Biochemistry, Genetics and Molecular Biology › Molecular Biology

Identification and Quantification in Food

Works Count: 66222

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Description

This cluster of papers focuses on the use of DNA barcoding and PCR-based methods for authenticating food products, detecting fraud, and identifying species in fish and meat. It addresses issues such as market substitution, mislabeling, and adulteration, with a specific emphasis on traceability and species identification in the food industry.

Keywords

DNA Barcoding; Food Authentication; Fraud Detection; Species Identification; Fish Species; Meat Products; PCR-based Methods; Adulteration; Market Substitution; Traceability

Evolution of the cytochromeb gene of mammals

1991-02-01

David M. Irwin , Thomas D. Kocher , Allan C. Wilson

A PHOTOMETRIC METHOD FOR THE DETERMINATION OF FREE PENTOSES IN ANIMAL TISSUES

1948-04-01

Joseph H. Roe , Eugene W. Rice

DETERMINATION OF CARBOHYDRATE METABOLISM OF MARINE BACTERIA

1963-05-01

Einar Leifson

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An inexpensive, automation‐friendly protocol for recovering high‐quality DNA

2006-07-07

Natalya Ivanova , Jeremy R deWaard , Paul D. N. Hebert

Abstract Although commercial kits are available for automated DNA extraction, ‘artisanal’ protocols are not. In this study, we present a silica‐based method that is sensitive, inexpensive and compliant with automation. … Abstract Although commercial kits are available for automated DNA extraction, ‘artisanal’ protocols are not. In this study, we present a silica‐based method that is sensitive, inexpensive and compliant with automation. The effectiveness of this protocol has now been tested on more than 5000 animal specimens with highly positive results.

Identifying Canadian Freshwater Fishes through DNA Barcodes

2008-06-17

Nicolas Hubert , Robert Hanner , Erling Holm +7 more

Background DNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 5′ region of the mitochondrial cytochrome c … Background DNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 5′ region of the mitochondrial cytochrome c oxidase I (COI) gene. The efficiency of the method hinges on the degree of sequence divergence among species and species-level identifications are relatively straightforward when the average genetic distance among individuals within a species does not exceed the average genetic distance between sister species. Fishes constitute a highly diverse group of vertebrates that exhibit deep phenotypic changes during development. In this context, the identification of fish species is challenging and DNA barcoding provide new perspectives in ecology and systematics of fishes. Here we examined the degree to which DNA barcoding discriminate freshwater fish species from the well-known Canadian fauna, which currently encompasses nearly 200 species, some which are of high economic value like salmons and sturgeons. Methodology/Principal Findings We bi-directionally sequenced the standard 652 bp “barcode” region of COI for 1360 individuals belonging to 190 of the 203 Canadian freshwater fish species (95%). Most species were represented by multiple individuals (7.6 on average), the majority of which were retained as voucher specimens. The average genetic distance was 27 fold higher between species than within species, as K2P distance estimates averaged 8.3% among congeners and only 0.3% among concpecifics. However, shared polymorphism between sister-species was detected in 15 species (8% of the cases). The distribution of K2P distance between individuals and species overlapped and identifications were only possible to species group using DNA barcodes in these cases. Conversely, deep hidden genetic divergence was revealed within two species, suggesting the presence of cryptic species. Conclusions/Significance The present study evidenced that freshwater fish species can be efficiently identified through the use of DNA barcoding, especially the species complex of small-sized species, and that the present COI library can be used for subsequent applications in ecology and systematics.

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Sensory Biology of Aquatic Animals

1988-01-01

Jelle Atema , Richard R. Fay , Arthur N. Popper +1 more

Defining the Public Health Threat of Food Fraud

2011-11-01

John Spink , Douglas C. Moyer

Abstract: Food fraud, including the more defined subcategory of economically motivated adulteration, is a food risk that is gaining recognition and concern. Regardless of the cause of the food risk, … Abstract: Food fraud, including the more defined subcategory of economically motivated adulteration, is a food risk that is gaining recognition and concern. Regardless of the cause of the food risk, adulteration of food is both an industry and a government responsibility. Food safety, food fraud, and food defense incidents can create adulteration of food with public health threats. Food fraud is an intentional act for economic gain, whereas a food safety incident is an unintentional act with unintentional harm, and a food defense incident is an intentional act with intentional harm. Economically motivated adulteration may be just that—economically motivated—but the food‐related public health risks are often more risky than traditional food safety threats because the contaminants are unconventional. Current intervention systems are not designed to look for a near infinite number of potential contaminants. The authors developed the core concepts reported here following comprehensive research of articles and reports, expert elicitation, and an extensive peer review. The intent of this research paper is to provide a base reference document for defining food fraud—it focuses specifically on the public health threat—and to facilitate a shift in focus from intervention to prevention. This will subsequently provide a framework for future quantitative or innovative research. The fraud opportunity is deconstructed using the criminology and behavioral science applications of the crime triangle and the chemistry of the crime . The research provides a food risk matrix and identifies food fraud incident types. This project provides a starting point for future food science, food safety, and food defense research. Practical Application: Food fraud, including the more defined subcategory of economically motivated adulteration, is a food protection threat that has not been defined or holistically addressed. The terrorist attacks of September 11, 2001, led to the development of food defense as an autonomous area of study and a new food protection discipline. As economically motivated adulteration grows in scope, scale, and awareness, it is conceivable that food fraud will achieve the same status as an autonomous concept, between food safety and food defense. This research establishes a starting point for defining food fraud and identifying the public health risks.

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Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals

2010-10-01

Hui Yao , Jingyuan Song , Chang Liu +7 more

Background The internal transcribed spacer 2 (ITS2) region of nuclear ribosomal DNA is regarded as one of the candidate DNA barcodes because it possesses a number of valuable characteristics, such … Background The internal transcribed spacer 2 (ITS2) region of nuclear ribosomal DNA is regarded as one of the candidate DNA barcodes because it possesses a number of valuable characteristics, such as the availability of conserved regions for designing universal primers, the ease of its amplification, and sufficient variability to distinguish even closely related species. However, a general analysis of its ability to discriminate species in a comprehensive sample set is lacking. Methodology/Principal Findings In the current study, 50,790 plant and 12,221 animal ITS2 sequences downloaded from GenBank were evaluated according to sequence length, GC content, intra- and inter-specific divergence, and efficiency of identification. The results show that the inter-specific divergence of congeneric species in plants and animals was greater than its corresponding intra-specific variations. The success rates for using the ITS2 region to identify dicotyledons, monocotyledons, gymnosperms, ferns, mosses, and animals were 76.1%, 74.2%, 67.1%, 88.1%, 77.4%, and 91.7% at the species level, respectively. The ITS2 region unveiled a different ability to identify closely related species within different families and genera. The secondary structure of the ITS2 region could provide useful information for species identification and could be considered as a molecular morphological characteristic. Conclusions/Significance As one of the most popular phylogenetic markers for eukaryota, we propose that the ITS2 locus should be used as a universal DNA barcode for identifying plant species and as a complementary locus for CO1 to identify animal species. We have also developed a web application to facilitate ITS2-based cross-kingdom species identification (http://its2-plantidit.dnsalias.org).

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Polymorphism in the Esterases of Atlantic Herring

1970-01-01

George J. Ridgway , Stuart W. Sherburne , R.D. Lewis

The esterase enzymes of the tissues of Atlantic herring (Clupea harengus harengus) were analyzed by starch gel electrophoresis. Four sets of esterase bands were distinguished by their electrophoretic mobility, their … The esterase enzymes of the tissues of Atlantic herring (Clupea harengus harengus) were analyzed by starch gel electrophoresis. Four sets of esterase bands were distinguished by their electrophoretic mobility, their relative activity with the two substrates, alpha-naphthyl acetate and alpha-naphthyl butyrate, and their relative concentrations in plasma, liver, and heart tissues. All of the esterases were inhibited by 10−4M solutions of dichlorvos, an organophosphate inhibitor, but none was inhibited by 10−4M eserine sulfate or by 10−4 M EDTA. Polymorphism was noted in all four sets of esterases. Evidence for the genetic control of the fastest migrating set was obtained from population genetic analyses. In this set of esterases, five distinct bands occurred either singly or in pairs. The observed distribution of the three most common bands fits the hypothesis that they are controlled by a set of autosomal alleles. The two rarest bands occurred only in the heterozygous state, as would be expected. Differences in frequencies of two of the genes were detected between herring taken in Western Maine waters and on Georges Bank.

Development and Application of a Database of Food Ingredient Fraud and Economically Motivated Adulteration from 1980 to 2010

2012-04-01

Jeffrey C. Moore , John Spink , Markus Lipp

Abstract: Food ingredient fraud and economically motivated adulteration are emerging risks, but a comprehensive compilation of information about known problematic ingredients and detection methods does not currently exist. The objectives … Abstract: Food ingredient fraud and economically motivated adulteration are emerging risks, but a comprehensive compilation of information about known problematic ingredients and detection methods does not currently exist. The objectives of this research were to collect such information from publicly available articles in scholarly journals and general media, organize into a database, and review and analyze the data to identify trends. The results summarized are a database that will be published in the US Pharmacopeial Convention's Food Chemicals Codex , 8th edition, and includes 1305 records, including 1000 records with analytical methods collected from 677 references. Olive oil, milk, honey, and saffron were the most common targets for adulteration reported in scholarly journals, and potentially harmful issues identified include spices diluted with lead chromate and lead tetraoxide, substitution of Chinese star anise with toxic Japanese star anise, and melamine adulteration of high protein content foods. High‐performance liquid chromatography and infrared spectroscopy were the most common analytical detection procedures, and chemometrics data analysis was used in a large number of reports. Future expansion of this database will include additional publically available articles published before 1980 and in other languages, as well as data outside the public domain. The authors recommend in‐depth analyses of individual incidents. Practical Application: This report describes the development and application of a database of food ingredient fraud issues from publicly available references. The database provides baseline information and data useful to governments, agencies, and individual companies assessing the risks of specific products produced in specific regions as well as products distributed and sold in other regions. In addition, the report describes current analytical technologies for detecting food fraud and identifies trends and developments.

