Design and flight testing of an integrated solar powered UAV and WSN for greenhouse gas monitoring emissions in agricultural farms

There is an increased interest in measuring the amount of greenhouse gases produced by farming practices . This paper describes an integrated solar powered Unmanned Air Vehicles (UAV) and Wireless Sensor Network (WSN) gas sensing system for greenhouse gas emissions in agricultural lands. The system uses a generic gas sensing system for CH4 and CO2 concentrations using metal oxide (MoX) and non-dispersive infrared sensors, and a new solar cell encapsulation method to power the unmanned aerial system (UAS)as well as a data management platform to store, analyze and share the information with operators and external users. The system was successfully field tested at ground and low altitudes, collecting, storing and transmitting data in real time to a central node for analysis and 3D mapping. The system can be used in a wide range of outdoor applications at a relatively low operational cost. In particular, agricultural environments are increasingly subject to emissions mitigation policies. Accurate measurements of CH4 and CO2 with its temporal and spatial variability can provide farm managers key information to plan agricultural practices. A video of the bench and flight test performed can be seen in the following link: https://www.youtube.com/watch?v=Bwas7stYIxQ

Functional correlation of bacterial LuxS with their quaternary associations: interface analysis of the structure networks

Background The genome of a wide variety of prokaryotes contains the luxS gene homologue, which encodes for the protein S-ribosylhomocysteinelyase (LuxS). This protein is responsible for the production of the quorum sensing molecule, AI-2 and has been implicated in a variety of functions such as flagellar motility, metabolic regulation, toxin production and even in pathogenicity. A high structural similarity is present in the LuxS structures determined from a few species. In this study, we have modelled the structures from several other species and have investigated their dimer interfaces. We have attempted to correlate the interface features of LuxS with the phenotypic nature of the organisms. Results The protein structure networks (PSN) are constructed and graph theoretical analysis is performed on the structures obtained from X-ray crystallography and on the modelled ones. The interfaces, which are known to contain the active site, are characterized from the PSNs of these homodimeric proteins. The key features presented by the protein interfaces are investigated for the classification of the proteins in relation to their function. From our analysis, structural interface motifs are identified for each class in our dataset, which showed distinctly different pattern at the interface of LuxS for the probiotics and some extremophiles. Our analysis also reveals potential sites of mutation and geometric patterns at the interface that was not evident from conventional sequence alignment studies. Conclusion The structure network approach employed in this study for the analysis of dimeric interfaces in LuxS has brought out certain structural details at the side-chain interaction level, which were elusive from the conventional structure comparison methods. The results from this study provide a better understanding of the relation between the luxS gene and its functional role in the prokaryotes. This study also makes it possible to explore the potential direction towards the design of inhibitors of LuxS and thus towards a wide range of antimicrobials.

Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis

Background: One of the major challenges in understanding enzyme catalysis is to identify the different conformations and their populations at detailed molecular level in response to ligand binding/environment. A detail description of the ligand induced conformational changes provides meaningful insights into the mechanism of action of enzymes and thus its function. Results: In this study, we have explored the ligand induced conformational changes in H. pylori LuxS and the associated mechanistic features. LuxS, a dimeric protein, produces the precursor (4,5-dihydroxy-2,3-pentanedione) for autoinducer-2 production which is a signalling molecule for bacterial quorum sensing. We have performed molecular dynamics simulations on H. pylori LuxS in its various ligand bound forms and analyzed the simulation trajectories using various techniques including the structure network analysis, free energy evaluation and water dynamics at the active site. The results bring out the mechanistic details such as co operativity and asymmetry between the two subunits, subtle changes in the conformation as a response to the binding of active and inactive forms of ligands and the population distribution of different conformations in equilibrium. These investigations have enabled us to probe the free energy landscape and identify the corresponding conformations in terms of network parameters. In addition, we have also elucidated the variations in the dynamics of water co-ordination to the Zn2+ ion in LuxS and its relation to the rigidity at the active sites. Conclusions: In this article, we provide details of a novel method for the identification of conformational changes in the different ligand bound states of the protein, evaluation of ligand-induced free energy changes and the biological relevance of our results in the context of LuxS structure-function. The methodology outlined here is highly generalized to illuminate the linkage between structure and function in any protein of known structure.

Novel approach for simultaneous measurement of strain and temperature using a single tapered fiber Bragg grating

A novel approach for simultaneous measurement of strain and temperature with a single tapered fiber Bragg grating is proposed. This method is based on the fact that the reflectivity at central wavelength of FBG reflection changes with chirp (strain gradient). A diode laser is locked to the central wavelength of FBG reflection. Central wavelength of the FBG shifts with temperature. Change in reflectivity & wavelength of the diode laser were used to measure strain and temperature on the FBG respectively.

