DNA from mollusc shell: a valuable and underutilised substrate for genetic analyses

Mollusc shells are an abundant resource that have been long used to predict the structures of ancient ecological communities, examine evolutionary processes, reconstruct paleoenvironmental conditions, track and predict responses to climatic change, and explore the movement of hominids across the globe. Despite the ubiquity of mollusc shell in many environments, it remains relatively unexplored as a substrate for molecular genetic analysis. Here we undertook a series of experiments using the New Zealand endemic greenshell mussel, Perna canaliculus, to explore the utility of fresh, aged, beach-cast and cooked mollusc shell for molecular genetic analyses. We find that reasonable quantities of DNA (0.002–21.48 ng/mg shell) can be derived from aged, beach-cast and cooked mussel shell and that this can routinely provide enough material to undertake PCR analyses of mitochondrial and nuclear gene fragments. Mitochondrial PCR amplification had an average success rate of 96.5% from shell tissue extracted thirteen months after the animal’s death. A success rate of 93.75% was obtained for cooked shells. Amplification of nuclear DNA (chitin synthase gene) was less successful (80% success from fresh shells, decreasing to 10% with time, and 75% from cooked shells). Our results demonstrate the promise of mollusc shell as a substrate for genetic analyses targeting both mitochondrial and nuclear genes.

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Relocation of the unusual VAR1 gene from the mitochondrion to the nucleus

Biochemistry and Cell Biology ◽

10.1139/o95-106 ◽

1995 ◽

Vol 73 (11-12) ◽

pp. 987-995 ◽

Cited By ~ 19

Author(s):

Marie Sanchirico ◽

Andrew Tzellas ◽

Thomas L. Mason ◽

Thomas D. Fox ◽

Heather Conrad-Webb ◽

...

Keyword(s):

Structure Function ◽

Molecular Genetic ◽

Ribosomal Subunit ◽

Nuclear Gene ◽

Genetic System ◽

Molecular Genetic Analysis ◽

Translation System ◽

Major Protein ◽

Mitochondrial Translation ◽

Var1 Gene

The Varl protein (Var1p) is an essential, stoichiometric component of the yeast mitochondrial small ribosomal subunit, and it is the only major protein product of the mitochondrial genetic system that is not part of an energy transducing complex of the inner membrane. Interestingly, no mutations have been reported that affect the function of Var1p, presumably because loss of a functional mitochondrial translation system leads to an instability of mtDNA. To study the structure, function and synthesis of Varlp, we have engineered yeast strains for the expression of this protein from a nuclear gene, VAR1U, in which 39 nonstandard mitochondrial codons were converted to the universal code. Immunoblot analysis using an epitope-tagged form of Var1Up showed that the nuclear-encoded protein was expressed and imported into the mitochondria. VAR1U was tested for its ability to complement a mutation in mtDNA, PZ206, which disrupts 3′-end processing of the VAR1 mRNA, causing greatly reduced synthesis of Var1p and a respiratory-deficient phenotype. Respiratory growth was restored in PZ206 mutants by transformation with a centromere plasmid carrying VAR1U under ADH1 promoter control, thus proving that VAR1 function can be relocated from the mitochondrion to the nucleus. Moreover, epitope-tagged Var1Up co-sedimented specifically with small ribosomal subunits in high salt sucrose gradients. The relocation of VAR1 from the mitochondrion to the nucleus provides an excellent system for the molecular genetic analysis of structure–function relationships in the unusual Var1 protein.Key words: Saccharomyces cerevisiae, VAR1 gene, mitochondria, ribosome assembly, gene relocation, RNA processing, nuclear–mitochondrial interaction.

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Variability in nuclear DNA among nonhuman primates: Application of molecular genetic techniques to intra- and inter-species genetic analyses

American Journal of Primatology ◽

10.1002/ajp.1350270205 ◽

1992 ◽

Vol 27 (2) ◽

pp. 93-105 ◽

Cited By ~ 7

Author(s):

J. Rogers ◽

G. Ruano ◽

K. K. Kidd

Keyword(s):

Nonhuman Primates ◽

Nuclear Dna ◽

Molecular Genetic ◽

Genetic Analyses ◽

Genetic Techniques

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DNA authentication of brewery products: basic principles and methodological approaches

Foods and raw materials ◽

10.21603/2308-4057-2019-2-364-374 ◽

2019 ◽

pp. 364-374 ◽

Cited By ~ 1

Author(s):

Lev Oganesyants ◽

Ramil Vafin ◽

Aram Galstyan ◽

Anastasia Ryabova ◽

Sergey Khurshudyan ◽

...

