scholarly journals Molecular Analysis of Forensically Important Blow Flies in Thailand

Insects ◽  
2018 ◽  
Vol 9 (4) ◽  
pp. 159 ◽  
Author(s):  
Narin Sontigun ◽  
Kabkaew Sukontason ◽  
Jens Amendt ◽  
Barbara Zajac ◽  
Richard Zehner ◽  
...  
Keyword(s):  
Species Identification ◽  
Developmental Stages ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Reference Database ◽  
Closely Related Species ◽  
Close Match ◽  
Blow Flies ◽  
Tree Methods ◽  
Species Specific

Blow flies are the first insect group to colonize on a dead body and thus correct species identification is a crucial step in forensic investigations for estimating the minimum postmortem interval, as developmental times are species-specific. Due to the difficulty of traditional morphology-based identification such as the morphological similarity of closely related species and uncovered taxonomic keys for all developmental stages, DNA-based identification has been increasing in interest, especially in high biodiversity areas such as Thailand. In this study, the effectiveness of long mitochondrial cytochrome c oxidase subunit I and II (COI and COII) sequences (1247 and 635 bp, respectively) in identifying 16 species of forensically relevant blow flies in Thailand (Chrysomya bezziana, Chrysomya chani, Chrysomya megacephala, Chrysomya nigripes, Chrysomya pinguis, Chrysomya rufifacies, Chrysomya thanomthini, Chrysomya villeneuvi, Lucilia cuprina, Lucilia papuensis, Lucilia porphyrina, Lucilia sinensis, Hemipyrellia ligurriens, Hemipyrellia pulchra, Hypopygiopsis infumata, and Hypopygiopsis tumrasvini) was assessed using distance-based (Kimura two-parameter distances based on Best Match, Best Close Match, and All Species Barcodes criteria) and tree-based (grouping taxa by sequence similarity in the neighbor-joining tree) methods. Analyses of the obtained sequence data demonstrated that COI and COII genes were effective markers for accurate species identification of the Thai blow flies. This study has not only demonstrated the genetic diversity of Thai blow flies, but also provided a reliable DNA reference database for further use in forensic entomology within the country and other regions where these species exist.

scholarly journals Song discrimination by nestling collared flycatchers during early development

2016 ◽  
Vol 12 (7) ◽  
pp. 20160234 ◽  
Author(s):  
S. Eryn McFarlane ◽  
Axel Söderberg ◽  
David Wheatcroft ◽  
Anna Qvarnström
Keyword(s):  
Metabolic Rate ◽  
Developmental Stages ◽  
Closely Related Species ◽  
Selective Learning ◽  
Collared Flycatcher ◽  
Song Perception ◽  
Song Discrimination ◽  
Novel Method ◽  
Species Specific ◽  
Early Developmental

Pre-zygotic isolation is often maintained by species-specific signals and preferences. However, in species where signals are learnt, as in songbirds, learning errors can lead to costly hybridization. Song discrimination expressed during early developmental stages may ensure selective learning later in life but can be difficult to demonstrate before behavioural responses are obvious. Here, we use a novel method, measuring changes in metabolic rate, to detect song perception and discrimination in collared flycatcher embryos and nestlings. We found that nestlings as early as 7 days old respond to song with increased metabolic rate, and, by 9 days old, have increased metabolic rate when listening to conspecific when compared with heterospecific song. This early discrimination between songs probably leads to fewer heterospecific matings, and thus higher fitness of collared flycatchers living in sympatry with closely related species.

scholarly journals Rapid, raw-read reference and identification (R4IDs): A flexible platform for rapid generic species ID using long-read sequencing technology

2018 ◽  
Author(s):  
Joe Parker ◽  
Andrew Helmstetter ◽  
James Crowe ◽  
John Iacona ◽  
Dion Devey ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Species Identification ◽  
Sequence Data ◽  
Vascular Plant ◽  
Reference Sequence ◽  
Read Length ◽  
Reference Database ◽  
Sequencing Technology ◽  
Long Read ◽  
Suitable Reference

