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Roumi Z, Mirzababaei A, Abaj F, Davaneghi S, Aali Y, Mirzaei K. The interaction between polyphenol intake and genes (MC4R, Cav-1, and Cry1) related to body homeostasis and cardiometabolic risk factors in overweight and obese women: a cross-sectional study. Front Nutr 2024; 11:1410811. [PMID: 39104759 PMCID: PMC11299215 DOI: 10.3389/fnut.2024.1410811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 07/10/2024] [Indexed: 08/07/2024] Open
Abstract
Background Cardiovascular disease (CVD), which is an important global health challenge, is expanding. One of the main factors in the occurrence of CVD is a high genetic risk. The interaction between genetic risk in CVD and nutrition is debatable. Polyphenols are one of the important dietary components that may have a protective role in people who have a high genetic risk score (GRS) for cardiometabolic risk factors. This study, conducted in overweight and obese women, examines the interaction between polyphenol intake and specific genes (MC4r, Cav-1, and Cry1) related to maintaining body balance and their interaction with cardiometabolic risk factors. Methods This cross-sectional study included 391 women who were overweight or obese, aged 18 to 48 years, with a body mass index (BMI) between 25 and 40 kg/m2. Body composition was measured using the InBody 770 scanner. Total dietary polyphenol intake (TDPI) was assessed with a validated 147-item food frequency questionnaire (FFQ), and polyphenol intakes were determined using the Phenol-Explorer database. Serum samples underwent biochemical tests. The Genetic Risk Score (GRS) was calculated based on the risk alleles of three genes: MC4r, Cav-1, and Cry1. Results The mean ± standard deviation (SD) age and BMI of women were 36.67 (9.1) years and 30.98 (3.9) kg/m2, respectively. The high GRS and high TDPI group had a significant negative interaction with fasting blood glucose (FBS) (p = 0.01). Individuals who had a high GRS and a high phenolic acid intake were found to have a significant negative interaction with Triglyceride (p = 0.04). Similarly, individuals with high GRS and a high intake of flavonoids had a significant negative interaction with TG (p < 0.01) and a significant positive interaction with High-density lipoprotein (HDL) (p = 0.01) in the adjusted model. Conclusion According to our findings, those with a high GRS may have a protective effect on cardiometabolic risk factors by consuming high amounts of polyphenols. Further studies will be necessary in the future to validate this association.
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Affiliation(s)
- Zahra Roumi
- Department of Nutrition, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Atieh Mirzababaei
- Department of Nutrition, Science and Research Branch, Islamic Azad University, Tehran, Iran
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Faezeh Abaj
- Department of Nutrition, Dietetics and Food, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Soheila Davaneghi
- MSC, School of Nutrition and Food Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yasaman Aali
- Department of Nutrition, Science and Research Branch, Islamic Azad University, Tehran, Iran
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Khadijeh Mirzaei
- Department of Nutrition, Science and Research Branch, Islamic Azad University, Tehran, Iran
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Rasaei N, Daneshzad E, Khadem A, Gholami F, Samadi M, Mirzaei K. Investigation of the interaction between genetic risk score (GRS) and fatty acid quality indices on metabolic syndrome among overweight and obese women. BMC Med Genomics 2024; 17:113. [PMID: 38685080 PMCID: PMC11057091 DOI: 10.1186/s12920-024-01838-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 02/27/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND AND AIM Metabolic syndrome is one of the major public-health challenges, affecting one-quarter of the world population. Fatty acid quality indices are novel determinants of this disease and their interactions with genetic factors may have an impact on metabolic syndrome risk. Therefore, we aimed to investigate the interaction between genetic risk score (GRS) and fatty acid quality indices with metabolic syndrome (MetS) among overweight and obese women. METHODS In the present cross-sectional study, 279 overweight and obese women (18-48 years old) were included. Several anthropometric measurements such as weight, height, body mass index (BMI), waist circumference (WC), and body fat percent (BF%) were measured. Also, systolic and diastolic blood pressure (SBP and DBP) were measured. Biochemical determination was performed for fasting blood glucose (FBS), triglyceride (TG), and high-density lipoprotein (HDL). MetS was determined according to National Cholesterol Education Program (NCEP ATP III) criteria. Dietary intake was evaluated by a validated and reliable 147-item semi-quantitative food frequency questionnaire. Cholesterol-saturated fat index (CSI) and the ratio of omega-6/omega-3 (ω-6/ω-3) essential fatty acids were considered as fat quality indices. The salting-out method was used to extract the total DNA. The unweighted GRS was calculated using the risk alleles of the three single nucleotide polymorphisms. The total average GRS value was 2 and the sum of the risk alleles of the 3 polymorphisms was 6. RESULT The results of our analysis showed that after controlling for age, energy intake, BMI, and physical activity, there was a positive interaction between T2 of GRS and T2 of N6/N3 ratio on WC (β = 7.95, 95%CI = 0.83,15.08, P = 0.029), T3 of GRS and T2 of N6/N3 ratio on DBP (β = 5.93, 95%CI= -0.76,12.63, P = 0.083), and FBS (β = 6.47, 95%CI = 0.59,13.53, P = 0.073), T3 of GRS and T3 of N6/N3 ratio on TG (β = 54.42, 95%CI = 1.76,107.08, P = 0.043), and T3 of GRS and T3 of CSI on BF% (β = 3.55, 95%CI= -0.35,7.45, P = 0.075). Also T2 of GRS in the interaction with T3 of CSI leads to an decrease - 8.35 mg/dl in HDL level after adjustment in (β= -8.35, 95%CI= -17.34,0.62, P = 0.068). CONCLUSION It seems the interaction of GRS and fatty acid quality indices is positively associated with several components of metabolic syndrome such as WC, TG and BF%. Our findings are of importance to public health, considering the high consumption of foods that are high on fatty acids. Conflicting evidence of many previous studies regarding the effect of fat intake and obesity and cardiovascular diseases could be because of the gene-diet interactions and genetic heterogeneity across various ethnic groups. Hence, the synergism effect of genetic and dietay intakes should be considered in future studies.
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Affiliation(s)
- Niloufar Rasaei
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), Tehran, P. O. Box: 14155-6117, Iran
| | - Elnaz Daneshzad
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Alireza Khadem
- Department of Nutrition, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Fatemeh Gholami
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), Tehran, P. O. Box: 14155-6117, Iran
| | - Mahsa Samadi
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), Tehran, P. O. Box: 14155-6117, Iran
| | - Khadijeh Mirzaei
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), Tehran, P. O. Box: 14155-6117, Iran.
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Jiao Y, Nigam D, Barry K, Daum C, Yoshinaga Y, Lipzen A, Khan A, Parasa SP, Wei S, Lu Z, Tello-Ruiz MK, Dhiman P, Burow G, Hayes C, Chen J, Brandizzi F, Mortimer J, Ware D, Xin Z. A large sequenced mutant library - valuable reverse genetic resource that covers 98% of sorghum genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1543-1557. [PMID: 38100514 DOI: 10.1111/tpj.16582] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/08/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023]
Abstract
Mutant populations are crucial for functional genomics and discovering novel traits for crop breeding. Sorghum, a drought and heat-tolerant C4 species, requires a vast, large-scale, annotated, and sequenced mutant resource to enhance crop improvement through functional genomics research. Here, we report a sorghum large-scale sequenced mutant population with 9.5 million ethyl methane sulfonate (EMS)-induced mutations that covered 98% of sorghum's annotated genes using inbred line BTx623. Remarkably, a total of 610 320 mutations within the promoter and enhancer regions of 18 000 and 11 790 genes, respectively, can be leveraged for novel research of cis-regulatory elements. A comparison of the distribution of mutations in the large-scale mutant library and sorghum association panel (SAP) provides insights into the influence of selection. EMS-induced mutations appeared to be random across different regions of the genome without significant enrichment in different sections of a gene, including the 5' UTR, gene body, and 3'-UTR. In contrast, there were low variation density in the coding and UTR regions in the SAP. Based on the Ka /Ks value, the mutant library (~1) experienced little selection, unlike the SAP (0.40), which has been strongly selected through breeding. All mutation data are publicly searchable through SorbMutDB (https://www.depts.ttu.edu/igcast/sorbmutdb.php) and SorghumBase (https://sorghumbase.org/). This current large-scale sequence-indexed sorghum mutant population is a crucial resource that enriched the sorghum gene pool with novel diversity and a highly valuable tool for the Poaceae family, that will advance plant biology research and crop breeding.
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Affiliation(s)
- Yinping Jiao
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, Texas, 79409, USA
| | - Deepti Nigam
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, Texas, 79409, USA
| | - Kerrie Barry
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Chris Daum
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Yuko Yoshinaga
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Anna Lipzen
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Adil Khan
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, Texas, 79409, USA
| | - Sai-Praneeth Parasa
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, Texas, 79409, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
| | - Zhenyuan Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
| | | | - Pallavi Dhiman
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, Texas, 79409, USA
| | - Gloria Burow
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, Texas, 79424, USA
| | - Chad Hayes
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, Texas, 79424, USA
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, Texas, 79424, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, Michigan, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Jenny Mortimer
- Joint BioEnergy Institute, Emeryville, California, 94608, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California, 94720, USA
- School of Agriculture, Food and Wine, Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, South Australia, 5064, Australia
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
- USDA-ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, New York, 14853, USA
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, Texas, 79424, USA
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Huang CC, Lin CH, Lin YC, Chang HX. Application of bulk segregant RNA-Seq (BSR-Seq) and allele-specific primers to study soybean powdery mildew resistance. BMC PLANT BIOLOGY 2024; 24:155. [PMID: 38424508 PMCID: PMC10905810 DOI: 10.1186/s12870-024-04822-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND Powdery mildew (PM) is one of the important soybean diseases, and host resistance could practically contribute to soybean PM management. To date, only the Rmd locus on chromosome (Chr) 16 was identified through traditional QTL mapping and GWAS, and it remains unclear if the bulk segregant RNA-Seq (BSR-Seq) methodology is feasible to explore additional PM resistance that might exist in other varieties. RESULTS BSR-Seq was applied to contrast genotypes and gene expressions between the resistant bulk (R bulk) and the susceptible bulk (S bulk), as well as the parents. The ∆(SNP-index) and G' value identified several QTL and significant SNPs/Indels on Chr06, Chr15, and Chr16. Differentially expressed genes (DEGs) located within these QTL were identified using HISAT2 and Kallisto, and allele-specific primers (AS-primers) were designed to validate the accuracy of phenotypic prediction. While the AS-primers on Chr06 or Chr15 cannot distinguish the resistant and susceptible phenotypes, AS-primers on Chr16 exhibited 82% accuracy prediction with an additive effect, similar to the SSR marker Satt431. CONCLUSIONS Evaluation of additional AS-primers in the linkage disequilibrium (LD) block on Chr16 further confirmed the resistant locus, derived from the resistant parental variety 'Kaohsiung 11' ('KS11'), not only overlaps with the Rmd locus with unique up-regulated LRR genes (Glyma.16G213700 and Glyma.16G215100), but also harbors a down-regulated MLO gene (Glyma.16G145600). Accordingly, this study exemplified the feasibility of BSR-Seq in studying biotrophic disease resistance in soybean, and showed the genetic makeup of soybean variety 'KS11' comprising the Rmd locus and one MLO gene.
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Affiliation(s)
- Cheng-Chun Huang
- Master Program for Plant Medicine, National Taiwan University, Taipei, 106319, Taiwan
| | - Chen-Hsiang Lin
- Taoyuan District Agricultural Research and Extension Station. Ministry of Agriculture, Taoyuan, 327005, Taiwan
| | - Yu-Cheng Lin
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 106319, Taiwan
- Department of Ecology and Evolutionary Biology, The University of Michigan, Ann Arbor, MI, 48109, USA
| | - Hao-Xun Chang
- Master Program for Plant Medicine, National Taiwan University, Taipei, 106319, Taiwan.
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 106319, Taiwan.
- Center of Biotechnology, National Taiwan University, Taipei, 106319, Taiwan.
