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Maciag T, Kozieł E, Otulak-Kozieł K, Jafra S, Czajkowski R. Looking for Resistance to Soft Rot Disease of Potatoes Facing Environmental Hypoxia. Int J Mol Sci 2024; 25:3757. [PMID: 38612570 PMCID: PMC11011919 DOI: 10.3390/ijms25073757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Plants are exposed to various stressors, including pathogens, requiring specific environmental conditions to provoke/induce plant disease. This phenomenon is called the "disease triangle" and is directly connected with a particular plant-pathogen interaction. Only a virulent pathogen interacting with a susceptible plant cultivar will lead to disease under specific environmental conditions. This may seem difficult to accomplish, but soft rot Pectobacteriaceae (SRPs) is a group virulent of pathogenic bacteria with a broad host range. Additionally, waterlogging (and, resulting from it, hypoxia), which is becoming a frequent problem in farming, is a favoring condition for this group of pathogens. Waterlogging by itself is an important source of abiotic stress for plants due to lowered gas exchange. Therefore, plants have evolved an ethylene-based system for hypoxia sensing. Plant response is coordinated by hormonal changes which induce metabolic and physiological adjustment to the environmental conditions. Wetland species such as rice (Oryza sativa L.), and bittersweet nightshade (Solanum dulcamara L.) have developed adaptations enabling them to withstand prolonged periods of decreased oxygen availability. On the other hand, potato (Solanum tuberosum L.), although able to sense and response to hypoxia, is sensitive to this environmental stress. This situation is exploited by SRPs which in response to hypoxia induce the production of virulence factors with the use of cyclic diguanylate (c-di-GMP). Potato tubers in turn reduce their defenses to preserve energy to prevent the negative effects of reactive oxygen species and acidification, making them prone to soft rot disease. To reduce the losses caused by the soft rot disease we need sensitive and reliable methods for the detection of the pathogens, to isolate infected plant material. However, due to the high prevalence of SRPs in the environment, we also need to create new potato varieties more resistant to the disease. To reach that goal, we can look to wild potatoes and other Solanum species for mechanisms of resistance to waterlogging. Potato resistance can also be aided by beneficial microorganisms which can induce the plant's natural defenses to bacterial infections but also waterlogging. However, most of the known plant-beneficial microorganisms suffer from hypoxia and can be outcompeted by plant pathogens. Therefore, it is important to look for microorganisms that can withstand hypoxia or alleviate its effects on the plant, e.g., by improving soil structure. Therefore, this review aims to present crucial elements of potato response to hypoxia and SRP infection and future outlooks for the prevention of soft rot disease considering the influence of environmental conditions.
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Affiliation(s)
- Tomasz Maciag
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland;
| | - Edmund Kozieł
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland;
| | - Katarzyna Otulak-Kozieł
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland;
| | - Sylwia Jafra
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama Street 58, 80-307 Gdansk, Poland;
| | - Robert Czajkowski
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama Street 58, 80-307 Gdansk, Poland;
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Moon YJ, Lee SY, Kim U, Oh SW. Naked-eye detection with loop-mediated isothermal amplification for P. carotovorum subsp. carotovorum in agricultural products. Food Sci Biotechnol 2024; 33:203-209. [PMID: 38186613 PMCID: PMC10766909 DOI: 10.1007/s10068-023-01315-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/04/2023] [Accepted: 04/17/2023] [Indexed: 01/09/2024] Open
Abstract
Pectobacterium carotovorum causing soft-rot disease requires on-site detection before the distribution of agricultural products. Loop-mediated isothermal amplification (LAMP), which is resistant to food inhibitors, is known for its high detection sensitivity for pathogens and when coupled with lateral flow immunoassay (LFA) enables visualizations. For detection of soft-rot disease, we developed a LAMP-LFA system targeting 16S ribosomal RNA, a partial sequence gene of P. carotovorum subsp. carotovorum. The LAMP-LFA was performed at 60 °C for 50 min followed by hybridization of digoxygenin-labeled LAMP amplicon and biotinylated probe. Detection sensitivity was 3.22 × 101 CFU/mL in pure culture, which specifically detected the target. In Chinese cabbage and potato, the target was detected up to low levels of 1.57 × 102 CFU/g and 1.29 × 102 CFU/g, respectively. This study showed potential applicability as a sensitive point-of-care system for soft-rot disease bacteria detection in agricultural products. Supplementary Information The online version contains supplementary material available at 10.1007/s10068-023-01315-z.