Simultaneous measurement of strain and temperature with a pair of matched fiber Bragg gratings

A novel approach for simultaneous measurement of static/dynamic strain and temperature with a pair of matched fiber Bragg grating(FBG)s is proposed. When a diode laser locked to the mid reflection frequency of reference FBG is used to illuminate the sensor FBG, reflected intensity changes with strain on sensor FBG. Reference FBG responds with temperature on sensor FBG and is immune to strain, hence, wavelength of the diode laser acts as a signature for temperature measurement. Theoretical sensitivity limit for static strain and temperature are 1.2n epsilon / root Hz and 0.0011 degrees C respectively. Proposed sensor shows a great potential in high sensitive strain measurements with a simplified experimental setup.

Highly sensitive and rapid detection of acetylcholine using an ITO plate modified with platinum-graphene nanoparticles

Determining the concentrations of acetylcholine (ACh) and choline (Ch) is clinically important. ACh is a neurotransmitter that acts as a key link in the communication between neurons in the spinal cord and in nerve skeletal junctions in vertebrates, and plays an important role in transmitting signals in the brain. A bienzymatic sensor for the detection of ACh was prepared by co-immobilizing choline oxidase (ChO) and acetylcholinesterase (AChE) on graphene matrix/platinum nanoparticles, and then electrodepositing them on an ITO-coated glass plate. Graphene nanoparticles were decorated with platinum nanoparticles and were electrodeposited on a modified ITO-coated glass plate to form a modified electrode. The modified electrode was characterized by scanning electron microscopy (SEM), cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) studies. The optimum response of the enzyme electrode was obtained at pH 7.0 and 35 degrees C. The response time of this ACh-sensing system was shown to be 4 s. The linear range of responses to ACh was 0.005-700 mu M. This biosensor exhibits excellent anti-interferential abilities and good stability, retaining 50% of its original current even after 4 months. It has been applied for the detection of ACh levels in human serum samples.

Novel Functions of (p)ppGpp and Cyclic di-GMP in Mycobacterial Physiology Revealed by Phenotype Microarray Analysis of Wild-Type and Isogenic Strains of Mycobacterium smegmatis

The bacterial second messengers (p)ppGpp and bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) regulate important functions, such as transcription, virulence, biofilm formation, and quorum sensing. In mycobacteria, they regulate long-term survival during starvation, pathogenicity, and dormancy. Recently, a Pseudomonas aeruginosa strain lacking (p) ppGpp was shown to be sensitive to multiple classes of antibiotics and defective in biofilm formation. We were interested to find out whether Mycobacterium smegmatis strains lacking the gene for either (p)ppGpp synthesis (Delta rel(Msm)) or c-di-GMP synthesis (Delta dcpA) would display similar phenotypes. We used phenotype microarray technology to compare the growth of the wild-type and the knockout strains in the presence of several antibiotics. Surprisingly, the Delta rel(Msm) and Delta dcpA strains showed enhanced survival in the presence of many antibiotics, but they were defective in biofilm formation. These strains also displayed altered surface properties, like impaired sliding motility, rough colony morphology, and increased aggregation in liquid cultures. Biofilm formation and surface properties are associated with the presence of glycopeptidolipids (GPLs) in the cell walls of M. smegmatis. Thin-layer chromatography analysis of various cell wall fractions revealed that the levels of GPLs and polar lipids were reduced in the knockout strains. As a result, the cell walls of the knockout strains were significantly more hydrophobic than those of the wild type and the complemented strains. We hypothesize that reduced levels of GPLs and polar lipids may contribute to the antibiotic resistance shown by the knockout strains. Altogether, our data suggest that (p)ppGpp and c-di-GMP may be involved in the metabolism of glycopeptidolipids and polar lipids in M. smegmatis.

光纤布拉格光栅传感系统在海洋平台监测中的应用研究

首先阐述了光纤布拉格光栅(FBG)传感系统的传感原理和基本组成。然后介绍了我们研制的FBG温度和应变传感器的特性以及关于它们应用于平台监测中的可靠性问题的研究结果，包括疲劳损伤、防水密封和机械防护。最后讨论了FBG传感系统在海洋工程中的其它潜在用途。Sensing mechanism of Fiber Bragg gratings (FBGs) and its sensing system are presented. Then, the performance of the FBG strain and temperature sensors we designed is described. Some results related to the reliability of the FBG sensor in the application to monitoring offshore platforms is also given, which involves fatigue damage, waterproof packing and mechanical protection. Finally, other potential applications of FBGs in offshore engineering are discussed.

