Freshwater monitoring by nanopore sequencing

While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges in cost and logistics. Here, we present a simple, fast, cost-effective and remotely accessible freshwater diagnostics workflow centred around the portable nanopore sequencing technology. Using defined compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), we provide optimised experimental and bioinformatics guidelines, including a benchmark with twelve taxonomic classification tools for nanopore sequences. We find that nanopore metagenomics can depict the hydrological core microbiome and fine temporal gradients in line with complementary physicochemical measurements. In a public health context, these data feature relevant sewage signals and pathogen maps at species level resolution. We anticipate that this framework will gather momentum for new environmental monitoring initiatives using portable devices.

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Freshwater monitoring by nanopore sequencing

10.1101/2020.02.06.936302 ◽

2020 ◽

Cited By ~ 1

Author(s):

Lara Urban ◽

Andre Holzer ◽

J Jotautas Baronas ◽

Michael Hall ◽

Philipp Braeuninger-Weimer ◽

...

Keyword(s):

Cost Effective ◽

Species Level ◽

Portable Devices ◽

Nanopore Sequencing ◽

Sequencing Technology ◽

Core Microbiome ◽

Bacterial Indicator ◽

Freshwater Monitoring ◽

Physicochemical Measurements

ABSTRACTWhile traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges in cost and logistics. Here we present a simple, fast, cost-effective and remotely accessible freshwater diagnostics workflow centred around the portable nanopore sequencing technology. Using defined compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), we provide optimised experimental and bioinformatics guidelines, including a benchmark with twelve taxonomic classification tools for nanopore sequences. We find that nanopore metagenomics can depict the hydrological core microbiome and fine temporal gradients in line with complementary physicochemical measurements. In a public health context, these data feature relevant sewage signals and pathogen maps at species level resolution. We anticipate that this framework will gather momentum for new environmental monitoring initiatives using portable devices.

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Development of a Two-Color Fluorescence In Situ Hybridization Technique for Species-Level Identification of Human-Infectious Cryptosporidium spp.

Applied and Environmental Microbiology ◽

10.1128/aem.00643-09 ◽

2009 ◽

Vol 75 (18) ◽

pp. 5996-5998 ◽

Cited By ~ 12

Author(s):

A. Alagappan ◽

P. L. Bergquist ◽

B. C. Ferrari

Keyword(s):

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Cryptosporidium Parvum ◽

Cost Effective ◽

Species Level ◽

Hybridization Technique ◽

Cryptosporidium Spp ◽

Simultaneous Identification ◽

Level Identification

ABSTRACT A two-color fluorescence in situ hybridization assay that allows for the simultaneous identification of Cryptosporidium parvum and C. hominis was developed. The assay is a simple, rapid, and cost-effective tool for the detection of the major Cryptosporidium species of concern to public health.

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Fabrication of a liquid cell for in situ transmission electron microscopy

Microscopy ◽

10.1093/jmicro/dfaa076 ◽

2020 ◽

Author(s):

Xiaoguang Li ◽

Kazutaka Mitsuishi ◽

Masaki Takeguchi

Keyword(s):

Electron Microscopy ◽

Transmission Electron Microscopy ◽

Cost Effective ◽

Production Method ◽

Microscopy Imaging ◽

Transmission Electron ◽

In Situ Electron Microscopy ◽

Liquid Cell ◽

Si Wafer

Abstract Liquid cell transmission electron microscopy (LCTEM) enables imaging of dynamic processes in liquid with high spatial and temporal resolution. The widely used liquid cell (LC) consists of two stacking microchips with a thin wet sample sandwiched between them. The vertically overlapped electron-transparent membrane windows on the microchips provide passage for the electron beam. However, microchips with imprecise dimensions usually cause poor alignment of the windows and difficulty in acquiring high-quality images. In this study, we developed a new and efficient microchip fabrication process for LCTEM with a large viewing area (180 µm × 40 µm) and evaluated the resultant LC. The new positioning reference marks on the surface of the Si wafer dramatically improve the precision of dicing the wafer, making it possible to accurately align the windows on two stacking microchips. The precise alignment led to a liquid thickness of 125.6 nm close to the edge of the viewing area. The performance of our LC was demonstrated by in situ transmission electron microscopy imaging of the dynamic motions of 2-nm Pt particles. This versatile and cost-effective microchip production method can be used to fabricate other types of microchips for in situ electron microscopy.

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Cost effective in-situ methane enrichment for chicken farm biogas system

Bioresource Technology Reports ◽

10.1016/j.biteb.2021.100773 ◽

2021 ◽

pp. 100773

Author(s):

Kamoldara Reansuwan ◽

Rotsukon Jawana ◽

Saoharit Nitayavardhana ◽

Sirichai Koonaphapdeelert

Keyword(s):

Cost Effective ◽

Chicken Farm

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Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions

Briefings in Bioinformatics ◽

10.1093/bib/bby017 ◽

2018 ◽

Vol 20 (4) ◽

pp. 1542-1559 ◽

Cited By ~ 44

Author(s):

Damla Senol Cali ◽

Jeremie S Kim ◽

Saugata Ghose ◽

Can Alkan ◽

Onur Mutlu

Keyword(s):