AbstractThe versatility of the current DNA sequencing platforms and the development of portable, nanopore sequencers means that it has never been easier to collect genetic data for unknown sample ID. DNA barcoding and meta-barcoding have become increasingly popular and barcode databases continue to grow at an impressive rate. However, the number of canonical genome assemblies (reference or draft) that are publically available is relatively tiny, hindering the more widespread use of genome scale DNA sequencing technology for accurate species identification and discovery. Here, we show that rapid raw-read reference datasets, or R4IDs for short, generated in a matter of hours on the Oxford Nanopore MinION, can bridge this gap and accelerate the generation of useable reference sequence data. By exploiting the long read length of this technology, shotgun genomic sequencing of a small portion of an organism’s genome can act as a suitable reference database despite the low sequencing coverage. These R4IDs can then be used for accurate species identification with minimal amounts of re-sequencing effort (1000s of reads). We demonstrated the capabilities of this approach with six vascular plant species for which we created R4IDs in the laboratory and then re-sequenced, live at the Kew Science Festival 2016. We further validated our method using simulations to determine the broader applicability of the approach. Our data analysis pipeline has been made available as a Dockerised workflow for simple, scalable deployment for a range of uses.

Identification of sea louse species of the genus Caligus using mtDNA

2005 ◽  
Vol 85 (1) ◽  
pp. 73-79 ◽  
Author(s):  
Øivind Øines ◽  
Peter Andreas Heuch
Keyword(s):  
Developmental Stages ◽  
Sequence Data ◽  
Coi Gene ◽  
Molecular Assay ◽  
Chain Reaction ◽  
Closely Related Species ◽  
The Common ◽  
Polymerase Chain ◽  
Louse Species ◽  
Sample Time

A molecular assay was designed to distinguish the common sea louse Caligus elongatus from its sympatric relatives. The method identifies the parasites at all developmental stages. Fragments of the mitochondrial Cytochrome C Oxidase 1 (COI) gene from identified adult caligids were amplified by polymerase chain reaction (PCR) and sequenced. Analysis of sequence data from unknown samples permitted identification by clustering of the samples with their appropriate genetic relative. Nucleotide sequences obtained were used for preliminary investigations of the population genetic structure of Caliguselongatus. Aligned sequences from the COI gene from this speciesindicate that our C. elongatus material divides into two distinct clades, possibly revealing two closely related species. The two genotypes do not appear to be associated with sample site, parasite gender, sample time or host species. Parasites from both groups were found on Atlantic salmon (Salmosalar), sea trout (Salmotrutta), pollack (Pollachiuspollachius), saithe (Pollachiusvirens), and Atlantic herring (Clupeaharengus).

scholarly journals Identification Pseudomonas aeruginosa by 16s rRNA gene for Differentiation from Other Pseudomonas Species that isolated from Patients and environment

2014 ◽  
Vol 11 (2) ◽  
pp. 1028-1034 ◽  
Author(s):  
Baghdad Science Journal
Keyword(s):  
Pseudomonas Aeruginosa ◽  
16S Rrna ◽  
Sequence Data ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Pseudomonas Species ◽  
Signature Sequences ◽  
Stable Part ◽  
Opportunistic Human Pathogen ◽  
Species Specific

Pseudomonas aeruginosa is a common and major opportunistic human pathogen, its causes many and dangersinfectious diseases due to death in some timesex: cystic fibrosis , wounds inflammation , burns inflammation , urinary tract infection , other many infections otitis external , Endocarditis , nosocomial infection and also causes other blood infections (Bacteremia). thereforebecomes founding fast and exact identification of P. aeruginosafrom samples culture very important.However, identification of this species may be problematic due to the marked phenotypic variabilitydemonstrated by samples isolates and the presence of other closely related species. To facilitate species identification, we used 16S ribosomal DNA(rRNA) sequence data toidentify genus- and species-specific 16S rRNA signature sequences,its account a stable part of the geneticcode. Based on these sequences we designed simple, rapid, and accurate PCR assays that allow the differentiation of P. aeruginosa from Pseudomonas species and other pathogen genus ,also this test considered as the most specific than the other diagnostic tests like API (20) which give 70% while the 16SrRNA test give more than 90 %.

