Biological Devices Research Articles

Suppressing variation in synthetic circuits

Mol Syst Biol. 7: 520 One of the challenges in engineering biological devices is to precisely control the number of parts in each cell. Automobile engineers do not worry about control mechanisms for variation in the number of wheels on a car—if an engineer designs a car with four wheels, then all the cars roll off the assembly line with four wheels. But biology is dynamic, and biological circuits change continuously. Therefore, synthetic biologists are faced with the challenge that the number of DNA, RNA, and protein components of their devices may vary between cells, possibly by several folds. Are there simple methods for ensuring that stoichiometric changes do not affect the proper functioning of the device? In a recent Molecular Systems Biology article, Bleris et al (2011) address this question by identifying useful circuits that can make biological output insensitive to DNA dosage. Although the network of interactions between the components of a cell is dazzlingly complex, biological networks contain smaller, recurrent subnetworks called motifs (Milo et al , 2002). Motifs often convey useful properties, such as altering the response time or magnitude of a propagated signal. A particular motif found in many biological contexts is a three‐node motif called a Type I incoherent feed‐forward loop (I1‐FFL; Figure 1A …

Fabrication of gold micro-spine structures for improvement of cell/device adhesion

Improvement of the interface contact between biological objects and electronic devices can significantly enhance the quality of electronic signal transfer. The surface of biosensor can be artificially modified in order to strengthen the adhesion of biological cells. We report on results of fabrication of micron and submicron golden spines by means of e-beam lithography and electroplating. The fabrication technique allows easy modification of the size and shape of golden spines by variation of processing parameters. The structures with different spine profiles and spacing have been fabricated for optimization of cell growth conditions. We present the results of growth of rat cortical neurons on the surface of spine modified samples. Well-defined cell guidance was established at the spine arrays. Furthermore, the results of transmission electron microscope and focused ion beam technique confirm the good adhesion between the spines and cell structures.

Small Cells—Big Future

Small Cells—Big Future

Biological electrochemical devices for production of current and hydrogen

Biological electrochemical devices for production of current and hydrogen

Effect of Low-Power Gallium–Aluminum–Arsenium Noncoherent Light (640 nm) on Muscle Activity: A Clinical Study

Studies have shown the significant effects of electromagnetic irradiation in the visible region, with laser as an irradiation source. However, the effect of LEDs (light-emitting diodes) irradiation in similar wavelengths is not known. The purpose of this clinical study was to verify the effects of the LED (640 nm with 40 nm full bandwidth at half maximum) on muscle activity. The study was done with 30 test subjects, of both genders, aged 23 ± 3 years, with a mean weight of 60 kg, divided into three groups (n = 10). Fatigue was induced through the maximum power of a bite, for 60 s in two overlaid occlusal platforms, coupled to a load cell and to a biologic signal-acquisition device. LED irradiation of the right masseter muscle was applied to all subjects. The left muscle received placebo treatment. Irradiation was applied in eight points on the right masseter muscle (transcutaneous), 1.044 J per point, 2.088 J per point, or 3.132 J per point, 0.116 W, 0.522 cm(2) spot size, 0.816 cm spot Ø, continuous wave, perpendicular to the skin. An increase in muscle activity was observed after irradiation with 1.044 J per point (p < 0.05). A significant increase (p < 0.01) in the time before fatigue was observed in the irradiated muscle with 2.088 J per point, without a change in the force of contraction (p > 0.05). This change was not observed with 1.044 J per point and 3.132 J per point. The results suggest a dose-dependent relation with this kind of noncoherent irradiation in the red region of the electromagnetic spectrum in the muscle-fatigue process. It was concluded that LED can be used as a clinical tool to increase muscle activity (1.044 J per point) and to prevent fatigue (2.088 J per point), without change in the muscle force.

