Monitoring fungal infection in maize with high resolution X-ray micro computed tomography

Orina, Irene Nyangoge (2018-03)

Thesis (PhD (Food Sc))--Stellenbosch University, 2018.

Thesis

ENGLISH ABSTRACT: Maize (Zea mays L.) is an important cereal crop used for human food as well as animal feed. Maize is however vulnerable to contamination by fungi that produce harmful mycotoxins. Fusarium verticillioides is among the most frequently isolated fungus from maize and maize-based products worldwide. Conventional methods for evaluation of fungal infection are destructive in nature and involve tedious sample preparation procedures. X-ray micro computed tomography (X-ray micro CT) was used as a non-destructive technique to monitor the effect of fungal damage on the internal structure of maize kernels infected with F. verticillioides. X-ray images of control and infected kernels were acquired post inoculation using high resolution X-ray micro CT over time. After image acquisition, consecutive two-dimensional (2D) cross sectional images were reconstructed into three dimensional (3D) volumes of the maize kernels. Qualitative results were presented as 2D projection images, and 3D volumes which enable visualisation in different views (top, front and side view). More voids were observed especially in the germ and floury endosperm regions of both the control and infected kernels over time. Quantitative parameters including total volume, mean grey value and total volume of voids were calculated. Total volume and mean grey value increased, while total volume decreased over time in both the control and infected kernels. No significant difference (P ≥ 0.05) was reported between the control and infected for the first four days scanned. Algorithms were developed to extract image textural features from selected 2D images of both the control and infected kernels. First order statistics (mean, standard deviation, kurtosis and skewness) and grey level co-occurrence matrix (GLCM) features were extracted from the side, front and top view of each kernel for the days scanned. The outputs from calculation of these textural features were used as inputs for calculating principal component analysis (PCA) and developing classification models using partial least square discriminant analysis (PLS-DA). Clear separation of the control from the infected was seen on day 8 post inoculation using the first order statistical features. Classification accuracies of 97.22% for control and 55.56% for infected kernels was achieved using the developed PLS-DA model. The GLCM extracted features gave a better classification accuracy of 79.16% for infected kernels with less infected kernels classified as controls compared to first order statistics features. This study demonstrated that, although X-ray micro CT cannot be used as a rapid technique for detection of fungal infection especially during early stages of infection, it allows monitoring of structural changes in the kernel over time, and therefore offer a better understanding of the effect of fungal damage on the microstructure of maize kernel at high resolution.

AFRIKAANSE OPSOMMING: Mielies (Zea mays L.) is ‘n belangrike graangewas wat gebruik word vir menslike voeding sowel as vir dierevoeding. Mielies is egter kwesbaar vir kontaminasie deur fungi wat skadelike mikotoksiene produseer. Fusarium verticillioides is een van die fungi wat wêreldwyd die gereeldste in mielies en mielie-gebasseerde produkte voorkom. Konvensionele metodes vir die evaluering van swaminfeksiesies is vernietigend van aard en sluit tydrowende monstervoorbereidingsprosedures in. X-straal mikro-berekende tomografie (X-straal mikro CT) is gebruik as ‘n nie-vernietigende tegniek om die effek van swamskade op die interne strukture van mieliepitte wat met F. verticillioides geïnfekteer is, te monitor. X-straal beelde van kontrole en geïnfekteerde pitte is na inokulasie verkry deur hoë resolusie X-straal mikro CT oor tyd. Na die beelde verkry is, is agtereenvolgende twee-dimensionele (2D) deursnee-beelde herbou in drie-dimensionele (3D) volumes van die mieliepitte. Kwalitatiewe resultate is aangebied as 2D projeksie beelde, en 3D volumes wat visualisering in verskeie aansigte (bo-, voor-, en syaansig) moontlik maak. Meer ruimtes is waargeneem in veral die kiem en melerige endosperm van beide die kontrole en geïnfekteerde pitte oor tyd. Kwantitatiewe parameters insluitende totale volume, gemiddelde gryswaarde en totale volume leemtes is bereken. Totale volume en gemiddelde gryswaarde het oor tyd toegeneem in beide die kontrole en geïnfekteerde pitte. Geen beduidende verskil (P≥ 0.05) is gerapporteer vir die kontrole en geïnfekteerde pitte vir die eerste vier dae waarop geskandeer is nie. Algoritmes is ontwikkel om beeld-tekstuur kenmerke van geselekteerde 2D beelde van beide kontrole en geïnfekteerde pitte te onttrek. Eerste-orde statistiek (gemiddeld, standaardafwyking, kurtoses en skeefheid) en grysvlak mede-voorkoms matriks (GLCM) kenmerke is onttrek uit die sy, voor- en bo-aansig van elke pit vir die dae waarop geskandeer is. Die uitsette van die berekening van hierdie tekstuur kenmerke is gebruik as insette vir die berekening van hoofkomponent analise (PCA) en vir die ontwikkeling van klassifikasie modelle deur die gebruik van parsiële kleinste kwadrate diskriminantanalise (PLS-DA). Duidelike skeiding tussen die kontrole en die geïnfekteerde pitte is gesien op dag 8 na inokulasie met die gebruik van eerste orde statistiese kenmerke. Klassifikasie akkuraatheid van 97% vir kontrole en 55% vir geïnfekteerde pitte is verkry met die ontwikkelde PLS-DA model. Die GLCM onttrekte kenmerke het ‘n beter klassifikasie akkuraatheid van 79% vir geïnfekteerde pitte, met minder geïnfekteerde pitte wat as kontrole geklassifiseer is in vergelyking met eerste orde statistiese kenmerke. Hierdie studie het gedemonstreer dat, al kan X-straal mikro CT nie as ‘n vinnige tegniek vir die opsporing van ‘n swaminfeksie - veral in die vroeë stadia van infeksie - gebruik word nie, sal dit die monitering van strukturele veranderinge in die mieliepit oor tyd toelaat, en sal dus ‘n beter begrip van die effek van swambeskadiging op die mikrostruktuur van die mieliepit teen hoë resolusie bied.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/103377
This item appears in the following collections: