scholarly journals Identification and Monitoring of Amomi Fructus and its Adulterants Based on DNA Barcoding Analysis and Designed DNA Markers

Molecules ◽  
2019 ◽  
Vol 24 (22) ◽  
pp. 4193 ◽  
Author(s):  
Eui Jeong Doh ◽  
Jung-Hoon Kim ◽  
Guemsan Lee
Keyword(s):  
Dna Barcoding ◽  
Dna Markers ◽  
Dna Marker ◽  
Intergenic Spacer ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Traditional Medicines ◽  
Amomum Villosum ◽  
Reliable Methods ◽  
A New Species

Amomi Fructus is one of the traditional medicines derived from the ripe fruits of the Zingiberaceae family of plants, which include Amomum villosum, A. villosum var. xanthioides, and A. longiligulare. Owing to their highly similar morphological traits, several kinds of adulterants of Amomi Fructus have been reported. Therefore, accurate and reliable methods of identification are necessary in order to ensure drug safety and quality. We performed DNA barcoding using five regions (ITS, matK, rbcL, rpoB, and trnL-F intergenic spacer) of 23 Amomi Fructus samples and 22 adulterants. We designed specific DNA markers for Amomi Fructus based on the single nucleotide polymorphisms (SNPs) in the ITS. Amomi Fructus was well separated from the adulterants and was classified with the species of origin based on the detected SNPs from the DNA barcoding results. The AVF1/ISR DNA marker for A. villosum produced a 270 bases amplified product, while the ALF1/ISF DNA marker produced a 350 bases product specific for A. longiligulare. Using these DNA markers, the monitoring of commercially distributed Amomi Fructus was performed, and the monitoring results were confirmed by ITS analysis. This method identified samples that were from incorrect origins, and a new species of adulterant was also identified. These results confirmed the accuracy and efficiency of the designed DNA markers; this method may be used as an efficient tool for the identification and verification of Amomi Fructus.

Sex Differences in Childhood Associations between DNA Markers and General Cognitive Ability

2007 ◽  
Vol 28 (3) ◽  
pp. 161-164 ◽  
Author(s):  
Rosalind Arden ◽  
Nicole Harlaar ◽  
Robert Plomin
Keyword(s):  
Sex Differences ◽  
Single Nucleotide Polymorphisms ◽  
Cognitive Ability ◽  
Dna Markers ◽  
Community Sample ◽  
Nucleotide Polymorphisms ◽  
General Cognitive Ability ◽  
Single Nucleotide ◽  
The Difference

Abstract. An association between intelligence at age 7 and a set of five single-nucleotide polymorphisms (SNPs) has been identified and replicated. We used this composite SNP set to investigate whether the associations differ between boys and girls for general cognitive ability at ages 2, 3, 4, 7, 9, and 10 years. In a longitudinal community sample of British twins aged 2-10 (n > 4,000 individuals), we found that the SNP set is more strongly associated with intelligence in males than in females at ages 7, 9, and 10 and the difference is significant at 10. If this finding replicates in other studies, these results will constitute the first evidence of the same autosomal genes acting differently on intelligence in the two sexes.

In search for polymorphic DNA markers to increase resistance and production level of hens

2020 ◽  
Vol 1 (12) ◽  
pp. 98-104
Author(s):  
I. I. Kochish ◽  
◽  
О. V. Myasnikova ◽  
V. V. Martynov ◽  
V. I. Smolensky ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Dopamine Receptor ◽  
Dna Markers ◽  
Production Level ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Pcr Rflp ◽  
Productive Traits ◽  
Pure Lines ◽  
The Relationship

In the article, the authors assess the prospect of using genetic polymorphisms to predict resistance to diseases and a possible enlarge in chicken production level. Using the PCR-RFLP method, we analyzed the SNP frequencies in the genes of myostatin (MSTN, or GDF-8), proopiomelanocortin (POMC), and dopamine receptor D2 (DRD2) in chickens of the pure lines of the Smena-8 broiler hybreed – B6, B7m / o (slow-feathering), B7b / o (fast-fledging) FSBI "Breeding and Genetic Center “Smena”. The relationship between the studied single nucleotide polymorphisms and the productive traits of chickens was determined. The assessment of the possibilities of using polymorphisms to increase the resistance and productivity of linear birds.