Nanoscale Biomolecular Structures on Self-Assembled Monolayers Generated from Modular Pegylated Disulfides

A solid-phase synthetic strategy was developed that uses modular building blocks to prepare symmetric oligo(ethylene glycol)-terminated disulfides with a variety of lengths and terminal functionalities. The modular disulfides, composed of alkyl amino groups linked by an amide group to oligoethylene chains were used to generate self-assembled monolayers (SAMs), which were characterised to determine their applicability for biomolecular applications. X-ray photoelectron spectroscopy (XPS) of the SAMs obtained from these molecules demonstrated improved stability towards displacement by 16-hexadecanethiol, while surface plasmon resonance (SPR) analyses of SAMs prepared with the hydroxy-terminated oligoethylene disulfide showed equal resistance to non-specific protein adsorption in comparison to 11-mercaptoundecyl tri(ethylene glycol). SAMs made from these adsorbates were amenable to nanoscale patterning by scanning near-field photolithography (SNP), facilitating the fabrication of nanopatterned, protein-functionalised surfaces. Such SAMs may be further developed for bionanotechnology applications such as the fabrication of nanoscale biological arrays and sensor devices.

Possible way to substantial improvement of early warning system in the International Odra (Oder) River Basin

Water ecosystems are threatened by accidental spills of pollution. Rapidity and trueness of information gathering the biological impact of accidental pollution is crucial for the efficiency of the minimisation of possible deterioration of ecosystems and for success in detecting the source of pollution. Due to the randomised occurrence of accidental spills the only way to quickly detect hazardous situations is to perform continuous monitoring of surface water quality. The current situation in the field of early warning in the International Odra (Oder) River basin is not satisfactory. The actual number of monitoring stations and list of routinely continuously monitored parameters are not able to meet the needs of sensitive and rapid detection of biological impact of accidental pollution spills. An effort to change this unfavourable situation was the reason for the offer survey, selection and a model operation of a commercially produced biological monitoring device. This apparatus was located on the border-line profile on the territory of the Czech Republic and represented the first and only one tool of continual biological monitoring of surface water quality in the International Odra (Oder) River Basin. The selected apparatus was the Daphnia Toximeter produced by the firm bbe Moldaenke (Kiel, Germany). This device exploited for rapid detection of changes of biological quality of surface water evaluation of behavioural response of monitoring organisms-daphnids. Five years of model operation proved its suitability for early warning purposes. The apparatus was reliable in function and sensitive enough to detect the deterioration of the biological quality of the river water. The given examples document its applicability not only for detection of accidental spills but also of illegal emissions of pollution, which are very often toxic.

High‐Throughput Near‐Field Optical Nanoprocessing of Solution‐Deposited Nanoparticles

The application of nanoscale electrical and biological devices will benefit from the development of nanomanufacturing technologies that are high-throughput, low-cost, and flexible. Utilizing nanomaterials as building blocks and organizing them in a rational way constitutes an attractive approach towards this goal and has been pursued for the past few years. The optical near-field nanoprocessing of nanoparticles for high-throughput nanomanufacturing is reported. The method utilizes fluidically assembled microspheres as a near-field optical confinement structure array for laser-assisted nanosintering and nanoablation of nanoparticles. By taking advantage of the low processing temperature and reduced thermal diffusion in the nanoparticle film, a minimum feature size down to approximately 100 nm is realized. In addition, smaller features (50 nm) are obtained by furnace annealing of laser-sintered nanodots at 400 degrees C. The electrical conductivity of sintered nanolines is also studied. Using nanoline electrodes separated by a submicrometer gap, organic field-effect transistors are subsequently fabricated with oxygen-stable semiconducting polymer.

