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First Report of Pectobacterium carotovorum and Pectobacterium aroidearum Causing Bacterial Soft Rot on Curly Dwarf Pak Choy (Brassica rapa var. Chinensis) in Malaysia

Teoh SH, Wong GR, Teo WFA, Mazumdar P

Plant Dis, 2023 Aug 03.
PMID: 37537794 DOI: 10.1094/PDIS-06-23-1239-PDN

Brassica rapa var. Chinensis (curly dwarf pak choy) is commonly grown in large-scale vertical farming aquaponic systems. In October 2022, soft rot symptoms and dark brown lesions were observed on B. rapa grown in a commercial aquaponic farm located in Perak, Malaysia. The infected stem appeared brown and water soaked. Severely infected plants produced creamy white ooze on the surface before collapsing entirely (Fig. 1A and B). Infected leaves displayed yellow-brown symptoms and eventually rotted (Fig. 1C); the healthy plants were symptomless (Fig. 1D). About 20 % of the 20,000 B. rapa plants on the farm exhibited symptoms. Ten randomly selected symptomatic plants, five with infected stems and five with infected leaves, were surface sterilized. Each tissue (1.0 cm2) was homogenized and suspended in a saline solution. The suspensions were then serially diluted and plated separately on Luria-Bertani agar. After a 16-h incubation period, stem tissue yielded 12 isolated colonies, while leaf tissue produced 8 colonies. These isolates were subjected to dereplication using RAPD-PCR (Krzewinski et al., 2001), revealing two distinct RAPD patterns. The cultures, named Pathogen Stem 2 (PS2, obtained from the stem) and Pathogen Leaf 2 (PL2, obtained from the leaf), were initially identified as Pectobacterium sp. through 16S rRNA sequence analysis (Frank et al., 2008) on the EzBioCloud 16S database (Yoon et al., 2017). Further identification of the Pectobacterium species was conducted using multilocus sequence analysis (MLSA) of the icdA, mdh, proA, and mltD genes (Ma et al., 2007). The sequences were deposited in GenBank (OQ660180, OQ660181, and OR206482-OR206489). Based on MLSA phylogeny, PS2 and PL2 were identified as Pectobacterium carotovorum and Pectobacterium aroidearum, respectively (Fig. 2A). Anaerobic assays confirmed their facultative anaerobic nature, while Gram staining revealed Gram-negative, rod-shaped morphology consistent with Pectobacterium (Fig. 2B and C). For the re-inoculation study, one-month-old healthy B. rapa plants were used. PS2 was inoculated into petioles, while PL2 was inoculated into leaves separately (3 biological replicates × 3 leaves for each replicate) using the prick inoculation method (Wei et al., 2019). Sterile needles were used to prick the plant tissues, and 10 µL of bacterial suspensions (2.40×109 CFU/mL) in saline were inoculated onto the pricked spots. Negative control using sterile saline was included. The inoculated plants were maintained in a controlled growth chamber (25 ± 1°C, relative humidity 80 ± 5%). After 48 hpi, the petiole tissue inoculated with PS2 showed bacterial soft rot symptoms (Fig. 1F) and leaves inoculated with PL2 appeared dark brown around the wound (Fig. 1G), similar to the symptoms observed in the commercial farm (Fig. 1B, C); while control plants remained asymptomatic (Fig. 1E). Bacteria were re-isolated from the inoculated petiole and leaf tissue and their identities were confirmed by RAPD-PCR. The RAPD profiles of the bacteria reisolated from the petiole and leaf tissues were the same as those of PS2 and PL2 respectively (Fig. 1H). The pathogenicity of PS2 and PL2 was thus confirmed. To our knowledge, this is the first report of bacterial soft rot on B. rapa in aquaponic systems caused by P. carotovorum and P. aroidearum in Malaysia. The identification of these pathogens is crucial for the prevention of disease outbreaks and to develop an effective disease management strategy.
Ectopic expression of a Musa acuminata root hair defective 3 (MaRHD3) in Arabidopsis enhances drought tolerance

