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Jasiewicz J, Piekarczyk J, Stępień Ł, Tkaczuk C, Sosnowska D, Urbaniak M, Ratajkiewicz H. Multidimensional discriminant analysis of species, strains and culture age of closely related entomopathogenic fungi using reflectance spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124135. [PMID: 38508072 DOI: 10.1016/j.saa.2024.124135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 03/22/2024]
Abstract
The diversity of fungal strains is influenced by genetic and environmental factors, growth conditions and mycelium age, and the spectral features of fungal mycelia are associated with their biochemical, physiological, and structural traits. This study investigates whether intraspecific differences can be detected in two closely related entomopathogenic species, namely Cordyceps farinosa and Cordyceps fumosorosea, using ultraviolet A to shortwave infrared (UVA-SWIR) reflectance spectra. Phylogenetic analysis of all strains revealed a high degree of uniformity among the populations of both species. The characteristics resulting from variation in the species, as well as those resulting from the age of the cultures were determined. We cultured fungi on PDA medium and measured the reflectance of mycelia in the 350-2500 nm range after 10 and 17 days. We subjected the measurements to quadratic discriminant analysis (QDA) to identify the minimum number of bands containing meaningful information. We found that when the age of the fungal culture was known, species represented by a group of different strains could be distinguished with no more than 3-4 wavelengths, compared to 7-8 wavelengths when the age of the culture was unknown. At least 6-8 bands were required to distinguish cultures of a known species among different age groups. Distinguishing all strains within a species was more demanding: at least 10 bands were required for C. fumosorosea and 21 bands for C. farinosa. In conclusion, fungal differentiation using point reflectance spectroscopy gives reliable results when intraspecific and age variations are taken into account.
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Affiliation(s)
- Jarosław Jasiewicz
- Adam Mickiewicz University in Poznań, Institute of Geoecology and Geoinformation, ul. Krygowskiego 10, 60-680 Poznań, Poland
| | - Jan Piekarczyk
- Adam Mickiewicz University in Poznań, Institute of Physical Geography and Environmental Planning, ul. Krygowskiego 10, 60-680 Poznań, Poland
| | - Łukasz Stępień
- Plant-Pathogen Interaction Team, Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479 Poznań, Poland
| | - Cezary Tkaczuk
- Institute of Agriculture and Horticulture, University in Siedlce, ul. Prusa 14, 08-110 Siedlce, Poland
| | - Danuta Sosnowska
- Institute of Plant Protection - National Research Institute, Department of Biological Control Methods and Organic Farming, ul. Władysława Węgorka 20, Poznań 60-318, Poland
| | - Monika Urbaniak
- Plant-Pathogen Interaction Team, Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479 Poznań, Poland
| | - Henryk Ratajkiewicz
- Poznan University of Life Sciences, Department of Entomology and Environmental Protection, ul. Dąbrowskiego 159, 60-594 Poznań, Poland.
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Tong C, Li T, Luo S, Chen R, Chen S, Wei J, Qing Y, Qin S, Pan G, Li C, Zhou Z. Detection of the pathogenic fungus Cordyceps farinosa in the Thitarodes armoricanus soil-rearing environment based on nucleic acid targets. Can J Microbiol 2023; 69:136-145. [PMID: 36638365 DOI: 10.1139/cjm-2022-0165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Cordyceps farinosa, an entomopathogenic fungus, infects and leads to high mortality of Thitarodes armoricanus larvae, which die soon after the infection of C. farinose, usually before the colonization of Ophiocordyceps sinensis owing to competitive inhibition and fruiting body formation. Therefore, monitoring C. farinosa in the O. sinensis cultivation environment is critical for minimizing the C. farinosa infection-induced losses. In this study, we initially designed a PCR primer pair (Tar-1F/Tar-1R) through open reading frame prediction and homology comparison of the C. farinosa genome sequence. This primer pair can detect both C. farinosa and Samsoniella hepiali. To further distinguish, primers (ITS5-172/ITS4-95) were then designed to selectively amplify the large ribosomal subunit sequences in the C. farinosa genome. All these primers were applied in combination for detection of C. farinosa in soil samples. The sensitivity reached a detection limit of 1 × 106 spores/g soil. In addition, these primers can detect the presence of C. farinosa in dead T. armoricanus larval samples. This newly established rapid detection method provides important information for C. farinosa control during O. sinensis cultivation.
