Programming living sensors for environment,health and biomanufacturing

Synthetic biology offers new tools and capabilities of engineering cells with desired functions for example as new biosensing platforms leveraging engineered microbes. In the last two decades, bacterial cells have been programmed to sense and respond to various input cues for versatile purposes including environmental monitoring, disease diagnosis and adaptive biomanufacturing. Despite demonstrated proof-of-concept success in the laboratory, the real-world applications of microbial sensors have been restricted due to certain technical and societal limitations. Yet, most limitations can be addressed by new technological developments in synthetic biology such as circuit design, biocontainment and machine learning. Here, we summarize the latest advances in synthetic biology and discuss how they could accelerate the development, enhance the performance and address the present limitations of microbial sensors to facilitate their use in the field. We view that programmable living sensors are promising sensing platforms to achieve sustainable, affordable and easy-to-use on-site detection in diverse settings.     

New highly sensitive and selective catalytic DNA biosensors for metal ions

While remarkable progress has been made in developing sensors for metal ions such as Ca(II) and Zn(II), designing and synthesizing sensitive and selective metal ion sensors remains a significant challenge. Perhaps the biggest challenge is the design and synthesis of a sensor capable of specific and strong metal binding. Since our knowledge about the construction of metal-binding sites in general is limited, searching for sensors in a combinatorial way is of significant value. Therefore, we have been able to use a combinatorial method called in vitro selection to obtain catalytic DNA that can bind a metal ion of choice strongly and specifically. The metal ion selectivity of the catalytic DNA was further improved using a 'negative selection' strategy where catalytic DNA that are selective for competing metal ions are discarded in the in vitro selection processes. By labeling the resulting catalytic DNA with a fluorophore/quencher pair, we have made a new class of metal ion fluorescent sensors that are the first examples of catalytic DNA biosensors for metal ions. The sensors combine the high selectivity of catalytic DNA with the high sensitivity of fluorescent detection, and can be applied to the quantitative detection of metal ions over a wide concentration range and with high selectivity. The use of DNA sensors in detection and quantification of lead ions in environmental samples such as water from Lake Michigan has been demonstrated. DNA is stable, cost-effective, environmentally benign, and easily adaptable to optical fiber and microarray technology for device manufacture. Thus, the DNA sensors explained here hold great promise for on-site and real-time monitoring of metal ions in the fields of environmental monitoring, developmental biology, clinical toxicology, wastewater treatment, and industrial process monitoring.     

Recent developments of genetically encoded optical sensors for cell biology

Optical sensors are powerful tools for live cell research as they permit to follow the location, concentration changes or activities of key cellular players such as lipids, ions and enzymes. Most of the current sensor probes are based on fluorescence which provides great spatial and temporal precision provided that high‐end microscopy is used and that the timescale of the event of interest fits the response time of the sensor. Many of the sensors developed in the past 20 years are genetically encoded. There is a diversity of designs leading to simple or sometimes complicated applications for the use in live cells. Genetically encoded sensors began to emerge after the discovery of fluorescent proteins, engineering of their improved optical properties and the manipulation of their structure through application of circular permutation. In this review, we will describe a variety of genetically encoded biosensor concepts, including those for intensiometric and ratiometric sensors based on single fluorescent proteins, Forster resonance energy transfer‐based sensors, sensors utilising bioluminescence, sensors using self‐labelling SNAP‐ and CLIP‐tags, and finally tetracysteine‐based sensors. We focus on the newer developments and discuss the current approaches and techniques for design and application. This will demonstrate the power of using optical sensors in cell biology and will help opening the field to more systematic applications in the future.     

