incoming light and recently inspired many imaging and display applications. A bioluminescent organ, such as a firefly lantern, helps to out-couple light from the body in a highly efficient fashion for delivering strong optical signals in sexual communication. However, the cuticular nanostructures, except the light-producing reactions, have not been well investigated for physical principles and engineering biomimetics. Here we report a unique observation of high-transmission nanostructures on a firefly lantern and its biological inspiration for highly efficient LED illumination. Both numerical and experimental results clearly reveal high transmission through the nanostructures inspired from the lantern cuticle. The nanostructures on an LED lens surface were fabricated by using a large-area nanotemplating and reconfigurable nanomolding with heat-induced shear thinning. The biologically inspired LED lens, distinct from a smooth surface lens, substantially increases light transmission over visible ranges, comparable to conventional antireflection coating. This biological inspiration can offer new opportunities for increasing the light extraction efficiency of high-power LED packages. PMID:23112185

Evolutionary game based control for biological systems with applications in drug delivery.

PubMed

Li, Xiaobo; Lenaghan, Scott C; Zhang, Mingjun

2013-06-07

Control engineering and analysis of biological systems have become increasingly important for systems and synthetic biology. Unfortunately, no widely accepted control framework is currently available for these systems, especially at the cell and molecular levels. This is partially due to the lack of appropriate mathematical models to describe the unique dynamics of biological systems, and the lack of implementation techniques, such as ultra-fast and ultra-small devices and corresponding control algorithms. This paper proposes a control framework for biological systems subject to dynamics that exhibit adaptive behavior under evolutionary pressures. The control framework was formulated based on evolutionary game based modeling, which integrates both the internal dynamics and the population dynamics. In the proposed control framework, the adaptive behavior was characterized as an internal dynamic, and the external environment was regarded as an external control input. The proposed open-interface control framework can be integrated with additional control algorithms for control of biological systems. To demonstrate the effectiveness of the proposed framework, an optimal control strategy was developed and validated for drug delivery using the pathogen Giardia lamblia as a test case. In principle, the proposed control framework can be applied to any biological system exhibiting adaptive behavior under evolutionary pressures. Copyright © 2013 Elsevier Ltd. All rights reserved.

A two-agent model applied to the biological control of the sugarcane borer (Diatraea saccharalis) by the egg parasitoid Trichogramma galloi and the larvae parasitoid Cotesia flavipes.

PubMed

Molnár, Sándor; López, Inmaculada; Gámez, Manuel; Garay, József

2016-03-01

The paper is aimed at a methodological development in biological pest control. The considered one pest two-agent system is modelled as a verticum-type system. Originally, linear verticum-type systems were introduced by one of the authors for modelling certain industrial systems. These systems are hierarchically composed of linear subsystems such that a part of the state variables of each subsystem affect the dynamics of the next subsystem. Recently, verticum-type system models have been applied to population ecology as well, which required the extension of the concept a verticum-type system to the nonlinear case. In the present paper the general concepts and technics of nonlinear verticum-type control systems are used to obtain biological control strategies in a two-agent system. For the illustration of this verticum-type control, these tools of mathematical systems theory are applied to a dynamic model of interactions between the egg and larvae populations of the sugarcane borer (Diatraea saccharalis) and its parasitoids: the egg parasitoid Trichogramma galloi and the larvae parasitoid Cotesia flavipes. In this application a key role is played by the concept of controllability, which means that it is possible to steer the system to an equilibrium in given time. In addition to a usual linearization, the basic idea is a decomposition of the control of the whole system into the control of the subsystems, making use of the verticum structure of the population system. The main aim of this study is to show several advantages of the verticum (or decomposition) approach over the classical control theoretical model (without decomposition). For example, in the case of verticum control the pest larval density decreases below the critical threshold value much quicker than without decomposition. Furthermore, it is also shown that the verticum approach may be better even in terms of cost effectiveness. The presented optimal control methodology also turned out to be an efficient tool for the "in silico" analysis of the cost-effectiveness of different biocontrol strategies, e.g. by answering the question how far it is cost-effective to speed up the reduction of the pest larvae density, or along which trajectory this reduction should be carried out. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Generating high-speed dynamic running gaits in a quadruped robot using an evolutionary search.