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Affiliation(s)
- Chaoqun Tong
- State Key Laboratory of Silkworm Genome Biology, Chongqing Key Laboratory of Microsporidia Infection and Prevention, Southwest University, Chongqing 400715, China
| | - Tian Li
- State Key Laboratory of Silkworm Genome Biology, Chongqing Key Laboratory of Microsporidia Infection and Prevention, Southwest University, Chongqing 400715, China
| | - Shisui Luo
- Taiji Medical Research Institute, Chongqing 401147, China
| | - Ruoni Chen
- Taiji Medical Research Institute, Chongqing 401147, China
| | - Shijiang Chen
- Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China
| | - Junhong Wei
- State Key Laboratory of Silkworm Genome Biology, Chongqing Key Laboratory of Microsporidia Infection and Prevention, Southwest University, Chongqing 400715, China
| | - Yuling Qing
- Taiji Medical Research Institute, Chongqing 401147, China
| | - Shaorong Qin
- Taiji Medical Research Institute, Chongqing 401147, China
| | - Guoqing Pan
- State Key Laboratory of Silkworm Genome Biology, Chongqing Key Laboratory of Microsporidia Infection and Prevention, Southwest University, Chongqing 400715, China
| | - Chunfeng Li
- State Key Laboratory of Silkworm Genome Biology, Chongqing Key Laboratory of Microsporidia Infection and Prevention, Southwest University, Chongqing 400715, China
| | - Zeyang Zhou
- State Key Laboratory of Silkworm Genome Biology, Chongqing Key Laboratory of Microsporidia Infection and Prevention, Southwest University, Chongqing 400715, China.,College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
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Gómez-Caro S, Mendoza-Vargas LA, Ramírez-Gil JG, Burbano-David D, Soto-Suárez M, Melgarejo LM. Close-Range Thermography and Reflectance Spectroscopy Support In Vitro and In Vivo Characterization of Colletotrichum spp. Isolates from Mango Fruits. PLANT DISEASE 2022; 106:2355-2369. [PMID: 35350902 DOI: 10.1094/pdis-08-21-1774-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Colletotrichum causing anthracnose in mango is known for its variable virulence that may have an effect on disease development and efficacy of management strategies. In this study, we characterized Colletotrichum spp. isolated from mango fruits under in vitro and in vivo conditions using close-range thermography and reflectance spectroscopy. Twenty-six isolates were phylogenetically characterized to ascertain species using the internal transcribed spacer sequence. Virulence, spectral (in vivo and in vitro), and thermographic responses (in vivo) of these isolates were analyzed. Isolates were grouped into the Colletotrichum gloeosporioides species complex and classified into eight morphotypes. Mycelial growth, conidia production, sporulation abundance, and area under disease progress curve (AUDPC) varied largely among isolates. Disease symptoms were observed 4 days after inoculation (dai), and, for most morphotypes, changes in tissue temperature were registered at 11 dai, with the greatest decrease at 14 dai with pathogen sporulation. In vitro and in vivo morphotypes shared changes in the spectrum range, and main variations were found in the number of informative spectral bands. In vivo average gross reflectance was higher in disease-inoculated tissue than in healthy uninoculated tissue. Morphotype responses varied depending on AUDPC values and postinoculation time. Discriminant analysis of the spectral response using principal component analysis and partial least squares regression explained 94 to 96.3 and 98 to 99.9% of the variance from in vitro and in vivo tests, respectively. Spectral markers were obtained for four distinct morphotype groups. We found three (550 to 650, 650.1 to 790, and 1,300 to 1,400 nm) and two (520 to 830 and 1,100 to 1,450 nm) regions with highly (P < 0.05) discriminant spectral bands for diseased fruits and morphotype characterization.
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Affiliation(s)
- Sandra Gómez-Caro
- Facultad de Ciencias Agrarias, Departamento de Agronomía, Universidad Nacional de Colombia-Sede Bogotá, Bogotá, Colombia
| | - Luis Alberto Mendoza-Vargas
- Facultad de Ciencias Agrarias, Departamento de Agronomía, Universidad Nacional de Colombia-Sede Bogotá, Bogotá, Colombia
| | - Joaquín Guillermo Ramírez-Gil
- Facultad de Ciencias Agrarias, Departamento de Agronomía, Universidad Nacional de Colombia-Sede Bogotá, Bogotá, Colombia
| | - Diana Burbano-David
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria-AGROSAVIA, 250047 Mosquera, Colombia
| | - Mauricio Soto-Suárez
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria-AGROSAVIA, 250047 Mosquera, Colombia
| | - Luz Marina Melgarejo
- Facultad de Ciencias, Departamento de Biología, Laboratorio de Fisiología y Bioquímica Vegetal, Universidad Nacional de Colombia-Sede Bogotá, Bogotá, Colombia
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Dyba K, Wąsala R, Piekarczyk J, Gabała E, Gawlak M, Jasiewicz J, Ratajkiewicz H. Reflectance spectroscopy and machine learning as a tool for the categorization of twin species based on the example of the Diachrysia genus. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 273:121058. [PMID: 35220048 DOI: 10.1016/j.saa.2022.121058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
In our work we used noninvasive point reflectance spectroscopy in the range from 400 to 2100 nm coupled with machine learning to study scales on the brown and golden iridescent areas on the dorsal side of the forewing of Diachrysia chrysitis and D. stenochrysis. We used our approach to distinguish between these species of moths. The basis for the study was a statistically significant collection of 95 specimens identified based on morphological feature and gathered during 23 years in Poland. The numerical part of an experiment included two independent discriminant analyses: stochastic and deterministic. The more sensitive stochastic approach achieved average compliance with the species identification made by entomologists at the level of 99-100%. It demonstrated high stability against the different configurations of training and validation sets, hence strong predictors of Diachrysia siblings distinctiveness. Both methods resulted in the same small set of relevant features, where minimal fully discriminating subsets of wavelengths were three for glass scales on the golden area and four for the brown. The differences between species in scales primarily concern their major components and ultrastructure. In melanin-absent glass scales, this is mainly chitin configuration, while in melanin-present brown scales, melanin reveals as an additional factor.