Wong GR, Mazumdar P, Lau SE, Harikrishna JA

J Plant Physiol, 2018 Dec;231:219-233.
PMID: 30292098 DOI: 10.1016/j.jplph.2018.09.018

Genetic improvement is an important approach for crop improvement towards yield stability in stress-prone areas. Functional analysis of candidate stress response genes can provide key information to allow the selection and modification of improved crop varieties. In this study, the constitutive expression of a banana cDNA, MaRHD3 in Arabidopsis improved the ability of transgenic lines to adapt to drought conditions. Transgenic Arabidopsis plants expressing MaRHD3 had roots with enhanced branching and more root hairs when challenged with drought stress. The MaRHD3 plants had higher biomass accumulation, higher relative water content, higher chlorophyll content and an increase in activity of reactive oxygen species (ROS) scavenging enzymes; SOD, CAT, GR, POD and APX with reduced water loss rates compared to control plants. The analysis of oxidative damage indicated lower cell membrane damage in transgenic lines compared to control plants. These findings, together with data from higher expression of ABF-3 and higher ABA content of drought-stressed transgenic MaRHD3 expressing plants, support the involvement of the ABA signal pathway and ROS scavenging enzyme systems in MaRHD3 mediated drought tolerance.
Audit of Turnaround Time for a Training Oral Histopathology Laboratory in Malaysia

Chan SW, Liew LH, Wong GR, Kallarakkal TG, Abraham MT, Ramanathan A, et al.

Int. J. Surg. Pathol., 2016 Aug;24(5):401-9.
PMID: 27006298 DOI: 10.1177/1066896916639372

BACKGROUND: Turnaround time (TAT) is the benchmark to assess the performance of a laboratory, pathologists, and pathology services, but there are few articles on TAT of surgical pathology, particularly in relation to oral or head and neck specimens. This study investigates the TAT for oral histopathology reporting in an academic institution's training laboratory and offers recommendations to achieve better overall quality of diagnostic services.

METHODS: This study examined data obtained from biopsy request forms for specimens received from the Oro-Maxillofacial Surgery Department of Hospital Tengku Ampuan Rahimah Klang in the Oral Pathology Diagnostic Laboratory of the Faculty of Dentistry, University of Malaya, over a period of 3 years between January 2012 and October 2014.

RESULTS: TAT for surgical and decalcified specimens were increased significantly compared to biopsies. Additional special handling did not influence TAT, but increased specimen volume resulted in greater TAT. Slide interpretation was the most time-consuming stage during histopathology reporting. Overall, mean TAT was acceptable for most specimens, but the TAT goals were less than satisfactory.

CONCLUSION: A TAT goal appropriate for this laboratory may hence be established based on this study. Collective efforts to improve the TAT for various specimens are essential for better laboratory performance in the future.
Fulltext Transcripts and MicroRNAs Responding to Salt Stress in Musa acuminata Colla (AAA Group) cv. Berangan Roots

Lee WS, Gudimella R, Wong GR, Tammi MT, Khalid N, Harikrishna JA

PLoS One, 2015;10(5):e0127526.
PMID: 25993649 DOI: 10.1371/journal.pone.0127526

Physiological responses to stress are controlled by expression of a large number of genes, many of which are regulated by microRNAs. Since most banana cultivars are salt-sensitive, improved understanding of genetic regulation of salt induced stress responses in banana can support future crop management and improvement in the face of increasing soil salinity related to irrigation and climate change. In this study we focused on determining miRNA and their targets that respond to NaCl exposure and used transcriptome sequencing of RNA and small RNA from control and NaCl-treated banana roots to assemble a cultivar-specific reference transcriptome and identify orthologous and Musa-specific miRNA responding to salinity. We observed that, banana roots responded to salinity stress with changes in expression for a large number of genes (9.5% of 31,390 expressed unigenes) and reduction in levels of many miRNA, including several novel miRNA and banana-specific miRNA-target pairs. Banana roots expressed a unique set of orthologous and Musa-specific miRNAs of which 59 respond to salt stress in a dose-dependent manner. Gene expression patterns of miRNA compared with those of their predicted mRNA targets indicated that a majority of the differentially expressed miRNAs were down-regulated in response to increased salinity, allowing increased expression of targets involved in diverse biological processes including stress signaling, stress defence, transport, cellular homeostasis, metabolism and other stress-related functions. This study may contribute to the understanding of gene regulation and abiotic stress response of roots and the high-throughput sequencing data sets generated may serve as important resources related to salt tolerance traits for functional genomic studies and genetic improvement in banana.
Evaluating the efficacy of OralDETECT training: Face-to-face versus online delivery in dental education

