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 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.

scholarly journals Recorded captures of American lobster (Homarus americanus) in Swedish waters and an observation of predation on the European lobster (Homarus gammarus)

2017 ◽  
Vol 74 (10) ◽  
pp. 1503-1506 ◽  
Author(s):  
Vidar Øresland ◽  
Mats Ulmestrand ◽  
Ann-Lisbeth Agnalt ◽  
Gert Oxby
Keyword(s):  
Native Species ◽  
Homarus Americanus ◽  
American Lobster ◽  
Swedish West Coast ◽  
Marine Research ◽  
European Lobster ◽  
Homarus Gammarus ◽  
Genetic Sampling ◽  
Identification Measurements ◽  
First Time

The intentional or unintentional release of American lobsters (Homarus americanus), imported through the European seafood trade, has resulted in findings of H. americanus in European waters. A total of 36 specimens was recorded within a smaller area, halfway along the Swedish west coast, between 2008 and 2016. The lobsters were caught by both recreational and professional fishermen and delivered to the Institute of Marine Research in Lysekil, where species identification, measurements, and genetic sampling were performed. Twenty-five of these lobsters were caught inside the sill of the Gullmar Fjord, most of them close to Lysekil harbor, where escapes from an illegal holding is suspected. Six females had eggs, which in two cases were hybrids. While there is no evidence to suggest that a population has been established in the Gullmar Fjord or elsewhere in Swedish waters, serious concerns must be raised regarding the possible consequences for the native species. An American lobster has for the first time been filmed eating a killed European lobster (Homarus gammarus) in Swedish waters.

Year-class detection reveals climatic modulation of settlement strength in the European lobster, Homarus gammarus

2002 ◽  
Vol 59 (7) ◽  
pp. 1132-1143 ◽  
Author(s):  
M R.J Sheehy ◽  
R C.A Bannister
Keyword(s):  
Stock Assessment ◽  
Global Climate ◽  
Larval Settlement ◽  
European Lobster ◽  
Homarus Gammarus ◽  
Cross Correlation Analysis ◽  
Age Dependent ◽  
Intractable Problem ◽  
First Time

Understanding the nature of recruitment relationships in the European lobster, Homarus gammarus, has been an intractable problem because of difficulties associated with quantification of its scarce planktonic larvae and early benthic phase. We attempt to address this problem by analyzing the age composition of a population off the northeast coast of England. Age-dependent in situ deposits of neurolipofuscin in the eyestalk are used as an age index. An approach is presented that accounts and (or) corrects for the two most important potential sources of error in age determinations by this technique, namely environmental temperature variation and unexplained individual variation. This yields, for the first time in very long-lived clawed lobsters, reproducible catch age structures with year-class resolution. The method should be generally applicable to crustaceans. Cross-correlation analysis shows that larval settlement strength in the European lobster is associated with local sea temperatures and onshore winds in a manner similar to that reported for other lobsters. These findings have important implications for stock assessment, particularly the use of traditional models dependent on size and steady state, yield forecasting, the effects of global climate change, arguments about spawner protection or restocking, and the spawner–recruit relationship.

scholarly journals Heterozygous Ile453Val codon mutation in exon 7, homozygous single nucleotide polymorphisms in intron 2 and 5 of cathepsin C are associated with Haim-Munk syndrome

2014 ◽  
Vol 08 (01) ◽  
pp. 079-084 ◽  
Author(s):  
Nalini Aswath ◽  
Bhuminathan Swamikannu ◽  
Sankar Narayanan Ramakrishnan ◽  
Rajendran Shanmugam ◽  
Jayakar Thomas ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Direct Sequencing ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Heterozygous Condition ◽  
South Indian ◽  
The Subject ◽  
First Time ◽  
Intron 2

ABSTRACT Objective: In the present study, we have investigated the genetic status of CTSC gene in a HMS subject, who along with her parents belonged to non-Jewish South Indian Dravidian community. Materials and Methods: Genomic deoxyribonucleic acid isolated from the peripheral blood of the subject was amplified with CTSC exon specific primers and were analyzed by direct sequencing. Results: Sequencing analysis identified Ile453Val mutation within exon 7 of CTSC gene in heterozygous condition, and two single nucleotide polymorphisms (SNPs) within intron 2 and 5 in homozygous condition. Conclusion: The present study has identified for the first time the association of Ile453Val mutation within exon 7 and the two SNPs in a subject with HMS.

