Identifying spawning activity in aquatic species based on environmental DNA spikes

Mapping Intimacies ◽

10.1101/2020.01.28.924167 ◽

2020 ◽

Author(s):

Satsuki Tsuji ◽

Naoki Shibata

Keyword(s):

Reproductive Biology ◽

Field Survey ◽

Aquatic Organisms ◽

Environmental Dna ◽

Reproductive Season ◽

Aquatic Species ◽

Spawning Activity ◽

Invasive Approach ◽

Non Invasive ◽

Management Actions

AbstractAn understanding of the reproductive biology of aquatic organisms is crucial for the efficient conservation and management of species and/or populations. Nevertheless, conventional spawning surveys such as visual- and capture-based monitoring generally require laborious, time-consuming work and are subject to monitoring biases such as observer bias, as well as miscounts due to false spawning. In addition, direct capture often damages eggs or individuals. Thus, an efficient non-invasive approach for monitoring spawning activity on aquatic species would be a valuable tool to understand their reproductive biology and conserving biodiversity. Here, we proposed an environmental DNA (eDNA)-based approach for monitoring and understanding spawning activity by observing spikes in eDNA concentration after spawning activity. We found in cross experiments using two medaka species (Oryzias latipes and O. sakaizumii, 1:1 individual per tank) that an eDNA spike occurred in only male species after spawning activity. In addition, the magnitude of the eDNA spike was dependent on the number of spawning activities with egg and sperm release. In the field survey during the reproductive season, eDNA concentration after spawning were 3–25 times higher than before spawning. On the other hand, there was no increase in eDNA concentration during the non-reproductive season. Therefore, our results demonstrated that spikes in the eDNA concentration are mainly caused by the release of sperm during spawning activity, and it can be used as evidence of spawning in field survey. The presented approach could be a practical tool for studying reproductive biology and provides an opportunity to design effective conservation and environmental management actions.

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Using Optimal Environmental DNA Method to Improve the Fish Diversity Survey—From Laboratory to Aquatic Life Reserve

Water ◽

10.3390/w13111468 ◽

2021 ◽

Vol 13 (11) ◽

pp. 1468

Author(s):

Wen-Pan Li ◽

Zi-Fang Liu ◽

Tong Guo ◽

He Chen ◽

Xin Xie

Keyword(s):

High Throughput Sequencing ◽

Field Survey ◽

Diversity Index ◽

Environmental Dna ◽

Fish Diversity ◽

Target Area ◽

Aquatic Species ◽

Aquatic Life ◽

Wiener Diversity Index ◽

Better Than

Conserving aquatic ecosystems requires efficient tools to accurately assess the biodiversity of aquatic species. However, existing knowledge is insufficient in terms of the reliability and the comparability of methods measuring fish diversity. Environmental DNA (eDNA), as a promising method, was used to detect fish taxa in this study. We optimized the eDNA method in the laboratory, and applied the optimal eDNA method to survey fish diversity in a natural aquatic life reserve. We simulated necessary steps of the eDNA method in the lab to increase the confidence of the field survey. Specifically, we compared different eDNA sampling, extraction, and sequencing strategies for accurately capturing fish species of the target area. We found that 1L water samples were sufficient for sampling eDNA information of the majority taxa. The filtration was more effective than the centrifugal precipitation for the eDNA extraction. The cloning sequencing was better than the high-throughput sequencing. The field survey showed that the Shannon–Wiener diversity index of fish taxa was the highest in Huairou Reservoir. The diversity index also showed seasonal changes. The accuracy rate of detecting fish taxa was positively correlated with the eDNA concentration. This study provides a scientific reference for an application of the eDNA method in terms of surveying and estimating the biodiversity of aquatic species.

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Passive sampling of environmental DNA in aquatic environments using 3D-printed hydroxyapatite samplers

10.1101/2021.05.12.443744 ◽

2021 ◽

Author(s):

Heloise Verdier ◽

Lara Konecny-Dupre ◽

Christophe Marquette ◽

Helen Reveron ◽

Solene Tadier ◽

...

Keyword(s):

Aquatic Organisms ◽

Environmental Dna ◽

Aquatic Environments ◽

Non Invasive ◽

Turbid Waters ◽

Physico Chemical ◽

Wide Range ◽

Artificial Dna ◽

3D Printed ◽

High Binding Affinity

1. The study of environmental DNA released by aquatic organisms in their habitat offers a fast, non-invasive and sensitive approach to monitor their presence. Common eDNA sampling methods such as filtration and precipitation are time consuming, require human intervention and are not applicable to a wide range of habitats such as turbid waters and poorly-accessible environments. To circumvent these limitations, we propose to use the binding properties of minerals to create a passive eDNA sampler. 2. We have designed 3D-printed samplers made of hydroxyapatite (HAp samplers), a mineral known for its high binding affinity with DNA. The shape and the geometry of the samplers have been designed to facilitate their handling in laboratory and field. Here we describe and test the ability of HAp samplers to recover artificial DNA and eDNA. 3. We show that HAp samplers efficiently recover DNA and are effective even on small amounts of eDNA (<1 ng). However, we also observed large variations in the amount of DNA recovered even under controlled conditions. 4. By better understanding the physico-chemical interactions between DNA and the HAp sampler surface, one could improve the repeatability of the sampling process and provide an easy-to-use eDNA sampling tool for aquatic environments.