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Technical improvements in two‐dimensional electrophoresis increase the level of genetic variation detected in wheat‐seedling proteins

1986-01-01

Catherine Damerval , Dominique de Vienne , Michel Zivy +1 more

Abstract The level of genetic variation revealed by two‐dimensional electrophoresis of proteins from seedlings of two wheat lines strongly depends on the technical procedures. Improvements in extraction and electrophoresis procedures … Abstract The level of genetic variation revealed by two‐dimensional electrophoresis of proteins from seedlings of two wheat lines strongly depends on the technical procedures. Improvements in extraction and electrophoresis procedures relative to earlier experiments on the same material led to a significant increase in the genetic variation revealed: 15.2 % instead of 6.7 % of the spots were genetically variable. The improved procedure is based on (i) precipipation of proteins from wheat seedlings with trichloroacetic acid and acetone, (ii) solubilization of the proteins with a solution containing urea, potassium carbonate and sodium dodecyl sulfate, (iii) isoelectric focusing in an optimized pH gradient, obtained with a mixture of carrier ampholytes (Pharmalyte and Servalyt), and (iv) running elecrophoresis in the second dimension on gels with increased surface.

Non-invasive genetic sampling and individual identification

1999-09-01

Pierre Taberlet , Gordon Luikart

Individual identification via non-invasive sampling is of prime importance in conservation genetics and in behavioural ecology. This approach allows for genetics studies of wild animals without having to catch them, … Individual identification via non-invasive sampling is of prime importance in conservation genetics and in behavioural ecology. This approach allows for genetics studies of wild animals without having to catch them, or even to observe them. The material used as a source of DNA is usually faeces, shed hairs, or shed feathers. It has been recendy shown that this material may lead to genotyping errors, mainly due to allelic dropout. In addition to these technical errors, there are problems with accurately estimating the probability of identity (PI, or the probability of two individuals having identical genotypes) because of the presence of close relatives in natural populations. As a consequence, before initiating an extensive study involving non-invasive sampling, we strongly suggest conducting a pilot study to assess both the technical difficulties and the PI for the genetic markers to be used. This pilot study could be carried out in three steps: (i) estimation of the PI using preliminary genetic data; (ii) simulations taking into account the PI and choosing the technical error rate mat is sufficiently low for assessing the scientific question; (iii) polymerase chain reaction (PCR) experiments to check if it is technically possible to achieve this error rate.

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Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test

1994-01-01

C. Ash , Fergus G. Priest , M. D. COLLINS

AllerTOP v.2—a server for in silico prediction of allergens

2014-05-30

Ivan Dimitrov , Ivan P. Bangov , Darren R. Flower +1 more

DNA Barcoding: Promise and Pitfalls

2004-09-21

Craig Moritz , Carla Cicero

In this issue of PLoS Biology, Hebert et al. (2004) have set out to test the resolution and performance of “DNA barcoding,” using a single mtDNA gene, cytochrome c oxidase … In this issue of PLoS Biology, Hebert et al. (2004) have set out to test the resolution and performance of “DNA barcoding,” using a single mtDNA gene, cytochrome c oxidase I (COI), for a sample of North American birds. Before turning to details of this study, it is useful as context to consider the following questions: What is DNA barcoding, and what does it promise? What is new about it? Why is it controversial? What are the potential pitfalls?

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Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species

2010-01-06

Shilin Chen , Hui Yao , Jianping Han +7 more

The plant working group of the Consortium for the Barcode of Life recommended the two-locus combination of rbcL+matK as the plant barcode, yet the combination was shown to successfully discriminate … The plant working group of the Consortium for the Barcode of Life recommended the two-locus combination of rbcL+matK as the plant barcode, yet the combination was shown to successfully discriminate among 907 samples from 550 species at the species level with a probability of 72%. The group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over.Here, we compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL, rpoC1, ycf5, ITS2, and ITS) from medicinal plant species. Our ranking criteria included PCR amplification efficiency, differential intra- and inter-specific divergences, and the DNA barcoding gap. Our data suggest that the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA represents the most suitable region for DNA barcoding applications. Furthermore, we tested the discrimination ability of ITS2 in more than 6600 plant samples belonging to 4800 species from 753 distinct genera and found that the rate of successful identification with the ITS2 was 92.7% at the species level.The ITS2 region can be potentially used as a standard DNA barcode to identify medicinal plants and their closely related species. We also propose that ITS2 can serve as a novel universal barcode for the identification of a broader range of plant taxa.

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The Genetic Structure of Ancient Human Populations

1993-08-01

Henry Harpending , Stephen T. Sherry , Alan R. Rogers +1 more

Choosing and Using a Plant DNA Barcode

2011-05-26

Peter M. Hollingsworth , Sean W. Graham , Damon P. Little

The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully … The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1 (CO1) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. In this paper, we review the process of selecting and refining a plant barcode; evaluate the factors which influence the discriminatory power of the approach; describe some early applications of plant barcoding and summarise major emerging projects; and outline tool development that will be necessary for plant DNA barcoding to advance.

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Identification of Birds through DNA Barcodes

2004-09-21

Paul D. N. Hebert , Mark Y. Stoeckle , Tyler Zemlak +1 more

Short DNA sequences from a standardized region of the genome provide a DNA barcode for identifying species. Compiling a public library of DNA barcodes linked to named specimens could provide … Short DNA sequences from a standardized region of the genome provide a DNA barcode for identifying species. Compiling a public library of DNA barcodes linked to named specimens could provide a new master key for identifying species, one whose power will rise with increased taxon coverage and with faster, cheaper sequencing. Recent work suggests that sequence diversity in a 648-bp region of the mitochondrial gene, cytochrome c oxidase I (COI), might serve as a DNA barcode for the identification of animal species. This study tested the effectiveness of a COI barcode in discriminating bird species, one of the largest and best-studied vertebrate groups. We determined COI barcodes for 260 species of North American birds and found that distinguishing species was generally straightforward. All species had a different COI barcode(s), and the differences between closely related species were, on average, 18 times higher than the differences within species. Our results identified four probable new species of North American birds, suggesting that a global survey will lead to the recognition of many additional bird species. The finding of large COI sequence differences between, as compared to small differences within, species confirms the effectiveness of COI barcodes for the identification of bird species. This result plus those from other groups of animals imply that a standard screening threshold of sequence difference (10x average intraspecific difference) could speed the discovery of new animal species. The growing evidence for the effectiveness of DNA barcodes as a basis for species identification supports an international exercise that has recently begun to assemble a comprehensive library of COI sequences linked to named specimens.

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A simplified protocol for routine total DNA isolation from salmonid fishes

1992-06-01

John B. Taggart , R. A. Hynes , P. A. Prodöuhl +1 more

An efficient total DNA isolation protocol, suitable for routine population genetic screening purposes is described. This phenol based extraction can utilize fresh, frozen or ethanol preserved tissues. An efficient total DNA isolation protocol, suitable for routine population genetic screening purposes is described. This phenol based extraction can utilize fresh, frozen or ethanol preserved tissues.

Redesign of <scp>PCR</scp> primers for mitochondrial cytochrome c oxidase subunit <scp>I</scp> for marine invertebrates and application in all‐taxa biotic surveys

2013-07-13

Jonathan B. Geller , Chris Meyer , Meaghan Parker +1 more

Abstract DNA barcoding is a powerful tool for species detection, identification and discovery. Metazoan DNA barcoding is primarily based upon a specific region of the cytochrome c oxidase subunit I … Abstract DNA barcoding is a powerful tool for species detection, identification and discovery. Metazoan DNA barcoding is primarily based upon a specific region of the cytochrome c oxidase subunit I gene that is PCR amplified by primers HCO 2198 and LCO 1490 (‘Folmer primers’) designed by Folmer et al . ( Molecular Marine Biology and Biotechnology , 3 , 1994, 294). Analysis of sequences published since 1994 has revealed mismatches in the Folmer primers to many metazoans. These sequences also show that an extremely high level of degeneracy would be necessary in updated Folmer primers to maintain broad taxonomic utility. In primers jg HCO 2198 and jg LCO 1490, we replaced most fully degenerated sites with inosine nucleotides that complement all four natural nucleotides and modified other sites to better match major marine invertebrate groups. The modified primers were used to amplify and sequence cytochrome c oxidase subunit I from 9105 specimens from Moorea, French Polynesia and San Francisco Bay, California, USA representing 23 phyla, 42 classes and 121 orders. The new primers, jg HCO 2198 and jg LCO 1490, are well suited for routine DNA barcoding, all‐taxon surveys and metazoan metagenomics.

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DNA fingerprinting in birds

1987-05-01

Terry Burke , Michael W. Bruford

Species identification by analysis of bone collagen using matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry

2009-11-09

Michael Buckley , Matthew J. Collins , Jane Thomas‐Oates +1 more

Species identification of fragmentary bone, such as in rendered meat and bone meal or from archaeological sites, is often difficult in the absence of clear morphological markers. Here we present … Species identification of fragmentary bone, such as in rendered meat and bone meal or from archaeological sites, is often difficult in the absence of clear morphological markers. Here we present a robust method of analysing genus-specific collagen peptides by mass spectrometry simply by using solid-phase extraction (a C18 ZipTip) for peptide purification, rather than liquid chromatography/mass spectrometry (LC/MS). Analysis of the collagen from 32 different mammal species identified a total of 92 peptide markers that could be used for species identification, for example, in processed food and animal feed. A set of ancient (>100 ka@10 degrees C) bone samples was also analysed to show that the proposed method has applications to archaeological bone identification.

A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System

2013-07-08

Sujeevan Ratnasingham , Paul D. N. Hebert

Because many animal species are undescribed, and because the identification of known species is often difficult, interim taxonomic nomenclature has often been used in biodiversity analysis. By assigning individuals to … Because many animal species are undescribed, and because the identification of known species is often difficult, interim taxonomic nomenclature has often been used in biodiversity analysis. By assigning individuals to presumptive species, called operational taxonomic units (OTUs), these systems speed investigations into the patterning of biodiversity and enable studies that would otherwise be impossible. Although OTUs have conventionally been separated through their morphological divergence, DNA-based delineations are not only feasible, but have important advantages. OTU designation can be automated, data can be readily archived, and results can be easily compared among investigations. This study exploits these attributes to develop a persistent, species-level taxonomic registry for the animal kingdom based on the analysis of patterns of nucleotide variation in the barcode region of the cytochrome c oxidase I (COI) gene. It begins by examining the correspondence between groups of specimens identified to a species through prior taxonomic work and those inferred from the analysis of COI sequence variation using one new (RESL) and four established (ABGD, CROP, GMYC, jMOTU) algorithms. It subsequently describes the implementation, and structural attributes of the Barcode Index Number (BIN) system. Aside from a pragmatic role in biodiversity assessments, BINs will aid revisionary taxonomy by flagging possible cases of synonymy, and by collating geographical information, descriptive metadata, and images for specimens that are likely to belong to the same species, even if it is undescribed. More than 274,000 BIN web pages are now available, creating a biodiversity resource that is positioned for rapid growth.