scholarly journals Evidence of adoption, monozygotic twinning, and low inbreeding rates in a large genetic pedigree of polar bears

2015 ◽  
Author(s):  
René M. Malenfant ◽  
David W. Coltman ◽  
Evan S. Richardson ◽  
Nicholas J. Lunn ◽  
Ian Stirling ◽  
...  
Keyword(s):  
Mating Systems ◽  
Parentage Analysis ◽  
Hudson Bay ◽  
Polar Bears ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Monozygotic Twinning ◽  
Close Relatives ◽  
Free Ranging ◽  
First Time

Multigenerational pedigrees have been developed for free-ranging populations of many species, are frequently used to describe mating systems, and are used in studies of quantitative genetics. Here, we document the development of a 4449-individual pedigree for the Western Hudson Bay subpopulation of polar bears (Ursus maritimus), created from relationships inferred from field and genetic data collected over six generations of bears sampled between 1966 and 2011. Microsatellite genotypes for 22-25 loci were obtained for 2945 individuals, and parentage analysis was performed using the program FRANZ, including additional offspring-dam associations known only from capture data. Parentage assignments for a subset of 859 individuals were confirmed using an independent medium-density set of single nucleotide polymorphisms. To account for unsampled males in our population, we performed half-sib/full-sib analysis to reconstruct males using the program COLONY, resulting in a final pedigree containing 2957 assigned maternities and 1861 assigned paternities with only one observed case of inbreeding between close relatives. During genotyping, we identified two independently captured two-year-old males with identical genotypes at all 25 loci, showing--for the first time--a case of monozygotic twinning among polar bears. In addition, we documented six new cases of cub adoption, which we attribute to cub misidentification or misdirected maternal care by a female bereaved of her young. Importantly, none of these adoptions could be attributed to reduced female vigilance caused by immobilization to facilitate scientific handling, as has previously been suggested.

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.

scholarly journals Role of GSPT1 and GSPT2 polymorphisms in different outcomes upon Hepatitis B virus infection and prognosis to lamivudine therapy

2019 ◽  
Vol 39 (3) ◽  
Author(s):  
Wenxuan Liu ◽  
Ning Ma ◽  
Xia Gao ◽  
Wencong Liu ◽  
Jinhai Jia ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Lamivudine Therapy ◽  
Single Nucleotide ◽  
Tumor Susceptibility ◽  
B Virus ◽  
First Time

Abstract Purpose. ERF3, having been found expressing differently in liver tissues in our previous work, including eRF3a and eRF3b, which are structural homologs named GSPT1 and GSPT2. Recent studies have indicated that eRF3b involved in the development and proliferation of HepG2 cell, and eRF3a may be associated with tumor susceptibility. Based on this, we tested the effects of GSPT1 and GSPT2 single-nucleotide polymorphisms for all major Hepatitis B virus (HBV) outcomes and lamivudine (LAM) treatment in Han Chinese. Method. A total of 1649 samples were enrolled, and peripheral blood samples were collected in the present study. The single-nucleotide polymorphisms in the GSPT1 and GSPT2 region were genotyped using MALDI-TOF MS. Results. Our study demonstrated there was no obvious relevance of either GSPT1-rs33635 or GSPT2-rs974285 polymorphisms with HBV susceptibility, spontaneous recovery, and development of HBV-related diseases. However, we showed for the first time to our knowledge that GSPT1-rs33635C was a predictor for LAM therapy (viral response: odds ratio (OR) = 2.436, P=0.022; biochemical response: OR = 3.328, P=1.73 × 10−4). Conclusions. These findings might provide potential implications for therapeutic guidance.

Polymorphisms in adipokine-related genes to predict treatment outcomes in patients (pts) with metastatic colorectal cancer (mCRC) treated with bevacizumab-based chemotherapy.

