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1. Technical note: Performing LR calculations when loci are missing between reference and trace DNA profiles

Author:
Irene Bouwman; Jerry Hoogenboom; Titia Sijen; Corina C.G. Benschop
Source:
Forensic science international 2022 v.5 pp. 100268
ISSN:
2665-9107
Subject:
DNA fingerprinting,   etc   ; forensic sciences; loci; weight-of-evidence;     Show all 4 Subjects
Abstract:
... The initial version of DNAStatistX calculated likelihood ratios (LRs) using only loci present in both the trace and reference profiles, thereby ignoring loci from the trace that are not present in the reference. Here, DNAStatistX was adapted to include all trace loci. At loci missing in the reference, an unknown contributor was invoked. Although this strategy is already incorporated in other syste ...
DOI:
10.1016/j.fsir.2022.100268

2. Kit‐Based Sampling by Trained Fishers Yields Successful DNA Identification of Depredating Shark Species in the Marianas

Author:
Maryann K. Webb; Derek W. Kraft; Madison N. Hampp; Carl G. Meyer
Source:
Marine and coastal fisheries 2022 v.14 no.3 pp. e10204
ISSN:
1942-5120
Subject:
DNA fingerprinting,   etc   ; corals; line fisheries; mitochondrial DNA; predation; sharks; transfer DNA;     Show all 7 Subjects
Abstract:
... Shark depredation is a worldwide yet not well understood problem that is responsible for economic losses in both commercial and recreational fisheries. We collaborated with fishers from the Mariana Islands in the western Pacific to identify depredating shark species via mitochondrial DNA (mtDNA) barcoding of partially consumed fish from real‐world depredation events. Trained fishers collected swab ...
DOI:
10.1002/mcf2.10204

3. DNA Identification and Diversity of the Vector Mosquitoes Culex pipiens s.s. and Culex torrentium in Belgium (Diptera: Culicidae)

Author:
Ann Vanderheyden; Nathalie Smitz; Katrien De Wolf; Isra Deblauwe; Wouter Dekoninck; Kenny Meganck; Sophie Gombeer; Adwine Vanslembrouck; Jacobus De Witte; Anna Schneider; Ingrid Verlé; Marc De Meyer; Thierry Backeljau; Ruth Müller; Wim Van Bortel
Source:
Diversity 2022 v.14 no.6 pp. -
ISSN:
1424-2818
Subject:
DNA fingerprinting,   etc   ; Culex pipiens; Wolbachia; biotypes; haplotypes; introgression; loci; surveys; sympatry; Belgium;     Show all 10 Subjects
Abstract:
... This survey reports on the DNA identification and occurrence of Culex torrentium and Cx. pipiens s.s. in Belgium. These native disease-vector mosquito species are morphologically difficult to separate, and the biotypes of Cx. pipiens s.s. are morphologically indistinguishable. Culex torrentium and Cx. pipiens s.s. were identified using the COI and ACE2 loci. We recorded 1248 Cx. pipiens s.s. and 4 ...
DOI:
10.3390/d14060486

4. A Pipeline NanoTRF as a New Tool for De Novo Satellite DNA Identification in the Raw Nanopore Sequencing Reads of Plant Genomes

Author:
Ilya Kirov; Elizaveta Kolganova; Maxim Dudnikov; Olga Yu. Yurkevich; Alexandra V. Amosova; Olga V. Muravenko
Source:
Plants 2022 v.11 no.16 pp. -
ISSN:
2223-7747
Subject:
DNA fingerprinting,   etc   ; bioinformatics; chromosomes; fish; genome; genome assembly; information sources; nanopores; satellite DNA; satellites;     Show all 10 Subjects
Abstract:
... High-copy tandemly organized repeats (TRs), or satellite DNA, is an important but still enigmatic component of eukaryotic genomes. TRs comprise arrays of multi-copy and highly similar tandem repeats, which makes the elucidation of TRs a very challenging task. Oxford Nanopore sequencing data provide a valuable source of information on TR organization at the single molecule level. However, bioinform ...
DOI:
10.3390/plants11162103

