Detection of buried explosives with immobilized bacterial bioreporters

The unchecked dispersal of antipersonnel landmines since the late 19th century has resulted in large areas contaminated with these explosive devices, creating a substantial worldwide humanitarian safety risk. The main obstacle to safe and effective landmine removal is the identification of their exact location, an activity that currently requires entry of personnel into the minefields; to date, there is no commercialized technology for an efficient stand-off detection of buried landmines. In this article, we describe the optimization of a microbial sensor strain, genetically engineered for the remote detection of 2,4,6-trinitrotoloune (TNT)-based mines. This bioreporter, designed to bioluminescence in response to minute concentrations of either TNT or 2,4-dinitotoluene (DNT), was immobilized in hydrogel beads and optimized for dispersion over the minefield. Following modifications of the hydrogel matrix in which the sensor bacteria are encapsulated, as well as their genetic reporting elements, these sensor bacteria sensitively detected buried 2,4-dinitrotoluene in laboratory experiments. Encapsulated in 1.5 mm 2% alginate beads containing 1% polyacrylic acid, they also detected the location of a real metallic antipersonnel landmine under field conditions. To the best of our knowledge, this is the first report demonstrating the detection of a buried landmine with a luminescent microbial bioreporter.     

Bioremoval of heavy metals by the use of microalgae

Bioremoval, the use of biological systems for the removal of metal ions from polluted waters, has the potential to achieve greater performance at lower cost than conventional wastewater treatment technologies for metal removal. Bioremoval capabilities of microalgae have been extensively studied, and some commercial applications have been initiated. Although microalgae are not unique in their bioremoval capabilities, they offer advantages over other biological materials in some conceptual bioremoval process schemes. Selected microalgae strains, purposefully cultivated and processed for specific bioremoval applications, have the potential to provide significant improvements in dealing with the world-wide problems of metal pollution. In addition to strain selection, significant advances in the technology appear possible by improving biomass containment or immobilization techniques and by developing bioremoval process steps utilizing metabolically active microalgae cultures. The latter approach is especially attractive in applications where extremely low levels of residual metal ions are desired. This review summarizes the current literature, highlighting the potential benefits and problems associated with the development of novel algal-based bioremoval processes for the abatement of heavy metal pollution.     

Electrical/electrochemical impedance for rapid detection of foodborne pathogenic bacteria

The realization of rapid, sensitive, and specific methods to detect foodborne pathogenic bacteria is central to implementing effective practice to ensure food safety and security. As a principle of transduction, the impedance technique has been applied in the field of microbiology as a means to detect and/or quantify foodborne pathogenic bacteria. The integration of impedance with biological recognition technology for detection of bacteria has led to the development of impedance biosensors that are finding wide-spread use in the recent years. This paper reviews the progress and applications of impedance microbiology for foodborne pathogenic bacteria detection, particularly the new aspects that have been added to this subject in the past few years, including the use of interdigitated microelectrodes, the development of chip-based impedance microbiology, and the use of equivalent circuits for analysis of the impedance systems. This paper also reviews the significant developments of impedance biosensors for bacteria detection in the past 5 years, focusing on microfabricated microelectrodes-based and microfluidic-based Faradaic electrochemical impedance biosensors, non-Faradaic impedance biosensors, and the integration of impedance biosensors with other techniques such as dielectrophoresis and electropermeabilization.     

Quantum-like interference effect in gene expression: glucose-lactose destructive interference

In this note we illustrate on a few examples of cells and proteins behavior that microscopic biological systems can exhibit a complex probabilistic behavior which cannot be described by classical probabilistic dynamics. These examples support authors conjecture that behavior of microscopic biological systems can be described by quantum-like models, i.e., models inspired by quantum-mechanics. At the same time we do not couple quantum-like behavior with quantum physical processes in bio-systems. We present arguments that such a behavior can be induced by information complexity of even smallest bio-systems, their adaptivity to context changes. Although our examples of the quantum-like behavior are rather simple (lactose-glucose interference in E. coli growth, interference effect for differentiation of tooth stem cell induced by the presence of mesenchymal cell, interference in behavior of PrP(C) and PrP(Sc) prions), these examples may stimulate the interest in systems biology to quantum-like models of adaptive dynamics and lead to more complex examples of nonclassical probabilistic behavior in molecular biology.     

Food consumption risks associated with animal clones: what should be investigated?