scholarly journals Strategy for Identification of Bacillus cereus and Bacillus thuringiensis Strains Closely Related to Bacillus anthracis

2006 ◽  
Vol 72 (2) ◽  
pp. 1295-1301 ◽  
Author(s):  
Daniele Daffonchio ◽  
Noura Raddadi ◽  
Maya Merabishvili ◽  
Ameur Cherif ◽  
Lorenzo Carmagnola ◽  
...  
Keyword(s):  
Bacillus Cereus ◽  
Restriction Site ◽  
Intergenic Spacer ◽  
23S Rrna ◽  
Trna Genes ◽  
Nucleotide Polymorphisms ◽  
Efficient Tool ◽  
Single Nucleotide ◽  
The Relationship ◽  
Different Origin

ABSTRACT Bacillus cereus strains that are genetically closely related to B. anthracis can display anthrax-like virulence traits (A. R. Hoffmaster et al., Proc. Natl. Acad. Sci. USA 101:8449-8454, 2004). Hence, approaches that rapidly identify these “near neighbors” are of great interest for the study of B. anthracis virulence mechanisms, as well as to prevent the use of such strains for B. anthracis-based bioweapon development. Here, a strategy is proposed for the identification of near neighbors of B. anthracis based on single nucleotide polymorphisms (SNP) in the 16S-23S rRNA intergenic spacer (ITS) containing tRNA genes, characteristic of B. anthracis. By using restriction site insertion-PCR (RSI-PCR) the presence of two SNP typical of B. anthracis was screened in 126 B. cereus group strains of different origin. Two B. cereus strains and one B. thuringiensis strain showed RSI-PCR profiles identical to that of B. anthracis. The sequencing of the entire ITS containing tRNA genes revealed two of the strains to be identical to B. anthracis. The strict relationship with B. anthracis was confirmed by multilocus sequence typing (MLST) of four other independent loci: cerA, plcR, AC-390, and SG-749. The relationship to B. anthracis of the three strains described by MLST was comparable and even higher to that of four B. cereus strains associated with periodontitis in humans and previously reported as the closest known strains to B. anthracis. SNP in ITS containing tRNA genes combined with RSI-PCR provide a very efficient tool for the identification of strains closely related to B. anthracis.

scholarly journals A Fresh Look at Grape Powdery Mildew (Erysiphe necator) A and B Genotypes Revealed Frequent Mixed Infections and Only B Genotypes in Flag Shoot Samples

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1156 ◽  
Author(s):  
Anett Csikós ◽  
Márk Z. Németh ◽  
Omer Frenkel ◽  
Levente Kiss ◽  
Kálmán Zoltán Váczy
Keyword(s):  
Powdery Mildew ◽  
Biological Significance ◽  
Intergenic Spacer ◽  
Nuclear Ribosomal Dna ◽  
Nucleotide Polymorphisms ◽  
Temporal Isolation ◽  
Single Nucleotide ◽  
Erysiphe Necator ◽  
The World ◽  
Genotype A

Erysiphe necator populations, causing powdery mildew of grapes, have a complex genetic structure. Two genotypes, A and B, were identified in most vineyards across the world on the basis of fixed single nucleotide polymorphisms (SNPs) in several DNA regions. It was hypothesized that A populations overwinter as mycelia in grapevine buds, giving rise to so-called flag shoots in spring, and are more sensitive to fungicides than B populations, which overwinter as ascospores and become widespread later in the season. Other studies concluded that the biological significance of these genotypes is unclear. In the spring of 2015, there was a unique opportunity to collect E. necator samples from flag shoots in Hungary. The same grapevines were sampled in summer and autumn as well. A total of 182 samples were genotyped on the basis of β-tubulin (TUB2), nuclear ribosomal DNA (nrDNA) intergenic spacer (IGS), and internal transcribed spacer (ITS) sequences. Genotypes of 56 samples collected in 2009–2011 were used for comparison. Genotype A was not detected at all in spring, and was present in only 19 samples in total, mixed with genotype B, and sometimes with another frequently found genotype, designated as B2. These results did not support the hypothesis about temporal isolation of the two genotypes and indicated that these are randomly distributed in vineyards.

