Physiological race characterisation of Fusarium oxysporum strains infecting tomato employing candidate pathogenicity genes and host resistance.

Physiological races of 14 strains of Fusarium oxysporum f.sp. lycopersici were established by PCR profiling SIX gene expressions. No amplification of the SIX4 (Avr1) gene was observed in any of the 14 strains. Based on amplification of the SIX3 (Avr2) gene, 6 strains were distinguished as race 2. Race 2 strains are known to contain identical SIX3 sequences and differ from race 3 strains by single point mutations. Hence, based on polymorphic amplicons of the SIX3 gene detected by stringent PCR conditions, 8 strains were identified as race 3. The identity of the physiological races of the strains was validated by inoculating on three germplasm lines, EC-814916, FEB-2 and Pusa Rohini carrying I-2, I-3 and no I gene, respectively. The race 2 and race 3 strains were avirulent on EC-814916 and FEB-2 lines, respectively. All the 14 fungal strains were pathogenic on Pusa Rohini, the Fusarium wilt susceptible cultivar lacking R genes and exhibited different levels of virulence. In evaluating two other potential pathogenicity genes, Fow1 and Fow2 as markers for virulence, their expressions were observed among both the races of the Fol strains, and hence are not potential candidates for physiological race discrimination. However, strong expressions of the genes in the root tissues inoculated with the highly virulent strain, TOFU-IHBT in comparison to the uninoculated control indicated their roles in fungal pathogenicity. To understand the role of these pathogenicity genes in countering the host defence mechanisms, their expressions in response to ROS and phenolics, the earliest known defence mechanisms of host plants were assessed. In H2O2, the Fow2 gene expressed 1.4-fold greater than that of the control. On the contrary, in relation to the control, the expressions of Fow1 were strongly repressed exhibiting 0.7-to 0.8-fold lesser at 0.1 mM through 3 mM concentrations than that of the control indicating that the gene is modulated by the phenolic acid indicating the roles of Fow2 and Fow1 in alleviating oxidative stress and targeted by the phenolic acid, respectively.

Molecular basis of genetic plasticity to varying environmental conditions on growing rice by dry/direct-sowing and exposure to drought stress: Insights for DSR varietal development.

Rice requires plenty of water for its cultivation by transplanting. This poses several challenges to its cultivation due to erratic rainfall resulting in drought, flood, and other abiotic stresses of varying intensity. Dry/direct-sown rice (DSR) has emerged as a water-saving/climate-smart alternative to transplanted rice (TPR). The performance of a rice cultivar on growing by different methods of planting under varying environmental conditions varies considerably. However, the molecular basis of the observed phenotypic plasticity of rice to varying environmental conditions is still elusive. Resilience to various environmental fluctuations is important to ensure sustainable rice production in the present era of global climate change. Our observations on exclusively up-regulated genes in leaf of Nagina 22 (N 22) grown by dry/direct-sowing and subjected to drought stress at panicle initiation stage (compared to that in leaf of IR 64), and another set of genes exclusively down-regulated in leaf of N 22 (compared to that in leaf of IR 64) indicate important roles of leaf in stress resilience. A large number of genes down-regulated exclusively in root of N 22 on dry/direct-sowing subjected to drought stress indicates a major contribution of roots in stress tolerance. The genes for redox-homeostasis, transcription factors, stress signaling, carbohydrate metabolism, and epigenetic modifications play important roles in making N 22 better adapted to DSR conditions. More importantly, the involvement of genes in rendering genetic plasticity to N 22 under changing environmental conditions was confirmed by reversal of the method of planting. To the best of our knowledge, this is the first report on decoding the molecular basis of genetic plasticity of rice grown by two different methods of planting subjected to drought stress at the reproductive stage of plant growth. This might help in DSR varietal development program to enhance water-productivity, conserve natural resources, and minimize the emission of greenhouse gases, thus achieving the objectives of negative-emission agriculture.

Metabolomic analysis of sheath blight disease of rice (Oryza sativa L.) induced by Rhizoctonia solani phytotoxin.