Somatic Cell Nuclear Transfer (SCNT), or cloning, is likely to be used for the expansion of elite breeding stock of agronomically important livestock used for food. The Center for Veterinary Medicine at the US Food and Drug Administration has been developing a risk assessment to identify hazards and characterize food consumption risks that may result from cloning. The risk assessment is comprised of two prongs. The first evaluates the health of animal clones, and is referred to as the Critical Biological Systems Approach. The second considers the composition of meat and milk from animal clones. Assessing the safety of food products from animal clones and their progeny, at least during these early stages of the development of the technology, is best accomplished by using both approaches: prospectively drawing on our knowledge of biological systems in development and maturation, and in retrograde, from an analysis of food products. Subtle hazards and potential risks that may be posed by animal clones must, however, be considered in the context of other mutations and epigenetic changes that occur in all food animal populations.     

Problems of biochemical organization]

Biological organization has been defined as a unity of structure, function and regulation. Biological organization of hierarchical multilevel biological systems is represented by a hierarchy of functioning controllable structures. The hierarchy of levels of material organization predetermines the existence of a hierarchy of regulatory mechanisms. Biochemical organization involves the levels of material organization corresponding to biomacromolecules, supramolecular complexes and cellular organelles. The levels of biomacromolecules and supramolecular structures effectuating elementary functions and controlled by basic regulatory mechanisms occupy key positions in biological systems. These levels play the role of standard functional blocks; their combination leads to hierarchically higher structural levels (cell, tissue, organ, systems of organs, organism) performing more complex functions and controlled by hierarchically more important regulatory mechanisms. The peculiarities of regulation of biological systems that are due to the existence of a hierarchy of regulatory mechanisms are discussed.     

Computer‐automated bird detection and counts in high‐resolution aerial images: a review

Bird surveys conducted using aerial images can be more accurate than those using airborne observers, but can also be more time‐consuming if images must be analyzed manually. Recent advances in digital cameras and image‐analysis software offer unprecedented potential for computer‐automated bird detection and counts in high‐resolution aerial images. We review the literature on this subject and provide an overview of the main image‐analysis techniques. Birds that contrast sharply with image backgrounds (e.g., bright birds on dark ground) are generally the most amenable to automated detection, in some cases requiring only basic image‐analysis software. However, the sophisticated analysis capabilities of modern object‐based image analysis software provide ways to detect birds in more challenging situations based on a variety of attributes including color, size, shape, texture, and spatial context. Some techniques developed to detect mammals may also be applicable to birds, although the prevalent use of aerial thermal‐infrared images for detecting large mammals is of limited applicability to birds because of the low pixel resolution of thermal cameras and the smaller size of birds. However, the increasingly high resolution of true‐color cameras and availability of small unmanned aircraft systems (drones) that can fly at very low altitude now make it feasible to detect even small shorebirds in aerial images. Continued advances in camera and drone technology, in combination with increasingly sophisticated image analysis software, now make it possible for investigators involved in monitoring bird populations to save time and resources by increasing their use of automated bird detection and counts in aerial images. We recommend close collaboration between wildlife‐monitoring practitioners and experts in the fields of remote sensing and computer science to help generate relevant, accessible, and readily applicable computer‐automated aerial photographic census techniques.     

Bacterial Community Composition of Biological Degreasing Systems and Health Risk Assessment for Workers

Biological degreasing system is a new technology based on the degradation capabilities of microorganisms to remove oil, grease, or lubricants from metal parts. No data is available about the potential biological health hazards in such system. Thus, a health risk assessment linked to the bacterial populations present in this new degreasing technology is, therefore, necessary for workers. We performed both cultural and molecular approaches in several biological degreasing systems for various industrial contexts to investigate the composition and dynamics of bacterial populations. These biological degreasing systems did not work with the original bacterial populations. Indeed, they were colonized by a defined and restricted group of bacteria. This group replaced the indigenous bacterial populations known for degrading complex substrates. Klebsiella pneumoniae, Klebsiella oxytoca, Pseudomonas aeruginosa, and Pantoea agglomerans were important members of the microflora found in most of the biological degreasing systems. These bacteria might represent a potential health hazard for workers.     

Biomechanics of Musculoskeletal System and Its Biomimetic Implications： A Review

Biological musculoskeletal system （MSK）, composed of numerous bones, cartilages, skeletal muscles, tendons, ligaments etc., provides form, support, movement and stability for human or animal body. As the result of million years of selection and evolution, the biological MSK evolves to be a nearly perfect mechanical mechanism to support and transport the human or animal body, and would provide enormously rich resources to inspire engineers to innovate new technology and methodology to develop robots and mechanisms as effective and economical as the biological systems. This paper provides a general review of the current status of musculoskeletal biomechanics studies using both experimental and computational methods. This includes the use of the latest three-dimensional motion analysis systems, various medical imaging modalities, and also the advanced rigid-body and continuum mechanics musculoskeletal modelling techniques. Afterwards, several representative biomimetic studies based on ideas and concepts inspired from the structures and biomechanical functions of the biological MSK are dis- cussed. Finally, the major challenges and also the future research directions in musculoskeletal biomechanics and its biomimetic studies are proposed.     