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PCR-DGGE fingerprinting: novel strategies for detection of microbes in food

2003-12-17

Danilo Ercolini

Free Competition and the Optimal Amount of Fraud

1973-04-01

Michael R. Darby , Edi Karni

Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification

2004-02-01

Kipling Will , Daniel Rubinoff

So-called DNA barcodes have recently been proposed to answer the problem of specimen identification and to quantify global biodiversity. We show that this proposition is wanting in terms of rationale, … So-called DNA barcodes have recently been proposed to answer the problem of specimen identification and to quantify global biodiversity. We show that this proposition is wanting in terms of rationale, methodology and interpretation of results. In addition to falling short of all its stated goals, the method abandons the benefits of morphological studies in favor of a limited molecular identification system that would ultimately impede our understanding of biodiversity.

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Universal primer cocktails for fish DNA barcoding

2007-03-19

Natalya Ivanova , Tyler Zemlak , Robert Hanner +1 more

Abstract Reliable recovery of the 5′ region of the cytochrome c oxidase 1 (COI) gene is critical for the ongoing effort to gather DNA barcodes for all fish species. In … Abstract Reliable recovery of the 5′ region of the cytochrome c oxidase 1 (COI) gene is critical for the ongoing effort to gather DNA barcodes for all fish species. In this study, we develop and test primer cocktails with a view towards increasing the efficiency of barcode recovery. Specifically, we evaluate the success of polymerase chain reaction amplification and the quality of resultant sequences using three primer cocktails on DNA extracts from representatives of 94 fish families. Our results show that M13‐tailed primer cocktails are more effective than conventional degenerate primers, allowing barcode work on taxonomically diverse samples to be carried out in a high‐throughput fashion.

Towards writing the encyclopaedia of life: an introduction to DNA barcoding

2005-09-08

Vincent Savolainen , Robyn S. Cowan , Alfried P. Vogler +2 more

An international consortium of major natural history museums, herbaria and other organizations has launched an ambitious project, the ‘Barcode of Life Initiative’, to promote a process enabling the rapid and … An international consortium of major natural history museums, herbaria and other organizations has launched an ambitious project, the ‘Barcode of Life Initiative’, to promote a process enabling the rapid and inexpensive identification of the estimated 10 million species on Earth. DNA barcoding is a diagnostic technique in which short DNA sequence(s) can be used for species identification. The first international scientific conference on Barcoding of Life was held at the Natural History Museum in London in February 2005, and here we review the scientific challenges discussed during this conference and in previous publications. Although still controversial, the scientific benefits of DNA barcoding include: (i) enabling species identification, including any life stage or fragment, (ii) facilitating species discoveries based on cluster analyses of gene sequences (e.g. cox1 = CO1 , in animals), (iii) promoting development of handheld DNA sequencing technology that can be applied in the field for biodiversity inventories and (iv) providing insight into the diversity of life.

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Use of DNA barcodes to identify flowering plants

2005-05-31

W. John Kress , Kenneth J. Wurdack , Elizabeth A. Zimmer +2 more

Methods for identifying species by using short orthologous DNA sequences, known as “DNA barcodes,” have been proposed and initiated to facilitate biodiversity studies, identify juveniles, associate sexes, and enhance forensic … Methods for identifying species by using short orthologous DNA sequences, known as “DNA barcodes,” have been proposed and initiated to facilitate biodiversity studies, identify juveniles, associate sexes, and enhance forensic analyses. The cytochrome c oxidase 1 sequence, which has been found to be widely applicable in animal barcoding, is not appropriate for most species of plants because of a much slower rate of cytochrome c oxidase 1 gene evolution in higher plants than in animals. We therefore propose the nuclear internal transcribed spacer region and the plastid trnH-psbA intergenic spacer as potentially usable DNA regions for applying barcoding to flowering plants. The internal transcribed spacer is the most commonly sequenced locus used in plant phylogenetic investigations at the species level and shows high levels of interspecific divergence. The trnH-psbA spacer, although short (≈450-bp), is the most variable plastid region in angiosperms and is easily amplified across a broad range of land plants. Comparison of the total plastid genomes of tobacco and deadly nightshade enhanced with trials on widely divergent angiosperm taxa, including closely related species in seven plant families and a group of species sampled from a local flora encompassing 50 plant families (for a total of 99 species, 80 genera, and 53 families), suggest that the sequences in this pair of loci have the potential to discriminate among the largest number of plant species for barcoding purposes.

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Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians.

2005-03-16

Miguel Vences , Meike Thomas , Arie van der Meijden +2 more

BACKGROUND: Identifying species of organisms by short sequences of DNA has been in the center of ongoing discussions under the terms DNA barcoding or DNA taxonomy. A C-terminal fragment of … BACKGROUND: Identifying species of organisms by short sequences of DNA has been in the center of ongoing discussions under the terms DNA barcoding or DNA taxonomy. A C-terminal fragment of the mitochondrial gene for cytochrome oxidase subunit I (COI) has been proposed as universal marker for this purpose among animals. RESULTS: Herein we present experimental evidence that the mitochondrial 16S rRNA gene fulfills the requirements for a universal DNA barcoding marker in amphibians. In terms of universality of priming sites and identification of major vertebrate clades the studied 16S fragment is superior to COI. Amplification success was 100% for 16S in a subset of fresh and well-preserved samples of Madagascan frogs, while various combination of COI primers had lower success rates.COI priming sites showed high variability among amphibians both at the level of groups and closely related species, whereas 16S priming sites were highly conserved among vertebrates. Interspecific pairwise 16S divergences in a test group of Madagascan frogs were at a level suitable for assignment of larval stages to species (1-17%), with low degrees of pairwise haplotype divergence within populations (0-1%). CONCLUSION: We strongly advocate the use of 16S rRNA as standard DNA barcoding marker for vertebrates to complement COI, especially if samples a priori could belong to various phylogenetically distant taxa and false negatives would constitute a major problem.

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The campaign to DNA barcode all fishes, FISH‐BOL

2009-01-29

Robert Ward , Robert Hanner , Paul D. N. Hebert

FISH-BOL, the Fish Barcode of Life campaign, is an international research collaboration that is assembling a standardized reference DNA sequence library for all fishes. Analysis is targeting a 648 base … FISH-BOL, the Fish Barcode of Life campaign, is an international research collaboration that is assembling a standardized reference DNA sequence library for all fishes. Analysis is targeting a 648 base pair region of the mitochondrial cytochrome c oxidase I (COI) gene. More than 5000 species have already been DNA barcoded, with an average of five specimens per species, typically vouchers with authoritative identifications. The barcode sequence from any fish, fillet, fin, egg or larva can be matched against these reference sequences using BOLD; the Barcode of Life Data System (http://www.barcodinglife.org). The benefits of barcoding fishes include facilitating species identification, highlighting cases of range expansion for known species, flagging previously overlooked species and enabling identifications where traditional methods cannot be applied. Results thus far indicate that barcodes separate c. 98 and 93% of already described marine and freshwater fish species, respectively. Several specimens with divergent barcode sequences have been confirmed by integrative taxonomic analysis as new species. Past concerns in relation to the use of fish barcoding for species discrimination are discussed. These include hybridization, recent radiations, regional differentiation in barcode sequences and nuclear copies of the barcode region. However, current results indicate these issues are of little concern for the great majority of specimens.

An holistic approach to fish stock identification

1999-10-01

Gavin A. Begg , John R. Waldman

Molecular identification of prey in predator diets

2002-04-01

William O. C. Symondson

Abstract In many situations prey choice by predators in the field cannot be established or quantified using direct observation. The remains of some prey may be visually identified in the … Abstract In many situations prey choice by predators in the field cannot be established or quantified using direct observation. The remains of some prey may be visually identified in the guts and faeces of predators but not all predators ingest such hard remains and even those that do consume them may also ingest soft‐bodies prey that leave no recognizable remnants. The result is, at best, a biased picture of prey choice. A range of molecular techniques and applications are reviewed that allow prey remains to be identified, often to the species and even stage level. These techniques, all of which are still in use, include enzyme electrophoresis, a range of immunological approaches using polyclonal and monoclonal antibodies to detect protein epitopes, and recently developed polymerase chain reaction (PCR)‐based methods for detecting prey DNA. Analyses may be postmortem, on invertebrate and vertebrate predators collected from the field, or noninvasive assays of the remains in regurgitated bird pellets or vertebrate faeces. It was concluded that although monoclonal antibodies are currently the most effective method in use today, PCR‐based techniques have proved to be highly effective and versatile in recent laboratory trials and are likely to rapidly displace all other approaches.

DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics

2007-02-21

Mehrdad Hajibabaei , Gregory A. C. Singer , Paul D. N. Hebert +1 more

Principles of Animal Taxonomy

1961-12-31

George Gaylord Simpson

The Perils of DNA Barcoding and the Need for Integrative Taxonomy

2005-10-01

Kipling Will , Brent D. Mishler , Quentin D. Wheeler

Your work, Sir, is both new and good, but what's new Your work, Sir, is both new and good, but what's new

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The Promise of DNA Barcoding for Taxonomy

2005-10-01

Paul D. N. Hebert , T. Ryan Gregory

DNA barcoding is a novel system designed to provide rapid, accurate, and automatable species identifications by using short, standardized gene regions as internal species tags. As a consequence, it will … DNA barcoding is a novel system designed to provide rapid, accurate, and automatable species identifications by using short, standardized gene regions as internal species tags. As a consequence, it will make the Linnaean taxonomic system more accessible, with benefits to ecologists, conservationists, and the diversity of agencies charged with the control of pests, invasive species, and food safety. More broadly, DNA barcoding allows a day to be envisioned when every curious mind, from professional biologists to schoolchildren, will have easy access to the names and biological attributes of any species on the planet. In addition to assigning specimens to known species, DNA barcoding will accelerate the pace of species discovery by allowing taxonomists to rapidly sort specimens and by highlighting divergent taxa that may represent new species. By augmenting their capabilities in these ways, DNA barcoding offers taxonomists the opportunity to greatly expand, and eventually complete, a global inventory of life’s diversity. Despite the potential benefits of DNA barcoding to both the practitioners and users of taxonomy, it has been controversial in some scientific circles (Wheeler, 2004; Will and Rubinoff, 2004; Ebach and Holdredge, 2005; Will et al., 2005). A few have even characterized DNA barcoding as being “anti-taxonomy,” arguing that its implementation will signal the death of a system 250 years in the making. We feel that this opposition stems from misconceptions about the DNA barcoding effort. As such, we welcome this opportunity to clarify both the rationale and potential impacts of DNA barcoding. In responding to this set of questions, we emphasize the multiple positive impacts of this approach for taxonomy and biodiversity science.

