scholarly journals Transgenes of genetically modified animals detected non-invasively via environmental DNA

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0249439
Author(s):  
Charles C. Y. Xu ◽  
Claire Ramsay ◽  
Mitra Cowan ◽  
Mehrnoush Dehghani ◽  
Paul Lasko ◽  
...  
Keyword(s):  
Genetically Modified ◽  
Pcr Amplification ◽  
Environmental Dna ◽  
Cost Effective ◽  
Laboratory Mice ◽  
Non Invasive ◽  
Aquarium Water ◽  
Food Media ◽  
Gm Animals ◽  
Genetically Modified Animals

We demonstrate that simple, non-invasive environmental DNA (eDNA) methods can detect transgenes of genetically modified (GM) animals from terrestrial and aquatic sources in invertebrate and vertebrate systems. We detected transgenic fragments between 82–234 bp through targeted PCR amplification of environmental DNA extracted from food media of GM fruit flies (Drosophila melanogaster), feces, urine, and saliva of GM laboratory mice (Mus musculus), and aquarium water of GM tetra fish (Gymnocorymbus ternetzi). With rapidly growing accessibility of genome-editing technologies such as CRISPR, the prevalence and diversity of GM animals will increase dramatically. GM animals have already been released into the wild with more releases planned in the future. eDNA methods have the potential to address the critical need for sensitive, accurate, and cost-effective detection and monitoring of GM animals and their transgenes in nature.

scholarly journals Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modelling

2018 ◽  
Author(s):  
Keiichi Fukaya ◽  
Hiroaki Murakami ◽  
Seokjin Yoon ◽  
Kenji Minami ◽  
Yutaka Osada ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Cost Effective ◽  
Population Monitoring ◽  
Fish Population ◽  
Abundance Estimation ◽  
Population Abundance ◽  
Jack Mackerel ◽  
Non Invasive ◽  
Quantitative Measurements ◽  
Japanese Jack Mackerel

AbstractWe propose a general framework of abundance estimation based on spatially replicated quantitative measurements of environmental DNA in which production, transport, and degradation of DNA are explicitly accounted for. Application to a Japanese jack mackerel (Trachurus japonicus) population in Maizuru Bay revealed that the method gives an estimate of population abundance comparable to that of a quantitative echo sounder method. These findings indicate the ability of environmental DNA to reliably reflect population abundance of aquatic macroorganisms and may offer a new avenue for population monitoring based on the fast, cost-effective, and non-invasive sampling of genetic information.

scholarly journals Tagsteady: a metabarcoding library preparation protocol to avoid false assignment of sequences to samples

2020 ◽  
Author(s):  
Christian Carøe ◽  
Kristine Bohmann
Keyword(s):  
Dna Polymerase ◽  
Pcr Amplification ◽  
Environmental Dna ◽  
Cost Effective ◽  
Ecological Interactions ◽  
Library Preparation ◽  
Bulk Specimen ◽  
Effective Generation ◽  
Illumina Library ◽  
Library Preparation Protocol

AbstractMetabarcoding of environmental DNA (eDNA) and DNA extracted from bulk specimen samples is a powerful tool in studies of biodiversity, diet and ecological interactions as its inherent labelling of amplicons allows sequencing of taxonomically informative genetic markers from many samples in parallel. However, the occurrence of so-called ‘tag-jumps’ can cause incorrect assignment of sequences to samples and artificially inflate diversity. Two steps during library preparation of pools of 5’ nucleotide-tagged amplicons have been suggested to cause tag-jumps; i) T4 DNA polymerase blunt-ending in the end-repair step and ii) post-ligation PCR amplification of amplicon libraries. The discovery of tag-jumps has led to recommendations to only carry out metabarcoding PCR amplifications with primers carrying twin-tags to ensure that tag-jumps cannot result in false assignments of sequences to samples. As this increases both cost and workload, a metabarcoding library preparation protocol which circumvents the two steps that causes tag-jumps is needed. Here, we demonstrate Tagsteady, a metabarcoding Illumina library preparation protocol for pools of nucleotide-tagged amplicons that enables efficient and cost-effective generation of metabarcoding data with virtually no tag-jumps. We use pools of twin-tagged amplicons to investigate the effect of T4 DNA polymerase blunt-ending and post-ligation PCR on the occurrence of tag-jumps. We demonstrate that both blunt-ending and post-ligation PCR, alone or together, can result in detrimental amounts of tag-jumps (here, up to ca. 49% of total sequences), while leaving both steps out (the Tagsteady protocol) results in amounts of sequences carrying new combinations of used tags (tag-jumps) comparable to background contamination.