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Kondo J, Tempaku PF, D'Almeida V, Kakazu VA, Andersen ML, Tufik S, Poyares D. Sleep patterns according to genetically determined ethnicity in the population of São Paulo, Brazil. Sleep Med 2024; 113:242-248. [PMID: 38064796 DOI: 10.1016/j.sleep.2023.11.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 01/07/2024]
Abstract
Sleep is a behavior expressed differently for each individual. However, studies have shown that some ethnic groups express common sleep patterns, which can be observed in different ethnic groups. Previous studies have shown the existence of sleep disparities in populations of different ethnicities. Most of these studies have considered self-reported ethnicity and assessed sleep subjectively. Therefore, the aim of this study was to evaluate sleep disparities in different ethnic groups based on an analysis of genetic ancestry and the use of objective sleep evaluation. To do this, we used data from the São Paulo Epidemiologic Sleep Study (EPISONO), which was undertaken in Brazil, a country that is known for its ethnic/racial diversity. All individuals completed a series of questionnaires, underwent full polysomnography and had their blood collected for DNA extraction. After genotyping and identifying samples with high-quality DNA suitable for genetic analysis, 31 ancestry-informative markers (AIMs) were selected. These markers exhibited substantial allelic frequency differences, enabling the characterization of the three primary founding populations of modern Brazil - Europeans, West-Africans, and Native Americans. Through this analysis, the genetic contribution of each of these ancestral groups was identified in respect of each participant. Based on this, a latent class cluster analysis (LCCA) was performed to define the three clusters that best classified the sample according to ethnic group: African (n = 255), Caucasian (n = 668) and Native American (n = 83). Applying the adjusted model for the confounding variables (age, socio-economic class and sex), statistically significant differences in sleep variables between ethnicities were found. Africans had higher sleep latency compared to the other groups (β = 4.46, CI = 1.18 to 7.74 and β = 7.83, CI = 3.50 to 12.15), while Caucasians had longer total sleep time (β = -16.47, CI = -29.94 to -2.99) and better sleep efficiency (β = -2.19, CI = -4.35 to -0.02) compared to Africans. Regarding the respiratory arousals index (β = -1.11, IC = -2.07 to -0.16) and periodic leg movements index (β = -7.48, CI = -12.08 to -2.88), both were higher among Caucasians compared to Africans. We were able to conclude that genetic ancestry might modulate sleep structure and the occurrence of sleep disorders.
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Affiliation(s)
- Julia Kondo
- Departamento de Psicobiologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Priscila F Tempaku
- Departamento de Psicobiologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Vânia D'Almeida
- Departamento de Psicobiologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Viviane A Kakazu
- Departamento de Psicobiologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Monica L Andersen
- Departamento de Psicobiologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Sergio Tufik
- Departamento de Psicobiologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Dalva Poyares
- Departamento de Psicobiologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil.
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Thai DA, Lee NY. A point-of-care platform for hair loss-related single nucleotide polymorphism genotyping. Anal Chim Acta 2023; 1283:341973. [PMID: 37977768 DOI: 10.1016/j.aca.2023.341973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/21/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]
Abstract
Rapid genotyping of single nucleotide polymorphism (SNP) is crucial for prognostics and disease management, enabling more rapid therapy selection and treatment determination. Here, we introduce a point-of-care platform for hair loss-related SNP genotyping based on allele-specific loop-mediated isothermal amplification (AS-LAMP) combined with naked-eye visualization. The specificity of the AS-LAMP assay was significantly enhanced by using mismatched allele-specific primers. AS-LAMP reaction and Schiff's reagent-based colorimetric detection were successfully performed using a thermoplastic genotyping chip. This strategy also showed potential for determining homozygotes and heterozygotes in a target sample. To assess SNP genotyping capacity, the genotyping chip was fabricated to visually detect rs6152 polymorphism of an androgen receptor gene associated with genetically induced hair loss. The genotyping platform rapidly identified the SNP within 40 min, and the detection limit was as low as 1 pg/μL of the target DNA contained in human serum. The introduced strategy showed high specificity and stability in discriminating low-abundance mutations, making it suitable as a portable and affordable point-of-care platform for rapid and accurate SNP discrimination applicable for bedside detection.
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Affiliation(s)
- Duc Anh Thai
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, South Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, South Korea.
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Rasaei N, Samadi M, Khadem A, Fatemi SF, Gholami F, Mirzaei K. Investigation of the interaction between Genetic Risk Score (GRS) and fatty acid quality indices on mental health among overweight and obese women. BMC Womens Health 2023; 23:413. [PMID: 37542261 PMCID: PMC10403951 DOI: 10.1186/s12905-023-02491-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 06/19/2023] [Indexed: 08/06/2023] Open
Abstract
BACKGROUND & AIMS Mental disorders are associated with dietary fatty acids and genome-wide association studies have found multiple risk loci robustly related to depression, anxiety, and stress. The aim of this study is to investigate the interaction of genetic risk score (GRS) and dietary fat quality indices on mental health. METHODS This cross-sectional study included 279 overweight and obese women for N6/N3 ratio and 378 overweight and obese women for CSI aged 18-68 years. Using reliable and verified standard protocols, body composition, anthropometric indices, blood pressure, physical activity, and dietary fat quality were measured. Serum samples were used to determine biochemical tests. A genetic risk score (GRS) was calculated using the risk alleles of the three SNPs. A generalized linear model (GLM) was applied to assess the interactions between GRS and fat quality indices. Mental health was evaluated using Depression Anxiety Stress Scales (DASS-21). RESULTS The mean (± SD) age and BMI of our participants were 36.48 (8.45) and 30.73 (3.72) kg/m2 respectively. There was a marginally significant mean difference among tertiles of the CSI in terms of stress (P = 0.051), DASS-21 (P = 0.078) in the crude model. After adjusting for age, energy intake, physical activity and BMI in model 1, there was a positive interaction between GRS and T3 of N6/N3 ratio on anxiety (β = 0.91, CI = 0.08,1.75, P = 0.031), depression (β = 1.05, CI = 0.06,2.04, P = 0.037), DASS-21 (β = 2.22, CI= -0.31,4.75, P = 0.086). CONCLUSION Our findings indicate that higher ratio of N-6 to N-3 considering genetics were predictive of mental disorder in our population.
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Affiliation(s)
- Niloufar Rasaei
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), Tehran, Iran
- Network of Interdisciplinarity in Neonates and Infants (NINI), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Mahsa Samadi
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Alireza Khadem
- Department of Nutrition, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Seyedeh Fatemeh Fatemi
- Department of Nutrition, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Gholami
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Khadijeh Mirzaei
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), Tehran, Iran
- Food Microbiology Research Center, Tehran University of Medical Sciences, Tehran, Iran
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Gholami F, Samadi M, Rasaei N, Yekaninejad MS, Keshavarz SA, Javdan G, Shiraseb F, Bahrampour N, Mirzaei K. Interactions Between Genetic Risk Score and Healthy Plant Diet Index on Cardiometabolic Risk Factors Among Obese and Overweight Women. Clin Nutr Res 2023; 12:199-217. [PMID: 37593209 PMCID: PMC10432161 DOI: 10.7762/cnr.2023.12.3.199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/19/2023] Open
Abstract
People with higher genetic predisposition to obesity are more susceptible to cardiovascular diseases (CVDs) and healthy plant-based foods may be associated with reduced risks of obesity and other metabolic markers. We investigated whether healthy plant-foods-rich dietary patterns might have inverse associations with cardiometabolic risk factors in participants at genetically elevated risk of obesity. For this cross-sectional study, 377 obese and overweight women were chosen from health centers in Tehran, Iran. We calculated a healthy plant-based diet index (h-PDI) in which healthy plant foods received positive scores, and unhealthy plant and animal foods received reversed scores. A genetic risk score (GRS) was developed based on 3 polymorphisms. The interaction between GRS and h-PDI on cardiometabolic traits was analyzed using a generalized linear model (GLM). We found significant interactions between GRS and h-PDI on body mass index (BMI) (p = 0.02), body fat mass (p = 0.04), and waist circumference (p = 0.056). There were significant gene-diet interactions for healthful plant-derived diets and BMI-GRS on high-sensitivity C-reactive protein (p = 0.03), aspartate aminotransferase (p = 0.04), alanine transaminase (p = 0.05), insulin (p = 0.04), and plasminogen activator inhibitor 1 (p = 0.002). Adherence to h-PDI was more strongly related to decreased levels of the aforementioned markers among participants in the second or top tertile of GRS than those with low GRS. These results highlight that following a plant-based dietary pattern considering genetics appears to be a protective factor against the risks of cardiometabolic abnormalities.
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Affiliation(s)
- Fatemeh Gholami
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), Tehran 14155-6117, Iran
| | - Mahsa Samadi
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), Tehran 14155-6117, Iran
| | - Niloufar Rasaei
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), Tehran 14155-6117, Iran
| | - Mir Saeid Yekaninejad
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences (TUMS), Tehran 14155-6117, Iran
| | - Seyed Ali Keshavarz
- Department of Clinical Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), Tehran 14155-6117, Iran
| | - Gholamali Javdan
- Food Health Research Center, Hormozgan University of Medical Sciences, Bandar ‘Abbas 79166-13885, Iran
| | - Farideh Shiraseb
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), Tehran 14155-6117, Iran
| | - Niki Bahrampour
- Department of Nutrition, Science and Research Branch, Islamic Azad University (SRBIAU), Tehran 14778-93855, Iran
| | - Khadijeh Mirzaei
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), Tehran 14155-6117, Iran
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Rasaei N, Khadem A, Masihi LS, Mirzaei K. Interaction of fatty acid quality indices and genes related to lipid homeostasis on mental health among overweight and obese women. Sci Rep 2023; 13:9580. [PMID: 37311812 DOI: 10.1038/s41598-023-35810-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/24/2023] [Indexed: 06/15/2023] Open
Abstract
The aim of this study is to investigate the interaction of fatty acid quality indices and genes related to lipid homeostasis on mental health among overweight and obese women. This cross-sectional study included 279 overweight and obese women for N6/N3 ratio and 378 overweight and obese women for CSI aged 18-58 years. Mental health were evaluated using Depression Anxiety Stress Scales (DASS-21). The anthropometric indices, biochemical parameters, body composition and dietary fat quality were measured. MC4R (rs17782313) and Caveolin-1 (CAV-1) (rs3807992) were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. The results of the study showed that after adjusting for age, energy intake, thyroid disease, physical activity, and BMI, a positive interaction between TC genotype of MC4R and CSI on depression (β = 0.39, CI = 0.12, 0.66, P = 0.004), and DASS-21 (β = 0.074, CI = 0.04, 1.44, P = 0.036). Also, there were a marginal significant interactions between AG genotype of CAV-1 and N6/N3 ratio on depression in adjustment model1 (β = 16.83, CI = - 0.19, 33.85, P = 0.053). Our findings showed that increasing adherence to fatty acid quality indices by considering genes related to lipid homeostasis was related to increasing depression in our population.
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Affiliation(s)
- Niloufar Rasaei
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), P.O. Box:14155-6117, Tehran, Iran
| | - Alireza Khadem
- Department of Nutrition, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Lilit Sardari Masihi
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), P.O. Box:14155-6117, Tehran, Iran
| | - Khadijeh Mirzaei
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), P.O. Box:14155-6117, Tehran, Iran.
- Food Microbiology Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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Khassanova G, Khalbayeva S, Serikbay D, Mazkirat S, Bulatova K, Utebayev M, Shavrukov Y. SNP Genotyping with Amplifluor-Like Method. Methods Mol Biol 2023; 2638:201-219. [PMID: 36781644 DOI: 10.1007/978-1-0716-3024-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
For SNP genotyping, amplification of fluorescence (Amplifluor) is a popular and actively developing method in the plant sciences. The "Amplifluor-like" is a "home-made" modification of the original commercial Amplifluor method. Amplifluor-like genotyping requires two essential components: (1) two allele-specific forward primers targeting the SNP site with one common reverse primer; and (2) a universal part with two non-allele-specific molecular probes containing one of the two used fluorophores and a quencher. Allele discrimination is based on the fluorescence score, where the dominance of one dye over the other confirms the presence of each specific SNP allele. The Amplifluor-like method is similar to commercial KASP and original Amplifluor methods but is much cheaper because all components can be ordered as regular and modified oligos. The easily adaptable Amplifluor-like method can be modified by any researcher to make it suitable for available instruments, reagents and conditions in low-budget laboratories for SNP genotyping of any plant species with identified genetic polymorphism.
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Affiliation(s)
- Gulmira Khassanova
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Sholpan Khalbayeva
- Kazakh Research Institute of Agriculture and Plant Production, Almalybak, Almaty, Kazakhstan
| | - Dauren Serikbay
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Shynar Mazkirat
- Kazakh Research Institute of Agriculture and Plant Production, Almalybak, Almaty, Kazakhstan
| | - Kulpash Bulatova
- Kazakh Research Institute of Agriculture and Plant Production, Almalybak, Almaty, Kazakhstan
| | - Maral Utebayev
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia.