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Affiliation(s)
- Ye-Ji Moon
- Department of Food and Nutrition, Kookmin University, Seoul, 02727 Republic of Korea
| | - So-Young Lee
- Department of Food and Nutrition, Kookmin University, Seoul, 02727 Republic of Korea
| | - Unji Kim
- Department of Food and Nutrition, Kookmin University, Seoul, 02727 Republic of Korea
| | - Se-Wook Oh
- Department of Food and Nutrition, Kookmin University, Seoul, 02727 Republic of Korea
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3
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Díaz D, Zamorano A, García H, Ramos C, Cui W, Carreras C, Beltrán MF, Sagredo B, Pinto M, Fiore N. Development of a Genome-Informed Protocol for Detection of Pseudomonas amygdali pv. morsprunorum Using LAMP and PCR. PLANTS (BASEL, SWITZERLAND) 2023; 12:4119. [PMID: 38140446 PMCID: PMC10747947 DOI: 10.3390/plants12244119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 12/24/2023]
Abstract
One of the causal agents of bacterial canker is Pseudomonas amygdali pv. morsprunorum-Pam (formerly Pseudomonas syringae pv. morsprunorum). Recently detected in Chile, Pam is known to cause lesions in the aerial parts of the plant, followed by more severe symptoms such as cankers and gummosis in the later stages of the disease. This study presents the design of PCR and LAMP detection methods for the specific and sensitive identification of Pseudomonas amygdali pv. morsprunorum (Pam) from cherry trees. Twelve Pseudomonas isolates were collected, sequenced, and later characterized by Multi-locus Sequence Analysis (MLSA) and Average Nucleotide Identity by blast (ANIb). Three of them (11116B2, S1 Pam, and S2 Pam) were identified as Pseudomonas amygdali pv. morsprunorum and were used to find specific genes through RAST server, by comparing their genome with that of other Pseudomonas, including isolates from other Pam strains. The effector gene HopAU1 was selected for the design of primers to be used for both techniques, evaluating sensitivity and specificity, and the ability to detect Pam directly from plant tissues. While the PCR detection limit was 100 pg of purified bacterial DNA per reaction, the LAMP assays were able to detect up to 1 fg of purified DNA per reaction. Similar results were observed using plant tissues, LAMP being more sensitive than PCR, including when using DNA extracted from infected plant tissues. Both detection methods were tested in the presence of 30 other bacterial genera, with LAMP being more sensitive than PCR.
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Affiliation(s)
- Daniela Díaz
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agropecuarias, Universidad de Chile, Avenida Santa Rosa 11315, Santiago 8820808, Chile; (D.D.); (A.Z.); (W.C.); (C.C.)
| | - Alan Zamorano
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agropecuarias, Universidad de Chile, Avenida Santa Rosa 11315, Santiago 8820808, Chile; (D.D.); (A.Z.); (W.C.); (C.C.)
| | - Héctor García
- Laboratorio Diagnofruit, Avenida Sucre 1521, Santiago 7770273, Chile; (H.G.); (C.R.)
| | - Cecilia Ramos
- Laboratorio Diagnofruit, Avenida Sucre 1521, Santiago 7770273, Chile; (H.G.); (C.R.)
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de las Américas, Campus Providencia, Manuel Montt 948, Santiago 7500975, Chile
| | - Weier Cui
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agropecuarias, Universidad de Chile, Avenida Santa Rosa 11315, Santiago 8820808, Chile; (D.D.); (A.Z.); (W.C.); (C.C.)
| | - Claudia Carreras
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agropecuarias, Universidad de Chile, Avenida Santa Rosa 11315, Santiago 8820808, Chile; (D.D.); (A.Z.); (W.C.); (C.C.)
| | - María Francisca Beltrán
- Instituto de Investigaciones Agropecuarias, INIA Rayentué, Avda. Salamanca s/n, Rengo 2940000, Chile; (M.F.B.); (B.S.)
| | - Boris Sagredo
- Instituto de Investigaciones Agropecuarias, INIA Rayentué, Avda. Salamanca s/n, Rengo 2940000, Chile; (M.F.B.); (B.S.)
| | - Manuel Pinto
- Instituto de Ciencias Agroalimentarias Animales y Ambientales (ICA3), Universidad de O’Higgins, Campus Colchagua, Ruta I-90 S/N, San Fernando 3072590, Chile;
| | - Nicola Fiore
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agropecuarias, Universidad de Chile, Avenida Santa Rosa 11315, Santiago 8820808, Chile; (D.D.); (A.Z.); (W.C.); (C.C.)
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Wang Y, Fu L, Tao D, Han X, Xu B, Deng M, Li S, Zhao C, Li X, Zhao S, Gong P, Yang Y, Khazalwa EM, Ma Y, Ruan J, Li C, Xie S. Development of a Naked Eye CRISPR-Cas12a and -Cas13a Multiplex Point-of-Care Detection of Genetically Modified Swine. ACS Synth Biol 2023; 12:2051-2060. [PMID: 37432138 DOI: 10.1021/acssynbio.3c00089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
The Rapid Visual CRISPR (RAVI-CRISPR) assay employs Cas12a and Cas13a enzymes for precise gene detection in a sample. However, RAVI-CRISPR is limited in single-tube multiplex detection applications due to the lack of specific single-strand (ss) DNA-fluorescently quenched (ssDNA-FQ) and RNA-fluorescently quenched (ssRNA-FQ) reporter cleavage mechanisms. We report the development of a sensitive and specific dual-gene Cas12a and Cas13a diagnostic system. To optimize the application for field testing, we designed a portable multiplex fluorescence imaging assay that could distinguish test results with the naked eye. Herein, dual gene amplified products from multiplex recombinase polymerase amplification (RPA) were simultaneously detected in a single tube using Cas12a and Cas13a enzymes. The resulting orthogonal DNA and RNA collateral cleavage specifically distinguishes individual and mixed ssDNA-FQ and ssRNA-FQ reporters using the green-red-yellow, fluorescent signal conversion reaction system, detectable with portable blue and ultraviolet (UV) light transilluminators. As a proof-of-concept, reliable multiplex RAVI-CRISPR detection of genome-edited pigs was demonstrated, exhibiting 100% sensitivity and specificity for the analysis of CD163 knockout, lactoferrin (LF) knock-in, and wild-type pig samples. This portable naked-eye multiplex RAVI-CRISPR detection platform can provide accurate point-of-care screening of genetically modified animals and infectious diseases in resource-limited settings.