scholarly journals Development of a 16S metabarcoding assay for the environmental DNA (eDNA) detection of aquatic reptiles across northern Australia

2020 ◽  
Author(s):  
Katrina West ◽  
Matthew Heydenrych ◽  
Rose Lines ◽  
Tony Tucker ◽  
Sabrina Fossette ◽  
...  
Keyword(s):  
Simultaneous Detection ◽  
Environmental Dna ◽  
Cost Effective ◽  
Distribution Data ◽  
Freshwater Turtles ◽  
Northern Australia ◽  
Non Invasive ◽  
Sea Snakes ◽  
Reptile Species ◽  
Species Specific

AbstractA severe lack of distribution data for aquatic reptiles in northern Australia leaves many taxa vulnerable to extirpation and extinction. Environmental DNA (eDNA) technologies offer sensitive and non-invasive genetic alternatives to trapping and visual surveys and are increasingly employed for the detection of aquatic and semi-aquatic reptiles. However, at present, these studies have largely applied species-specific primers which do not provide a cost-effective avenue for the simultaneous detection of multiple reptilian taxa. Here, we present a 16S rRNA metabarcoding assay for the broad detection of aquatic and semi-aquatic reptile species. This assay is tested on water samples collected at multiple sampling sites at two tropical locations: 12 marine/estuarine sites in Roebuck Bay, Western Australia, and 4 estuarine sites in Cooktown, Queensland, Australia. A total of nine reptile taxa were detected from 10 of the 16 sampled sites, including marine and freshwater turtles, aquatic and semi-aquatic/terrestrial snakes, and terrestrial skinks. However, inconsistencies in the detection of previously observed aquatic reptiles at our sampled sites, such as saltwater crocodile and sea snakes, indicates that further research is required to assess the reliability, strengths and limitations of eDNA methods for aquatic reptile detection before it can be integrated as a broad-scale bioassessment tool.

A novel use of contrast-enhanced ultrasound in uterine artery embolization

2020 ◽  
Vol 4 ◽  
pp. 8
Author(s):  
Jemianne Bautista Jia ◽  
Eric Mastrolonardo ◽  
Mateen Soleman ◽  
Ilya Lekht
Keyword(s):  
Uterine Artery Embolization ◽  
Uterine Artery ◽  
Imaging Modality ◽  
Cost Effective ◽  
Contrast Enhanced Ultrasound ◽  
Artery Embolization ◽  
Non Invasive ◽  
Contrast Enhanced

Contrast-enhanced ultrasound (CEUS) is a cost-effective, quick, and non-invasive imaging modality that has yet to be incorporated in uterine artery embolization (UAE). We present two cases that demonstrate the utility of CEUS in UAE for the identification of uterine-ovarian collaterals which otherwise can result in ineffective fibroid treatment and non-target embolization.

Review of Various Tasks Performed in the Preprocessing Phase of a Diabetic Retinopathy Diagnosis System

2020 ◽  
Vol 16 (4) ◽  
pp. 397-426
Author(s):  
Muhammad Nadeem Ashraf ◽  
Muhammad Hussain ◽  
Zulfiqar Habib
Keyword(s):  
Diabetic Retinopathy ◽  
Blood Vessels ◽  
Early Stage ◽  
Spherical Shape ◽  
Cost Effective ◽  
Lesion Detection ◽  
Diabetic Patients ◽  
Cad System ◽  
Non Invasive ◽  
Optic Discs

