DeNovoMass Spectrometry Sequencing and Characterization of Species-Specific Peptides from Nucleoside Diphosphate Kinase B for the Classification of Commercial Fish Species Belonging to the Family Merlucciidae

2007 ◽  
Vol 6 (8) ◽  
pp. 3070-3080 ◽  
Author(s):  
Mónica Carrera ◽  
Benito Cañas ◽  
Carmen Piñeiro ◽  
Jesús Vázquez ◽  
José Manuel Gallardo
Keyword(s):  
Fish Species ◽  
Nucleoside Diphosphate Kinase ◽  
Commercial Fish ◽  
Nucleoside Diphosphate Kinase B ◽  
The Family ◽  
Species Specific

scholarly journals Heterochromatin characterization of four fish species of the family Loricariidae (Siluriformes)

Hereditas ◽  
2005 ◽  
Vol 141 (3) ◽  
pp. 237-242 ◽  
Author(s):  
KARINE FREHNER KAVALCO ◽  
RUBENS PAZZA ◽  
LUIZ ANTONIO CARLOS BERTOLLO ◽  
ORLANDO MOREIRA-FILHO
Keyword(s):  
Fish Species ◽  
The Family

Otoliths of Common Australian Temperate Fish

2007 ◽  
Author(s):  
Dianne Furlani ◽  
Rosemary Gales ◽  
David Pemberton
Keyword(s):  
Fish Species ◽  
Marine Mammal ◽  
Comparative Anatomy ◽  
Age And Growth ◽  
Accurate Identification ◽  
Fish Prey ◽  
Commercial Fish ◽  
Surface Features ◽  
Species Specific ◽  
Temperate Fish

The accurate identification of fish ‘ear-bones’, known as otoliths, is essential to determine the fish prey of marine and terrestrial predators. Fish otoliths are species-specific when combining size, shape and surface features, and can remain undigested for long periods. As a result, they can indicate which fish make up the diet of various predators, including cephalopod, seabird, marine mammal and fish species. Such studies are crucial for understanding marine ecosystems, and trophodynamics in particular. Increasingly, these methods are being used to understand the diet of some terrestrial predators, also extending to that of humans in archaelogical studies. Otoliths of Common Australian Temperate Fish offers users a verified reference collection to assist in the accurate identification of species and size of fish using otoliths. It covers 141 fish species from a broad geographic range of the Australian temperate region and includes commercial and non-commercial fish species. A standardised written description of the otolith structure, size and surface features is provided for each species. Included are brief distribution and ecology notes, and regression for both otolith and fish lengths, together with high-quality SEM photographs of the otolith described. This guide will be an essential reference for marine scientists and marine mammal researchers; ornithologists, fisheries researchers and fish biologists studying age and growth or comparative anatomy; and archaeologists. Winner of the 2008 Whitley Award for Zoological Manual.

scholarly journals Detection and Characterization of Porcine Sapelovirus in Italian Pig Farms

Animals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 966
Author(s):  
Eleonora Chelli ◽  
Luca De Sabato ◽  
Gabriele Vaccari ◽  
Fabio Ostanello ◽  
Ilaria Di Bartolo
Keyword(s):  
Phylogenetic Analyses ◽  
Whole Genome Sequence ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Genetic Characteristics ◽  
The Family ◽  
Polymerase Chain ◽  
Porcine Sapelovirus

Porcine sapelovirus (PSV) belongs to the genus Sapelovirus of the family Picornaviridae. PSV infects pigs asymptomatically, but it can also cause severe neurologic, enteric, and respiratory symptoms or reproductive failure. Sapelovirus infections have been reported worldwide in pigs. The objective of this study was to investigate the presence and the prevalence of PSV in Italian swine farms in animals of different ages to clarify the occurrence of the infection and the genetic characteristics of circulating strains. In the present study, 92 pools of fecal samples, collected from pigs across three farms, were analyzed by Reverse Transcriptase-polymerase Chain Reaction-PCR (RT-PCR). Fecal pools from young growers (63/64) were found positive for Sapelovirus in all farms while detection in sows (4/28) was observed in only one farm. Phylogenetic analyses of the 19 partial capsid protein nucleotide sequences (VP1) (6–7 each farm) enable the classification of the virus sequences into three distinct clades and highlighted the high heterogeneity within one farm. The whole genome sequence obtained from one strain showed the highest correlation with the Italian strain detected in 2015. The study adds novel information about the circulation and heterogeneity of PSV strains in Italy and considering the movement of pigs across Europe would also be informative for other countries.