Sequence Analysis ◽

Genome Assembly ◽

Sequence Data ◽

Error Rates ◽

Nanopore Sequencing ◽

Memory Usage ◽

Sequencing Technology ◽

Assembly Pipeline ◽

And Performance ◽

Polishing Tool

Abstract Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating accurate genome assemblies. The tools used for nanopore sequence analysis are of critical importance, as they should overcome the high error rates of the technology. Our goal in this work is to comprehensively analyze current publicly available tools for nanopore sequence analysis to understand their advantages, disadvantages and performance bottlenecks. It is important to understand where the current tools do not perform well to develop better tools. To this end, we (1) analyze the multiple steps and the associated tools in the genome assembly pipeline using nanopore sequence data, and (2) provide guidelines for determining the appropriate tools for each step. Based on our analyses, we make four key observations: (1) the choice of the tool for basecalling plays a critical role in overcoming the high error rates of nanopore sequencing technology. (2) Read-to-read overlap finding tools, GraphMap and Minimap, perform similarly in terms of accuracy. However, Minimap has a lower memory usage, and it is faster than GraphMap. (3) There is a trade-off between accuracy and performance when deciding on the appropriate tool for the assembly step. The fast but less accurate assembler Miniasm can be used for quick initial assembly, and further polishing can be applied on top of it to increase the accuracy, which leads to faster overall assembly. (4) The state-of-the-art polishing tool, Racon, generates high-quality consensus sequences while providing a significant speedup over another polishing tool, Nanopolish. We analyze various combinations of different tools and expose the trade-offs between accuracy, performance, memory usage and scalability. We conclude that our observations can guide researchers and practitioners in making conscious and effective choices for each step of the genome assembly pipeline using nanopore sequence data. Also, with the help of bottlenecks we have found, developers can improve the current tools or build new ones that are both accurate and fast, to overcome the high error rates of the nanopore sequencing technology.

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A facile approach to fabricate halloysite/metal nanocomposites with preformed and in situ synthesized metal nanoparticles: a comparative study of their enhanced catalytic activity

Dalton Transactions ◽

10.1039/c5dt00830a ◽

2015 ◽

Vol 44 (19) ◽

pp. 8906-8916 ◽

Cited By ~ 29

Author(s):

Sankar Das ◽

Subhra Jana

Keyword(s):

Catalytic Activity ◽

Comparative Study ◽

Metal Nanoparticles ◽

Heterogeneous Catalysts ◽

Cost Effective ◽

Environmentally Benign ◽

Metal Nanocomposites

Halloysite/metal nanocomposites have been synthesized through the immobilization of preformed and in situ synthesized metal nanoparticles over halloysite surfaces, which in turn produce efficient, cost-effective, and environmentally benign heterogeneous catalysts.

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Application of Epoxy Resin for Improvement of the Banana Stem-Acoustic Panel

Recent Innovations in Chemical Engineering (Formerly Recent Patents on Chemical Engineering) ◽

10.2174/2405520415666211229125344 ◽

2021 ◽

Vol 15 ◽

Author(s):

Mohd Azril Riduan ◽

Mohd Jumain Jalil ◽

Intan Suhada Azmi ◽

Afifudin Habulat ◽

Danial Nuruddin Azlan Raofuddin ◽

...

Keyword(s):

Oleic Acid ◽

Kinetic Modelling ◽

Low Cost ◽

Cost Effective ◽

Performic Acid ◽

High Yield ◽

Renewable Materials ◽

Runge Kutta Method ◽

To Come

Background: Greener epoxidation by using vegetable oil to create an eco-friendly epoxide is being studied because it is a more cost-effective and environmentally friendly commodity that is safer than non-renewable materials. The aim of this research is to come up with low-cost solutions for banana trunk acoustic panels with kinetic modelling of epoxy-based palm oil. Method: In this study, the epoxidation of palm oleic acid was carried out by in situ performic acid to produce epoxidized palm oleic acid. Results: Banana trunk acoustic panel was successfully innovated based on the performance when the epoxy was applied. Lastly, a mathematical model was developed by using the numerical integration of the 4th order Runge-Kutta method, and the results showed that there is a good agreement between the simulation and experimental data, which validates the kinetic model. Conclusion: Overall, the peracid mechanism was effective in producing a high yield of epoxy from palm oleic acid that is useful for the improvement of acoustic panels based on the banana trunk.

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IoT Based Bus Tracking System

International Journal for Research in Applied Science and Engineering Technology ◽

10.22214/ijraset.2021.35613 ◽

2021 ◽

Vol 9 (VI) ◽

pp. 2889-2893

Author(s):

Miss Payal W. Paratpure

Keyword(s):

Tracking System ◽

Cost Effective ◽

Raspberry Pi ◽

Accurate Estimation ◽

Time Of Arrival ◽

Test Results ◽

Cloud Server ◽

Bus Operator ◽

Gps Device

Tracking of public bus location requires a GPS device to be installed, and lots of bus operators in developing countries don't have such an answer in situ to supply an accurate estimation of bus time of arrival (ETA). Without ETA information, it's very difficult for the overall public to plan their journey effectively. In this paper, implementation of an innovative IOT solution to trace the real time location of buses without requiring the deployment of a GPS device is discussed. It uses Bluetooth Low Energy (BLE) proximity beacon to trace the journey of a bus by deploying an Estimate location beacon on the bus. BLE detection devices (Raspberry Pi 4) are installed at selected bus stops along the path to detect the arrival of buses. Once detected, the situation of the bus is submitted to a cloud server to compute the bus ETAs. A field trial is currently being conducted in Johor, Malaysia together with an area bus operator on one single path. Our test results showed that the detection of BLE beacons is extremely accurate and it's feasible to trace the situation of buses without employing a GPS device during a cost-effective way.

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