scholarly journals Tubulin-Based DNA Barcode: Principle and Applications to Complex Food Matrices

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 229 ◽  
Author(s):  
Laura Morello ◽  
Luca Braglia ◽  
Floriana Gavazzi ◽  
Silvia Gianì ◽  
Diego Breviario
Keyword(s):  
Dna Sequencing ◽  
Cell Biology ◽  
Animal Species ◽  
Analytical Procedure ◽  
Dna Barcode ◽  
Gene Families ◽  
Genomic Profile ◽  
Complex Matrix ◽  
Universal Primer ◽  
Food Matrices

The DNA polymorphism diffusely present in the introns of the members of the Eukaryotic beta-tubulin gene families, can be conveniently used to establish a DNA barcoding method, named tubulin-based polymorphism (TBP), that can reliably assign specific genomic fingerprintings to any plant or/and animal species. Similarly, many plant varieties can also be barcoded by TBP. The method is based on a simple cell biology concept that finds a conveniently exploitable molecular basis. It does not depend on DNA sequencing as the most classically established DNA barcode strategies. Successful applications, diversified for the different target sequences or experimental purposes, have been reported in many different plant species and, of late, a new a version applicable to animal species, including fishes, has been developed. Also, the TBP method is currently used for the genetic authentication of plant material and derived food products. Due to the use of a couple of universal primer pairs, specific for plant and animal organisms, respectively, it is effective in metabarcoding a complex matrix allowing an easy and rapid recognition of the different species present in a mixture. A simple, dedicated database made up by the genomic profile of reference materials is also part of the analytical procedure. Here we will provide some example of the TBP application and will discuss its features and uses in comparison with the DNA sequencing-based methods.

scholarly journals Phylogenetic Study of Bufonidae (Amphibia: Anura) from Sumatera and Asia Based on Cytochrome B Gene

2021 ◽  
Vol 11 (3) ◽  
pp. 383-387
Author(s):  
Djong Tjong ◽  
◽  
Dewi Roesma ◽  
Silvia Indra ◽  
◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Cytochrome B ◽  
Cell Biology ◽  
Sequence Divergence ◽  
Phylogenetic Study ◽  
Tissue Samples ◽  
Duttaphrynus Melanostictus ◽  
Level Increase ◽  
West Sumatra ◽  
Biology Laboratory

Bufonidae is widely distributed amphibian family around the world, including Indonesia (Sumatra) and Asia. Sumatra is an island which has separated because of sea level increase and create gene flows barrier for amphibian in Sumatra and Asia. The purpose of this research is to analyse Bufonidae phylogenetic which exist in several locations in Sumatra and Asia based on gene cytochrome b analysis. Samples were collected from six localities in West Sumatra. DNA extraction and amplification has been done in Genetics and Cell Biology Laboratory, Andalas University, whereas DNA sequencing were analyzed at MacroGen USA DNA Sequencing Laboratory, South Korea. About 14 tissue samples of Bufonidae from West Sumatra has been analyzed. The relationship of Bufonidae phylogenetics in Sumatra and Asia were divided into three main clusters. Duttaphrynus melanostictus in Sumatra is closer to Duttaphrynus melanostictus from India with 0,3-0,5% sequence divergence and it is a group of paraphyletic with Duttaphrynus melanostictus from Vietnam, Taiwan, and China.

scholarly journals A PCR Method That Can Be Further Developed into PCR-RFLP Assay for Eight Animal Species Identification

2018 ◽  
Vol 2018 ◽  
pp. 1-6 ◽  
Author(s):  
Feng Guan ◽  
Yu-Ting Jin ◽  
Jin Zhao ◽  
Ai-Chun Xu ◽  
Yuan-Yuan Luo
Keyword(s):  
Species Identification ◽  
Animal Species ◽  
Limit Of Detection ◽  
Cost Effective ◽  
Universal Primers ◽  
Universal Primer ◽  
Routine Identification ◽  
Pcr Rflp ◽  
Fast Processing ◽  
Rflp Assay