scholarly journals A symbolic projection of Langton's Ant

2003 ◽  
Vol DMTCS Proceedings vol. AB,... (Proceedings) ◽  
Author(s):  
Anahi Gajardo
Keyword(s):  
Point Of View ◽  
Algebraic Characterization ◽  
Transition Rule ◽  
Regular Graphs ◽  
New Approach ◽  
The Family ◽  
International Audience ◽  
Topological Dynamical Systems

International audience The Langton's ant is studied from the point of view of topological dynamical systems. A new approach which associate a subshift to the system is proposed.The transition rule is generalized to the family of bi-regular graphs $\Gamma(k,d)$ and the dependence of the dynamical system on $k$ and $d$ is analyzed. A classification of the $\Gamma (k,d)$ graphs based on the dynamical properties of the subshift is established. Also a hierarchy is defined on the graphs through the subset relation of the respective subshifts. The analysis are worked out by establishing an algebraic characterization of the forbidden words of the subshift.

scholarly journals A Rapid Method for the Identification of Fresh and Processed Pagellus erythrinus Species against Frauds

Foods ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1397
Author(s):  
Marina Ceruso ◽  
Celestina Mascolo ◽  
Pasquale De Luca ◽  
Iolanda Venuti ◽  
Giorgio Smaldone ◽  
...  
Keyword(s):  
Fish Species ◽  
Hamming Distance ◽  
Specific Primers ◽  
Pagellus Erythrinus ◽  
Fish Species Identification ◽  
The Family ◽  
The Common ◽  
Processed Products ◽  
Species Specific ◽  
Complete Mtdna

The commercialization of porgies or seabreams of the family Sparidae has greatly increased in the last decade, and some valuable species have become subject to seafood substitution. DNA regions currently used for fish species identification in fresh and processed products belong to the mitochondrial (mt) genes cytochrome b (Cytb), cytochrome c oxidase I (COI), 16S and 12S. However, these markers amplify for fragments with lower divergence within and between some species, failing to provide informative barcodes. We adopted comparative mitogenomics, through the analysis of complete mtDNA sequences, as a compatible approach toward studying new barcoding markers. The intent is to develop a specific and rapid assay for the identification of the common pandora Pagellus erythrinus, a sparid species frequently subject to fraudulent replacement. The genetic diversity analysis (Hamming distance, p-genetic distance, gene-by-gene sequence variability) between 16 sparid mtDNA genomes highlighted the discriminating potential of a 291 bp NAD2 gene fragment. A pair of species-specific primers were successfully designed and tested by end-point and real-time PCR, achieving amplification only in P. erythrinus among several fish species. The use of the NAD2 barcoding marker provides a rapid presence/absence method for the identification of P. erythrinus.

scholarly journals Identification and genome characterization of Heliothis armigera cypovirus types 5 and 14 and Heliothis assulta cypovirus type 14

2006 ◽  
Vol 87 (2) ◽  
pp. 387-394 ◽  
Author(s):  
Yang Li ◽  
Li Tan ◽  
Yanqiu Li ◽  
Wuguo Chen ◽  
Jiamin Zhang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Heliothis Armigera ◽  
Amino Acid Sequences ◽  
Nucleotide Sequencing ◽  
Sequencing Analysis ◽  
Electrophoretic Patterns ◽  
The Family ◽  
Genomic Characterization