Ramanathan A, Zaini ZM, Ghani WMN, Wong GR, Zainuddin NI, Yang YH, et al.

Oral Dis, 2024 Mar 15.
PMID: 38488212 DOI: 10.1111/odi.14927

OBJECTIVE: This study evaluated the effectiveness of face-to-face (F2F) and online OralDETECT training programme in enhancing early detection skills for oral cancer.
METHODS: A total of 328 final-year dental students were trained across six cohorts. Three cohorts (175 students) received F2F training from the academic years 2016/2017 to 2018/2019, and the remaining three (153 students) underwent online training during the Covid-19 pandemic from 2019/2020 to 2021/2022. Participant scores were analysed using the Wilcoxon signed rank test, the Mann-Whitney test, Cohen's d effect size, and multiple linear regression.
RESULTS: Both F2F and online training showed increases in mean scores from pre-test to post-test 3: from 67.66 ± 11.81 to 92.06 ± 5.27 and 75.89 ± 11.03 to 90.95 ± 5.22, respectively. Comparison between F2F and online methods revealed significant differences in mean scores with large effect sizes at the pre-test stage (p
Fulltext Homeobox Genes in Odontogenic Lesions: A Scoping Review

Hii EPW, Ramanathan A, Pandarathodiyil AK, Wong GR, Sekhar EVS, Binti Talib R, et al.

Head Neck Pathol, 2023 Mar;17(1):218-232.
PMID: 36344906 DOI: 10.1007/s12105-022-01481-2

BACKGROUND: Homeobox genes play crucial roles in tooth morphogenesis and development and thus mutations in homeobox genes cause developmental disorders such as odontogenic lesions. The aim of this scoping review is to identify and compile available data from the literatures on the topic of homeobox gene expression in odontogenic lesions.
METHOD: An electronic search to collate all the information on studies on homeobox gene expression in odontogenic lesions was carried out in four databases (PubMed, EBSCO host, Web of Science and Cochrane Library) with selected keywords. All papers which reported expression of homeobox genes in odontogenic lesions were considered.
RESULTS: A total of eleven (11) papers describing expression of homeobox genes in odontogenic lesions were identified. Methods of studies included next generation sequencing, microarray analysis, RT-PCR, Western blotting, in situ hybridization, and immunohistochemistry. The homeobox reported in odontogenic lesions includes LHX8 and DLX3 in odontoma; PITX2, MSX1, MSX2, DLX, DLX2, DLX3, DLX4, DLX5, DLX6, ISL1, OCT4 and HOX C in ameloblastoma; OCT4 in adenomatoid odontogenic tumour; PITX2 and MSX2 in primordial odontogenic tumour; PAX9 and BARX1 in odontogenic keratocyst; PITX2, ZEB1 and MEIS2 in ameloblastic carcinoma while there is absence of DLX2, DLX3 and MSX2 in clear cell odontogenic carcinoma.
CONCLUSIONS: This paper summarized and reviews the possible link between homeobox gene expression in odontogenic lesions. Based on the current available data, there are insufficient evidence to support any definite role of homeobox gene in odontogenic lesions.
Seropositivity of HPV 16 E6 and E7 and the risk of oral cancer

Wong GR, Ha KO, Himratul-Aznita WH, Yang YH, Wan Mustafa WM, Yuen KM, et al.