There are many PCR-based methods for animal species identification; however, their detection numbers are limited or could not identify unknown species. We set out to solve this problem by developing a universal primer PCR assay for simultaneous identification of eight animal species, including goat, sheep, deer, buffalo, cattle, yak, pig, and camel. In this assay, the variable lengths of mitochondrial DNA were amplified using a pair of universal primers. PCR amplifications yielded 760 bp, 737 bp, 537 bp, 486 bp, 481 bp, 464 bp, 429 bp, and 359 bp length fragments for goat, sheep, deer, buffalo, cattle, yak, pig, and camel, respectively. This primer pair had no cross-reaction with other common domestic animals and fish. The limit of detection varied from 0.01 to 0.05 ng of genomic DNA for eight animal species in a 20 µl PCR mixture. Each PCR product could be further digested into fragments with variable sizes and qualitative analysis by SspI restriction enzyme. This developed PCR-RFLP assay was sufficient to distinguish all targeted species. Compared with the previous published related methods, this approach is simple, with high throughput, fast processing rates, and more cost-effective for routine identification of meat in foodstuffs.

scholarly journals The problems and promise of DNA barcodes for species diagnosis of primate biomaterials

2005 ◽  
Vol 360 (1462) ◽  
pp. 1869-1877 ◽  
Author(s):  
Joseph G Lorenz ◽  
Whitney E Jackson ◽  
Jeanne C Beck ◽  
Robert Hanner
Keyword(s):  
Quality Control ◽  
Dna Barcode ◽  
Control Process ◽  
Dna Barcodes ◽  
Universal Primer ◽  
Dna And Rna ◽  
Quality Control Process ◽  
Primate Cell ◽  
Identification Technique ◽  
Extraction Processes

The Integrated Primate Biomaterials and Information Resource ( www.IPBIR.org ) provides essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing DNA and RNA derived from primate cell cultures. The IPBIR uses mitochondrial cytochrome c oxidase subunit I sequences to verify the identity of samples for quality control purposes in the accession, cell culture, DNA extraction processes and prior to shipping to end users. As a result, IPBIR is accumulating a database of ‘DNA barcodes’ for many species of primates. However, this quality control process is complicated by taxon specific patterns of ‘universal primer’ failure, as well as the amplification or co-amplification of nuclear pseudogenes of mitochondrial origins. To overcome these difficulties, taxon specific primers have been developed, and reverse transcriptase PCR is utilized to exclude these extraneous sequences from amplification. DNA barcoding of primates has applications to conservation and law enforcement. Depositing barcode sequences in a public database, along with primer sequences, trace files and associated quality scores, makes this species identification technique widely accessible. Reference DNA barcode sequences should be derived from, and linked to, specimens of known provenance in web-accessible collections in order to validate this system of molecular diagnostics.

scholarly journals A Universal Primer Set for PCR Amplification of Nuclear Histone H4 Genes from All Animal Species

2004 ◽  
Vol 22 (3) ◽  
pp. 582-588 ◽  
Author(s):  
Pascal Pineau ◽  
Michel Henry ◽  
Rodolphe Suspène ◽  
Agnès Marchio ◽  
Agnès Dettai ◽  
...  
Keyword(s):  
Animal Species ◽  
Pcr Amplification ◽  
Histone H4 ◽  
Universal Primer ◽  
Nuclear Histone

scholarly journals Optogenetic Technology and Its In Vivo Applications

2016 ◽  
Vol 27 (2) ◽  
pp. 78
Author(s):  
Simon Gelman
Keyword(s):  
Cell Biology ◽  
Nonhuman Primates ◽  
Animal Species ◽  
Neural Circuits ◽  
Neuronal Cell ◽  
Cell Types ◽  
Whole Cells ◽  
Neuronal Populations ◽  
Novel Technology

Optogenetics is a novel technology with the widely acknowledged potential to revolutionize cell biology and neuroscience. Essentially, optogenetic methods integrate optical and genetic tools to control the activity of whole cells or subcellular events. In recent years, optogenetics has been used to activate and to inhibit genetically defined neuronal populations within neural circuits. As such, it has been used to show the sufficiency or the necessity of specific neuronal cell types in generating behaviors across a number of animal species. When employed in rodent models of human neurological and psychiatric disorders, optogenetics has provided clinically relevant insights into the function of pathologic neural circuits. Recent progress in the in vivo applications of this methodology is reviewed in this article, with particular focus on behavioral applications in nematodes, fish, rodents, and nonhuman primates.