AIM: To understand the mechanism of necrosis incited by a host-selective phytotoxin designated as Rhizoctonia solani toxin (RST) identified to be a potential pathogenic factor of R. solani AG1 IA, causing sheath blight (ShB) of rice. METHODS AND RESULTS: The metabolomic changes induced by the phytotoxic metabolite in a ShB susceptible rice cultivar were elucidated by gas chromatography-mass spectrometry analysis and compared with that of the pathogen to identify rice metabolites targeted by the phytotoxin. The profiles of about 29 metabolites with various physiological roles in rice plants have been identified worldwide. Unsupervised and supervised multivariate chemometrics (principal component analysis and partial least squares-discriminant analysis) and cluster (Heat maps) analyses were used to compare the metabolites obtained from chemical profiles of the treatments with sterile distilled water (SDW) control. The results indicated that the rice plant expressed more metabolites in response to the pathogen than the phytotoxin and was lowest in SDW control. The key metabolites expressed in rice in response to the treatments were investigated by the variable importance in projection (VIP) analysis using p < 0.05 VIP >15. The analysis identified 7 and 11 upregulating metabolites in the phytotoxin and the pathogen treatments, respectively, compared to the untreated control. Among the phytotoxin-treated and the pathogen inoculated samples, the phytotoxin-treated sample recorded upregulation of six metabolites, whereas nine metabolites were upregulated in the pathogen-inoculated samples. These upregulating metabolites are speculated for the necrotic symptoms characteristic to both the phytotoxin and pathogen. In this analysis, hexadecanoic acid and dotriacontane were highly expressed metabolites specific to the phytotoxin and pathogen-treated samples, respectively. Besides upregulation, the metabolites also have a VIP score of >1.5 and hence fulfilled the criteria of classifying them as reliable potential biomarkers. In the pathway analysis, hexadecanoic acid and dotriacontane were identified to be involved in several important biosynthetic pathways of rice, such as the biosynthesis of saturated fatty acid and unsaturated fatty acids cutin, suberin and wax. CONCLUSIONS: The study concludes that though certain metabolites induced by the phytotoxin in the susceptible variety during necrosis shares with that of the pathogen, the identification of metabolites specific to the phytotoxin in comparison to the pathogenic and SDW controls indicated that the phytotoxin modulates the host metabolism differently and hence can be a potential pathogenicity factor of the ShB fungus. SIGNIFICANCE AND IMPACT OF THE STUDY: Due to lack of knowledge on the pathway genes of RST and in the absence of an ShB-resistant variety, understanding differentially expressed metabolic changes induced in the susceptible variety by the phytotoxin in comparison to that of the pathogenic and uninoculated controls enables us to identify the key metabolite changes during the ShB infection. Such metabolomic changes can further be used to infer gene functions for exploitation in ShB control.

Under or overpressure: an audit of endotracheal cuff pressure monitoring at the tertiary care center.

BACKGROUND: Mechanical ventilation is a lifesaving intervention for critically ill patients but can produce the major complication of ventilator-associated pneumonia (VAP). Inappropriately inflated endotracheal tubes cause potential harm due to high or low pressure; this can be prevented through monitoring protocols. METHODS: A cross-sectional study of 348 cuff pressure readings was performed with intubated and mechanically ventilated patients to evaluate the exact proportion of patients in intensive care units (ICUs) where the cuff pressure is optimal and to identify the ICUs where device-based monitoring is available to produce a lower proportion of sub-optimal cuff pressure cases. Every three days, cuff pressure was assessed with a handheld cuff pressure manometer. The corresponding VAP rates of those ICUs were obtained from the hospital infection control department. RESULTS: Cuff pressure of 40.2% was the lower cutoff for the high category, that of optimal was 35.3%, and the highest cutoff of sub-optimal was 24.4%. This study also showed ICUs that had cuff pressure monitoring devices and protocols. Active measurement protocols had a higher proportion of optimal cuff pressure (58.5%) and a lower proportion of sub-optimal and high cuff pressure (19.5% and 22.0%) compared to ICUs with no device-based monitoring protocols. Furthermore, the VAP rate of ICUs exhibited a weak positive correlation with sub-optimal cuff pressure. CONCLUSIONS: Device-based cuff pressure monitoring is essential in maintaining adequate cuff pressure but often is inadequate, resulting in high readings. Therefore, this study suggests that device-based cuff pressure monitoring be practiced.

LINEZOLID-INDUCED MITOCHONDRIAL TOXICITY PRESENTING AS RETINAL NERVE FIBER LAYER MICROCYSTS AND OPTIC AND PERIPHERAL NEUROPATHY IN A PATIENT WITH CHRONIC GRANULOMATOUS DISEASE.

