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Lee H, Ozbulak U, Park H, Depuydt S, De Neve W, Vankerschaver J. Assessing the reliability of point mutation as data augmentation for deep learning with genomic data. BMC Bioinformatics 2024; 25:170. [PMID: 38689247 PMCID: PMC11059627 DOI: 10.1186/s12859-024-05787-6] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Deep neural networks (DNNs) have the potential to revolutionize our understanding and treatment of genetic diseases. An inherent limitation of deep neural networks, however, is their high demand for data during training. To overcome this challenge, other fields, such as computer vision, use various data augmentation techniques to artificially increase the available training data for DNNs. Unfortunately, most data augmentation techniques used in other domains do not transfer well to genomic data. RESULTS Most genomic data possesses peculiar properties and data augmentations may significantly alter the intrinsic properties of the data. In this work, we propose a novel data augmentation technique for genomic data inspired by biology: point mutations. By employing point mutations as substitutes for codons, we demonstrate that our newly proposed data augmentation technique enhances the performance of DNNs across various genomic tasks that involve coding regions, such as translation initiation and splice site detection. CONCLUSION Silent and missense mutations are found to positively influence effectiveness, while nonsense mutations and random mutations in non-coding regions generally lead to degradation. Overall, point mutation-based augmentations in genomic datasets present valuable opportunities for improving the accuracy and reliability of predictive models for DNA sequences.
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Affiliation(s)
| | - Utku Ozbulak
- Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, South Korea
| | - Homin Park
- Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, South Korea
- IDLab, Department of Electronics and Information Systems, Ghent University, Ghent, Belgium
| | - Stephen Depuydt
- Erasmus Brussels University of Applied Sciences and Arts, Brussels, Belgium
| | - Wesley De Neve
- Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, South Korea
- IDLab, Department of Electronics and Information Systems, Ghent University, Ghent, Belgium
| | - Joris Vankerschaver
- Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, South Korea.
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.
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2
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Zhang F, Liu ZY, Liu S, Zhang WG, Wang BB, Li CL, Xu JZ. Rapid screening of point mutations by mismatch amplification mutation assay PCR. Appl Microbiol Biotechnol 2024; 108:190. [PMID: 38305911 PMCID: PMC10837254 DOI: 10.1007/s00253-024-13036-2] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 08/18/2023] [Accepted: 01/25/2024] [Indexed: 02/03/2024]
Abstract
Metabolic engineering frequently makes use of point mutation and saturation mutation library creation. At present, sequencing is the only reliable and direct technique to detect point mutation and screen saturation mutation library. In this study, mismatch amplification mutation assay (MAMA) PCR was used to detect point mutation and screen saturation mutation library. In order to fine-tune the expression of odhA encoding 2-oxoglutarate dehydrogenase E1 component, a saturating mutant library of the RBS of odhA was created in Corynebacterium glutamicum P12 based on the CRISPR-Cas2a genome editing system, which increased the L-proline production by 81.3%. MAMA PCR was used to filter out 42% of the non-mutant transformants in the mutant library, which effectively reduced the workload of the subsequent fermentation test and the number of sequenced samples. The rapid and sensitive MAMA-PCR method established in this study provides a general strategy for detecting point mutations and improving the efficiency of mutation library screening. KEY POINTS: • MAMA PCR was optimized and developed to detect point mutation. • MAMA PCR greatly improves the screening efficiency of point mutation. • Attenuation of odhA expression in P12 effectively improves proline production.
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Affiliation(s)
- Feng Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Zhen Yang Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Shuai Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Wei Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China.
| | - Bing Bing Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Chang Lon Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Jian Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
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Shi N, Zhao D, Qiu D, Wang H, Wu L, Chen F, Chen Q, Du Y. Resistance risk and resistance-related point mutations in cytochrome b of florylpicoxamid in Colletotrichum scovillei. Pestic Biochem Physiol 2023; 196:105617. [PMID: 37945253 DOI: 10.1016/j.pestbp.2023.105617] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/07/2023] [Accepted: 09/09/2023] [Indexed: 11/12/2023]
Abstract
Anthracnose caused by Colletotrichum scovillei is one of the most destructive diseases of chili worldwide. Florylpicoxamid is a new quinone inside inhibitor (QiI) fungicide, which shows intensively inhibitory activity against C. scovillei. Currently, florylpicoxamid is in the registration process to control chili anthracnose in China. This study investigated the risk of resistance and resistance genetic mechanism of C. scovillei to florylpicoxamid. Baseline sensitivity of 141C. scovillei isolates to florylpicoxamid was established with an average EC50 value of 0.2328 ± 0.0876 μg/mL. A total of seven stable florylpicoxamid-resistant mutants were obtained with resistance factors ranging from 41 to 276. The mutants showed similar or weaker traits in mycelial growth, sporulation, conidial germination and pathogenicity than their parental isolates. Generally, the resistance risk of C. scovillei to florylpicoxamid would be moderate. In addition, there was no cross-resistance between florylpicoxamid and the commercially available fungicides tested. A37V and S207L mutations in the cytochrome b protein were detected in four high-resistance and three moderate-resistance mutants, respectively, of which, S207L is a new mutation. Molecular docking showed that the two mutations conferred different resistance levels to florylpicoxamid. These results provide a new perspective for QiI fungicide-resistance mechanism and may help in the reasonable use of florylpicoxamid against chili anthracnose in the future.
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Affiliation(s)
- Niuniu Shi
- Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China; Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou, Fujian 350013, China
| | - Deyou Zhao
- Corteva (China) Investment Co., Ltd., Shanghai 200120, China
| | - Dezhu Qiu
- Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China
| | - Haihong Wang
- Corteva (China) Investment Co., Ltd., Shanghai 200120, China
| | - Liting Wu
- Corteva (China) Investment Co., Ltd., Shanghai 200120, China
| | - Furu Chen
- Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China
| | - Qing Chen
- Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China
| | - Yixin Du
- Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China; Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou, Fujian 350013, China.
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Carrington B, Sood R. Fluorescent PCR-based Screening Methods for Precise Knock-in of Small DNA Fragments and Point Mutations in Zebrafish. Bio Protoc 2023; 13:e4732. [PMID: 37575394 PMCID: PMC10415208 DOI: 10.21769/bioprotoc.4732] [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: 02/22/2023] [Revised: 03/29/2023] [Accepted: 05/10/2023] [Indexed: 08/15/2023] Open
Abstract
Generation of zebrafish (Danio rerio) models with targeted insertion of epitope tags and point mutations is highly desirable for functional genomics and disease modeling studies. Currently, CRISPR/Cas9-mediated knock-in is the method of choice for insertion of exogeneous sequences by providing a repair template for homology-directed repair (HDR). A major hurdle in generating knock-in models is the labor and cost involved in screening of injected fish to identify the precise knock-in events due to low efficiency of the HDR pathway in zebrafish. Thus, we developed fluorescent PCR-based high-throughput screening methods for precise knock-in of epitope tags and point mutations in zebrafish. Here, we provide a step-by-step guide that describes selection of an active sgRNA near the intended knock-in site, design of single-stranded oligonucleotide (ssODN) templates for HDR, quick validation of somatic knock-in using injected embryos, and screening for germline transmission of precise knock-in events to establish stable lines. Our screening method relies on the size-based separation of all fragments in an amplicon by fluorescent PCR and capillary electrophoresis, thus providing a robust and cost-effective strategy. Although we present the use of this protocol for insertion of epitope tags and point mutations, it can be used for insertion of any small DNA fragments (e.g., LoxP sites, in-frame codons). Furthermore, the screening strategy described here can be used to screen for precise knock-in of small DNA sequences in any model system, as PCR amplification of the target region is its only requirement. Key features This protocol expands the use of fluorescent PCR and CRISPR-STAT for screening of precise knock-in of small insertions and point mutations in zebrafish. Allows validation of selected sgRNA and HDR template within two weeks by somatic knock-in screening. Allows robust screening of point mutations by combining restriction digest with CRISPR-STAT. Graphical overview Overview of the three-phase knock-in pipeline in zebrafish (created with BioRender.com).
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Affiliation(s)
- Blake Carrington
- Zebrafish Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Raman Sood
- Zebrafish Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Sasaguri H. Introduction of Genetic Mutations Into Mice by Base Editor and Target-AID. Methods Mol Biol 2023; 2637:111-124. [PMID: 36773142 DOI: 10.1007/978-1-0716-3016-7_9] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Generating genetically modified animal models that precisely recapitulate disease characteristics forms an integral and indispensable tool to understanding disease pathophysiology. Recently, important advances in genome editing technologies have enabled us to efficiently create sophisticated animal models in short periods of time. Base editing is a modified CRISPR/Cas system that induces base substitution at targeted genomic regions. Here I describe a basic protocol to introduce disease-relevant pathogenic mutations into mice utilizing two representative base editing tools, Base Editor and Target-AID.
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Affiliation(s)
- Hiroki Sasaguri
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Saitama, Japan.