Masterminds or minions? Cysteine proteinases in plant programmed cell deathThis review is one of a selection of papers published in the Special Issue on Plant Cell Biology.

2006 ◽  
Vol 84 (4) ◽  
pp. 651-667 ◽  
Author(s):  
Christopher P. Trobacher ◽  
Adriano Senatore ◽  
John S. Greenwood
Keyword(s):  
Cell Death ◽  
Cell Biology ◽  
Apoptotic Cell ◽  
Gene Families ◽  
Cysteine Proteinases ◽  
Special Issue ◽  
Multicellular Organisms ◽  
Protease Expression ◽  
Signalling Cascade ◽  
Selection Of

Cysteine proteinases are ubiquitously involved in programmed cell death (PCD) in multicellular organisms. In animals, one group of cysteine proteinases, the cysteine-dependent aspartate-specific proteinases (caspases), are involved in a proteolytic signalling cascade that controls apoptosis, the most studied form of PCD. The enzymes act as both masterminds and executioners in apoptotic cell death. In plants, members of the metacaspase family, as well as those of the papain-like and legumain families, of cysteine proteinases have all been implicated in PCD. These enzymes often belong to sizeable gene families, with Arabidopsis having 9 metacaspase, 32 papain-like, and 4 legumain genes. This redundancy has made it difficult to ascertain the functional importance of any particular enzyme in plant PCD, as many are often expressed in a given tissue undergoing PCD. As yet, mechanisms similar to the apoptotic caspase cascade in animals have not been uncovered in plants and, indeed, may not exist. Are the various cysteine proteinases, so often implicated in plant PCD, merely acting as minions in the process? This review will outline reports of cysteine proteinases associated with plant PCD, discuss problems in determining the function of specific proteases, and suggest avenues for determining how these enzymes might be regulated and how PCD pathways upstream of protease expression and activation might operate.

scholarly journals Semi-Automated Library Preparation for High-Throughput DNA Sequencing Platforms

2010 ◽  
Vol 2010 ◽  
pp. 1-8 ◽  
Author(s):  
Eveline Farias-Hesson ◽  
Jonathan Erikson ◽  
Alexander Atkins ◽  
Peidong Shen ◽  
Ronald W. Davis ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Dna Sequencing ◽  
High Throughput ◽  
Magnetic Beads ◽  
Dna Barcode ◽  
Cost Effective ◽  
Dna Libraries ◽  
Emulsion Pcr ◽  
High Throughput Dna Sequencing ◽  
Sequencing Platforms

Next-generation sequencing platforms are powerful technologies, providing gigabases of genetic information in a single run. An important prerequisite for high-throughput DNA sequencing is the development of robust and cost-effective preprocessing protocols for DNA sample library construction. Here we report the development of a semi-automated sample preparation protocol to produce adaptor-ligated fragment libraries. Using a liquid-handling robot in conjunction with Carboxy Terminated Magnetic Beads, we labeled each library sample using a unique 6 bp DNA barcode, which allowed multiplex sample processing and sequencing of 32 libraries in a single run using Applied Biosystems' SOLiD sequencer. We applied our semi-automated pipeline to targeted medical resequencing of nuclear candidate genes in individuals affected by mitochondrial disorders. This novel method is capable of preparing as much as 32 DNA libraries in 2.01 days (8-hour workday) for emulsion PCR/high throughput DNA sequencing, increasing sample preparation production by 8-fold.