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11
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Kim JJ, Park HM, Kyoung AY, Lim SK, Cha SH, Lee JE, Park BC. Com probe implemented STexS II greatly enhances specificity in SARS-CoV-2 variant detection. Sci Rep 2023; 13:1036. [PMID: 36658190 PMCID: PMC9850334 DOI: 10.1038/s41598-022-24530-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/16/2022] [Indexed: 01/20/2023] Open
Abstract
The initial introduction of utilizing double helix structural oligonucleotides known as SNP typing with excellent specificity (STexS) in a standard PCR greatly improved the detection of single nucleotide polymorphisms (SNP) by enhancing amplification rates of primer-matching strands and interrupting mismatched strands by constant instability of kinetics regarding alignment attaching and detaching. The model was beneficial overall in detecting SNP variants consisting of large amounts of wildtype strands such as EGFR mutation genotyping for early detection of non-small cell lung cancer. While the STexS PCR is advantageous in detecting SNPs and biomarkers, limitations were yet observed. Despite the ability to detect variants 10 times more effective than a typical amplification-refractory mutation system PCR, it could only perform optimally in DNA concentrations around 101 ~ 105. To further enhance STexS specificity to perform detecting viral-RNA variants such as the infamous SARS-CoV-2, a novel improvement of the regular TaqMan Probe using Com-probes to inhibit high copy wild targets and amplify low copy mutant targets. By introducing the novel STexS II, omicron variants of SARS-CoV-2 were able to be successfully detected in high concentrations of normal genes.
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Affiliation(s)
- Jae Jong Kim
- GenoTech Corporation, 26-69, Gajeongbuk-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Hyoung-Min Park
- Biometrology Group, Korea Research Institute of Standards and Science, 267 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - A Young Kyoung
- GenoTech Corporation, 26-69, Gajeongbuk-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Si-Kyu Lim
- GenoTech Corporation, 26-69, Gajeongbuk-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
| | - Sun Ho Cha
- GenoTech Corporation, 26-69, Gajeongbuk-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - J Eugene Lee
- Biometrology Group, Korea Research Institute of Standards and Science, 267 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Byoung Chul Park
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34145, Republic of Korea.
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Gholami F, Rasaei N, Samadi M, Yekaninejad MS, Keshavarz SA, Javdan G, Karimi Z, Mirzaei K. The relationship of genetic risk score with cardiometabolic risk factors: a cross-sectional study. BMC Cardiovasc Disord 2022; 22:459. [PMID: 36324080 PMCID: PMC9632045 DOI: 10.1186/s12872-022-02888-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Background & aims For more than eight decades, cardiovascular disease (CVD) has remained the leading cause of death in the world. CVD risk factors are multifaceted, with genetics and lifestyle both playing a role. The aim of this study was to investigate the association between a genetic profile risk score for obesity GRS and cardio-metabolic risk factors in overweight and obese women. Methods The current cross-sectional study was conducted on 391 overweight and obese women. The genetic risk score was created by combining three single nucleotide polymorphisms [MC4R (rs17782313), CAV-1 (rs3807992), and Cry-1 (rs2287161)]. Anthropometric measurements, blood pressure, and some blood parameters were measured by standard protocols. Results A significant association between the GRS and some of cardiometabolic risk factors variables such as body mass index (β = 0. 49, 95%CI = 0.22 to 0.76, p < 0.001), waist circumference (β = 0. 86, 95%CI = 0.18 to 1.54, p = 0.01), body fat mass (β = 0. 82, 95%CI = 0.25 to 1.39, p = 0.005), %body fat (β = 0. 44, 95%CI = 0.06 to 0.82, p = 0.02), and hs-CRP (β = 0.46, 95% CI = 0.14 to 0.78, p = 0.005) was observed in crude model. After adjustment for confounding factors (age, BMI, and physical activity), a significant positive association was observed between BMI (p = 0.004), WC (p = 0.02), body fat mass (p = 0.01), %BF (p = 0.01), hs-CRP (p = 0.009), and GRS. In addition, we discovered a significant negative association between the GRS and BMC (= -0.02, 95%CI = -0.05 to -0.001, p = 0.04). But other variables did not show any significant association with GRS among obese and overweight women. Conclusion We found a significant positive association between GRS, including MC4R (rs17782313), CAV-1 (rs3807992), and Cry-1 (rs2287161) and cardiometabolic risk factors among overweight and obese Iranian women.
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Affiliation(s)
- Fatemeh Gholami
- grid.411705.60000 0001 0166 0922Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), P. O Box 6446, 14155 Tehran, Iran
| | - Niloufar Rasaei
- grid.411705.60000 0001 0166 0922Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), P. O Box 6446, 14155 Tehran, Iran
| | - Mahsa Samadi
- grid.411705.60000 0001 0166 0922Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), P. O Box 6446, 14155 Tehran, Iran
| | - Mir Saeid Yekaninejad
- grid.411705.60000 0001 0166 0922Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Science, Tehran, Iran
| | - Seyed Ali Keshavarz
- grid.411705.60000 0001 0166 0922Department of Clinical Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences, Tehran, Iran
| | - Gholamali Javdan
- grid.412237.10000 0004 0385 452XFood Health Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Zahra Karimi
- grid.411705.60000 0001 0166 0922Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Science, Tehran, Iran
| | - Khadijeh Mirzaei
- grid.411705.60000 0001 0166 0922Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), P. O Box 6446, 14155 Tehran, Iran ,grid.411705.60000 0001 0166 0922 Food Microbiology Research Center, Tehran University of Medical Sciences, Tehran, Iran
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13
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Gholami F, Samadi M, Soveid N, Mirzaei K. Healthy beverages may reduce the genetic risk of abdominal obesity and related metabolic comorbidities: a gene-diet interaction study in Iranian women. Diabetol Metab Syndr 2022; 14:143. [PMID: 36167582 PMCID: PMC9516810 DOI: 10.1186/s13098-022-00911-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND & AIMS The nutrition transition in developing countries like Iran causes the increasing rise of obesity and abdominal obesity rates. However, it is not yet well proven that environmental modifications like improving the quality of beverage intake can be effective in people who have a genetic predisposition to obesity. So, in the present study, we examine the interaction between genetic predisposition and healthy beverage index (HBI) with abdominal obesity and obesity-related metabolic risk factors in overweight and obese women. METHOD Based on inclusion and exclusion criteria, 202 overweight or obese females were chosen for this cross-sectional study. Body composition, anthropometric measures, physical activity, and beverage intake data were collected and analyzed using recognized and trustworthy methodologies. Biochemical tests were performed on serum samples. A genetic risk score (GRS) was calculated based on the results of genetic tests. The predetermined HBI was calculated based on previous studies. A generalized linear model was used to estimate the interactions between GRS and HBI (GLM). RESULTS We found significant interactions between GRS and HBI on WHR (β = - 0.39, CI: -0.07 to 0.001, P = 0.05) and WC (β = - 6.18, CI: - 13.41 to 1.05, P = 0.09). Also, there were significant gene-diet interactions for HBI and GRS on HDL (β = 7.09, CI: - 0.73 to 14.92, P = 0.07) and FBS (β = - 9.07, CI: - 18.63 to 0.47, P = 0.06). CONCLUSIONS These findings emphasize the HBI considering genetics appears to protect against the risks of abdominal obesity and metabolic associated obesity markers.
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Affiliation(s)
- Fatemeh Gholami
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), P.O Box 6446, 14155 Tehran, I.R. of Iran
| | - Mahsa Samadi
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), P.O Box 6446, 14155 Tehran, I.R. of Iran
| | - Neda Soveid
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), P.O Box 6446, 14155 Tehran, I.R. of Iran
| | - Khadijeh Mirzaei
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), P.O Box 6446, 14155 Tehran, I.R. of Iran
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Offornedo Q, Menkir A, Babalola D, Gedil M. Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries. Gates Open Res 2022. [DOI: 10.12688/gatesopenres.13338.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Molecular breeding is an essential tool for accelerating genetic gain in crop improvement towards meeting the need to feed an ever-growing world population. Establishing low-cost, flexible genotyping platforms in small, public and regional laboratories can stimulate the application of molecular breeding in developing countries. These laboratories can serve plant breeding projects requiring low- to medium-density markers for marker-assisted selection (MAS) and quality control (QC) activities. Methods: We performed two QC and MAS experiments consisting of 637 maize lines, using an optimised genotyping workflow involving an in-house competitive allele-specific PCR (KASP) genotyping system with an optimised sample collection, preparation, and DNA extraction and quantitation process. A smaller volume of leaf-disc size plant samples was collected directly in 96-well plates for DNA extraction, using a slightly modified CTAB-based DArT DNA extraction protocol. DNA quality and quantity analyses were performed using a microplate reader, and the KASP genotyping and data analysis was performed in our laboratory. Results: Applying the optimized genotyping workflow expedited the QC and MAS experiments from over five weeks (when outsourcing) to two weeks and eliminated the shipping cost. Using a set of 28 KASP single nucleotide polymorphisms (SNPs) validated for maize, the QC experiment revealed the genetic identity of four maize varieties taken from five seed sources. Another set of 10 KASP SNPs was sufficient in verifying the parentage of 390 F1 lines. The KASP-based MAS was successfully applied to a maize pro-vitamin A (PVA) breeding program and for introgressing the aflatoxin resistance gene into elite tropical maize lines. Conclusion: This improved workflow has helped accelerate maize improvement activities of IITA's Maize Improvement Program and facilitated DNA fingerprinting for tracking improved crop varieties. National Agricultural Research Systems (NARS) in developing countries can adopt this workflow to fast-track molecular marker-based genotyping for crop improvement.
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15
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Yoshiki A, Ballard G, Perez AV. Genetic quality: a complex issue for experimental study reproducibility. Transgenic Res 2022; 31:413-430. [PMID: 35751794 PMCID: PMC9489590 DOI: 10.1007/s11248-022-00314-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/30/2022] [Indexed: 11/29/2022]
Abstract
Laboratory animal research involving mice, requires consideration of many factors to be controlled. Genetic quality is one factor that is often overlooked but is essential for the generation of reproducible experimental results. Whether experimental research involves inbred mice, spontaneous mutant, or genetically modified strains, exercising genetic quality through careful breeding, good recordkeeping, and prudent quality control steps such as validation of the presence of mutations and verification of the genetic background, will help ensure that experimental results are accurate and that reference controls are representative for the particular experiment. In this review paper, we will discuss various techniques used for the generation of genetically altered mice, and the different aspects to be considered regarding genetic quality, including inbred strains and substrains used, quality check controls during and after genetic manipulation and breeding. We also provide examples for when to use the different techniques and considerations on genetic quality checks. Further, we emphasize on the importance of establishing an in-house genetic quality program.
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Affiliation(s)
- Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, 3050074, Japan.
| | - Gregory Ballard
- Comparative Medicine and Quality, The Jackson Laboratory, Bar Harbor, ME 04609, USA
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Offornedo Q, Menkir A, Babalola D, Gedil M. Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries. Gates Open Res 2022. [DOI: 10.12688/gatesopenres.13338.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Molecular breeding is an essential tool for accelerating genetic gain in crop improvement, towards meeting the need to feed an ever-growing world population. Establishing low-cost, flexible genotyping platforms in small, public and regional laboratories can stimulate the application of molecular breeding in developing countries. These laboratories can serve plant breeding projects requiring low- to medium-density markers for marker-assisted selection (MAS) and quality control (QC) activities. Methods: We performed two QC and MAS experiments consisting of 637 maize lines, using an optimised genotyping workflow involving an in-house competitive allele-specific PCR (KASP) genotyping system with an optimised sample collection, preparation, and DNA extraction and quantitation process. A smaller volume of leaf-disc size plant samples was collected directly in 96-well plates for DNA extraction, using a slightly modified CTAB-based DArT DNA extraction protocol. DNA quality and quantity analyses were performed using a microplate reader, and the KASP genotyping and data analysis was performed in our laboratory. Results: Applying the optimized genotyping workflow expedited the QC and MAS experiments from over five weeks (when outsourcing) to two weeks and eliminated the shipping cost. Using a set of 28 KASP single nucleotide polymorphisms (SNPs) validated for maize, the QC experiment revealed the genetic identity of four maize varieties taken from five seed sources. Another set of 10 KASP SNPs was sufficient in verifying the parentage of 390 F1 lines. The KASP-based MAS was successfully applied to a maize pro-vitamin A (PVA) breeding program and for introgressing the aflatoxin resistance gene into elite tropical maize lines. Conclusion: This improved workflow has helped accelerate maize improvement activities of IITA's Maize Improvement Program and facilitated DNA fingerprinting for tracking improved crop varieties. National Agricultural Research Systems (NARS) in developing countries can adopt this workflow to fast-track molecular marker-based genotyping for crop improvement.