Keyword(s):

Hordeum Vulgare ◽

Nucleic Acids ◽

Dna Extraction ◽

Nuclear Dna ◽

Molecular Genetic ◽

Molecular Genetic Analysis ◽

Snp Markers ◽

Pcr Analysis ◽

Malting Barley ◽

Barley Malt

Beer DNA authentication is the process of authentication by identification of barley malt Hordeum vulgare or its substitutes, as well as hops and yeast. The method is based on molecular genetic analysis of residual quantities of nucleic acids extracted from the cellular debris of the final product. The aim of the study was to analyse scientific and methodical approaches to extraction of residual quantities of beer raw materials nucleic acids and beer DNA authentication for their later application in determining brewing products authenticity. The technological level discloses the method of DNA extraction from wines, modified for extraction of nucleic acids from beer samples. The method includes the following characteristic peculiarities: stage enzymatic hydrolysis of polysaccharides and polypeptides of dissolved lyophilisate, multiple sedimentation and resursuspension of nucleoproteid complex, RNA removal followed by DNA extraction by organic solvents, and additional DNA purification by magnetic particle adsorption. This review presents the analysis of genetic targets used as molecular markers for gene identification of malting barley varieties and beer DNA authentication. We also provided the interpretation of PCR analysis of Hordeum vulgare varieties and samples of commercial beer. Data on SSR- and SNP-markers of Hordeum vulgare nuclear DNA, used for barley varieties identification and potentially suitable for beer DNA authentication, are also presented. We also analysed genetic targets used in malting barley substitute detection, as well as hops and yeast identification in beer. Data on correlation of amplified DNA targets with beer quality indicators were systematised.

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Taxonomic Evaluation of Hedera crebrescens: A Potentially Invasive Ivy in Central Europe

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.8935 ◽

2020 ◽

Vol 89 (3) ◽

Cited By ~ 1

Author(s):

Enikő Ibolya Major ◽

Endre György Tóth ◽

Márta Bényei-Himmer ◽

Mária Höhn

Keyword(s):

Central Europe ◽

Invasive Plant ◽

Nuclear Dna ◽

Molecular Genetic ◽

Phylogenetic Reconstruction ◽

Diploid Species ◽

Taxonomic Status ◽

Molecular Genetic Analysis ◽

Reproductive Capacity ◽

Species Specific

Although Hedera helix is the only native ivy distributed in Central Europe, other ivy species are cultivated in this region and have horticultural importance, including H. hibernica, H. colchica, and H. azorica. On the basis of morphological, cytological, and phenological studies, a newly identified diploid species of ivy, H. crebrescens Bényei-Himmer & Höhn, was recently described from Hungary. Due to its high reproductive capacity and vigorous growth, this species can be considered a potentially invasive plant that could readily supplant H. helix in its native habitats. To characterize the molecular taxonomic status of H. crebrescens, we conducted a molecular genetic analysis based on five chloroplast and one nuclear DNA regions. Our phylogenetic reconstruction supported the monophyly of Hedera, with a tree topology similar to that previously obtained based on phylogenetic cpDNA analyses. Mediterranean species of ivy were well separated from the remainder of the European species, as well as from Asian species. Hedera crebrescens represented a single independent haplotype within the Asian–European cluster, whereas H. helix proved to be polyphyletic. The detected species-specific haplotype and invariability among studied specimens obtained from different geographical locations, provide support for the taxonomical autonomy of H. crebrescens.

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Pathology of Adult and Paediatric Mitochondrial Myopathies

10.20944/preprints201706.0059.v1 ◽

2017 ◽

Author(s):

Rahul Phadke

Keyword(s):