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Affiliation(s)
- Krzysztof Dyba
- Institute of Geoecology and Geoinformation, Adam Mickiewicz University in Poznań, Poland
| | - Roman Wąsala
- Department of Entomology and Environment Protection, Poznań University of Life Sciences, Poland
| | - Jan Piekarczyk
- Institute of Physical Geography and Environmental Planning, Adam Mickiewicz University in Poznań, Poland
| | - Elżbieta Gabała
- Research Centre of Quarantine, Invasive and Genetically Modified Organisms, Institute of Plant Protection - National Research Institute, Poland
| | - Magdalena Gawlak
- Research Centre of Quarantine, Invasive and Genetically Modified Organisms, Institute of Plant Protection - National Research Institute, Poland
| | - Jarosław Jasiewicz
- Institute of Geoecology and Geoinformation, Adam Mickiewicz University in Poznań, Poland.
| | - Henryk Ratajkiewicz
- Department of Entomology and Environment Protection, Poznań University of Life Sciences, Poland.
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Naderlou E, Salouti M, Amini B, Amini A, Narmani A, Jalilvand A, Shahbazi R, Zabihian S. Enhanced sensitivity and efficiency of detection of Staphylococcus aureus based on modified magnetic nanoparticles by photometric systems. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2021; 48:810-817. [PMID: 32476515 DOI: 10.1080/21691401.2020.1748638] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Staphylococcus aureus is an important infectious factor in the food industry and hospital infections. Many methods are used for detecting bacteria but they are mostly time-consuming, poorly sensitive. In this study, a nano-biosensor based on iron nanoparticles (MNPs) was designed to detect S. aureus. MNPs were synthesized and conjugated to Biosensors. Then S. aureus was lysed and nano-biosensor (MNP-TiO2-AP-SMCC-Biosensors) was added to the lysed bacteria. After bonding the bacterial genome to the nano-biosensor, MNPs were separated by a magnet. Bacterial DNA was released from the surface of nano-biosensor and researched by Nano-drop spectrophotometry. The results of SEM and DLS revealed that the size of MNPs was 20-25 nm which increased to 38-43 nm after modification and addition of biosensors. The designed nano-biosensor was highly sensitive and specific for the detection of S. aureus. The limit of detection (LOD) was determined as 230 CFU mL-1. There was an acceptable linear correlation between bacterial concentration and absorption at 3.7 × 102-3.7× 107 whose linear diagram and regression was Y = 0.242X + 2.08 and R2 = .996. Further, in the presence of other bacteria as a negative control, it was absolutely specific. The sensitivity of the designed nano-biosensor was investigated and compared through PCR.