5. 18S ribosomal DNA-based PCR test for avian and mammalian DNA identification in meat products

Author:
Irina M. Zyrianova; Oleg G. Zaripov
Source:
Veterinary and Animal Science 2022 v.15 pp. 100234
ISSN:
2451-943X
Subject:
DNA fingerprinting,   etc   ; Amphibia; Mammalia; Reptilia; agarose; chickens; gels; meat; phylogeny; ribosomal RNA; sausages; sheep; statistical analysis;     Show all 13 Subjects
Abstract:
... This work has aimed to create a PCR test to identify avian and mammalian DNA in meat products. The test is based on phylogenetic analysis of 18S ribosomal RNA (rRNA) of four major groups of Tetrapod: Amphibia, Reptilia, Mammalia, and Aves. 18S rDNA complete coding sequences from GenBank have been used for phylogenetic analysis by the Maximum Likelihood method. The alignment of these 18S rDNA seque ...
DOI:
10.1016/j.vas.2022.100234

6. Label-free detection of DNA methylation by surface-enhanced Raman spectroscopy using zirconium-modified silver nanoparticles

Author:
Yuan Zhang; De-Sheng Zhan; Xiao-Ying Xu; Zhe Zhang; Mahmoud Elsayed Hafez; Yue He; Yang Li; Da-Wei Li
Source:
Talanta 2023 v.253 pp. 123941
ISSN:
0039-9140
Subject:
DNA fingerprinting,   etc   ; DNA; DNA methylation; Raman spectroscopy; adenine; cytosine; epigenetics; genes; hydrophobicity; nanosilver; principal component analysis; zirconium;     Show all 12 Subjects
Abstract:
... DNA methylation is an important feature of gene epigenetics that affects the metabolic process of organisms. Although surface-enhanced Raman spectroscopy (SERS) has demonstrated great potential in label-free DNA detection, discriminating the various processes involved in DNA methylation remains a challenge. DNA molecules fold themselves, wrapping the hydrophobic bases, thus making it difficult for ...
DOI:
10.1016/j.talanta.2022.123941

7. Elevated temperature may reduce functional but not taxonomic diversity of fungal assemblages on decomposing leaf litter in streams

Author:
Encarnación Fenoy; Arunava Pradhan; Cláudia Pascoal; Juan Rubio‐Ríos; Daniela Batista; Francisco J. Moyano‐López; Fernanda Cássio; J. Jesús Casas
Source:
Global change biology 2022 v.28 no.1 pp. 115-127
ISSN:
1354-1013
Subject:
DNA fingerprinting,   etc   ; carbon; cold; ecosystems; functional diversity; global change; leaves; plant litter; riparian vegetation; species richness; temperature; water;     Show all 12 Subjects
Abstract:
... Mounting evidence points to a linkage between biodiversity and ecosystem functioning (B‐EF). Global drivers, such as warming and nutrient enrichment, can alter species richness and composition of aquatic fungal assemblages associated with leaf‐litter decomposition, a key ecosystem process in headwater streams. However, effects of biodiversity changes on ecosystem functions might be countered by th ...
DOI:
10.1111/gcb.15931

8. New problems of environmental ecology: ticks and tick‐borne pathogens in city parks of Ukraine

Author:
Valentyna Kolomiiets; Patrycja Rakowska; Anna Rymaszewska
Source:
Environmental microbiology reports 2022 v.14 no.4 pp. 591-594
ISSN:
1758-2229
Subject:
DNA fingerprinting,   etc   ; Dermacentor reticulatus; Rickettsia; epidemiology; gene amplification; habitats; host seeking; humans; microbiology; risk; summer; urban areas; Ukraine;     Show all 13 Subjects
Abstract:
... City parks of Vinnytsia, Ukraine, were examined for the occurrence of host‐seeking ticks and collected specimens were examined for presence of rickettsial pathogens. In the summer season, the only collected individuals were Dermacentor reticulatus adults (n = 203). DNA identification of pathogens was conducted with the use of 16S rRNA gene amplification. Molecular analyses confirmed the presence o ...
DOI:
10.1111/1758-2229.13075