光纤光栅滤波的瓦斯传感系统的研究

差分吸收法是进行瓦斯远距离监测的重要方法，根据瓦斯在近红外波段的吸收特性，报道了一种新型的远距离光纤瓦斯传感系统。采用1．3μm超辐射发光二极管为光源，利用光纤布拉格光栅(FBG)优良的窄带滤波特性实现了对瓦斯的差分吸收测量。和传统的干涉滤光片相比，光纤光栅滤波器插入损耗低、制备简单。系统具有全光纤化、结构简单、工作距离远、稳定性好的特点。工作距离10km，测量灵敏度为0．1％，是瓦斯爆炸极限的2％。

Quantitative, Time-Resolved Proteomic Analysis Using Bio-Orthogonal Non-Canonical Amino Acid Tagging

Bio-orthogonal non-canonical amino acid tagging (BONCAT) is an analytical method that allows the selective analysis of the subset of newly synthesized cellular proteins produced in response to a biological stimulus. In BONCAT, cells are treated with the non-canonical amino acid L-azidohomoalanine (Aha), which is utilized in protein synthesis in place of methionine by wild-type translational machinery. Nascent, Aha-labeled proteins are selectively ligated to affinity tags for enrichment and subsequently identified via mass spectrometry. The work presented in this thesis exhibits advancements in and applications of the BONCAT technology that establishes it as an effective tool for analyzing proteome dynamics with time-resolved precision.

Chapter 1 introduces the BONCAT method and serves as an outline for the thesis as a whole. I discuss motivations behind the methodological advancements in Chapter 2 and the biological applications in Chapters 2 and 3.

Chapter 2 presents methodological developments that make BONCAT a proteomic tool capable of, in addition to identifying newly synthesized proteins, accurately quantifying rates of protein synthesis. I demonstrate that this quantitative BONCAT approach can measure proteome-wide patterns of protein synthesis at time scales inaccessible to alternative techniques.

In Chapter 3, I use BONCAT to study the biological function of the small RNA regulator CyaR in Escherichia coli. I correctly identify previously known CyaR targets, and validate several new CyaR targets, expanding the functional roles of the sRNA regulator.

In Chapter 4, I use BONCAT to measure the proteomic profile of the quorum sensing bacterium Vibrio harveyi during the time-dependent transition from individual- to group-behaviors. My analysis reveals new quorum-sensing-regulated proteins with diverse functions, including transcription factors, chemotaxis proteins, transport proteins, and proteins involved in iron homeostasis.

Overall, this work describes how to use BONCAT to perform quantitative, time-resolved proteomic analysis and demonstrates that these measurements can be used to study a broad range of biological processes.

Radio over fibre technologies for wideband in-building wireless coverage

This paper describes the use of radio over multimode fibre networks to allow wideband wireless coverage in building environments. It will cover basic principles, commercial applications of such networks and their extension to provide a converged communications/sensing system. © 2009 Optical Society of America.

Anticancer Drug-DNA Interactions Measured Using a Photoinduced Electron-Transfer Mechanism Based on Luminescent Quantum Dots

A sensing system based on the photoinduced electron transfer of quantum dots (QDs) was designed to measure the interaction of anticancer drug and DNA, taking mitoxantrone (MTX) as a model drug. MTX adsorbed on the surface of QDs can quench the photoluminescence (PL) of QDs through the photoinduced electron-transfer process; and then the addition of DNA will bring the restoration of QDs PL intensity, as DNA can bind with MTX and remove it from QDs. Sensitive detection of MTX with the detection limit of 10 nmol L-1 and a linear detection range from 10 nmol L-1 to 4.5 mu mol L-1 was achieved. The dependence of PL intensity on DNA amount was successfully utilized to investigate the interactions between MTX and DNA. Both the binding constants and the sizes of binding site of MTX-DNA interactions were calculated based on the equations deduced for the PL recovery process. The binding constant obtained in our experiment was generally consistent with previous reports. The sensitive and speedy detection of MTX as well as the avoidance of modification or immobilization process made this system suitable and promising in the drug-DNA interaction studies.