Unraveling the Effects of Size, Composition, and Substrate on the Localized Surface Plasmon Resonance Frequencies of Gold and Silver Nanocubes: A Systematic Single-Particle Approach

Localized surface plasmon resonances (LSPRs), resulting from the interaction of light with metal nanoparticles, are powerful tools for biological sensors, surface-enhanced spectroscopies, and optical devices. LSPR frequencies are strongly dependent on a nanoparticle’s structure, composition, and local dielectric environment. However, these relationships are prohibitively difficult or impossible to probe from bulk solutions due to the heterogeneity of chemically synthesized products. In this study, systematic single-particle structure−property measurements, coupled with a statistical analysis and FDTD calculations, are performed on silver and gold nanocubes. The dependencies of LSPR frequencies on nanocube size, composition, and substrate dielectric constant are determined. The results obtained represent the most quantitative measurements and analysis to date, yielding predictive rules and fundamental insights into the interactions between nanoparticles and substrates.

An introduction device for the aphidophagous hoverfly Episyrphus balteatus (De Geer) (Diptera: Syrphidae)

Augmentative biocontrol constitutes a safe option to reduce pest populations through the enhancement of natural enemies’ activity. In this context, the aphidophagous syrphid Episyrphus baltetaus (De Geer) (Diptera: Syrphidae) is a promising candidate for aphid biological control: larvae of this syrphid attack and consume a wide range of aphid species and are found on many vegetable crops. Because natural populations of beneficial insects are not always sufficient to regulate the pest infestations, this work has focused on the conception of a biological control device containing syrphid eggs which ones can easily be introduced in fields or greenhouses. Using semiochemicals [E-(β)-farnesene, R-(+)-limonene and (Z)-3-hexenol], honeydews and “artificial honeydews” (10% or 30% aqueous solutions of sucrose, fructose and glucose), the syrphid oviposition was artificially induced on an inert surface. Specifically, E-(β)-farnesene and concentrated mono-sugars (30%) were identified as the most efficient ovipositional stimulants. To test and validate the biological control device described above, laboratory and field experiments were performed: a plastic lamella covered with syrphid eggs was suspended on aphid infested plants in order to measure the efficiency of the device. The results obtained were promising since populations of 500 aphids were eliminated in 10 days when 15 syrphid eggs were introduced. The use of such a biological control device could certainly contribute to the biological control to reduce the aphid infestations.

Effects of moisture content and compression positions on mechanical properties of carob pod (Ceratonia siliqua L.)

Mechanical properties should be investigated for the harvest and post harvest operations of carob pod which is the fruit of carob trees (Ceratonia siliqua L.). These properties are pre-requisite for the design and development of harvesting, transportation, storage, and grinding machines used for carob pod. In this study, rupture force, bioyield force, rupture deformation, bioyield deformation, modulus of elasticity and rupture energy were determined for carob pod as functions of moisture content at four different levels of 8.3, 13.2, 14.1, 16.8% wet basis (w.b.) and compression positions of Horizantal1 (H1), Horizantal2 (H2), Vertical1 (V1), and Vertical2 (V2). The biological material test device was used to measure the mechanical properties of carob pod. Results showed that rupture force, bioyield force, modulus of elasticity and rupture energy decreased with increase in moisture content of carob pod. The rupture force ranged from 101.0 to 197.0 N while the bioyield force varies between 84.0 and 159.0 N. The modulus of elasticity changed between 22.5 and 43.8 N mm -2 . The range of the rupture energy calculated was between 268 and 419 J. The results showed that rupture force measured at the horizontal positions (H1 and H2) were higher than that of the vertical positions (V1 and V2).

A Highly Sensitive Enzyme-Amplified Immunosensor Based on a Nanoporous Niobium Oxide (Nb2O5) Electrode

We report on the development of an enzyme-amplified sandwich-type immunosensor based on a thin gold film sputtered on an anodic nanoporous niobium oxide (Au@Nb2O5) electrode. The electrocatalytic activity of enzymatically amplified electroactive species and a stable electrode consisting of Au@Nb2O5 were used to obtain a powerful signal amplification of the electrochemical immunobiosensor. The method using this electrochemical biosensor based on an Au@Nb2O5 electrode provides a much better performance than those based on conventional bulk gold or niobium oxide electrodes. Our novel approach does not require any time-consuming cleaning steps to yield reproducible electrochemical signals. In addition, the strong adhesion of gold films on the niobium oxide electrodes offers a very stable substrate during electrochemical biosensing. Cyclic voltammetry measurements indicate that non-specific binding of proteins to the modified Au@Nb2O5 surface is sufficiently low to be ignored in the case of our novel system. Finally, we demonstrated the ability of the biosensor based on an Au@Nb2O5 offering the enhanced performance with a high resolution and sensitivity. Therefore, it is expected that the biosensor based on an Au@Nb2O5 has great potential for highly efficient biological devices.

