1
|
Filatov DA. ProSeq4: A user-friendly multiplatform program for preparation and analysis of large-scale DNA polymorphism datasets. Mol Ecol Resour 2024:e13962. [PMID: 38646687 DOI: 10.1111/1755-0998.13962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024]
Abstract
Preparation of DNA polymorphism datasets for analysis is an important step in evolutionary genetic and molecular ecology studies. Ever-growing dataset sizes make this step time consuming, but few convenient software tools are available to facilitate processing of large-scale datasets including thousands of sequence alignments. Here I report "processor of sequences v4" (proSeq4)-a user-friendly multiplatform software for preparation and evolutionary genetic analyses of genome- or transcriptome-scale sequence polymorphism datasets. The program has an easy-to-use graphic user interface and is designed to process and analyse many thousands of datasets. It supports over two dozen file formats, includes a flexible sequence editor and various tools for data visualization, quality control and most commonly used evolutionary genetic analyses, such as NJ-phylogeny reconstruction, DNA polymorphism analyses and coalescent simulations. Command line tools (e.g. vcf2fasta) are also provided for easier integration into bioinformatic pipelines. Apart of molecular ecology and evolution research, proSeq4 may be useful for teaching, e.g. for visual illustration of different shapes of phylogenies generated with coalescent simulations in different scenarios. ProSeq4 source code and binaries for Windows, MacOS and Ubuntu are available from https://sourceforge.net/projects/proseq/.
Collapse
|
2
|
Bose D, Banerjee N, Roy A, Sengupta P, Chatterjee S. Switchable tetraplex elements in the heterogeneous nuclear ribonucleoprotein K promoter: micro-environment dictated structural transitions of G/C rich elements. J Biomol Struct Dyn 2024:1-18. [PMID: 38235706 DOI: 10.1080/07391102.2024.2303378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
We have elucidated the hnRNP K promoter as a hotspot for tetraplex-based molecular switches receptive to micro-environmental stimuli. We have characterised the structural features of four tetraplex-forming loci and identified them as binding sites of transcription factors. These segments form either G-quadruplex or i-motif structures, the structural dynamicity of which has been studied in depth via several biophysical techniques. The tetraplexes display high dynamicity and are influenced by both pH and KCl concentrations in vitro. The loci complementary to these sequences form additional non-canonical secondary structures. In the cellular context, the most eminent observation of this study is the binding of hnRNP K to the i-motif forming sequences in its own promoter. We are the first to report a probable transcriptional autoregulatory function of hnRNP K in coordination with higher-order DNA structures. Herein, we also report the positive interaction of the endogenous tetraplexes with Sp1, a well-known transcriptional regulator. Treatment with tetraplex-specific small molecule ligands further uncovered G-quadruplexes' functioning as repressors and i-motifs as activators in this context. Together, our findings strongly indicate the critical regulatory role of the identified tetraplex elements in the hnRNP K promoter.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Debopriya Bose
- Department of Biological Sciences, Bose Institute, Kolkata, West Bengal, India
| | - Nilanjan Banerjee
- Department of Biological Sciences, Bose Institute, Kolkata, West Bengal, India
| | - Ananya Roy
- Department of Biological Sciences, Bose Institute, Kolkata, West Bengal, India
| | - Pallabi Sengupta
- Department of Medical Biochemistry and Biophysics, Kemihuset (K), Campus, Umeå, Umeå universitet, Umeå, Sweden
| | | |
Collapse
|
3
|
Paganová V, Hus M, Lichtnerová H, Žiarovská J, Moravčíková D, Kučka M, Ražná K, Abbas A. Physiological and Molecular Responses of Pyrus pyraster Seedlings to Salt Treatment Analyzed by miRNA and Cytochrome P450 Gene-Based Markers. Plants (Basel) 2024; 13:261. [PMID: 38256814 PMCID: PMC10820964 DOI: 10.3390/plants13020261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024]
Abstract
Physiological and molecular marker-based changes were studied in the tissues of two-year-old Pyrus pyraster (L.) Burgsd. seedlings under salt treatment. For 60 days, 5 mL of 100 mM NaCl solution was applied to each plant per day to a cumulative volume of 300 mL in the substrate. In response to osmotic stress, the seedlings increased their water use efficiency (WUE) on day 20 of regular NaCl application and maintained a stable net photosynthetic rate (An) per unit area. Under conditions of increasing salinity, the young plants maintained a balanced water regime of the leaf tissues (Ψwl). The seedlings invested mass to their root growth (R/S), retained a substantial portion (72%) of Na+ ions in the roots, and protected their leaves against intoxication and damage. A significant decrease in the leaf gas exchange parameters (gs, E, An) was manifested on day 60 of the experiment when the cumulative NaCl intake was 300 mL per plant. The variability in the reactions of the seedlings to salinity is related to the use of open-pollinated progeny (54 genotypes) in the experiment. Lus-miR168 showed tissue- and genotype-specific genome responses to the applied stress. Polymorphic miRNA-based loci were mostly detected in the root samples on the 20th and 35th days of the experiment. The cumulative effect of the salt treatment was reflected in the predominance of polymorphic loci in the leaves. We can confirm that miRNA-based markers represent a sensitive detection tool for plant stress response on an individual level. The screening and selection of the optimal type of miRNA for this type of research is crucial. The cytochrome P450-Based Analog (PBA) techniques were unable to detect polymorphism among the control and treated seedlings, except for the primer pair CYP2BF+R, where, in the roots of the stressed plant, insertions in the amplicons were obtained. The expression ratios of cytochrome P450 in the salt-stressed plants were higher in the roots in the case of 20/100 mL and in the leaves with higher doses. The observed physiological and molecular responses to salinity reflect the potential of P. pyraster seedlings in adaptation to osmotic and ionic stress.
Collapse
Affiliation(s)
- Viera Paganová
- Institute of Landscape Architecture, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, 949 76 Nitra, Slovakia; (M.H.); (H.L.)
| | - Marek Hus
- Institute of Landscape Architecture, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, 949 76 Nitra, Slovakia; (M.H.); (H.L.)
| | - Helena Lichtnerová
- Institute of Landscape Architecture, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, 949 76 Nitra, Slovakia; (M.H.); (H.L.)
| | - Jana Žiarovská
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia; (J.Ž.); (D.M.); (M.K.); (K.R.); (A.A.)
| | - Dagmar Moravčíková
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia; (J.Ž.); (D.M.); (M.K.); (K.R.); (A.A.)
| | - Matúš Kučka
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia; (J.Ž.); (D.M.); (M.K.); (K.R.); (A.A.)
| | - Katarína Ražná
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia; (J.Ž.); (D.M.); (M.K.); (K.R.); (A.A.)
| | - Aqsa Abbas
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia; (J.Ž.); (D.M.); (M.K.); (K.R.); (A.A.)
| |
Collapse
|
4
|
Zubova EA, Strelnikov IA. Experimental detection of conformational transitions between forms of DNA: problems and prospects. Biophys Rev 2023; 15:1053-1078. [PMID: 37974981 PMCID: PMC10643659 DOI: 10.1007/s12551-023-01143-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/06/2023] [Indexed: 11/19/2023] Open
Abstract
Under different conditions, the DNA double helix can take different geometric forms. Of the large number of its conformations, in addition to the "canonical" B form, the A, C, and Z forms are widely known, and the D, Hoogsteen, and X forms are less known. DNA locally takes the A, C, and Z forms in the cell, in complexes with proteins. We compare different methods for detecting non-canonical DNA conformations: X-ray, IR, and Raman spectroscopy, linear and circular dichroism in both the infrared and ultraviolet regions, as well as NMR (measurement of chemical shifts and their anisotropy, scalar and residual dipolar couplings and inter-proton distances from NOESY (nuclear Overhauser effect spectroscopy) data). We discuss the difficulties in applying these methods, the problems of theoretical interpretation of the experimental results, and the prospects for reliable identification of non-canonical DNA conformations.
Collapse
Affiliation(s)
- Elena A. Zubova
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin St., Moscow, 119991 Russia
| | - Ivan A. Strelnikov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin St., Moscow, 119991 Russia
| |
Collapse
|
5
|
Hromadová Z, Gálová Z, Mikolášová L, Balážová Ž, Vivodík M, Chňapek M. Efficiency of RAPD and SCoT Markers in the Genetic Diversity Assessment of the Common Bean. Plants (Basel) 2023; 12:2763. [PMID: 37570917 PMCID: PMC10420954 DOI: 10.3390/plants12152763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023]
Abstract
Knowledge about the genetic diversity of the available common bean germplasm can help breeders properly direct the choice of genetic material in the breeding process. The aim of the present work was to estimate the usefulness of 10 RAPD and 10 SCoT markers in genetic diversity detection among 33 common bean genotypes. Both molecular marker systems were able to generate high levels of polymorphism in the genetic material, which was supported by the relatively high polymorphic information content (PIC) values observed for the used markers. The Diversity Detection Index (DDI) and Marker Index (MI) were used to compare the effectiveness of RAPD and SCoT markers. For both techniques, high values of MI and DDI were calculated, representing their effectivity. The SCoT markers showed higher values of the parameters used (MI = 7.474, DI = 2.265) than the RAPD markers (MI = 5.323, DDI = 1.612), indicating their higher efficiency in the detection of molecular variability. Three constructed dendrograms and PCoA plots were created using RAPD and SCoT, and both methods combined confirmed sufficient separation of the bean genotypes from each other. At the same time, a higher efficiency of SCoT markers compared to RAPD markers in the detection of the genetic diversity of beans was also proven. The results may be of future interest in the choice of genetically distant material for breeding purposes.
Collapse
Affiliation(s)
| | | | | | | | | | - Milan Chňapek
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia; (Z.H.); (Z.G.); (L.M.); (Ž.B.); (M.V.)
| |
Collapse
|
6
|
Fevereiro-Martins M, Santos AC, Marques-Neves C, Guimarães H, Bicho M, On Behalf Of The GenE-Rop Study Group. Genetic Modulation of the Erythrocyte Phenotype Associated with Retinopathy of Prematurity-A Multicenter Portuguese Cohort Study. Int J Mol Sci 2023; 24:11817. [PMID: 37511576 PMCID: PMC10380881 DOI: 10.3390/ijms241411817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
The development of retinopathy of prematurity (ROP) may be influenced by anemia or a low fetal/adult hemoglobin ratio. We aimed to analyze the association between DNA methyltransferase 3 β (DNMT3B) (rs2424913), methylenetetrahydrofolate reductase (MTHFR) (rs1801133), and lysine-specific histone demethylase 1A (KDM1A) (rs7548692) polymorphisms, erythrocyte parameters during the first week of life, and ROP. In total, 396 infants (gestational age < 32 weeks or birth weight < 1500 g) were evaluated clinically and hematologically. Genotyping was performed using a MicroChip DNA on a platform employing iPlex MassARRAY®. Multivariate regression was performed after determining risk factors for ROP using univariate regression. In the group of infants who developed ROP red blood cell distribution width (RDW), erythroblasts, and mean corpuscular volume (MCV) were higher, while mean hemoglobin and mean corpuscular hemoglobin concentration (MCHC) were lower; higher RDW was associated with KDM1A (AA), MTHFR (CC and CC + TT), KDM1A (AA) + MTHFR (CC), and KDM1A (AA) + DNMT3B (allele C); KDM1A (AA) + MTHFR (CC) were associated with higher RDW, erythroblasts, MCV, and mean corpuscular hemoglobin (MCH); higher MCV and MCH were also associated with KDM1A (AA) + MTHFR (CC) + DNMT3B (allele C). We concluded that the polymorphisms studied may influence susceptibility to ROP by modulating erythropoiesis and gene expression of the fetal/adult hemoglobin ratio.