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6
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Omuut G, Mollel HG, Kanyesigye D, Akohoue F, Adumo Aropet S, Wagaba H, Otim MH. Genetic analyses and detection of point mutations in the acetylcholinesterase-1 gene associated with organophosphate insecticide resistance in fall armyworm (Spodoptera frugiperda) populations from Uganda. BMC Genomics 2023; 24:22. [PMID: 36646998 PMCID: PMC9841645 DOI: 10.1186/s12864-022-09093-4] [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: 01/26/2022] [Accepted: 12/21/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The fall armyworm (FAW), Spodoptera frugiperda; J.E. Smith (Lepidoptera: Noctuidae), is now an economically important pest that causes huge losses to maize productivity in sub-Saharan Africa. Variations in sub-population genetics and the processes of rapid adaptation underpinning the invasion remain unclear. For this, the genetic identity and diversity of FAW populations in Uganda were revealed by sequencing 87 samples (collected across the country). Based on the partial mitochondrial cytochrome oxidase I (COI) gene polymorphisms, we further examined the mitochondrial haplotype configuration and compared the FAW in Uganda with sequences from other parts of the world. The molecular target for organophosphate and carbamate resistance, acetylcholinesterase, was also investigated. RESULTS Analysis of the partial COI gene sequences showed the presence of both rice (predominant) and corn strain haplotypes, with a haplotype diversity of 0.382. Based on the COI marker, pairwise difference distribution analyses, and neutrality tests, showed that the FAW populations in Uganda and the rest of Africa are evolving neutrally, but those in America and Asia are undergoing expansion. Our findings support observations that invasive FAW populations throughout the rest of Africa and Asia share a common origin. Sequencing of the S. frugiperda ace-1 gene revealed four amino acid substitutions, two of which (A201S and F290V) were previously shown to confer organophosphate resistance in both S. frugiperda and several other insect species. The other two previously reported new variations in positions g-396 and g-768, are presumed to be related to the development of insecticide resistance. CONCLUSIONS This research has increased our knowledge of the genetics of FAW in Uganda, which is critical for pest surveillance and the detection of resistance. However, due to the low gene polymorphism of COI, more evolutionary studies incorporating the Spodoptera frugiperda whole-genome sequence are required to precisely understand the FAW population dynamics, introduction paths, origin, and subsequent spread.
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Affiliation(s)
- Geresemu Omuut
- grid.463519.c0000 0000 9021 5435National Agricultural Research Organization, National Crops Resources Research Institute, P. O Box, 7084 Kampala, Uganda
| | - Happyness G. Mollel
- Tanzania Agricultural Research Institute-Mikocheni, P. O. Box, 6226 Dar es Salaam, Tanzania
| | - Dalton Kanyesigye
- grid.463519.c0000 0000 9021 5435National Agricultural Research Organization, National Crops Resources Research Institute, P. O Box, 7084 Kampala, Uganda
| | - Félicien Akohoue
- grid.412037.30000 0001 0382 0205Laboratory of Genetics, Biotechnology and Seed Science (GBioS), Faculty of Agronomic Sciences, University of Abomey-Calavi, Abomey-Calavi, Benin ,grid.9464.f0000 0001 2290 1502State Plant Breeding Institute, University of Hohenheim, 70599 Stuttgart, Germany
| | - Stella Adumo Aropet
- grid.463387.d0000 0001 2229 1011National Agricultural Research Organization, National Agricultural Research Laboratories, P.O. Box 7065, Kampala, Uganda
| | - Henry Wagaba
- grid.463519.c0000 0000 9021 5435National Agricultural Research Organization, National Crops Resources Research Institute, P. O Box, 7084 Kampala, Uganda
| | - Michael H. Otim
- grid.463519.c0000 0000 9021 5435National Agricultural Research Organization, National Crops Resources Research Institute, P. O Box, 7084 Kampala, Uganda
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Sasaguri H. Use of the Representative Base Editing Tool Target-AID to Introduce Pathogenic Mutations into Mice. Methods Mol Biol 2023; 2606:87-97. [PMID: 36592310 DOI: 10.1007/978-1-0716-2879-9_8] [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: 01/03/2023]
Abstract
Base editing technology is a modified CRISPR/Cas system that directly introduces point mutations into targeted genomic regions without causing double-stranded DNA breaks. Target-AID (activation-induced cytidine deaminase) is a representative base editing tool and may serve as a potent option to create genetically modified animals that harbor disease-causing pathogenic point mutations. In this chapter, I describe the basic protocol used to introduce disease-relevant pathogenic mutations into mice by Target-AID.
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Affiliation(s)
- Hiroki Sasaguri
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Saitama, Japan.
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8
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Abstract
In this chapter, we describe a protocol to estimate the thermal stability of single domain antibodies (sdAbs) using molecular dynamics (MD) simulations. This method measures the Q-value, the fraction of the native contacts, along the trajectory of high-temperature MD simulations starting from the experimental X-ray structure. We show a good correlation between the Q-value and the experimental melting temperature (Tm) in seven sdAbs. Assessing the Q-value on a per-residue level enabled us to identify residues that contribute to the instability and thus demonstrate which residues could be mutated to improve the stability and have later been validated by experiments. Our protocol extends beyond the application on sdAbs, as it is also suitable for other proteins and to determine the interfacial stability between protein and ligand.
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Affiliation(s)
- Gert-Jan Bekker
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Narutoshi Kamiya
- Graduate School of Information Science, University of Hyogo, Kobe, Hyogo, Japan.
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Al-Raawi D, Kanhere A. Site-Directed Mutagenesis Protocol to Determine the Role of Amino Acid Residues in Polycomb Group (PcG) Protein Function. Methods Mol Biol 2023; 2655:79-89. [PMID: 37212990 DOI: 10.1007/978-1-0716-3143-0_7] [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] [Indexed: 05/23/2023]
Abstract
Site-directed mutagenesis (SDM) is a technique in molecular biology and protein engineering that is widely used to determine the significance of specific residues involved in post-translational modifications (PTMs), protein structure, function, and stability. Here, we describe a simple and cost-effective polymerase chain reaction (PCR)-based SDM method. This method can be used to introduce point mutation, short addition, or deletions in protein sequences. Using polycomb repressive complex-2 (PRC2)-associated protein JARID2 as an example, we demonstrate how SDM can be used to study structural and consequently functional changes in a protein.
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Affiliation(s)
| | - Aditi Kanhere
- Institute of System, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
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Carrington B, Ramanagoudr-Bhojappa R, Bresciani E, Han TU, Sood R. A robust pipeline for efficient knock-in of point mutations and epitope tags in zebrafish using fluorescent PCR based screening. BMC Genomics 2022; 23:810. [PMID: 36476416 DOI: 10.1186/s12864-022-08971-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 10/26/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Genome editing using CRISPR/Cas9 has become a powerful tool in zebrafish to generate targeted gene knockouts models. However, its use for targeted knock-in remains challenging due to inefficient homology directed repair (HDR) pathway in zebrafish, highlighting the need for efficient and cost-effective screening methods. RESULTS: Here, we present our fluorescent PCR and capillary electrophoresis based screening approach for knock-in using a single-stranded oligodeoxynucleotide donor (ssODN) as a repair template for the targeted insertion of epitope tags, or single nucleotide changes to recapitulate pathogenic human alleles. For the insertion of epitope tags, we took advantage of the expected change in size of the PCR product. For point mutations, we combined fluorescent PCR with restriction fragment length polymorphism (RFLP) analysis to distinguish the fish with the knock-in allele. As a proof-of-principle, we present our data on the generation of fish lines with insertion of a FLAG tag at the tcnba locus, an HA tag at the gata2b locus, and a point mutation observed in Gaucher disease patients in the gba gene. Despite the low number of germline transmitting founders (1-5%), combining our screening methods with prioritization of founder fish by fin biopsies allowed us to establish stable knock-in lines by screening 12 or less fish per gene. CONCLUSIONS We have established a robust pipeline for the generation of zebrafish models with precise integration of small DNA sequences and point mutations at the desired sites in the genome. Our screening method is very efficient and easy to implement as it is PCR-based and only requires access to a capillary sequencer.
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Vázquez-García JG, de Portugal J, Torra J, Osuna MD, Palma-Bautista C, Cruz-Hipólito HE, De Prado R. Comparison between the mechanisms of Clearfield ® wheat and Lolium rigidum multiple resistant to acetyl CoA carboxylase and acetolactate synthase inhibitors. Environ Pollut 2022; 306:119438. [PMID: 35561797 DOI: 10.1016/j.envpol.2022.119438] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 04/28/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Clearfield® wheat (Triticum aestivum) have helped eliminate the toughest grasses and broadleaf weeds in Spain since 2005. This crop production system includes other tolerant cultivars to the application of imidazolinone (IMI) herbicides. However, the continuous use and off-label rates of IMI herbicides can contribute to the development of resistance in Lolium rigidum and other weed species. In this research, the main objectives were to study the resistance mechanisms to acetolactate synthase (ALS) and acetyl coenzyme A carboxylase (ACCase) inhibitors in a L. rigidum accession (LrR) from a Clearfield® wheat field, with a long history rotating these IMI-tolerant crops and compare them with those present in the IMI-tolerant wheat. The resistance to ACCase inhibitors in LrR was due to point mutations (Ile1781Leu plus Asp2078Gly) of the target site gene plus an enhanced herbicide metabolism (EHM), on the other hand, in wheat accessions was due only by EHM. Mechanisms involved in the resistance to ALS inhibitors were both point mutations of the target gene and EHM in the IMI-tolerant wheat, while only evidence of mutation (Trp574Leu) was found in the multiple herbicide resistant L. rigidum accession. This research demonstrates that if crop rotation is not accompanied by the use of alternative sites of action in herbicide-tolerant crops, resistant weeds to herbicide to which crops are tolerant, can easily be selected. Moreover, repeated and inappropriate use of Clearfield® crops and herbicide rotations can lead to the evolution of multiple resistant weeds, as shown in this study, and have also inestimable environmental impacts.