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17
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Nobusawa K, Han HW, Takei F, Chu TC, Hashida N, Yamashita I. Electrochemical Impedimetric Real-Time Polymerase Chain Reactions Using Anomalous Charge Transfer Enhancement. Anal Chem 2022; 94:7747-7751. [PMID: 35609246 DOI: 10.1021/acs.analchem.2c01659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We developed a new electrochemical impedimetric method for the real-time detection of polymerase chain reactions (PCR) based on our recent discovery that the DNA intercalator, [Ru(bpy)2DPPZ]2+, anomalously enhances charge transfer between redox mediators, K4[Fe(CN)6]/K3[Fe(CN)6], and a carbon electrode. Three mM [Fe(CN)6]3-/4- and 5 μM [Ru(bpy)2DPPZ]2+ were added to the PCR solution, and electrochemical impedance spectroscopy (EIS) measurements were performed at each elongation heat cycle. The charge transfer resistance (Rct) was initially low due to the presence of [Ru(bpy)2DPPZ]2+ in the solution. As PCR progressed, amplicon dsDNA was produced exponentially, and intercalated [Ru(bpy)2DPPZ]2+ ions, which could be detected as a steep Rct, increased at specific heat cycles depending on the amount of template DNA. The Rct increase per heat cycle, ΔRct, showed a peak at the same heat cycle as optical detection, proving that PCR can be accurately monitored in real time by impedance measurement. This simple method will enable a cost-effective and portable PCR device.
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Affiliation(s)
- Kazuyuki Nobusawa
- Graduate School of Engineering, Osaka University 2-8 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Huan-Wen Han
- Graduate School of Engineering, Osaka University 2-8 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Fumie Takei
- National Defense Medical College, 3-2 Namiki, Tokorozawa-shi, Saitama 359-8513, Japan
| | - Ting-Chieh Chu
- Graduate School of Engineering, Osaka University 2-8 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Noriyasu Hashida
- Department of Ophthalmology, Osaka University Graduate School of Medicine, 2-2 E7 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ichiro Yamashita
- Graduate School of Engineering, Osaka University 2-8 Yamadaoka, Suita, Osaka 565-0871, Japan
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18
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Kalendar R, Shustov AV, Akhmetollayev I, Kairov U. Designing Allele-Specific Competitive-Extension PCR-Based Assays for High-Throughput Genotyping and Gene Characterization. Front Mol Biosci 2022; 9:773956. [PMID: 35300118 PMCID: PMC8921500 DOI: 10.3389/fmolb.2022.773956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/02/2022] [Indexed: 12/03/2022] Open
Abstract
Polymerase chain reaction (PCR) is a simple and rapid method that can detect nucleotide polymorphisms and sequence variation in basic research applications, agriculture, and medicine. Variants of PCR, collectively known as allele-specific PCR (AS-PCR), use a competitive reaction in the presence of allele-specific primers to preferentially amplify only certain alleles. This method, originally named by its developers as Kompetitive Allele Specific PCR (KASP), is an AS-PCR variant adapted for fluorescence-based detection of amplification results. We developed a bioinformatic tool for designing probe sequences for PCR-based genotyping assays. Probe sequences are designed in both directions, and both single nucleotide polymorphisms (SNPs) and insertion-deletions (InDels) may be targeted. In addition, the tool allows discrimination of up to four-allelic variants at a single SNP site. To increase both the reaction specificity and the discriminative power of SNP genotyping, each allele-specific primer is designed such that the penultimate base before the primer's 3' end base is positioned at the SNP site. The tool allows design of custom FRET cassette reporter systems for fluorescence-based assays. FastPCR is a user-friendly and powerful Java-based software that is freely available (http://primerdigital.com/tools/). Using the FastPCR environment and the tool for designing AS-PCR provides unparalleled flexibility for developing genotyping assays and specific and sensitive diagnostic PCR-based tests, which translates into a greater likelihood of research success.
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Affiliation(s)
- Ruslan Kalendar
- Institute of Biotechnology HiLIFE, University of Helsinki, Helsinki, Finland
- PrimerDigital Ltd., Helsinki, Finland
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | | | | | - Ulykbek Kairov
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
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Offornedo Q, Menkir A, Babalola D, Gedil M. Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries. Gates Open Res 2022. [DOI: 10.12688/gatesopenres.13338.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Molecular breeding is an essential tool for accelerating genetic gain in crop improvement, towards meeting the need to feed an ever-growing world population. Establishing low-cost, flexible genotyping platforms in small, public and regional laboratories can stimulate the application of molecular breeding in developing countries. These laboratories can serve plant breeding projects requiring low- to medium-density markers for marker-assisted selection (MAS) and quality control (QC) activities. Methods: We performed two QC and MAS experiments consisting of 637 maize lines, using an optimised genotyping workflow involving an in-house competitive allele-specific PCR (KASP) genotyping system with an optimised sample collection, preparation, and DNA extraction and quantitation process. A smaller volume of leaf-disc size plant samples was collected directly in 96-well plates for DNA extraction, using a slightly modified CTAB-based DArT DNA extraction protocol. DNA quality and quantity analyses were performed using a microplate reader, and the KASP genotyping and data analysis was performed in our laboratory. Results: Applying the optimized genotyping workflow expedited the QC and MAS experiments from over five weeks (when outsourcing) to two weeks and eliminated the shipping cost. Using a set of 28 KASP single nucleotide polymorphisms (SNPs) validated for maize, the QC experiment revealed the genetic identity of four maize varieties taken from five seed sources. Another set of 10 KASP SNPs was sufficient in verifying the parentage of 390 F1 lines. The KASP-based MAS was successfully applied to a maize pro-vitamin A (PVA) breeding program and for introgressing the aflatoxin resistance gene into elite tropical maize lines. Conclusion: This improved workflow has helped accelerate maize improvement activities of IITA's Maize Improvement Program and facilitated DNA fingerprinting for tracking improved crop varieties. National Agricultural Research Systems (NARS) in developing countries can adopt this workflow to fast-track molecular marker-based genotyping for crop improvement.
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20
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Wang G, Estrella A, Hakim O, Milazzo P, Patel S, Pintagro C, Li D, Zhao R, Vance DE, Li W. Mini-Mental State Examination and Montreal Cognitive Assessment as Tools for Following Cognitive Changes in Alzheimer's Disease Neuroimaging Initiative Participants. J Alzheimers Dis 2022; 90:263-270. [PMID: 36093696 DOI: 10.3233/jad-220397] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Mini-Mental State Examination (MMSE) and Montreal Cognitive Assessment (MoCA) are two commonly used cognitive screening and diagnostic tools. OBJECTIVE Our goal was to assess their efficacy for monitoring cognitive changes, as well as the correlation between the two tests. METHODS At baseline, participants in the Alzheimer's Disease Neuroimaging Initiative (ADNI) were divided into four groups based on their cognitive diagnoses: healthy control (HC), early mild cognitive impairment (EMCI), late mild cognitive impairment (LMCI), and Alzheimer's disease (AD). MMSE or MoCA scores were compared among the four groups using an analysis of variance (ANOVA) model with repeated measures with post-hoc Bonferroni correction. For those participants who had both MMSE and MoCA assessments done, a Pearson correlation analysis was performed between the two assessments for each visit. RESULTS The MMSE scores were significantly different among the four groups at baseline, which was true for each of the three annual follow-up visits. By contrast, the MoCA scores were not significantly different between HC and EMCI groups at either baseline or any of the follow-up visits. For participants with a diagnosis of LMCI, the cognitive performance deteriorated in a linear manner 12 months after the baseline, which was independent of MMSE or MoCA. At last, the MMSE scores were moderately related to MoCA scores, which got stronger along with the time of follow-up. CONCLUSION MMSE and MoCA are comparable as cognitive assessment tools to monitor cognitive changes. In addition, the measurements of MMSE and MoCA are moderately correlated for the follow-up visits.
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Affiliation(s)
- Ge Wang
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Alliyah Estrella
- School of Health Professions, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ornin Hakim
- School of Health Professions, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Paul Milazzo
- School of Health Professions, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sonali Patel
- School of Health Professions, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Clara Pintagro
- School of Health Professions, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Daniel Li
- The College, University of California at Los Angeles, Los Angeles, CA, USA
| | - Rui Zhao
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - David E Vance
- School of Nursing, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Wei Li
- School of Health Professions, University of Alabama at Birmingham, Birmingham, AL, USA
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21
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Han H, Nobusawa K, Yamashita I. Anomalous Enhancement of Electrochemical Charge Transfer by a Ru Complex Ion Intercalator. Anal Chem 2021; 94:571-576. [PMID: 34928123 DOI: 10.1021/acs.analchem.1c03681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have found that the DNA intercalator [Ru(bpy)2DPPZ]2+ (bpy = 2,2'-bipyridine; DPPZ = dipyrido[3,2-a:2',3'-c]phenazine) causes an anomalous increase in charge transfer in electrochemical impedance spectroscopy (EIS). With a carbonaceous electrode and a 1 mM hexacyanoferrate (1 mM [Fe(CN)6]3- and 1 mM [Fe(CN)6]4-) mediator, we found that adding only 1 μM [Ru(bpy)2DPPZ]2+ greatly enhanced the charge transfer between the electrode and hexacyanoferrate mediator, independently of other electrolytes or buffer components. The effect started with a one millionth amount of hexacyanoferrate. Since [Ru(bpy)2DPPZ]2+ can intercalate with dsDNA, the effect is highly applicable for dsDNA detection or PCR monitoring. With further developments of this method, EIS sensors not requiring specific electrode modifications should be possible.
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Affiliation(s)
- HuanWen Han
- Graduate School of Engineering, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kazuyuki Nobusawa
- Graduate School of Engineering, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Ichiro Yamashita
- Graduate School of Engineering, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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22
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Saleem S, Tahir IM, Iqbal T, Jamil A, Mehboob H, Akram M, Oladoye PO. Genetic polymorphism of NAT1 in local Pakistani population. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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Sun G, Cao H, Bai Y, Wang J, Zhou Y, Li K, Xiao JH. A novel multiplex qPCR method for assessing the comparative lengths of telomeres. J Clin Lab Anal 2021; 35:e23929. [PMID: 34347924 PMCID: PMC8418462 DOI: 10.1002/jcla.23929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/21/2021] [Accepted: 07/20/2021] [Indexed: 11/10/2022] Open
Abstract
Background The comparative length of telomeres is considered to be related to diseases such as cancer, aging, and cardiovascular diseases. qPCR is currently one of the main methods for detecting telomere length. However, due to the unique sequence of telomeres (highly repetitive six‐base sequence), it is difficult to design primers and probes to expand and detect telomere and to put internal reference gene and telomere into the same tube for detection to reduce the possible inter‐pore errors and improve amplification efficiency. Besides, the stability and accuracy of the test results are greatly affected by the difference between reference genes and telomere copy number. Methods In this study, the single‐copy genes were replaced with high‐copy genes (300 copies) as the internal control to reduce the copy number difference of the internal genes and telomere. In addition, a multiplex qPCR system was constructed to detect the telomeres and an internal reference gene product. We also detected the lengths of telomeres in the genomic DNA in immortalized cells (293T and Hela) from different generations of cells. Results We detected the comparative telomere lengths of 1500 random Chinese volunteers of different ages with the multiplex qPCR method; the result shows that the comparative length of telomeres is negatively related to age. In addition, we compared our qPCR detection method with a terminal restriction fragmentation (TRF) method. Both of them were highly consistent, indicating that the qPCR method was reliable. Conclusions In conclusion, we developed a stable, convenient, and accurate comparative telomere length detection method.