Recent advances in the development of biosensor for phenol: a review

Phenol and its derivatives are widespread contaminants whose sources are both natural and industrial. Phenol is massively produced and used as a starting material for synthetic polymers and fibers. Although phenolic compounds play important biochemical and physiological roles in living systems, their accumulation in the environment as a result of intensive human activity may result in drastic ecological problem. Various analytical techniques are available for the detection of phenol in environmental samples. But they need complex sample pre-treatment so as are time consuming, costly and use heavy devices. On the other hand a biosensor is a device that gives rapid detection, cost effective and easy. A review study was carried out to accumulate the possible biosensors for the detection of phenolic compounds in environmental samples. A number of biological components including microorganisms, enzymes, antibodies, antigens, nucleic acids etc. can be used for the construction of biosensors that was found to detect phenolic compounds. Of all type of biological components microorganisms and enzymes are mostly used. The microorganisms are Pseudomonas, Moraxella, Arthrobacter, Rhodococcus, and Trichosporon. The most used enzymes are tyrosinase, peroxidase, laccase, glucose dehydrogenase, cellobiose dehydrogenase etc. Antibody sensors can detect a very trace level. The biorecognition of DNA biosensors occur by hybridization of DNA. Biosensors are found to work well when the biological sensing element is immobilized. A variety of immobilization techniques were found to use as adsorption, covalent binding, entrapment, cross-linking etc. For immobilization the matrices used was polyvinyl alcohol, Osmium complex, nafion/sol?Cgel silicate, chitosan, silica gel etc.     

Review: Current status and future prospects of associative nitrogen fixation in rice

Biological sources of nutrients are gaining importance over the chemical and organic sources from the standpoint of environmental safety and quality, and sustainable agriculture. The nutrient input for a growing rice crop can largely be met by promoting the activities of physiologically diverse microorganisms in the aerobic, anaerobic and interface zones in the ecologically important flooded soils. Associative bacteria contribute from 10 to 80 kg N per hectare per cropping season depending upon the ecosystem, cultural practices and rice variety grown. In addition to N contribution, these bacterial associations can improve the nutrient transformations and contribute to plant growth-promoting effects. Current improved agronomic and crop production management systems greatly affect the contributions of biological sources to the overall soil nutrient status. Azospirillum and other associative bacterial systems have been intensively researched using various evaluation techniques to understand the diazotrophic rhizocoenosis. Researches clearly indicate that these associations are governed by several soil, water, nutrient, agrochemical, plant genotype and other biological factors. Considerable efforts have been made so far in selecting efficient bacterial strains as inoculants and identifying host genotypes which support maximum nitrogenase activity in addition to other beneficial traits of effective associative relationships. Knowledge gained so far on how the N2-fixing system in rice functions suggests the need for providing optimum management practices to ensure greater contribution from the plant-microbe associations. Holistic approaches integrating technological developments and achievements in biological sciences could lead to crop improvement. Research on extending nitrogen-fixing symbiosis to rice using molecular and genetic approaches is underway, albeit at a slow pace. The need for further fine-tuning and developing management practices, innovative approaches to improve rice-bacterial systems and the strategies to sustain the benefits from associative diazotrophy are discussed.     

The analysis of distributed control and information processing in adaptive systems: a biologically motivated approach.

Biological systems have evolved hierarchical, distributed control structures that greatly enhance their adaptability. Two important determinants of biological adaptability considered here are: (i) the pattern of distribution of self-control capabilities; (ii) the degree of programmability of information processing. In this paper we model organizations as goal-oriented, adaptive systems, possessing properties similar to those of biological systems. We use the notion of implicit control (defined as the capability of self-control that is embedded in a system's own dynamics) in the analysis of the impact of specific patterns of distribution of control and information processing on the adaptability of organizations. A principle of design of organizational information systems, that captures important aspects of adaptability-preserving strategies of information processing in biological systems, is stated in terms of the implicit control concept.     

Does quantum mechanics play a non-trivial role in life?

There have been many claims that quantum mechanics plays a key role in the origin and/or operation of biological organisms, beyond merely providing the basis for the shapes and sizes of biological molecules and their chemical affinities. These range from Schr?dinger's suggestion that quantum fluctuations produce mutations, to Hameroff and Penrose's conjecture that quantum coherence in microtubules is linked to consciousness. I review some of these claims in this paper, and discuss the serious problem of decoherence. I advance some further conjectures about quantum information processing in bio-systems. Some possible experiments are suggested.     