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Affiliation(s)
- José G Vázquez-García
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, 14014, Córdoba, Spain.
| | - Joao de Portugal
- Biosciences Department, Polytechnic Institute of Beja, Beja, Portugal; VALORIZA-Research Centre for Endogenous Resource Valorization, Polytechnic Institute of Portalegre, Portalegre, Portugal
| | - Joel Torra
- Department d'Hortofructicultura, Botànica i Jardineria, Agrotecnio-CERCA Center, Universitat de Lleida, Lleida, Spain
| | - Maria D Osuna
- Plant Protection Department, Extremadura Scientific and Technological Research Center (CICYTEX), Ctra. de AV, km 372, Badajoz, 06187, Guadajira, Spain
| | - Candelario Palma-Bautista
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, 14014, Córdoba, Spain
| | | | - Rafael De Prado
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, 14014, Córdoba, Spain
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Bernasocchi T, Theurillat JPP. SPOP-mutant prostate cancer: Translating fundamental biology into patient care. Cancer Lett 2021; 529:11-18. [PMID: 34974131 DOI: 10.1016/j.canlet.2021.12.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 03/16/2021] [Revised: 11/30/2021] [Accepted: 12/21/2021] [Indexed: 02/06/2023]
Abstract
Comprehensive cancer genome studies have revealed genetically-defined subtypes of prostate cancer with distinct truncal driver mutations. Because prostate cancer has been largely seen as a rather uniform disease, the clinical significance of this discovery remained largely obscure. However, recent findings imply distinct biological features and therapeutic vulnerabilities linked to specific truncal mutations. Here we review our current understanding of prostate cancers harboring recurrent point mutations in the ubiquitin ligase adaptor protein SPOP and discuss opportunities for future clinical translation. More specifically, activation of the androgen receptor (AR) signaling emerges as the key oncogenic pathway. SPOP-mutant prostate cancer patients respond to AR inhibition in various clinical settings. Molecular insights on how mutant SPOP promotes tumorigenesis may open more specific therapeutic avenues which, in combination with conventional AR-targeting agents, could improve the outcome of patients with SPOP-mutant prostate cancer.
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Affiliation(s)
- Tiziano Bernasocchi
- Institute of Oncology Research, Bellinzona, TI, 6500, Switzerland; Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, TI, 6900, Lugano, Switzerland
| | - Jean-Philippe P Theurillat
- Institute of Oncology Research, Bellinzona, TI, 6500, Switzerland; Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, TI, 6900, Lugano, Switzerland.
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Rogers C, Morrissette JJD, Sussman RT. NTRK point mutations and their functional consequences. Cancer Genet 2021; 262-263:5-15. [PMID: 34972036 DOI: 10.1016/j.cancergen.2021.12.002] [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: 07/09/2021] [Revised: 11/15/2021] [Accepted: 12/13/2021] [Indexed: 12/27/2022]
Abstract
The neurotrophic receptor tyrosine kinase (NTRK) family of genes, including NTRK1, NTRK2, and NTRK3, encodes membrane-bound receptors that normally regulate cell survival and differentiation upon binding of growth factors. Not surprisingly, mutations in these genes are known to contribute to the growth of a diverse number of cancers. With the recent FDA approval of two first-generation tyrosine-kinase inhibitors (TKIs) for adult and pediatric patients with solid tumors harboring NTRK gene fusions, much of the literature has focused on the biology behind these types of NTRK abnormalities; however, point mutations can also contribute to oncogenesis or resistance to TKI therapy, albeit at a lower frequency than fusions. This review focuses on NTRK gene mutations that are associated with resistance to directed therapies, mutations detected in the primary setting that confer increased oncogenic activity, and evidence that suggests that some of these variants may be treated using specific targeted therapies. Finally, this review focuses on the detection of point mutations, including the utility of cell-free DNA (cfDNA) for monitoring the acquisition of resistance mutations.
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Affiliation(s)
- Corey Rogers
- Department of Pathology and Laboratory Medicine, Division of Precision and Computational Diagnostics, University of Pennsylvania, 3020 Market Street, Suite 220, Philadelphia, PA 19104, USA.
| | - Jennifer J D Morrissette
- Department of Pathology and Laboratory Medicine, Division of Precision and Computational Diagnostics, University of Pennsylvania, 3020 Market Street, Suite 220, Philadelphia, PA 19104, USA
| | - Robyn T Sussman
- Department of Pathology and Laboratory Medicine, Division of Precision and Computational Diagnostics, University of Pennsylvania, 3020 Market Street, Suite 220, Philadelphia, PA 19104, USA
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Fimmel E, Gumbel M, Starman M, Strüngmann L. Robustness against point mutations of genetic code extensions under consideration of wobble-like effects. Biosystems 2021; 208:104485. [PMID: 34280517 DOI: 10.1016/j.biosystems.2021.104485] [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: 06/16/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 11/25/2022]
Abstract
Many theories of the evolution of the genetic code assume that the genetic code has always evolved in the direction of increasing the supply of amino acids to be encoded (Barbieri, 2019; Di Giulio, 2005; Wong, 1975). In order to reduce the risk of the formation of a non-functional protein due to point mutations, nature is said to have built in control mechanisms. Using graph theory the authors have investigated in Blazej et al. (2019) if this robustness is optimal in the sense that a different codon-amino acid assignment would not generate a code that is even more robust. At present, efforts to expand the genetic code are very relevant in biotechnological applications, for example, for the synthesis of new drugs (Anderson et al., 2004; Chin, 2017; Dien et al., 2018; Kimoto et al., 2009; Neumann et al., 2010). In this paper we generalize the approach proposed in Blazej et al. (2019) and will explore hypothetical extensions of the standard genetic code with respect to their optimal robustness in two ways: (1) We keep the usual genetic alphabet but move from codons to longer words, such as tetranucleotides. This increases the supply of coding words and thus makes it possible to encode non-canonical amino acids. (2) We expand the genetic alphabet by introducing non-canonical base pairs. In addition, the approach from Blazej et al. (2019) and Blazej et al. (2018) is extended by incorporating the weights of single point-mutations into the model. The weights can be interpreted as probabilities (appropriately normalized) or degrees of severity of a single point mutation. In particular, this new approach allows us to take a closer look at the wobble effects in the translation of codons into amino acids. According to the results from Blazej et al. (2019) and Blazej et al. (2018), the standard genetic code is not optimal in terms of its robustness to point mutations if the weights of single point mutations are not taken into account. After incorporation into the model weights that mimic the wobble effect, the results of the present work show that it is much more robust, almost optimal in that respect. We hope, that this theoretical analysis might help to assess extended genetic codes and their abilities to encode new amino acids.
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Affiliation(s)
- E Fimmel
- Competence Center in Medicine, Biology, and Biotechnology, Mannheim University of Applied Sciences, 68163 Mannheim, Germany.
| | - M Gumbel
- Competence Center in Medicine, Biology, and Biotechnology, Mannheim University of Applied Sciences, 68163 Mannheim, Germany.
| | - M Starman
- Competence Center in Medicine, Biology, and Biotechnology, Mannheim University of Applied Sciences, 68163 Mannheim, Germany.
| | - L Strüngmann
- Competence Center in Medicine, Biology, and Biotechnology, Mannheim University of Applied Sciences, 68163 Mannheim, Germany.
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15
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Alexandrov ID, Alexandrova MV. The dose-, LET-, and gene-dependent patterns of DNA changes underlying the point mutations in spermatozoa of Drosophila melanogaster. I. Autosomal gene black. Mutat Res 2021; 823:111755. [PMID: 34217017 DOI: 10.1016/j.mrfmmm.2021.111755] [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: 10/20/2020] [Revised: 04/23/2021] [Accepted: 05/24/2021] [Indexed: 11/26/2022]
Abstract
Sequence analysis of 7 spontaneous, 27 γ-ray- and 20 neutron/neutron+γ-ray-induced black (b) point mutants was carried out. All these mutants were isolated as non-mosaic transmissible recessive visibles in the progeny of irradiated males from the wild-type high-inbred laboratory D32 strain of Drosophila melanogaster. Among spontaneous mutants, there were two (28.5 %) mutants with copia insertion in intron 1 and exon 2, three (42.8 %) with replacement of b+D32 paternal sequence with maternal b1 sequence (gene conversion), one (14.3 %) with 142-bp-long insertion in exon 2, and one (14.3 %) with a short deletion and two single-base substitutions in exon 3. Among γ-ray-induced mutants, there were 1 (3.7 %) with copia insertion in intron 2, 6 (22.2 %) with gene conversion, and the remaining 20 (74.1 %) mutants had 37 different small-scale DNA changes. There were 20 (54.1 %) single- or double-base substitutions, 7 (18.9 %) frameshifts (indels), 9 (24.3 %) extended deletions or insertions, and 1(2.7 %) mutant with a short insertion instead of a short deletion. Remarkably, clusters of independent small-scale changes inside the gene or within one DNA helical turn were recovered. The spectrum of DNA changes in 20 neutron/ neutron+γ-ray-induced mutants was drastically different from that induced by γ-rays in that 18 (90.0 %) mutants had the b1sequence. In addition, 2 (10.0 %) with gene conversion had 600- or 19-bp-long deletion in exon 3 and 1 (5.0 %) mutant with a short insertion instead of a short deletion. Analysis of all 27 mutants with gene conversion events shows that 20 (74.1 %) had full b1 sequence whereas 7 others (25.9 %) contained a partial b1 sequence. These data are the first experimental evidence for gene conversion in the early stages of animal embryogenesis in the first diploid cleavage nucleus after male and female pronuclei have united. The gene conversion, frameshifts (indels), and deletions between short repeats were considered as products of a relevant DNA repair pathways described in the literature. As the first step, the gametic doubling doses for phenotypic black point mutations and for intragenic base substitution mutations in mature sperm cells irradiated by 40 Gy of γ-rays were estimated as 5.8 and 1.2 Gy, respectively, showing that doubling dose for mutations at the molecular level is about 5 times lower than that at the phenotypic level.