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Affiliation(s)
- Guozhu Sun
- School of Chemistry and Bioengineering, Donghua University, Shanghai, China
| | - Hui Cao
- Department of Clinical Laboratory, Shanghai Songjiang District Central Hospital, Shanghai, China
| | - Yang Bai
- Shanghai Biowing Applied Biotechnology CO.LTD, Shanghai, China
| | - Jueheng Wang
- School of Chemistry and Bioengineering, Donghua University, Shanghai, China
| | - Yuxun Zhou
- School of Chemistry and Bioengineering, Donghua University, Shanghai, China
| | - Kai Li
- School of Chemistry and Bioengineering, Donghua University, Shanghai, China
| | - Jun-Hua Xiao
- School of Chemistry and Bioengineering, Donghua University, Shanghai, China
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24
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Wang G, Vance DE, Li W. A Cross-Sectional Analysis of APOE Gene Polymorphism and the Risk of Cognitive Impairments in the Alzheimer's Disease Neuroimaging Initiative Study. JAR LIFE 2021; 10:26-31. [PMID: 36923510 PMCID: PMC10002875 DOI: 10.14283/jarlife.2021.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/12/2021] [Indexed: 03/18/2023]
Abstract
Background It is inconclusive on how apolipoprotein epsilon (APOE) gene polymorphism is associated with the risk of having mild cognitive impairment (MCI) or Alzheimer's disease (AD). Objectives To investigate how APOE genotype is associated with the risk of MCI or AD using the data collected from the Alzheimer's Disease Neuroimaging Initiative (ADNI) participants. Methods A cross-sectional design was used to analyze the baseline data collected from the 1,720 ADNI participants. APOE gene polymorphism was analyzed on how they are related to the risk of cognitive impairments of either MCI or AD using a percent yield (PY) method. Then cognitive functions were compared among six different APOE genotypes using a two-way ANCOVA by controlling possible confounding factors. Results The prevalence of six APOE genotypes in 1,720 participants is as following: e2/e2 (0.3%), e2/e3 (7.4%), e3/e3 (45.4%), e2/e4 (2%), e3/e4 (35%) and e4/e4 (9.9%). The e2/e2 and e4/e4 genotypes were associated with the lowest and the highest risk respectively for cognitive impairments of either MCI or AD. Further, a worse cognitive diagnosis was associated with an increasing number of APOE e4 allele in a dose dependent manner. Participants with genotype e3/e3 had a better memory measure than those with the genotype of e3/e4. Conclusions APOE gene polymorphism is associated with different level of risks for cognitive impairments. The heterozygous genotype e3/e4 is associated with a worse memory function compared to the genotype of e3/e3. Further investigations are needed to intervene the cognitive deteriorations in those with at risk APOE genotypes.
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Affiliation(s)
- G Wang
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - D E Vance
- Office of Research and Scholarship, School of Nursing, University of Alabama at Birmingham, Birmingham, Alabama
| | - W Li
- Physician Assistant Studies, School of Health Professions, University of Alabama at Birmingham, Birmingham, Alabama
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25
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Lavrinenko A, Sheck E, Kolesnichenko S, Azizov I, Turmukhambetova A. Antibiotic Resistance and Genotypes of Nosocomial Strains of Acinetobacter baumannii in Kazakhstan. Antibiotics (Basel) 2021; 10:antibiotics10040382. [PMID: 33916831 PMCID: PMC8065490 DOI: 10.3390/antibiotics10040382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/25/2021] [Accepted: 04/01/2021] [Indexed: 12/17/2022] Open
Abstract
The aim of this study was to determine the prevalence of A. baumannii antibiotic-resistant strains in Kazakhstan and to characterize genotypes related to epidemic “high-risk” clones. Two hundred and twenty four A. baumannii isolates from four cities of Kazakhstan in 2011–2019 were studied. Antibiotic susceptibility testing was performed by using broth microdilutions method according to EUCAST (v 11.0) recommendations. The presence of blaOXA-23-like, blaOXA-24/40-like,blaOXA-58-like,blaVIM,blaIMP, and blaNDM genes was determined by PCR. Genotyping was performed using high-throughput real-time PCR detection of 21 SNPs at 10 chromosomal loci used in existing MLST schemes. Resistance rates to imipenem, meropenem, amikacin, gentamicin, and ciprofloxacin were 81.3%, 78.6%, 79.9%, 65.2%, and 89.3%, respectively. No colistin resistant isolates were detected. The values of the MIC 50% and the MIC 90% of tigecycline were 0.125 mg/L, only four isolates (1.8%) had the ECOFF value >0.5 mg/L. The presence of acquired carbapenemase genes was found in 82.2% strains, including blaOXA-23-like (78.6%) or blaOXA-58-like (3.6%) genes. The spreading of carbapenem resistant A. baumannii strains in Kazakhstan was associated with epidemic “high-risk” clonal groups, predominantly, CG208(92)OXF/CG2PAS (80.8%) and less often CG231(109)OXF/CG1PAS (1.8%).
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Affiliation(s)
- Alyona Lavrinenko
- Share Resource Laboratory, Karaganda Medical University, Karaganda 100008, Kazakhstan; (A.L.); (A.T.)
| | - Eugene Sheck
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214014 Smolensk, Russia; (E.S.); (I.A.)
| | - Svetlana Kolesnichenko
- Share Resource Laboratory, Karaganda Medical University, Karaganda 100008, Kazakhstan; (A.L.); (A.T.)
- Correspondence: ; Tel.: +7-721-251-3479
| | - Ilya Azizov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214014 Smolensk, Russia; (E.S.); (I.A.)
| | - Anar Turmukhambetova
- Share Resource Laboratory, Karaganda Medical University, Karaganda 100008, Kazakhstan; (A.L.); (A.T.)
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26
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Li JS, Wu LY, Zhang H, Song XS, Wang JX, Zhou MG, Hou YP. PCR-RFLP for Detection of Fusarium graminearum Genotypes with Resistance to Phenamacril. PLANT DISEASE 2021; 105:889-895. [PMID: 33044138 DOI: 10.1094/pdis-06-20-1156-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Phenamacril is a cyanoacrylate fungicide that provides excellent control of Fusarium head blight (FHB) or wheat scab, which is caused predominantly by Fusarium graminearum and F. asiaticum. Previous studies revealed that codon mutations of the myosin-5 gene of Fusarium spp. conferred resistance to phenamacril in in vitro lab experiments. In this study, PCR restriction fragment length polymorphism (RFLP) was developed to detect three common mutations (A135T, GCC to ACC at codon 135; S217L, TCA to TTA at codon 217; and E420K, GAA to AAA at codon 420) in F. graminearum induced by fungicide domestication in vitro. PCR products of 841 bp (for mutation of A135T), 802 bp (for mutation of S217L), or 1,649 bp (for mutation of E420K) in the myosin-5 gene were amplified by appropriate primer pairs. Restriction enzyme KpnI, TasI, or DraI was used to distinguish phenamacril-sensitive and -resistant strains with mutation genotypes of A135T, S217L, and E420K, respectively. KpnI digested the 841-bp PCR products of phenamacril-resistant strains with codon mutation A135T into two fragments of 256 and 585 bp. In contrast, KpnI did not digest the PCR products of sensitive strains. TasI digested the 802-bp PCR products of phenamacril-resistant strains with codon mutation S217L into three fragments of 461, 287, and 54 bp. In contrast, TasI digestion of the 802-bp PCR products of phenamacril-sensitive strains resulted in only two fragments of 515 and 287 bp. DraI digested the 1,649-bp PCR products of phenamacril-resistant strains with codon mutation E420K into two fragments of 932 and 717 bp, while the PCR products of phenamacril-sensitive strains was not digested. The three genotypes of resistance mutations were determined by analyzing electrophoresis patterns of the digestion fragments of PCR products. The PCR-RFLP method was evaluated on 48 phenamacril-resistant strains induced by fungicide domestication in vitro and compared with the conventional method (mycelial growth on fungicide-amended agar). The accuracy of the PCR-RFLP method for detecting the three mutation genotypes of F. graminearum resistant to phenamacril was 95.12% compared with conventional method. Bioinformatics analysis revealed that the PCR-RFLP method could also be used to detect the codon mutations of A135T and E420K in F. asiaticum.
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Affiliation(s)
- Jiao-Sheng Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Luo-Yu Wu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Hui Zhang
- College of Agronomy, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xiu-Shi Song
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jian-Xin Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ming-Guo Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yi-Ping Hou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
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27
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Associations of the Rate of Change in Geriatric Depression Scale with Amyloid and Cerebral Glucose Metabolism in Cognitively Normal Older Adults: A Longitudinal Study. J Affect Disord 2021; 280:77-84. [PMID: 33202341 DOI: 10.1016/j.jad.2020.10.078] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/09/2020] [Accepted: 10/31/2020] [Indexed: 01/10/2023]
Abstract
BACKGROUND Depression is considered a psychological risk factor for Alzheimer's disease (AD). We sought to examine the differential associations of depression severity with cognitive decline, clinical progression to mild cognitive impairment (MCI) or AD, and neuroimaging markers of AD in cognitively normal older adults. METHODS A total of 522 cognitively normal (CN) participants who underwent assessments for depression (longitudinal geriatric depression scale [GDS] ) and cognitive assessments were included from the Alzheimer Disease Neuroimaging Initiative (ADNI) cohort. The cross-sectional and longitudinal associations of the rate of change in GDS with amyloid-β (Aβ)-positron emission tomography (PET), tau-PET, and 18F-fluorodeoxyglucose (FDG)-PET were explored. Kaplan-Meier survival curves of clinical progression and Aβ accumulation were plotted based on mean annual changes in GDS. Mediation analyses were utilized to explore the mediation effects of AD markers. RESULTS Higher rate of increase in GDS was associated with faster cognitive decline and higher risk of progression to MCI or AD. Moreover, the rate of change in GDS was significantly associated with Aβ accumulation and cerebral glucose metabolism. The influences of the rate of change in GDS on cognition and clinical progression were partially mediated by Aβ accumulation and cerebral glucose metabolism. LIMITATIONS GDS is a self-reported questionnaire and not the same as a clinical diagnosis of depression. CONCLUSIONS The cognitive and clinical consequences of changes in depressive symptoms partly stem from Aβ accumulation and cerebral glucose metabolism, which increases our understanding of how depressive symptoms may increase vulnerability to dementia.
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Kalendar R, Baidyussen A, Serikbay D, Zotova L, Khassanova G, Kuzbakova M, Jatayev S, Hu YG, Schramm C, Anderson PA, Jenkins CLD, Soole KL, Shavrukov Y. Modified "Allele-Specific qPCR" Method for SNP Genotyping Based on FRET. FRONTIERS IN PLANT SCIENCE 2021; 12:747886. [PMID: 35082803 PMCID: PMC8784781 DOI: 10.3389/fpls.2021.747886] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/22/2021] [Indexed: 05/02/2023]
Abstract
The proposed method is a modified and improved version of the existing "Allele-specific q-PCR" (ASQ) method for genotyping of single nucleotide polymorphism (SNP) based on fluorescence resonance energy transfer (FRET). This method is similar to frequently used techniques like Amplifluor and Kompetitive allele specific PCR (KASP), as well as others employing common universal probes (UPs) for SNP analyses. In the proposed ASQ method, the fluorophores and quencher are located in separate complementary oligonucleotides. The ASQ method is based on the simultaneous presence in PCR of the following two components: an allele-specific mixture (allele-specific and common primers) and a template-independent detector mixture that contains two or more (up to four) universal probes (UP-1 to 4) and a single universal quencher oligonucleotide (Uni-Q). The SNP site is positioned preferably at a penultimate base in each allele-specific primer, which increases the reaction specificity and allele discrimination. The proposed ASQ method is advanced in providing a very clear and effective measurement of the fluorescence emitted, with very low signal background-noise, and simple procedures convenient for customized modifications and adjustments. Importantly, this ASQ method is estimated as two- to ten-fold cheaper than Amplifluor and KASP, and much cheaper than all those methods that rely on dual-labeled probes without universal components, like TaqMan and Molecular Beacons. Results for SNP genotyping in the barley genes HvSAP16 and HvSAP8, in which stress-associated proteins are controlled, are presented as proven and validated examples. This method is suitable for bi-allelic uniplex reactions but it can potentially be used for 3- or 4-allelic variants or different SNPs in a multiplex format in a range of applications including medical, forensic, or others involving SNP genotyping.
