FTIR spectroscopy for detection and identification of fungal phytopathogenes

Soil-borne fungi are considered as major pathogens to many plants and can cause a severe economic damage. Early detection and identification of these pathogens is very important and might be critical for their control. The available methods for identification of fungi like molecular biology, serological tests and PCRs tests (polymerase chain reaction) are time consuming and not always very specific. Fourier-transform infrared (FTIR) attenuated total reflection (ATR) spectroscopy, is considered to be a comprehensive and sensitive method for detection of molecular changes in intact cells.In the present study we used FTIR–ATR as a sensitive and effective assay for the detection and discrimination between different fungal genera. Our results showed significant spectral differences between the various examined fungi genera. These results proved the possibility of discrimination between these fungi on the genus level.

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Discrimination of Soil-Borne Fungi Using Fourier Transform Infrared Attenuated Total Reflection Spectroscopy

Applied Spectroscopy ◽

10.1366/000370208783759678 ◽

2008 ◽

Vol 62 (3) ◽

pp. 302-305 ◽

Cited By ~ 25

Author(s):

Raphael Linker ◽

Leah Tsror(LAHKIM)

Keyword(s):

Fourier Transform ◽

Success Rate ◽

Fourier Transform Infrared ◽

Total Reflection ◽

Attenuated Total Reflection ◽

Economic Damage ◽

Genus Level ◽

Ft Ir ◽

Atr Spectroscopy ◽

Soil Borne Fungi

Fourier transform infrared (FT-IR) attenuated total reflection (ATR) spectroscopy was used to discriminate five commonly encountered soil-borne fungi that cause severe economic damage to agriculture: Colletotrichum, Fusarium, Pythium, Rhizoctonia, and Verticillium. Contrary to previous studies related to microorganism discrimination using FT-IR-ATR spectroscopy, the pathogen samples were not dried on the ATR crystal, which is a time-consuming operation. Rather, after removing some pathogen filaments from the solution using tweezers, these were placed directly on a flat ATR crystal and pressure was applied using a pressure clamp. Following water subtraction, baseline correction, and normalization of the spectra, principal component analysis was used as a data-reduction step and canonical variate analysis was used for discrimination. Discrimination was performed at the genus level and at the strain level for Colletotrichum. For discrimination between the five fungi at the genus level, the success rate for the validation samples ranged from 75% to 89%. For discrimination between the two Colletotrichum strains, the success rate was 78%. Comparison with spectra of similar fungi dried on the ATR crystal showed that both types of spectra were very similar, indicating that drying the samples on the ATR crystal is not required and can be replaced by mathematical post-processing of the spectra. For routine analyses that involve rapid screening of very large amounts of samples, this approach allows for increasing significantly the number of samples that can be analyzed daily.

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Detection ofFusarium oxysporumFungal Isolates Using ATR Spectroscopy

Spectroscopy An International Journal ◽

10.1155/2012/109708 ◽

2012 ◽

Vol 27 ◽

pp. 551-556 ◽

Cited By ~ 9

Author(s):

A. Salman ◽

I. Lapidot ◽

A. Pomerantz ◽

L. Tsror ◽

Z. Hammody ◽

...

Keyword(s):

Fusarium Oxysporum ◽

Economic Damage ◽

Mathematical Principle ◽

Success Rates ◽

Linear Discriminant ◽

Detection And Identification ◽

Identification Of Fungi ◽

Atr Spectroscopy ◽

Different Strains ◽

Leave One Out

Fungi are considered as serious pathogens for many plants, potentially causing severe economic damage. Early detection and identification of these pathogens is crucial for their timely control. The methods available for identification of fungi are time consuming and not always very specific. In this study, the potential of FTIR-ATR spectroscopy was examined together with advanced mathematical principle component analysis (PCA) and statistical linear discriminant analysis (LDA) to differentiate among 10 isolates of Fusarium oxysporum. The results are encouraging and indicate that FTIR-ATR can successfully detect different isolates of Fusarium oxysporum. Based on PCA and LDA calculations in the region 850–1775 cm-1with 16 PC's, the different strains from the same fungal genus could be classified with 75.3% and 69.5% success rates using the “leave one out” method and “20–80% algorithm” respectively.

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Direct identification of potato's fungal phyto-pathogens by Fourier-transform infrared (FTIR) microscopy

Spectroscopy An International Journal ◽

10.1155/2010/507295 ◽

2010 ◽

Vol 24 (6) ◽

pp. 609-619 ◽

Cited By ~ 9

Author(s):

V. Erukhimovitch ◽

L. Tsror (Lahkim) ◽

M. Hazanovsky ◽

M. Huleihel

Keyword(s):

Fungal Pathogens ◽

Direct Detection ◽

Economic Damage ◽

Potato Tubers ◽

Direct Identification ◽

Ftir Microscopy ◽

Spectral Bands ◽

Detection And Identification ◽

Identification Of Fungi ◽

Potato Pathogens

Fungi are considered as serious pathogens to many plants and can cause a severe economic damage. The available methods for identification of fungi are time consuming and not always very specific. In the present study we examined the potential of FTIR microscopy for direct detection and identification of different fungal potato pathogens on the surface of potato tubers. Unique spectral bands for each of the examined fungal pathogens appeared in the spectra of naturally infected potatoes. These results strongly support the potential of FTIR microscopy for successful detection and probably discrimination between different fungal pathogens directly from the infected tissue.