Diabetic Retinopathy (DR) is a major cause of blindness in diabetic patients. The increasing population of diabetic patients and difficulty to diagnose it at an early stage are limiting the screening capabilities of manual diagnosis by ophthalmologists. Color fundus images are widely used to detect DR lesions due to their comfortable, cost-effective and non-invasive acquisition procedure. Computer Aided Diagnosis (CAD) of DR based on these images can assist ophthalmologists and help in saving many sight years of diabetic patients. In a CAD system, preprocessing is a crucial phase, which significantly affects its performance. Commonly used preprocessing operations are the enhancement of poor contrast, balancing the illumination imbalance due to the spherical shape of a retina, noise reduction, image resizing to support multi-resolution, color normalization, extraction of a field of view (FOV), etc. Also, the presence of blood vessels and optic discs makes the lesion detection more challenging because these two artifacts exhibit specific attributes, which are similar to those of DR lesions. Preprocessing operations can be broadly divided into three categories: 1) fixing the native defects, 2) segmentation of blood vessels, and 3) localization and segmentation of optic discs. This paper presents a review of the state-of-the-art preprocessing techniques related to three categories of operations, highlighting their significant aspects and limitations. The survey is concluded with the most effective preprocessing methods, which have been shown to improve the accuracy and efficiency of the CAD systems.

scholarly journals Prostate Cancer Liquid Biopsy Biomarkers’ Clinical Utility in Diagnosis and Prognosis

Cancers ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 3373
Author(s):  
Milena Matuszczak ◽  
Jack A. Schalken ◽  
Maciej Salagierski
Keyword(s):  
Prostate Cancer ◽  
Liquid Biopsy ◽  
Current Knowledge ◽  
Prostate Gland ◽  
Specific Antigen ◽  
Transrectal Ultrasound ◽  
Digital Rectal Examination ◽  
Cost Effective ◽  
Non Invasive ◽  
Diagnosis And Prognosis

Prostate cancer (PCa) is the most common cancer in men worldwide. The current gold standard for diagnosing PCa relies on a transrectal ultrasound-guided systematic core needle biopsy indicated after detection changes in a digital rectal examination (DRE) and elevated prostate-specific antigen (PSA) level in the blood serum. PSA is a marker produced by prostate cells, not just cancer cells. Therefore, an elevated PSA level may be associated with other symptoms such as benign prostatic hyperplasia or inflammation of the prostate gland. Due to this marker’s low specificity, a common problem is overdiagnosis, which leads to unnecessary biopsies and overtreatment. This is associated with various treatment complications (such as bleeding or infection) and generates unnecessary costs. Therefore, there is no doubt that the improvement of the current procedure by applying effective, sensitive and specific markers is an urgent need. Several non-invasive, cost-effective, high-accuracy liquid biopsy diagnostic biomarkers such as Progensa PCA3, MyProstateScore ExoDx, SelectMDx, PHI, 4K, Stockholm3 and ConfirmMDx have been developed in recent years. This article compares current knowledge about them and their potential application in clinical practice.

scholarly journals The effect of silica desiccation under different storage conditions on filter-immobilized environmental DNA

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Michael J. Allison ◽  
Jessica M. Round ◽  
Lauren C. Bergman ◽  
Ali Mirabzadeh ◽  
Heather Allen ◽  
...  
Keyword(s):  
Silica Gel ◽  
Storage Temperature ◽  
Environmental Dna ◽  
Cost Effective ◽  
Storage Conditions ◽  
Systematic Evaluation ◽  
Silica Bead ◽  
Gel Beads ◽  
Polymerase Chain

Abstract Objective Silica gel beads have promise as a non-toxic, cost-effective, portable method for storing environmental DNA (eDNA) immobilized on filter membranes. Consequently, many ecological surveys are turning to silica bead filter desiccation rather than ethanol preservation. However, no systematic evaluation of silica bead storage conditions or duration past 1 week has been published. The present study evaluates the quality of filter-immobilized eDNA desiccated with silica gel under different storage conditions for over a year using targeted quantitative real-time polymerase chain reaction (qPCR)-based assays. Results While the detection of relatively abundant eDNA target was stable over 15 months from either ethanol- or silica gel-preserved filters at − 20 and 4 °C, silica gel out-performed ethanol preservation at 23 °C by preventing a progressive decrease in eDNA sample quality. Silica gel filter desiccation preserved low abundance eDNA equally well up to 1 month regardless of storage temperature (18, 4, or − 20 °C). However only storage at − 20 °C prevented a noticeable decrease in detectability at 5 and 12 months. The results indicate that brief storage of eDNA filters with silica gel beads up to 1 month can be successfully accomplished at a range of temperatures. However, longer-term storage should be at − 20 °C to maximize sample integrity.