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Affiliation(s)
- Yuan Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Lanting Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Dagang Tao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Xiaosong Han
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Bingrong Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Manfei Deng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Sheng Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Changzhi Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Ping Gong
- Institute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan 430208, P. R. China
| | - Yu Yang
- Institute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan 430208, P. R. China
| | | | - Yunlong Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Jinxue Ruan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Changchun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
- Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, P. R. China
- Key Laboratory of Prevention and Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Wuhan 430070, P. R. China
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5
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DeLude A, Wells R, Boomla S, Chuang SC, Urena F, Shipman A, Rubas N, Kuehu DL, Bickerton B, Peterson T, Dobhal S, Arizala D, Klair D, Ochoa-Corona F, Ali ME, Odani J, Bingham JP, Jenkins DM, Fletcher J, Stack JP, Alvarez AM, Arif M. Loop-mediated isothermal amplification (LAMP) assay for specific and rapid detection of Dickeya fangzhongdai targeting a unique genomic region. Sci Rep 2022; 12:19193. [PMID: 36357509 PMCID: PMC9649655 DOI: 10.1038/s41598-022-22023-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/07/2022] [Indexed: 11/11/2022] Open
Abstract
Dickeya fangzhongdai, a bacterial pathogen of taro (Colocasia esculenta), onion (Allium sp.), and several species in the orchid family (Orchidaceae) causes soft rot and bleeding canker diseases. No field-deployable diagnostic tool is available for specific detection of this pathogen in different plant tissues. Therefore, we developed a field-deployable loop-mediated isothermal amplification (LAMP) assay using a unique genomic region, present exclusively in D. fangzhongdai. Multiple genomes of D. fangzhongdai, and other species of Dickeya, Pectobacterium and unrelated genera were used for comparative genomic analyses to identify an exclusive and conserved target sequence from the major facilitator superfamily (MFS) transporter gene region. This gene region had broad detection capability for D. fangzhongdai and thus was used to design primers for endpoint PCR and LAMP assays. In-silico validation showed high specificity with D. fangzhongdai genome sequences available in the NCBI GenBank genome database as well as the in-house sequenced genome. The specificity of the LAMP assay was determined with 96 strains that included all Dickeya species and Pectobacterium species as well as other closely related genera and 5 hosts; no false positives or false negatives were detected. The detection limit of the assay was determined by performing four sensitivity assays with tenfold serially diluted purified genomic DNA of D. fangzhongdai with and without the presence of crude host extract (taro, orchid, and onion). The detection limit for all sensitivity assays was 100 fg (18-20 genome copies) with no negative interference by host crude extracts. The assays were performed by five independent operators (blind test) and on three instruments (Rotor-Gene, thermocycler and dry bath); the assay results were concordant. The assay consistently detected the target pathogen from artificially inoculated and naturally infected host samples. The developed assay is highly specific for D. fangzhongdai and has applications in routine diagnostics, phytosanitary and seed certification programs, and epidemiological studies.
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Affiliation(s)
- Anuhea DeLude
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Riley Wells
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Sherine Boomla
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Shu-Cheng Chuang
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Frank Urena
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA ,grid.410445.00000 0001 2188 0957Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, HI USA
| | - Aaron Shipman
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Noelle Rubas
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Donna Lee Kuehu
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA ,grid.410445.00000 0001 2188 0957Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, HI USA
| | - Buster Bickerton
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Taylor Peterson
- grid.410445.00000 0001 2188 0957Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Shefali Dobhal
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Dario Arizala
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Diksha Klair
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Francisco Ochoa-Corona
- grid.65519.3e0000 0001 0721 7331Institute for Biosecurity & Microbial Forensics, Oklahoma State University, Stillwater, OK USA
| | - Md Emran Ali
- grid.213876.90000 0004 1936 738XDepartment of Plant Pathology, University of Georgia, Tifton, GA USA
| | - Jenee Odani
- grid.410445.00000 0001 2188 0957Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Jon-Paul Bingham
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Daniel M. Jenkins
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Jacqueline Fletcher
- grid.65519.3e0000 0001 0721 7331Institute for Biosecurity & Microbial Forensics, Oklahoma State University, Stillwater, OK USA
| | - James P. Stack
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA
| | - Anne M. Alvarez
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Mohammad Arif
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
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