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DNA barcoding Australia's fish species

2005-09-15

Robert Ward , Tyler Zemlak , B. H. Innes +2 more

Two hundred and seven species of fish, mostly Australian marine fish, were sequenced (barcoded) for a 655 bp region of the mitochondrial cytochrome oxidase subunit I gene (cox1). Most species … Two hundred and seven species of fish, mostly Australian marine fish, were sequenced (barcoded) for a 655 bp region of the mitochondrial cytochrome oxidase subunit I gene (cox1). Most species were represented by multiple specimens, and 754 sequences were generated. The GC content of the 143 species of teleosts was higher than the 61 species of sharks and rays (47.1% versus 42.2%), largely due to a higher GC content of codon position 3 in the former (41.1% versus 29.9%). Rays had higher GC than sharks (44.7% versus 41.0%), again largely due to higher GC in the 3rd codon position in the former (36.3% versus 26.8%). Average within-species, genus, family, order and class Kimura two parameter (K2P) distances were 0.39%, 9.93%, 15.46%, 22.18% and 23.27%, respectively. All species could be differentiated by their cox1 sequence, although single individuals of each of two species had haplotypes characteristic of a congener. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data. In the neighbour-joining tree for all 754 sequences, four major clusters were apparent: chimaerids, rays, sharks and teleosts. Species within genera invariably clustered, and generally so did genera within families. Three taxonomic groups-dogfishes of the genus Squalus, flatheads of the family Platycephalidae, and tunas of the genus Thunnus-were examined more closely. The clades revealed after bootstrapping generally corresponded well with expectations. Individuals from operational taxonomic units designated as Squalus species B through F formed individual clades, supporting morphological evidence for each of these being separate species. We conclude that cox1 sequencing, or 'barcoding', can be used to identify fish species.

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The Ecology of Teleost Fishes

1991-12-13

Gary D. Grossman , R. J. Wooten

The Principles of Classification and a Classification of Mammals

1946-08-01

E. Raymond Hall , George Gaylord Simpson

Simpson, George Gaylord. The Principles of Classification and a Classification op Mammals. Bull. Amer. Mus. Nat. Hist.> vol. 85, pp. xvi + 350, October 5,1945. Simpson George Gaylord. The Principles … Simpson, George Gaylord. The Principles of Classification and a Classification op Mammals. Bull. Amer. Mus. Nat. Hist.> vol. 85, pp. xvi + 350, October 5,1945. Simpson George Gaylord. The Principles of Classification and a Classification op Mammals. Bull. Amer. Mus. Nat. Hist. vol. 85, pp. xvi + 350, October 5, 1945. E. Raymond Hall E. Raymond Hall Search for other works by this author on: Oxford Academic Google Scholar Journal of Mammalogy, Volume 27, Issue 3, 14 August 1946, Pages 287–288, https://doi.org/10.2307/1375443 Published: 14 August 1946

Future challenges on the use of blockchain for food traceability analysis

2018-08-30

J. F. Gálvez , J. C. Mejuto , Jesús Simal‐Gándara

PCR protocols — A guide to methods and applications

1990-01-01

Analysis and Management of Animal Populations

2003-07-01

James B. Grand , Byron K. Williams , James D. Nichols +1 more

Ecology of Teleost Fishes

1990-10-01

J. M. Elliott , R. J. Wootton

Immunodiagnostics for Food Safety

2025-06-24

Inderpal Kaur , Manmeet Kaur , Sumeet Singh +1 more | CRC Press eBooks

Genomic Adaptation of Marine Medaka (Oryzias melastigma) Under Artificial Life‐History Selection

2025-06-23

Peng Sun , Guochen Gan , Yongjun Tian +3 more | Molecular Ecology

Size-selective harvesting imposes indirect selection on life-history traits and has profound evolutionary and ecological implications for fish populations, influencing traits such as body size, reproductive success, hatchability, and driving significant … Size-selective harvesting imposes indirect selection on life-history traits and has profound evolutionary and ecological implications for fish populations, influencing traits such as body size, reproductive success, hatchability, and driving significant genetic shifts. Here, we investigated the long-term effects of three harvesting strategies, large-harvested (LH), small-harvested (SH), and random-harvested (RH), on marine medaka (Oryzias melastigma) populations over five generations. We observed declines in body length and weight in the LH group, whereas these traits increased in the SH group, with the RH group remaining relatively stable. In terms of hatchability, SH surpassed LH but remained below RH. Genome-wide analyses identified key selective regions on chromosomes 8, 13, and 21, which were associated with growth and reproductive fitness. Genome-wide association studies (GWAS) identified significant loci on chromosome 13 linked to genes such as fat3a, kcnj13, and gucy1a2, which are strongly correlated with body weight. These findings suggest a close link between selective harvesting and life-history evolution, indicating that fishing behaviour may drive genetic shifts within populations. Furthermore, our results imply that selective pressures could influence phenotypic traits and allele frequencies, potentially leading to long-term or even irreversible genetic changes that might affect growth and survival, traits important for population sustainability.

Stort behov for nasjonal overvåkning av fremmede marine arter

2025-06-23

Vivian Husa , Frode Fossøy | Naturen

Oportunidades y errores en el uso de la genética para conocer el origen de una especie: el cangrejo italiano en la península ibérica

2025-06-22

Miguel Clavero , Sergio Bedmar , Francisco J. Oficialdegui | Ecosistemas

En ocasiones ocurre que el carácter nativo de una especie es incierto, siendo esta duda más frecuente cuando las posibles introducciones hubiesen ocurrido en tiempos remotos. Para resolver estas incertezas, … En ocasiones ocurre que el carácter nativo de una especie es incierto, siendo esta duda más frecuente cuando las posibles introducciones hubiesen ocurrido en tiempos remotos. Para resolver estas incertezas, es importante integrar conocimientos generados desde diferentes disciplinas, incluyendo análisis de ADN. Sin embargo, la información genética requiere interpretaciones y tiene una serie de limitaciones que hay que tener en cuenta para identificar correctamente el origen de una especie. Para ello es fundamental i) asegurar un muestreo representativo del acervo genético nativo, ii) priorizar el análisis de la estructura genética sobre la diversidad o la exclusividad de haplotipos, y iii) enmarcar los resultados genéticos en el conocimiento existente. Una interpretación sesgada de los patrones genéticos puede dar lugar a errores en la evaluación del carácter nativo de una especie, con importantes implicaciones para la gestión y la conservación de la biodiversidad. Esta situación la ejemplificamos aquí con caso del cangrejo italiano (Austropotamobius fulcisianus) en la península ibérica. Tradicionalmente, en España se ha tratado al cangrejo italiano como especie autóctona, y aún se gestiona como tal. Sin embargo, existen evidencias, numerosas y coherentes, de que la especie fue introducida desde la Toscana en el siglo XVI. Contradiciendo esta narrativa, diferentes trabajos han usado ADN mitocondrial para afirmar que esta especie es en realidad nativa en España, enfatizando una elevada riqueza y exclusividad entre los haplotipos detectados. En este trabajo mostramos que estas interpretaciones se basan en métricas poco informativas y que, además, están lastradas por la pobre representación de muestras italianas, un sesgo que se acentúa notablemente en los trabajos más recientes. De hecho, los patrones genéticos observados en el cangrejo italiano son muy similares a los descritos para el cangrejo rojo (Procambarus clarkii), y en los dos casos solo son compatibles con el hecho de ser especies introducidas en la península ibérica.

Molecular detection of some Staphylococcal enterotoxins in the meat of slaughtered animals in abattoirs, Mosul- Iraq

2025-06-21

Rana M. Dawood , Raad A. ِAlsanjary | Al-mağallaẗ al-ʻirāqiyyaẗ li-l-ʻulūm al-bayṭariyyaẗ/Iraqi journal of veterinary sciences

Generative AI in Predicting and Preventing Foodborne Illnesses

2025-06-20

Shweta Koparde , P. Selvakumar , Ravi Prakash Jha +4 more | IGI Global eBooks

Foodborne illnesses, often referred to as food poisoning, each year. These illnesses result from consuming contaminated food or beverages. Understanding the causes, consequences, and challenges associated with foodborne illnesses is … Foodborne illnesses, often referred to as food poisoning, each year. These illnesses result from consuming contaminated food or beverages. Understanding the causes, consequences, and challenges associated with foodborne illnesses is essential for developing effective prevention strategies and protecting public healthThe primary causes of foodborne illnesses can be broadly categorized into biological, chemical, and physical agents. Biological agents include bacteria, viruses, parasites, and fungi, which are responsible for the majority of foodborne infections. Common culprits such as pathogens often thrive in conditions that promote their growth, such as improper food handling, inadequate cooking, and cross-contamination. For instance, undercooked meat may harbor Salmonella, while raw vegetables can be contaminated with E. coli if exposed to contaminated water or soil.Chemical agents, including pesticides, food additives, and environmental contaminants, can also lead to foodborne illnesses.