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Affiliation(s)
- Ruslan Kalendar
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
- Institute of Biotechnology HiLIFE, University of Helsinki, Helsinki, Finland
- *Correspondence: Ruslan Kalendar
| | - Akmaral Baidyussen
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Dauren Serikbay
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Lyudmila Zotova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Gulmira Khassanova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Marzhan Kuzbakova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Yin-Gang Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Carly Schramm
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Peter A. Anderson
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Colin L. D. Jenkins
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Kathleen L. Soole
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
- Yuri Shavrukov
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29
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Liu N, Zhang X, Tang X, Liu Y, Huang D, Xiao X. A double-stranded DNA catalyzed strand displacement system for detection of small genetic variations. Chem Commun (Camb) 2020; 56:14397-14400. [PMID: 33140767 DOI: 10.1039/d0cc06216b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A double-stranded DNA catalyzed strand displacement system (dsCSD) was established for the detection of small genetic variations, which showed greatly enhanced specificity compared to the conventional single-stranded DNA catalyzed strand displacement (ssCSD) system. The system achieved limits of detection (LODs) of 0.05% and 0.1% for synthesized DNA samples and clinical gene samples, respectively.
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Affiliation(s)
- Na Liu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China.
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30
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Zhang K, Deng R, Gao H, Teng X, Li J. Lighting up single-nucleotide variation in situ in single cells and tissues. Chem Soc Rev 2020; 49:1932-1954. [PMID: 32108196 DOI: 10.1039/c9cs00438f] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ability to 'see' genetic information directly in single cells can provide invaluable insights into complex biological systems. In this review, we discuss recent advances of in situ imaging technologies for visualizing the subtlest sequence alteration, single-nucleotide variation (SNV), at single-cell level. The mechanism of recently developed methods for SNV discrimination are summarized in detail. With recent developments, single-cell SNV imaging methods have opened a new door for studying the heterogenous and stochastic genetic information in individual cells. Furthermore, SNV imaging can be used on morphologically preserved tissue, which can provide information on histological context for gene expression profiling in basic research and genetic diagnosis. Moreover, the ability to visualize SNVs in situ can be further developed into in situ sequencing technology. We expect this review to inspire more research work into in situ SNV imaging technologies for investigating cellular phenotypes and gene regulation at single-nucleotide resolution, and developing new clinical and biomedical applications.
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Affiliation(s)
- Kaixiang Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China. and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ruijie Deng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China.
| | - Hua Gao
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China. and Department of Pathogeny Biology, Medical College, Zhengzhou University, Zhengzhou 450001, China
| | - Xucong Teng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China.
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China.
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Yokouchi Y, Suzuki S, Ohtsuki N, Yamamoto K, Noguchi S, Soejima Y, Goto M, Ishioka K, Nakamura I, Suzuki S, Takenoshita S, Era T. Rapid repair of human disease-specific single-nucleotide variants by One-SHOT genome editing. Sci Rep 2020; 10:13927. [PMID: 32811847 PMCID: PMC7435196 DOI: 10.1038/s41598-020-70401-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 07/24/2020] [Indexed: 12/26/2022] Open
Abstract
Many human diseases ranging from cancer to hereditary disorders are caused by single-nucleotide mutations in critical genes. Repairing these mutations would significantly improve the quality of life for patients with hereditary diseases. However, current procedures for repairing deleterious single-nucleotide mutations are not straightforward, requiring multiple steps and taking several months to complete. In the current study, we aimed to repair pathogenic allele-specific single-nucleotide mutations using a single round of genome editing. Using high-fidelity, site-specific nuclease AsCas12a/Cpf1, we attempted to repair pathogenic single-nucleotide variants (SNVs) in disease-specific induced pluripotent stem cells. As a result, we achieved repair of the Met918Thr SNV in human oncogene RET with the inclusion of a single-nucleotide marker, followed by absolute markerless, scarless repair of the RET SNV with no detected off-target effects. The markerless method was then confirmed in human type VII collagen-encoding gene COL7A1. Thus, using this One-SHOT method, we successfully reduced the number of genetic manipulations required for genome repair from two consecutive events to one, resulting in allele-specific repair that can be completed within 3 weeks, with or without a single-nucleotide marker. Our findings suggest that One-SHOT can be used to repair other types of mutations, with potential beyond human medicine.
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Affiliation(s)
- Yuji Yokouchi
- Pluripotent Stem Cell Research Unit in Department of Thyroid and Endocrinology, School of Medicine, Fukushima Medical University, 1 Hikariga-oka, Fukushima, 960-1295, Japan. .,Department of Thyroid and Endocrinology, School of Medicine, Fukushima Medical University, Fukushima, Japan.
| | - Shinichi Suzuki
- Department of Thyroid and Endocrinology, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Noriko Ohtsuki
- Pluripotent Stem Cell Research Unit in Department of Thyroid and Endocrinology, School of Medicine, Fukushima Medical University, 1 Hikariga-oka, Fukushima, 960-1295, Japan.,Department of Thyroid and Endocrinology, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Kei Yamamoto
- Pluripotent Stem Cell Research Unit in Department of Thyroid and Endocrinology, School of Medicine, Fukushima Medical University, 1 Hikariga-oka, Fukushima, 960-1295, Japan.,Department of Thyroid and Endocrinology, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Satomi Noguchi
- Pluripotent Stem Cell Research Unit in Department of Thyroid and Endocrinology, School of Medicine, Fukushima Medical University, 1 Hikariga-oka, Fukushima, 960-1295, Japan.,Department of Thyroid and Endocrinology, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Yumi Soejima
- Department of Cell Modulation, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan
| | - Mizuki Goto
- Department of Cell Modulation, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan.,Department of Dermatology, Faculty of Medicine, Oita University, Yufu, Japan
| | - Ken Ishioka
- Department of Microbiology, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Izumi Nakamura
- Pluripotent Stem Cell Research Unit in Department of Thyroid and Endocrinology, School of Medicine, Fukushima Medical University, 1 Hikariga-oka, Fukushima, 960-1295, Japan.,Department of Thyroid and Endocrinology, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Satoru Suzuki
- Office of Thyroid Ultrasound Examination Promotion, Radiation Medical Science Centre for the Fukushima Health Management Survey, Fukushima Medical University, Fukushima, Japan
| | | | - Takumi Era
- Pluripotent Stem Cell Research Unit in Department of Thyroid and Endocrinology, School of Medicine, Fukushima Medical University, 1 Hikariga-oka, Fukushima, 960-1295, Japan.,Department of Thyroid and Endocrinology, School of Medicine, Fukushima Medical University, Fukushima, Japan.,Department of Cell Modulation, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan
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32
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Wu Y, Li M, He Z, Dreisigacker S, Wen W, Jin H, Zhai S, Li F, Gao F, Liu J, Wang R, Zhang P, Wan Y, Cao S, Xia X. Development and validation of high-throughput and low-cost STARP assays for genes underpinning economically important traits in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2431-2450. [PMID: 32451598 DOI: 10.1007/s00122-020-03609-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 05/13/2020] [Indexed: 05/12/2023]
Abstract
We developed and validated 56 gene-specific semi-thermal asymmetric reverse PCR (STARP) markers for 46 genes of important wheat quality, biotic and abiotic stress resistance, grain yield, and adaptation-related traits for marker-assisted selection in wheat breeding. Development of high-throughput, low-cost, gene-specific molecular markers is important for marker-assisted selection in wheat breeding. In this study, we developed 56 gene-specific semi-thermal asymmetric reverse PCR (STARP) markers for wheat quality, tolerance to biotic and abiotic stresses, grain yield, and adaptation-related traits. The STARP assays were validated by (1) comparison of the assays with corresponding diagnostic STS/CAPS markers on 40 diverse wheat cultivars and (2) characterization of allelic effects based on the phenotypic and genotypic data of three segregating populations and 305 diverse wheat accessions from China and 13 other countries. The STARP assays showed the advantages of high-throughput, accuracy, flexibility, simple assay design, low operational costs, and platform compatibility. The state-of-the-art assays of this study provide a robust and reliable molecular marker toolkit for wheat breeding programs.
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Affiliation(s)
- Yuying Wu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Ming Li
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Susanne Dreisigacker
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
| | - Weie Wen
- Department of Cell Biology, Zunyi Medical University, 201 Dalian Road, Zunyi, 563099, Guizhou, China
| | - Hui Jin
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, 368 Xuefu Street, Harbin, 150086, Heilongjiang, China
| | - Shengnan Zhai
- Crop Research Institute, National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement in the Northern Yellow-Huai Rivers Valley of Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, Shandong, China
| | - Faji Li
- Crop Research Institute, National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement in the Northern Yellow-Huai Rivers Valley of Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, Shandong, China
| | - Fengmei Gao
- Crop Research Institute, Heilongjiang Academy of Agricultural Sciences, 368 Xuefu Street, Harbin, 150086, Heilongjiang, China
| | - Jindong Liu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Shenzhen, 518120, Guangdong, China
| | - Rongge Wang
- Farm of Seed Production of Gaoyi County, Gaoyi, 051330, Hebei, China
| | - Pingzhi Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, 40 Nongke South Street, Hefei, 230001, Anhui, China
| | - Yingxiu Wan
- Crop Research Institute, Anhui Academy of Agricultural Sciences, 40 Nongke South Street, Hefei, 230001, Anhui, China
| | - Shuanghe Cao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
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Rapid and sensitive screening and identification of CRISPR/Cas9 edited rice plants using quantitative real-time PCR coupled with high resolution melting analysis. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107088] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Jung S, Kim WJ, Kim BK, Kim J, Kim MJ, Kim KP, Kim SK. In-particle stem-loop RT-qPCR for specific and multiplex microRNA profiling. Biosens Bioelectron 2020; 163:112301. [PMID: 32568699 DOI: 10.1016/j.bios.2020.112301] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/23/2020] [Accepted: 05/13/2020] [Indexed: 01/15/2023]
Abstract
Here we report a novel method of microRNA (miRNA) profiling with particle-based multiplex quantitative reverse transcription polymerase chain reaction (RT-qPCR). To achieve target-specific reaction in a particle, the stem-loop RT primer and forward primer for each target miRNA were chemically immobilized to the particle. Target-specific cDNA synthesis proceeds with the stem-loop RT primer and then qPCR subsequently proceeds with the forward primer to rapidly achieve a quantitative result. High-fidelity multiplex assay was also accomplished in a single PCR process by loading multiple particles for each specific miRNA. The method for primer supply in the particles, involving confinement of the target-specific RT and PCR primers in the matrix of particles, led to the reduction of nonspecific reactions and improved the selectivity of the miRNA assay while minimizing labor in a multiple target assay. Specifically, this particle-based assay enabled the differentiation of mature miRNA from precursor with selectivity of 270:1 in terms of amplification speed. This advanced method also showed good discrimination among highly homologous let-7 family members, with cross-reaction rates of less than 5%. We demonstrated a very simple process of five-plex miRNA profiling in total RNA, and the measured changes in expression level were consistent with those from a conventional singleplex method.
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Affiliation(s)
- Seungwon Jung
- Center for Molecular Recognition Research, Materials and Life Science Research Division, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Applied Chemistry, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Won Jin Kim
- Center for Molecular Recognition Research, Materials and Life Science Research Division, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Applied Chemistry, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Bong Kyun Kim
- Center for Molecular Recognition Research, Materials and Life Science Research Division, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Biomedical Engineering, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Junsun Kim
- Center for Molecular Recognition Research, Materials and Life Science Research Division, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Mi Jung Kim
- Center for Molecular Recognition Research, Materials and Life Science Research Division, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Kwang Pyo Kim
- Applied Chemistry, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Sang Kyung Kim
- Center for Molecular Recognition Research, Materials and Life Science Research Division, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Biomedical Engineering, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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DNA methylation and one-carbon metabolism related nutrients and polymorphisms: analysis after mandatory flour fortification with folic acid. Br J Nutr 2020; 123:23-29. [PMID: 31583988 DOI: 10.1017/s0007114519002526] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
There is a growing research interest in determining whether changes in the global status of DNA methylation are related to the environment, in particular, to one-carbon metabolism. So, our aim was to investigate the effect of dietary methyl-group donor intake (methionine, folate, choline, betaine, vitamins B2, B6 and B12), biomarkers (total folate, unmetabolised folic acid (FA), 5-methyltetrahydrofolate, homocysteine, vitamins B6 and B12 concentrations) and genetic variants (polymorphisms involved in one-carbon metabolism) on global DNA methylation in a population exposed to mandatory flour fortification with FA. A cross-sectional study of health and living conditions was conducted among a representative sample of residents in São Paulo, Brazil. The mean of global DNA methylation was lower in young people than in adults and the elderly (P = 0·049). No differences between genotypes of polymorphism and global DNA methylation mean were identified. We observed that the increase in betaine intake led to an absolute change in percentage of DNA methylation (β = 0·0005, P = 0·024) using multiple regression. Betaine intake alone was associated with an absolute change in percentage of global DNA methylation. The study did not find an association between global DNA methylation and folate status even in a population exposed to mandatory flour fortification with FA.