Beyond the diffraction limit: far-field fluorescence imaging with ultrahigh resolution

Fluorescence microscopy is an important and extensively utilised tool for imaging biological systems. However, the image resolution that can be obtained has a limit as defined through the laws of diffraction. Demand for improved resolution has stimulated research into developing methods to image beyond the diffraction limit based on far-field fluorescence microscopy techniques. Rapid progress is being made in this area of science with methods emerging that enable fluorescence imaging in the far-field to possess a resolution well beyond the diffraction limit. This review outlines developments in far-field fluorescence methods which enable ultrahigh resolution imaging and application of these techniques to biology. Future possible trends and directions in far-field fluorescence imaging with ultrahigh resolution are also outlined.     

农药残留检测关键用酶固定化研究进展

为保障消费者食用安全,迫切需要研发农产品和食品中的农药残留快速检测技术.酶抑制法检测是目前农药残留快速检测技术中的主要研究方向之一,而酶的固定化是用基于酶抑制法原理对农药残留检测研究中的重要步骤.通过物理或化学的方法高效地将酶固定于载体上,同时保持酶的催化活性是开发各类基于酶抑制法检测农药残留传感器的关键.本文将从固定...     

Solid-state NMR structure determination

Biological applications of solid-state NMR (SS-NMR) have been predominantly in the area of model membrane systems. Increasingly the focus has been membrane peptides and proteins. SS-NMR is able to provide information about how the peptides or proteins interact with the lipids or other peptides/proteins in the membrane, their effect on the membrane and the location of the peptides or proteins relative to the membrane surface. Recent developments in biological SS-NMR have been made possible by improvements in labelling and NMR techniques. This review discusses aligned systems and magic angle spinning techniques, bilayers and bicelles, and measurement of chemical shift anisotropy and dipolar coupling. A number of specific experiments such as cross polarization, rotational resonance, REDOR, PISEMA, MAOSS and multidimensional experiments are described. In addition to 2H, 13C and 15N, recent solid-sate 1H, 19F and 17O NMR work is discussed. Several examples of the use of SS-NMR to determine the structure of membrane peptides and proteins are given.     

Microfluidics Approaches in Modern Developmental Biology

Modern automated microsystems based on microhydrodynamic (microfluidic) technologies— labs on chips—make it possible to solve various basic and applied research problems. In the last 15 years, the development of these approaches in application to the problems of modern quantitative (systems) development biology has been observed. In this field, high-throughput experiments aimed at accumulating ample quantitative data for their subsequent computer analysis are important. In this review, the main directions in the development and application of microfluidics approaches for solving problems of modern developmental biology using the classical model object, Drosophila embryo, as an example is discussed. Microfluidic systems provide an opportunity to perform experiments that can hardly be performed using other approaches. These systems allow automated, rapid, reliable, and proper placing of many live embryos on a substrate for their simultaneous confocal scanning, sorting them, or injecting them with various agents. Such systems make it possible, in particular, to create controlled gradients of microenvironmental parameters along a series of developing embryos or even to introduce discontinuity in parameters within the microenvironment of one embryo, so that the head half is under other conditions compared to the tail half (at continuous scanning). These approaches are used both in basic research of the functions of gene ensembles that control early development, including the problems of resistance of early patterns to disturbances, and in test systems for screening chemical agents on developing embryos. The problems of integration of microfluidic devices in systems for automated performance of experiments simultaneously on many developing embryos under conditions of their continuous scanning using modern fluorescence microscopy instruments will be discussed. The methods and approaches developed for Drosophila are also applicable to other model objects, even mammalian embryos.     

Developmental imaging: Insights into the avian embryo

The study of embryonic events using different animal model systems is crucial for gaining insights into human development and birth defects. Biological imaging plays a major role in this effort by providing a spatiotemporal framework to link complex cell movements with molecular data. However, depending on the age of the embryo and the location of a morphogenetic event, visualization often requires the design of novel culture and imaging techniques. One of the primary model systems for biological imaging is the avian embryo, due to its accessibility to manipulation, relatively two-dimensional morphogenesis early on, and viability when grown in culture. Significant work in avian embryo culture and cell labeling, together with advances in imaging technology, now make it possible to monitor many developmental events within the period from egg laying to hatching. Here, we present the latest in avian developmental imaging, focusing on cell labeling, embryo culture, and imaging technologies.