scholarly journals Species detection using environmental DNA from water samples

2008 ◽  
Vol 4 (4) ◽  
pp. 423-425 ◽  
Author(s):  
Gentile Francesco Ficetola ◽  
Claude Miaud ◽  
François Pompanon ◽  
Pierre Taberlet
Keyword(s):  
Dna Sequences ◽  
Developmental Stages ◽  
Rana Catesbeiana ◽  
Environmental Dna ◽  
Species Detection ◽  
Novel Approach ◽  
Molecular Imprint ◽  
Massive Sequencing ◽  
Natural Wetlands ◽  
Controlled Environments

The assessment of species distribution is a first critical phase of biodiversity studies and is necessary to many disciplines such as biogeography, conservation biology and ecology. However, several species are difficult to detect, especially during particular time periods or developmental stages, potentially biasing study outcomes. Here we present a novel approach, based on the limited persistence of DNA in the environment, to detect the presence of a species in fresh water. We used specific primers that amplify short mitochondrial DNA sequences to track the presence of a frog ( Rana catesbeiana ) in controlled environments and natural wetlands. A multi-sampling approach allowed for species detection in all environments where it was present, even at low densities. The reliability of the results was demonstrated by the identification of amplified DNA fragments, using traditional sequencing and parallel pyrosequencing techniques. As the environment can retain the molecular imprint of inhabiting species, our approach allows the reliable detection of secretive organisms in wetlands without direct observation. Combined with massive sequencing and the development of DNA barcodes that enable species identification, this approach opens new perspectives for the assessment of current biodiversity from environmental samples.

The Culture in vitro of Urogenital Organs of Pleurodeles waltlii

Development ◽  
1962 ◽  
Vol 10 (4) ◽  
pp. 465-470
Author(s):  
Charles L. Foote ◽  
Florence M. Foote
Keyword(s):  
Organ Culture ◽  
Germ Cells ◽  
Culture Medium ◽  
Developmental Stages ◽  
Rana Catesbeiana ◽  
Sex Differentiation ◽  
Organ Cultures ◽  
Tissue And Organ Culture ◽  
Pleurodeles Waltlii

Earlier reports (Foote & Foote, 1958a, b, 1959) describe growth and maintenance in vitro of larval organs, particularly gonads, of Rana catesbeiana and Xenopus laevis. Immature germ cells of both testes and ovaries are well maintained in vitro, especially if the culture medium is supplemented with watersoluble sex-hormonal substances, although germ cells in process of maturation become necrotic. Recently some urogenital organs from the salamander, Pleurodeles waltlii, have been grown in vitro. Tissues and organs from this amphibian might prove to be more suitable for tissue and organ culture investigations than those of Anurans. Animals at three different ages were used in this study: recently hatched larvae, metamorphosing animals, and adults. To determine whether sex differentiation would occur in vitro, trunk portions of young larvae of Pleurodeles waltlii of developmental stages 37–38 (Gallien & Durocher, 1957) were placed in organ cultures.

Elimination of micronuclear specific DNA sequences early in anlagen development

1985 ◽  
Vol 5 (1) ◽  
pp. 93-98
Author(s):  
C F Brunk ◽  
R K Conover
Keyword(s):  
Developmental Stage ◽  
Dna Sequences ◽  
Developmental Stages ◽  
Tetrahymena Thermophila ◽  
Southern Analysis ◽  
Limited Sequence

After conjugation in Tetrahymena thermophila, the old macronuclei degenerate, and new macronuclei (anlagen) develop. During anlagen development a number of DNA sequences found in the micronuclear genome (micronuclear limited sequences) are eliminated from the anlagen. A cloned copy of a repetitive micronuclear limited sequence has been used to determine the developmental stage at which micronuclear limited sequences are eliminated. DNAs from anlagen of various developmental stages were examined by Southern analysis. It was found that micronuclear limited sequences are present in 4C anlagen and essentially absent in 8C and 16C anlagen. The precipitous loss of these sequences in the 8C anlagen rules out under-replication as the mechanism for the loss and suggests that these sequences are specifically degraded early during anlagen development.

scholarly journals Overcoming limitations to environmental DNA studies: A coastal temperate reference sequence database for multiple chloroplast gene regions generated in a single assay.