Collapse
Affiliation(s)
- Mariza Fevereiro-Martins
- Ecogenetics and Human Health Unit, Environmental Health Institute-ISAMB, Associate Laboratory TERRA, Faculty of Medicine, University of Lisbon, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
- Institute for Scientific Research Bento Rocha Cabral, Calçada Bento da Rocha Cabral 14, 1250-012 Lisboa, Portugal
- Department of Ophthalmology, Cuf Descobertas Hospital, Rua Mário Botas, 1998-018 Lisboa, Portugal
| | - Ana Carolina Santos
- Ecogenetics and Human Health Unit, Environmental Health Institute-ISAMB, Associate Laboratory TERRA, Faculty of Medicine, University of Lisbon, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Carlos Marques-Neves
- Ecogenetics and Human Health Unit, Environmental Health Institute-ISAMB, Associate Laboratory TERRA, Faculty of Medicine, University of Lisbon, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
- Center for the Study of Vision Sciences, Ophthalmology Clinic, Faculty of Medicine, University of Lisbon, Av. Professor Egas Moniz, Piso 1C, 1649-028 Lisboa, Portugal
| | - Hercília Guimarães
- Department of Gynecology-Obstetrics and Pediatrics, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Manuel Bicho
- Ecogenetics and Human Health Unit, Environmental Health Institute-ISAMB, Associate Laboratory TERRA, Faculty of Medicine, University of Lisbon, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
- Institute for Scientific Research Bento Rocha Cabral, Calçada Bento da Rocha Cabral 14, 1250-012 Lisboa, Portugal
| | | |
Collapse
|
7
|
Jocienė L, Krokaitė E, Rekašius T, Vilčinskas R, Judžentienė A, Marozas V, Kupčinskienė E. Ionomic Parameters of Populations of Common Juniper ( Juniperus communis L.) Depending on the Habitat Type. Plants (Basel) 2023; 12:961. [PMID: 36840309 PMCID: PMC9963431 DOI: 10.3390/plants12040961] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/17/2023] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
For the study of the ionomic parameters of Juniperus communis needles, fourteen sites covering most of the territory of Lithuania and belonging to distinct habitats (coastal brown dunes covered with natural Scots pine forests (G), Juniperus communis scrubs (F), transition mires and quaking bogs (D), subcontinental moss Scots pine forests (G), and xero-thermophile fringes) were selected. Concentrations of macro-, micro-, and non-essential elements were analyzed in current-year needles, sampled in September. According to the concentrations of elements in J. communis needles, the differences between the most contrasting populations were as follows: up to 2-fold for Mg, N, K, Ca, and Zn; 2- to 7-fold for P, Na, Fe, Cu, Al, Cr, Ni, and Pb; and 26- to 31-fold for Mn and Cd. The concentrations of Cd, Cr, and Ni in needles of J. communis did not reach levels harmful for conifers. When compared to all other habitats (B, F, G, and E), the populations from transition mires and quaking bogs (D) had significantly lower concentrations of main nutritional elements N (12176 µg/g d. m.), P (1054 µg/g d. m.), and K (2916 µg/g d. m.). In Juniperus communis scrubs (F), a habitat protected by EUNIS, the concentration of K in the needles was highest, while Zn and Cu concentrations were the lowest. Principal component (PC) analyses using concentrations of 15 elements as variables for the discrimination of populations or habitats allowed authors to distinguish F and B habitats from the E habitat (PC1) and F and D habitats from the G habitat (PC2). Discriminating between populations, the most important variables were concentrations of P, N, Mg, Ca, Cu, and K. Discriminating between habitats, the important variables were concentrations of N and P.
Collapse
Affiliation(s)
- Lina Jocienė
- Department of Biology, Faculty of Natural Sciences, Vytautas Magnus University, K. Donelaičio Str. 58, 44248 Kaunas, Lithuania
| | - Edvina Krokaitė
- Department of Biology, Faculty of Natural Sciences, Vytautas Magnus University, K. Donelaičio Str. 58, 44248 Kaunas, Lithuania
| | - Tomas Rekašius
- Department of Mathematics and Statistics, Faculty of Informatics, Vytautas Magnus University, K. Donelaičio Str. 58, 44248 Kaunas, Lithuania
- Department of Mathematical Statistics, Faculty of Fundamental Sciences, Vilnius Gediminas Technical University, Saulėtekio Ave. 11, 10223 Vilnius, Lithuania
| | - Ramūnas Vilčinskas
- Department of Biology, Faculty of Natural Sciences, Vytautas Magnus University, K. Donelaičio Str. 58, 44248 Kaunas, Lithuania
| | - Asta Judžentienė
- Department of Organic Chemistry, Center for Physical Sciences and Technology, Saulėtekio Ave. 3, 10257 Vilnius, Lithuania
- Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio Ave. 7, 10257 Vilnius, Lithuania
| | - Vitas Marozas
- Department of Environment and Ecology, Faculty of Forest Sciences and Ecology, Vytautas Magnus University, K. Donelaičio Str. 58, 44248 Kaunas, Lithuania
| | - Eugenija Kupčinskienė
- Department of Biology, Faculty of Natural Sciences, Vytautas Magnus University, K. Donelaičio Str. 58, 44248 Kaunas, Lithuania
| |
Collapse
|
8
|
Braglia L, Gavazzi F, Gianì S, Morello L, Breviario D. Tubulin-Based Polymorphism (TBP) in Plant Genotyping. Methods Mol Biol 2023; 2638:387-401. [PMID: 36781658 DOI: 10.1007/978-1-0716-3024-2_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Tubulin-based polymorphism (TBP) is an intron length polymorphism (ILP) method widely applicable to any plant species and particularly suitable for a first and rapid classification of any plant genome. It is based on the selective, polymerase chain reaction (PCR)-based amplification of the two introns present at conserved positions within the coding sequences of plant β-tubulin genes. Amplification releases a simple yet distinctive genomic profile.
Collapse
Affiliation(s)
- Luca Braglia
- Institute of Agricultural Biology and Biotechnology (IBBA), Milan, Italy
| | - Floriana Gavazzi
- Institute of Agricultural Biology and Biotechnology (IBBA), Milan, Italy
| | - Silvia Gianì
- Institute of Agricultural Biology and Biotechnology (IBBA), Milan, Italy
| | - Laura Morello
- Institute of Agricultural Biology and Biotechnology (IBBA), Milan, Italy
| | - Diego Breviario
- Institute of Agricultural Biology and Biotechnology (IBBA), Milan, Italy.
| |
Collapse
|
9
|
Jacob EO, Hegele RA. How reliable are polygenic risk scores for risk prediction in patients with heart disease? Expert Rev Mol Diagn 2023; 23:105-107. [PMID: 36734990 DOI: 10.1080/14737159.2023.2176753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Erin O Jacob
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University.,Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Robert A Hegele
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University.,Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| |
Collapse
|
10
|
Mavlyutov Y, Kostenko S, Shamustakimova A, Klimenko I. Genetic variability analysis of Russian cultivars of ryegrass (Lolium) based on SCoT markers. J Genet Eng Biotechnol 2022; 20:163. [PMID: 36512171 PMCID: PMC9748000 DOI: 10.1186/s43141-022-00446-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/04/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Ryegrass is a promising crop for the development of meadow farming in the world. More than 1000 cultivated varieties widely used in feed production have been developed, based on the main species - perennial ryegrass (Lolium perenne L.) and annual one (Lolium multiflorum Lam.). Development and implementation of the modern methods of plant varietal and species identification are of great importance. In recent years, molecular markers have been successfully used for these purposes, which increase the accuracy of the breeding material evaluation at a significant reduction of time and labor costs. The aim of this study was to assess the discriminatory potential of the new SCoT marking technique for the identification of Russian perennial (Lolium perenne L.) and annual (Lolium multiflorum Lam.) ryegrass varieties. RESULTS Out of the total number of the tested SCoT-primers, 8 polymorphic ones were selected, which demonstrates the high stability and reproducibly amplified DNA fragments. These primers generated 107 PCR products, where 37 were found to be polymorphic. The average number of amplicons per primer was 13. The size of the PCR products varied from 349 to 2718 bp (see Table 3). The polymorphic ratio of the tested markers was 30.8%. The marker SCoT-06 was characterized by the maximum number of PCR products and the highest level of polymorphism (50%). The effective number of alleles (ne) ranged from 1.35 to 1.58 with a mean of 1.48 per locus. The average value of the PIC and Shannon index (I) were 0.35 and 0.46, respectively. The unique PCR fragments were revealed for the identification of tested varieties. Analysis of molecular variance (AMOVA) showed that the level of genetic diversity between ryegrass species (59%) was more than between varieties within a species (41%). Based on binary matrix data, clustering and PCoA analysis (see Figs. 1 and 2) of the samples were carried out that divided them into two groups according to species. CONCLUSIONS We found a set of markers that can be useful tools for ryegrass varieties identification. The level of intravarietal polymorphism turned out to be higher than the differences between varieties because of the possible significant heterogeneity of the varietal material. The information obtained can be used in breeding programs to create improved ryegrass varieties adapted to Russian climatic conditions.
Collapse
Affiliation(s)
- Yulian Mavlyutov
- grid.494809.8Federal Williams Research Center of Forage Production & Agroecology (FWRC FPA), Lobnya, Moscow region Russia
| | - Sergey Kostenko
- grid.494809.8Federal Williams Research Center of Forage Production & Agroecology (FWRC FPA), Lobnya, Moscow region Russia
| | - Anastasia Shamustakimova
- grid.494809.8Federal Williams Research Center of Forage Production & Agroecology (FWRC FPA), Lobnya, Moscow region Russia
| | - Irina Klimenko
- grid.494809.8Federal Williams Research Center of Forage Production & Agroecology (FWRC FPA), Lobnya, Moscow region Russia
| |
Collapse
|
11
|
Bao B, Hu H, Chen L, Lu S, Tang Q, Liang Z. SNP and DNA methylation analyses of a monozygotic twins discordant for complete endocardial cushion defect: a case report. Am J Transl Res 2022; 14:8271-8278. [PMID: 36505317 PMCID: PMC9730093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/24/2022] [Indexed: 12/15/2022]
Abstract
The exact cause of complete endocardial cushion defect (ECD) is still unknown. This report describes a unique pair of monozygotic twins (MZ twins) discordant for ECD. The chromosome karyotyping analysis revealed normal karyotype of 46, XY, 16qh+ and mat in both MZ twins. A genome-wide analysis of DNA using the Affymetrix SNP 6.0 revealed identical genotyping of single nucleotide polymorphisms (SNPs) and copy number variations (CNVs). An extensive methylation assay was carried out by NimbleGen 3 × 720 K CpG Island Plus RefSeq Promoter Arrays to analyze the potential epigenetic differences. The DNA methylation profiles of the affected twin seemed increased compared with that of the unaffected twin. However, further validation of Notch1 promoter hypermethylation and six top-ranked differentially methylated CpG sites by sodium bisulfate modification and methylation-specific PCR, failed to reveal consistent methylation differences between the twins. Other relevant factors, such as heritability and penetrance of the condition that place the MZ twins near to a threshold for ECD or variations in local epigenetic events in the twins' heart tissues, are probably responsible for the phenotypic discordance.
Collapse
Affiliation(s)
- Bihui Bao
- Department of Obstetrics and Gynecology, Qingbaijiang Women’s and Children’s Hospital (Maternal and Child Health Hospital), West China Second University Hospital, Sichuan UniversityChengdu 610300, Sichuan, China
| | - Hua Hu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital (Xinqiao Hospital), Army Medical UniversityChongqing 400037, China
| | - Limei Chen
- Department of Obstetrics and Gynecology, Qingbaijiang Women’s and Children’s Hospital (Maternal and Child Health Hospital), West China Second University Hospital, Sichuan UniversityChengdu 610300, Sichuan, China
| | - Shiyong Lu
- Department of Obstetrics and Gynecology, Qingbaijiang Women’s and Children’s Hospital (Maternal and Child Health Hospital), West China Second University Hospital, Sichuan UniversityChengdu 610300, Sichuan, China
| | - Qifeng Tang
- Department of Anesthesiology, Shanghai Hechuan-Rhine TCM HospitalShanghai 201103, China
| | - Zhiqing Liang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital (Southwest Hospital), Army Medical UniversityChongqing 400038, China
| |
Collapse
|
12
|
Jax E, Franchini P, Sekar V, Ottenburghs J, Monné Parera D, Kellenberger RT, Magor KE, Müller I, Wikelski M, Kraus RHS. Comparative genomics of the waterfowl innate immune system. Mol Biol Evol 2022; 39:6649919. [PMID: 35880574 PMCID: PMC9356732 DOI: 10.1093/molbev/msac160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Animal species differ considerably in their ability to fight off infections. Finding the genetic basis of these differences is not easy, as the immune response is comprised of a complex network of proteins that interact with one another to defend the body against infection. Here, we used population- and comparative genomics to study the evolutionary forces acting on the innate immune system in natural hosts of the avian influenza virus (AIV). For this purpose, we used a combination of hybrid capture, next- generation sequencing and published genomes to examine genetic diversity, divergence, and signatures of selection in 127 innate immune genes at a micro- and macroevolutionary time scale in 26 species of waterfowl. We show across multiple immune pathways (AIV-, toll-like-, and RIG-I -like receptors signalling pathways) that genes involved genes in pathogen detection (i.e., toll-like receptors) and direct pathogen inhibition (i.e., antimicrobial peptides and interferon-stimulated genes), as well as host proteins targeted by viral antagonist proteins (i.e., mitochondrial antiviral-signaling protein, [MAVS]) are more likely to be polymorphic, genetically divergent, and under positive selection than other innate immune genes. Our results demonstrate that selective forces vary across innate immune signaling signalling pathways in waterfowl, and we present candidate genes that may contribute to differences in susceptibility and resistance to infectious diseases in wild birds, and that may be manipulated by viruses. Our findings improve our understanding of the interplay between host genetics and pathogens, and offer the opportunity for new insights into pathogenesis and potential drug targets.