scholarly journals JUSTIFICATION OF CANDIDATE POLYMORPHISMS USAGE IN MARKER-ASSISTED SELECTION OF UKRAINIAN MEATY PIG BREED

2020 ◽  
pp. 149-156
Author(s):  
Vladimir Rossokha ◽  
Yelyzaveta Oliinychenko ◽  
Yelena Boyko ◽  
Elena Zaderikhina
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Dna Markers ◽  
Population Analysis ◽  
Farm Animals ◽  
Nucleotide Polymorphisms ◽  
Economic Traits ◽  
Genetic Population ◽  
Single Nucleotide ◽  
Marker Selection ◽  
Genotype Frequencies

Effective selection in pig breeding is not possible without involvement of new approaches which involve the assessment animal genotypes at the DNA level. The development of methods for determining the polymorphisms in candidate genes that are responsible for the manifestation of economic traits is the basis of modern marker selection technology (MAS). Currently, a number of DNA markers have been developed for use in the breeding of farm animals. In this case, the most informative were single nucleotide polymorphisms (SNPs) of genes. However, despite the significant amount of scientific research, the problem of development and implementation of DNA markers for breeds of Ukrainian selection remains relevant. The results of SNPs study of RYR1, CTSF and CTSD genes by PCR-RFLP method are presented. The initial stage for implementing marker selection for single nucleotide polymorphisms is conducting genetic-population analysis in the studied population of Ukrainian Meaty pig breed. It was found that SNP RYR1 g. 1843 C>T was characterized by low polymorphism, the minor allele g. 1843 T met with a frequency of q = 0.05. SNP CTSD g. 70 G>A had a low level of representativeness, allele g. 70 A prevailed at a frequency of q = 0.92. It was found that SNP CTSF g. 22 G>C was characterized by a sufficient level of representativeness, both alleles were detected with a predominance of the allele frequency g. 22 G (q=0.80). In the population of Ukrainian Meaty pig breed, there was a statistically confirmed deviation of genotype frequencies from SNP-balanced CTSF g. 22 G> C (χ2 = 28.125) and CTSD g. 70 G> A (χ2 = 26,518). In the future, SNPs of CTSF, CTSD genes can be used for associative studies to find a link between markers and signs of pig productivity and the introduction of marker-associated selection in the UM pig breed.

scholarly journals Single Nucleotide Polymorphisms Are Suitable For Assessing The Success of Restocking Efforts of The European Lobster (Homarus Gammarus, L.)

2021 ◽  
Author(s):  
Pierre De Wit ◽  
Linda Svanberg ◽  
Isabel Casties ◽  
Susanne P Eriksson ◽  
Kristina Sundell ◽  
...  
Keyword(s):  
Dna Marker ◽  
Nucleotide Polymorphisms ◽  
Population Assignment ◽  
Single Nucleotide ◽  
Swedish West Coast ◽  
European Lobster ◽  
Homarus Gammarus ◽  
Snp Panel ◽  
First Time ◽  
A Current

Abstract The European lobster (Homarus gammarus) forms the base of an important fishery along the coasts of Europe. However, stocks have been in decline for many years, prompting new regulations in the fishery and also restocking efforts. An important feature of any restocking effort is the assessment of success in the number of released juveniles that stay and become adult over time. Here, we tested the power of a SNP DNA marker panel developed for population assignment to correctly infer parentage on the maternal side of lobster larvae, in the absence of known fathers, using lobsters included in a current restocking effort on the Swedish west coast. We also examined the power to reconstruct the unknown paternal genotypes, and examined the number of fathers for each larval clutch. We found that the 96-SNP panel, despite only containing 78 informative markers, allowed us to assign all larvae to the correct mother. Furthermore, with 10 genotyped larvae or more, confident paternal genotypes could be reconstructed. We also found that 15 out of 17 clutches were full siblings, whereas two clutches had two fathers. To our knowledge, this is the first time a SNP panel of this size has been used to assess parentage in a crustacean restocking effort. Our conclusion is that the panel works well, and that it could be an important tool for the assessment of restocking success of H. gammarus in the future.