Phenotypic and Genotypic Detection of Zoonotic Foodborne Pathogens from Dairy Environment and Raw Milk with Special Reference to Biofilm Production

2025-06-19

Parul , Barkha Sharma , A. K. Singh +4 more | Deleted Journal

Mitochondrial Perspective on Species Complexes and Evolutionary Dynamics Within Genus Channa

2025-06-18

Sonakshi Modeel , Meenu Chaurasia , Sneha Siwach +3 more | Biochemical Genetics

A simple and cost-effective detection of capsule origin source using FTIR-ATR

2025-06-18

Radhiahtul Raehan Mustafa , Mohammad Naqib Hamdan , Siti Nur Hadis A. Rahman +3 more | Journal of Food Science and Technology

Abstract The adulteration of food by undeclared ingredients is a major problem for both consumers and regulatory authorities. The increasing demand for halal pharmaceuticals emphasises the need for a robust … Abstract The adulteration of food by undeclared ingredients is a major problem for both consumers and regulatory authorities. The increasing demand for halal pharmaceuticals emphasises the need for a robust technique to identify porcine-derived components in samples. Fourier transform infrared spectroscopy coupled with attenuated total reflectance (FTIR-ATR) has emerged as a rapid, non-destructive and cost-effective technique for the detection of porcelain-derived components. In this study, 13 gelatine capsule samples from different sources were analysed with FTIR-ATR to investigate the presence of porcine and non-porcine. The application of discriminant analysis to the FTIR-ATR data allowed successful differentiation between porcine and non-porcine components in the samples. The infrared spectra revealed prominent functional groups, such as the amino group and the carbonyl group, which are characteristic of gelatin. While the spectra of the samples showed striking similarities due to their common major component, subtle differences were observed in the specific ranges of 3600–3000 cm −1 and 1700–1000 cm −1 . This integrated approach of FTIR-ATR and discriminant analysis proved to be a robust and reliable method for authenticating capsule origin and a useful tool for tracing halal detection in capsule products.

Meat Authentication Based on Animal Species and Other Quality Meat Attributes (Protected Geographical Indication, Organic Production, and Halal and Kosher Products) by HPLC–UV Fingerprinting and Chemometrics

2025-06-18

Alexandra Santomá-Martí , Nil Aijon , Óscar Núñez | Food Analytical Methods

Abstract A simple and economic high-performance liquid chromatography with UV–vis detection (HPLC–UV) metabolomic fingerprinting methodology was developed and applied after a water extraction procedure to obtain sample chemical descriptors suitable … Abstract A simple and economic high-performance liquid chromatography with UV–vis detection (HPLC–UV) metabolomic fingerprinting methodology was developed and applied after a water extraction procedure to obtain sample chemical descriptors suitable for meat authentication by chemometrics. Three hundred meat samples involving different species (lamb, beef, pork, rabbit, quail, chicken, turkey, and duck) as well as different non-genetic attributes (protected geographical indications, organic production, and Halal and Kosher meats) were analyzed, and the obtained HPLC–UV fingerprints subjected to PCA and PLS-DA for classification and authentication. Excellent PLS-DA discrimination and classification performance was accomplished for calibration and cross-validation, with sensitivity and specificity values higher than 100% and 99.3%, respectively, and classification errors below 0.4%, when meat species were considered. The prediction capability when employing a classification decision tree consisting on consecutive dual PLS-DA models built using a hierarchical model builder was of 100% accuracy when 48 meat samples were subjected to the model as unknown samples. Multiclass PLS-DA classification performances when addressing meat geographical origin, organic productions and Halal and Kosher products were also very acceptable, with overall sensitivity and specificity values higher than 91.2%, and classification errors below 6.9%. Finally, fraudulent meat adulteration cases involving PGI, organic and Halal and Kosher adulterated meats were evaluated by partial least squares (PLS) regression, allowing the detection and quantitation of adulteration levels within the range from 15 to 85% with prediction errors below 6.6%, demonstrating the suitability of the proposed methodology to assess meat authenticity.

First Specimen-Based Japanese Record of the Sponge-Dwelling Goby Sueviota minersorum (Teleostei: Gobiidae) from Iriomote Island, Yaeyama Islands

2025-06-18

Masayuki C. Sato , Hiroyuki Motomura | Species Diversity

Lesser Antillean Bullfinch (Loxigilla noctis)

2025-06-18

Zoya E. A. Buckmire , Kenrith D. Carter | Birds of the World

Seaside Cinclodes (Cinclodes nigrofumosus)

2025-06-18

Fernando Medrano , Sarah Saldanha , Vicente Pantoja +4 more | Birds of the World

Quality control and origin traceability of Tibetan yak meat using mid-infrared spectroscopy combined with multivariate analysis and machine learning

2025-06-18

Wanli Zong , Shanshan Zhao , Yalan Li +4 more | Journal of Consumer Protection and Food Safety

The first complete mitochondrial genome of Rohanella titteya (Cypriniformes: Cyprinidae) and its phylogenetic analysis

2025-06-18

Yu-Hui Tao , J. Cheng , J Li +3 more | Mitochondrial DNA Part B

We report the first complete mitochondrial genome of Rohanella titteya (Deraniyagala 1929), revealing a 16,715 bp genome containing 37 genes (13 protein-coding genes, 22 tRNA genes, 2 rRNA genes). Phylogenetic … We report the first complete mitochondrial genome of Rohanella titteya (Deraniyagala 1929), revealing a 16,715 bp genome containing 37 genes (13 protein-coding genes, 22 tRNA genes, 2 rRNA genes). Phylogenetic analysis based on mitochondrial genomic data of R. titteya and 11 Cyprinidae species showed that it clustered most closely with the mitogenome of Puntius eugrammus, offering no support for the recent transfer of this species to the new genus Rohanella. The mitogenome presented here provides a useful resource for both conservation and future Cyprinidae taxonomy.

Clarifying species identity in Aphanopus using wavelet-based otolith shape analysis

2025-06-18

Joana Vasconcelos , Javier Martı́nez , Airam Guerra‐Marrero +6 more | PLoS ONE

Accurate species identification is crucial for effective fisheries management, particularly for cryptic species with overlapping ranges and similar morphologies. This study explores the coexistence and distribution of Aphanopus carbo and … Accurate species identification is crucial for effective fisheries management, particularly for cryptic species with overlapping ranges and similar morphologies. This study explores the coexistence and distribution of Aphanopus carbo and Aphanopus intermedius in the northeastern Atlantic over four decades using otolith contour analysis. Otolith samples were collected from Madeira and the African coast between 1990 and 2021 and analyzed using a wavelet-based method, which improves species discrimination by capturing finer morphological details. The analysis revealed stable species proportions over time, with A. carbo generally dominating the catches ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" id="M1"><mml:mrow><mml:mi>~</mml:mi></mml:mrow></mml:math> 55–60%), except in 2010 when a decline was observed. A higher presence of A. intermedius in offshore areas may be associated with increased salinity near Madeira Island during the spawning season (October–December). Environmental changes, including variations in temperature and salinity at depths greater than 800 m, and the progressive expansion of the drifting longline fishery to new grounds, likely influenced these patterns. This study demonstrates that combining otolith contour analysis with genetically identified reference specimens enhances species discrimination and provides valuable insights into population dynamics and habitat use. These findings contribute to more effective fisheries management and stock assessments for these economically important scabbardfish in the northeastern Atlantic.

¡MARTINES AL AGUA!: Estrategias de partición de nicho en cinco especies de martines pescadores (Alcedinidae) que coexisten en Caño Negro, San José del Guaviare, Colombia

2025-06-17

Luis Miguel Murcia-Betancourt | Ornitología colombiana

El concepto de nicho ecológico es fundamental en el estudio de comunidades. La partición de nicho ayuda a comprender cómo las especies reparten los recursos en un ecosistema, reduciendo la … El concepto de nicho ecológico es fundamental en el estudio de comunidades. La partición de nicho ayuda a comprender cómo las especies reparten los recursos en un ecosistema, reduciendo la competencia y coexistiendo en un mismo lugar. En este estudio examinamos las estrategias de partición de nicho de cinco especies de martín pescador (Alcedinidae) que coexisten en un tramo de dos kilómetros en Caño Negro, ubicado en la Vereda Playa Güio de San José del Guaviare, Colombia. Durante dos temporadas, correspondientes a la época de aguas altas en septiembre y la temporada de aguas bajas en marzo, evaluamos diferentes estrategias de partición de nicho de estas cinco especies. Realizamos un análisis morfológico que agrupó a las especies según su tamaño. Estudiamos la abundancia estacional de las especies, encontrando diferencias significativas entre las dos temporadas. Calculamos el índice de Pianka para analizar el horario de actividad de pesca de las especies, revelando segregación de nicho entre algunas. Se evaluó la estratificación espacial de las especies, encontrando claras diferencias entre el uso del hábitat. Además, se estudió la ubicación espacial de los martines pescadores, encontrando que algunos prefieren zonas abiertas, mientras que otros prefieren aguas estancadas con vegetación densa. Cabe resaltar que no se encontraron martines pescadores en áreas donde se presentaban florecimientos algales en el agua. Nuestros hallazgos indican que estas especies emplean diferentes estrategias de partición de nicho, lo que responde a su coexistencia efectiva en Caño Negro. Además, se sugiere que estas especies pueden ser importantes bioindicadores de la calidad de los ecosistemas acuáticos. Estos resultados resaltan la necesidad de considerar el estudio de las estrategias de partición de nicho en las comunidades de aves acuáticas para la conservación de la avifauna neotropical y la importancia de mantener hábitats acuáticos saludables para su supervivencia a largo plazo.

Taxonomic status of nominal species of the hair-fin anchovy genus Setipinna previously regarded as synonyms of Setipinna tenuifilis (Valenciennes, 1848) and Setipinna paxtoni Wongratana, 1987 (Teleostei: Clupeiformes: Engraulidae: Coiliinae)

2025-06-17

Harutaka Hata , Sébastien Lavoué , Sharon A. Appleyard +1 more | Marine Biodiversity

Post-Slaughter Age Classification and Sex Determination in Deboned Beef Using Lipofuscin Autofluorescence and Amelogenin Gene Analysis

2025-06-17

Büşra Cumhur , Mustafa Yenal Akkurt , Tuğçe Anteplioğlu +3 more | Veterinary Sciences

Beef meat quality and value are influenced by the breed, sex, and age of slaughtered animals. This study aimed to evaluate lipofuscin pigment autofluorescence as a method for age classification … Beef meat quality and value are influenced by the breed, sex, and age of slaughtered animals. This study aimed to evaluate lipofuscin pigment autofluorescence as a method for age classification in beef meat samples and to determine the sex of market-obtained meat using PCR-based amelogenin gene amplification. Deboned beef meat samples from M. longissimus dorsi and M. biceps femoris were collected from 67 slaughtered cows with known age and sex. Additionally, 48 market samples were tested for sex identification and age classification using the same methods. Lipofuscin deposition was first observed at 1.5 years, and autofluorescence analysis effectively distinguished between meat from younger animals (1.5-2.2 years) and older ones (3-13 years), with a statistically significant difference (p < 0.001). Lipofuscin levels and excitation intensity increased with age, and no differences were found between the two muscles analyzed. The sex determination results were fully consistent with the records, and 55.2% of animals aged 3 years and older were identified as female. These findings demonstrate the reliability of lipofuscin autofluorescence for binary age determination in beef and support the potential of combining age and sex classification to identify meat derived from older dairy cows in the marketplace.