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Affiliation(s)
- I D Alexandrov
- Dzhelepov Laboratory of Nuclear Problems, Joint Institute for Nuclear Research, 141980, Dubna, Moscow Region, Russia.
| | - M V Alexandrova
- Dzhelepov Laboratory of Nuclear Problems, Joint Institute for Nuclear Research, 141980, Dubna, Moscow Region, Russia
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16
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Zimowski JG, Purzycka J, Pawelec M, Ozdarska K, Zaremba J. Small mutations in Duchenne/Becker muscular dystrophy in 164 unrelated Polish patients. J Appl Genet 2021; 62:289-295. [PMID: 33420945 DOI: 10.1007/s13353-020-00605-0] [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] [Received: 07/25/2020] [Revised: 12/09/2020] [Accepted: 12/22/2020] [Indexed: 10/22/2022]
Abstract
In the 164 patients with Duchenne/Becker muscular dystrophy, we found 142 different small mutations including 51 novel mutations not listed in the LOVD, the UMD-DMD, the ClinVar, and the HGMD databases. Among all mutations, nonsense mutations occurred in 45.7%, frameshift mutations in 32.9%, and splicing mutations in 19.5%. Small mutations were distributed throughout the whole dystrophin gene. Splicing mutations were twice more common in BMD patients than in DMD patients. Eighty-two percent of mothers of the males affected with DMD/BMD were found to be carriers of small mutations.
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Affiliation(s)
- Janusz G Zimowski
- Department of Genetics, Institute of Psychiatry and Neurology, 02-957, Sobieskiego 9, Warsaw, Poland. .,, Warsaw, Poland.
| | - Joanna Purzycka
- Department of Genetics, Institute of Psychiatry and Neurology, 02-957, Sobieskiego 9, Warsaw, Poland
| | - Magdalena Pawelec
- Department of Genetics, Institute of Psychiatry and Neurology, 02-957, Sobieskiego 9, Warsaw, Poland
| | - Katarzyna Ozdarska
- Department of Genetics, Institute of Psychiatry and Neurology, 02-957, Sobieskiego 9, Warsaw, Poland
| | - Jacek Zaremba
- Department of Genetics, Institute of Psychiatry and Neurology, 02-957, Sobieskiego 9, Warsaw, Poland
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17
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Chernova OA, Chernov VM, Mouzykantov AA, Baranova NB, Edelstein IA, Aminov RI. Antimicrobial drug resistance mechanisms among Mollicutes. Int J Antimicrob Agents 2020; 57:106253. [PMID: 33264670 DOI: 10.1016/j.ijantimicag.2020.106253] [Citation(s) in RCA: 7] [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: 08/09/2019] [Revised: 07/08/2020] [Accepted: 11/22/2020] [Indexed: 12/11/2022]
Abstract
Representatives of the Mollicutes class are the smallest, wall-less bacteria capable of independent reproduction. They are widespread in nature, most are commensals, and some are pathogens of humans, animals and plants. They are also the main contaminants of cell cultures and vaccine preparations. Despite limited biosynthetic capabilities, they are highly adaptable and capable of surviving under various stress and extreme conditions, including antimicrobial selective pressure. This review describes current understanding of antibiotic resistance (ABR) mechanisms in Mollicutes. Protective mechanisms in these bacteria include point mutations, which may include non-target genes, and unique gene exchange mechanisms, contributing to transfer of ABR genes. Better understanding of the mechanisms of emergence and dissemination of ABR in Mollicutes is crucial to control these hypermutable bacteria and prevent the occurrence of highly ABR strains.
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Affiliation(s)
- Olga A Chernova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Centre of RAS, Kazan, Russian Federation
| | - Vladislav M Chernov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Centre of RAS, Kazan, Russian Federation
| | - Alexey A Mouzykantov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Centre of RAS, Kazan, Russian Federation
| | - Natalya B Baranova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Centre of RAS, Kazan, Russian Federation
| | - Inna A Edelstein
- Smolensk State Medical University, Ministry of Health of Russian Federation, Smolensk, Russian Federation
| | - Rustam I Aminov
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation.
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18
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Espinosa Reyes TM, Collazo Mesa T, Lantigua Cruz PA, Agramonte Machado A, Domínguez Alonso E, Falhammar H. Molecular diagnosis of patients with congenital adrenal hyperplasia due to 21-hydroxylase deficiency. BMC Endocr Disord 2020; 20:165. [PMID: 33168061 PMCID: PMC7653887 DOI: 10.1186/s12902-020-00643-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/22/2020] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Congenital adrenal hyperplasia (CAH) is an autosomal recessive group of diseases. 21-Hydroxylase deficiency (21OHD) accounts for between 95 and 99% of all CAH cases. OBJECTIVES To characterize the genotype of patients clinically diagnosed with 21OHD and to identify the most frequent mutations in the Cuban population. METHODS Cross-sectional descriptive study that included all patients diagnosed with 21OHD from January 2000 to December 2018. For the molecular analysis of the CYP21A2 gene, a protocol was used that used the polymerase chain reaction in 2 stages; in the first stage genomic DNA was amplified and 5 point mutations were detected in the second stage (Intron 2, Deletion of 8 bp, G318X, I172N and P30L). RESULTS The 5 point mutations were identified in 31 of the 55 (56%) studied patients, 16/21 (76%) in the salt-wasting, 12/18 (67%) in the simple virilizing and 3/16 (19%) in the nonclassical form. The Intron 2 mutation was the most frequent, followed by G318X and 8 bp deletion. Compound heterozygotes were found in 10 patients, all corresponded to classic forms of the disease. CONCLUSIONS The causal CYP21A2 gene mutation was detected in 56% (72% in classic CAH), which makes the method encouraging. The most frequent mutations observed were Intron 2 and G318X. The detection of mutations offers confirmation of diagnosis, prediction of phenotype and genetic counseling.
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Affiliation(s)
| | - Teresa Collazo Mesa
- National Institute of Endocrinology, Zapata Street and D, Vedado, 10400, Havana, Cuba
| | | | | | - Emma Domínguez Alonso
- National Institute of Endocrinology, Zapata Street and D, Vedado, 10400, Havana, Cuba
| | - Henrik Falhammar
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Endocrinology, Metabolism and Diabetes, Karolinska University Hospital, Stockholm, Sweden
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Tripathi K, Goel A, Singhai A, Garg M. Mutational analysis of Ras hotspots in patients with urothelial carcinoma of the bladder. World J Clin Oncol 2020; 11:614-628. [PMID: 32879848 PMCID: PMC7443835 DOI: 10.5306/wjco.v11.i8.614] [Citation(s) in RCA: 4] [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] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/21/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Mutational activation of Ras genes is established as a prognostic factor for the genesis of a constitutively active RAS-mitogen activated protein kinase pathway that leads to cancer. Heterogeneity among the distribution of the most frequent mutations in Ras isoforms is reported in different patient populations with urothelial carcinoma of the bladder (UCB).
AIM To determine the presence/absence of mutations in Ras isoforms in patients with UCB in order to predict disease outcome.
METHODS This study was performed to determine the mutational spectrum at the hotspot regions of H-Ras, K-Ras and N-Ras genes by polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) and DNA sequencing followed by their clinical impact (if any) by examining the relationship of mutational spectrum with clinical histopathological variables in 87 UCB patients.
RESULTS None of the 87 UCB patients showed point mutations in codon 12 of H-Ras gene; codon 61 of N-Ras gene and codons 12, 13 of K-Ras gene by PCR-RFLP. Direct DNA sequencing of tumor and normal control bladder mucosal specimens followed by Blastn alignment with the reference wild-type sequences failed to identify even one nucleotide difference in the coding exons 1 and 2 of H-Ras, N-Ras and K-Ras genes in the tumor and control bladder mucosal specimens.
CONCLUSION Our findings on the lack of mutations in H-Ras, K-Ras and N-Ras genes could be explained on the basis of different etiological mechanisms involved in tumor development/progression, inherent genetic susceptibility, tissue specificity or alternative Ras dysfunction such as gene amplification and/or overexpression in a given cohort of patients.
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Affiliation(s)
- Kiran Tripathi
- Department of Biochemistry, University of Lucknow, Lucknow 226007, India
| | - Apul Goel
- Department of Urology, King George Medical University, Lucknow 226003, India
| | - Atin Singhai
- Department of Pathology, King George Medical University, Lucknow 226003, India
| | - Minal Garg
- Department of Biochemistry, University of Lucknow, Lucknow 226007, India
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20
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Levi T, Sloutskin A, Kalifa R, Juven-Gershon T, Gerlitz O. Efficient In Vivo Introduction of Point Mutations Using ssODN and a Co-CRISPR Approach. Biol Proced Online 2020; 22:14. [PMID: 32684853 PMCID: PMC7362497 DOI: 10.1186/s12575-020-00123-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/06/2020] [Indexed: 12/20/2022] Open
Abstract
Background The generation of point mutations is a major tool for evaluating the roles of specific nucleotides or amino acids within the regulatory or functional landscape. However, examination of these mutations in vivo requires the generation of animals carrying only the relevant point mutations at the endogenous genomic loci, which is technically challenging. The CRISPR-Cas9 based genome editing greatly facilitates the generation of such genetically modified animals; however, most of the described methods use double-strand DNA (dsDNA) as the donor template. The dsDNA plasmids frequently undergo undesired integration events into the targeted genomic locus. The use of a single-strand oligodeoxynucleotide (ssODN) as the donor template prevents this complication and is therefore the preferred choice for introducing point mutations, as well as short sequences such as protein tags. Results We successfully applied the CRISPR-based white co-conversion strategy with a ssODN template, instead of the originally described dsDNA plasmid, to create genetically modified Drosophila melanogaster strains. We used the technique to easily introduce point mutations in two distinct chromosomes. Using the generated flies, we were able to demonstrate the in vivo importance of the respective mutations. For the Nucleoporin107 (Nup107) gene, the 1090G > A mutation was confirmed to affect ovarian development, while for the tinman (tin) gene, the regulatory role of the downstream core promoter element (DPE) was demonstrated within the developing Drosophila melanogaster embryo. Conclusions The described approach has facilitated the successful generation of point mutations in two different chromosomes, by two different labs. Distinct phenotypes associated with the newly-generated genotype were identified, thus exemplifying the importance of investigating the in vivo role of specific nucleotides. In addition, detailed guidelines, recommendations and crossing schemes are provided in order to support the generation of additional genetically modified animals by the scientific community.