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Ding X, Yin K, Chen J, Wang K, Liu C. A ribonuclease-dependent cleavable beacon primer triggering DNA amplification for single nucleotide mutation detection with ultrahigh sensitivity and selectivity. Chem Commun (Camb) 2019; 55:12623-12626. [PMID: 31580354 DOI: 10.1039/c9cc06296c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We described a ribonuclease-dependent cleavable beacon primer, an energy-transfer-tagged oligonucleotide inserted with a ribonucleotide, which can be cleaved by ribonuclease to generate enhanced fluorescence signals and initiate DNA amplification for single nucleotide mutation detection with ultrahigh sensitivity and selectivity.
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Affiliation(s)
- Xiong Ding
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut 06030, USA.
| | - Kun Yin
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut 06030, USA.
| | - Ju Chen
- Department of Immunology, School of Medicine, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Kepeng Wang
- Department of Immunology, School of Medicine, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Changchun Liu
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut 06030, USA.
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Benavides F, Rülicke T, Prins JB, Bussell J, Scavizzi F, Cinelli P, Herault Y, Wedekind D. Genetic quality assurance and genetic monitoring of laboratory mice and rats: FELASA Working Group Report. Lab Anim 2019; 54:135-148. [PMID: 31431136 PMCID: PMC7160752 DOI: 10.1177/0023677219867719] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Genetic quality assurance (QA), including genetic monitoring (GeMo) of inbred
strains and background characterization (BC) of genetically altered (GA) animal
models, should be an essential component of any QA programme in laboratory
animal facilities. Genetic quality control is as important for ensuring the
validity of the animal model as health and microbiology monitoring are. It
should be required that studies using laboratory rodents, mainly mice and rats,
utilize genetically defined animals. This paper, presented by the FELASA Working
Group on Genetic Quality Assurance and Genetic Monitoring of Laboratory Murines,
describes the objectives of and available methods for genetic QA programmes in
rodent facilities. The main goals of any genetic QA programme are: (a) to verify
the authenticity and uniformity of inbred stains and substrains, thus ensuring a
genetically reliable colony maintenance; (b) to detect possible genetic
contamination; and (c) to precisely describe the genetic composition of GA
lines. While this publication focuses mainly on mouse and rat genetic QA, the
principles will apply to other rodent species some of which are briefly
mentioned within the context of inbred and outbred stocks.
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Affiliation(s)
- Fernando Benavides
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas, MD Anderson Cancer Center, USA
| | - Thomas Rülicke
- Institute of Laboratory Animal Science, University of Veterinary Medicine, Vienna, Austria
| | - Jan-Bas Prins
- The Francis Crick Institute, London, UK.,Leiden University Medical Centre, Leiden, The Netherlands
| | - James Bussell
- Biomedical and Veterinary Services Department, University of Oxford, Oxford, UK
| | | | - Paolo Cinelli
- Department of Trauma Surgery, University of Zurich, Zurich, Switzerland
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique Biologie Moléculaire et Cellulaire, IGBMC, Illkirch, France.,Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, CELPHEDIA-PHENOMIN-ICS, Illkirch, France
| | - Dirk Wedekind
- Institute of Laboratory Animal Science, Hannover Medical School, Hannover, Germany
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The association between genetic risk score and blood pressure is modified by coffee consumption: Gene–diet interaction analysis in a population-based study. Clin Nutr 2019; 38:1721-1728. [DOI: 10.1016/j.clnu.2018.07.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 07/17/2018] [Accepted: 07/25/2018] [Indexed: 12/19/2022]
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Ehnert S, Linnemann C, Braun B, Botsch J, Leibiger K, Hemmann P, Nussler AAK. One-Step ARMS-PCR for the Detection of SNPs-Using the Example of the PADI4 Gene. Methods Protoc 2019; 2:mps2030063. [PMID: 31349745 PMCID: PMC6789486 DOI: 10.3390/mps2030063] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/22/2019] [Accepted: 07/22/2019] [Indexed: 12/16/2022] Open
Abstract
In eukaryotes, cellular functions are tightly controlled by diverse post-translational modifications (PTMs) of proteins. One such PTM affecting many proteins is the deimination of arginine to citrulline. This process, called citrullination is catalyzed by a group of hydrolases called protein arginine deiminases (PADs), of which five isoforms have been identified. Hypercitrullination, as a result of increased PAD expression or activity, is associated with autoimmune diseases e.g., rheumatoid arthritis, lupus, Alzheimer’s disease, ulcerative colitis, multiple sclerosis, and certain cancers. Three common single nucleotide polymorphisms (SNPs) in the PADI4 gene have been described, namely rs874881, rs11203366, and rs11203367, which are thought to affect PAD4 expression and activity. We here compared the suitability of four methods for the screening of SNPs in the PADI4 gene: (i) SYBR-green based real-time polymerase chain reaction followed by high resolution melting curve analysis (HRM-PCR); (ii) PCR followed by detection of restriction fragment length polymorphisms (PCR-RFLP); (iii) conventional tetra-primer amplification refractory mutation system PCR (ARMS-PCR); and (iv) real-time PCR based on the one-step ARMS-PCR. Of these, ARMS-PCR proved to be the most suitable method regarding handling, duration, and cost of experiments. Using the method with SYBR-green based real-time PCR reagents further diminished handling steps and thus potential sources of error.
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Affiliation(s)
- Sabrina Ehnert
- Siegfried Weller Research Institute, Department of Trauma and Reconstructive Surgery, Eberhard Karls University Tübingen, BG Trauma Center Tübingen, 72076 Tübingen, Germany.
| | - Caren Linnemann
- Siegfried Weller Research Institute, Department of Trauma and Reconstructive Surgery, Eberhard Karls University Tübingen, BG Trauma Center Tübingen, 72076 Tübingen, Germany
| | - Bianca Braun
- Siegfried Weller Research Institute, Department of Trauma and Reconstructive Surgery, Eberhard Karls University Tübingen, BG Trauma Center Tübingen, 72076 Tübingen, Germany
| | - Josephine Botsch
- Siegfried Weller Research Institute, Department of Trauma and Reconstructive Surgery, Eberhard Karls University Tübingen, BG Trauma Center Tübingen, 72076 Tübingen, Germany
| | - Karolin Leibiger
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Philipp Hemmann
- Siegfried Weller Research Institute, Department of Trauma and Reconstructive Surgery, Eberhard Karls University Tübingen, BG Trauma Center Tübingen, 72076 Tübingen, Germany
| | - And Andreas K Nussler
- Siegfried Weller Research Institute, Department of Trauma and Reconstructive Surgery, Eberhard Karls University Tübingen, BG Trauma Center Tübingen, 72076 Tübingen, Germany
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Wang M, Xu F, Chen K, Li X, Li K, Zhou Y, Xiao J. A multiplex SNP genotyping by allele-specificspecific PCR based on stem-loop and universal fluorescent primers of Chr1 daxin mice. Electrophoresis 2019; 40:1600-1605. [PMID: 30801725 DOI: 10.1002/elps.201900052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 02/23/2019] [Accepted: 02/18/2019] [Indexed: 01/16/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are one of the most common markers in mammals. Rapid, accurate, and multiplex typing of SNPs is critical for subsequent biological and genetic research. In this study, we have developed a novel method for multiplex genotyping SNPs in mice. The method involves allele-specific PCR amplification of genomic DNA with two stem-loop primers accompanied by two different universal fluorescent primers. Blue and green fluorescent signals were conveniently detected on a DNA sequencer. We verified four SNPs of 65 mice based on the novel method, and it is well suited for multiplex genotyping as it requires only one reaction per sample in a single tube with multiplex PCR. The use of universal fluorescent primers greatly reduces the cost of designing different fluorescent probes for each SNP. Therefore, this method can be applied to many biological and genetic studies, such as multiple candidate gene testing, genome-wide association study, pharmacogenetics, and medical diagnostics.
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Affiliation(s)
- Maochun Wang
- Institute of Biological Science and Biotechnology, Donghua University, Shanghai, P. R. China
| | - Fuyi Xu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, USA
| | - Ke Chen
- College of Environmental Science and Engineering, Donghua University, Shanghai, P. R. China
| | - Xiaoning Li
- Institute of Biological Science and Biotechnology, Donghua University, Shanghai, P. R. China
| | - Kai Li
- Institute of Biological Science and Biotechnology, Donghua University, Shanghai, P. R. China
| | - Yuxun Zhou
- Institute of Biological Science and Biotechnology, Donghua University, Shanghai, P. R. China
| | - Junhua Xiao
- Institute of Biological Science and Biotechnology, Donghua University, Shanghai, P. R. China
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Carmona-Antoñanzas G, Helgesen KO, Humble JL, Tschesche C, Bakke MJ, Gamble L, Bekaert M, Bassett DI, Horsberg TE, Bron JE, Sturm A. Mutations in voltage-gated sodium channels from pyrethroid resistant salmon lice (Lepeophtheirus salmonis). PEST MANAGEMENT SCIENCE 2019; 75:527-536. [PMID: 30062864 DOI: 10.1002/ps.5151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/22/2018] [Accepted: 07/19/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Parasitic salmon lice (Lepeophtheirus salmonis) cause high economic losses in Atlantic salmon farming. Pyrethroids, which block arthropod voltage-gated sodium channels (Nav 1), are used for salmon delousing. However, pyrethroid resistance is common in L. salmonis. The present study characterized Nav 1 homologues in L. salmonis in order to identify channel mutations associated to resistance, called kdr (knockdown) mutations. RESULTS Genome scans identified three L. salmonis Nav 1 homologues, LsNav 1.1, LsNav 1.2 and LsNav 1.3. Arthropod kdr mutations map to specific Nav 1 regions within domains DI-III, namely segments S5 and S6 and the linker helix connecting S4 and S5. The above channel regions were amplified by RT-PCR and sequenced in deltamethrin-susceptible and deltamethrin-resistant L. salmonis. While LsNav 1.1 and LsNav 1.2 lacked nucleotide polymorphisms showing association to resistance, LsNav 1.3 showed a non-synonymous mutation in S5 of DII occurring in deltamethrin-resistant parasites. The mutation is homologous to a previously described kdr mutation (I936V, numbering according to Musca domestica Vssc1) and was present in two pyrethroid-resistant L. salmonis strains (allele frequencies of 0.800 and 0.357), but absent in two pyrethroid-susceptible strains. CONCLUSIONS The present study indicates that a kdr-mutation in LsNaV 1.3 may contribute to deltamethrin resistance in L. salmonis. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Greta Carmona-Antoñanzas
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK
- Imegen, Parc Científic de la Universitat de València, Paterna, Spain
| | - Kari O Helgesen
- Department of Epidemiology, Norwegian Veterinary Institute, Oslo, Norway
| | - Joseph L Humble
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - Claudia Tschesche
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - Marit J Bakke
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Sea Lice Research Centre, Oslo, Norway
| | - Louise Gamble
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - Michaël Bekaert
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - David I Bassett
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - Tor E Horsberg
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Sea Lice Research Centre, Oslo, Norway
| | - James E Bron
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - Armin Sturm
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK
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Identification of Thermus aquaticus DNA polymerase variants with increased mismatch discrimination and reverse transcriptase activity from a smart enzyme mutant library. Sci Rep 2019; 9:590. [PMID: 30679705 PMCID: PMC6345897 DOI: 10.1038/s41598-018-37233-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/02/2018] [Indexed: 12/13/2022] Open
Abstract
DNA polymerases the key enzymes for several biotechnological applications. Obviously, nature has not evolved these enzymes to be compatible with applications in biotechnology. Thus, engineering of a natural scaffold of DNA polymerases may lead to enzymes improved for several applications. Here, we investigated a two-step approach for the design and construction of a combinatorial library of mutants of KlenTaq DNA polymerase. First, we selected amino acid sites for saturation mutagenesis that interact with the primer/template strands or are evolutionarily conserved. From this library, we identified mutations that little interfere with DNA polymerase activity. Next, these functionally active mutants were combined randomly to construct a second library with enriched sequence diversity. We reasoned that the combination of mutants that have minuscule effect on enzyme activity and thermostability, will result in entities that have an increased mutation load but still retain activity. Besides activity and thermostability, we screened the library for entities with two distinct properties. Indeed, we identified two different KlenTaq DNA polymerase variants that either exhibit increased mismatch extension discrimination or increased reverse transcription PCR activity, respectively.