Sarcasm Detection with Contextual-Representation Multihop-Attention network

2025-06-17

Yufeng Diao , Xingliang Su , Shiqi Li +4 more | Research Square (Research Square)

<title>Abstract</title> Sarcasm is a delicate and implicit form of expression where what people say often runs counter to what they really mean. With this intentional ambiguity and complexity, sarcasm detection … <title>Abstract</title> Sarcasm is a delicate and implicit form of expression where what people say often runs counter to what they really mean. With this intentional ambiguity and complexity, sarcasm detection has always been a challenging task, even for humans. The importance of sarcasm detection has been realized by industry and academia. However, existing methodologies for automatic sarcasm detection predominantly rely on lexical and linguistic indicators, which prove to be insufficiently effective in addressing the complexities of sarcasm recognition.This paper focuses on tackling the challenging problem of sarcasm detection by leveraging a novel Contextual-Representation Multihop-Attention (CRMA) network based on bidirectional GRU. CRMA not only understands the ambiguity of sarcasm by the combination of contextual representation and word representation, but also learns the semantic complexity among sentences by the multihop attention mechanism. We perform comprehensive experimental evaluations on IAC dataset collected from popular website.The empirical findings reveal that our proposed framework achieves a substantial performance advantage over existing cutting-edge approaches, while supplementary case analyses further corroborate the robustness of our network architecture in identifying sarcastic expressions.

Comparison of Sarcasm Detection Models Based on Lightweight BERT Model - Differences between ALBERT-Chinese-tiny and TinyBERT in Small Sample Scenarios

2025-06-17

Mingyu Li | Science and Technology of Engineering Chemistry and Environmental Protection

Large Language models have excellent performance in processing NLP tasks, but there are not many references for lightweight models to process NLP tasks due to performance differences. In this article, … Large Language models have excellent performance in processing NLP tasks, but there are not many references for lightweight models to process NLP tasks due to performance differences. In this article, I selected two lightweight BERT models, ALBERT-Chinese-tiny and TinyBERT, to process the Chinese sarcasm detection task, using annotated public Chinese sarcasm detection datasets, collecting F1 indicators, training time and other data for comparative analysis, and verifying the performance of TinyBERT in processing Chinese sentiment analysis tasks, and supplementing the training data of lightweight BERT models in Chinese sarcasm detection tasks.

Microbial Assessment of Traditionally and Scientifically Dried Fish Products of East Midnapore, West Bengal, India

2025-06-17

Pijush Payra , Priyanka Kar , Sandipana Pati | Asian Journal of Dairy and Food Research

Background: The purpose of the present investigation was to compare the microbial load of three traditionally and scientifically dried fish. In traditional drying, sometimes good hygienic practices are compromised. But … Background: The purpose of the present investigation was to compare the microbial load of three traditionally and scientifically dried fish. In traditional drying, sometimes good hygienic practices are compromised. But in case of solar drying or scientifically drying like-drying in a food dryer/can control the drying environment and suitable hygienic condition is alsoensured. Methods: Present investigation was carried out for a period of 6 months, from October, 2023 to March, 2024. The study focused on three commonly consumed fish species: Bombay duck, Scaly hairfin and Ribbon fish and the microbial populations were assessed using three types of media: Nutrient broth, Thiosulfate citrate bile salts sucrose agar and MacConkey agar. The results from the serial dilution and spread plate methods were used to determine the colony-forming units (CFU) per milliliter (ml) at different dilution levels. Result: The findings of the study revealed that fish dried using traditional methods had higher (p less than 0.001) microbial loads as compared to those dried using a food dryer machine. The overall decrease of microbial loads with the food dryer machine suggests that it offers improved safety and better colour, texturefor dried fish products which was attributed to the controlled and consistent drying conditions provided to the fish product dried in food dryer machine.

A Cost-Effective LLM-based Approach to Identify Wildlife Trafficking in Online Marketplaces

2025-06-17

J Barbosa , Ulhas Gondhali , Gohar A. Petrossian +4 more | Proceedings of the ACM on Management of Data

Wildlife trafficking remains a critical global issue, significantly impacting biodiversity, ecological stability, and public health. Despite efforts to combat this illicit trade, the rise of e-commerce platforms has made it … Wildlife trafficking remains a critical global issue, significantly impacting biodiversity, ecological stability, and public health. Despite efforts to combat this illicit trade, the rise of e-commerce platforms has made it easier to sell wildlife products, putting new pressure on wild populations of endangered and threatened species. The use of these platforms also opens a new opportunity: as criminals sell wildlife products online, they leave digital traces of their activity that can provide insights into trafficking activities as well as how they can be disrupted. The challenge lies in finding these traces. Online marketplaces publish ads for a plethora of products, and identifying ads for wildlife-related products is like finding a needle in a haystack. Learning classifiers can automate ad identification, but creating them requires costly, time-consuming data labeling that hinders support for diverse ads and research questions. This paper addresses a critical challenge in the data science pipeline for wildlife trafficking analytics: generating quality labeled data for classifiers that select relevant data. While large language models (LLMs) can directly label advertisements, doing so at scale is prohibitively expensive. We propose a cost-effective strategy that leverages LLMs to generate pseudo labels for a small sample of the data and uses these labels to create specialized classification models. Our novel method automatically gathers diverse and representative samples to be labeled while minimizing the labeling costs. Our experimental evaluation shows that our classifiers achieve up to 95% F1 score, outperforming LLMs at a lower cost. We present real use cases that demonstrate the effectiveness of our approach in enabling analyses of different aspects of wildlife trafficking.

Traditional preparation of Na.kam su.a - an ethnic fermented fish product of Garo tribes of Meghalaya in Northeast India

2025-06-16

| Indian Journal of Traditional Knowledge

Combined effects of pretreatment and type of protease on the chemical and bioactive properties of edible bird’s nest glycopeptides

2025-06-16

Chin Huan Ng , Pei Ling Tang , Yien Yien Ong | Journal of Food Measurement & Characterization

Genetic Diversity of Mudskipper Species (Periophthalmus spp.) from the Southern Coast of Java, Indonesia, Based on the Mitochondrial 16S Gene

2025-06-16

Tuty Arisuryanti , Tasya Nuraliyah , Vindi Dwijayanti +3 more | HAYATI Journal of Biosciences

The genus Periophthalmus (Bloch & Schneider, 1801) comprises a diverse group of mudskippers within the family Oxudercidae and subfamily Oxudercinae. It includes 20 verified species globally, with 11 of these … The genus Periophthalmus (Bloch & Schneider, 1801) comprises a diverse group of mudskippers within the family Oxudercidae and subfamily Oxudercinae. It includes 20 verified species globally, with 11 of these species originating from Indonesia. Among them, P. kalolo and P. argentilineatus are prevalent across seven major islands. However, P. novemradiatus is less documented, with limited distribution records. The morphological similarities among Periophthalmus spp. complicate recognition, often leading to misidentification. To address this challenge, this study investigated the phylogenetic relationships and genetic diversity among these three species, utilizing the 16S rRNA gene as a marker. PCR amplification of the DNA from samples collected from seven regions along Java's southern coast employed primers 16Sar and 16Sbr. Phylogenetic analysis revealed three monophyletic clades corresponding to each species, with genetic divergences ranging from 3.66 to 5.40%. P. argentilineatus displayed a relatively high intraspecific divergence of 0.21-2.26%, suggesting the potential identification of cryptic species within this lineage, even with a conserved gene like 16S rRNA. We identified 47 variable sites within the 552-bp 16S rRNA sequence, including four singleton sites and 43 parsimony-informative sites. We discovered a unique marker at position 172 that could serve as a genetic identifier for distinguishing these species. These findings suggest that the 16S rRNA gene has potential as an alternative marker for species identification while also revealing genetic diversity, thereby complementing or even serving as an alternative to the commonly used COI gene in Periophthalmus spp.

eDNA-Based Evaluation of the Haplotypic Diversity of Orange-Spotted Grouper (Epinephelus coioides) in Stock Enhancement Areas of Wanshan Archipelago

2025-06-16

Chun Hui Ai , Yi Long Lin , Ming Chen +1 more | Marine Biotechnology

Unveiling the putative porcine myosin-based peptide markers for non-halal meat through chemometrics-assisted MRM-based proteomics

2025-06-16

Mohd Hafis Yuswan , Nasima Ali , Syaiful Izwan Ismail +2 more | European Food Research and Technology

Population Structure of the Dog Snapper, Lutjanus jocu (Bloch & Schneider, 1801), an Important Fishery Resource in the North of Bahia, Brazil: Influence of Habitat Suitability, Larvae Retention, and Fishing Pressure

2025-06-16

Glaciane Conceição Marques , Juliana Beltramin De Biasi , Carlos Werner Hackradt +1 more | Coasts

The Lutjanidae family includes multiple species highly important to the global fishing industry. In Brazil, approximately 40% of the fishing landings come from a species of this family, the dog … The Lutjanidae family includes multiple species highly important to the global fishing industry. In Brazil, approximately 40% of the fishing landings come from a species of this family, the dog snapper, Lutjanus jocu, among the most abundant in the northeast-region fisheries. This study aimed to analyze the genetic diversity and population structure of this species in the states of Bahia and Espírito Santo through the use of microsatellite markers. The dog snapper presented a high genetic variability in the studied populations, with the presence of a distinct population stock in northern Bahia probably driven by habitat suitability, larvae retention, and fishing pressure. The L. jocu sampling sites exhibited an excess of heterozygosity, a low allelic richness, and M-ratio values close to critical levels, probably indicating a recent population decline. Additionally, the low inbreeding indices and high genetic diversity values suggest a significant connectivity and considerably effective population sizes. Although these characteristics may reflect population stability, anthropogenic factors such as habitat loss, fragmentation, and overfishing may pose threats to the sustainability of the species, particularly along the northeastern coast of Brazil.