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Affiliation(s)
- Tgst Levi
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, Institute for Medical Research Israel-Canada, Hebrew University, Jerusalem, Israel
| | - Anna Sloutskin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Rachel Kalifa
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, Institute for Medical Research Israel-Canada, Hebrew University, Jerusalem, Israel
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Offer Gerlitz
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, Institute for Medical Research Israel-Canada, Hebrew University, Jerusalem, Israel
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21
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Tovilla-Coutiño DB, Momany C, Eiteman MA. Engineered citrate synthase alters Acetate Accumulation in Escherichia coli. Metab Eng 2020; 61:171-80. [PMID: 32569710 DOI: 10.1016/j.ymben.2020.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/24/2020] [Accepted: 06/10/2020] [Indexed: 12/15/2022]
Abstract
Metabolic engineering is used to improve titers, yields and generation rates for biochemical products in host microbes such as Escherichia coli. A wide range of biochemicals are derived from the central carbon metabolite acetyl-CoA, and the largest native drain of acetyl-CoA in most microbes including E. coli is entry into the tricarboxylic acid (TCA) cycle via citrate synthase (coded by the gltA gene). Since the pathway to any biochemical derived from acetyl-CoA must ultimately compete with citrate synthase, a reduction in citrate synthase activity should facilitate the increased formation of products derived from acetyl-CoA. To test this hypothesis, we integrated into E. coli C ΔpoxB twenty-eight citrate synthase variants having specific point mutations that were anticipated to reduce citrate synthase activity. These variants were assessed in shake flasks for growth and the production of acetate, a model product derived from acetyl-CoA. Mutations in citrate synthase at residues W260, A267 and V361 resulted in the greatest acetate yields (approximately 0.24 g/g glucose) compared to the native citrate synthase (0.05 g/g). These variants were further examined in controlled batch and continuous processes. The results provide important insights on improving the production of compounds derived from acetyl-CoA.
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22
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Dhar BC, Reed AJ, Mitra S, Rodriguez Sanchez P, Nedorezova DD, Connelly RP, Rohde KH, Gerasimova YV. Cascade of deoxyribozymes for the colorimetric analysis of drug resistance in Mycobacterium tuberculosis. Biosens Bioelectron 2020; 165:112385. [PMID: 32729510 DOI: 10.1016/j.bios.2020.112385] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 05/24/2020] [Revised: 06/06/2020] [Accepted: 06/09/2020] [Indexed: 02/01/2023]
Abstract
A visual cascade detection system has been applied to the detection and analysis of drug-resistance profile of Mycobacterium tuberculosis complex (MTC), a causative agent of tuberculosis. The cascade system utilizes highly selective split RNA-cleaving deoxyribozyme (sDz) sensors. When activated by a complementary nucleic acid, sDz releases the peroxidase-like deoxyribozyme apoenzyme, which, in complex with a hemin cofactor, catalyzes the color change of the sample's solution. The excellent selectivity of the cascade has allowed for the detection of point mutations in the sequences of the MTC rpoB, katG, and gyrA genes, which are responsible for resistance to rifampin, isoniazid, and fluoroquinolone, respectively. When combined with isothermal nucleic acid sequence based amplification (NASBA), the assay was able to detect amplicons of 16S rRNA and katG mRNA generated from 0.1 pg and 10 pg total RNA taken for NASBA, respectively, in less than 2 h, producing a signal detectable with the naked eye. The proposed assay may become a prototype for point-of-care diagnosis of drug resistant bacteria with visual signal output.
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Affiliation(s)
- Bidhan C Dhar
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Adam J Reed
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Suvra Mitra
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | | | - Daria D Nedorezova
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Ryan P Connelly
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Kyle H Rohde
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Yulia V Gerasimova
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA.
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Salim B, Chatanga E, Jannot G, Mossaad E, Nakao R, Weitzman JB. Mutations in the TaPIN1 peptidyl prolyl isomerase gene in Theileria annulata parasites isolated in Sudan. Int J Parasitol Drugs Drug Resist 2019; 11:101-105. [PMID: 31794951 PMCID: PMC6904843 DOI: 10.1016/j.ijpddr.2019.11.001] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/26/2019] [Accepted: 11/14/2019] [Indexed: 11/27/2022]
Abstract
The tick-borne parasite Theileria annulata is the causative agent of tropical theileriosis or Mediterranean theileriosis. Infection of bovine leukocytes by the obligate intracellular parasites induces proliferative and invasive phenotypes associated with activated signaling pathways. The transformed phenotypes of infected cells are reversible by treatment with the theilericidal drug buparvaquone. Recent reports of resistance to buparvaquone in Africa and Asia highlight the need to investigate the mechanisms and prevalence of drug resistance. We screened 67 T. annulata isolates from Sudan to investigate mutations in the T. annulata prolyl isomerase I gene (TaPIN1). The secreted TaPin1 interacts with host proteins to induce pathways driving oncogenic transformation and metabolic reprogramming. We found an Alanine-to-Proline mutation at position 53 (A53P) in the catalytic loop that was previously found in Tunisian drug-resistant samples. This is the first study reporting independent confirmation of the A53P mutation in geographically isolated samples. We found several additional mutations in the predicted N-terminal signal peptide that might affect TaPin1 processing or targeting. We found that many parasites also share mutations in both the TaPIN1 and the cytochrome b genes, suggesting that these two genes represent important biomarkers to follow the spread of resistance in Africa, the Middle East and Asia.
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Affiliation(s)
- Bashir Salim
- Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum, P.O. Box 32, Khartoum North, Sudan.
| | - Elisha Chatanga
- Laboratory of Parasitology, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, N18 W9, Sapporo, Hokkaido, 060-0818, Japan
| | - Guillaume Jannot
- Université de Paris, Epigenetics and Cell Fate, CNRS, F-75013, Paris, France
| | - Ehab Mossaad
- Department of Pathology, Parasitology and Microbiology, College of Veterinary Medicine, Sudan University of Science and Technology, P.O. Box 204, Khartoum, Sudan
| | - Ryo Nakao
- Laboratory of Parasitology, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, N18 W9, Sapporo, Hokkaido, 060-0818, Japan
| | - Jonathan B Weitzman
- Université de Paris, Epigenetics and Cell Fate, CNRS, F-75013, Paris, France.
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24
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Ming Z, Chen Q, Chen N, Lin M, Liu N, Hu J, Xiao X. Eliminating the secondary structure of targeting strands for enhancement of DNA probe based low-abundance point mutation detection. Anal Chim Acta 2019; 1075:137-143. [PMID: 31196419 DOI: 10.1016/j.aca.2019.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 02/24/2019] [Revised: 04/25/2019] [Accepted: 05/05/2019] [Indexed: 10/26/2022]
Abstract
Nucleic acid probes are very useful tools in biological and medical science. However, the essential sensing mechanism of nucleic acid probes was prone to the interference of surrounding sequences. Especially when the target sequences formed secondary structures such as hairpin or quadruplex, the nucleic acid probes were hindered from hybridizing with target strands, greatly disabled the function of probes. Herein, we have established an Open strand based strategy for eliminating the influence of secondary structures on the performance of nucleic acid probes. The strategy was general toward different lengths, secondary structures and sequences of the targeting strand, and we found that the improvement was higher when the secondary structure of the targeting strand was more complicated. Experiments on synthetic single stranded DNA and real clinical genomic DNA samples were conducted for low abundance mutation detection, and the limit of detection for TERT-C228T and BRCA2 rs80359065 mutations could be 0.02% and 0.05% respectively, demonstrating the clinical practicability of our proposed strategy in low abundance mutation detection.
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Affiliation(s)
- Zhihao Ming
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Qianzhi Chen
- Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Na Chen
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Meng Lin
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Na Liu
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Junbo Hu
- Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Xianjin Xiao
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China.
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25
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Pathak B, Zhao S, Manoharan M, Srivastava V. Dual-targeting by CRISPR/Cas9 leads to efficient point mutagenesis but only rare targeted deletions in the rice genome. 3 Biotech 2019; 9:158. [PMID: 30944805 DOI: 10.1007/s13205-019-1690-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 03/20/2019] [Indexed: 11/05/2022] Open
Abstract
The present study investigated the efficiency of CRISPR/Cas9 in creating genomic deletions as the basis of its application in removing selection marker genes or the intergenic regions. Three loci, representing a transgene and two rice genes, were targeted at two sites each, in separate experiments, and the deletion of the defined fragments was investigated by PCR and sequencing. Genomic deletions were found at a low rate among the transformed callus lines that could be isolated, cultured, and regenerated into plants harboring the deletion. However, randomly regenerated plants showed mixed genomic effects, and generally did not harbor heritable genomic deletions. To determine whether point mutations occurred at each targeted site, a total of 114 plants consisting of primary transgenic lines and their progeny were analyzed. Ninety-three plants showed targeting, 60 of which were targeted at both sites. The presence of point mutations at both sites was correlated with the guide RNA efficiency. In summary, genomic deletions through dual-targeting by the paired-guide RNAs were generally observed in callus, while de novo point mutations at one or both sites occurred at high rates in transgenic plants and their progeny, generating a variety of insertion–deletions or single-nucleotide variations. In this study, point mutations were exceedingly favored over genomic deletions; therefore, for the recovery of plant lines harboring targeted deletions, identifying early transformed clones harboring the deletions, and isolating them for plant regeneration is recommended.