PubMed

Krasny, Darren P; Orin, David E

2004-08-01

Over the past several decades, there has been a considerable interest in investigating high-speed dynamic gaits for legged robots. While much research has been published, both in the biomechanics and engineering fields regarding the analysis of these gaits, no single study has adequately characterized the dynamics of high-speed running as can be achieved in a realistic, yet simple, robotic system. The goal of this paper is to find the most energy-efficient, natural, and unconstrained gallop that can be achieved using a simulated quadrupedal robot with articulated legs, asymmetric mass distribution, and compliant legs. For comparison purposes, we also implement the bound and canter. The model used here is planar, although we will show that it captures much of the predominant dynamic characteristics observed in animals. While it is not our goal to prove anything about biological locomotion, the dynamic similarities between the gaits we produce and those found in animals does indicate a similar underlying dynamic mechanism. Thus, we will show that achieving natural, efficient high-speed locomotion is possible even with a fairly simple robotic system. To generate the high-speed gaits, we use an efficient evolutionary algorithm called set-based stochastic optimization. This algorithm finds open-loop control parameters to generate periodic trajectories for the body. Several alternative methods are tested to generate periodic trajectories for the legs. The combined solutions found by the evolutionary search and the periodic-leg methods, over a range of speeds up to 10.0 m/s, reveal "biological" characteristics that are emergent properties of the underlying gaits.

Effect of Different Substrates and Casing Materials on the Growth and Yield of Calocybe indica.

PubMed

Amin, Ruhul; Khair, Abul; Alam, Nuhu; Lee, Tae Soo

2010-06-01

Calocybe indica, a tropical edible mushroom, is popular because it has good nutritive value and it can be cultivated commercially. The current investigation was undertaken to determine a suitable substrate and the appropriate thickness of casing materials for the cultivation of C. indica. Optimum mycelial growth was observed in coconut coir substrate. Primordia initiation with the different substrates and casing materials was observed between the 13th and 19th day. The maximum length of stalk was recorded from sugarcane leaf, while diameter of stalk and pileus, and thickness of pileus were found in rice straw substrate. The highest biological and economic yield, and biological efficiency were also obtained in the rice straw substrate. Cow dung and loamy soil, farm-yard manure, loamy soil and sand, and spent oyster mushroom substrates were used as casing materials to evaluate the yield and yield-contributing characteristics of C. indica. The results indicate that the number of effective fruiting bodies, the biological and economic yield, and the biological efficiency were statistically similar all of the casing materials used. The maximum biological efficiency was found in the cow dung and loamy soil casing material. The cow dung and loamy soil (3 cm thick) was the best casing material and the rice straw was the best substrate for the commercial cultivation of C. indica.

Effect of Different Substrates and Casing Materials on the Growth and Yield of Calocybe indica

PubMed Central

Amin, Ruhul; Khair, Abul; Alam, Nuhu

2010-01-01

Calocybe indica, a tropical edible mushroom, is popular because it has good nutritive value and it can be cultivated commercially. The current investigation was undertaken to determine a suitable substrate and the appropriate thickness of casing materials for the cultivation of C. indica. Optimum mycelial growth was observed in coconut coir substrate. Primordia initiation with the different substrates and casing materials was observed between the 13th and 19th day. The maximum length of stalk was recorded from sugarcane leaf, while diameter of stalk and pileus, and thickness of pileus were found in rice straw substrate. The highest biological and economic yield, and biological efficiency were also obtained in the rice straw substrate. Cow dung and loamy soil, farm-yard manure, loamy soil and sand, and spent oyster mushroom substrates were used as casing materials to evaluate the yield and yield-contributing characteristics of C. indica. The results indicate that the number of effective fruiting bodies, the biological and economic yield, and the biological efficiency were statistically similar all of the casing materials used. The maximum biological efficiency was found in the cow dung and loamy soil casing material. The cow dung and loamy soil (3 cm thick) was the best casing material and the rice straw was the best substrate for the commercial cultivation of C. indica. PMID:23956634

Systems Biology of Industrial Microorganisms

NASA Astrophysics Data System (ADS)

Papini, Marta; Salazar, Margarita; Nielsen, Jens

The field of industrial biotechnology is expanding rapidly as the chemical industry is looking towards more sustainable production of chemicals that can be used as fuels or building blocks for production of solvents and materials. In connection with the development of sustainable bioprocesses, it is a major challenge to design and develop efficient cell factories that can ensure cost efficient conversion of the raw material into the chemical of interest. This is achieved through metabolic engineering, where the metabolism of the cell factory is engineered such that there is an efficient conversion of sugars, the typical raw materials in the fermentation industry, into the desired product. However, engineering of cellular metabolism is often challenging due to the complex regulation that has evolved in connection with adaptation of the different microorganisms to their ecological niches. In order to map these regulatory structures and further de-regulate them, as well as identify ingenious metabolic engineering strategies that full-fill mass balance constraints, tools from systems biology can be applied. This involves both high-throughput analysis tools like transcriptome, proteome and metabolome analysis, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies. It is in fact expected that systems biology may substantially improve the process of cell factory development, and we therefore propose the term Industrial Systems Biology for how systems biology will enhance the development of industrial biotechnology for sustainable chemical production.