Effectiveness of Soaking Time and Bait Type on Dragon Trap Catch Results in Semarang Waters

2025-06-16

Syerly Niken Rukhayati , Bogi Budi Jayanto , Faik Kurohman +1 more | Asian Journal of Fisheries and Aquatic Research

Aims: The problem addressed in this research is the lack of empirical data on the optimal immersing duration and bait type to maximize the efficiency of dragon trap fishing for … Aims: The problem addressed in this research is the lack of empirical data on the optimal immersing duration and bait type to maximize the efficiency of dragon trap fishing for banana prawns (Penaeus merguiensis) in the coastal waters of Semarang. To analyze the effect of immersing duration and bait type on the catch of Banana Prawn (Penaeus merguiensis) in the waters of Semarang Study Design: Experimental fishing. Place and Duration of Study: This research was conducted in November 2024 at Tambak Lorok, Semarang City, Central Java, Indonesia. Methodology: The method used in this study was experimental fishing, involving two variables: immersing duration and bait type, with seven repetitions. The immersing durations were set at 12 hours and 24 hours, and the bait type used were discarded catch, chicken intestines, and green mussel shells. Results: The catch composition of the dragon trap includes banana prawn (Penaeus merguiensis), tiger shrimp (Penaeus monodon), dory snapper (Lutjanus fulviflamma), green mud crab (Scylla paramamosain), mangrove stone crab (Myomenippe hardwickii), barracuda (Sphyraena barracuda), and orange-spotted grouper (Epinephelus coioides). The highest average catch was obtained with a soaking time of 6 hours using discarded catch as bait, yielding a mean catch of 2.8 kg per trap. This was followed by the 8-hour soaking duration with discarded catch, which resulted in a slightly lower average catch of 2.5 kg. The 4-hour soaking time consistently produced the lowest yields across all bait types, with an average of 1.2 kg per trap. The Mann-Whitney test results showed an Asymp. Sig value of 0,018 (<0,05) for immersing duration, indicating a significant difference. Meanwhile, the Kruskal-Wallis test fir bait type resulted in a Asymp. Sig value of 0,173 (>0,05), indicating No. significant effect. The interaction between immersing duration and bait type using the Friedman test showed a significant effect with a value of ,0,000 (<0,05). Conclusion: The study demonstrates that a 12-hour immersion period using discarded catch as bait is the most effective combination for maximizing banana prawn catch in dragon trap fishing operations, with immersion duration having a significant impact on catch efficiency.

Is Pinna rudis Linnaeus, 1758 Spreading Towards the North (Adriatic Sea, Montenegro)

2025-06-16

Slavica Petović , Nikola Djordjević | Thalassas An International Journal of Marine Sciences

New Distributional Records of 31 Marine Fish Species from Rocky Reefs of Kerala: Insights from Underwater Visual Census on the Southwest Coast of India

2025-06-16

Baiju PT , Benno Pereira FG , S.A. Hama Amin Mr +3 more | Species

Legislative Requirements for Detection of Milk Counterfeit in Ukraine

2025-06-16

Roma Sybіrna , Andriy Sybirnyy , Zoriana Hrytsak | Visnik Nacional’nogo universitetu «Lvivska politehnika» Seria Uridicni nauki

The article, based on scientific literature, expert research and current legislation of Ukraine, analyzes the concept and content of falsification of goods, in particular milk, during the examination. The features … The article, based on scientific literature, expert research and current legislation of Ukraine, analyzes the concept and content of falsification of goods, in particular milk, during the examination. The features of the purpose and conduct of commodity examination in order to detect falsified dairy products are highlighted. The main methods of falsification of milk are analyzed. In particular, qualitative analysis of the determination of soda using indicators in milk, determination of the presence of biopolymers (starch, flour and others) in milk by heat treatment, as well as a qualitative method for determining the presence of hydrogen peroxide in dairy products. The study analyzed the responsibility for violation of consumer protection legislation, as well as for falsification of milk and dairy products. Changes to the Requirements for the safety and quality of milk and dairy products, which provide for clear rules for the sale of milk, mechanisms for conducting laboratory research and testing raw milk for antibiotic residues, freezing point and alkaline phosphatase during the study of milk after heat treatment, were worked out. An important moment was the approval of the specific functions of the national reference laboratory, which is designed to provide organizational and methodological guidance, as well as advisory and practical assistance to the network of laboratories authorized to test raw milk within the framework of the raw milk control program. Keywords: milk adulteration, adulterated products, product quality, quality losses, milk quality indicators, forensic commodity examination.

Population genetics of Pomatomus saltatrix (Linnaeus, 1766) in the seas of Türkiye based on microsatellite DNA

2025-06-15

İlyas Kutlu , Zehra Duygu Düzgüneş , Şirin Firidin +3 more | Ege Journal of Fisheries and Aquatic Sciences

Bluefish, (Pomatomus saltatrix (Linnaeus, 1766)) a commercially important and highly migratory predatory fish species, is found along the coasts of Türkiye. Despite it’s widespread presence along these coasts, there has … Bluefish, (Pomatomus saltatrix (Linnaeus, 1766)) a commercially important and highly migratory predatory fish species, is found along the coasts of Türkiye. Despite it’s widespread presence along these coasts, there has been no detailed study on the genetic structure of bluefish populations in Türkiye. In order to protect the biological diversity of countries, the genetic diversity present in natural resources must be identified. In this study, we examined the population structure of bluefish in the coastal regions of Türkiye; We aimed to identify bluefish samples collected from 14 regions along Türkiye coast by analyzing microsatellit DNA. For the microsatellite analysis, eight loci (ELF 17, ELF 37, ELF 49, ELF 19, ELF 39, ELF 46, ELF 44, ELF 50) were analyzed. A total of 433 samples from 14 populations were studied. In total 207 alleles and 61 specific alleles were identified across all populations and all loci. The highest observed (Ho) heterozygous values are ELF 50 (Ho: 0,991) while the lowest value is ELF 19 (Ho: 0.716). The highest expected (He) heterozygous values are ELF 39 (He: 0.952) while the lowest value is ELF 50 (He: 0.518). According to the Hardy-Weinberg analysis results, it was determined that there was a significant deviation in all populations. When bluefish populations are clustered according to their phylogenetic lineages by applying principal coordinate analysis (PCoA), the first three axes show 94% of the total genetic variation. The highest variation values and eigenvalues were found on the 3rd axis. When the analysis results are examined, it is clearly seen that the Mersin bluefish population is clustered differently from other populations. According to the Mantel test, a low correlation (R2 = 0.3061, P = 0.01) was detected between genetic and geographical distance. Admixed individuals and low genetic differentiation were observed in all populations.

Evaluation of ELISA for Detecting Porcine Content in Halal Compliance

2025-06-14

Meily C. Setyawati , Hendrik Setia Budi , Tantiana Tantiana +1 more | Journal of Current Science and Technology

Pork is strictly forbidden for consumption by the Muslim population. According to the Quran, the consumption is strictly prohibited, even in trace amounts or minimal concentrations. In this study, we … Pork is strictly forbidden for consumption by the Muslim population. According to the Quran, the consumption is strictly prohibited, even in trace amounts or minimal concentrations. In this study, we aimed to evaluate the sensitivity of ELISA to detect porcine in food. We used six types of pork-containing food samples: raw pork meat, grilled pork skewers, pork oil, pork fat, pork fried rice, and pork meatballs. To ensure sensitivity and reproducibility, each sample was tested in duplicate using undiluted, 10x, and 100x dilutions. Samples were evaluated using spectrometry at an absorbance wavelength of 450 nm. As a result, porcine antigen was detected in raw pork meat, grilled pork skewers, and pork meatballs at OD values > 0.07 (1.012; 1.1266; 0.8166) respectively. In pork meatballs, the presence of porcine antigen at high dilutions was inconsistently observed. Moreover, porcine antigen was not detected in pork oil, pork lard, pork fried rice, or beef soup even in undiluted samples at OD value < 0.07. This study successfully detected the presence of porcine antigens, however, its application is currently limited to meat products. Detection was also less sensitive when applied to processed food. Porcine protein was not detectable in oil and lard samples, nor in processed pork meat products at higher dilutions.

Eel consumption in Japan: Insights from genetic species identification and trade data

2025-06-13

Hiromi Shiraishi , Yu‐San Han , Kenzo Kaifu | Fisheries Science

Data Fusion for Integrative Species Identification Using Deep Learning

2025-06-13

Lara M Ko ̈sters , Kevin Karbstein , Martin Hofmann +3 more | Systematic Biology

Abstract DNA analyses have revolutionized species identification and taxonomic work. Yet, persistent challenges arise from little differentiation among and considerable variation within species, particularly among closely related groups. While images … Abstract DNA analyses have revolutionized species identification and taxonomic work. Yet, persistent challenges arise from little differentiation among and considerable variation within species, particularly among closely related groups. While images are commonly used as an alternative modality for automated identification tasks, their usability is limited by the same concerns. An integrative strategy, fusing molecular and image data through machine learning, holds significant promise for fine-grained species identification. However, a systematic overview and rigorous statistical testing concerning molecular and image preprocessing and fusion techniques, including practical advice for biologists, are missing so far. We introduce a machine learning scheme that integrates both molecular and image data for species identification. Initially, we systematically assess and compare three different DNA arrangements (aligned, unaligned, SNP-reduced) and two encoding methods (fractional, ordinal). Additionally, artificial neural networks are used to extract visual and molecular features, and we propose strategies for fusing this information. Specifically, we investigate three strategies: I) fusing directly after feature extraction, II) fusing features that passed through a fully connected layer after feature extraction, and III) fusing the output scores of both unimodal models. We systematically and statistically evaluate these strategies for four eukaryotic datasets, including two plant (Asteraceae, Poaceae) and two animal families (Lycaenidae, Coccinellidae) using Leave-One-Out Cross-Validation (LOOCV). In addition, we developed an approach to understand molecular- and image-specific identification failure. Aligned sequences with nucleotides encoded as decimal number vectors achieved the highest identification accuracy among DNA data preprocessing techniques in all four datasets. Fusing molecular and visual features directly after feature extraction yielded the best results for three out of four datasets (52-99%).Overall, combining DNA with image data significantly increased accuracy in three out of four datasets, with plant datasets showing the most substantial improvement (Asteraceae: +19%, Poaceae: +13.6%). Even for Lycaenidae with high identification accuracy based on molecular data (&gt;96%), a statistically significant improvement (+2.1%) was observed.Detailed analysis of confusion rates between and within genera shows that DNA alone tends to identify the genus correctly, but often fails to recognize the species. The failure to resolve species is alleviated by including image data in the training. This increase in resolution hints at a hierarchical role of modalities in which molecular data coarsely groups the specimens to then be guided towards a more fine-grained identification by the connected image. We systematically showed and explained, for the first time, that optimizing the preprocessing and integration of molecular and image data offers significant benefits, particularly for genetically similar and morphologically indistinguishable species, enhancing species identification by reducing modality-specific failure rates and information gaps. Our results can inform integration efforts for various organism groups, improving automated identification across a wide range of eukaryotic species.