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Affiliation(s)
- Ebrahim Naderlou
- Faculty of Sciences, Department of Microbiology, Islamic Azad University, Zanjan, Iran
| | - Mojtaba Salouti
- Faculty of Sciences, Department of Microbiology, Islamic Azad University, Zanjan, Iran
| | - Bahram Amini
- Department of Biochemistry, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Ali Amini
- Department of Biochemistry, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Asghar Narmani
- Faculty of New Sciences and Technologies, Department of Life Science Engineering, University of Tehran, Tehran, Iran
| | - Ahmad Jalilvand
- Department of Pathology, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Reza Shahbazi
- Faculty of Sciences, Department of Microbiology, Islamic Azad University, Zanjan, Iran
| | - Saeid Zabihian
- Department of Pathology, Zanjan University of Medical Sciences, Zanjan, Iran
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Taheri H, Amini B, Kamali M, Asadi M, Naderlou E. Functionalization of anti-Brucella antibody based on SNP and MNP nanoparticles for visual and spectrophotometric detection of Brucella. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 229:117891. [PMID: 31818642 DOI: 10.1016/j.saa.2019.117891] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/01/2019] [Indexed: 06/10/2023]
Abstract
An Immuno-Nano-Biosensor with high sensitivity was designed based on iron and silica nanoparticles to detect B. abortus. Briefly explain, primary polyclonal antibody (IgG1) was conjugated on surface magnetic nanoparticles (MNPs) to form MNP-IgG1. Secondary polyclonal antibody (IgG2) and Horseradish Peroxidase enzyme were conjugated on silica nanoparticles (SNPs) to form HRP-SNP-IgG2. HRP-SNP-IgG2. MNP-IgG1 and HRP-SNP-IgG2 were added to B. abortus. The MNP-IgG1-B.abortus-IgG2-SNP-HRP complex was isolated from the reaction mixture using a magnet. After that, tetramethylbenzidine was added to the complex. The reaction was stopped with HCl and investigated using UV-Vis spectrophotometry. The nanoparticles' structure and size were investigated using SEM and DLS. Immuno-Nano-Biosensor sensitivity and specificity were determined. The SEM and DLS results indicated that the SNPs, MNPs, HRP-SNP-IgG2 and MNP-IgG1 size and structure were 35, 44, 60 and 56 nm, respectively. In addition, a good linear correlation was observed at 102-107 CFU mL-1 concentrations, which their linear equation and regression were Y = 0.3× + 0.18 and R2 0.982, respectively. The limitation of detecting B. abortus was 160 CFU mL-1. Finally, the results demonstrated that those designed Immuno-Nano-Biosensor could be specifically detected B. abortus and B. melitensis in real samples.
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Affiliation(s)
- Hamidreza Taheri
- Nano biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Bahram Amini
- Department of biochemistry, Zanjan University of Medical Sciences, Zanjan, Iran.
| | - Mehdi Kamali
- Nano biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Masoud Asadi
- Department of biochemistry, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Ebrahim Naderlou
- Department of biochemistry, Zanjan University of Medical Sciences, Zanjan, Iran
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Gurbanov R, Tunçer S, Mingu S, Severcan F, Gozen AG. Methylation, sugar puckering and Z-form status of DNA from a heavy metal-acclimated freshwater Gordonia sp. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2019; 198:111580. [DOI: 10.1016/j.jphotobiol.2019.111580] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 07/07/2019] [Accepted: 07/29/2019] [Indexed: 01/27/2023]
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Rasskazov IL, Singh R, Carney PS, Bhargava R. Extended Multiplicative Signal Correction for Infrared Microspectroscopy of Heterogeneous Samples with Cylindrical Domains. APPLIED SPECTROSCOPY 2019; 73:859-869. [PMID: 31149835 DOI: 10.1177/0003702819844528] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Optical scattering corrections are invoked to computationally distinguish between scattering and absorption contributions to recorded data in infrared (IR) microscopy, with a goal to obtain an absorption spectrum that is relatively free of the effects of sample morphology. Here, we present a modification of the extended multiplicative signal correction (EMSC) approach that allows for spectral recovery from fibers and cylindrical domains in heterogeneous samples. The developed theoretical approach is based on exact Mie theory for infinite cylinders. Although rigorous Mie theory implies utilization of comprehensive and time-consuming calculations, we propose to change the workflow of the original EMSC algorithm to minimize extensive calculations for each recorded spectrum at each iteration step. This makes the modified EMSC approach practical for routine use. First, we tested our approach using synthetic data derived from a rigorous model of scattering from cylinders in an IR microscope. Second, we applied the approach to Fourier transform IR (FT-IR) microspectroscopy data recorded from filamentous fungal and cellulose samples with pronounced fiber-like shapes. While the corrected spectra show greatly reduced baseline offsets and consistency, strongly absorbing regions of the spectrum require further refinement. The modified EMSC algorithm broadly mitigates the effects of scattering, offering a practical approach to more consistent and accurate spectra from cylindrical objects or heterogeneous samples with cylindrical domains.
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Affiliation(s)
- Ilia L Rasskazov
- 1 The Institute of Optics, University of Rochester, Rochester, NY, USA
| | - Rajveer Singh
- 2 Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- 3 Department of Civil, Architectural and Environmental Engineering, Drexel University, Philadelphia, PA, USA
| | - P Scott Carney
- 1 The Institute of Optics, University of Rochester, Rochester, NY, USA
| | - Rohit Bhargava
- 2 Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- 4 Departments of Bioengineering, Electrical & Computer Engineering, Chemistry, Chemical and Biomolecular Engineering, and Mechanical Science and Engineering, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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