A Powerful Method to Describe Transport Properties of Nano and Bio Materials

A key factor for the efficiency in nanostructured devices is charge transport. Despite considerable attention to this subject, the precise nature of transport processes in these systems has remained unresolved. To understand the microscopic aspects of carrier dynamics, we suggest a method for the calculation of correlation functions. They can be expressed as the Fourier transform of a kernel containing the frequency-dependent conductivity (). We present results for the velocity correlation functions &lt;v(o)v(t)&gt;, the mean square deviation of position R2 = &lt;[R(t)-R(o)]2&gt; and the diffusion coefficient D = (R2/t) in materials, like TiO2, ZnO, Si, for which a Drude-Lorentz description or its generalizations applies with a good agreement with experiments. We find that D = 0, indicating absence of diffusion at long times, except in the Drude case (o = 0). For small times t/ &lt; 1, however, diffusion can occur even when o 0, within a limited region of size increasing with the value of o. The quantum mechanical extension of this method allows applications for the nanodiffusion in nanostructured, porous and cellular materials, as for biological, medical and nanopiezotronic devices.

A Counter-WMD Strategy for the Future

past year has witnessed a renewed emphasis by US government agencies addressing threat of weapons of mass destruction (WMD). In December 2009, Obama Administration released its second presidential policy directive, a National Strategy to Counter Biological Threats, which addressed challenge of combating infectious diseases, regardless of whether they were natural or manmade. In February 2010, Quadrennial Defense Review stressed how proliferation of WMD continues to undermine global In April, Nuclear Posture Review was released for first time as an unclassified document, along with a newly signed Strategic Arms Reduction Treaty, reducing deployable number of Russian and US nuclear weapons. In May, representatives from across globe met to renew Nuclear Nonproliferation Treaty, which attempts to reduce (and eventually eliminate) total number of nuclear-owning weapon in world. It has been a busy spring. During talks related to these initiatives, President Barack Obama directly connected threat of nuclear terrorism to success of nuclear proliferation efforts. He declared, The greatest threat to US and global security is no longer a nuclear exchange between nations, but nuclear terrorism by violent extremists and nuclear proliferation to an increasing number of states. (1) current focus on nonproliferation activities, however, does not stop terrorists from seeking and potentially obtaining nuclear and biological materials, technology, and devices. For that matter, emphasis on combating terrorism has not resulted in a reduction of terrorist ambitions to obtain these materials, either. US government, and Department of Defense (DOD) in particular, needs to review its strategy to combat weapons of mass destruction. combating WMD framework is based on a counterproliferation strategy developed in response to threat of nuclear, biological, and chemical (NBC) weapons to military forces in 1990s, however, its scope was broadened after September 2001 to address concerns relating to homeland security. For talk about the most dangerous weapons in hands of most dangerous people, there has been little discussion on whether combating WMD strategy is adequate against current and future threats. This article will review development of combating WMD strategy from its initiation in 1990s, as a result of post-conflict analysis of Persian Gulf War in 1991. It will outline creation of combating WMD strategy during George W. Bush Administration. article focuses on challenges in interpretation, largely due to thesis that terrorists were actively seeking WMD materials and technology from rogue states that had developed this capability (or were in process of doing so). Last, it will offer suggestions on how to improve framework, largely by defining strategy to counter nation-state WMD programs as distinct from strategy to counter terrorist pursuit of WMD. If US government clearly articulates these two strategies as separate but related, as opposed to being one single strategy to counter WMD, agencies responsible for executing these strategies will be much more effective. Genesis of DOD's Combating WMD Strategy In 1993, Office of Secretary of Defense (OSD) initiated a Defense Counterproliferation Initiative with image of ill-prepared US forces facing Iraq's chemical and biological (CB) weapons still fresh in its mind. There was some initial concern by nonproliferation community that DOD was attempting to usurp its role that a focus on developing offensive and defensive capabilities to counter adversarial use of CB weapons would come at cost of reducing nonproliferation efforts. (2) After a few years of discussion, OSD tasked Joint Staff in 1996 to develop a counterproliferation strategy, stating in Defense Planning Guidance that all US forces must be prepared to conduct wartime operations against adversaries armed with chemical or biological weapons. …