Nuclear Dna ◽

Molecular Genetic ◽

Mitochondrial Diseases ◽

Molecular Genetic Analysis ◽

Muscle Pathology ◽

Respiratory Chain Enzyme ◽

Metabolic Functions ◽

Atp Generation ◽

Next Generation Sequencing Ngs

Mitochondria are dynamic organelles ubiquitously present in nucleated eukaryotic cells, subserving multiple metabolic functions, including cellular ATP generation by oxidative phosphorylation (OXPHOS). The OXPHOS machinery comprises five transmembrane respiratory chain enzyme complexes (RC). Defective OXPHOS gives rise to mitochondrial diseases (mtD). The incredible phenotypic and genetic diversity of mtD can be attributed at least in part to the RC dual genetic control (nuclear DNA [nDNA] and mitochondrial DNA [mtDNA]) and the complex interaction between the two genomes. Despite the increasing use of next-generation-sequencing (NGS) and various -omics platforms in unraveling novel mtD genes and pathomechanisms, current clinical practice for investigating mtD essentially involves a multipronged approach including clinical assessment, metabolic screening, imaging, pathological, biochemical and functional testing to guide molecular genetic analysis. This review addresses the broad muscle pathology landscape including genotype-phenotype correlations in adult and paediatric mtD, the role of immunodiagnostics in understanding some of the pathomechanisms underpinning the canonical features of mtD, and recent diagnostic advances in the field.

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Molecular Characterization and Genetic Diversity Study in F3 Population of Rice

Progressive Agriculture ◽

10.3329/pa.v20i1-2.16839 ◽

2013 ◽

Vol 20 (1-2) ◽

pp. 1-8

Author(s):

MM Rahman ◽

L Rahman ◽

SN Begum ◽

F Nur

Keyword(s):

Genetic Distance ◽

Gene Diversity ◽

Random Amplified Polymorphic Dna ◽

Molecular Genetic ◽

Molecular Genetic Analysis ◽

Polymorphic Loci ◽

Rice Genotypes ◽

High Level ◽

Genetic Diversity Study ◽

Diversity Study

Random Amplified Polymorphic DNA (RAPD) assay was initiated for molecular genetic analysis among 13 F3 rice lines and their parents. Four out of 15 decamer random primers were used to amplify genomic DNA and the primers yielded a total of 41 RAPD markers of which 37 were considered as polymorphic with a mean of 9.25 bands per primer. The percentage of polymorphic loci was 90.24. The highest percentage of polymorphic loci (14.63) and gene diversity (0.0714) was observed in 05-6 F3 line and the lowest polymorphic loci (0.00) and gene diversity (0.00) was found in 05-12 and 05-15 F3 lines. So, relatively high level of genetic variation was found in 05-6 F3 line and it was genetically more diverse compared to others. The average co-efficient of gene differentiation (GST) and gene flow (Nm) values across all the loci were 0.8689 and 0.0755, respectively. The UPGMA dendrogram based on the Neis genetic distance differentiated the rice genotypes into two main clusters: PNR-519, 05-19, 05-14, 05-12 and 05-17 grouped in cluster 1. On the other hand, Baradhan, 05-9, 05-13, 05-11, 05-5, 05-6, 05-1, 05-4, 05-15 and 05-25 were grouped in cluster 2. The highest genetic distance (0.586) was found between 05-4 and 05-17 F3 lines and they remain in different cluster.DOI: http://dx.doi.org/10.3329/pa.v20i1-2.16839 Progress. Agric. 20(1 & 2): 1 8, 2009

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Diagnosis and Management of Cardiomyopathies – A Focus on Genetics, Cardiac Magnetic Resonance and Clinical Features

European Cardiology Review ◽

10.15420/ecr.2011.7.3.225 ◽

2011 ◽

Vol 7 (3) ◽

pp. 225

Author(s):

Gianfranco Sinagra ◽

Michele Moretti ◽

Giancarlo Vitrella ◽

Marco Merlo ◽

Rossana Bussani ◽

...

Keyword(s):

Clinical Practice ◽

Cardiac Magnetic Resonance ◽

Magnetic Resonance ◽

Imaging Techniques ◽

Molecular Genetic ◽

Molecular Genetic Analysis ◽

Routine Clinical Practice ◽

Clinical Approach ◽

Diagnosis And Management ◽

Made In

In recent years, outstanding progress has been made in the diagnosis and treatment of cardiomyopathies. Genetics is emerging as a primary point in the diagnosis and management of these diseases. However, molecular genetic analyses are not yet included in routine clinical practice, mainly because of their elevated costs and execution time. A patient-based and patient-oriented clinical approach, coupled with new imaging techniques such as cardiac magnetic resonance, can be of great help in selecting patients for molecular genetic analysis and is crucial for a better characterisation of these diseases. This article will specifically address clinical, magnetic resonance and genetic aspects of the diagnosis and management of cardiomyopathies.

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