Isolation and Characterization of Fungal Strains from Tilapia (Oreochromis niloticus) and Machoiron (Chrysichthys nigrodigitatus) Fish in Taabo Lake, Kossou Lake, and Tagba Lagoon of Grand Lahou, Côte d’Ivoire

2025-06-13

Rosly Sahi Bolou , Ettien Léon Hamian , Kouamé Kouadio +2 more | Microbiology Research Journal International

This study aimed to isolate and characterize fungal strains contaminating freshwater fish (Tilapia and Machoiron) in three water bodies in Côte d'Ivoire: Lake Taabo, Lake Kossou, and the Tagba Lagoon … This study aimed to isolate and characterize fungal strains contaminating freshwater fish (Tilapia and Machoiron) in three water bodies in Côte d'Ivoire: Lake Taabo, Lake Kossou, and the Tagba Lagoon in Grand-Lahou. A total of 120 samples were collected during four seasonal campaigns (dry and rainy seasons) and analyzed in the laboratory. Molds were isolated on acidified Potato Dextrose Agar (PDA) medium (pH 3.5) at 30°C and identified through macroscopic (color, texture) and microscopic (spore morphology, hyphae) observations. Contamination frequencies were calculated for each fungal genus. Among the 156 isolated strains, five dominant genera were identified: Aspergillus (57.69%), Rhizopus (25%), Fusarium (11.54%), Penicillium (3.85%), and Absidia (1.92%). Aspergillus was ubiquitous, while Rhizopus and Fusarium were more abundant during the rainy seasons. The analyzed fish showed high contamination rates: 75% for Aspergillus, 32.5% for Rhizopus, and 15% for Fusarium. These results confirm the presence of potentially toxigenic molds in fish, with associated risks of mycotoxin production (aflatoxins, ochratoxins). The contamination reflects environmental conditions and local practices. The study recommends establishing regulatory standards to limit consumer exposure and improve food safety.

A new record of the blackfin goby (Egglestonichthys melanoptera, Gobiidae) from China, with complete mitochondrial genomes of two Egglestonichthys species and their phylogenetic implications

2025-06-13

Jiajie Chen , Sheng Zeng , R. Passmore +7 more | Zoosystematics and Evolution

This study documents the northernmost record of Egglestonichthys melanoptera in the South China Sea (Hainan Island, China), thereby extending its distribution in the Indo-Pacific region from the Indian Ocean, and … This study documents the northernmost record of Egglestonichthys melanoptera in the South China Sea (Hainan Island, China), thereby extending its distribution in the Indo-Pacific region from the Indian Ocean, and confirms the sympatric occurrence of E. bombylios . The morphological characteristics of E. melanoptera are described in detail, and measurable data is presented. The complete mitochondrial genomes of both species have been presented for the first time (17,743 bp for E. bombylios , 17,350 bp for E. melanoptera ), revealing a conserved gobiid genomic architecture with a pronounced A+T bias (60.3–62.7%) and codon position-specific nucleotide preferences. A further objective of this study was to construct a phylogeny of 110 species of the family Gobiidae, extending previous studies. Phylogenetic analyses resolved E. melanoptera within Gobiidae, supported by osteological synapomorphies (single epural; pterygo-phore formula 3-22110), and placed Egglestonichthys within the Priolepis lineage. The validity of Benthophilinae remains contentious due to conflicting swim bladder and spine morphology, necessitating integrative reassessment. Comparative mitogenomic analyses reveal that the mitochondrial genome currently attributed to Oxyurichthys formosanus in GenBank (accession: KC237282) does not represent the genus Oxyurichthys but should be reassigned to Cryptocentrus yatsui . A revised diagnostic key has been synthesised, synthesising historical descriptions with novel morphological-molecular data, giving taxonomy for Egglestonichthys species. These findings contribute to our understanding of the evolutionary trajectories of gobiid fish, emphasising the synergy of mitogenomic and morphological approaches in resolving complex marine fish systematics.

Integrated Enzymatic and Biotechnological Strategies for Sustainable Extraction and Enrichment of Functional Components in Edible Bird’s Nest: A Review

2025-06-12

G. Fang , Nan Qian , M. Yuan +5 more | Food Reviews International

Genetic Diversity in Commercial Danio rerio and Its Implications for Ecotoxicology

2025-06-12

Carmen M. Flores‐Farfan , Alejandro J. Condori‐Flores , Sergio B. Bernuy‐Rodriguez +7 more | Environmental Toxicology

ABSTRACT The zebrafish ( Danio rerio ) is a widely used aquatic model organism. However, fish from confined groups may experience inbreeding and loss of heterozygosity, which could affect biological … ABSTRACT The zebrafish ( Danio rerio ) is a widely used aquatic model organism. However, fish from confined groups may experience inbreeding and loss of heterozygosity, which could affect biological responses and research outcomes. Therefore, we aimed to investigate the genetic differences among zebrafish populations from different commercial suppliers and assess their influence on responses to copper exposure. Seven groups of 3‐month‐old zebrafish were obtained from the major commercial breeders in the Arequipa region, Peru, and coded as zfRS , zfRN , zfHN , zfHV , zfHS , zfDN , and zfCN . Morphometric and morphological analyses were performed on a subsample, while genetic assessments focused on the mitochondrial cytochrome oxidase I (COI) gene, examining phylogeny, haplotypes, and polymorphisms. Additionally, mortality, sublethal effects, and liver histology were evaluated in response to four copper concentrations (ranging from 0.125 to 1.0 mg/L). No evident morphometric or morphological distinctions were observed between groups. On the contrary, COI gene assessment classified the seven groups into two main genetic clades, with the zfRS group being genetically distinct from the others. Two primary origins (Asian and North American) were identified, and moderate haplotype diversity (0.43 ± 0.06) and low nucleotide diversity (0.00137 ± 0.00) were observed. The zfHS and zfRN groups exhibited the highest intra‐group variability. Significant differences in lethal and sublethal responses to copper exposure were found, along with distinct forms of histological damage (e.g., steatosis, hemorrhages, fibrosis, and nuclear damage). Notably, the most genetically diverse groups ( zfHS and zfRN ) exhibited the highest resistance to copper‐induced stress. Relying exclusively on fish from commercial breeders with uncontrolled confined populations for ecotoxicology research may lead to biased conclusions, as these factors affect the consistency and reliability of biological responses in laboratory testing. Therefore, the use of fish from potentially long‐standing confined groups in research must be avoided.

Hook, line, and spectra: machine learning for fish species identification and body part classification using rapid evaporative ionization mass spectrometry

2025-06-12

Jesse Wood , Bach Hoai Nguyen , Bing Xue +2 more | Intelligent Marine Technology and Systems

Abstract Marine biomass composition analysis traditionally requires time-consuming processes and domain expertise. This study demonstrates the effectiveness of rapid evaporative ionization mass spectrometry (REIMS) combined with advanced machine learning (ML) … Abstract Marine biomass composition analysis traditionally requires time-consuming processes and domain expertise. This study demonstrates the effectiveness of rapid evaporative ionization mass spectrometry (REIMS) combined with advanced machine learning (ML) techniques for accurate marine biomass composition determination. Using fish species and body parts as model systems representing diverse biochemical profiles, we investigate various ML methods, including unsupervised pretraining strategies for transformers. The deep learning approaches consistently outperformed traditional machine learning across all tasks. For fish species classification, the pretrained transformer achieved 99.62% accuracy, and for fish body parts classification, the transformer achieved 84.06% accuracy. We further explored the explainability of the best-performing and predominantly black box models using local interpretable model-agnostic explanations and gradient-weighted class activation mapping to identify the important features driving the decisions behind each of the best performing classifiers. REIMS analysis with ML can be an accurate and potentially explainable technique for automated marine biomass composition analysis. Thus, REIMS analysis with ML has potential applications in quality control, product optimization, and food safety monitoring in marine-based industries.

Detection and identification of foreign objects by infrared scanning: literature review and own research

2025-06-12

Yu. V. Іvanova , Б. Б. Бандурян , К. V. Miasoiedov +2 more | The Ukrainian Journal of Clinical Surgery

Objective. To develop and test a method for recording temperature with high spatial resolution under the influence of ultrahighfrequency hyperthermia. Materials and methods. An in vitro experiment was conducted, which … Objective. To develop and test a method for recording temperature with high spatial resolution under the influence of ultrahighfrequency hyperthermia. Materials and methods. An in vitro experiment was conducted, which consisted of placing foreign objects (plastic, wood, metal) into the pig muscle tissue. A standard medical device LUCH3 with a frequency of electromagnetic oscillations of 2.45 GHz was used as an ultrahigh frequency generator. The objects of study were identified using a spectralanalytical setup based on the ICS21 spectrometer and the LAND814 thermal imager. The developed method provided visualization of spectral components, increased sensitivity and spectral resolution when measuring the infrared radiation spectrum. Results. It has been established that under the influence of ultrahigh frequency radiation on objects with different coefficients of transmission, absorption, reflection of heat, as well as with different heat capacity and thermal conductivity, temperature gradients are anomalous. The methods of microwave hyperthermia, infrared sensing, spectral analysis, and dynamic thermal imaging allow detecting and identifying objects not only on the surface but also at different depths.