scholarly journals A Universal Approach to Molecular Identification of Rumen Fluke Species Across Hosts, Continents, and Sample Types

2021 ◽  
Vol 7 ◽  
Author(s):  
Gillian Mitchell ◽  
Ruth N. Zadoks ◽  
Philip J. Skuce
Keyword(s):  
Species Identification ◽  
Molecular Identification ◽  
Sequence Data ◽  
Intergenic Spacer ◽  
Pairwise Comparison ◽  
Reference Database ◽  
Life Cycle Stages ◽  
Wide Range ◽  
Universal Approach ◽  
Species Comparisons

Rumen fluke are parasitic trematodes that affect domestic and wild ruminants across a wide range of countries and habitats. There are 6 major genera of rumen fluke and over 70 recognized species. Accurate species identification is important to investigate the epidemiology, pathophysiology and economic impact of rumen fluke species but paramphistomes are morphologically plastic, which has resulted in numerous instances of misclassification. Here, we present a universal approach to molecular identification of rumen fluke species, including different life-cycle stages (eggs, juvenile and mature fluke) and sample preservation methods (fresh, ethanol- or formalin-fixed, and paraffin wax-embedded). Among 387 specimens from 173 animals belonging to 10 host species and originating from 14 countries on 5 continents, 10 rumen fluke species were identified based on ITS-2 intergenic spacer sequencing, including members of the genera Calicophoron, Cotylophoron, Fischeroedius, Gastrothylax, Orthocoelium, and Paramphistomum. Pairwise comparison of ITS-2 sequences from this study and GenBank showed >98.5% homology for 80% of intra-species comparisons and <98.5% homology for 97% of inter-species comparisons, suggesting that some sequence data may have been entered into public repositories with incorrect species attribution based on morphological analysis. We propose that ITS-2 sequencing could be used as a universal tool for rumen fluke identification across host and parasite species from diverse technical and geographical origins and form the basis of an international reference database for accurate species identification.

scholarly journals Mitochondrial DNA-Based Identification of Forensically Important Flesh Flies (Diptera: Sarcophagidae) in Thailand

Insects ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 2 ◽  
Author(s):  
Chutharat Samerjai ◽  
Kabkaew L. Sukontason ◽  
Narin Sontigun ◽  
Kom Sukontason ◽  
Tunwadee Klong-klaew ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Strong Support ◽  
Reference Database ◽  
Close Match ◽  
Flesh Fly ◽  
Death Scene ◽  
Tree Topologies ◽  
Species Specific ◽  
Entomological Research ◽  
Flesh Flies