Controls of Hair Follicle Cycling

2001 ◽  
Vol 81 (1) ◽  
pp. 449-494 ◽  
Author(s):  
K. S. Stenn ◽  
R. Paus
Keyword(s):  
Growth Factor ◽  
Hair Follicle ◽  
Cell Biology ◽  
Transforming Growth Factor ◽  
Gene Families ◽  
Transforming Growth Factor Β ◽  
Follicle Growth ◽  
Modern Biology ◽  
Hair Follicle Growth

Nearly 50 years ago, Chase published a review of hair cycling in which he detailed hair growth in the mouse and integrated hair biology with the biology of his day. In this review we have used Chase as our model and tried to put the adult hair follicle growth cycle in perspective. We have tried to sketch the adult hair follicle cycle, as we know it today and what needs to be known. Above all, we hope that this work will serve as an introduction to basic biologists who are looking for a defined biological system that illustrates many of the challenges of modern biology: cell differentiation, epithelial-mesenchymal interactions, stem cell biology, pattern formation, apoptosis, cell and organ growth cycles, and pigmentation. The most important theme in studying the cycling hair follicle is that the follicle is a regenerating system. By traversing the phases of the cycle (growth, regression, resting, shedding, then growth again), the follicle demonstrates the unusual ability to completely regenerate itself. The basis for this regeneration rests in the unique follicular epithelial and mesenchymal components and their interactions. Recently, some of the molecular signals making up these interactions have been defined. They involve gene families also found in other regenerating systems such as fibroblast growth factor, transforming growth factor-β, Wnt pathway, Sonic hedgehog, neurotrophins, and homeobox. For the immediate future, our challenge is to define the molecular basis for hair follicle growth control, to regenerate a mature hair follicle in vitro from defined populations, and to offer real solutions to our patients' problems.

scholarly journals BARCODE TAXONOMY AT THE GENUS LEVEL

2019 ◽  
Vol 21 ◽  
pp. 17-37
Author(s):  
Rainer Breitling
Keyword(s):  
Animal Species ◽  
Dna Barcode ◽  
Morphological Evidence ◽  
Cryptic Diversity ◽  
Complementary Information ◽  
Genus Level ◽  
Taxonomic Decision ◽  
Taxonomic Groups ◽  
Barcode Sequencing ◽  
Sequence Similarities

DNA barcode sequencing has rapidly become one of the most powerful tools for biodiversity assessments. Beyond its original uses for the identification of animal species, including the discovery of cryptic diversity in difficult taxonomic groups, the growing public sequence datasets also offer opportunities for more wide-ranging applications. This contribution shows how barcode data can provide useful complementary information to assist taxonomic decision making at the genus level. An analysis of public barcode datasets for 10 diverse spider families, covering more than 3400 species and morphospecies, reveals numerous examples where sequence similarities either strongly support or convincingly refute recent controversial genus assignments. The following nomenclatorial changes are suggested based on a combined assessment of morphological evidence and the barcode analysis: Acantholycosa = Pardosa (syn. nov.); Piratula = Pirata (syn. nov.); Pulchellodromus, Philodromimus, Tibellomimus, Artanes, and Emargidromus = subgenera of Philodromus (stat. nov.); Cryptachaea riparia = Parasteatoda riparia (comb. nov.); Ohlertidion = Heterotheridion (syn. nov.); Saaristoa = Aphileta (syn. nov.); Aphileta microtarsa = Eulaira microtarsa (comb. conf.); Centromerita and Tallusia = Centromerus (syn. conf.); Obscuriphantes, Agnyphantes, and Acanthoneta = Poeciloneta (syn. nov.); Bolyphantes bipartitus = Poeciloneta bipartita (comb. nov.); Anguliphantes, Improphantes, Piniphantes, and Mansuphantes = Oryphantes (syn. nov.), Palliduphantes antroniensis = Oryphantes antroniensis (comb. nov.), Lepthyphantes nodifer = Oryphantes nodifer (comb. nov.), Hypositticus, Sittipub, Calositticus, Sittisax, Sittiflor, and Attulus = Sitticus (syn. nov.).

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