Biomolecular Computing Devices in Synthetic Biology

Synthetic biology and biomolecular computation are disciplines that fuse when it comes to designing and building information processing devices. In this chapter, we study several devices that are representative of this fusion. These are three gene circuits implementing logic gates, a DNA nanodevice and a biomolecular automaton. The operation of these devices is based on gene expression regulation, the so-called competitive hybridization and the workings of certain biomolecules like restriction enzymes or regulatory proteins. Synthetic biology, biomolecular computation, systems biology and standard molecular biology concepts are also defined to give a better understanding of the chapter. The aim is to acquaint readers with these biomolecular devices born of the marriage between synthetic biology and biomolecular computation.

INVESTIGATION INTO THE AIR TREATMENT EFFICIENCY OF BIOFILTERS OF DIFFERENT STRUCTURES

Biological air treatment devices, biofilters, of four different structures with different origin charges, composed of natural zeolite granules, foam cubes and wood chips, were used for the experimental investigation. Biological and ad‐sorptive air treatment methods are employed to clean the air from volatile organic compounds by mixing foam and zeolite with wood chips. The use of complex cleaning technologies improves the efficiency of the device and extends the useful life of a charge. The investigation showed that microorganisms predominant in the process of biocleaning could also propagate in the charges of inorganic origin composed of natural zeolite. The dependences of biofilter treatment efficiency on the nature, concentration and filtration time of the fed pollutant were determined when cultivating associations of spontaneous microorganisms in a charge. The best filtration efficiency of the charge was achieved when acetone‐polluted air was fed into the device at a speed of 0.3 m/s. The treatment efficiency of a biofilter with a humidifying chamber reached 98% when cleaning the air from acetone with an initial concentration of the pollutant of 305 mg/m3. The cleaning efficiency of the device increases when reducing the concentrations of pollutants fed into the device and increasing the time of their filtration. Santrauka Eksperimentiniams tyrimams atlikti naudota keturi skirtingu konstrukciju biologiniai oro valymo irenginiai - biofiltrai su skirtingos kilmes ikrovomis, sudarytomis iš gamtines kilmes ceolito granuliu, porolono kubeliu bei medienos skiedru. Porolona ir ceolita maišant su medienos skiedromis, lakiesiems organiniams junginiams iš oro valyti taikomi biologinis ir adsorbcinis oro valymo metodai. Irenginio valymo efektyvumas pagerinamas bei ikrovos naudojimo trukme ilgeja naudojant kompleksines valymo technologijas. Ištyrus nustatyta, kad biologinio valymo procese vyraujantys mikroorganizmai gali daugintis ir neorganines kilmes ikrovose, sudarytose iš gamtinio ceolito. Ikrovoje kultivuojant savaiminiu mikroorganizmu asociacijas nustatytos biofiltru valymo efektyvumo priklausomybes nuo i irengini tiekiamo teršalo prigimties, koncentracijos, filtracijos laiko. Geriausiai ikrova filtravo 0,3 m/s greičiu i biofiltra tiekiama acetono garais užteršta ora. Šalinant iš oro acetona, kai pradine teršalo koncentracija 305 mg/m3, biofiltro su drekinimo kamera valymo efektyvumas sieke 98 %. Mažinant i biofiltrus tiekiamu teršalu koncentracijas bei didinant ju filtracijos laika irenginiu valymo efektyvumas dideja. Резюме Для экспериментальных исследований использовались четыре устройства для биологической очистки воздуха – биофильтры разных конструкций. Загрузку биофильтров составляли гранулы естественного цеолита, поролон и древесина, которые использовались для очистки воздуха от летучих органических веществ. В случае применения для очистки воздуха поролона и цеолита в смеси с древесиной применялся биологический и адсорбционный методы. Применение комплексных технологий способствует улучшению эффективности очистки воздуха и продлению срока применения загрузки. Исследования показали, что в процессе биоочистки микроорганизмы могут размножаться и в неорганической загрузке, состоящей из природного цеолита. Культивируя в загрузке ассоциации микроорганизмов, найдены зависимости эффективности биофильтра от характера загрязнителя, его концентрации, времени фильтрации. Лучше всего загрузка фильтровала воздух, загрязненный парами ацетона и подаваемый в установку со скоростью 0,3 м/с. Эффективность очистки воздуха от ацетона при начальной концентрации загрязняющих веществ в 305 мг/м3 для биофильтра с камерой увлажнения составляла 98%. При снижении концентрации загрязняющих веществ, подаваемых в биофильтр, и повышении времени фильтрации загрязненного воздуха эффективность установки увеличивается.

