scholarly journals A lab in the field: applications of real-time, in situ metagenomic sequencing

2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Adriel Latorre-Pérez ◽  
Javier Pascual ◽  
Manuel Porcar ◽  
Cristina Vilanova

Abstract High-throughput metagenomic sequencing is considered one of the main technologies fostering the development of microbial ecology. Widely used second-generation sequencers have enabled the analysis of extremely diverse microbial communities, the discovery of novel gene functions, and the comprehension of the metabolic interconnections established among microbial consortia. However, the high cost of the sequencers and the complexity of library preparation and sequencing protocols still hamper the application of metagenomic sequencing in a vast range of real-life applications. In this context, the emergence of portable, third-generation sequencers is becoming a popular alternative for the rapid analysis of microbial communities in particular scenarios, due to their low cost, simplicity of operation, and rapid yield of results. This review discusses the main applications of real-time, in situ metagenomic sequencing developed to date, highlighting the relevance of this technology in current challenges (such as the management of global pathogen outbreaks) and in the next future of industry and clinical diagnosis.

Author(s):  
J. Craig Prather ◽  
Michael Bolt ◽  
Haley Harrell ◽  
Tyler Horton ◽  
Mark L. Adams

Weather affects many aspects of our daily lives from our individual commutes to the global economy. Although much progress has been made in understanding atmospheric physics and weather forecasting, there is still a need for better in situ atmospheric data. Forecasts are based on high performance computer models which solve the differential equations that represent the dynamics of the atmosphere. In all of these models, initial conditions based on the current state of the atmosphere are ingested into the models. The initial conditions are based on data from many sources including remote sensing satellites, ground based weather stations, weather balloons and even aircraft. However, the amount of in situ atmospheric data is very limited and so often times the initial conditions for the models are not truly representative of the current atmosphere. This is especially true for severe storms such as super cell thunderstorms, tornadoes, and hurricanes. Severe weather impacts millions of people every year costing both human life and substantial resources. A better understanding of severe weather will have a significant impact on human safety and infrastructure protection. Electronics miniaturization and advances in manufacturing such as 3D printing have allowed for the development of low-cost, light-weight probes capable of providing real-time in situ information about the atmosphere which can improve forecasts models and provide a better understanding to atmospheric scientists. The probes provide temperature, relative humidity, pressure, position, and velocity data. MEMS sensors are used to monitor the ambient weather conditions and an on-board GPS receiver provides position information. The sensors are combined with a microcontroller and radio to transmit data back to a receiver on the ground. Power is provided by zinc-air batteries and antennas for both the GPS and data radio are integrated into the package. In order to ensure correct operation of the electronics, 3D printing is used to generate a custom electronics/mechanical package that is both functional and robust while maintaining low weight and high drag coefficient. The desire is for the probes to stay airborne as long as possible without any active means of propulsion or buoyancy. The probes designed are small, light-weight, and low cost. They can be deployed from aircraft, weather balloons, or dropped directly into a storm. The design of the probes was simulated through CFD to determine the optimal mechanical packaging of the device. The probes have been tested to validate the range of the probes and the accuracy of the measurements. Although most probes can be recovered after testing, designs focus on minimizing the environmental impact of unrecovered probes. This was done by utilizing 3D printing to create custom mechanical packaging for the electronics that is environmentally friendly along with using zinc air batteries which are a less hazardous battery chemistry. The devices have been designed, fabricated, and tested and the results will be presented. This paper will explain the design processes, design decisions, and testing procedures utilized along with the testing results.


2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Alyse A. Larkin ◽  
Catherine A. Garcia ◽  
Nathan Garcia ◽  
Melissa L. Brock ◽  
Jenna A. Lee ◽  
...  

AbstractDetailed descriptions of microbial communities have lagged far behind physical and chemical measurements in the marine environment. Here, we present 971 globally distributed surface ocean metagenomes collected at high spatio-temporal resolution. Our low-cost metagenomic sequencing protocol produced 3.65 terabases of data, where the median number of base pairs per sample was 3.41 billion. The median distance between sampling stations was 26 km. The metagenomic libraries described here were collected as a part of a biological initiative for the Global Ocean Ship-based Hydrographic Investigations Program, or “Bio-GO-SHIP.” One of the primary aims of GO-SHIP is to produce high spatial and vertical resolution measurements of key state variables to directly quantify climate change impacts on ocean environments. By similarly collecting marine metagenomes at high spatiotemporal resolution, we expect that this dataset will help answer questions about the link between microbial communities and biogeochemical fluxes in a changing ocean.