Oral Dis, 2014 Nov;20(8):762-7.
PMID: 24320099 DOI: 10.1111/odi.12218

The objective of the study was to determine the prevalence of HPV seropositivity among patients with oral squamous cell carcinoma (OSCC) and healthy individuals and to correlate the association between HPV 16 seropositivity and risk of OSCC.
Effectiveness of "OralDETECT": a Repetitive Test-enhanced, Corrective Feedback Method Competency Assessment Tool for Early Detection of Oral Cancer

Zain RB, Pateel DGS, Ramanathan A, Kallarakkal TG, Wong GR, Yang YH, et al.

J Cancer Educ, 2020 Aug 21.
PMID: 32821988 DOI: 10.1007/s13187-020-01814-1

Early diagnosis of oral cancer results in less aggressive treatment and improves the quality of life and overall 5-year survival rate. Well-trained dental professionals can play a crucial role in the early detection of oral cancers. The present study aims to determine the effectiveness of the training program "OralDETECT", a spaced repetitive, test-enhanced learning tool with a corrective feedback mechanism for early detection of oral cancer. Thirty-two dentists and 259 dental students from three Malaysian dental schools were involved in this study. All participants were trained and calibrated to recognize oral potentially malignant disorders (OPMD) and oral cancer using "OralDETECT", which is comprised of a series of pre-test, lecture, post-tests and review sessions. The percentage of correct answers (scores) for each test given by the participants was calculated and analysed using a paired t test. It was found that the overall percentage of diagnostic accuracy for both dental professionals and student groups increased to above 80% from the pre-tests to the final post-tests. There was a significant improvement in overall scores between the pre-tests and all three post-tests for the dental professional groups and the student groups. The diagnostic accuracy for individual OPMD and lesions suspicious of oral cancer also increased to above 80% for both groups. The results of our study demonstrate that the "OralDETECT" is an efficient and effective competency tool which can be used to train dental professionals and students for the early detection of OPMD and oral cancer.
Association of Interleukin-10 Genotypes and Oral Cancer Susceptibility in Selected Malaysian Population: A Case- Control Study

Goud EVSS, Malleedi S, Ramanathan A, Wong GR, Hwei Ern BT, Yean GY, et al.

Asian Pac J Cancer Prev, 2019 Mar 26;20(3):935-941.
PMID: 30912418

Background: Interleukin-10 (IL10) genotypes have been closely correlated to the susceptibility for oral squamous cell
carcinoma. More than half of oral cancers in the world occur in Asia with estimated 168,850 new cases were diagnosed
in this geographical region alone. Considering the rising numbers of oral cancer cases in Malaysia, association of IL10
A1082G gene polymorphism was correlated. Methodology: 41 oral squamous cell carcinoma (OSCC) cases and 48
healthy controls of comparable age, gender, and with habits like smoking, alcohol consumption and betel quid chewing
were selected. In this case-control study, samples were collected from the Oral Cancer Research and Coordinating
Centre (OCRCC), Faculty of Dentistry, University of Malaya, Malaysia. Genotyping conditions were evaluated by
polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP). The PCR products were subjected
to digestion by MnlI enzyme (NEB, UK) to screen for the IL10 A-1082G. Digested DNA products were analyzed by
electrophoresis on 4% (w/v) agarose gel, stained with ethidium bromide and imaged under UV illumination. Chi-square
test and Fisher’s Exact test were used in statistical analysis. Results: AG genotypes were present in 81.3% and 86.0% of
healthy control and OSCC cases respectively (OR=0.468, 95% CI=0.133-1.653). No significant association was found
between IL10 A1082G polymorphism with risk habits, clinico-pathological parameters and 5-years overall survival.
The findings also show no significant correlation between the IL10 genotype and features of OSCC within the case
group as measured by tumor size, lymph node involvement, stage, invasive front, grading, depth, pattern of invasion.
Conclusion: This study suggests that functional polymorphism AG of IL10 A1082G may have no influence with OSCC
susceptibility. However, further investigation with larger sample sizes can be conducted to provide additional evidence
to support the lack of association of IL10 A1082G polymorphism in oral cancer.