9. Microsatellite marker based diversity analysis and DNA fingerprinting of Asiatic cotton (Gossypium arboreum) varieties of India

Author:
H. B. Santosh; M. Meshram; V. Santhy; V. N. Waghmare
Source:
Journal of plant biochemistry and biotechnology 2022 v.31 no.2 pp. 421-428
ISSN:
0971-7811
Subject:
DNA fingerprinting,   etc   ; DNA; Gossypium arboreum; biotechnology; climate; cotton; diploidy; genetic markers; genetic variation; pedigree; plant biochemistry; probability; India;     Show all 13 Subjects
Abstract:
... Asiatic cotton (G. arboreum) is one of the important cultivated species of cotton originated in Indian subcontinent. Owing to its climate resilience, Asiatic cotton in particular and desi cotton in general, constitutes valuable genetic resources for cotton improvement to achieve sustainable cotton production in India. In the present study, 24 popular Asiatic cotton varieties were profiled using 30 ...
DOI:
10.1007/s13562-021-00675-z

10. Rapid, Highly Sensitive, and Label-Free Pathogen Assay System Using a Solid-Phase Self-Interference Recombinase Polymerase Amplification Chip and Hyperspectral Interferometry

Author:
Xiangyu Jin; Rongxin Fu; Wenli Du; Xiaohui Shan; Zeyin Mao; Anni Deng; Xue Lin; Ya Su; Han Yang; Wenqi Lv; Hao Zhong; Guoliang Huang
Source:
Analytical chemistry 2022 v.94 no.6 pp. 2926-2933
ISSN:
1520-6882
Subject:
DNA fingerprinting,   etc   ; Plasmodium falciparum; analytical chemistry; detection limit; fluorescence; genes; genotyping; interferometry; mutants; pathogen identification; pathogens; recombinase polymerase amplification; single nucleotide polymorphism;     Show all 13 Subjects
Abstract:
... Recombinase polymerase amplification (RPA) is a useful pathogen identification method. Several label-free detection methods for RPA amplicons have been developed in recent years. However, these methods still lack sensitivity, specificity, efficiency, or simplicity. In this study, we propose a rapid, highly sensitive, and label-free pathogen assay system based on a solid-phase self-interference RPA ...
DOI:
10.1021/acs.analchem.1c04858

11. Full Width at Half Maximum of Nanopore Current Blockage Controlled by a Single-Biomolecule Interface

Author:
Jun-Ge Li; Meng-Yin Li; Xin-Yi Li; Xue-Yuan Wu; Yi-Lun Ying; Yi-Tao Long
Source:
Langmuir 2022 v.38 no.3 pp. 1188-1193
ISSN:
1520-5827
Subject:
DNA fingerprinting,   etc   ; DNA; models; mutants; nanopores;     Show all 5 Subjects
Abstract:
... A biological nanopore is one of the predominant single-molecule approaches as a result of its controllable single-biomolecule interface, which could reflect the “intrinsic” information on an individual molecule in a label-free way. Because the current blockage is normally treated as the most important parameter for nanopore identification of every single molecule, the fluctuation of current blocka ...
DOI:
10.1021/acs.langmuir.1c02900

12. Rubus aetnicus Cupani ex Weston and R. canescens DC. (Rosaceae): an analysis

Author:
Abraham van de Beek; Gianniantonio Domina
Source:
Nordic journal of botany 2021 v.39 no.10 pp. -
ISSN:
0107-055X
Subject:
DNA fingerprinting,   etc   ; DNA; Rubus; botany; fields; journals; loci;     Show all 7 Subjects
Abstract:
... Beek (2016) argued that Rubus aetnicus Cupani ex Weston was the correct name of the taxon that was then called R. canescens DC., and which was previously known as R. tomentosus Borkh. Moreover, R. canescens was stated to be not identical with R. aetnicus, but rather a form of R. × collinus DC. Matzke‐Hajek (2016) raised objections to both statements. Therefore, the aim of this study was to thoroug ...
DOI:
10.1111/njb.03288