Systems biology of industrial microorganisms.

PubMed

Papini, Marta; Salazar, Margarita; Nielsen, Jens

2010-01-01

The field of industrial biotechnology is expanding rapidly as the chemical industry is looking towards more sustainable production of chemicals that can be used as fuels or building blocks for production of solvents and materials. In connection with the development of sustainable bioprocesses, it is a major challenge to design and develop efficient cell factories that can ensure cost efficient conversion of the raw material into the chemical of interest. This is achieved through metabolic engineering, where the metabolism of the cell factory is engineered such that there is an efficient conversion of sugars, the typical raw materials in the fermentation industry, into the desired product. However, engineering of cellular metabolism is often challenging due to the complex regulation that has evolved in connection with adaptation of the different microorganisms to their ecological niches. In order to map these regulatory structures and further de-regulate them, as well as identify ingenious metabolic engineering strategies that full-fill mass balance constraints, tools from systems biology can be applied. This involves both high-throughput analysis tools like transcriptome, proteome and metabolome analysis, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies. It is in fact expected that systems biology may substantially improve the process of cell factory development, and we therefore propose the term Industrial Systems Biology for how systems biology will enhance the development of industrial biotechnology for sustainable chemical production.

Controlled ecological life-support system - Use of plants for human life-support in space

NASA Technical Reports Server (NTRS)

Chamberland, D.; Knott, W. M.; Sager, J. C.; Wheeler, R.

1992-01-01

Scientists and engineers within NASA are conducting research which will lead to development of advanced life-support systems that utilize higher plants in a unique approach to solving long-term life-support problems in space. This biological solution to life-support, Controlled Ecological Life-Support System (CELSS), is a complex, extensively controlled, bioengineered system that relies on plants to provide the principal elements from gas exchange and food production to potable water reclamation. Research at John F. Kennedy Space Center (KSC) is proceeding with a comprehensive investigation of the individual parts of the CELSS system at a one-person scale in an approach called the Breadboard Project. Concurrently a relatively new NASA sponsored research effort is investigating plant growth and metabolism in microgravity, innovative hydroponic nutrient delivery systems, and use of highly efficient light emitting diodes for artificial plant illumination.

Requirements for modeling airborne microbial contamination in space stations

NASA Astrophysics Data System (ADS)

Van Houdt, Rob; Kokkonen, Eero; Lehtimäki, Matti; Pasanen, Pertti; Leys, Natalie; Kulmala, Ilpo

2018-03-01

Exposure to bioaerosols is one of the facets that affect indoor air quality, especially for people living in densely populated or confined habitats, and is associated to a wide range of health effects. Good indoor air quality is thus vital and a prerequisite for fully confined environments such as space habitats. Bioaerosols and microbial contamination in these confined space stations can have significant health impacts, considering the unique prevailing conditions and constraints of such habitats. Therefore, biocontamination in space stations is strictly monitored and controlled to ensure crew and mission safety. However, efficient bioaerosol control measures rely on solid understanding and knowledge on how these bioaerosols are created and dispersed, and which factors affect the survivability of the associated microorganisms. Here we review the current knowledge gained from relevant studies in this wide and multidisciplinary area of bioaerosol dispersion modeling and biological indoor air quality control, specifically taking into account the specific space conditions.

Lysine-based polycation:heparin coacervate for controlled protein delivery.

PubMed

Johnson, Noah Ray; Ambe, Trisha; Wang, Yadong

2014-01-01

Polycations have good potential as carriers of proteins and genetic material. However, poor control over the release rate and safety issues currently limit their use as delivery vehicles. Here we introduce a new lysine-based polycation, poly(ethylene lysinylaspartate diglyceride) (PELD), which exhibits high cytocompatibility. PELD self-assembles with the biological polyanion heparin into a coacervate that incorporates proteins with high loading efficiency. Coacervates of varying surface charge were obtained by simple alteration of the PELD:heparin ratio and resulted in diverse release profiles of the model protein bovine serum albumin. Therefore, coacervate charge represents a direct means of control over release rate and duration. The PELD coacervate also rapidly adsorbed onto a porous polymeric scaffold, demonstrating potential use in tissue engineering applications. This coacervate represents a safe and tunable protein delivery system for biomedical applications. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Precise through-space control of an abiotic electrophilic aromatic substitution reaction

NASA Astrophysics Data System (ADS)

Murphy, Kyle E.; Bocanegra, Jessica L.; Liu, Xiaoxi; Chau, H.-Y. Katharine; Lee, Patrick C.; Li, Jianing; Schneebeli, Severin T.