scholarly journals RoboEye, an Efficient, Reliable and Safe Semi-Autonomous Gaze Driven Wheelchair for Domestic Use

Technologies ◽  
2021 ◽  
Vol 9 (1) ◽  
pp. 16
Author(s):  
Luca Maule ◽  
Alessandro Luchetti ◽  
Matteo Zanetti ◽  
Paolo Tomasin ◽  
Marco Pertile ◽  
...  
Keyword(s):  
Mobile Robotics ◽  
Cost Effective ◽  
Continuous Control ◽  
Eye Tracker ◽  
Motor Disability ◽  
Non Invasive ◽  
Severe Motor ◽  
Core Elements ◽  
Domestic Use ◽  
User Friendly

Any severe motor disability is a condition that limits the ability to interact with the environment, even the domestic one, caused by the loss of control over one’s mobility. This work presents RoboEYE, a power wheelchair designed to allow users to move easily and autonomously within their homes. To achieve this goal, an innovative, cost-effective and user-friendly control system was designed, in which a non-invasive eye tracker, a monitor, and a 3D camera represent some of the core elements. RoboEYE integrates functionalities from the mobile robotics field into a standard power wheelchair, with the main advantage of providing the user with two driving options and comfortable navigation. The most intuitive and direct modality foresees the continuous control of frontal and angular wheelchair velocities by gazing at different areas of the monitor. The second, semi-autonomous modality allows navigation toward a selected point in the environment by just pointing and activating the wished destination while the system autonomously plans and follows the trajectory that brings the wheelchair to that point. The purpose of this work was to develop the control structure and driving interface designs of the aforementioned driving modalities taking into account also uncertainties in gaze detection and other sources of uncertainty related to the components to ensure user safety. Furthermore, the driving modalities, in particular the semi-autonomous one, were modeled and qualified through numerical simulations and experimental verification by testing volunteers, who are regular users of standard electric wheelchairs, to verify the efficiency, reliability and safety of the proposed system for domestic use. RoboEYE resulted suitable for environments with narrow passages wider than 1 m, which is comparable with a standard domestic door and due to its properties with large commercialization potential.

scholarly journals Proteins and microRNAs are differentially expressed in tear fluid from patients with Alzheimer’s disease

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Aidan Kenny ◽  
Eva M. Jiménez-Mateos ◽  
María Ascensión Zea-Sevilla ◽  
Alberto Rábano ◽  
Pablo Gili-Manzanaro ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Unmet Need ◽  
Cost Effective ◽  
Specific Protein ◽  
Tear Fluid ◽  
Initiation Factor ◽  
Non Invasive ◽  
A Genome ◽  
Potential Biomarker

Abstract Alzheimer’s disease (AD) is characterized by a progressive loss of neurons and cognitive functions. Therefore, early diagnosis of AD is critical. The development of practical and non-invasive diagnostic tests for AD remains, however, an unmet need. In the present proof-of-concept study we investigated tear fluid as a novel source of disease-specific protein and microRNA-based biomarkers for AD development using samples from patients with mild cognitive impairment (MCI) and AD. Tear protein content was evaluated via liquid chromatography-mass spectrometry and microRNA content was profiled using a genome-wide high-throughput PCR-based platform. These complementary approaches identified enrichment of specific proteins and microRNAs in tear fluid of AD patients. In particular, we identified elongation initiation factor 4E (eIF4E) as a unique protein present only in AD samples. Total microRNA abundance was found to be higher in tears from AD patients. Among individual microRNAs, microRNA-200b-5p was identified as a potential biomarker for AD with elevated levels present in AD tear fluid samples compared to controls. Our study suggests that tears may be a useful novel source of biomarkers for AD and that the identification and verification of biomarkers within tears may allow for the development of a non-invasive and cost-effective diagnostic test for AD.

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