13. Y-Chromosome Markers in Population Genetics: Fundamental and Applied Results of Ethnogenomic Research

Author:
V. N. Kharkov
Source:
Russian journal of genetics 2021 v.57 no.9 pp. 989-1001
ISSN:
1022-7954
Subject:
DNA fingerprinting,   etc   ; DNA; Y chromosome; genes; humans; males; monophyly; phylogeography;     Show all 8 Subjects
Abstract:
... The Y chromosome is a unique tool for studying the structure of gene pools and the evolutionary history of human populations. Patrilinearity ensures the sequential accumulation of mutations, as a result of which the Y chromosome is a fairly simple marker system for reconstructing evolutionary changes, migration, and other demographic processes in human populations. The analysis of Y-chromosome hap ...
DOI:
10.1134/S1022795421090040

14. A novel twisted bud mutant from Ziziphus jujubaMill. ‘Dongzao’

Author:
Zhi Luo; LiHu Wang; FenFen Yan; ZhiGuo Liu; LiLi Wang; Xuan Zhao; LiXin Wang; Jin Zhao; JiuRui Wang; MengJun Liu
Source:
Scientia horticulturae 2022 v.295 pp. 110774
ISSN:
0304-4238
Subject:
DNA fingerprinting,   etc   ; Ziziphus jujuba; ascorbic acid; cultivars; fruits; germplasm; internode length; mutants;     Show all 8 Subjects
Abstract:
... The twisted growth of organs is a distinctive and attractive trait for woody plants. A bud mutant with twisted branches was discovered from ‘Dongzao’, the most popular and tasty table cultivar of Chinese jujube (Ziziphus jujuba Mill.). This study explored the morphological and nutritional characteristics and SSR marker changes of the novel variant. Compared to its mother plant and an external cont ...
DOI:
10.1016/j.scienta.2021.110774

15. Efficacy of a novel bone preprocessing method for better DNA yield

Author:
Subhasish Sahoo; Rashmita Samal; Sumit Biswas
Source:
Forensic science international 2021 v.325 pp. 110887
ISSN:
0379-0738
Subject:
DNA fingerprinting,   etc   ; DNA; bones; boning; disasters; forensic sciences; grinding; materials; people; sampling; teeth;     Show all 11 Subjects
Abstract:
... In cases involving identification of missing persons, mass disasters and ancient DNA investigations, bone and teeth samples are often the only, and almost always the best, biological material available for DNA profiling. Standard methods for extraction of DNA from such samples involve grinding of the bone and teeth samples. Here, we present an extremely efficient protocol for recovery of DNA from ...
DOI:
10.1016/j.forsciint.2021.110887

16. Geographical distribution and genetic diversity of Bradyrhizobium spp. isolated from Korean soybean root nodules

Author:
Ye-eun Kim; Hanseob Shin; Youri Yang; Hor-Gil Hur
Source:
Applied biological chemistry 2022 v.65 no.1 pp. 39
ISSN:
2468-0834
Subject:
DNA fingerprinting,   etc   ; DNA; agricultural land; chemistry; cultivars; genetic variation; geographical distribution; soybeans; temperature;     Show all 9 Subjects
Abstract:
... This study investigated the distribution and genetic diversity of the indigenous Bradyrhizobium spp. in the Korean agricultural field. A total of 254 Bradyrhizobium strains were isolated from 97 soybean samples (9 cultivars) collected in 14 regions. B. elkanii dominated in the southern regions, while B. diazoefficiens dominated in most central and northern regions. Through non-parametric multidime ...
DOI:
10.1186/s13765-022-00708-8

17. Identification and characterization of white onion (Allium cepa L.) genotypes for high total soluble solid content through molecular markers