Collapse
Affiliation(s)
- Elinor Jax
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Biology and Biotechnologies "Charles Darwin", Sapienza University, Rome, Italy
| | - Vaishnovi Sekar
- Department of Biology, Lund University, Lund, Sweden.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Jente Ottenburghs
- Wildlife Ecology and Conservation Group, Wageningen University, Wageningen, The Netherlands.,Forest Ecology and Forest Management Group, Wageningen University, Wageningen, The Netherlands
| | | | - Roman T Kellenberger
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Katharine E Magor
- Department of Biological Sciences and Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - Inge Müller
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Martin Wikelski
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
| | - Robert H S Kraus
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| |
Collapse
|
13
|
Dieter C, Lemos NE, de Faria Corrêa NR, Pellenz FM, Canani LH, Crispim D, Bauer AC. The A allele of the rs759853 single nucleotide polymorphism in the AKR1B1 gene confers risk for diabetic kidney disease in patients with type 2 diabetes from a Brazilian population. Arch Endocrinol Metab 2022; 66:12-18. [PMID: 35029856 PMCID: PMC9991038 DOI: 10.20945/2359-3997000000432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
OBJECTIVE The AKR1B1 gene encodes an enzyme that catalyzes the reduction of glucose into sorbitol. Chronic hyperglycemia in patients with diabetes mellitus (DM) leads to increased AKR1B1 affinity for glucose and, consequently, sorbitol accumulation. Elevated sorbitol increases oxidative stress, which is one of the main pathways related to chronic complications of diabetes, including diabetic kidney disease (DKD). Accordingly, some studies have suggested the rs759853 polymorphism in the AKR1B1 gene is associated with DKD; however, findings are still contradictory. The aim was to investigate the association of the rs759853 polymorphism in the AKR1B1 gene and DKD. METHODS The sample comprised 695 patients with type 2 DM (T2DM) and DKD (cases) and 310 patients with T2DM of more than 10 years' duration, but no DKD (controls). The polymorphism was genotyped by real-time PCR. RESULTS Allelic and genotype frequencies of this polymorphism did not differ significantly between groups. However, the A/A genotype was associated with risk for DKD after adjustment for gender, triglycerides, BMI, presence of hypertension and diabetic retinopathy, and duration of DM, under both recessive (P = 0.048) and additive (P = 0.037) inheritance models. CONCLUSION Our data suggest an association between the AKR1B1 rs759853A/A genotype and risk for DKD in Brazilians T2DM patients.
Collapse
Affiliation(s)
- Cristine Dieter
- Divisão Endócrina do Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brasil.,Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Clínica Médica, Programa de Pós-graduação em Ciências Médicas: Endocrinologia, Porto Alegre, RS, Brasil
| | - Natália Emerim Lemos
- Divisão Endócrina do Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brasil.,Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Clínica Médica, Programa de Pós-graduação em Ciências Médicas: Endocrinologia, Porto Alegre, RS, Brasil
| | | | - Felipe Mateus Pellenz
- Divisão Endócrina do Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brasil.,Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Clínica Médica, Programa de Pós-graduação em Ciências Médicas: Endocrinologia, Porto Alegre, RS, Brasil
| | - Luís Henrique Canani
- Divisão Endócrina do Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brasil.,Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Clínica Médica, Programa de Pós-graduação em Ciências Médicas: Endocrinologia, Porto Alegre, RS, Brasil
| | - Daisy Crispim
- Divisão Endócrina do Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brasil.,Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Clínica Médica, Programa de Pós-graduação em Ciências Médicas: Endocrinologia, Porto Alegre, RS, Brasil
| | - Andrea Carla Bauer
- Divisão Endócrina do Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brasil.,Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Clínica Médica, Programa de Pós-graduação em Ciências Médicas: Endocrinologia, Porto Alegre, RS, Brasil.,Serviço de Nefrologia do Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brasil,
| |
Collapse
|
14
|
Alexandrov OS, Karlov GI. The Development of New Species-Specific Molecular Markers Based on 5S rDNA in Elaeagnus L. Species. Plants (Basel) 2021; 10:plants10122713. [PMID: 34961186 PMCID: PMC8704621 DOI: 10.3390/plants10122713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/23/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
The Elaeagnus L. species are trees and bushes that mainly grow in temperate zones of Western Europe; Minor, Central, and Southeast Asia; the Far East; and North America. Some species are used as fruit or ornamental plants and have economic value. Problems with the identification of species in the Elaeagnus genus by molecular genetical methods arise in the study of populations, systematics, breeding, and other areas of plant science and practice. Recently, the polymorphism of 5S ribosomal DNA non-transcribed spacers (5S rDNA NTSs) in Elaeagnaceae Adans. has been described. The results were used in our study as a basis for development of new species-specific molecular markers for some members of the Elaeagnus genus. The author's method was applied for finding regions that were potentially applicable for species-specific primer design. As a result, some species-specific molecular markers were developed for Elaeagnus angustifolia L., E. commutata Bernh., E. pungens Thunb., and E. multiflora Thunb. These markers were tested in a range of samples and showed the presence of amplified fragments in lanes of the marked species only. Samples of other species showed no amplifications. Thus, the developed markers may be useful for the species identification of the studied Elaeagnus plants in botanical, dendrological, and genetic research (especially in a leafless period of year), as well as in breeding and hybridization experiments.
Collapse
Affiliation(s)
- Oleg S Alexandrov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia
| | - Gennady I Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia
| |
Collapse
|
15
|
Pushkova EN, Krasnov GS, Lakunina VA, Novakovskiy RO, Povkhova LV, Dvorianinova EM, Beniaminov AD, Fedorova MS, Snezhkina AV, Kudryavtseva AV, Dmitriev AA, Melnikova NV. Genome and Transcriptome Sequencing of Populus × sibirica Identified Sex-Associated Allele-Specific Expression of the CLC Gene. Front Genet 2021; 12:676935. [PMID: 34456967 PMCID: PMC8385651 DOI: 10.3389/fgene.2021.676935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/28/2021] [Indexed: 12/04/2022] Open
Abstract
Transcriptome sequencing of leaves, catkin axes, and flowers from male and female trees of Populus × sibirica and genome sequencing of the same plants were performed for the first time. The availability of both genome and transcriptome sequencing data enabled the identification of allele-specific expression. Such an analysis was performed for genes from the sex-determining region (SDR). P. × sibirica is an intersectional hybrid between species from sections Aigeiros (Populus nigra) and Tacamahaca (Populus laurifolia, Populus suaveolens, or Populus × moskoviensis); therefore, a significant number of heterozygous polymorphisms were identified in the SDR that allowed us to distinguish between alleles. In the SDR, both allelic variants of the TCP (T-complex protein 1 subunit gamma), CLC (Chloride channel protein CLC-c), and MET1 (DNA-methyltransferase 1) genes were expressed in females, while in males, two allelic variants were expressed for TCP and MET1 but only one allelic variant prevailed for CLC. Targeted sequencing of TCP, CLC, and MET1 regions on a representative set of trees confirmed the sex-associated allele-specific expression of the CLC gene in generative and vegetative tissues of P. × sibirica. Our study brings new knowledge on sex-associated differences in Populus species.
Collapse
Affiliation(s)
- Elena N Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Valentina A Lakunina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Roman O Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Liubov V Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Ekaterina M Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Artemy D Beniaminov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria S Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
16
|
Chowdhury S, Bhuiya S, Das S. Comparative binding studies on the interaction of the indoloquinoline alkaloid cryptolepine with the B and the non-canonical protonated form of DNA: A spectroscopic insight. Biochim Biophys Acta Gen Subj 2021; 1865:129993. [PMID: 34453987 DOI: 10.1016/j.bbagen.2021.129993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 07/16/2021] [Accepted: 08/22/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Low pH induced nucleic acid polymorphism and the interaction of naturally occurring small molecules with different polymorphic forms of DNA have been the focus in developing new drugs. Recent studies have revealed that low pH plays an active role in growth and development of cancer cells. Our target is to find whether and how the indoloquinoline alkaloid cryptolepine (CRP) interact with different polymorphic forms of natural DNA, in hope to explore this group of alkaloids as new therapeutics. METHODS Multiple spectroscopic techniques that include UV-visible absorption spectrophotometry, fluorimetry, CD spectroscopy along with thermal melting studies were employed to characterize the interaction between the alkaloid cryptolepine with the B and protonated forms of DNA. RESULTS & CONCLUSIONS Cryptolepine has been found to interact with either forms of DNA. The nature of binding is non-cooperative in both cases. Data show that the affinity of CRP to B form of DNA is relatively higher than that for the protonated form of DNA. Circular dichroic studies reveal that the alkaloid converts the left handed protonated DNA into bound right handed form. Fluorescence quenching experiments reveal that cryptolepine intercalates within the DNA base pairs. Thermal melting studies show that the alkaloid stabilises the DNA structures. GENERAL SIGNIFICANCE Such non-B DNA structures are often present at the 'mutation hotspots' that are associated with genetic instability related diseases such as cancer. The ability of cryptolepine to interact to such non-B DNA structures makes it a useful substrate in the designing of potential chemotherapeutic agents.
Collapse
Affiliation(s)
- Susmita Chowdhury
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, 188 Raja S. C. Mallick Road, Kolkata 700032, India
| | - Sutanwi Bhuiya
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, 188 Raja S. C. Mallick Road, Kolkata 700032, India
| | - Suman Das
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, 188 Raja S. C. Mallick Road, Kolkata 700032, India.
| |
Collapse
|
17
|
Gintoni I, Vassiliou S, Avgoustidis D, Adamopoulou M, Zavras N, Papakosta V, Vlachakis D, Yapijakis C. Lack of Association Between the ACE2 G8790A Gene Variation and Risk for Basal Cell Carcinoma. Anticancer Res 2021; 41:4021-4026. [PMID: 34281868 DOI: 10.21873/anticanres.15201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM The G8790A (rs2285666) functional polymorphism of the angiotensin-converting enzyme 2 (ACE2) gene influences alternative mRNA splicing and quantitatively affects the enzyme's production. Specifically, the presence of the A allele has been associated with higher ACE2 plasma levels. In this study, we investigated the possible association of the functional polymorphism ACE2-G8790A with the pathogenesis of basal cell carcinoma (BCC). PATIENTS AND METHODS A total of 190 DNA samples were studied, including 91 BCC patients and 99 controls of Greek origin. Molecular genotyping for the ACE2 G8790A polymorphism was carried out by PCR amplification, followed by AluI enzyme digestion and agarose gel electrophoresis of the DNA fragments. RESULTS The allelic and genotypic frequencies presented no statistical difference between the patient and the control group. CONCLUSION There is no association between the ACE2 G8790A polymorphism and pathogenesis of BCC.