Quantitative imaging using genetically encoded sensors for small molecules in plants

Quantitative imaging in live cells is a powerful method for monitoring the dynamics of biomolecules at an excellent spatio-temporal resolution. Such an approach, initially limited to a small number of substrates for which specific dyes were available, has become possible for a large number of biomolecules due to the development of genetically encoded, protein-based sensors. These sensors, which can be introduced into live cells through a transgenic approach, offer the benefits of quantitative imaging, with an extra advantage of non-invasiveness. In the past decade there has been a drastic expansion in the number of biomolecules for which genetically encoded sensors are available, and the functional properties of existing sensors are being improved at a dramatic pace. A number of technical improvements have now made the application of genetically encoded sensors in plants rather straightforward, and some of the sensors such as calcium indicator proteins have become standard analytical tools in many plant laboratories. The use of a handful of probes has already revealed an amazing specificity of cellular biomolecule dynamics in plants, which leads us to believe that there are many more discoveries to be made using genetically encoded sensors. In this short review, we will summarize the progress made in the past 15?years in the development in genetically encoded sensors, and highlight significant discoveries made in plant biology.     

Synthetic tissue biology: tissue engineering meets synthetic biology

We propose the term "synthetic tissue biology" to describe the use of engineered tissues to form biological systems with metazoan-like complexity. The increasing maturity of tissue engineering is beginning to render this goal attainable. As in other synthetic biology approaches, the perspective is bottom-up; here, the premise is that complex functional phenotypes (on par with those in whole metazoan organisms) can be effected by engineering biology at the tissue level. To be successful, current efforts to understand and engineer multicellular systems must continue, and new efforts to integrate different tissues into a coherent structure will need to emerge. The fruits of this research may include improved understanding of how tissue systems can be integrated, as well as useful biomedical technologies not traditionally considered in tissue engineering, such as autonomous devices, sensors, and manufacturing.     

生物传感器应用于食源性致病菌检测研究进展

生物传感器技术是一种由生物、化学、物理、医学、电子技术等多种学科互相渗透形成起来的高新微量分析技术,具有选择性好、灵敏度高、分析速度快、成本低、能在复杂的体系中进行在线连续监测的特点.本文根据生物传感器的分子识别元件将生物传感器分为DNA传感器、免疫传感器、细胞传感器三大类,简要介绍各种生物传感器的原理及其在检测食源性致病菌方面的应用情况,并对未来生物传感器应用于实际检测进行了展望.     

Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways

Cells are filled with biosensors, molecular systems that measure the state of the cell and respond by regulating host processes. In much the same way that an engineer would monitor a chemical reactor, the cell uses these sensors to monitor changing intracellular environments and produce consistent behavior despite the variable environment. While natural systems derive a clear benefit from pathway regulation, past research efforts in engineering cellular metabolism have focused on introducing new pathways and removing existing pathway regulation. Synthetic biology is a rapidly growing field that focuses on the development of new tools that support the design, construction, and optimization of biological systems. Recent advances have been made in the design of genetically-encoded biosensors and the application of this class of molecular tools for optimizing and regulating heterologous pathways. Biosensors to cellular metabolites can be taken directly from natural systems, engineered from natural sensors, or constructed entirely in vitro. When linked to reporters, such as antibiotic resistance markers, these metabolite sensors can be used to report on pathway productivity, allowing high-throughput screening for pathway optimization. Future directions will focus on the application of biosensors to introduce feedback control into metabolic pathways, providing dynamic control strategies to increase the efficient use of cellular resources and pathway reliability.     

Synthetic biology with RNA: progress report

One of the long-term goals in synthetic biology is the construction of large-scale gene networks to control and manipulate cells. Such networks often tweak natural regulatory mechanisms, or 'switches', in order to achieve the desired function. Regulatory mechanisms that involve RNA building blocks such as messenger RNA, microRNA and riboswitches have become increasingly prominent in this regard. Recent achievements include prototype mRNA sensors, logic circuits that respond to small molecule cues to affect cell fate, and cell-state classifier networks that identify physiological states using multiple microRNA inputs. This Review describes these and other results in RNA-based synthetic biology.     