2021 ◽  
Author(s):  
Nicole Foster ◽  
Kor-jent Dijk ◽  
Ed Biffin ◽  
Jennifer Young ◽  
Vicki Thomson ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Reference Sequence ◽  
Reference Database ◽  
Chloroplast Gene ◽  
Coastal Plants ◽  
Reference Databases ◽  
Targeted Capture ◽  
Comprehensive Reference

A proliferation in environmental DNA (eDNA) research has increased the reliance on reference sequence databases to assign unknown DNA sequences to known taxa. Without comprehensive reference databases, DNA extracted from environmental samples cannot be correctly assigned to taxa, limiting the use of this genetic information to identify organisms in unknown sample mixtures. For animals, standard metabarcoding practices involve amplification of the mitochondrial Cytochrome-c oxidase subunit 1 (CO1) region, which is a universally amplifyable region across majority of animal taxa. This region, however, does not work well as a DNA barcode for plants and fungi, and there is no similar universal single barcode locus that has the same species resolution. Therefore, generating reference sequences has been more difficult and several loci have been suggested to be used in parallel to get to species identification. For this reason, we developed a multi-gene targeted capture approach to generate reference DNA sequences for plant taxa across 20 target chloroplast gene regions in a single assay. We successfully compiled a reference database for 93 temperate coastal plants including seagrasses, mangroves, and saltmarshes/samphire’s. We demonstrate the importance of a comprehensive reference database to prevent species going undetected in eDNA studies. We also investigate how using multiple chloroplast gene regions impacts the ability to discriminate between taxa.

scholarly journals Development of species-specific Cichla species eDNA primers for alien invasive species (AIS) monitoring in Malaysia

2021 ◽  
Vol 4 ◽  
Author(s):  
O. Nurul Fizatul Nabilah ◽  
A. R. Ramizah ◽  
A. B. Adibah ◽  
S. Syazwan ◽  
A.G. Intan Faraha ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Environmental Dna ◽  
Coi Gene ◽  
Alien Invasive Species ◽  
Survey Method ◽  
Specific Primers ◽  
Invasive Fishes ◽  
Specific Amplification ◽  
Species Specific ◽  
High Level

Peacock bass or the cichlids are known locally as top predator fishes which are invasive in Malaysia freshwater system. Detection probabilities for these fishes are typically low, especially using conventional capture-survey method due to the fish’s behaviour of hiding beneath the water’s surface. Hence, the environmental DNA (eDNA) monitoring is a relatively new approach that can be used to assess the distribution of these invasive fishes. Here, we report the strategy to develop small fragment (280- 400 bp) specific-specific primers for three selected invasive Cichla species namely, C. ocellaris, C. monoculus, and C. kelberi based on mitochondrial DNA (mtDNA) sequences. Current research showed that the developed species-specific primers from cytochrome oxidase I (COI) gene has high resolution at species level. Species-specific amplification tests also proved the specificity of the developed primers, securing the high- level species identification potential which may help in controlling the spread of alien invasive fish species.

COMPARING VIRUS CLASSIFICATION USING GENOMIC MATERIALS ACCORDING TO DIFFERENT TAXONOMIC LEVELS

2013 ◽  
Vol 11 (06) ◽  
pp. 1343003 ◽  
Author(s):  
JING-DOO WANG
Keyword(s):  
Molecular Biology ◽  
Dna Sequences ◽  
Protein Sequences ◽  
Experimental Results ◽  
Virus Classification ◽  
Taxonomic Level ◽  
Biological Classification ◽  
Novel Approach

In this paper, three genomic materials — DNA sequences, protein sequences, and regions (domains) are used to compare methods of virus classification. Virus classes (categories) are divided by various taxonomic level of virus into three datasets for 6 order, 42 family, and 33 genera. To increase the robustness and comparability of experimental results of virus classification, the classes are selected that contain at least 10 instances, and meanwhile each instance contains at least one region name. Experimental results show that the approach using region names achieved the best accuracies — reaching 99.9%, 97.3%, and 99.0% for 6 orders, 42 families, and 33 genera, respectively. This paper not only involves exhaustive experiments that compare virus classifications using different genomic materials, but also proposes a novel approach to biological classification based on molecular biology instead of traditional morphology.

Environmental DNA (eDNA): A Promising Biological Survey Tool for Aquatic Species Detection

2018 ◽  
Vol 72 (3) ◽  
pp. 211-228 ◽  
Author(s):  
Debabrata Senapati ◽  
Manojit Bhattacharya ◽  
Avijit Kar ◽  
Deep Sankar Chini ◽  
Basanta Kumar Das ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Aquatic Species ◽  
Species Detection ◽  
Survey Tool ◽  
Biological Survey

scholarly journals MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies

BMC Genomics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 461 ◽  
Author(s):  
Manuel Stark ◽  
Simon A Berger ◽  
Alexandros Stamatakis ◽  
Christian von Mering
Keyword(s):  
Maximum Likelihood ◽  
Dna Sequences ◽  
Environmental Dna

Developmental stages of Sphaerospora ohlmacheri (Whinery, 1893) n.comb. (Myxozoa: Myxosporea) in the renal tubules of bullfrog tadpoles, Rana catesbeiana, from Lake of Two Rivers, Algonquin Park, Ontario