2017-04-01

Nature has evolved selective enzymes for the efficient biosynthesis of complex products. This exceptional ability stems from adapted enzymatic pockets, which geometrically constrain reactants and stabilize specific reactive intermediates by placing electron-donating/accepting residues nearby. Here we perform an abiotic electrophilic aromatic substitution reaction, which is directed precisely through space. Ester arms--positioned above the planes of aromatic rings--enable it to distinguish between nearly identical, neighbouring reactive positions. Quantum mechanical calculations show that, in two competing reaction pathways, both [C-H...O]-hydrogen bonding and electrophile preorganization by coordination to a carbonyl group likely play a role in controlling the reaction. These through-space-directed mechanisms are inspired by dimethylallyl tryptophan synthases, which direct biological electrophilic aromatic substitutions by preorganizing dimethylallyl cations and by stabilizing reactive intermediates with [C-H...N]-hydrogen bonding. Our results demonstrate how the third dimension above and underneath aromatic rings can be exploited to precisely control electrophilic aromatic substitutions.

A polyhedron made of tRNAs.

PubMed

Severcan, Isil; Geary, Cody; Chworos, Arkadiusz; Voss, Neil; Jacovetty, Erica; Jaeger, Luc

2010-09-01

Supramolecular assembly is a powerful strategy used by nature to build nanoscale architectures with predefined sizes and shapes. With synthetic systems, however, numerous challenges remain to be solved before precise control over the synthesis, folding and assembly of rationally designed three-dimensional nano-objects made of RNA can be achieved. Here, using the transfer RNA molecule as a structural building block, we report the design, efficient synthesis and structural characterization of stable, modular three-dimensional particles adopting the polyhedral geometry of a non-uniform square antiprism. The spatial control within the final architecture allows the precise positioning and encapsulation of proteins. This work demonstrates that a remarkable degree of structural control can be achieved with RNA structural motifs for the construction of thermostable three-dimensional nano-architectures that do not rely on helix bundles or tensegrity. RNA three-dimensional particles could potentially be used as carriers or scaffolds in nanomedicine and synthetic biology.

A polyhedron made of tRNAs

PubMed Central

Severcan, Isil; Geary, Cody; Chworos, Arkadiusz; Voss, Neil; Jacovetty, Erica; Jaeger, Luc

2010-01-01

Supra-molecular assembly is a powerful strategy used by nature for building nano-scale architectures with predefined sizes and shapes. Numerous challenges remain however to be solved in order to demonstrate precise control over the synthesis, folding and assembly of rationally designed three-dimensional (3D) nano-objects made of RNA. Using the transfer RNA molecule as a structural building block, we report the design, efficient synthesis and structural characterization of stable, modular 3D particles adopting the polyhedral geometry of a non-uniform square antiprism. The spatial control within the final architecture allows precise positioning and encapsulation of proteins. This work demonstrates that a remarkable degree of structural control can be achieved with RNA structural motifs to build thermostable 3D nano-architectures that do not rely on helix bundles or tensegrity. RNA 3D particles can potentially be used as carriers or scaffolds in nano-medicine and synthetic biology. PMID:20729899

Protozoacidal Trojan-Horse: use of a ligand-lytic peptide for selective destruction of symbiotic protozoa within termite guts.

PubMed

Sethi, Amit; Delatte, Jennifer; Foil, Lane; Husseneder, Claudia

2014-01-01

For novel biotechnology-based termite control, we developed a cellulose bait containing freeze-dried genetically engineered yeast which expresses a protozoacidal lytic peptide attached to a protozoa-recognizing ligand. The yeast acts as a 'Trojan-Horse' that kills the cellulose-digesting protozoa in the termite gut, which leads to the death of termites, presumably due to inefficient cellulose digestion. The ligand targets the lytic peptide specifically to protozoa, thereby increasing its protozoacidal efficiency while protecting non-target organisms. After ingestion of the bait, the yeast propagates in the termite's gut and is spread throughout the termite colony via social interactions. This novel paratransgenesis-based strategy could be a good supplement for current termite control using fortified biological control agents in addition to chemical insecticides. Moreover, this ligand-lytic peptide system could be used for drug development to selectively target disease-causing protozoa in humans or other vertebrates.