Flesh flies (Sarcophagidae) are necrophagous insects initially colonizing on a corpse. The species-specific developmental data of the flies collected from a death scene can be used to estimate the minimum postmortem interval (PMImin). Thus, the first crucial step is to correctly identify the fly species. Because of the high similarity among species of flesh flies, DNA-based identification is considered more favorable than morphology-based identification. In this study, we demonstrated the effectiveness of combined sequences (2216 to 2218 bp) of cytochrome c oxidase subunit I and II genes (COI and COII) for identification of the following 14 forensically important flesh fly species in Thailand: Boettcherisca nathani Lopes, Fengia ostindicae (Senior-White), Harpagophalla kempi (Senior-White), Liopygia ruficornis (Fabricius), Lioproctia pattoni (Senior-White), Lioproctia saprianovae (Pape & Bänziger), Parasarcophaga albiceps (Meigen), Parasarcophaga brevicornis (Ho), Parasarcophaga dux (Thomson), Parasarcophaga misera (Walker), Sarcorohdendorfia antilope (Böttcher), Sarcorohdendorfia inextricata (Walker), Sarcorohdendorfia seniorwhitei (Ho) and Seniorwhitea princeps (Wiedemann). Nucleotide variations of Thai flesh flies were evenly distributed throughout the COI-COII genes. Mean intra- and interspecific variations ranged from 0.00 to 0.96% and 5.22% to 12.31%, respectively. Using Best Match (BM) and Best Close Match (BCM) criteria, identification success for the combined genes was 100%, while the All Species Barcodes (ASB) criterion showed 76.74% success. Maximum Likelihood (ML) and Bayesian Inference (BI) phylogenetic analyses yielded similar tree topologies of monophyletic clades between species with very strong support values. The achieved sequences covering 14 forensically important flesh fly species including newly submitted sequences for B. nathani, F. ostindicae and S. seniorwhitei, can serve as a reliable reference database for further forensic entomological research in Thailand and in other areas where those species occur.

scholarly journals cpn60 barcode sequences accurately identify newly defined genera within the Lactobacillaceae

2021 ◽  
Author(s):  
Ishika Shukla ◽  
Janet E. Hill
Keyword(s):  
Species Identification ◽  
Sequence Data ◽  
Sequence Diversity ◽  
Reference Sequence ◽  
Reference Database ◽  
New Genera ◽  
Accurate Identification ◽  
Detection And Identification ◽  
Taxonomic Framework ◽  
Definition Of

AbstractThe cpn60 barcode sequence is established as an informative target for microbial species identification. Applications of cpn60 barcode sequencing are supported by the availability of “universal” PCR primers for its amplification and a curated reference database of cpn60 sequences, cpnDB. A recent reclassification of lactobacilli involving the definition of 23 new genera provided an opportunity to update cpnDB and to determine if the cpn60 barcode could be used for accurate identification of species consistent with the new framework. Analysis of 275 cpn60 sequences representing 258/269 of the validly named species in Lactobacillus, Paralactobacillus and the 23 newer genera showed that cpn60-based sequence relationships were consistent with the whole-genome-based phylogeny. Aligning or mapping full length barcode sequences or a 150 bp subsequence resulted in accurate and unambiguous species identification in almost all cases. Taken together, our results show that the combination of available reference sequence data, “universal” barcode amplification primers, and the inherent sequence diversity within the cpn60 barcode make it a useful target for the detection and identification of lactobacilli as defined by the latest taxonomic framework.Significance and Impact of the StudyThe genus Lactobacillus recently underwent a major reorganization resulting in the definition of 23 new genera. Lactobacilli are widespread in environmental and host-associated microbiomes and are exploited in food and biotechnology applications, making methods for their accurate identification desirable. Here we show that the combination of a reference sequence database, “universal” barcode amplification primers, and the inherent sequence diversity within the cpn60 barcode make it a useful target for the detection and identification of lactobacilli as defined by the latest taxonomic framework.

scholarly journals A multi-bioassay integrated approach to assess antifouling potential of extracts from the Mediterranean sponge Ircinia oros

2021 ◽  
Author(s):  
Lucia De Marchi ◽  
Carlo Pretti ◽  
Alessia Cuccaro ◽  
Matteo Oliva ◽  
Federica Tardelli ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Integrated Approach ◽  
Common Species ◽  
Marine Diatom ◽  
Cellular Damage ◽  
Inhibition Of Growth ◽  
Aliivibrio Fischeri ◽  
The Mediterranean ◽  
Ircinia Oros ◽  
Species Specific