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Uruburu M, Mastrangelo E, Bolognesi M, Ferrara S, Bertoni G, Milani M. Structural and functional characterization of TgpA, a critical protein for the viability of Pseudomonas aeruginosa. J Struct Biol 2019; 205:18-25. [PMID: 30599211 DOI: 10.1016/j.jsb.2018.12.004] [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] [Received: 08/29/2018] [Revised: 12/06/2018] [Accepted: 12/07/2018] [Indexed: 11/29/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen associated with severe diseases, such as cystic fibrosis. During an extensive search for novel essential genes, we identified tgpA (locus PA2873) in P. aeruginosa PAO1, as a gene playing a critical role in bacterial viability. TgpA, the translated protein, is an internal membrane protein with a periplasmic soluble domain, predicted to be endowed with a transglutaminase-like fold, hosting the Cys404, His448, and Asp464 triad. We report here that Cys404 mutation hampers the essential role of TgpA in granting P. aeruginosa viability. Moreover, we present the crystal structure of the TgpA periplasmic domain at 1.6 Å resolution as a first step towards structure-activity analysis of a new potential target for the discovery of antibacterial compounds.
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Affiliation(s)
- Mónica Uruburu
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133 Milano, Italy
| | - Eloise Mastrangelo
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133 Milano, Italy; CNR-IBF, Istituto di Biofisica, Via Celoria 26, I-20133 Milano, Italy
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133 Milano, Italy; Centro di Ricerca Pediatrica R.E. Invernizzi, Università di Milano, Via Celoria 26, I-20133 Milano, Italy
| | - Silvia Ferrara
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133 Milano, Italy
| | - Giovanni Bertoni
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133 Milano, Italy.
| | - Mario Milani
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133 Milano, Italy; CNR-IBF, Istituto di Biofisica, Via Celoria 26, I-20133 Milano, Italy.
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Oza G, Krishnajyothi K, Merupo VI, Bracamontes KAC, Olmos PC, Garrido E, Velumani S, Sridharan M, Sharma A, Arriaga LG, Ramirez JT. Gold-Iron oxide yolk-shell nanoparticles (YSNPs) as magnetic probe for fluorescence-based detection of 3 base mismatch DNA. Colloids Surf B Biointerfaces 2019; 176:431-438. [PMID: 30665097 DOI: 10.1016/j.colsurfb.2019.01.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/04/2019] [Accepted: 01/05/2019] [Indexed: 01/26/2023]
Abstract
Seed-mediated Gold-Iron oxide yolk-shell nanoparticles (YSNPs) were synthesized and functionalized with cy5 attached- thiolated single strand DNA probe for the detection of mutated DNA. The optimum concentration of thiolated DNA determined from a bathochromic shift of surface plasmon resonance (SPR) peak, was 0.177μM. The effect of pH (2-10), temperature (4, 37, 60 and 100 °C), and ionic strengths (1 M to 4 M) on the stability of ssDNA probe tethered YSNPs, studied with the assistance of flocculation parameter. The detection of mutation in DNA was possible using such ssDNA probe functionalized and stabilized nanoparticles. The hybridization of the oligonucleotide probe with the complementary, non-complementary and mutated DNA strands are determined via their respective intensities of the fluorescence of cy5, an efficient fluorescent marker. The intensities help in the comprehension of the specificity of the system. The report predicts controlled efficiency of hybridization with the aid of Hamaker constant, which is determined as 1.15 × 10-20 J for DNA functionalized YSNPs. The minimum concentration of target DNA detected using this methodology was 1.2 × 10-11 mol/L.
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Affiliation(s)
- Goldie Oza
- Centro de Investigación y Desarrollo Tecnológico en Electroquímica (CIDETEQ), Parque Tecnológico Querétaro s/n, Sanfandila, Pedro Escobedo, C.P. 76703, Querétaro, Qro, Mexico.
| | - Kaligotla Krishnajyothi
- Centre for Nanotechnology and Advanced Biomaterials, SASTRA Deemed to be University, Thanjavur, India
| | - Victor Ishrayelu Merupo
- Institut catholique d'arts et métiers-Nantes, 35 Avenue du Champ de Manœuvre, 44470, Carquefou, France
| | - Karen A Chavez Bracamontes
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio González No. 500, Fracc. San Pablo, Queretaro CP 76130, Mexico
| | - Pedro Chavez Olmos
- Department of Genetics and Molecular Biology, CINVESTAV-IPN, Avenida IPN 6508, San Pedro Zacatenco, Mexico
| | - Efrain Garrido
- Department of Genetics and Molecular Biology, CINVESTAV-IPN, Avenida IPN 6508, San Pedro Zacatenco, Mexico
| | - S Velumani
- Program on Nanoscience and Nanotechnology, Department of Electrical Engineering (SEES), CINVESTAV-IPN, Avenida IPN 6508, San Pedro Zacatenco, Mexico
| | - M Sridharan
- Centre for Nanotechnology and Advanced Biomaterials, SASTRA Deemed to be University, Thanjavur, India
| | - Ashutosh Sharma
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio González No. 500, Fracc. San Pablo, Queretaro CP 76130, Mexico
| | - L G Arriaga
- Centro de Investigación y Desarrollo Tecnológico en Electroquímica (CIDETEQ), Parque Tecnológico Querétaro s/n, Sanfandila, Pedro Escobedo, C.P. 76703, Querétaro, Qro, Mexico
| | - Jose Tapia Ramirez
- Department of Genetics and Molecular Biology, CINVESTAV-IPN, Avenida IPN 6508, San Pedro Zacatenco, Mexico.
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Queralt-Martín M, Bergdoll L, Jacobs D, Bezrukov SM, Abramson J, Rostovtseva TK. Assessing the role of residue E73 and lipid headgroup charge in VDAC1 voltage gating. Biochim Biophys Acta Bioenerg 2019; 1860:22-29. [PMID: 30412693 PMCID: PMC8283775 DOI: 10.1016/j.bbabio.2018.11.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/05/2018] [Accepted: 11/04/2018] [Indexed: 12/25/2022]
Abstract
The voltage-dependent anion channel (VDAC) is the most abundant protein of the mitochondrial outer membrane (MOM) where it regulates transport of ions and metabolites in and out of the organelle. VDAC function is extensively studied in a lipid bilayer system that allows conductance monitoring of reconstituted channels under applied voltage. The process of switching from a high-conductance state, open to metabolites, to a variety of low-conducting states, which excludes metabolite transport, is termed voltage gating and the mechanism remains poorly understood. Recent studies have implicated the involvement of the membrane-solvated residue E73 in the gating process through β-barrel destabilization. However, there has been no direct experimental evidence of E73 involvement in VDAC1 voltage gating. Here, using electrophysiology measurements, we exclude the involvement of E73 in murine VDAC1 (mVDAC1) voltage gating process. With an established protocol of assessing voltage gating of VDACs reconstituted into planar lipid membranes, we definitively show that mVDAC1 gating properties do not change when E73 is replaced by either a glutamine or an alanine. We further demonstrate that cholesterol has no effect on mVDAC1 gating characteristics, though it was shown that E73 is coordinating residue in the cholesterol binding site. In contrast, we found a pronounced gating effect based on the charge of the phospholipid headgroup, where the positive charge stimulates and negative charge suppresses gating. These findings call for critical evaluation of the existing models of VDAC gating and contribute to our understanding of VDAC's role in control of MOM permeability and regulation of mitochondrial respiration and metabolism.
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Affiliation(s)
- María Queralt-Martín
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Lucie Bergdoll
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
| | - Daniel Jacobs
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sergey M. Bezrukov
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeff Abramson
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
| | - Tatiana K. Rostovtseva
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA,To whom correspondence should be addressed: Tatiana K. Rostovtseva, Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bldg. 9, Room 1E-106, Bethesda, MD 20892-0924. Phone: (301) 402-4702, ; Jeff Abramson, Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095. Phone: (310) 825-3913,
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Abstract
The zebrafish is an increasingly popular model organism for human genetic disease research. CRISPR/Cas9-based approaches are currently used for multiple gene-editing purposes in zebrafish, but few studies have developed reliable ways to introduce precise mutations. Point mutation knock-in using CRISPR/Cas9 and single-stranded oligodeoxynucleotides (ssODNs) is currently the most promising technology for this purpose. Despite some progress in applying this technique to zebrafish, there is still a great need for improvements in terms of its efficiency, optimal design of sgRNA and ssODNs and broader applicability. The papers discussed in this Editorial provide excellent case studies on identifying problems inherent in the mutation knock-in technique, quantifying these issues and proposing strategies to overcome them. These reports also illustrate how the procedures for introducing specific mutations can be straightforward, such that ssODNs with only the target mutation are sufficient for generating the intended knock-in animals. Two of the studies also develop interesting point mutant knock-in models for cardiac diseases, validating the translational relevance of generating knock-in mutations and opening the door to many possibilities for their further study.
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Affiliation(s)
- Sergey V Prykhozhij
- Department of Pediatrics, Dalhousie University, IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Jason N Berman
- Department of Pediatrics, Dalhousie University, IWK Health Centre, Halifax, NS B3K 6R8, Canada .,Department of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada.,Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
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Mira F, Dowgier G, Purpari G, Vicari D, Di Bella S, Macaluso G, Gucciardi F, Randazzo V, Decaro N, Guercio A. Molecular typing of a novel canine parvovirus type 2a mutant circulating in Italy. Infect Genet Evol 2018; 61:67-73. [PMID: 29548803 PMCID: PMC7185394 DOI: 10.1016/j.meegid.2018.03.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 03/08/2018] [Accepted: 03/11/2018] [Indexed: 01/20/2023]
Abstract
Canine parvovirus (CPV) is the etiological agent of a severe viral disease of dogs. After its emergence in late 1970s, the CPV original type (CPV-2) was rapidly and totally replaced by three antigenic variants named CPV-2a, CPV-2b and CPV-2c. CPV has an evolutionary rate nearest to those of RNA viruses, with consequences on disease diagnosis and epidemiology. This paper reports the molecular characterization of eight CPV-2a strains collected from dogs in Italy in 2016–2017. Genetic analysis was conducted on a CPV genomic region encompassing both open reading frames (ORFs) encoding for nonstructural (NS1-NS2) and structural proteins (VP1-VP2). Sequence analysis indicates new and unreported sequence changes, mainly affecting the VP2 gene, which included the mutation Tyr324Leu. This study represents the first evidence of a new CPV-2a mutant (VP2 324Leu) and illustrates the importance of a continuous molecular survey in order to obtain more information on effective spread of new CPV mutants. Canine parvovirus strains collected from dogs in southern Italy were analyzed. Nearly complete genome sequences of the CPV strains were obtained and comparatively analyzed. A novel CPV-2a mutant with unreported sequence changes has been characterized. This study reports a novel CPV-2a mutant in genus Protoparvovirus. Our data confirmed the importance of the continuous epidemiological survey.