Light it up: highly efficient multigene delivery in mammalian cells

Multigene delivery and expression systems are emerging as key technologies for many applications in contemporary biology. We have developed new methods for multigene delivery and expression in eukaryotic hosts for a variety of applications, including production of protein complexes for structural biology and drug development, provision of multicomponent protein biologics, and cell-based assays. We implemented tandem recombineering to facilitate rapid generation of multicomponent gene expression constructs for efficient transformation of mammalian cells, resulting in homogenous cell populations. Analysis of multiple parameters in living cells may require co-expression of fluorescently tagged sensors simultaneously in a single cell, at defined and ideally controlled ratios. Our method enables such applications by overcoming currently limiting challenges. Here, we review recent multigene delivery and expression strategies and their exploitation in mammalian cells. We discuss applications in drug discovery assays, interaction studies, and biologics production, which may benefit in the future from our novel approach.     

Sensor heavy metal from natural resources for a green environment: A review relation between synthesis method and luminescence properties of carbon dots

Carbon dots (CDs) are 10-nm nanomaterial classes as excellent candidates in various applications: physics, biology, chemistry, and food science due to high stable biocompatibility and high surface expansive. CDs produced from natural materials have received wide attention due to their unique benefits, easy availabilities, sufficient costs, and harmless to the ecosystem. The various properties of CDs can be obtained from various synthesis methods: hydrothermal, microwave-assisted, and pyrolysis. The CDs have shown enormous potential in metal particle detection, colorimetric sensors, electrochemical sensors, and pesticide sensors. This review provides systematic information on a synthesis method based on natural resources and the application to the environmental sensors for supporting the clean environment. We hope this review will be useful as a reference source in providing the guidance or roadmap for new researchers to develop new strategies in increasing luminescence properties CDs for multi detection of heavy metals in the environment.     

Molecular and mechanical bases of focal lipid accumulation in arterial wall

Mechanical forces such as shear stress can modulate gene and protein expressions and hence cellular functions by activating membrane sensors and intracellular signaling. Using cultured endothelial cells, we have shown that laminar shear stress causes a transient increase in monocyte chemotactic protein-1 (MCP-1) expression, which involves the Ras-MAP kinase signaling pathway. We have demonstrated that integrins and the vascular endothelial growth factor receptor Flk-1 can sense shear stress, with integrins being upstream to Flk-1. Other possible membrane components involved in the sensing of shear stress include G-protein coupled receptors, intercellular junction proteins, membrane glycocalyx, and the lipid bilayer. Mechano-transduction involves the participation of a multitude of sensors, signaling molecules, and genes. Microarray analysis has demonstrated that shear stress can upregulate and downregulate different genes. Sustained shear stress downregulates atherogenic genes (e.g., MCP-1 and the genes that facilitate lipid accumulation) and upregulates growth-arrest genes. In contrast, disturbed flow observed at branch points and simulated in step-flow channels causes sustained activation of MCP-1 and the genes facilitating cell turnover and lipid accumulation. These findings provide a molecular basis for the explanation of the preferential localization of atherosclerotic lesions at regions of disturbed flow, such as the arterial branch points. The combination of mechanics and biology (from molecules-cells to organs-systems) can help to elucidate the physiological processes of mechano-chemical transduction and improving the methods of the management of important clinical conditions such as coronary artery disease.     

Regulation and protection of mitochondrial physiology by sirtuins

The link between sirtuin activity and mitochondrial biology has recently emerged as an important field. This conserved family of NAD(+)-dependent deacetylase proteins has been described to be particularly involved in metabolism and longevity. Recent studies on protein acetylation have uncovered a high number of acetylated mitochondrial proteins indicating that acetylation/deacetylation processes may be important not only for the regulation of mitochondrial homeostasis but also for metabolic dysfunction in the context of various diseases such as metabolic syndrome/diabetes and cancer. The functional involvement of sirtuins as sensors of the redox/nutritional state of mitochondria and their role in mitochondrial protection against stress are hereby described, suggesting that pharmacological manipulation of sirtuins is a viable strategy against several pathologies.     