AbstractThe phylum Porifera and their symbionts produce a wide variety of bioactive compounds, playing a central role in their ecology and evolution. In this study, four different extracts (obtained by non-polar and semi-polar extraction methodologies) of the Mediterranean sponge Ircinia oros were tested through a multi-bioassay integrated approach to assess their antifouling potential. Tests were performed using three common species, associated with three different endpoints: the marine bacterium Aliivibrio fischeri (inhibition of bioluminescence), the marine diatom Phaeodactylum tricornutum (inhibition of growth), and different development stages of the brackish water serpulid Ficopomatus enigmaticus (gametes: sperm motion, vitality inhibition and cellular damage; larvae: development; adults: AChE (acetylcholinesterase)-inhibitory activity). The effects of extracts were species specific and did not vary among different extraction methodologies. In particular, no significant reduction of bioluminescence of A. fischeri was observed for all tested samples. By contrast, extracts inhibited P. tricornutum growth and had toxic effects on different F. enigmaticus’ developmental stages. Our results suggest that the proposed test battery can be considered a suitable tool as bioactivity screening of marine natural products.

scholarly journals The Effect of an Anthropogenic Magnetic Field on the Early Developmental Stages of Fishes—A Review

2021 ◽  
Vol 22 (3) ◽  
pp. 1210
Author(s):  
Krzysztof Formicki ◽  
Agata Korzelecka-Orkisz ◽  
Adam Tański
Keyword(s):  
Magnetic Fields ◽  
Developmental Stages ◽  
Negative Influence ◽  
Pigment Cells ◽  
Egg Activation ◽  
Industrial Equipment ◽  
Positive Effects ◽  
Early Developmental Stages ◽  
Species Specific ◽  
Early Developmental

The number of sources of anthropogenic magnetic and electromagnetic fields generated by various underwater facilities, industrial equipment, and transferring devices in aquatic environment is increasing. These have an effect on an array of fish life processes, but especially the early developmental stages. The magnitude of these effects depends on field strength and time of exposure and is species-specific. We review studies on the effect of magnetic fields on the course of embryogenesis, with special reference to survival, the size of the embryos, embryonic motor function, changes in pigment cells, respiration hatching, and directional reactions. We also describe the effect of magnetic fields on sperm motility and egg activation. Magnetic fields can exert positive effects, as in the case of the considerable extension of sperm capability of activation, or have a negative influence in the form of a disturbance in heart rate or developmental instability in inner ear organs.

scholarly journals Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dimitri Boeckaerts ◽  
Michiel Stock ◽  
Bjorn Criel ◽  
Hans Gerstmans ◽  
Bernard De Baets ◽  
...  
Keyword(s):  
Machine Learning ◽  
Predictive Model ◽  
Receptor Binding ◽  
Bacterial Infections ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Area Under The Curve ◽  
Local Alignment ◽  
Search Tool ◽  
Different Levels

AbstractNowadays, bacteriophages are increasingly considered as an alternative treatment for a variety of bacterial infections in cases where classical antibiotics have become ineffective. However, characterizing the host specificity of phages remains a labor- and time-intensive process. In order to alleviate this burden, we have developed a new machine-learning-based pipeline to predict bacteriophage hosts based on annotated receptor-binding protein (RBP) sequence data. We focus on predicting bacterial hosts from the ESKAPE group, Escherichia coli, Salmonella enterica and Clostridium difficile. We compare the performance of our predictive model with that of the widely used Basic Local Alignment Search Tool (BLAST). Our best-performing predictive model reaches Precision-Recall Area Under the Curve (PR-AUC) scores between 73.6 and 93.8% for different levels of sequence similarity in the collected data. Our model reaches a performance comparable to that of BLASTp when sequence similarity in the data is high and starts outperforming BLASTp when sequence similarity drops below 75%. Therefore, our machine learning methods can be especially useful in settings in which sequence similarity to other known sequences is low. Predicting the hosts of novel metagenomic RBP sequences could extend our toolbox to tune the host spectrum of phages or phage tail-like bacteriocins by swapping RBPs.

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