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Affiliation(s)
- Francesco Mira
- Istituto Zooprofilattico Sperimentale della Sicilia, Via Gino Marinuzzi 3, 90129 Palermo, Italy.
| | - Giulia Dowgier
- Department of Veterinary Medicine, University of Bari, Strada provinciale per Casamassima Km 3, 70010 Valenzano, Bari, Italy
| | - Giuseppa Purpari
- Istituto Zooprofilattico Sperimentale della Sicilia, Via Gino Marinuzzi 3, 90129 Palermo, Italy
| | - Domenico Vicari
- Istituto Zooprofilattico Sperimentale della Sicilia, Via Gino Marinuzzi 3, 90129 Palermo, Italy
| | - Santina Di Bella
- Istituto Zooprofilattico Sperimentale della Sicilia, Via Gino Marinuzzi 3, 90129 Palermo, Italy
| | - Giusi Macaluso
- Istituto Zooprofilattico Sperimentale della Sicilia, Via Gino Marinuzzi 3, 90129 Palermo, Italy
| | - Francesca Gucciardi
- Istituto Zooprofilattico Sperimentale della Sicilia, Via Gino Marinuzzi 3, 90129 Palermo, Italy
| | - Vincenzo Randazzo
- Istituto Zooprofilattico Sperimentale della Sicilia, Via Gino Marinuzzi 3, 90129 Palermo, Italy
| | - Nicola Decaro
- Department of Veterinary Medicine, University of Bari, Strada provinciale per Casamassima Km 3, 70010 Valenzano, Bari, Italy
| | - Annalisa Guercio
- Istituto Zooprofilattico Sperimentale della Sicilia, Via Gino Marinuzzi 3, 90129 Palermo, Italy
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Śliwinska M, Robaszkiewicz K, Czajkowska M, Zheng W, Moraczewska J. Functional effects of substitutions I92T and V95A in actin-binding period 3 of tropomyosin. Biochim Biophys Acta Proteins Proteom 2018; 1866:558-568. [PMID: 29496559 DOI: 10.1016/j.bbapap.2018.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 02/12/2018] [Accepted: 02/23/2018] [Indexed: 01/10/2023]
Affiliation(s)
- Małgorzata Śliwinska
- Department of Biochemistry and Cell Biology, Faculty of Natural Sciences, Kazimierz Wielki University in Bydgoszcz, Ks. J. Poniatowskiego 12 Str., 85-671 Bydgoszcz, Poland
| | - Katarzyna Robaszkiewicz
- Department of Biochemistry and Cell Biology, Faculty of Natural Sciences, Kazimierz Wielki University in Bydgoszcz, Ks. J. Poniatowskiego 12 Str., 85-671 Bydgoszcz, Poland
| | - Marta Czajkowska
- Department of Biochemistry and Cell Biology, Faculty of Natural Sciences, Kazimierz Wielki University in Bydgoszcz, Ks. J. Poniatowskiego 12 Str., 85-671 Bydgoszcz, Poland
| | - Wenjun Zheng
- Department of Physics, University at Buffalo, SUNY, Buffalo, NY 14260, United States
| | - Joanna Moraczewska
- Department of Biochemistry and Cell Biology, Faculty of Natural Sciences, Kazimierz Wielki University in Bydgoszcz, Ks. J. Poniatowskiego 12 Str., 85-671 Bydgoszcz, Poland.
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Di Sotto A, Di Giacomo S, Abete L, Božović M, Parisi OA, Barile F, Vitalone A, Izzo AA, Ragno R, Mazzanti G. Genotoxicity assessment of piperitenone oxide: An in vitro and in silico evaluation. Food Chem Toxicol 2017; 106:506-13. [PMID: 28606765 DOI: 10.1016/j.fct.2017.06.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/20/2017] [Accepted: 06/09/2017] [Indexed: 01/24/2023]
Abstract
Piperitenone oxide, a natural flavouring agent also known as rotundifolone, has been studied for the genotoxicity assessment by an integrated in vitro and in silico experimental approach, including the bacterial reverse mutation assay, the micronucleus test, the comet assay and the computational prediction by Toxtree and VEGA tools. Under our experimental conditions, the monoterpene showed to induce both point mutations (i.e. frameshift, base-substitution and/or oxidative damage) and DNA damage (i.e. clastogenic or aneuploidic damage, or single-strand breaks). Computational prediction for piperitenone oxide agreed with the toxicological data, and highlighted the presence of the epoxide function and the α,β-unsaturated carbonyl as possible structural alerts for DNA damage. However, improving the toxicological libraries for natural occurring compounds is required in order to favour the applicability of in silico models to the toxicological predictions. Further in vivo evaluations are strictly needed in order to evaluate the role of the bioavailability of the substance and the metabolic fate on its genotoxicity profile. To the best of our knowledge, these data represent the first evaluation of the genotoxicity for this flavour compound and suggest the need of further studies to assess the safety of piperitenone oxide as a flavouring agent.
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Pan CY, Xu N, He BL, Cao R, Liao LB, Yin CX, Lan YQ, Lu ZY, Huang JX, Sun J, Feng R, Liu QF, Liu XL. [Clinical significance of cytogenetic monitoring in chronic myeloid leukemia]. Zhonghua Xue Ye Xue Za Zhi 2017; 38:112-117. [PMID: 28279034 PMCID: PMC7354167 DOI: 10.3760/cma.j.issn.0253-2727.2017.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Objective: To analyze the association of cytogenetic abnormalities with the prognosis of chronic myeloid leukemia (CML) patients in tyrosine kinase inhibitors (TKI) era. Methods: Karyotype analysis of chromosome G-banding was carried out in 387 newly diagnosed CML patients by short-term culture of bone marrow cells. The correlation of cytogenetic abnormalities and CML progression was explored in combination with ABL tyrosine point mutations. Result: Of 387 patients with positive BCR-ABL fusion gene assayed by fluorescence in situ hybridization (FISH) technique, 94.1% (364/387) patients were Ph positive and 5.9% (23/387) Ph negative; 320 patients (87.9%) had a translocation t (9;22) (q34;q11) and 5 (1.4%) a variant translocation t (v;22) . Additional cytogenetic aberrations (ACA) at diagnosis were found in 10.7% (39/387) Ph(+) patients, major route ACA in 22 (56.4%) cases and minor route ACA in 15 (38.5%) cases and 2 patients (5.1%) lacked the Y chromosome (-Y) ; 23.4% (71/303) patients occurred ACA during TKI treatment and the most frequent abnormalities were abnormal chromosome numbersd, which were likely associated with high proportion of disease progression (χ(2)=168.21, P<0.001) and ABL tyrosine point mutations (χ(2)=29.04, P<0.001) . Newly diagnosed CML-CP patients with t (9;22) (q34;q11) had a longer event-free survival (EFS) and disease-free survival (DFS) rates than that of patients with ACA (P=0.037; P=0.003) , while the overall survival (OS) had no significant differences (P=0.209) . As for CML-CP patients that occurred ACA during TKI therapy would have a marked low OS, EFS and DFS (all P<0.001) compared with no ACA occurred patients. Survival of advanced patients that occurred ACA were dramatically reduced. Conclusion: ACA often emerged during the disease progress in CML patients, regular and timely detection of chromosomes karyotype and ABL tyrosine point mutations during TKI treatment was important for therapeutic evaluation, progress and prognosis of CML.
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Affiliation(s)
- C Y Pan
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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Metzeler KH, Bloomfield CD. Clinical Relevance of RUNX1 and CBFB Alterations in Acute Myeloid Leukemia and Other Hematological Disorders. Adv Exp Med Biol 2017; 962:175-99. [PMID: 28299658 DOI: 10.1007/978-981-10-3233-2_12] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The translocation t(8;21), leading to a fusion between the RUNX1 gene and the RUNX1T1 locus, was the first chromosomal translocation identified in cancer. Since the first description of this balanced rearrangement in a patient with acute myeloid leukemia (AML) in 1973, RUNX1 translocations and point mutations have been found in various myeloid and lymphoid neoplasms. In this chapter, we summarize the currently available data on the clinical relevance of core binding factor gene alterations in hematological disorders. In the first section, we discuss the prognostic implications of the core binding factor translocations RUNX1-RUNX1T1 and CBFB-MYH11 in AML patients. We provide an overview of the cooperating genetic events in patients with CBF-rearranged AML and their clinical implications, and review current treatment approaches for CBF AML and the utility of minimal residual disease monitoring. In the next sections, we summarize the available data on rare RUNX1 rearrangements in various hematologic neoplasms and the role of RUNX1 translocations in therapy-related myeloid neoplasia. The final three sections of the chapter cover the spectrum and clinical significance of RUNX1 point mutations in AML and myelodysplastic syndromes, in familial platelet disorder with associated myeloid malignancy, and in acute lymphoblastic leukemia.