scholarly journals Detection of one large insertion/deletion (indel) and two novel SNPs within the <i>SPEF2</i> gene and their associations with male piglet reproduction traits

2016 ◽  
Vol 59 (2) ◽  
pp. 275-283 ◽  
Author(s):  
Rui Chen ◽  
Shuai Yu ◽  
Fa Ren ◽  
Xiao Yan Lv ◽  
Chuan Ying Pan
Keyword(s):  
Dna Marker ◽  
Male Reproduction ◽  
Nucleotide Polymorphisms ◽  
Chromosome 16 ◽  
Large White ◽  
Single Nucleotide ◽  
Association Testing ◽  
Normal Sperm ◽  
Reproduction Traits ◽  
Large Insertion

Abstract. The sperm flagella 2 (SPEF2) gene is essential for normal sperm tail development and male fertility. To fully characterize the structure of the mutation and to further study the function of the pig SPEF2 gene, we explored the insertion/deletion (indel) and novel single-nucleotide polymorphisms (SNPs) within the pig SPEF2 gene, and tested their associations with the testicular sizes in male Large White (LW) and Landrace (LD) pigs from China. Herein, a large insertion located at the SPEF2 gene in chromosome 16 was found, and two alleles of "I" (insertion) and "D" (deletion) were designated. Allele "D" was dominant in all analyzed pigs. Two novel SNPs (namely (NC_010458) g.19642G > A, resulting in AfaI aCRS PCR–PFLP, and g.19886C > G, resulting in EcoRI aCRS PCR–PFLP) were found in LW and LD pigs. Association testing revealed that g.19886C > G was significantly associated with the testis long circumference (TLC) in LW pigs (P < 0.05), suggesting that this SNP would be the DNA marker for the marker-assisted selection (MAS) in reproduction traits. This preliminary result indicates that the pig SPEF2 gene had significant effects on male reproduction traits. These findings could not only extend the spectrum of genetic variations in the pig SPEF2 gene but also contribute to implementing MAS in genetics and breeding in pigs.

Intergenic Spacer Single Nucleotide Polymorphisms for Genotyping Amylostereum areolatum (Russulales: Amylostereacea) Symbionts of Native and Non-native Sirex Species

2020 ◽  
Vol 113 (4) ◽  
pp. 280-287 ◽  
Author(s):  
Rabiu O Olatinwo ◽  
Timothy D Schowalter ◽  
Daniel Doucet ◽  
Susan Bowman ◽  
Wood C Johnson ◽  
...  
Keyword(s):  
North America ◽  
Single Nucleotide Polymorphisms ◽  
Genetic Markers ◽  
Native Species ◽  
Intergenic Spacer ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Sirex Noctilio ◽  
Single Nucleotide ◽  
Sirex Nigricornis

Abstract In North America Amylostereum areolatum (Chaillet ex Fr.) Boidin is a fungal symbiont associated with both the non-native Sirex noctilio Fabricius (Hymenoptera: Siricidae) and less commonly the native Sirex nigricornis Fabricius (Hymenoptera: Siricidae) woodwasps. The relationship between S. noctilio and A. areolatum constitutes a serious threat to pine plantation in the southern hemisphere. Studies have shown evidence of exchange of symbionts between non-native and native Sirex species. Our objectives were 1) to identify and assemble a panel of rDNA intergenic spacer–single nucleotide polymorphisms (IGS-SNPs) for genotyping strains of A. areolatum symbionts associated with Sirex species in North America, and 2) to develop genetic markers for monitoring the spread of specific A. areolatum haplotypes associated with S. noctilio across regions. The IGS-SNPs panel analyzed included haplotypes B1, B2, D1, D2 (from known IGS type B and D), E, and F. Genetic markers and haplotype-specific primers were designed to detect the IGS haplotypes D and E of A. areolatum. We found that haplotype D was absent in A. areolatum from S. nigricornis in Louisiana, while haplotype E was detected in all A. areolatum from S. nigricornis in Canada and Louisiana. Both haplotype D and E were co-detected in approximately 5% of samples from Canada. The IGS-SNP markers detected specific haplotypes accurately. Observing haplotype D in any A. areolatum from the native S. nigricornis likely indicates the presence of the potentially harmful S. noctilo-A. areolatum complex. The work highlights how IGS-SNPs can help in early detection without direct occurrence/observations of the non-native species of concern.