Genomic characterization of Heliothis armigera cypovirus (HaCPV) isolated from China showed that insects were co-infected with several cypoviruses (CPVs). One of the CPVs (HaCPV-5) could be separated from the others by changing the rearing conditions of the Heliothis armigera larvae. This finding was further confirmed by nucleotide sequencing analysis. Genomic sequences of segments S10–S7 from HaCPV-14, S10 and S7 from HaCPV-5, and S10 from Heliothis assulta CPV-14 were compared. Results from database searches showed that the nucleotide sequences and deduced amino acid sequences of the newly identified CPVs had high levels of identity with those of reported CPVs of the same type, but not with CPVs of different types. Putative amino acid sequences of HaCPV-5 S7 were similar to that of the protein from Rice ragged stunt virus (genus Oryzavirus, family Reoviridae), suggesting that CPVs and oryzaviruses are related more closely than other genera of the family Reoviridae. Conserved motifs were also identified at the ends of each RNA segment of the same virus type: type 14, 5′-AGAAUUU…CAGCU-3′; and type 5, 5′-AGUU…UUGC-3′. Our results are consistent with classification of CPV types based on the electrophoretic patterns of CPV double-stranded RNA.

scholarly journals Identification of Commercial Fish Species Belonging to the Orders Pleuronectiformes and Gadiformes: Library of Isoelectric Focusing Patterns

2001 ◽  
Vol 84 (5) ◽  
pp. 1600-1607 ◽  
Author(s):  
Valentina Tepedino ◽  
Anna Berrini ◽  
Vitaliano Borromeo ◽  
Daniela Gaggioli ◽  
Carlo Cantoni ◽  
...  
Keyword(s):  
Image Analysis ◽  
Computer Program ◽  
Isoelectric Focusing ◽  
Fish Species ◽  
Subjective Evaluation ◽  
Protein Profiles ◽  
Commercial Fish ◽  
Sarcoplasmic Protein ◽  
Flat Fish ◽  
Species Specific

Abstract Isoelectric focusing in polyacrylamide gel was used to establish an identification archive of fish species belonging to the orders Pleuronectiformes, or flat fish, and Gadiformes, or gadoid fish. The 2 orders include species of different commercial value and interest that are frequently requested in European fish markets, but are susceptible to substitution either because they are morphologically similar or because they arrive on the markets already filleted or sliced. The sarcoplasmic protein profiles are species-specific and reproducible. The use of densitometry and image analysis coupled with a simple computer program overcomes the subjective evaluation of the patterns, making it possible to identify species correctly.

scholarly journals Isolation and Characterization of 27 Novel Microsatellite Loci in Critically Endangered Wyoming Toad

2019 ◽  
Vol 10 (2) ◽  
pp. 563-566
Author(s):  
Renee M. Martin ◽  
Heidi Meador ◽  
Lee Bender ◽  
Lacey Hopper
Keyword(s):  
Captive Breeding ◽  
Captive Breeding Program ◽  
Isolation And Characterization ◽  
The Family ◽  
Hardy Weinberg Equilibrium ◽  
Laramie Basin ◽  
Species Specific ◽  
Wyoming Toad ◽  
Paired End Sequencing

Abstract Wyoming toad Anaxyrus baxteri is a federally endangered amphibian endemic to the Laramie basin in southwestern Wyoming, USA. A captive breeding program propagates A. baxteri, and the monitoring of genetic diversity in the captive stock can assist in guiding conservation measures of this species. Illumina paired-end sequencing lead to 27 species-specific polymorphic microsatellite genetic markers being developed. Across 24 samples, A. baxteri exhibited two to eight alleles per locus, and observed and expected heterozygosities per locus ranged from 0.292 to 0.958 and from 0.344 to 0.787, respectively. Tests for Hardy–Weinberg equilibrium were nonsignificant except for Abax_13 and Abax_39. These microsatellite markers will be useful for genetic monitoring to aid recovery efforts of A. baxteri captive and wild populations as well as other amphibians in the family Bufonidae.