Author(s):  
Xingjun Ma ◽  
Sudanthi Wijewickrema ◽  
Shuo Zhou ◽  
Yun Zhou ◽  
Zakaria Mhammedi ◽  
...  

Simulation-based training (SBT) is gaining popularity as a low-cost and convenient training technique in a vast range of applications. However, for a SBT platform to be fully utilized as an effective training tool, it is essential that feedback on performance is provided automatically in real-time during training. It is the aim of this paper to develop an efficient and effective feedback generation method for the provision of real-time feedback in SBT. Existing methods either have low effectiveness in improving novice skills or suffer from low efficiency, resulting in their inability to be used in real-time. In this paper, we propose a neural network based method to generate feedback using the adversarial technique. The proposed method utilizes a bounded adversarial update to minimize a L1 regularized loss via back-propagation. We empirically show that the proposed method can be used to generate simple, yet effective feedback. Also, it was observed to have high effectiveness and efficiency when compared to existing methods, thus making it a promising option for real-time feedback generation in SBT.


2021 ◽  
Vol 2079 (1) ◽  
pp. 012032
Author(s):  
Rui Su ◽  
Yawen Dai

Abstract In the era of the Internet of Everything, applications based on real-time location continue to appear in various industries. The indoor and outdoor positioning, analysis and management of personnel and objects can effectively improve the efficiency of production and management, which is of great significance to many industries. The use of Bluetooth beacon positioning has the advantages of low energy consumption, low cost, and fast data transmission speed. However, in real life, there are two obstacles to receiving signals, which are easily affected by the environment and the need for frequent on-site maintenance. This paper designs and implements a new type of LoRa-based smart Bluetooth beacon, which can be quickly connected to LoRa. Online monitoring and remote control can achieve better adaptation to the environment, and can fit a better signal attenuation model in the deployment environment in real time. Traditional signal strength positioning solutions have their own limitations. In order to improve the positioning accuracy of the Bluetooth beacon and the universality of the algorithm, in view of the low deployment density of beacons, the positioning accuracy is not good and the anchor circle has various situations, an optimized weighted centroid positioning scheme integrating greedy strategy is proposed.


Sensors ◽  
2019 ◽  
Vol 19 (2) ◽  
pp. 296 ◽  
Author(s):  
Leire Francés ◽  
Paz Morer ◽  
Maria Rodriguez ◽  
Aitor Cazón

Wearables are gaining widespread use and technologies are making it possible to monitor human physical activity and behaviour as part of connected infrastructures. Many companies see wearables as an opportunity to enhance worker safety since they can monitor their workers’ activity in real life scenarios. One of the goals of this technology is to integrate existing electronic components, such as sensors or conductors, in order to create fully wearable systems. This integration is constrained not only by technical factors but also by user requirements and internal company standards. This paper considers such constraints and presents preliminary research for the design of a wearable glove as a new tool to track forces exerted by workers in car assembly lines. The objective of the glove is to measure forces and compare these to maximum forces already identified by the company. Thus, the main objectives are to: (1) integrate the components based on the requirements of the users and the context of application, and (2) provide a new tool that can be used “in situ” to track workers. This study was carried out in close collaboration with Volkswagen through a human-centred iterative design process. Thus, this paper presents the development of a wearable device glove based on a specific design methodology where both the human and technological aspects are considered.


2019 ◽  
Author(s):  
Chengdong Xu ◽  
Sneha P. Couvillion ◽  
Ryan L. Sontag ◽  
Nancy G. Isern ◽  
Yukari Maezato ◽  
...  

Metabolites have essential roles in microbial communities, including as mediators of nutrient and energy exchange, cell-to-cell communication, and antibiosis. However, detecting and quantifying metabolites and other chemicals in samples having extremes in salt or mineral content using liquid chromatography-mass spectrometry (LC-MS)-based methods remains a significant challenge. Here we report a facile method based on in situ chemical derivatization followed by extraction for analysis of metabolites and other chemicals in hypersaline samples, enabling for the first time direct LC-MS-based exo-metabolomics analysis in sample matrices containing up to 2 molar total dissolved salts. The method, MetFish, is applicable to molecules containing amine, carboxylic acid, carbonyl, or hydroxyl functional groups, and can be integrated into either targeted or untargeted analysis pipelines. In targeted analyses, MetFish provided limits of quantification as low as 1 nM, broad linear dynamic ranges (up to 5-6 orders of magnitude) with excellent linearity, and low median inter-day reproducibility (e.g. 2.6%). MetFish was successfully applied in targeted and untargeted exo-metabolomics analyses of microbial consortia, quantifying amino acid dynamics in the exo-metabolome during community succession; in situ in a native prairie soil, whose exo-metabolome was isolated using a hypersaline extraction; and in input and produced fluids from a hydraulically fractured well, identifying dramatic changes in the exo-metabolome over time in the well.