Mammalian synthetic biology – from tools to therapies

Mammalian synthetic biology holds the promise of providing novel therapeutic strategies, and the first success stories are beginning to be reported. Here we focus on the latest generation of mammalian transgene control devices, highlight state-of-the-art synthetic gene network design, and cover prototype therapeutic circuits. These will have an impact on future gene- and cell-based therapies and help bring drug discovery into a new era. The inventory of biological parts that are essential for life on this planet is becoming increasingly complete. The postgenomic era has provided encyclopedic information on gene-function correlations and systems biology is now delivering comprehensive details on the dynamics of biochemical reaction networks in living organisms. The time has come to reassemble these catalogued items and design new biological devices and systems with novel and useful functionality in a rational and systematic manner. This is the premise of synthetic biology, a constructive systems biology discipline likely to become the life science revolution of the 21(st) century.

Synthetic protocols for nano sensor transmitting platforms using enzyme and DNA based computing

The ability to create communication networks of biological nanoscale devices has the potential to open up new opportunities and applications, particularly in areas such as health care and information processing. Inspired by recent developments in molecular communication and biomolecular computing, we present in this paper a biological cell based molecular communication transmitting platform using synthetic molecular computing techniques. We investigated two protocol solutions which include DNA based computing coupled with viral particles and enzyme based computing coupled with calcium signaling. Each of these solutions is designed for different applications and environments. For each of these approaches we demonstrate how elements from various layers in the communication stack are developed using the molecular computing mechanisms. Simulation results are also presented to illustrate the functionality and performance of each solution.

Liver Transplantation for Acute Liver Failure: A Spanish Perspective

The Spanish characteristics of organ donation (high accessibility to a transplant) and the different proportion in the etiologies of acute liver failure (ALF), namely, the very low incidence of paracetamol overdose causing this syndrome in contrast with other Western countries, are the causes of some specific features of emergency liver transplantation for ALF. The most relevant are the short time between the need for a graft and effective urgent liver transplant, and the high proportion of patients who undergo this therapy. This paper analyzes these characteristics and provides information about the use of biological and nonbiological extracorporeal liver support devices in acute liver failure, suggesting that these systems should be tested in countries with a long waiting times for urgent liver transplantation, or in patients with ALF and contraindications for transplantation.

Paving the way for synthetic biology‐based bioremediation in Europe

Paving the way for synthetic biology‐based bioremediation in Europe