Plant protection and growth stimulation by microorganisms: biotechnological applications of Bacilli in agriculture.

PubMed

Pérez-García, Alejandro; Romero, Diego; de Vicente, Antonio

2011-04-01

The increasing demand for a steady, healthy food supply requires an efficient control of the major pests and plant diseases. Current management practices are based largely on the application of synthetic pesticides. The excessive use of agrochemicals has caused serious environmental and health problems. Therefore, there is a growing demand for new and safer methods to replace or at least supplement the existing control strategies. Biological control, that is, the use of natural antagonists to combat pests or plant diseases has emerged as a promising alternative to chemical pesticides. The Bacilli offer a number of advantages for their application in agricultural biotechnology. Several Bacillus-based products have been marketed as microbial pesticides, fungicides or fertilisers. Bacillus-based biopesticides are widely used in conventional agriculture, by contrast, implementation of Bacillus-based biofungicides and biofertilizers is still a pending issue. Copyright © 2010 Elsevier Ltd. All rights reserved.

Maximum Drawdown of Atmospheric CO2 due to Biological Uptake in the Ocean and the Ocean Temperature Effect

NASA Astrophysics Data System (ADS)

Odalen, M.; Nycander, J.; Oliver, K. I. C.; Nilsson, J.; Brodeau, L.; Ridgwell, A.

2016-02-01

During glacials, atmospheric CO2 is significantly lowered; the decrease is about 1/3 or 90 ppm during the last four glacial cycles. Since the ocean reservoir of carbon, and hence the ocean capacity for storing carbon, is substantially larger than the atmospheric and terrestrial counterparts, it is likely that this lowering was caused by ocean processes, drawing the CO2 into the deep ocean. The Southern Ocean circulation and biological efficiency are widely accepted as having played an important part in this CO2 drawdown. However, the relative effects of different processes contributing to this oceanic uptake have not yet been well constrained. In this work, we focus on better constraining two of these processes; 1) the effect of increased efficiency of the biological carbon uptake, and 2) the effect of changes in global mean ocean temperature on the abiotic ocean-atmosphere CO2 equilibrium. By performing ensemble runs using an Earth System Model of Intermediate Complexity (EMIC) we examine the changes in atmospheric pCO2 achieved by 100% nutrient utilization efficiency of biology. The simulations display different ocean circulation patterns and hence different global ocean mean temperatures. By restoring the atmospheric pCO2 to a target value during the spin-up phase, the total carbon content differs between each of the ensemble members. The difference is due to circulation having direct effects on biology, but also on global ocean mean temperature, changing the solubility of CO2. This study reveals the relative importance of of the processes 1 and 2 (mentioned above) for atmospheric pCO2 in a changed climate. The results of this study also show that a difference in carbon content after spin-up can have a significant effect on the drawdown potential of a maximised biological efficiency. Thus, the choice of spin-up characteristics in a model study of climate change CO2 dynamics may significantly affect the outcome of the study.

Controllability and observability of Boolean networks arising from biology

NASA Astrophysics Data System (ADS)

Li, Rui; Yang, Meng; Chu, Tianguang

2015-02-01

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

Near-infrared light-responsive nanomaterials in cancer therapeutics.

PubMed

Shanmugam, Vijayakumar; Selvakumar, S; Yeh, Chen-Sheng

2014-09-07

Noninvasive techniques, such as breath tests (urea breath test), blood pressure measurements using a sphygmomanometer and electrocardiography, were employed by a physician to perform classical diagnosis. The use of state-of-the-art noninvasive therapies at the organ level in modern medicine has gradually become possible. However, cancer treatment demands spatially and temporally controlled noninvasive therapy at the cell level because nonspecific toxicity often causes complicated side effects. To increase survival in cancer patients further, combination therapy and combination drugs are explored which demand high specificity to avoid combined-drug side effects. We believe that high specificity could be obtained by implementing near-infrared (NIR) light-assisted nanoparticles in photothermal therapy, chemotherapy, and photodynamic therapy. To refine this therapy and subsequently achieve high efficiency, novel nanomaterials have been designed and modified either to enhance the uptake and drug delivery to the cancer site, or control treatment to administer therapy efficiently. These modifications and developments have been demonstrated to achieve spatial and temporal control when conducting an in vivo xenograft, because the NIR light penetrated effectively the biological tissue. The nanoplatforms discussed in this review are grouped under the following subheadings: Au nanorods (NRs), Au nanoshells, other Au-related nanomaterials, graphene oxide, upconversion nanoparticles, and other related materials (including materials such as CuS, Fe3O4-related systems, and carbon nanotubes (CNTs)).