迟缓爱德华氏菌(Edwardsiella tarda) LuxS/AI-2群体感应系统研究

从患病牙鲆中分离出迟缓爱德华氏菌株TX1，经报告菌株检测发现TX1有AI-2活性。用梯度PCR和Genome walking的方法克隆了TX1 luxS基因，将luxS基因在大肠杆菌DH5α中表达，证明其具有功能活性。在TX1中，luxS的表达与AI-2的活性基本是一致的，二者均受生长时期和生长条件的调节，即在glucose存在的条件下luxS表达和AI-2活性升高，而在高温条件下luxS表达和AI-2活性降低。glucose对AI-2活性以及luxS表达的影响经过荧光定量PCR，启动子活性检测，AI-2活性检测以及凝胶滞缓等一系列的实验证实是由cAMP-CRP复合物介导的，该复合物可以通过与luxS启动子相互作用而抑制luxS的表达。RNA干扰表明，TX1中luxS表达被干扰以后，对细菌产生了多方面的影响，包括：(1) 降低AI-2水平；(2) 降低细菌的生长能力；(3) 降低Ⅲ型分泌系统相关基因的表达水平以及生物膜的形成能力；(4) 减弱细菌毒力。外源AI-2的添加可以回复Ⅲ型分泌系统相关基因的表达水平以及生物膜的形成，但是并不能修复生长状况，表明LuxS在TX1中具有双重功能，即参与细胞代谢以及群体感应信号传导。基于LuxS/AI-2群体感应系统对细菌毒力的重要性，设计并筛选了一个该系统的阻遏因子5411。Pull-down实验证明5411可以和LuxS特异性结合。研究表明5411在TX1中表达导致细菌毒力显著下降。将5411克隆至牙鲆共生菌FP3中，发现5411可以被分泌到胞外并能被TX1吸收。将表达5411的共生菌导入牙鲆，发现其能够有效阻遏TX1对牙鲆的侵染。 这些结果表明：(1) TX1中AI-2的活性受控于LuxS，而后者则受生长时期和生长条件的调控；(2) luxS的正常表达对于细菌的正常生长和侵染是必需的；(3) LuxS/AI-2群体感应系统调控Ⅲ型分泌系统相关毒力因子的表达；(4) 通过阻遏LuxS/AI-2群体感应系统来抑制病原菌侵染是一种具有潜力的新型病害防控方法。

PHOTOREFRACTIVE CRYSTAL-BASED ACOUSTO-OPTIC IMAGING IN THE NEAR-INFRARED AND ITS APPLICATIONS

Acousto-optic (AO) sensing and imaging (AOI) is a dual-wave modality that combines ultrasound with diffusive light to measure and/or image the optical properties of optically diffusive media, including biological tissues such as breast and brain. The light passing through a focused ultrasound beam undergoes a phase modulation at the ultrasound frequency that is detected using an adaptive interferometer scheme employing a GaAs photorefractive crystal (PRC). The PRC-based AO system operating at 1064 nm is described, along with the underlying theory, validating experiments, characterization, and optimization of this sensing and imaging apparatus. The spatial resolution of AO sensing, which is determined by spatial dimensions of the ultrasound beam or pulse, can be sub-millimeter for megahertz-frequency sound waves.A modified approach for quantifying the optical properties of diffuse media with AO sensing employs the ratio of AO signals generated at two different ultrasound focal pressures. The resulting “pressure contrast signal” (PCS), once calibrated for a particular set of pressure pulses, yields a direct measure of the spatially averaged optical transport attenuation coefficient within the interaction volume between light and sound. This is a significant improvement over current AO sensing methods since it produces a quantitative measure of the optical properties of optically diffuse media without a priori knowledge of the background illumination. It can also be used to generate images based on spatial variations in both optical scattering and absorption. Finally, the AO sensing system is modified to monitor the irreversible optical changes associated with the tissue heating from high intensity focused ultrasound (HIFU) therapy, providing a powerful method for noninvasively sensing the onset and growth of thermal lesions in soft tissues. A single HIFU transducer is used to simultaneously generate tissue damage and pump the AO interaction. Experimental results performed in excised chicken breast demonstrate that AO sensing can identify the onset and growth of lesion formation in real time and, when used as feedback to guide exposure parameters, results in more predictable lesion formation.

Miniaturised multi-MEMS sensor development

Complex systems, from environmental behaviour to electronics reliability, can now be monitored with Wireless Sensor Networks (WSN), where multiple environmental sensors are deployed in remote locations. This ensures aggregation and reading of data, at lower cost and lower power consumption. Because miniaturisation of the sensing system is hampered by the fact that discrete sensors and electronics consume board area, the development of MEMS sensors offers a promising solution. At Tyndall, the fabrication flow of multiple sensors has been made compatible with CMOS circuitry to further reduce size and cost. An ideal platform on which to host these MEMS environmental sensors is the Tyndall modular wireless mote. This paper describes the development and test of the latest sensors incorporating temperature, humidity, corrosion, and gas. It demonstrates their deployment on the Tyndall platform, allowing real-time readings, data aggregation and cross-correlation capabilities. It also presents the design of the next generation sensing platform using the novel 10mm wireless cube developed by Tyndall.