Collapse
Affiliation(s)
- Iphigenia Gintoni
- Unit of Orofacial Genetics, 1 Department of Pediatrics, National Kapodistrian University of Athens, "Hagia Sophia" Children's Hospital, Athens, Greece.,Department of Molecular Genetics, Cephalogenetics Center, Athens, Greece
| | - Stavros Vassiliou
- Department of Oral and Maxillofacial Surgery, School of Medicine, National and Kapodistrian University of Athens, Attikon Hospital, Athens, Greece
| | - Dimitris Avgoustidis
- Department of Oral and Maxillofacial Surgery, Evangelismos General Hospital, Athens, Greece
| | - Mary Adamopoulou
- Department of Molecular Genetics, Cephalogenetics Center, Athens, Greece
| | - Nikolaos Zavras
- Department of Pediatric Surgery, School of Medicine, National and Kapodistrian University of Athens, Attikon Hospital, Athens, Greece
| | - Veronica Papakosta
- Department of Oral and Maxillofacial Surgery, School of Medicine, National and Kapodistrian University of Athens, Attikon Hospital, Athens, Greece
| | - Dimitris Vlachakis
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Christos Yapijakis
- Unit of Orofacial Genetics, 1 Department of Pediatrics, National Kapodistrian University of Athens, "Hagia Sophia" Children's Hospital, Athens, Greece .,Department of Molecular Genetics, Cephalogenetics Center, Athens, Greece.,Department of Oral and Maxillofacial Surgery, School of Medicine, National and Kapodistrian University of Athens, Attikon Hospital, Athens, Greece
| |
Collapse
|
18
|
Monteiro J, Pratas D, Videira A, Pereira F. Revisiting the Neurospora crassa mitochondrial genome. Lett Appl Microbiol 2021; 73:495-505. [PMID: 34265094 DOI: 10.1111/lam.13538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 11/30/2022]
Abstract
The mitochondrial genome of Neurospora crassa has been less studied than its nuclear counterpart, yet it holds great potential for understanding the diversity and evolution of this important fungus. Here we describe a new mitochondrial DNA (mtDNA) complete sequence of a N. crassa wild type strain. The genome with 64 839 bp revealed 21 protein-coding genes and several hypothetical open reading frames with no significant homology to any described gene. Five large repetitive regions were identified across the genome, including partial or complete genes. The largest repeated region holds a partial nd2 section that was also detected in Neurospora intermedia, suggesting a rearrangement that occurred before the N. crassa speciation. Interestingly, N. crassa has a palindrome adjacent to the partial nd2 repeated region possibly related to the genomic rearrangement, which is absent in N. intermedia. Finally, we compared the sequences of the three available N. crassa complete mtDNAs and found low levels of intraspecific variability. Most differences among strains were due to small indels in noncoding regions. The revisiting of the N. crassa mtDNA forms the basis for future studies on mitochondrial genome organization and variability.
Collapse
Affiliation(s)
- J Monteiro
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal.,Department of Molecular Biology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - D Pratas
- Department of Virology, University of Helsinki, Helsinki, Finland.,Department of Electronics, Telecommunications and Informatics, University of Aveiro, Aveiro, Portugal.,Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, Aveiro, Portugal
| | - A Videira
- Department of Molecular Biology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal.,Institute for Cellular and Molecular Biology (IBMC), University of Porto, Porto, Portugal.,Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal
| | - F Pereira
- IDENTIFICA Genetic Testing, Maia, Portugal.,Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| |
Collapse
|
19
|
Yoshie Y, Ando H, Tamura T, Fukuda K, Igarashi M, Hishida A, Kawahara N, Sasaki Y. Polymorphism analysis of TCP gene region to intraspecific analysis of Paeonia lactiflora, and application for authentication of Paeoniae Radix. J Nat Med 2021; 75:985-993. [PMID: 34003415 DOI: 10.1007/s11418-021-01521-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
We attempted to conduct an intraspecific analysis of 30 peony cultivars in Japan and to authenticate five herbal medicine samples derived from Paeoniae Radix by polymorphism analysis of the TEOSINTE BRANCHED1, CYCLOIDEA, and PCF (TCP) gene region. We focused on cultivar-dependent differences in leaf margin undulation and analyzed the sequence of the related TCP gene region. As a result, we found that the nucleotide sequences of 29 cultivars of Paeonia lactiflora except 'America' exhibit interspecific variations compared with the nucleotide sequences of Paeonia suffruticosa and Paeonia tenuifolia. Therefore, in the dendrogram constructed on the basis of the sequence similarity in the TCP gene region, the 29 cultivars of P. lactiflora were separated from P. suffruticosa, P. tenuifolia, and 'America', and clustered into three subgroups. There were 16 variations containing heterogenous DNA sequences within P. lactiflora species, and two characteristic variations in subgroup I. Some P. lactiflora cultivars showed the same nucleotide sequence in the TCP gene region, whereas the five herbal medicine samples showed different sequences, although all of them could be authenticated. The results suggest that Paeoniae Radix in the Japanese crude drug market can be authenticated by analysis of the TCP gene region.
Collapse
Affiliation(s)
- Yuina Yoshie
- Laboratory of Molecular Pharmacognosy, Division of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Hirokazu Ando
- Laboratory of Molecular Pharmacognosy, Division of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Takayuki Tamura
- Center for Medicinal Plant Resources, Toyama Prefectural Institute for Pharmaceutical Research, 2732 Hirono, Kamiichi-machi, Nakaniikawa, Toyama, 930-0412, Japan
| | - Kozo Fukuda
- Fukuda Shoten, 477 Abe, Sakurai, Nara, 633-0054, Japan
| | - Motoko Igarashi
- Hokkaido Division, Research Center for Medicinal Plant Resources, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 108-4 Ohashi, Nayoro, Hokkaido, 096-0065, Japan
| | - Atsuyuki Hishida
- Hokkaido Division, Research Center for Medicinal Plant Resources, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 108-4 Ohashi, Nayoro, Hokkaido, 096-0065, Japan
| | - Nobuo Kawahara
- Research Center for Medicinal Plant Resources, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 1-2 Hachimandai, Tsukuba, Ibaraki, 305-0843, Japan
| | - Yohei Sasaki
- Laboratory of Molecular Pharmacognosy, Division of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan.
| |
Collapse
|
20
|
Nowacka-Woszuk J, Mackowski M, Stefaniuk-Szmukier M, Cieslak J. The equine graying with age mutation of the STX17 gene: A copy number study using droplet digital PCR reveals a new pattern. Anim Genet 2021; 52:223-227. [PMID: 33550611 DOI: 10.1111/age.13044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2021] [Indexed: 01/05/2023]
Abstract
The equine graying with age causative mutation in the syntaxin-17 gene (STX17) has been known for over a decade, but proper genotyping of this variant remains challenging due to its molecular character (4.6-kb tandem duplication). Precise information on gray mutation status is important for horse breeders and veterinarians, since gray homozygous horses are more prone to developing aggressive melanoma tumors than heterozygotes. Since recent studies have confirmed that droplet digital PCR is a valuable technique for copy number analysis, we decided to investigate whether this method can be used for accurate genotyping of the horse graying-related variant and established the copy numbers of the 4.6-kb fragment in the available cohort (n = 75) of gray and nongray horses of various breeds. Surprisingly, we found that our STX17 genotype results varied from what has been previously published, suggesting that gray phenotype is associated with the presence of six (GG) or four (Gg) copies of studied region. All the examined nongray horses (gg) have the two copies of these fragments. This new pattern and its inheritance were also confirmed by an analysis conducted for the Polish Warmblood horse family. We noted no further copy number variation in the entire tested samples set. Our study confirmed the usefulness and accuracy of droplet digital PCR for genotyping STX17 gene variant. Further studies on a broader range of materials are needed to fully understand the origin and molecular structure of the graying causative mutation in the horse STX17.
Collapse
Affiliation(s)
- J Nowacka-Woszuk
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, Poznan, 60-637, Poland
| | - M Mackowski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, Poznan, 60-637, Poland.,Horse Genetic Markers Laboratory, Poznan University of Life Sciences, Wolynska 33, Poznan, 60-637, Poland
| | - M Stefaniuk-Szmukier
- Department of Animal Reproduction, Anatomy and Genomics, University of Agriculture in Krakow, Mickiewicza 24/28, Krakow, 30-059, Poland
| | - J Cieslak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, Poznan, 60-637, Poland
| |
Collapse
|
21
|
Abstract
Size, structure, and sequence content lability of plant mitochondrial genome (mtDNA) across species has sharply limited its use in taxonomic studies. Historically, mtDNA variation has been first investigated with RFLPs, while the development of universal primers then allowed studying sequence polymorphisms within short genomic regions (<3 kb). The recent advent of NGS technologies now offers new opportunities by greatly facilitating the assembly of longer mtDNA regions, and even full mitogenomes. Phylogenetic works aiming at comparing signals from different genomic compartments (i.e., nucleus, chloroplast, and mitochondria) have been developed on a few plant lineages, and have been shown especially relevant in groups with contrasted inheritance of organelle genomes. This chapter first reviews the main characteristics of mtDNA and the application offered in taxonomic studies. It then presents tips for best sequencing protocol based on NGS data to be routinely used in mtDNA-based phylogenetic studies.
Collapse
Affiliation(s)
- Jérôme Duminil
- DIADE, University of Montpellier, IRD, Montpellier, France.
| | - Guillaume Besnard
- CNRS-UPS-IRD, UMR5174, EDB, Université Paul Sabatier, Toulouse, France
| |
Collapse
|
22
|
Dmitriev AA, Novakovskiy RO, Pushkova EN, Rozhmina TA, Zhuchenko AA, Bolsheva NL, Beniaminov AD, Mitkevich VA, Povkhova LV, Dvorianinova EM, Snezhkina AV, Kudryavtseva AV, Krasnov GS, Melnikova NV. Transcriptomes of Different Tissues of Flax ( Linum usitatissimum L.) Cultivars With Diverse Characteristics. Front Genet 2020; 11:565146. [PMID: 33363567 PMCID: PMC7755106 DOI: 10.3389/fgene.2020.565146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 10/20/2020] [Indexed: 12/18/2022] Open
Affiliation(s)
- Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Roman O Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena N Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana A Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Federal Research Center for Bast Fiber Crops, Torzhok, Russia
| | - Alexander A Zhuchenko
- Federal Research Center for Bast Fiber Crops, Torzhok, Russia.,All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, Moscow, Russia
| | - Nadezhda L Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Artemy D Beniaminov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir A Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Liubov V Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ekaterina M Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | | | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
23
|
Shang Z, Horovitz DJ, McKenzie RH, Keisler JL, Felder MR, Davis SW. Using genomic resources for linkage analysis in Peromyscus with an application for characterizing Dominant Spot. BMC Genomics 2020; 21:622. [PMID: 32912160 PMCID: PMC7488232 DOI: 10.1186/s12864-020-06969-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 08/03/2020] [Indexed: 11/16/2022] Open
Abstract
Background Peromyscus are the most common mammalian species in North America and are widely used in both laboratory and field studies. The deer mouse, P. maniculatus and the old-field mouse, P. polionotus, are closely related and can generate viable and fertile hybrid offspring. The ability to generate hybrid offspring, coupled with developing genomic resources, enables researchers to conduct linkage analysis studies to identify genomic loci associated with specific traits. Results We used available genomic data to identify DNA polymorphisms between P. maniculatus and P. polionotus and used the polymorphic data to identify the range of genetic complexity that underlies physiological and behavioral differences between the species, including cholesterol metabolism and genes associated with autism. In addition, we used the polymorphic data to conduct a candidate gene linkage analysis for the Dominant spot trait and determined that Dominant spot is linked to a region of chromosome 20 that contains a strong candidate gene, Sox10. During the linkage analysis, we found that the spot size varied quantitively in affected Peromyscus based on genetic background. Conclusions The expanding genomic resources for Peromyscus facilitate their use in linkage analysis studies, enabling the identification of loci associated with specific traits. More specifically, we have linked a coat color spotting phenotype, Dominant spot, with Sox10, a member the neural crest gene regulatory network, and that there are likely two genetic modifiers that interact with Dominant spot. These results establish Peromyscus as a model system for identifying new alleles of the neural crest gene regulatory network.