Endometrial 'scratching': what the data show.

PubMed

Santamaria, Xavier; Katzorke, Nora; Simón, Carlos

2016-08-01

Since its first description in 2003, the endometrial scratching procedure has been the topic of over 1000 studies. This procedure, used to improve endometrial receptivity for assisted reproduction, is accessible - any gynecologist can easily perform it - and has been adapted into clinical routine by some reproductive units. However, the available data are controversial, and no biological plausibility exists to support the use of this intervention. This study aims to critically review the existing data, focusing on the last 2 years, regarding the efficiency of endometrial scratching. A total of five randomized controlled studies, one meta-analysis, and a systematic review related to endometrial scratching/injury were published in 2014 and 2015. Considerable heterogeneity exists among these studies regarding the selected population, type of treatment, and even timing and devices used to perform the endometrial injury. Importantly, none of these studies reported improved reproductive outcomes in terms of live birth rates following endometrial scratching. Overall, data from properly designed and powered randomized controlled studies demonstrate no beneficial effect of this intervention that is based on unknown biological effects. Endometrial scratching produces pain, costs money, and the side-effects of systematic scratching in the production of Asherman syndrome remain to be seen. Think before scratching.

Peripersonal Space and Margin of Safety around the Body: Learning Visuo-Tactile Associations in a Humanoid Robot with Artificial Skin

PubMed Central

Roncone, Alessandro; Fadiga, Luciano; Metta, Giorgio

2016-01-01

This paper investigates a biologically motivated model of peripersonal space through its implementation on a humanoid robot. Guided by the present understanding of the neurophysiology of the fronto-parietal system, we developed a computational model inspired by the receptive fields of polymodal neurons identified, for example, in brain areas F4 and VIP. The experiments on the iCub humanoid robot show that the peripersonal space representation i) can be learned efficiently and in real-time via a simple interaction with the robot, ii) can lead to the generation of behaviors like avoidance and reaching, and iii) can contribute to the understanding the biological principle of motor equivalence. More specifically, with respect to i) the present model contributes to hypothesizing a learning mechanisms for peripersonal space. In relation to point ii) we show how a relatively simple controller can exploit the learned receptive fields to generate either avoidance or reaching of an incoming stimulus and for iii) we show how the robot can select arbitrary body parts as the controlled end-point of an avoidance or reaching movement. PMID:27711136

Load-sensitive impairment of working memory for biological motion in schizophrenia.

PubMed

Lee, Hannah; Kim, Jejoong

2017-01-01

Impaired working memory (WM) is a core cognitive deficit in schizophrenia. Nevertheless, past studies have reported that patients may also benefit from increasing salience of memory stimuli. Such efficient encoding largely depends upon precise perception. Thus an investigation on the relationship between perceptual processing and WM would be worthwhile. Here, we used biological motion (BM), a socially relevant stimulus that schizophrenics have difficulty discriminating from similar meaningless motions, in a delayed-response task. Non-BM stimuli and static polygons were also used for comparison. In each trial, one of the three types of stimuli was presented followed by two probes, with a short delay in between. Participants were asked to indicate whether one of them was identical to the memory item or both were novel. The number of memory items was one or two. Healthy controls were more accurate in recognizing BM than non-BM regardless of memory loads. Patients with schizophrenia exhibited similar accuracy patterns to those of controls in the Load 1 condition only. These results suggest that information contained in BM could facilitate WM encoding in general, but the effect is vulnerable to the increase of cognitive load in schizophrenia, implying inefficient encoding driven by imprecise perception.

Serial analysis of gene expression (SAGE) in bovine trypanotolerance: preliminary results

PubMed Central

2003-01-01

In Africa, trypanosomosis is a tsetse-transmitted disease which represents the most important constraint to livestock production. Several indigenous West African taurine (Bos taurus) breeds, such as the Longhorn (N'Dama) cattle are well known to control trypanosome infections. This genetic ability named "trypanotolerance" results from various biological mechanisms under multigenic control. The methodologies used so far have not succeeded in identifying the complete pool of genes involved in trypanotolerance. New post genomic biotechnologies such as transcriptome analyses are efficient in characterising the pool of genes involved in the expression of specific biological functions. We used the serial analysis of gene expression (SAGE) technique to construct, from Peripheral Blood Mononuclear Cells of an N'Dama cow, 2 total mRNA transcript libraries, at day 0 of a Trypanosoma congolense experimental infection and at day 10 post-infection, corresponding to the peak of parasitaemia. Bioinformatic comparisons in the bovine genomic databases allowed the identification of 187 up- and down- regulated genes, EST and unknown functional genes. Identification of the genes involved in trypanotolerance will allow to set up specific microarray sets for further metabolic and pharmacological studies and to design field marker-assisted selection by introgression programmes. PMID:12927079

Serial analysis of gene expression (SAGE) in bovine trypanotolerance: preliminary results.