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Insidensi Virus dan Cendawan pada Biji dan Umbi Bawang Merah

Jurnal Fitopatologi Indonesia ◽

10.14692/jfi.14.6.222 ◽

2019 ◽

Vol 14 (6) ◽

pp. 222

Author(s):

Ana Septiana Saputri ◽

Efi Toding Tondok ◽

Sri Hendrastuti Hidayat

Keyword(s):

Seed Quality ◽

Disease Incidence ◽

Virus Detection ◽

Test Method ◽

Assay Method ◽

Planting Material ◽

Detection And Identification ◽

Identification Of Fungi ◽

Polymerase Chain ◽

Rhizopus Sp

Incidence of Viruses and Fungi on True Shallot Seed and Shallot Bulb Shallot is an important vegetable in Indonesia. Shallot farmers generally use bulbs as planting material even though there is an option to use true shallot seed (TSS). One important criteria for a good seed quality as planting material is pathogen free. Research was conducted to detect and identify viruses and fungi from TSS and shallot seed bulbs cultivars Bima, Bauji, Thailand, and Tuk-Tuk. Virus detection was carried out by DIBA (dot immunobinding assay) method using specific antiserum to OYDV, SLV, SYSV, and GCLV. Detection and identification of fungi was carried out by blotter test method and polymerase chain reaction. Infection of OYDV, GCLV, SYSV, and SLV were only detected in shallot bulbs with infection rates ranging from 66% to 100%. Four species of fungi were detected in TSS and bulbs, i.e. Aspergillus niger, A.flavus, F. solani, and Rhizopus sp; whereas F.oxysporum was only found in bulbs. All isolates of F. oxysporum was pathogenic and cause disease incidence up to 55%. Pathogenic isolate of F. oxysporum had 100% homology to those isolate from China and USA on the spesies level and 91.2% to those isolate from India and USA to the forma spesies level.

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Diagnostic Accuracy of a Direct Panfungal Polymerase Chain Reaction Assay Performed on Stained Cytology Slides

Veterinary Pathology ◽

10.1177/0300985821991562 ◽

2021 ◽

pp. 030098582199156

Author(s):

Alexandra N. Myers ◽

Unity Jeffery ◽

Zachary G. Seyler ◽

Sara D. Lawhon ◽

Aline Rodrigues Hoffmann

Keyword(s):

Polymerase Chain Reaction ◽

Diagnostic Accuracy ◽

Molecular Techniques ◽

Fungal Culture ◽

Chain Reaction ◽

Identification Of Fungi ◽

Fungal Dna ◽

Polymerase Chain ◽

Panfungal Pcr ◽

Pcr Targeting

Molecular techniques are increasingly being applied to stained cytology slides for the diagnosis of neoplastic and infectious diseases. Such techniques for the identification of fungi from stained cytology slides have not yet been evaluated. This study aimed to assess the diagnostic accuracy of direct (without nucleic acid isolation) panfungal polymerase chain reaction (PCR) followed by sequencing for identification of fungi and oomycetes on stained cytology slides from dogs, cats, horses, and other species. Thirty-six cases were identified with cytologically identifiable fungi/oomycetes and concurrent identification via fungal culture or immunoassay. Twenty-nine controls were identified with no cytologically or histologically visible organisms and a concurrent negative fungal culture. Direct PCR targeting the internal transcribed spacer region followed by sequencing was performed on one cytology slide from each case and control, and the sensitivity and specificity of the assay were calculated. The sensitivity of the panfungal PCR assay performed on stained cytology slides was 67% overall, 73% excluding cases with oomycetes, and 86% when considering only slides with abundant fungi. The specificity was 62%, which was attributed to amplification of fungal DNA from control slides with no visible fungus and negative culture results. Direct panfungal PCR is capable of providing genus- or species-level identification of fungi from stained cytology slides. Given the potential of panfungal PCR to amplify contaminant fungal DNA, this assay should be performed on slides with visible fungi and interpreted in conjunction with morphologic assessment by a clinical pathologist.

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Diffusion Measurements Using FT-IR ATR Spectroscopy: Lubricant Diffusion in Polypropylene

Applied Spectroscopy ◽

10.1366/0003702021954962 ◽

2002 ◽

Vol 56 (4) ◽

pp. 509-514 ◽

Cited By ~ 3

Author(s):

Xiaohua Yi ◽

Karen Nerbonne ◽

John Pellegrino

Keyword(s):