Author:
Puthem Robindro Singh; Vijay Mahajan; Annu Verma; R. Sagar; Kuldip Jayaswall; Neeraj Shukla; Pranjali Gedam; Major Singh
Source:
Genetic resources and crop evolution 2021 v.68 no.3 pp. 957-967
ISSN:
0925-9864
Subject:
DNA fingerprinting,   etc   ; Allium cepa; DNA; bulbs; evolution; heterozygosity; introns; loci; onions; total soluble solids;     Show all 10 Subjects
Abstract:
... Onion (Allium cepa L.) is one of the most important bulbous vegetable used in global kitchen. Although it has various important traits but among them the high total soluble solid content (HTSS) of white onion is highly preferred by the industries for processing purpose. Looking into the broader use of the white onion; we utilized a total of 23 polymorphic simple sequence repeats (SSRs) and intron ...
DOI:
10.1007/s10722-020-01037-9

18. First case of a Great Spotted Woodpecker (Dendrocopos major) egg in a Cinereous Tit (Parus cinereus) nest

Author:
Jian Fang; Xudong Li; Wei Liang; Jiangping Yu; Haitao Wang; Guodong Yi; Romain Lorrilliere
Source:
Wilson journal of ornithology 2021 v.133 no.2 pp. 300-303
ISSN:
1559-4491
Subject:
DNA fingerprinting,   etc   ; Dendrocopos major; Parus; chicks; conservation areas; death; eggs; nests; ornithology; woodpeckers; China;     Show all 11 Subjects
Abstract:
... In the breeding season f 2018, we found a much larger egg in one nest of Cinereous Tit (Parus cinereus) in Zuojia Nature Reserve, Jilin Province, China. The tit pair abandoned their nest soon after the alien egg hatched, which resulted in the death of the foreign chick. Based on DNA identification, this foreign chick was confirmed as a Great Spotted Woodpecker (Dendrocopos major), suggesting that ...
DOI:
10.1676/19-00121

19. Intraspecific trait variability and genetic diversity in the adaptive strategies of serpentine and non-serpentine populations of Silene paradoxa L.

Author:
Lorenzo Lazzaro; Ilaria Colzi; Daniele Ciampi; Cristina Gonnelli; Lorenzo Lastrucci; Nadia Bazihizina; Daniele Viciani; Andrea Coppi
Source:
Plant and soil 2021 v.460 no.1-2 pp. 105-121
ISSN:
0032-079X
Subject:
DNA fingerprinting,   etc   ; Silene; gene pool; genetic drift; genetic variation; genome; leaves; serpentine; soil types;     Show all 9 Subjects
Abstract:
... AIMS: We investigated whether individuals of Silene paradoxa L., grown in serpentine and non-serpentine soils, displayed variation in functional traits and adaptive strategies together with a differentiation of the gene pool. We hypothesised that individuals growing in serpentine sites may be exposed to a higher degree of stress, resulting in measurable differences in leaf traits and adaptive stra ...
DOI:
10.1007/s11104-020-04780-1

20. Statistical Evaluation of Paternity Using Most Recent STR-Based Multiplex Systems

Author:
Pankaj Shrivastava; R. K. Kumawat; Shivani Dixit
Source:
Proceedings of the National Academy of Sciences, India, Section B: biological sciences 2021 v.91 no.3 pp. 575-580
ISSN:
0369-8211
Subject:
DNA fingerprinting,   etc   ; DNA; capillary electrophoresis; children; forensic sciences; humans; paternity; polymerase chain reaction; India;     Show all 9 Subjects
Abstract:
... Short Tandem Repeats (STRs) are widely accepted genetic tool for human identification. The present DNA technique based on STR, Polymerase Chain reaction (PCR) and capillary electrophoresis is the backbone of criminal investigation today. We present here statistical evaluation of a case of parentage determination in a trio match (mother, child and father) using different STR-based assays. DNA profi ...
DOI:
10.1007/s40011-021-01233-2