PubMed

Berthier, David; Quéré, Ronan; Thevenon, Sophie; Belemsaga, Désiré; Piquemal, David; Marti, Jacques; Maillard, Jean-Charles

2003-01-01

In Africa, trypanosomosis is a tsetse-transmitted disease which represents the most important constraint to livestock production. Several indigenous West African taurine Bos taurus) breeds, such as the Longhorn (N'Dama) cattle are well known to control trypanosome infections. This genetic ability named "trypanotolerance" results from various biological mechanisms under multigenic control. The methodologies used so far have not succeeded in identifying the complete pool of genes involved in trypanotolerance. New post genomic biotechnologies such as transcriptome analyses are efficient in characterising the pool of genes involved in the expression of specific biological functions. We used the serial analysis of gene expression (SAGE) technique to construct, from Peripheral Blood Mononuclear Cells of an N'Dama cow, 2 total mRNA transcript libraries, at day 0 of a Trypanosoma congolense experimental infection and at day 10 post-infection, corresponding to the peak of parasitaemia. Bioinformatic comparisons in the bovine genomic databases allowed the identification of 187 up- and down- regulated genes, EST and unknown functional genes. Identification of the genes involved in trypanotolerance will allow to set up specific microarray sets for further metabolic and pharmacological studies and to design field marker-assisted selection by introgression programmes.

Expression of single-chain Fv gene specific for gamma-seminoprotein by RTS and its biological activity identification.

PubMed

Han, Yuedong; Haun, Yi; Deng, Jinlan; Gao, Feng; Pan, Bifeng; Cui, Daxiang

2006-01-01

Fabricating a single-chain variable fragment specific for human seminoprotein is very important in antibody-directed enzyme prodrug therapy and NMR imaging for prostate cancer. Here a single-chain Fv specific for gamma-seminoprotein was expressed by RTS. Its activity and the efficiency of entry into prostate cancer cells are investigated by immunoprecipitation and Western blotting and immunofluorescent staining, as well as entry of conjugated magnetic beads into cells. Results showed that ScFv peptides specific for gamma-seminoprotein were successfully prepared, which can bind with the prostate cells specifically and can bring magnetic beads into prostate cancer cells within 15 min, the amount of magnetic beads inside prostate cancer cells increased as the culture time prolonged. ScFv-conjugated magnetic beads did not enter into control cells. In conclusion, the ScFv peptide against human gamma-seminoprotein with biological activity was successfully fabricated, which can take magnetic beads to prostate cancer cells specifically and not to the control cells. This ScFv peptide against human gamma-seminoprotein should be useful in improving the detection and therapy of prostate cancer at early stages and NMR imaging.

Physical constraints on biological integral control design for homeostasis and sensory adaptation.

PubMed

Ang, Jordan; McMillen, David R

2013-01-22

Synthetic biology includes an effort to use design-based approaches to create novel controllers, biological systems aimed at regulating the output of other biological processes. The design of such controllers can be guided by results from control theory, including the strategy of integral feedback control, which is central to regulation, sensory adaptation, and long-term robustness. Realization of integral control in a synthetic network is an attractive prospect, but the nature of biochemical networks can make the implementation of even basic control structures challenging. Here we present a study of the general challenges and important constraints that will arise in efforts to engineer biological integral feedback controllers or to analyze existing natural systems. Constraints arise from the need to identify target output values that the combined process-plus-controller system can reach, and to ensure that the controller implements a good approximation of integral feedback control. These constraints depend on mild assumptions about the shape of input-output relationships in the biological components, and thus will apply to a variety of biochemical systems. We summarize our results as a set of variable constraints intended to provide guidance for the design or analysis of a working biological integral feedback controller. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Practical applications of sulfate-reducing bacteria to control acid mine drainage at the Lilly/Orphan Boy Mine near Elliston, Montana

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

Canty, M.