scholarly journals Single nucleotide polymorphisms are suitable for assessing the success of restocking efforts of the European lobster (Homarus gammarus, L.)

2021 ◽  
Author(s):  
Pierre De Wit ◽  
Linda Svanberg ◽  
Isabel Casties ◽  
Susanne P. Eriksson ◽  
Kristina Sundell ◽  
...  
Keyword(s):  
Dna Marker ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Swedish West Coast ◽  
European Lobster ◽  
Homarus Gammarus ◽  
Snp Panel ◽  
First Time ◽  
A Current

AbstractThe European lobster (Homarus gammarus) forms the base of an important fishery along the coasts of Europe. However, stocks have been in decline for many years, prompting new regulations in the fishery and also restocking efforts. An important feature of any restocking effort is the assessment of success in the number of released juveniles that stay and become adult over time. Here, we tested the power of a single nucleotide polymorphism (SNP) DNA marker panel developed for population assignment to correctly infer parentage on the maternal side of lobster larvae, in the absence of known fathers, using lobsters included in a current restocking effort on the Swedish west coast. We also examined the power to reconstruct the unknown paternal genotypes, and examined the number of fathers for each larval clutch. We found that the 96-SNP panel, despite only containing 78 informative markers, allowed us to assign all larvae to the correct mother. Furthermore, with ten genotyped larvae or more, confident paternal genotypes could be reconstructed. We also found that 15 out of 17 clutches were full siblings, whereas two clutches had two fathers. To our knowledge, this is the first time a SNP panel of this size has been used to assess parentage in a crustacean restocking effort. Our conclusion is that the panel works well, and that it could be an important tool for the assessment of restocking success of H. gammarus in the future.

Nuclear receptors in disease: the oestrogen receptors

2004 ◽  
Vol 40 ◽  
pp. 157-167 ◽  
Author(s):  
Maria Nilsson ◽  
Karin Dahlman-Wright ◽  
Jan-Åke Gustafsson
Keyword(s):  
Nuclear Receptors ◽  
Target Genes ◽  
Receptor Subtype ◽  
Target Tissue ◽  
Oestrogen Receptors ◽  
Nucleotide Polymorphisms ◽  
Cell Type ◽  
Single Nucleotide ◽  
Beneficial Effects ◽  
The Family

For several decades, it has been known that oestrogens are essential for human health. The discovery that there are two oestrogen receptors (ERs), ERalpha and ERbeta, has facilitated our understanding of how the hormone exerts its physiological effects. The ERs belong to the family of ligand-activated nuclear receptors, which act by modulating the expression of target genes. Studies of ER-knockout (ERKO) mice have been instrumental in defining the relevance of a given receptor subtype in a certain tissue. Phenotypes displayed by ERKO mice suggest diseases in which dysfunctional ERs might be involved in aetiology and pathology. Association between single-nucleotide polymorphisms (SNPs) in ER genes and disease have been demonstrated in several cases. Selective ER modulators (SERMs), which are selective with regard to their effects in a certain cell type, already exist. Since oestrogen has effects in many tissues, the goal with a SERM is to provide beneficial effects in one target tissue while avoiding side effects in others. Refined SERMs will, in the future, provide improved therapeutic strategies for existing and novel indications.

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