Collapse
Affiliation(s)
- Zhenhua Shang
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - David J Horovitz
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Ronald H McKenzie
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Jessica L Keisler
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Michael R Felder
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Shannon W Davis
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA.
| |
Collapse
|
24
|
Vyhnánek T, Nevrtalová E, Bjelková M, Balgová B. SSR loci survey of technical hemp cultivars: The optimization of a cost-effective analyses to study genetic variability. Plant Sci 2020; 298:110551. [PMID: 32771162 DOI: 10.1016/j.plantsci.2020.110551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
Our study aimed to optimize a selection of a suitable combination of SSRs (Simple Sequence Repeats) for determination of technical Cannabis cultivars and genetic variability level. We used sequences of 23 published SSR families (107 alleles) and amplified them in 28 cultivars. One of the alleles possesses no selective information (SSR family CAN1660) due to its presence in every single tested cultivar. We excluded it, together with another 11 least informative alleles. After data filtration, we used 96 alleles to do recursive sub-sampling of random alleles' sets. We found a minimal set of 8 alleles (in three different combinations) to distinguish 28 analyzed cultivars from each other. Our results contribute to saving resources and to reduce the performance time of the molecular analysis.
Collapse
Affiliation(s)
- Tomáš Vyhnánek
- Department of Plant Biology, Faculty of AgriSciences, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
| | - Eva Nevrtalová
- Department of Plant Biology, Faculty of AgriSciences, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic.
| | - Marie Bjelková
- Agritec Plant Research, Ltd. Šumperk, Zemědělská 6, 787 01 Šumperk, Czech Republic
| | - Barbora Balgová
- Department of Plant Biology, Faculty of AgriSciences, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
| |
Collapse
|
25
|
Nunziata A, Ruggieri V, Petriccione M, De Masi L. Single Nucleotide Polymorphisms as Practical Molecular Tools to Support European Chestnut Agrobiodiversity Management. Int J Mol Sci 2020; 21:ijms21134805. [PMID: 32646057 PMCID: PMC7370276 DOI: 10.3390/ijms21134805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 12/12/2022] Open
Abstract
European chestnut orchards are multifunctional agroforestry systems with a key role in environmental management. Their biodiversity is at risk of erosion and farmers do not have enough tools to protect and valorize traditional ecotypes. In particular, cost effective and reliable molecular markers for cultivar identification are lacking. The aim of this research was to develop a new molecular tool for varietal identification in European chestnuts. A set of cultivars was preliminarily characterized to evaluate the range of genetic diversity using random amplified polymorphic DNA (RAPD) markers. The genetic distances indicated a sufficiently wide variability range among tested genotypes and confirmed they were suitable for our goal. A single nucleotide polymorphism (SNP) mining within 64 expressed sequence tags (EST), covering all the linkage groups, was performed by high-resolution melting (HRM) and validated by target resequencing. Fifty-six SNPs were retrieved by monitoring the variability present on the whole set of considered cultivars in loci uniformly distributed on the genome. A subset of 37 SNPs was finally transformed into kompetitive allele-specific PCR (KASP) markers that were successfully evaluated for varietal discrimination. Three assays (C1083, G0115 and A5096) were identified as necessary and sufficient for distinguishing among the tested cultivars. The developed tools can be effectively exploited by stakeholders for improving the management of the European chestnut genetic resources.
Collapse
Affiliation(s)
- Angelina Nunziata
- C.R.E.A. Council for Agricultural Research and Economics—Research Centre for Olive, Fruits and Citrus Crops, Via Torrino 2, 81100 Caserta, Italy;
- Correspondence: (A.N.); (L.D.M.); Tel.: +39-0823-256228 (A.N.); +39-081-2539494 (L.D.M.)
| | | | - Milena Petriccione
- C.R.E.A. Council for Agricultural Research and Economics—Research Centre for Olive, Fruits and Citrus Crops, Via Torrino 2, 81100 Caserta, Italy;
| | - Luigi De Masi
- National Research Council (CNR), Institute of Biosciences and BioResources (IBBR), Via Università 133, 80055 Portici (NA), Italy
- Correspondence: (A.N.); (L.D.M.); Tel.: +39-0823-256228 (A.N.); +39-081-2539494 (L.D.M.)
| |
Collapse
|
26
|
Monteiro J, Videira A, Pereira F. Quantification of Neurospora crassa mitochondrial DNA using quantitative real-time PCR. Lett Appl Microbiol 2020; 71:171-178. [PMID: 32270506 DOI: 10.1111/lam.13294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/26/2020] [Accepted: 03/31/2020] [Indexed: 11/28/2022]
Abstract
The filamentous fungus Neurospora crassa is a popular model organism used in a wide range of biochemical and genetic studies and vastly used in mitochondrial research. Despite the relevance of mitochondria in N. crassa biology, no method for quantification of mitochondrial DNA (mtDNA) is currently available. Quantitative real-time PCR (qPCR) is a powerful tool, with a wide range of applications, and has been used for the quantification of nucleic acids in humans and a few other species. Here we present a new qPCR assay for relative quantification of N. crassa mtDNA. Three sets of qPCR primers targeting different regions of the mitochondrial genome were tested for mtDNA quantification. The qPCR was successfully validated in N. crassa strains from different geographical locations, representing the vast genetic diversity of this species, and knockout mutant strains. Moreover the assay proved to be efficient in templates with varied amounts of mitochondria, obtained through different DNA extraction methods. The qPCR performed well in all tested samples revealing a higher amount of mtDNA than nuclear DNA in all cases. This technique will facilitate the characterization of mtDNA of N. crassa in future studies and can be used as a tool to validate methods of mitochondria isolation. SIGNIFICANCE AND IMPACT OF THE STUDY: The standardization of quantitative real-time PCR (qPCR) techniques is essential to enable and facilitate future comparisons. Neurospora crassa is a model organism with a lot of potential in different fields of study. Here we use N. crassa to develop and establish an assay to quantify mitochondrial DNA using qPCR. We tested strains with different geographical background and our data demonstrated the usefulness of this assay to quantify mitochondrial DNA in N. crassa. This technique can be useful in a wide variety of applications and in different types of studies.
Collapse
Affiliation(s)
- J Monteiro
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Porto, Portugal.,ICBAS-Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Porto, Portugal
| | - A Videira
- ICBAS-Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - F Pereira
- IDENTIFICA, Science and Technology Park of the University of Porto - UPTEC, Porto, Portugal
| |
Collapse
|
27
|
Tsukuda K, Mano S, Yamamoto T. Bayesian approach to discriminant problems for count data with application to multilocus short tandem repeat dataset. Stat Appl Genet Mol Biol 2020; 19:sagmb-2018-0044. [PMID: 32364524 DOI: 10.1515/sagmb-2018-0044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 03/23/2020] [Indexed: 11/15/2022]
Abstract
Short Tandem Repeats (STRs) are a type of DNA polymorphism. This study considers discriminant analysis to determine the population of test individuals using an STR database containing the lengths of STRs observed at more than one locus. The discriminant method based on the Bayes factor is discussed and an improved method is proposed. The main issues are to develop a method that is relatively robust to sample size imbalance, identify a procedure to select loci, and treat the parameter in the prior distribution. A previous study achieved a classification accuracy of 0.748 for the g-mean (geometric mean of classification accuracies for two populations) and 0.867 for the AUC (area under the receiver operating characteristic curve). We improve the maximum values for the g-mean to 0.830 and the AUC to 0.935. Computer simulations indicate that the previous method is susceptible to sample size imbalance, whereas the proposed method is more robust while achieving almost identical classification accuracy. Furthermore, the results confirm that threshold adjustment is an effective countermeasure to sample size imbalance.
Collapse
Affiliation(s)
- Koji Tsukuda
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, 153-8902, Tokyo, Japan.,Faculty of Mathematics, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka-shi, 819-0395, Fukuoka, Japan
| | - Shuhei Mano
- The Institute of Statistical Mathematics, 10-3 Midori-cho, Tachikawa-shi, 190-8562, Tokyo, Japan
| | - Toshimichi Yamamoto
- Department of Legal Medicine and Bioethics, Graduate School of Medicine, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya-shi, 466-8550, Aichi, Japan
| |
Collapse
|
28
|
Cakina S, Ocak O, Ozkan A, Yucel S, Ozısık Karaman HI. Relationship between genetic polymorphisms MTHFR (C677T, A1298C), MTR (A2756G) and MTRR (A66G) genes and multiple sclerosis: a case-control study. Folia Neuropathol 2019; 57:36-40. [PMID: 31038186 DOI: 10.5114/fn.2019.83829] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Recent studies have reported elevated plasma homocysteine and reduced folate and vitamin B levels in patients with multiple sclerosis (MS). In this study, we aimed to investigate the association between MS and the following four DNA polymorphisms: MTR A[2756]G, MTHFR C[677]T, MTHFR A[1298]C and MTRR A[66]G. The DNA polymorphisms were genotyped in 80 patients with confirmed MS and 80 healthy control age- and gender-matched subjects using PCR-RFLP approach. Our results show that the frequency of the T/T genotype homozygotes for the MTHFR C[677]T polymorphism was significantly higher in patients than in controls (p = 0.04, OR: 3.16, 95% CI: 1.23-8.17). In turn, the A/A genotype of the MTHFR A[1298]C polymorphism was more frequent in controls than in patients (41.3% vs. 32.5%, p = 0.04). There were no differences in distribution of genotypes for the MTR A[66]G and MTR A[2756]C polymorphisms between patients with MS and controls (p > 0.05). Our findings suggested that the MTHFR C[677]T and MTHFR A[1298]C gene polymorphisms might be associated with MS as genetic factors influencing the risk of the disease.
Collapse
|
29
|
Brondani LA, Crispim D, Pisco J, Guimarães JA, Berger M. The G Allele of the rs12050217 Polymorphism in the BDKRB1 Gene Is Associated with Protection for Diabetic Retinopathy. Curr Eye Res 2019; 44:994-999. [PMID: 31017477 DOI: 10.1080/02713683.2019.1610178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Purpose: The plasma kallikrein-kinin system is activated during vascular injury caused by diabetic retinopathy (DR), being involved in hyperpermeability and inflammation. Bradykinin B1 receptor (B1R) is expressed in human retina, and its levels are increased in murine models of diabetes. Experimental studies reveal that B1R antagonists ameliorate retinal injury caused by diabetes in rodents. Thus, the aim of this study was to investigate the association between the rs12050217A/G polymorphism in the BDKRB1 gene, the gene that codifies B1R, and DR in type 2 diabetes mellitus (T2DM) patients. Methods: We analyzed 636 T2DM patients and 443 non-diabetic subjects. T2DM patients were categorized by the presence of non-proliferative DR (NPDR, n = 267), proliferative DR (PDR, n = 197), and absence of DR (n = 172). The BDKRB1 rs12050217A/G polymorphism was genotyped by real-time PCR using TaqMan MGB probes. Results: The genotype frequencies of the BDKRB1 rs12050217A/G polymorphism are in Hardy-Weinberg equilibrium and did not differ between T2DM patients and non-diabetic subjects (P > 0.05). The presence of the genotypes containing the rs12050217 G allele was less frequent in patients with PDR when compared to patients with NPDR and without DR (32.0%, 41.9%, and 43.0%, P = 0.045, respectively). Interestingly, the presence of G allele was associated with ~40% protection for PDR, which was confirmed after correction for the presence of hypertension, ethnicity, age, HDL, and gender (odds ratio = 0.616, 95% confidence interval 0.385-0.986, P = 0.043). Conclusion: For the first time, we showed that BDKRB1 rs12050217 G allele is associated with protection for the advanced stage of DR in T2DM patients; however, further studies are needed to confirm this finding.