mSystems ◽  
2021 ◽  
Vol 6 (3) ◽  
Author(s):  
Chengdong Xu ◽  
Sneha P. Couvillion ◽  
Ryan L. Sontag ◽  
Nancy G. Isern ◽  
Yukari Maezato ◽  
...  

ABSTRACT Metabolites have essential roles in microbial communities, including as mediators of nutrient and energy exchange, cell-to-cell communication, and antibiosis. However, detecting and quantifying metabolites and other chemicals in samples having extremes in salt or mineral content using liquid chromatography-mass spectrometry (LC-MS)-based methods remains a significant challenge. Here, we report a facile method based on in situ chemical derivatization followed by extraction for analysis of metabolites and other chemicals in hypersaline samples, enabling for the first time direct LC-MS-based exometabolomics analysis in sample matrices containing up to 2 M total dissolved salts. The method, MetFish, is applicable to molecules containing amine, carboxylic acid, carbonyl, or hydroxyl functional groups, and it can be integrated into either targeted or untargeted analysis pipelines. In targeted analyses, MetFish provided limits of quantification as low as 1 nM, broad linear dynamic ranges (up to 5 to 6 orders of magnitude) with excellent linearity, and low median interday reproducibility (e.g., 2.6%). MetFish was successfully applied in targeted and untargeted exometabolomics analyses of microbial consortia, quantifying amino acid dynamics in the exometabolome during community succession; in situ in a native prairie soil, whose exometabolome was isolated using a hypersaline extraction; and in input and produced fluids from a hydraulically fractured well, identifying dramatic changes in the exometabolome over time in the well. IMPORTANCE The identification and accurate quantification of metabolites using electrospray ionization-mass spectrometry (ESI-MS) in hypersaline samples is a challenge due to matrix effects. Clean-up and desalting strategies that typically work well for samples with lower salt concentrations are often ineffective in hypersaline samples. To address this gap, we developed and demonstrated a simple yet sensitive and accurate method—MetFish—using chemical derivatization to enable mass spectrometry-based metabolomics in a variety of hypersaline samples from varied ecosystems and containing up to 2 M dissolved salts.


Author(s):  
Jonathan Teague ◽  
Thomas B. Scott ◽  
Sanjay Sharma ◽  
George Graham ◽  
Michael J. Allen

The development of low-cost, open-source Remotely Operated Vehicle (ROV) systems has provided almost unrestricted access for researchers looking to monitor the marine environment in ever greater resolution. Sampling microbial communities from the marine environment, however, still usually relies on Niskin-bottle sampling (ROV or CTD based), a method which introduces an inaccuracy and variability that is incompatible with metatranscriptomic analysis. Here, we describe a versatile, easily-replicated platform which achieves in situ mRNA preservation, via the addition of RNAlater to filtered microbial cells, to enhance ROV or CTD functionality.


2020 ◽  
Author(s):  
Alyse A. Larkin ◽  
Catherine A. Garcia ◽  
Melissa L. Brock ◽  
Jenna A. Lee ◽  
Nathan Garcia ◽  
...  

AbstractDetailed descriptions of microbial communities have lagged far behind physical and chemical measurements in the marine environment. Here, we present 720 globally distributed surface ocean metagenomes collected at high spatio-temporal resolution. Our low-cost metagenomic sequencing protocol produced 2.75 terabases of data, where the median number of base pairs per sample was 3.48 billion. The median distance between sampling stations was 26 km. The metagenomic libraries described here were collected as a part of a biological initiative for the Global Ocean Ship-based Hydrographic Investigations Program, or “Bio-GO-SHIP.” One of the primary aims of GO-SHIP is to produce high spatial and vertical resolution measurements of key state variables to directly quantify climate change impacts on ocean environments. By similarly collecting marine metagenomes at high spatiotemporal resolution, we expect that this dataset will help answer questions about the link between microbial communities and biogeochemical fluxes in a changing ocean.


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