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Teixeira JA, Steluti J, Gorgulho BM, Carioca AAF, Alencar GP, Fisberg RM, Marchioni DM. Prudent dietary pattern influences homocysteine level more than folate, vitamin B12, and docosahexaenoic acid: a structural equation model approach. Eur J Nutr 2019; 59:81-91. [DOI: 10.1007/s00394-018-1886-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 12/19/2018] [Indexed: 12/20/2022]
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44
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Lee J. Development and Evolution of Molecular Markers and Genetic Maps in Capsicum Species. COMPENDIUM OF PLANT GENOMES 2019. [DOI: 10.1007/978-3-319-97217-6_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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45
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Zhang X, Yang L, Wang F, Liu Z, Liu R, Ying Q, Fan C, Wu X. Development of a Simple and Cost-Effective Method Based on T7 Endonuclease Cleavage for Detection of Single Nucleotide Polymorphisms. Genet Test Mol Biomarkers 2018; 22:719-723. [PMID: 30484704 DOI: 10.1089/gtmb.2018.0181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
AIMS Single nucleotide polymorphisms (SNP) can be used as genetic markers and for risk assessment of allele-linked diseases, which can provide information for clinical diagnosis. Large-scale microarray and next-generation sequencing methods have made genome-wide SNP genotyping possible. However, in addition to their high cost, these techniques are dependent on having specialized equipment. Thus, there is a need for a simple genotyping method that can be implemented in a resource-limited environment. METHODS We developed a strategy for SNP genotyping based on T7 Endonuclease I cleavage and an enzyme-linked microparticle immune assay. Using this method, we genotyped two common SNP sites (rs11526468 and rs12979860). The quality of the genotyping process was validated. RESULTS Although a 70% false-negative rate was observed, no false-positive reactions were found. Therefore, multiple parallel repeat reactions can offset the possibility of mutation detection failure. DISCUSSION This method employs a duplicate reagent-dependent procedure, and therefore has the potential for integration into a portable kit for field utilization.
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Affiliation(s)
- Xiaoxiao Zhang
- 1 Department of Microbiology, Fourth Military Medical University, Xi'an, China
| | - Lina Yang
- 2 Institute for Hygiene of Ordernance Industry, Xi'an, China
| | - Fang Wang
- 1 Department of Microbiology, Fourth Military Medical University, Xi'an, China
| | - Ziyu Liu
- 1 Department of Microbiology, Fourth Military Medical University, Xi'an, China
| | - Rongrong Liu
- 1 Department of Microbiology, Fourth Military Medical University, Xi'an, China
| | - Qikang Ying
- 1 Department of Microbiology, Fourth Military Medical University, Xi'an, China
| | - Chao Fan
- 3 Department of Infectious Diseases and Center of Liver Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Xingan Wu
- 1 Department of Microbiology, Fourth Military Medical University, Xi'an, China
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Presence of circulating folic acid in plasma and its relation with dietary intake, vitamin B complex concentrations and genetic variants. Eur J Nutr 2018; 58:3069-3077. [DOI: 10.1007/s00394-018-1852-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 10/29/2018] [Indexed: 12/28/2022]
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Zotova L, Kurishbayev A, Jatayev S, Khassanova G, Zhubatkanov A, Serikbay D, Sereda S, Sereda T, Shvidchenko V, Lopato S, Jenkins C, Soole K, Langridge P, Shavrukov Y. Genes Encoding Transcription Factors TaDREB5 and TaNFYC-A7 Are Differentially Expressed in Leaves of Bread Wheat in Response to Drought, Dehydration and ABA. FRONTIERS IN PLANT SCIENCE 2018; 9:1441. [PMID: 30319682 PMCID: PMC6171087 DOI: 10.3389/fpls.2018.01441] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/10/2018] [Indexed: 05/18/2023]
Abstract
Two groups of six spring bread wheat varieties with either high or low grain yield under the dry conditions of Central and Northern Kazakhstan were selected for analysis. Experiments were set up with the selected wheat varieties in controlled environments as follows: (1) slowly progressing drought imposed on plants in soil, (2) rapid dehydration of whole plants grown in hydroponics, (3) dehydration of detached leaves, and (4) ABA treatment of whole plants grown in hydroponics. Representatives of two different families of transcription factors (TFs), TaDREB5 and TaNFYC-A7, were found to be linked to yield-under-drought using polymorphic Amplifluor-like SNP marker assays. qRT-PCR revealed differing patterns of expression of these genes in the leaves of plants subjected to the above treatments. Under drought, TaDREB5 was significantly up-regulated in leaves of all high-yielding varieties tested and down-regulated in all low-yielding varieties, and the level of expression was independent of treatment type. In contrast, TaNFYC-A7 expression levels showed different responses in the high- and low-yield groups of wheat varieties. TaNFYC-A7 expression under dehydration (treatments 2 and 3) was higher than under drought (treatment 1) in all high-yielding varieties tested, while in all low-yielding varieties the opposite pattern was observed: the expression levels of this gene under drought were higher than under dehydration. Rapid dehydration of detached leaves and intact wheat plants grown in hydroponics produced similar changes in gene expression. ABA treatment of whole plants caused rapid stomatal closure and a rise in the transcript level of both genes during the first 30 min, which decreased 6 h after treatment. At this time-point, expression of TaNFYC-A7 was again significantly up-regulated compared to untreated controls, while TaDREB5 returned to its initial level of expression. These findings reveal significant differences in the transcriptional regulation of two drought-responsive and ABA-dependent TFs under slowly developing drought and rapid dehydration of wheat plants. The results obtained suggest that correlation between grain yield in dry conditions and TaNFYC-A7 expression levels in the examined wheat varieties is dependent on the length of drought development and/or strength of drought; while in the case of TaDREB5, no such dependence is observed.
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Affiliation(s)
- Lyudmila Zotova
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Akhylbek Kurishbayev
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Gulmira Khassanova
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Askar Zhubatkanov
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Dauren Serikbay
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Sergey Sereda
- Karaganda Research Institute of Plant Industry and Breeding, Karaganda, Kazakhstan
| | - Tatiana Sereda
- Karaganda Research Institute of Plant Industry and Breeding, Karaganda, Kazakhstan
| | - Vladimir Shvidchenko
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Sergiy Lopato
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Colin Jenkins
- College of Science and Engineering, Biological Sciences, Flinders University, Bedford Park, SA, Australia
| | - Kathleen Soole
- College of Science and Engineering, Biological Sciences, Flinders University, Bedford Park, SA, Australia
| | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Bedford Park, SA, Australia
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Jatayev S, Kurishbayev A, Zotova L, Khasanova G, Serikbay D, Zhubatkanov A, Botayeva M, Zhumalin A, Turbekova A, Soole K, Langridge P, Shavrukov Y. Advantages of Amplifluor-like SNP markers over KASP in plant genotyping. BMC PLANT BIOLOGY 2017; 17:254. [PMID: 29297326 PMCID: PMC5751575 DOI: 10.1186/s12870-017-1197-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
BACKGROUND KASP (KBioscience Competitive Allele Specific PCR) and Amplifluor (Amplification with fluorescence) SNP markers are two prominent technologies based upon a shared identical Allele-specific PCR platform. METHODS Amplifluor-like SNP and KASP analysis was carried out using published and own design of Universal probes (UPs) and Gene-specific primers (GSPs). RESULTS Advantages of the Amplifluor-like system over KASP include the significantly lower costs and much greater flexibility in the adjustment and development of 'self-designed' dual fluorescently-labelled UPs and regular GSPs. The presented results include optimisation of 'tail' length in UPs and GSPs, protocol adjustment, and the use of various fluorophores in different qPCR instruments. The compatibility of the KASP Master-mix in both original and Amplifluor-like systems has been demonstrated in the presented results, proving their similar principles. Results of SNP scoring with rare alleles in addition to more frequently occurring alleles are shown. CONCLUSIONS The Amplifluor-like system produces SNP genotyping results with a level of sensitivity and accuracy comparable to KASP but at a significantly cheaper cost and with much greater flexibility for UPs with self-designed GSPs.
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Affiliation(s)
- Satyvaldy Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Akhylbek Kurishbayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Lyudmila Zotova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Gulmira Khasanova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Dauren Serikbay
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Askar Zhubatkanov
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Makpal Botayeva
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Aibek Zhumalin
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Arysgul Turbekova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Kathleen Soole
- School of Biological Sciences, Flinders University, Bedford Park, SA Australia
| | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA Australia
| | - Yuri Shavrukov
- School of Biological Sciences, Flinders University, Bedford Park, SA Australia
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA Australia
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Locked Nucleic Acid Technology for Highly Sensitive Detection of Somatic Mutations in Cancer. Adv Clin Chem 2017; 83:53-72. [PMID: 29304903 DOI: 10.1016/bs.acc.2017.10.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The molecular diagnosis of the cancer mutational status is essential for modern clinical laboratory medicine. Mutations in EGFR, KRAS, BRAF, and PIK3CA genes are widely analyzed in solid tumors such as lung cancer, colorectal cancer, breast cancer, and melanoma. The allele-specific polymerase chain reaction, high-resolution melting, and Sanger sequencing are used for detecting and identifying gene mutations in many clinical laboratories. The locked nucleic acid (LNA) is a class of nucleic acid analogs that contain a methylene bridge connecting the 2' oxygen and 4' carbon in the ribose moiety. This methylene bridge locks the ribose group into a C3'-endo conformation. LNA, including an oligonucleotide, increases the thermal stability of hybrid strands. The use of LNA technology in molecular diagnostic methods improves the specificity and sensitivity of assays. This review describes routinely analyzed mutations and molecular diagnostic methods used in the clinical laboratory along with the performance improvement of mutational analysis with LNA.
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He G, Li J, Qi C, Guo X. Single Nucleotide Polymorphism Genotyping in Single-Molecule Electronic Circuits. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2017; 4:1700158. [PMID: 29201610 PMCID: PMC5700462 DOI: 10.1002/advs.201700158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/20/2017] [Indexed: 05/08/2023]
Abstract
Establishing low-cost, high-throughput, simple, and accurate single nucleotide polymorphism (SNP) genotyping techniques is beneficial for understanding the intrinsic relationship between individual genetic variations and their biological functions on a genomic scale. Here, a straightforward and reliable single-molecule approach is demonstrated for precise SNP authentication by directly measuring the fluctuations in electrical signals in an electronic circuit, which is fabricated from a high-gain field-effect silicon nanowire decorated with a single hairpin DNA, in the presence of different target DNAs. By simply comparing the proportion difference of a probe-target duplex structure throughout the process, this study implements allele-specific and accurate SNP detection. These results are supported by the statistical analyses of different dynamic parameters such as the mean lifetime and the unwinding probability of the duplex conformation. In comparison with conventional polymerase chain reaction and optical methods, this convenient and label-free method is complementary to existing optical methods and also shows several advantages, such as simple operation and no requirement for fluorescent labeling, thus promising a futuristic route toward the next-generation genotyping technique.
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Affiliation(s)
- Gen He
- Beijing National Laboratory for Molecular SciencesState Key Laboratory for Structural Chemistry of Unstable and Stable SpeciesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871P. R. China
- Key Laboratory of RadiopharmaceuticalsMinistry of EducationCollege of ChemistryBeijing Normal UniversityBeijing100875P. R. China
| | - Jie Li
- Beijing National Laboratory for Molecular SciencesState Key Laboratory for Structural Chemistry of Unstable and Stable SpeciesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871P. R. China
- Key Laboratory of RadiopharmaceuticalsMinistry of EducationCollege of ChemistryBeijing Normal UniversityBeijing100875P. R. China
| | - Chuanmin Qi
- Key Laboratory of RadiopharmaceuticalsMinistry of EducationCollege of ChemistryBeijing Normal UniversityBeijing100875P. R. China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular SciencesState Key Laboratory for Structural Chemistry of Unstable and Stable SpeciesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871P. R. China
- Department of Materials Science and EngineeringCollege of EngineeringPeking UniversityBeijing100871P. R. China
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