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Aquatic Organisms Research with DNA Barcodes

Diversity ◽

10.3390/d13070306 ◽

2021 ◽

Vol 13 (7) ◽

pp. 306

Author(s):

Manuel Elías-Gutiérrez ◽

Nicolas Hubert ◽

Rupert A. Collins ◽

Camilo Andrade-Sossa

Keyword(s):

Food Security ◽

Aquatic Ecosystems ◽

Sustainable Use ◽

Aquatic Organisms ◽

Environmental Dna ◽

Aquatic Species ◽

Dna Barcodes ◽

Aquatic Resources ◽

Further Development ◽

Made In

Since their inception, DNA barcodes have become a powerful tool for understanding the biodiversity and biology of aquatic species, with multiple applications in diverse fields such as food security, fisheries, environmental DNA, conservation, and exotic species detection. Nevertheless, most aquatic ecosystems, from marine to freshwater, are understudied, with many species disappearing due to environmental stress, mostly caused by human activities. Here we highlight the progress that has been made in studying aquatic organisms with DNA barcodes, and encourage its further development in assisting sustainable use of aquatic resources and conservation.

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Salivary cortisol as a non-invasive approach to assess stress in dystocic dairy calves

Scientific Reports ◽

10.1038/s41598-021-85666-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Levente Kovács ◽

Fruzsina Luca Kézér ◽

Szilárd Bodó ◽

Ferenc Ruff ◽

Rupert Palme ◽

...

Keyword(s):

Birth Weight ◽

Body Condition ◽

Salivary Cortisol ◽

Sampling Period ◽

Dairy Calves ◽

Birth Process ◽

Invasive Approach ◽

Non Invasive ◽

Saliva Cortisol ◽

Cortisol Levels

AbstractThe intensity and the magnitude of saliva cortisol responses were investigated during the first 48 h following birth in newborn dairy calves which underwent normal (eutocic, EUT, n = 88) and difficult (dystocic, DYS, n = 70) calvings. The effects of parity and body condition of the dam, the duration of parturition, the time spent licking the calf, the sex and birth weight of the calf were also analyzed. Neonatal salivary cortisol concentrations were influenced neither by factors related to the dam (parity, body condition) nor the calf (sex, birth weight). The duration of parturition and the time spent licking the calf also had no effect on salivary cortisol levels. Salivary cortisol concentrations increased rapidly after delivery in both groups to reach their peak levels at 45 and 60 min after delivery in EUT and DYS calves, respectively supporting that the birth process means considerable stress for calves and the immediate postnatal period also appears to be stressful for newborn calves. DYS calves exhibited higher salivary cortisol concentrations compared to EUT ones for 0 (P = 0.022), 15 (P = 0.016), 30 (P = 0.007), 45 (P = 0.003), 60 (P = 0.001) and 120 min (P = 0.001), and for 24 h (P = 0.040), respectively. Peak levels of salivary cortisol and the cortisol release into saliva calculated as AUC were higher in DYS than in EUT calves for the 48-h of the sampling period (P = 0.009 and P = 0.003, respectively). The greater magnitude of saliva cortisol levels in DYS calves compared to EUT ones suggest that difficult parturition means severe stress for bovine neonates and salivary cortisol could be an opportunity for non-invasive assessment of stress during the early neonatal period in cattle.

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The Cat Mandible (II): Manipulation of the Jaw, with a New Prosthesis Proposal, to Avoid Iatrogenic Complications

Animals ◽

10.3390/ani11030683 ◽

2021 ◽

Vol 11 (3) ◽

pp. 683

Author(s):

Matilde Lombardero ◽

Mario López-Lombardero ◽

Diana Alonso-Peñarando ◽

María del Mar Yllera

Keyword(s):

Imaging Techniques ◽

Recovery Period ◽

Prosthesis Design ◽

Patient Specific ◽

Mandibular Fractures ◽

Rigid Fixation ◽

Invasive Approach ◽

Non Invasive ◽

Iatrogenic Complications ◽

Mandibular Body

The cat mandible is relatively small, and its manipulation implies the use of fixing methods and different repair techniques according to its small size to keep its biomechanical functionality intact. Attempts to fix dislocations of the temporomandibular joint should be primarily performed by non-invasive techniques (repositioning the bones and immobilisation), although when this is not possible, a surgical method should be used. Regarding mandibular fractures, these are usually concurrent with other traumatic injuries that, if serious, should be treated first. A non-invasive approach should also first be considered to fix mandibular fractures. When this is impractical, internal rigid fixation methods, such as osteosynthesis plates, should be used. However, it should be taken into account that in the cat mandible, dental roots and the mandibular canal structures occupy most of the volume of the mandibular body, a fact that makes it challenging to apply a plate with fixed screw positions without invading dental roots or neurovascular structures. Therefore, we propose a new prosthesis design that will provide acceptable rigid biomechanical stabilisation, but avoid dental root and neurovascular damage, when fixing simple mandibular body fractures. Future trends will include the use of better diagnostic imaging techniques, a patient-specific prosthesis design and the use of more biocompatible materials to minimise the patient’s recovery period and suffering.