Current Model ◽

Mineral Oil ◽

Attenuated Total Reflection ◽

Lubricant Layer ◽

Polymer Interfaces ◽

Time Resolved ◽

Polymer Sample ◽

Ft Ir ◽

Atr Spectroscopy ◽

Poly Propylene

We present an experimental method for measuring diffusion of lubricants (or any highly viscous fluid) in polymers using Fourier transform infrared (FT-IR) attenuated total reflection (ATR) spectroscopy. Unlike the conventional FT-IR ATR diffusion measurement, in which a polymer sample is sandwiched between the penetrant and an internal reflection element (IRE), in this method, a thin layer of penetrant (for example, a lubricant) is sandwiched between the IRE and the polymer sample. This allows accurate control and measurement of the thickness of the lubricant layer, which, in turn, facilitates subsequent data analysis. The diffusion is studied by monitoring the time-resolved change in absorbance of either a unique polymer or penetrant band. A feature of this new method is that it can provide an estimate of solubility, as well as an estimate of the diffusivity of the penetrant in the polymer. Using this method, we studied the diffusion of mineral oil and a commercial fluorocarbon ether lubricant (Krytox® 143AC‡) in poly(propylene) (PP) film at room temperature. The experimental data was modeled using a Fickian model with impermeable and saturated boundary conditions applied at the IRE/lubricant and lubricant/polymer interfaces, respectively. The diffusivity and solubility of mineral oil in PP were found to be 1.34 ± 0.35 (×10−10) cm2/s and 0.77 ± 0.13 (×10−2) g/g of PP, respectively. The current model was unable to quantitatively describe the diffusion of the Krytox® 143AC in the PP, possibly due to excessive swelling.

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Model Optimization and Stability of Hemoglobin Analysis in Human Soluble Blood Samples by FTIR/ATR Spectroscopy

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.55-57.1168 ◽

2011 ◽

Vol 55-57 ◽

pp. 1168-1171

Author(s):

Tao Pan ◽

Ai Hong Peng ◽

Wen Jie Huang

Keyword(s):

Signal To Noise Ratio ◽

Attenuated Total Reflection ◽

Partial Least Square ◽

Least Square ◽

Model Optimization ◽

Optimal Model ◽

Blood Samples ◽

Quantification Method ◽

Atr Spectroscopy ◽

Pls Method

Using Fourier transform infrared spectroscopy (FTIR), attenuated total reflection (ATR) technology and partial least square (PLS) method, the rapid quantification method of hemoglobin (HGB) in human soluble blood samples was established. Based on the distribution of samples’ HGB chemical value and absorbance on 1543 cm-1 which had the highest signal to noise ratio for HGB, all samples were divided into calibration set and prediction set for 50 times. PLS models were established for all divisions, based on the average data RMSEPAve, the stable optimal model was selected, the corresponding PLS factor, RMSEPAve and RP,Ave were 2, 6.81 g/L and 0.943 respectively.

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Detection and identification of Candida spp. in human serum by LightCycler® real-time polymerase chain reaction

Diagnostic Microbiology and Infectious Disease ◽

10.1016/j.diagmicrobio.2007.09.014 ◽

2008 ◽

Vol 60 (3) ◽

pp. 263-271 ◽

Cited By ~ 37

Author(s):

Catherine Dunyach ◽

Sébastien Bertout ◽

Cécile Phelipeau ◽

Pascal Drakulovski ◽

Jacques Reynes ◽

...

Keyword(s):

Polymerase Chain Reaction ◽

Human Serum ◽

Real Time ◽

Chain Reaction ◽

Candida Spp ◽

Detection And Identification ◽

Polymerase Chain

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Application Of Systems With Total Internal Reflection At Novosibirsk Free Electron Laser For Spectroscopy In The Terahertz Range

Siberian Journal of Physics ◽

10.54362/1818-7919-2016-11-3-72-82 ◽

2016 ◽

Vol 11 (3) ◽

pp. 72-82

Author(s):

Vasily Gerasimov ◽

Elvira Grigorieva ◽

Boris Knyazev ◽

Yuliya Choporova

Keyword(s):

Free Electron ◽

Free Electron Laser ◽

Quantum Cascade Lasers ◽

Attenuated Total Reflection ◽

Terahertz Range ◽

Optical Systems ◽

Early Diagnosis Of Cancer ◽

Infrared Spectral ◽

Atr Spectroscopy ◽

Spectral Ranges

Attenuated total reflection (ATR) spectroscopy is widely used in the visible and infrared spectral ranges. Progress in the development of laboratory scale monochromatic sources of terahertz radiation, such as quantum cascade lasers, suggests that in the near future this kind of spectrometers will be widely spread in the terahertz range. For this reason, the development of ATR based methods and devices is highly relevant. In this paper, we discuss the features of the use of ATR spectroscopy in the terahertz range, and describe some of the optical systems, designed for experiments at the Novosibirsk free electron laser (NovoFEL). We show that in the terahertz range the ATR spectroscopy has a number of significant advantages over the absorption spectroscopy. As an example, we are discussing the possibility of using terahertz polarimetry to develop a method for early diagnosis of cancer via the detection of left-handed to right-handed polysaccharide enantiomers ratio. Spectra of selected polysaccharides were recorded with a standard Fourier spectrometer using developed by us an ATR unit. The possibility of studying the polarization characteristics of polysaccharides in aqueous solutions using spectrally selective polarimeter with the NovoFEL as a tunable radiation source was demonstrated.

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