RNA synthetic biology

RNA molecules play important and diverse regulatory roles in the cell by virtue of their interaction with other nucleic acids, proteins and small molecules. Inspired by this natural versatility, researchers have engineered RNA molecules with new biological functions. In the last two years efforts in synthetic biology have produced novel, synthetic RNA components capable of regulating gene expression in vivo largely in bacteria and yeast, setting the stage for scalable and programmable cellular behavior. Immediate challenges for this emerging field include determining how computational and directed-evolution techniques can be implemented to increase the complexity of engineered RNA systems, as well as determining how such systems can be broadly extended to mammalian systems. Further challenges include designing RNA molecules to be sensors of intracellular and environmental stimuli, probes to explore the behavior of biological networks and components of engineered cellular control systems.     

Living electronics: A catalogue of engineered living electronic components

Biology leverages a range of electrical phenomena to extract and store energy, control molecular reactions and enable multicellular communication. Microbes, in particular, have evolved genetically encoded machinery enabling them to utilize the abundant redox-active molecules and minerals available on Earth, which in turn drive global-scale biogeochemical cycles. Recently, the microbial machinery enabling these redox reactions have been leveraged for interfacing cells and biomolecules with electrical circuits for biotechnological applications. Synthetic biology is allowing for the use of these machinery as components of engineered living materials with tuneable electrical properties. Herein, we review the state of such living electronic components including wires, capacitors, transistors, diodes, optoelectronic components, spin filters, sensors, logic processors, bioactuators, information storage media and methods for assembling these components into living electronic circuits.     

无人机遥感在生态学中的应用进展

无人机与遥感技术的结合,即无人机遥感。与传统的以卫星和有人机遥感相比,无人机遥感具有高时效、高时空分辨率、云下低空飞行、高机动性等优势,是传统卫星和有人机遥感手段所无法比拟的。这些优点使得无人机在生态学和保护生物学等领域获得迅速发展。首先对无人机遥感技术的发展历程、系统组成、分类与选型、应用优势等进行了介绍。在此基础上,对无人机在生态学中的应用案例进行了总结,内容涉及生境监测、植物物候调查、动物监测等方面。最后通过比较国内外相关领域的研究进展对无人机生态学存在的问题(技术门槛较高和法律法规不完善等)和潜在应用前景进行了探讨。     

Analysis of undergraduate cell biology contents in Brazilian public universities

The enormous amount of information available in cell biology has created a challenge in selecting the core concepts we should be teaching our undergraduates. One way to define a set of essential core ideas in cell biology is to analyze what a specific cell biology community is teaching their students. Our main objective was to analyze the cell biology content currently being taught in Brazilian universities. We collected the syllabi of cell biology courses from public universities in Brazil and analyzed the frequency of cell biology topics in each course. We also compared the Brazilian data with the contents of a major cell biology textbook. Our analysis showed that while some cell biology topics such as plasma membrane and cytoskeleton was present in ～100% of the Brazilian curricula analyzed others such as cell signaling and cell differentiation were present in only ～35%. The average cell biology content taught in the Brazilian universities is quite different from what is presented in the textbook. We discuss several possible explanations for these observations. We also suggest a list with essential cell biology topics for any biological or biomedical undergraduate course. The comparative discussion of cell biology topics presented here could be valuable in other educational contexts.     

Photochemical tools for studying metal ion signaling and homeostasis

Metal ions have well-established catalytic and structural roles in proteins. Much of the knowledge acquired about metalloenzymes has been derived using spectroscopic techniques and X-ray crystallography, but these methodologies are less effective for studying metal ions that are not tightly bound to biomacromolecules. In order to prevent deleterious chemistry, cells tightly regulate the uptake, distribution, and intracellular concentrations of metal ions. Investigation into these homeostasis mechanisms has necessitated the development of alternative ways to study metal ions. Photochemical tools such as small molecule and protein-based fluorescent sensors as well as photocaged complexes have provided insight into the homeostasis and signaling mechanisms of Ca(2+), Zn(2+), and Cu(+), but a comprehensive picture of metal ions in biology will require additional development of these techniques, which are reviewed in this Current Topics article.