Collapse
Affiliation(s)
- Leticia A Brondani
- Endocrine Division, Hospital de Clínicas de Porto Alegre , Porto Alegre , Rio Grande do Sul , Brazil.,Postgraduate Program in Medical Science: Endocrinology, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul , Porto Alegre , Rio Grande do Sul , Brazil
| | - Daisy Crispim
- Endocrine Division, Hospital de Clínicas de Porto Alegre , Porto Alegre , Rio Grande do Sul , Brazil.,Postgraduate Program in Medical Science: Endocrinology, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul , Porto Alegre , Rio Grande do Sul , Brazil
| | - Julia Pisco
- Endocrine Division, Hospital de Clínicas de Porto Alegre , Porto Alegre , Rio Grande do Sul , Brazil
| | - Jorge A Guimarães
- Biochemical Pharmacology Lab, Center for Experimental Research, Hospital de Clínicas de Porto Alegre , Porto Alegre , Rio Grande do Sul , Brazil.,Postgraduate Program in Cell and Molecular Biology, Center of Biotechnology, Instituto de Biociências, Universidade Federal do Rio Grande do Sul , Porto Alegre , Rio Grande do Sul , Brazil
| | - Markus Berger
- Biochemical Pharmacology Lab, Center for Experimental Research, Hospital de Clínicas de Porto Alegre , Porto Alegre , Rio Grande do Sul , Brazil.,Postgraduate Program in Health Sciences: Gynecology and Obstetrics, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul , Porto Alegre , Rio Grande do Sul , Brazil
| |
Collapse
|
30
|
Abstract
INTRODUCTION Among various human tissue identity testing platforms, short tandem repeat (STR) genotyping has emerged as the most powerful and cost-effective method. Beyond forensic applications, tissue identity testing has become increasingly important in modern medical practice, in areas such as diagnostic pathology. Areas covered: A brief overview of various molecular/genetic techniques for identity testing is provided. This includes restriction fragment length polymorphism, single nucleotide polymorphism array and STR genotyping by multiplex PCR. Diagnostic applications of STR genotyping are covered in greater details: genotyping diagnosis of gestational trophoblastic disease, resolving tissue specimen mislabeling or histologic contaminant or 'floaters', bone marrow engraftment/chimerism analysis and interrogation of the primary source of malignancy in patients receiving organ donation. Four clinical cases are then presented to further illustrate these important clinical applications along with discussion of the interpretation, limitations, and pitfalls of STR genotyping. Expert commentary: STR genotyping is currently the most applicable method of identity testing and has extended its role well into the practice of diagnostic pathology with novel and powerful applications beyond forensics.
Collapse
Affiliation(s)
- Ian Baine
- a Department of Pathology , Yale University School of Medicine , New Haven , CT , USA
| | - Pei Hui
- a Department of Pathology , Yale University School of Medicine , New Haven , CT , USA
| |
Collapse
|
31
|
Mackowski M, Wodas L, Brooks SA, Cieslak J. TBX3 and ASIP genotypes reveal discrepancies in officially recorded coat colors of Hucul horses. Animal 2019; 13:1811-6. [PMID: 30614426 DOI: 10.1017/S1751731118003506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although only a few specific pigmentation types are allowed within the Hucul horse registry, accurate determination of particular coat colors can be uncertain due to the presence of variation in color shades and segregation of multiple dun dilution variants. Herein, we genotyped the previously identified polymorphisms within two coat color loci TBX3 (T-box 3) and ASIP (Agouti Signaling Protein) in 462 Hucul individuals and compared the genotype predicted phenotypes with observed pigmentation types provided in the Polish Horse Breeders Association database. We identified disagreement between the predicted and recorded coat color in 157 horses (34%). The most common error was misclassification of horses with the nd1/nd1 and nd1/nd2 genotypes, what may be related with the occurrence of some 'intermediate' dilution phenotypes in such individuals. We have also proven that the frequency of the dominant dun dilution allele (D) (0.30) is higher than previously predicted by available studbooks. The D allele(s) is easily 'hidden' in various phenotypic groups including dark bay and black, therefore we hypothesized that the dun dilution effect itself is not as strongly epistatic in the Hucul horse as described in other horse breeds. This may be the result of an additional genetic modifier suppressing D allele phenotypic effect.
Collapse
|
32
|
Dewir YH, Naidoo Y, Teixeira da Silva JA. Thidiazuron-induced abnormalities in plant tissue cultures. Plant Cell Rep 2018; 37:1451-1470. [PMID: 30051285 DOI: 10.1007/s00299-018-2326-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
Thidiazuron (TDZ) is a proven effective and potent synthetic plant growth regulator for organogenic, regeneration, and developmental pathways, including axillary and adventitious shoot proliferation, somatic embryogenesis, and in vitro flowering. TDZ has facilitated the establishment of in vitro cultures for several plant species, especially woody and recalcitrant plants, which has enabled their genetic transformation and improvement. Despite the effectiveness and advantages of using TDZ, several drawbacks are associated with its application in plant tissue culture. This review addresses the morphological, physiological, and cytogenetic abnormalities associated with the use of TDZ in vitro, and provides a summary of these abnormalities in several plant species.
Collapse
Affiliation(s)
- Yaser Hassan Dewir
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia.
- Department of Horticulture, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh, 33516, Egypt.
| | - Yougasphree Naidoo
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban, 4000, South Africa.
| | | |
Collapse
|
33
|
Amer A, Taha H, Ammar N, Salama M, El-Alfy T. Applicability of Different Molecular Markers Techniques for Genetic Distinguish Between Two Genera <I>Cressa</I> Linn. and <I>Cuscuta</I> Yunck. Family Convolvulaceae. Pak J Biol Sci 2018; 21:179-186. [PMID: 30311474 DOI: 10.3923/pjbs.2018.179.186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVE The DNA fingerprinting is used to determine the relationship between species in the same genus or between genera related to the same family. The aim of this study was to determine the relationships between two samples related to the same family Convolvulaceae, representing two genera, Cressa Linn. and Cuscuta Yunck. by RAPD, ISSR and SCoT molecular techniques (PCR based DNA fingerprint). MATERIALS AND METHODS The RAPD, ISSR and SCoT based DNA fingerprinting techniques were implemented to identify the fingerprint diversity between two genera, Cressa Linn. and Cuscuta Yunck-belonging to the family Convolvulaceae. RESULTS Applying of RAPD technique revealed that using OP-A02, OP-A09, OP-A10, OP-C04 and OP-M01 primers recorded 60, 83.33, 100, 50 and 70.66% polymorphism, respectively. On the other hand, ISSR technique recorded 40, 50, 100, 66.67, 33.33 and 37.5% polymorphism with 44B, HB-08, HB-09, HB-10, HB-11 and HB-12 primers, respectively. However, amplification of SCoT technique, SCoT 1, SCoT 2, SCoT 3, SCoT 4, SCoT 6, SCoT 8, SCoT 10 and SCoT 12 primers recorded 33.33, 28.57, 14.28, 66.66, 25, 40, 42.85 and 50%, respectively . The total polymorphism recorded 73.33, 54.58 and 37.7% for RAPD, ISSR and SCoT techniques, respectively. CONCLUSION The result of this study indicated that SCoT technique was more efficient and sustainable for distinguish between two genera under investigation.
Collapse
|
34
|
Nakamura H, Teshima K, Tachida H. Effects of cyclic changes in population size on neutral genetic diversity. Ecol Evol 2018; 8:9362-9371. [PMID: 30377507 PMCID: PMC6194295 DOI: 10.1002/ece3.4436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 07/09/2018] [Indexed: 01/29/2023] Open
Abstract
Recurrent changes in population size are often observed in nature, influencing the efficiency of selection and consequently affecting organismal evolution. Thus, it is important to know whether such changes occurred in the past history of a focal population of evolutionary interests. Here, we focused on cyclic changes in population size and investigated the distributional properties of Tajima's D and its power to distinguish a cyclic change model compared with the standard neutral model, changing the frequency and magnitude of the cyclic change. With very low or very high frequencies of the cycle, the distribution of Tajima's D was similar to that in a constant size population, as demonstrated by previous theoretical works. Otherwise, its mean was negative or positive, and its variance was smaller or larger depending on the time of sampling. The detection rate of the cyclic change against the constancy in size by Tajima's D depended on the sample size, the number of loci, and the time of sampling in addition to the frequency and amplitude of the cycle. Using sequence data of several tens of loci, the detection rate was fairly high if the frequency was intermediate and the sampling was made when population size was large; otherwise, the detection rate was not high. We also found that cyclic change could be discriminated from simple expansion or shrinkage of a population by Tajima's D only if the frequency was in a limited range and the sampling was made when the population was large.
Collapse
Affiliation(s)
- Haruna Nakamura
- Graduate School of Systems Life SciencesKyushu UniversityFukuokaJapan
| | - Kosuke Teshima
- Department of BiologyFaculty of ScienceKyushu UniversityFukuokaJapan
| | - Hidenori Tachida
- Department of BiologyFaculty of ScienceKyushu UniversityFukuokaJapan
| |
Collapse
|
35
|
Abstract
Population size is one of the main factors that determine the amount of DNA polymorphism. We examined a model under which the population size changed linearly. Because of the simplicity of this model, we could analytically obtain the expectation of nucleotide diversity, E(π), and the expectation of the amount of DNA polymorphism, E(θ), based on the number of segregating sites. The results suggest that E(π) is larger than E(θ) when the population size decreased and that E(π) is smaller than E(θ) when the population size increased. The expected time to the most recent common ancestor could also be obtained under this model.
Collapse
Affiliation(s)
- Takuya Takahashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Fumio Tajima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| |
Collapse
|
36
|
Wirtwein M, Melander O, Sjőgren M, Hoffmann M, Narkiewicz K, Gruchala M, Sobiczewski W. Elevated ambulatory systolic-diastolic pressure regression index is genetically determined in hypertensive patients with coronary heart disease. Blood Press 2017; 26:174-180. [PMID: 28092973 DOI: 10.1080/08037051.2016.1273741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
OBJECTIVES Ambulatory systolic-diastolic pressure regression index (ASDPRI) as a composite marker of cardiovascular (CV) properties is related to CV complications. However, genetic determinants of ASDPRI are not known. The aim of this study is to report the relationship between certain single nucleotide polymorphisms (SNP) and ASDPRI in hypertensive patients with CAD confirmed by coronary angiography. METHODS A total of 1345 hypertensive subjects with CAD were included. SNPs were selected from genome-wide association studies. SNPs were reported to be associated with coronary artery disease risk. There were significant differences in 24 h and daytime and nighttime ASDPRIs for PHCTR1, LPA and ADAMTS7 polymorphisms. Genetic risk score (GRS18) was constructed to evaluate additive effect of 18 SNPs for ASDPRI. RESULTS Analysis of covariance revealed a significant relationship between the PPAB2B (β - 0.85; 95 CI -1.85--0.16, p < 0.02), WDR12 (β - 1.31; 95 CI -2.19--0.43, p < 0.01) polymorphisms and nighttime ASDPRI dipping. Analysis of covariance revealed a significant relationship between GRS 18 and 24-h ASDPRI (β 0.34; 95 CI 0.16-0.31, p < 0.01). CONCLUSIONS In conclusion, ADAMTS7 and LPA polymorphisms are related to 24-h ASDPRI but PPAB2B and WDR12 gene polymorphisms are associated with nighttime ASDPRI dipping. A total of 24-h ASDPRI is determined by GRS18.
Collapse
Affiliation(s)
- Marcin Wirtwein
- a Department of Pharmacology , Medical University of Gdansk , Gdansk , Poland
| | - Olle Melander
- b Department of Clinical Sciences , Lund University , Malmö , Sweden
| | - Marketa Sjőgren
- b Department of Clinical Sciences , Lund University , Malmö , Sweden
| | - Michal Hoffmann
- c Department of Hypertension and Diabetology , Medical University of Gdansk , Gdansk , Poland
| | - Krzysztof Narkiewicz
- c Department of Hypertension and Diabetology , Medical University of Gdansk , Gdansk , Poland
| | - Marcin Gruchala
- d 1st Department of Cardiology , Medical University of Gdansk , Gdansk , Poland
| | | |
Collapse
|
37
|
Thirugnanasambandam A, Karthik S, Artheswari G, Gautham N. DNA polymorphism in crystals: three stable conformations for the decadeoxynucleotide d(GCATGCATGC). Acta Crystallogr D Struct Biol 2016; 72:780-8. [PMID: 27303798 DOI: 10.1107/s2059798316006306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/14/2016] [Indexed: 11/11/2022]
Abstract
High-resolution structures of DNA fragments determined using X-ray crystallography or NMR have provided descriptions of a veritable alphabet of conformations. They have also shown that DNA is a flexible molecule, with some sequences capable of adopting two different structures. Here, the first example is presented of a DNA fragment that can assume three different and distinct conformations in crystals. The decanucleotide d(GCATGCATGC) was previously reported to assume a single-stranded double-fold structure. In one of the two crystal structures described here the decamer assumes both the double-fold conformation and, simultaneously, the more conventional B-type double-helical structure. In the other crystal the sequence assumes the A-type double-helical conformation. These results, taken together with CD spectra, which were recorded as the decamer was titrated against four metal ions and spermine, indicate that the molecule may exist as a mixed population of structures in solution. Small differences in the environmental conditions, such as the concentration of metal ion, may decide which of these crystallizes out. The results also support the idea that it may be possible for DNA to change its structure to suit the binding requirements of proteins or drugs.