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Holistic description of new deep sea megafauna (Cephalopoda: Cirrata) using a minimally invasive approach

BMC Biology ◽

10.1186/s12915-021-01000-9 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Alexander Ziegler ◽

Christina Sagorny

Keyword(s):

Minimally Invasive ◽

Dna Barcoding ◽

Deep Sea ◽

Imaging Techniques ◽

Structural Complexity ◽

Micro Computed Tomography ◽

Invasive Approach ◽

Non Invasive ◽

Additional Support ◽

Holistic Description

Abstract Background In zoology, species descriptions conventionally rely on invasive morphological techniques, frequently leading to damage of the specimens and thus only a partial understanding of their structural complexity. More recently, non-destructive imaging techniques have successfully been used to describe smaller fauna, but this approach has so far not been applied to identify or describe larger animal species. Here, we present a combination of entirely non-invasive as well as minimally invasive methods that permit taxonomic descriptions of large zoological specimens in a more comprehensive manner. Results Using the single available representative of an allegedly novel species of deep-sea cephalopod (Mollusca: Cephalopoda), digital photography, standardized external measurements, high-field magnetic resonance imaging, micro-computed tomography, and DNA barcoding were combined to gather all morphological and molecular characters relevant for a full species description. The results show that this specimen belongs to the cirrate octopod (Octopoda: Cirrata) genus Grimpoteuthis Robson, 1932. Based on the number of suckers, position of web nodules, cirrus length, presence of a radula, and various shell characters, the specimen is designated as the holotype of a new species of dumbo octopus, G. imperator sp. nov. The digital nature of the acquired data permits a seamless online deposition of raw as well as derived morphological and molecular datasets in publicly accessible repositories. Conclusions Using high-resolution, non-invasive imaging systems intended for the analysis of larger biological objects, all external as well as internal morphological character states relevant for the identification of a new megafaunal species were obtained. Potentially harmful effects on this unique deep-sea cephalopod specimen were avoided by scanning the fixed animal without admixture of a contrast agent. Additional support for the taxonomic placement of the new dumbo octopus species was obtained through DNA barcoding, further underlining the importance of combining morphological and molecular datasets for a holistic description of zoological specimens.

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Platelet production estimation in thrombocytopenic patient: a non-invasive or invasive approach?

Nuclear Medicine Communications ◽

10.1097/00006231-200404000-00103 ◽

2004 ◽

Vol 25 (4) ◽

pp. 422 ◽

Cited By ~ 1

Author(s):

M. Todorovic-Tirnanic ◽

V. Obradovic ◽

N. Suvajdzic ◽

I. Elezovic ◽

M. Rolovic ◽

...

Keyword(s):

Invasive Approach ◽

Platelet Production ◽

Non Invasive ◽

Thrombocytopenic Patient

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Alterations of 5-hydroxymethylation in circulating cell-free DNA reflect molecular distinctions of subtypes of non-Hodgkin lymphoma

npj Genomic Medicine ◽

10.1038/s41525-021-00179-8 ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Brian C.-H. Chiu ◽

Chang Chen ◽

Qiancheng You ◽

Rudyard Chiu ◽

Girish Venkataraman ◽

...

Keyword(s):

B Cell Lymphoma ◽

Cell Free Dna ◽

Invasive Approach ◽

Non Invasive ◽

Signature Genes ◽

Non Hodgkin Lymphoma ◽

Free Dna ◽

Genome Wide ◽

Circulating Cell Free Dna

AbstractThe 5-methylcytosines (5mC) have been implicated in the pathogenesis of diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL). However, the role of 5-hydroxymethylcytosines (5hmC) that are generated from 5mC through active demethylation, in lymphomagenesis is unknown. We profiled genome-wide 5hmC in circulating cell-free DNA (cfDNA) from 73 newly diagnosed patients with DLBCL and FL. We identified 294 differentially modified genes between DLBCL and FL. The differential 5hmC in the DLBCL/FL-differentiating genes co-localized with enhancer marks H3K4me1 and H3K27ac. A four-gene panel (CNN2, HMG20B, ACRBP, IZUMO1) robustly represented the overall 5hmC modification pattern that distinguished FL from DLBCL with an area under curve of 88.5% in the testing set. The median 5hmC modification levels in signature genes showed potential for separating patients for risk of all-cause mortality. This study provides evidence that genome-wide 5hmC profiles in cfDNA differ between DLBCL and FL and could be exploited as a non-invasive approach.

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