1986 ◽  
Vol 64 (10) ◽  
pp. 2213-2217 ◽  
Author(s):  
Sherwin S. Desser ◽  
Jǐrí Lom ◽  
Iva Dyková
Keyword(s):  
Developmental Stages ◽  
Renal Tubule ◽  
Rana Catesbeiana ◽  
Renal Tubules ◽  
Histological Sections ◽  
Tubule Cells ◽  
Bowman's Capsule

Pseudoplasmodia and mature spores of Sphaerospora ohlmacheri (Whinery, 1893) n.comb. were found in the renal tubules and in the space of the Bowman's capsule of 2nd-year tadpoles of the bullfrog, Rana catesbeiana. Fresh spores and the sporogenic stages of S. ohlmacheri from tissue imprints and histological sections are described and illustrated. Dystrophic changes of renal tubule cells characterized by degeneration associated with hyaline droplets often accompanied the presence of the parasite. Features of the genera Leptotheca, Wardia, and Sphaerospora are discussed.

Patterns of polyembryony and frequency of surviving multiple embryos of the Brazilian pine Araucaria angustifolia

2011 ◽  
Vol 59 (8) ◽  
pp. 749 ◽  
Author(s):  
Sarah Zanon Agapito-Tenfen ◽  
Neusa Steiner ◽  
Miguel Pedro Guerra ◽  
Rubens Onofre Nodari
Keyword(s):  
Microsatellite Markers ◽  
Developmental Stages ◽  
Rare Event ◽  
Morphological Characteristics ◽  
Immature Embryos ◽  
Araucaria Angustifolia ◽  
Embryo Survival ◽  
Major Mechanism ◽  
Novel Approach ◽  
Nuclear Microsatellite

The development of polyembryony is a common reproductive strategy in conifers. Multiple embryos are observed during early seed developmental stages. However, upon seed maturation, only the dominant embryo survives, with few exceptions. Although programmed cell death has been reported as the major mechanism responsible for elimination of subordinate embryos, the genetics of surviving embryos and the probabilities of survival remain unclear. The aim of this study is to determine patterns of polyembryony and survival frequency in Araucaria angustifolia (Bert) O. Ktze. Thus, we investigate the morphogenetic parameters that might be related to embryo survival using nuclear microsatellite markers and morphological characteristics of immature embryos and seedlings. Our novel approach couples genotype frequency analysis with the number of surviving embryos, presence of embryo dominance and number of cotyledons present within a single seed. Polyembryonic seedling frequency was low (0.022%) and 91% of surviving embryos were monozygotic. From all monozygotic embryos, 98% showed differences in growth rate (height) in relation to each other. Concrescent tissues were common in the monozygotic polyembryony patterns observed (80%) but not for those with polyzygotic polyembryony. We demonstrate that the survival of multiple embryos is a rare event in A. angustifolia seeds. To the best of our knowledge this study represents the first evidence of cleavage polyembryony in immature embryos and seedlings from A. angustifolia. Our novel approach using a combined set of morphological parameters and microsatellite markers was successful in investigating polyembryony patterns and survival.

scholarly journals Enzymatic Weight Update Algorithm for DNA-Based Molecular Learning

Molecules ◽  
2019 ◽  
Vol 24 (7) ◽  
pp. 1409 ◽  
Author(s):  
Christina Baek ◽  
Sang-Woo Lee ◽  
Beom-Jin Lee ◽  
Dong-Hyun Kwak ◽  
Byoung-Tak Zhang
Keyword(s):  
Machine Learning ◽  
Dna Sequences ◽  
Dna Nanotechnology ◽  
Search Space ◽  
Molecular Computing ◽  
Training Data ◽  
Molecular Systems ◽  
Novel Approach ◽  
Biological Substrates

Recent research in DNA nanotechnology has demonstrated that biological substrates can be used for computing at a molecular level. However, in vitro demonstrations of DNA computations use preprogrammed, rule-based methods which lack the adaptability that may be essential in developing molecular systems that function in dynamic environments. Here, we introduce an in vitro molecular algorithm that ‘learns’ molecular models from training data, opening the possibility of ‘machine learning’ in wet molecular systems. Our algorithm enables enzymatic weight update by targeting internal loop structures in DNA and ensemble learning, based on the hypernetwork model. This novel approach allows massively parallel processing of DNA with enzymes for specific structural selection for learning in an iterative manner. We also introduce an intuitive method of DNA data construction to dramatically reduce the number of unique DNA sequences needed to cover the large search space of feature sets. By combining molecular computing and machine learning the proposed algorithm makes a step closer to developing molecular computing technologies for future access to more intelligent molecular systems.

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