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Hao D, Yang S, Huang Y, Su Y. Identification of structural elements involved in fine-tuning of the transport activity of the rice ammonium transporter OsAMT1;3. Plant Physiol Biochem 2016; 108:99-108. [PMID: 27423220 DOI: 10.1016/j.plaphy.2016.07.003] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/01/2016] [Accepted: 07/03/2016] [Indexed: 05/13/2023]
Abstract
Ammonium transporters (AMTs) are major routes for plant uptake of the NH4+-form nitrogen. Plant AMTs mediate predominantly the uptake of NH4+ and to a lesser extent, its organic analog methylammonium (MeA+). Mutagenesis studies on potential phosphorylation residues have achieved solid recognition that alteration of the phosphorylation status can result in allosteric regulation and impair the functionality of plant AMTs. However, molecular insights to the fine-tuning of a functional ammonium transporter remain less clear. In this report, we demonstrate that the rice root expressed OsAMT1;3 (Oryza sativa ammonium transporter 1;3) functions as a typical high-affinity NH4+ transporter and is weakly permeable to MeA+ using growth assays in NH4+ uptake defective yeast cells and electrophysiological measurements in Xenopus oocytes. Upon screening of six point mutations generated with the transporter, we identified two amino acid residues involved in the functional modulation of OsAMT1;3. The H199E mutation caused loss of transport activity whereas other five mutations retained the functionality of OsAMT1;3. Furthermore, the L56F mutation enabled respectively 5- and 3.5 -fold increased capability for NH4+ and MeA+ uptake with several-fold decreased affinity (Km) and accelerated Vmax values. Surprisingly, yeast cells expressing the L56F mutation shown increased Na+ toxicity leading to a speculation that enhanced Na+ permeation occurred with this mutation. The phenomenon was further supported by the observation of significant Na+ uptake current in oocytes. Our results seemingly support a speculation that the L56F mutation of OsAMT1;3 widens the substrate passage tunnel and allows enhanced permeability to NH4+ and larger ions MeA+ and Na+.
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Affiliation(s)
- Dongli Hao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shunying Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yanan Huang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanhua Su
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
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Yörüker EE, Holdenrieder S, Gezer U. Blood-based biomarkers for diagnosis, prognosis and treatment of colorectal cancer. Clin Chim Acta 2016; 455:26-32. [PMID: 26797671 DOI: 10.1016/j.cca.2016.01.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [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: 10/28/2015] [Revised: 01/15/2016] [Accepted: 01/16/2016] [Indexed: 02/07/2023]
Abstract
The global burden of colorectal cancer (CRC)-associated morbidity and mortality is increasing, in part due to a lack of early detection. Direct structural examination techniques, such as colonoscopy, are invasive and can therefore affect the willingness of patients to participate in screening. Recently, the use of "liquid biopsy" has gained considerable attention as a novel source of biomarkers. Blood-based biomarkers could prove to be practical tools for CRC detection, as the monitoring of biomarkers in biological fluids offers many advantages, including minimal invasiveness and easy accessibility. Biomarkers with high specificity and sensitivity can enable the detection of CRC at an early stage, thereby improving prognosis, prediction of treatment response, and recurrence risk. In this review, we summarize that the biomarkers currently thought to have potential for the early detection and monitoring of CRC, including circulating tumor cells, DNA, RNA and proteins.
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Affiliation(s)
- Ebru E Yörüker
- Department of Basic Oncology, Oncology Institute, Istanbul University, Istanbul, Turkey
| | - Stefan Holdenrieder
- Institute of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Ugur Gezer
- Department of Basic Oncology, Oncology Institute, Istanbul University, Istanbul, Turkey.
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37
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Vecoli C, Pulignani S, Foffa I, Andreassi MG. Congenital heart disease: the crossroads of genetics, epigenetics and environment. Curr Genomics 2014; 15:390-9. [PMID: 25435801 PMCID: PMC4245698 DOI: 10.2174/1389202915666140716175634] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [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: 03/20/2014] [Revised: 06/24/2014] [Accepted: 07/07/2014] [Indexed: 02/07/2023] Open
Abstract
Congenital heart diseases (CHDs) are recognized as the most common type of birth malformations. Although recent advances in pre- and neonatal diagnosis as well as in surgical procedures have reduced the morbidity and mortality for many CHD, the etiology for CHD remains undefined. In non-syndromic and isolated (without a familial history or a Mendelian inheritance) forms of CHDs, a multifactorial pathogenesis with interplay between inherited and non-inherited causes is recognized. In this paper, we discuss the current knowledge of the potential molecular mechanisms, mediating abnormal cardiac development in non-syndromic and isolated CHD, including mutations in cardiac transcription factors, the role of somatic mutations and epigenetic alterations as well as the influence of gene-environment interactions. In the near future, the advent of high-throughput genomic technologies with the integration of system biology will expand our understanding of isolated, non-syndromic CHDs for their prevention, early diagnosis and therapy.
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Affiliation(s)
| | | | - Ilenia Foffa
- CNR, Institute of Clinical Physiology, Massa, Italy
| | - Maria Grazia Andreassi
- CNR, Institute of Clinical Physiology, Pisa, Italy ; Fondazione Toscana G.Monasterio, Massa, Italy
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38
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Parker JE, Warrilow AGS, Price CL, Mullins JGL, Kelly DE, Kelly SL. Resistance to antifungals that target CYP51. J Chem Biol 2014; 7:143-61. [PMID: 25320648 DOI: 10.1007/s12154-014-0121-1] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [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: 05/14/2014] [Accepted: 08/06/2014] [Indexed: 12/23/2022] Open
Abstract
Fungal diseases are an increasing global burden. Fungi are now recognised to kill more people annually than malaria, whilst in agriculture, fungi threaten crop yields and food security. Azole resistance, mediated by several mechanisms including point mutations in the target enzyme (CYP51), is increasing through selection pressure as a result of widespread use of triazole fungicides in agriculture and triazole antifungal drugs in the clinic. Mutations similar to those seen in clinical isolates as long ago as the 1990s in Candida albicans and later in Aspergillus fumigatus have been identified in agriculturally important fungal species and also wider combinations of point mutations. Recently, evidence that mutations originate in the field and now appear in clinical infections has been suggested. This situation is likely to increase in prevalence as triazole fungicide use continues to rise. Here, we review the progress made in understanding azole resistance found amongst clinically and agriculturally important fungal species focussing on resistance mechanisms associated with CYP51. Biochemical characterisation of wild-type and mutant CYP51 enzymes through ligand binding studies and azole IC50 determinations is an important tool for understanding azole susceptibility and can be used in conjunction with microbiological methods (MIC50 values), molecular biological studies (site-directed mutagenesis) and protein modelling studies to inform future antifungal development with increased specificity for the target enzyme over the host homologue.
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Affiliation(s)
- Josie E Parker
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, College of Medicine, Swansea University, Swansea, Wales SA2 8PP UK
| | - Andrew G S Warrilow
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, College of Medicine, Swansea University, Swansea, Wales SA2 8PP UK
| | - Claire L Price
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, College of Medicine, Swansea University, Swansea, Wales SA2 8PP UK
| | - Jonathan G L Mullins
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, College of Medicine, Swansea University, Swansea, Wales SA2 8PP UK
| | - Diane E Kelly
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, College of Medicine, Swansea University, Swansea, Wales SA2 8PP UK
| | - Steven L Kelly
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, College of Medicine, Swansea University, Swansea, Wales SA2 8PP UK
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39
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Stephan BI, Lozano ME, Goñi SE. Watching every step of the way: junín virus attenuation markers in the vaccine lineage. Curr Genomics 2014; 14:415-24. [PMID: 24396274 PMCID: PMC3867718 DOI: 10.2174/138920291407131220153526] [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: 07/08/2013] [Revised: 08/26/2013] [Accepted: 08/26/2013] [Indexed: 01/19/2023] Open
Abstract
The Arenaviridae family includes several hemorrhagic fever viruses which are important emerging pathogens. Junín virus, a member of this family, is the etiological agent of Argentine Hemorrhagic Fever (AHF). A collaboration between the Governments of Argentina and the USA rendered the attenuated Junín virus vaccine strain Candid#1. Arenaviruses are enveloped viruses with genomes consisting of two single-stranded RNA species (L and S), each carrying two coding regions separated by a stably structured, non-coding intergenic region. Molecular characterization of the vaccine strain and of its more virulent ancestors, XJ13 (prototype) and XJ#44, allows a systematic approach for the discovery of key elements in virulence attenuation. We show comparisons of sequence information for the S RNA of the strains XJ13, XJ#44 and Candid#1 of Junín virus, along with other strains from the vaccine lineage and a set of Junín virus field strains collected at the AHF endemic area. Comparisons of nucleotide and amino acid sequences revealed different point mutations which might be linked to the attenuated phenotype. The majority of changes are consistent with a progressive attenuation of virulence between XJ13, XJ#44 and Candid#1. We propose that changes found in genomic regions with low natural variation frequencies are more likely to be associated with the virulence attenuation process. We partially sequenced field strains to analyze the genomic variability naturally occurring for Junín virus. This information, together with the sequence analysis of strains with intermediate virulence, will serve as a starting point to study the molecular bases for viral attenuation.
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Affiliation(s)
- Betina Inés Stephan
- Área de Virosis Emergentes y Zoonóticas, Laboratorio de Biología Celular y Molecular, Universidad Nacional de Quilmes, Argentina
| | - Mario Enrique Lozano
- Área de Virosis Emergentes y Zoonóticas, Laboratorio de Biología Celular y Molecular, Universidad Nacional de Quilmes, Argentina
| | - Sandra Elizabeth Goñi
- Área de Virosis Emergentes y Zoonóticas, Laboratorio de Biología Celular y Molecular, Universidad Nacional de Quilmes, Argentina
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