scholarly journals A Novel Bioinformatics Method for Efficient Knowledge Discovery by BLSOM from Big Genomic Sequence Data

2014 ◽  
Vol 2014 ◽  
pp. 1-11
Author(s):  
Yu Bai ◽  
Yuki Iwasaki ◽  
Shigehiko Kanaya ◽  
Yue Zhao ◽  
Toshimichi Ikemura
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Self Organizing Map ◽  
Genome Signature ◽  
A Genome ◽  
Wide Range ◽  
Oligonucleotide Composition ◽  
Species Specific

With remarkable increase of genomic sequence data of a wide range of species, novel tools are needed for comprehensive analyses of the big sequence data. Self-Organizing Map (SOM) is an effective tool for clustering and visualizing high-dimensional data such as oligonucleotide composition on one map. By modifying the conventional SOM, we have previously developed Batch-Learning SOM (BLSOM), which allows classification of sequence fragments according to species, solely depending on the oligonucleotide composition. In the present study, we introduce the oligonucleotide BLSOM used for characterization of vertebrate genome sequences. We first analyzed pentanucleotide compositions in 100 kb sequences derived from a wide range of vertebrate genomes and then the compositions in the human and mouse genomes in order to investigate an efficient method for detecting differences between the closely related genomes. BLSOM can recognize the species-specific key combination of oligonucleotide frequencies in each genome, which is called a “genome signature,” and the specific regions specifically enriched in transcription-factor-binding sequences. Because the classification and visualization power is very high, BLSOM is an efficient powerful tool for extracting a wide range of information from massive amounts of genomic sequences (i.e., big sequence data).

scholarly journals Morphology and Molecular Studies of Contracaecum Larvae (Nematoda: Anisakidae) in Some Fish species from Sulaimani Province, Kurdistan Region, Iraq

2021 ◽  
Vol 34 (1) ◽  
pp. 93-110
Author(s):  
Younis S. Abdullah ◽  
Shamall M. A. Abdullah ◽  
Ridha H. Hussein
Keyword(s):  
Fish Species ◽  
Larval Stage ◽  
Genetic Characterization ◽  
Kurdistan Region ◽  
Chain Reaction ◽  
Contracaecum Rudolphii ◽  
The Family ◽  
Polymerase Chain ◽  
Paratenic Hosts

Contracaecum is a genus of nematodes belonging to the family Anisakidae, that parasitise many fishes which act as an intermediate or paratenic hosts, while the piscivorous birds and mammals are definitive hosts. A total of 44 third larval stage of Contracaecum were collected from 13 infected freshwater fishes belonging to five different species in different water bodies in Sulaimani Province, Kurdistan Region, Iraq from January to the end of December 2018. In this investigation, 966 fishes were collected including six species of Nemacheilidae, five species of Cyprinidae, three species of Leuciscidae, two species of Xenocyprididae, one species of each of Bagridae, Heteropneustidae, Mastacembelidae, Mugilidae, Siluridae and Sisoridae. This study revealed that five fish species (Cyprinus carpio, Luciobarbus barbulus, L. esocinus, L. xanthopterus and Mastacembelus mastacembelus) were infected with Contracaecum larvae with the prevalence of 2.05%, 0.92%, 1.92%, 19.35% and 1.06%, respectively. The Contracaecum larvae were morphologically studied by compound light microscope and the molecular analyses was done by amplification, sequencing and comparing different gene loci (ITS1, ITS2 and COX2) of isolated third larval stage of Contracaecum. The ITS1, ITS2 and COX2 were amplified by polymerase chain reaction (PCR) and sequenced. The sequences of ITS1, ITS2 and COX2 reveal that all Contracaecum larvae from all infected fishes represented exactly one species (Contracaecum rudolphii B) based on compering and identity percentage in Gene Bank database. Phylogenetic analysis of the genotype (for ITS1) was described. The genetic characterization of the Contracaecum larvae in the present study is available in the GenBank database and they were deposited in GenBank and their accession numbers were demonstrated.

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