2017 ◽  
Vol 35 (4_suppl) ◽  
pp. 600-600
Author(s):  
Yuji Miyamoto ◽  
Sebastian Stintzing ◽  
Wu Zhang ◽  
Shu Cao ◽  
Yan Ning ◽  
...  
Keyword(s):  
Direct Sequencing ◽  
Univariate Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Prognostic Effect ◽  
Low Bmi ◽  
Molecular Effects ◽  
First Time ◽  
High Bmi

600 Background: The molecular effects of obesity are mediated by alterations in the levels of adipokines, which are produced mainly by adipose tissue. Adipokines have multiple effects, including insulin sensitivity, cell proliferation, inflammation, and angiogenesis. We previously reported that single-nucleotide polymorphisms (SNPs) in obesity-related genes were associated with the recurrence probability of CRC treated with 5-FU based adjuvant chemotherapy. This study aimed to evaluate whether SNPs in adipokine-related genes may predict clinical outcomes in bevacizumab treated mCRC pts. Methods: Genomic DNA was obtained from mCRC pts receiving bevacizumab plus FOLFIRI as first-line treatment and analyzed by using PCR-based direct sequencing. Eleven functional SNPs in 7 genes ( LEP, LEPR, ADIPOQ, ADIPOR1, RETN, TNFa and NAMPT) were tested in 291 pts in FIRE3 trial bevacizumab cohort (NCT00433927). Main characteristics were the following: male/female = 193/98; median age = 65; High BMI pts (BMI ≥ 25 Kg/m2)/low BMI pts (BMI < 25 Kg/m2) = 162/129; median PFS = 10.1 months; median OS = 24.2 months, median follow-up time = 40.8 months. Results: LEPR rs1137100 G/G variants (n = 24) showed worse PFS than any A variants (n = 246) in univariate (10.4 months (M) vs. 9.2 M, HR = 1.75, 95%CI = 1.12-2.74, P = 0.011) and multivariate analyses (HR = 1.75, 95%CI = 1.11-2.74, P = 0.016). NAMPT rs61330082 T/T (n = 24) showed worse PFS than any C variants (n = 243) in multivariate analysis (HR = 1.65, 95% = 1.02-2.67, P = 0.042). RETN rs1862513 C/C (n = 23) showed worse OS than any G variants (n = 246) in univariate analysis (14.1 m vs. 25.1 M, HR = 1.65, 95%CI = 1.04-2.60, P = 0.029). In subgroup analyses of high BMI pts, the prognostic effect of LEPR rs1137100 G/G and RETN rs1862513 C/C was confirmed and no association was observed among low BMI pts. Conclusions: Our study showed for the first time that genetic variations in adipokine-related genes are associated with prognosis of mCRC pts treated with bevacizumab based chemotherapy.

scholarly journals TNF-α, IL-4Rα AND IL-4 Polymorphisms in Mild to Severe Asthma from Italian Caucasians

2013 ◽  
Vol 26 (1) ◽  
pp. 75-84 ◽  
Author(s):  
F.L.M. Ricciardolo ◽  
V. Sorbello ◽  
M. Silvestri ◽  
M. Giacomelli ◽  
V.M.G. Debenedetti ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Protein Coding ◽  
Cytokine Genes ◽  
Asthmatic Patients ◽  
Tnf Α ◽  
Snp Mapping ◽  
Polymerase Chain ◽  
First Time

Asthma is a chronic airway inflammatory disease associated with airway hyperresponsiveness which affects subjects with genetic predisposition. An association has been reported between some polymorphisms in various cytokine genes and asthma. Most of them are single nucleotide polymorphisms (SNPs). These polymorphisms are detected in the protein coding sequence or in the promoter region thus influencing cytokine production. We investigated the involvement of SNP mapping in 5 cytokine genes in mild to severe asthmatics of Italian Caucasians. The frequency of alleles and genotypes, relatively to 10 allelic specificities of the cytokine genes, was defined in 57 asthmatics and in 124 control subjects by a Polymerase Chain Reaction-Sequence Specific Primer method. TNF-α -308A and TNF-α -238A allele frequencies were higher in asthmatics than in controls (p<0.001). Significant differences in the frequency of IL-4 -590T allele and of IL-4Rα + 1902A allele were also detected in asthmatics in comparison with controls (p<0.001 and p=0.005, respectively). Similarly, IL-1α -889C allele was present in 84.1% of asthmatics and in 70.2% of controls (p=0.013). Furthermore, the IL-4Rα + 1902A/A and IL-1α -889C/C homozygous conditions and the TNF-α -308G/A, TNF-α -238G/A, IL-4 -590T/C and IL-10 -1082G/A heterozygous conditions were significantly associated with asthma (p<0.05). ACA haplotype of IL-10 was observed only in asthmatic patients. This study reports, for the first time, the frequency of 10 different single nucleotide polymorphisms in 5 cytokine genes in the Italian Caucasians. Furthermore, we also indicate that in our population some single nucleotide polymorphisms are associated with mild to severe bronchial asthma.

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