The overall purpose of this document is to provide a detailed technical description of a technology, biological sulfate reduction, which is being demonstrated under the Mine Waste Technology Pilot Program, and provide the technology evaluation process undertaken to select this technology for demonstration. In addition, this document will link the use of the selected technology to an application at a specific site. The purpose of this project is to develop technical information on the ability of biological sulfate reduction to slow the process of acid generation and, thus, improve water quality at a remote mine site. Several technologies are screenedmore » for their potential to treat acid mine water and to function as a source control for a specific acid-generating situation: a mine shaft and associated underground workings flooded with acid mine water and discharging a small flow from a mine opening. The preferred technology is the use of biological sulfate reduction. Sulfate-reducing bacteria are capable of reducing sulfate to sulfide, as well as increasing the pH and alkalinity of water affected by acid generation. Soluble sulfide reacts with the soluble metals in solution to form insoluble metal sulfides. The environment needed for efficient sulfate-reducing bacteria growth decreases acid production by reducing the dissolved oxygen in water and increasing pH. A detailed technical description of the sulfate-reducing bacteria technology, based on an extensive review of the technical literature, is presented. The field demonstration of this technology to be performed at the Lilly/Orphan Boy Mine is also described. Finally, additional in situ applications of biological sulfate reduction are presented.« less

Polarization control of high order harmonics in the EUV photon energy range.

PubMed

Vodungbo, Boris; Barszczak Sardinha, Anna; Gautier, Julien; Lambert, Guillaume; Valentin, Constance; Lozano, Magali; Iaquaniello, Grégory; Delmotte, Franck; Sebban, Stéphane; Lüning, Jan; Zeitoun, Philippe

2011-02-28

We report the generation of circularly polarized high order harmonics in the extreme ultraviolet range (18-27 nm) from a linearly polarized infrared laser (40 fs, 0.25 TW) focused into a neon filled gas cell. To circularly polarize the initially linearly polarized harmonics we have implemented a four-reflector phase-shifter. Fully circularly polarized radiation has been obtained with an efficiency of a few percents, thus being significantly more efficient than currently demonstrated direct generation of elliptically polarized harmonics. This demonstration opens up new experimental capabilities based on high order harmonics, for example, in biology and materials science. The inherent femtosecond time resolution of high order harmonic generating table top laser sources renders these an ideal tool for the investigation of ultrafast magnetization dynamics now that the magnetic circular dichroism at the absorption M-edges of transition metals can be exploited.

Screening of antagonistic bacteria for biological control of nursery wilt of black pepper (Piper nigrum).

PubMed

Anith, K N; Radhakrishnan, N V; Manomohandas, T P

2003-01-01

Bacterial antagonists of Phytophthora capsici were isolated from underground shoot portions of rooted cuttings of black pepper. Initially isolates were screened by dual culture on potato dextrose agar and carrot agar. Further, a screening was done on black pepper shoots for supression of lesion caused by the pathogen. Most of the antagonists showed varying levels of antagonism in the dual culture and the shoot assay. Isolate PN-026, showing the highest suppression of lesion development in the shoot assay was found to be the most efficient antagonist in reducing Phytophthora capsici induced nursery wilt of black pepper. This screening involving the host, pathogen, and the antagonist, performed on black pepper shoot (the planting material for this vegetatively propagated crop), could be used as a rapid and reliable method for the isolation of efficient bacterial antagonists of P. capsici.

Effect of rhizobacteria on arsenic uptake by macrophyte Eichhornia crassipes (Mart.) Solms.

PubMed

Kaur, Parvinder; Singh, Simranjeet; Kumar, Vivek; Singh, Nasib; Singh, Joginder

2018-01-28

Wastewater flowing in streams and nallahs across India carries several trace metals, including metalloid arsenic (As), which are considered serious environmental contaminants due to their toxicity, and recalcitrant nature. In this study, we determined the phytoremediation of As by Eichhornia crassipes (Mart.) Solms either alone or in association with plant growth-promoting rhizobacteria. Pseudomonas and Azotobacter inoculation to E. crassipes resulted in enhanced As removal compared to uninoculated control. Co-inoculation with a consortium of Pseudomonas, Azotobacter, Azospirillum, Actinomyces, and Bacillus resulted in a higher As (p < 0.05) phytoaccumulation efficiency. P. aeruginosa strain jogii was found particularly effective in augmenting As removal by E. crassipes. Our findings indicate that the synergistic association of E. crassipes and various rhizobacteria is an effective strategy to enhance removal of As and thus may be utilized as an efficient biological alternative for the removal of this metalloid from wastewaters.