Collapse
Affiliation(s)
| | - Selvam Karthik
- CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
| | - Gunanithi Artheswari
- CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
| | - Namasivayam Gautham
- CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
| |
Collapse
|
38
|
Khrunin AV, Filippova IN, Aliev AM, Tupitsina TV, Slominsky PA, Limborska SA. GSTM1 copy number variation in the context of single nucleotide polymorphisms in the human GSTM cluster. Mol Cytogenet 2016; 9:30. [PMID: 27099630 PMCID: PMC4837583 DOI: 10.1186/s13039-016-0241-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/01/2016] [Indexed: 02/06/2023] Open
Abstract
Background GSTM1 gene deletion is one of the most known copy number polymorphisms in human genome. It is most likely caused by homologous recombination between the repeats flanking the gene. However, taking into account that the deletion has no crucial effects on human well-being, and the ability of other GSTMs to compensate for the lack of GSTM1, a role for additional factors affecting GSTM1 deletion can be proposed. Our goal was to explore the relationships between GSTM1 deletion polymorphism and single nucleotide polymorphisms (SNPs) in the region of the GSTM cluster that includes GSTM2, GSTM3, GSTM4, and GSTM5 in addition to GSTM1. Results Real-time polymerase chain reaction was used to quantify the number of GSTM1 copies. Fourteen SNPs from the region were tested and their allelic patterns were compared in groups of Russian individuals subdivided according to their GSTM1 deletion genotypes. Linkage disequilibrium-based haplotype analysis showed substantial differences of haplotype frequencies between the groups, especially between individuals with homozygous GSTM1 −/− and +/+ genotypes. Exploration of the results of phasing of GSTM1 and SNP genotypes revealed unequal segregation of GSTM1 + and − alleles at different haplotypes. Conclusions The observed differences in haplotype patterns suggest the potential role of genetic context in GSTM1 deletion frequency (appearance) and in the determination of the deletion-related effects.
Collapse
Affiliation(s)
- Andrey V Khrunin
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 Russia
| | - Irina N Filippova
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 Russia
| | - Aydar M Aliev
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 Russia
| | - Tat'yana V Tupitsina
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 Russia
| | - Petr A Slominsky
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 Russia
| | - Svetlana A Limborska
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 Russia
| |
Collapse
|
39
|
Gholap PN, Kale DS, Krishnamurthi K, Sirothia AR, Kothekar MD. Screening the partial coding region of metallothionein isoform-2 gene in Zebu cattle. Iran J Vet Res 2016; 17:155-159. [PMID: 27822243 PMCID: PMC5090147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 02/18/2016] [Accepted: 02/27/2016] [Indexed: 06/06/2023]
Abstract
Metallothionein (MT) is important because it binds tightly to heavy metals to decrease their toxicity. DNA was isolated from 30 toxic metal exposed and 30 toxic metal unexposed Zebu cows. The amplified metallothionein isoform-2 (MT-2) PCR product (489 bp) was further used for PCR-RFLP and DNA sequencing. MT-2 TaqI PCR-RFLP revealed homozygous genotype (AA) except for the E23 animal (AB). The genotype frequency of AA and AB (E23) genotypes in the exposed groups was 0.967 and 0.033 respectively. DNA sequencing was carried out for the toxic metal exposed sample (E23) and the control group sample (C13). Blast comparisons of the sequences were then aligned against a nucleotide database which revealed 150 nucleotide substitutions consisting of 70 transitions and around 80 transversions. DNA sequencing followed by PCR-RFLP for MT-2 revealed a higher number of nucleotide substitutions (150) for the AB genotype of E23 as compared to the AA genotype (38) of E21. The proportions of transversion mutations in the AB genotype were higher as compared to the MT-2 AA genotype. DNA sequencing was carried out based on random sampling for E21 and C13. Alignment analysis of the E21 and C13 sample revealed 38 nucleotide substitutions consisting of equal numbers of transition and transversion. BLAST analysis of the identified partial sequence revealed 89% identity with Bos taurus, 85% identity with sheep, 98% identity with buffalos and 100% identity with goat MT-2 sequences. Overall findings of the present study revealed DNA sequence variation in the coding region of the MT-2 gene of Zebu cattle which can be utilised to characterize and explore markers for heavy metal homeostasis in Zebu cattle.
Collapse
Affiliation(s)
- P. N. Gholap
- MVSc, Department of Animal Genetics and Breeding, Nagpur Veterinary College, Maharashtra Animal and Fishery Sciences University (MAFSU), Seminary Hills, Nagpur-440006, Maharashtra State, India
| | - D. S. Kale
- Department of Animal Genetics and Breeding, Nagpur Veterinary College, Maharashtra Animal and Fishery Sciences University (MAFSU), Seminary Hills, Nagpur-440006, Maharashtra State, India
| | - K. Krishnamurthi
- Environmental Health Division, National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur-440020, Maharashtra State, India
| | - A. R. Sirothia
- Department of Animal Genetics and Breeding, Nagpur Veterinary College, Maharashtra Animal and Fishery Sciences University (MAFSU), Seminary Hills, Nagpur-440006, Maharashtra State, India
| | - M. D. Kothekar
- Department of Animal Genetics and Breeding, Nagpur Veterinary College, Maharashtra Animal and Fishery Sciences University (MAFSU), Seminary Hills, Nagpur-440006, Maharashtra State, India
| |
Collapse
|
40
|
Bonanni A, Pividori MI, del Valle M. DNA polymorphism sensitive impedimetric detection on gold-nanoislands modified electrodes. Talanta 2015; 136:95-101. [PMID: 25702990 DOI: 10.1016/j.talanta.2015.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 12/30/2014] [Accepted: 01/03/2015] [Indexed: 10/24/2022]
Abstract
Nanocomposite materials are being increasingly used in biosensing applications as they can significantly improve biosensor performance. Here we report the use of a novel impedimetric genosensor based on gold nanoparticles graphite-epoxy nanocomposite (nanoAu-GEC) for the detection of triple base mutation deletion in a cystic-fibrosis (CF) related human DNA sequence. The developed platform consists of chemisorbing gold nano-islands surrounded by rigid, non-chemisorbing, and conducting graphite-epoxy composite. The ratio of the gold nanoparticles in the composite was carefully optimized by electrochemical and microscopy studies. Such platform allows the very fast and stable thiol immobilization of DNA probes on the gold islands, thus minimizing the steric and electrostatic repulsion among the DNA probes and improving the detection of DNA polymorphism down to 2.25fmol by using electrochemical impedance spectroscopy. These findings are very important in order to develop new and renewable platforms to be used in point-of-care devices for the detection of biomolecules.
Collapse
Affiliation(s)
- Alessandra Bonanni
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 63737, Singapore.
| | - Maria Isabel Pividori
- Sensors and Biosensors Group, Department of Chemistry, Universitat Autònoma de Barcelona, Edifici Cn, 08193 Bellaterra, Barcelona, Spain
| | - Manel del Valle
- Sensors and Biosensors Group, Department of Chemistry, Universitat Autònoma de Barcelona, Edifici Cn, 08193 Bellaterra, Barcelona, Spain.
| |
Collapse
|
41
|
Berisha N, Millaku F, Gashi B, Krasniqi E, Novak J. Initial determination of DNA polymorphism of some Primula veris L. populations from Kosovo and Austria. Physiol Mol Biol Plants 2015; 21:117-22. [PMID: 25650329 PMCID: PMC4312321 DOI: 10.1007/s12298-014-0275-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 12/07/2014] [Indexed: 06/04/2023]
Abstract
Primula veris L. (Primulaceae) is a long lived perennial and well known pharmaceutical plant, widely collected for these reasons in almost all SE Europe and particularly in Kosovo. The aim of the study is to determine molecular polymorphism of cowslip (P. veris L.) populations from Kosovo. DNA extracted from leaves were investigated in details for presence of polymorphism. RAPD analyses were conducted using 20 different short primers. Genomic DNA amplification profiles were analyzed and processed using data labelling. Comparison between cowslip populations in genetic composition revealed that samples from Bogaj were too distinct on their own. Molecular variation was observed to be more within populations (73 %) as compared to among populations (27 %). On the other hand, genetic distance of populations revealed that the highest genetic distance is between Leqinat and Maja e Madhe. Mean values of expected heterozygosity were highest in Bogaj population, while lowest in Maja e Madhe population. The obtained results indicated that Bogaj population are more polymorphic. From the obtained data it can be concluded that RAPD markers provided a useful technique to study genetic diversity in P. veris L. populations. This technology allows identification and assessment of the genetic similarities and differences among plant populations.
Collapse
Affiliation(s)
- Naim Berisha
- />Department of Biology, Faculty of Mathematics and Natural Sciences, University of Prishtina “Hasan Prishtina”, Mother Teresa, str., n.n., 10 000 Prishtina, Republic of Kosovo
- />Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Fadil Millaku
- />Department of Biology, Faculty of Mathematics and Natural Sciences, University of Prishtina “Hasan Prishtina”, Mother Teresa, str., n.n., 10 000 Prishtina, Republic of Kosovo
| | - Bekim Gashi
- />Department of Biology, Faculty of Mathematics and Natural Sciences, University of Prishtina “Hasan Prishtina”, Mother Teresa, str., n.n., 10 000 Prishtina, Republic of Kosovo
| | - Elez Krasniqi
- />Department of Biology, Faculty of Mathematics and Natural Sciences, University of Prishtina “Hasan Prishtina”, Mother Teresa, str., n.n., 10 000 Prishtina, Republic of Kosovo
| | - Johannes Novak
- />Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Veterinärplatz 1, A-1210 Vienna, Austria
| |
Collapse
|
42
|
Bachmann K, Neumann A, Hinsch A, Nentwich MF, El Gammal AT, Vashist Y, Perez D, Bockhorn M, Izbicki JR, Mann O. Cyclin D1 is a strong prognostic factor for survival in pancreatic cancer: analysis of CD G870A polymorphism, FISH and immunohistochemistry. J Surg Oncol 2014; 111:316-23. [PMID: 25470788 DOI: 10.1002/jso.23826] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 09/30/2014] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND OBJECTIVE Cyclin D1 is an important regulator protein for the G1-S cell cycle phase transition. The aim of this trial was to evaluate the impact of the CCND1 polymorphism G870A and corresponding protein expression and CCND1 amplification on the survival of the patients. METHODS 425 patients with ductal pancreatic adenocarcinoma who underwent resection were included after histopathological confirmation. DNA was analyzed for Cyclin D1 polymorphisms, immunhistochemical examination and fluorescence in situ hybridization analysis of the tumor were performed. RESULTS Overall, the mean survival was 22.9 months (20.5-25.3). The survival in patients with Cyclin D1 G870A polymorphism Adenine/Adenine was 15.1 months (95% CI 11.3-18.9), 21.5 months (17.4-25.6) for Adenine/Guanine, and 29.4 months (95% CI 23.8-35.0) for Guanine/Guanine (P = 0.003). A shorter survival was associated with strong/moderate protein expression in immunohistochemistry (IHC) compared to weak/no expression (P = 0.028). Additionally, a significant coherency between unfavourable polymorphism (AA/AG) and increased protein expression was detected (P = 0.005). CONCLUSIONS A strong impact on survival of Cyclin D1 G870A polymorphism and the detected corresponding protein expression was found. The biological mechanism of CCND1 in carcinogenesis has not been fully examined; but at present Cyclin D1 seems to be an interesting biomarker for the prognosis of ductal adenocarcinoma.
Collapse
Affiliation(s)
- Kai Bachmann
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Miwa M, Honjo S, You G, Tanaka M, Uchida K, Srivatanakul P, Khuhaprema T, Loilome W, Techasen A, Wongkham C, Limpaiboon T, Yongvanit P, Wongkham S. Genetic and environmental determinants of risk for cholangiocarcinoma in Thailand. World J Gastrointest Pathophysiol 2014; 5:570-578. [PMID: 25401000 PMCID: PMC4231521 DOI: 10.4291/wjgp.v5.i4.570] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 05/01/2014] [Accepted: 09/10/2014] [Indexed: 02/06/2023] Open
Abstract
Cholangiocarcinoma (CCA) is a difficult cancer to diagnose in the early stage and to treat by curative resection. The incidence of CCA in the northeast of Thailand is the highest in the world. To make progress in detecting a high risk group and in the prevention and detection of CCA, we have been analyzing the risk factors for CCA. Although liver fluke infection is known to be a risk factor, there are patients who are not infected with the liver fluke and not all people infected with the liver fluke will suffer from the disease. Therefore, it is of the utmost importance to analyze the risk factors and the mechanism to prevent the disease and also to detect the disease in its early stage to save patients’ lives. Through collaboration among Thai and Japanese researchers, we analyzed the genetic and environmental determinants of risks for CCA. Also, we have been trying to develop methods to detect the disease in a non-invasive way. Without repeating findings reported in various reviews on CCA, we will first discuss the environmental and genetic determinants of the risks for CCA. Second, we will discuss the properties of CCA, including the etiological agents and the mechanism of cholangiocarcinogenesis, and finally, we will discuss future approaches to prevent and cure CCA from the standpoint of evidence-based medicine. We will discuss these points by including the data from our laboratories. We would like to emphasize the importance of the genetic data, especially whole genome approaches, to understand the properties of CCA, to find a high risk population for CCA and to develop effective preventative methods to stop the carcinogenic steps toward CCA in the near future. In addition, it is of the upmost importance to develop a non-invasive, specific and sensitive method to detect CCA in its early stage for the application of modern medical approaches to help patients with CCA.
Collapse
|
44
|
Wang B, Khalili Mahani M, Ng WL, Kusumi J, Phi HH, Inomata N, Wang XR, Szmidt AE. Extremely low nucleotide polymorphism in Pinus krempfii Lecomte, a unique flat needle pine endemic to Vietnam. Ecol Evol 2014; 4:2228-38. [PMID: 25360263 PMCID: PMC4201436 DOI: 10.1002/ece3.1091] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 03/21/2014] [Accepted: 04/02/2014] [Indexed: 11/07/2022] Open
Abstract
Pinus krempfii Lecomte is a morphologically and ecologically unique pine, endemic to Vietnam. It is regarded as vulnerable species with distribution limited to just two provinces: Khanh Hoa and Lam Dong. Although a few phylogenetic studies have included this species, almost nothing is known about its genetic features. In particular, there are no studies addressing the levels and patterns of genetic variation in natural populations of P. krempfii. In this study, we sampled 57 individuals from six natural populations of P. krempfii and analyzed their sequence variation in ten nuclear gene regions (approximately 9 kb) and 14 mitochondrial (mt) DNA regions (approximately 10 kb). We also analyzed variation at seven chloroplast (cp) microsatellite (SSR) loci. We found very low haplotype and nucleotide diversity at nuclear loci compared with other pine species. Furthermore, all investigated populations were monomorphic across all mitochondrial DNA (mtDNA) regions included in our study, which are polymorphic in other pine species. Population differentiation at nuclear loci was low (5.2%) but significant. However, structure analysis of nuclear loci did not detect genetically differentiated groups of populations. Approximate Bayesian computation (ABC) using nuclear sequence data and mismatch distribution analysis for cpSSR loci suggested recent expansion of the species. The implications of these findings for the management and conservation of P. krempfii genetic resources were discussed.
Collapse
Affiliation(s)
- Baosheng Wang
- Department of Ecology and Environmental Science, Umeå University Umeå, Sweden
| | | | - Wei Lun Ng
- Department of Biology, Kyushu University Fukuoka, Japan
| | - Junko Kusumi
- Department of Biology, Kyushu University Fukuoka, Japan
| | - Hai Hong Phi
- Vietnamese Academy of Forest Sciences Hanoi, Vietnam
| | - Nobuyuki Inomata
- Department of Biology, Kyushu University Fukuoka, Japan ; Department of Environmental Science, International College of Arts and Sciences, Fukuoka Women's University Fukuoka, Japan
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå University Umeå, Sweden
| | | |
Collapse
|
45
|
Hanna MOF, Shahin RMH, Meshaal SS, Kostandi IF. Susceptibility and progression of end stage renal disease are not associated with angiotensin II type 1 receptor gene polymorphism. J Recept Signal Transduct Res 2014; 35:381-5. [PMID: 25316403 DOI: 10.3109/10799893.2014.956757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
CONTEXT The role of the angiotensin II type 1 receptor (AT1R) gene polymorphism, A1166C, has been shown to be associated with end stage renal disease (ESRD) and its progression. There is also some evidence that HLA class II alleles are associated with ESRD independent of other factors. OBJECTIVE To examine the association between AT1R gene polymorphism in the susceptibility and progression to ESRD in patients with chronic renal failure and to investigate if the AT1R genotypes and HLA-DR alleles predict the time to ESRD. MATERIALS AND METHODS Genotyping was performed in 50 ESRD patients and 44 control subjects for the AT1R A1166C gene polymorphism using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). ESRD patients were examined for HLA-DRB1 alleles according to a reverse hybridization line probe assay. RESULTS Allele and genotype frequencies of the AT1R polymorphism did not differ significantly between ESRD patients and controls. Furthermore, there was no association between the AT1R gene polymorphism or HLA-DRB1 alleles with the time to the occurrence of end stage failure. DISCUSSION AND CONCLUSION We concluded that the AT1R genotype does not contribute to the genetic susceptibility of ESRD and is not associated with progression of chronic kidney failure to ESRD.
Collapse
Affiliation(s)
| | | | | | - Inas F Kostandi
- b Department of Internal Medicine , Faculty of Medicine, Cairo University , Kasr Al Ainy , Cairo , Egypt
| |
Collapse
|
46
|
Aviñó A, Portella G, Ferreira R, Gargallo R, Mazzini S, Gabelica V, Orozco M, Eritja R. Specific loop modifications of the thrombin-binding aptamer trigger the formation of parallel structures. FEBS J 2014; 281:1085-99. [PMID: 24304855 DOI: 10.1111/febs.12670] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 11/11/2013] [Accepted: 11/27/2013] [Indexed: 01/31/2023]
Abstract
Guanine-rich sequences show large structural variability, with folds ranging from duplex to triplex and quadruplex helices. Quadruplexes are polymorphic, and can show multiple stoichiometries, parallel and antiparallel strand alignments, and different topological arrangements. We analyze here the equilibrium between intramolecular antiparallel and intermolecular parallel G-quadruplexes in the thrombin-binding aptamer (TBA) sequence. Our theoretical and experimental studies demonstrate that an apparently simple modification at the loops of TBA induces a large change in the monomeric antiparallel structure of TBA to yield a parallel G-quadruplex showing a novel T-tetrad. The present results illustrate the extreme polymorphism of G-quadruplexes and the ease with which their conformation in solution can be manipulated by nucleotide modification.
Collapse
Affiliation(s)
- Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Novák K. Functional polymorphisms in Toll-like receptor genes for innate immunity in farm animals. Vet Immunol Immunopathol 2013; 157:1-11. [PMID: 24268689 DOI: 10.1016/j.vetimm.2013.10.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 10/21/2013] [Accepted: 10/28/2013] [Indexed: 01/05/2023]
Abstract
The exploitation of the genetic factors affecting the health status of farm animals represents an alternative approach to controlling the diseases caused by microbial pathogens. The determination of innate immunity based on the genotype of the germplasm cells is a constraint for specificity but becomes an advantage in breeding schemes. The structural deviations among Toll-like receptors (TLRs), as the most frequently studied innate immunity components, have been documented at all levels, i.e., interspecific, inter- and intravarietal, in the main farm species. The current computational methods facilitate the prediction of the functional consequences of the observed mutations. Subsequently, these predictions can be verified through immunological responsiveness and population-wide association studies. The frequency and haplotype grouping of individual polymorphisms are used to track the origin and selection coefficient as independent indicators of functional changes. The Toll-like receptor variants associated with mastitis and mycobacterial infection have been identified in cattle, consequently, the targeting of these proteins in breeding could contribute to disease control. The range of infections affected by TLR polymorphisms suggests that the improvement of innate resistance is feasible in more species. Thus, the traditional breeds and wild populations should be regarded as the resources of genetic variability accessible for these purposes.
Collapse
Affiliation(s)
- Karel Novák
- Department of Molecular Genetics, Institute of Animal Science, Prague-Uhříněves, Czech Republic.
| |
Collapse
|
48
|
Wang Z, Wang Y, Wang N, Wang J, Wang Z, Vallejos CE, Wu R. Towards a comprehensive picture of the genetic landscape of complex traits. Brief Bioinform 2012; 15:30-42. [PMID: 22930650 DOI: 10.1093/bib/bbs049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The formation of phenotypic traits, such as biomass production, tumor volume and viral abundance, undergoes a complex process in which interactions between genes and developmental stimuli take place at each level of biological organization from cells to organisms. Traditional studies emphasize the impact of genes by directly linking DNA-based markers with static phenotypic values. Functional mapping, derived to detect genes that control developmental processes using growth equations, has proven powerful for addressing questions about the roles of genes in development. By treating phenotypic formation as a cohesive system using differential equations, a different approach-systems mapping-dissects the system into interconnected elements and then map genes that determine a web of interactions among these elements, facilitating our understanding of the genetic machineries for phenotypic development. Here, we argue that genetic mapping can play a more important role in studying the genotype-phenotype relationship by filling the gaps in the biochemical and regulatory process from DNA to end-point phenotype. We describe a new framework, named network mapping, to study the genetic architecture of complex traits by integrating the regulatory networks that cause a high-order phenotype. Network mapping makes use of a system of differential equations to quantify the rule by which transcriptional, proteomic and metabolomic components interact with each other to organize into a functional whole. The synthesis of functional mapping, systems mapping and network mapping provides a novel avenue to decipher a comprehensive picture of the genetic landscape of complex phenotypes that underlie economically and biomedically important traits.
Collapse
Affiliation(s)
- Zhong Wang
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA 17033, USA.
| | | | | | | | | | | | | |
Collapse
|
49
|
Abstract
Molecular markers serve to assign individual samples to specific groups. Such markers should be easily identified and have a high discrimination power, being highly conserved within groups while showing sufficient variability between the groups that are to be distinguished. The availability of a large number of complete genomic sequences now enables the informed selection of genes as molecular markers based on the observed patterns of variability. We derived a new scoring system based on observed DNA polymorphic differences, and which uses the Bayes theorem as adapted by Wilcox. For validation, we applied this system to the problem of identifying individual species within a prokaryotic (Vibrio) and a eukaryotic (Diphyllobothrium) genus for validation. Top-scoring candidates genes Chromosome segregation ATPase and ATPase-subunit 6 showed better discrimination power in Vibrio and Diphyllobothrium, respectively, as compared to standard molecular markers (recA, dnaJ and atpA for Vibrio, and 18s rRNA, ITS and COX1 for Diphyllobothrium).
Collapse
Affiliation(s)
- Harry M Bohle
- Bioinformática, Universidad Internacional de Andalucía, Málaga, Spain
| | | |
Collapse
|
50
|
Silva-Brandão KL, Lyra ML, Santos TV, Seraphim N, Albernaz KC, Pavinato VAC, Martinelli S, Cônsoli FL, Omoto C. Exploitation of mitochondrial nad6 as a complementary marker for studying population variability in Lepidoptera. Genet Mol Biol 2011; 34:719-25. [PMID: 22215980 PMCID: PMC3229131 DOI: 10.1590/s1415-47572011000400028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 07/31/2011] [Indexed: 11/22/2022] Open
Abstract
The applicability of mitochondrial nad6 sequences to studies of DNA and population variability in Lepidoptera was tested in four species of economically important moths and one of wild butterflies. The genetic information so obtained was compared to that of cox1 sequences for two species of Lepidoptera. nad6 primers appropriately amplified all the tested DNA targets, the generated data proving to be as informative and suitable in recovering population structures as that of cox1. The proposal is that, to obtain more robust results, this mitochondrial region can be complementarily used with other molecular sequences in studies of low level phylogeny and population genetics in Lepidoptera.
Collapse
Affiliation(s)
- Karina L Silva-Brandão
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, Brazil
| | | | | | | | | | | | | | | | | |
Collapse
|