PURPOSE: To report a case with unique changes in the retinal nerve fiber layer observed on optical coherence tomography in a 22-year-old patient on chronic linezolid therapy for recurrent pyogenic liver abscesses with underlying chronic granulomatous disease. METHODS: History and clinical examination, laboratory evaluation, fluorescein angiography, and optical coherence tomography. RESULTS: The patient presented with best-corrected visual acuity of 20/200 in the right eye and 20/125 in the left eye. He had moderate optic disk edema and superotemporal field defects bilaterally. Swept-source optical coherence tomography revealed the presence of retinal nerve fiber layer microcystic spaces. Laboratory tests showed no positive findings except for an elevated lactic acid level. Linezolid-induced optic neuropathy was suspected, and the drug was discontinued. Six weeks after termination of oral linezolid therapy, the optic disk edema and the microcystic spaces in the retinal nerve fiber layer resolved, and the best-corrected visual acuity improved to 20/50 in the right and 20/40 in the left eye, respectively. CONCLUSION: Linezolid is a widely used antibiotic with broad-spectrum action. However, chronic use can lead to mitochondrial toxicity that may have protean manifestations. Ocular examination, particularly of the optic nerve and nerve fiber layer using multimodal imaging, is critical in diagnosing such toxicity.

Allele-specific analysis of single parent backcross population identifies HOX10 transcription factor as a candidate gene regulating rice root growth.

Understanding the molecular and physiological mechanisms of trait diversity is crucial for crop improvement to achieve drought adaptation. Root traits such as high biomass and/or deep rootedness are undoubtedly important drought adaptive traits. The major aim of this investigation was to functionally characterize a set of ethyl methane sulfonate-induced rice mutants for root traits. We report the identification of a high-root biomass mutant through a novel screening strategy for yield and Δ13 C measurements. The high-root mutant (392-9-1) thus identified, had a 66% higher root biomass compared to wild-type (Nagina-22). Better maintenance of leaf turgor and carbon assimilation rates resulted in lower drought susceptibility index in 392-9-1. Targeted resequencing revealed three non-synonymous single nucleotide variations in 392-9-1 for the genes HOX10, CITRATE SYNTHASE and ZEAXANTHIN EPOXIDASE. Segregation pattern of phenotype and mutant alleles in a single parent backcross F2 population revealed a typical 3:1 segregation for each of the mutant alleles. The number of F2 progeny with root biomass equal to or greater than that of 392-9-1 represented approximately one-third of the population indicating a major role played by HOX10 gene in regulating root growth in rice. Allele-specific Sanger sequencing in contrasting F2 progenies confirmed the co-segregation of HOX10 allele with the root biomass. The non-synonymous mutations in the other two genes did not reveal any specific pattern of co-segregation with root phenotype, indicating a strong role of HOX10, an upstream transcription factor, in regulating root biomass in rice.

Integrated pathway analysis of nasopharyngeal carcinoma implicates the axonemal dynein complex in the Malaysian cohort.

Nasopharyngeal carcinoma (NPC) is an epithelial squamous cell carcinoma on the mucosal lining of the nasopharynx. The etiology of NPC remains elusive despite many reported studies. Most studies employ a single platform approach, neglecting the cumulative influence of both the genome and transcriptome toward NPC development. We aim to employ an integrated pathway approach to identify dysregulated pathways linked to NPC. Our approach combines imputation NPC GWAS data from a Malaysian cohort as well as published expression data GSE12452 from both NPC and non-NPC nasopharynx tissues. Pathway association for GWAS data was performed using MAGENTA while for expression data, GSA-SNP was used with gene p values derived from differential expression values from GEO2R. Our study identified NPC association in the gene ontology (GO) axonemal dynein complex pathway (pGWAS-GSEA = 1.98 × 10(-2) ; pExpr-GSEA = 1.27 × 10(-24) ; pBonf-Combined = 4.15 × 10(-21) ). This association was replicated in a separate cohort using gene expression data from NPC and non-NPC nasopharynx tissues (pAmpliSeq-GSEA = 6.56 × 10(-4) ). Loss of function in the axonemal dynein complex causes impaired cilia function, leading to poor mucociliary clearance and subsequently upper or lower respiratory tract infection, the former of which includes the nasopharynx. Our approach illustrates the potential use of integrated pathway analysis in detecting gene sets involved in the development of NPC in the Malaysian cohort.

Inclusion bodies of recombinant Epstein-Barr virus capsid antigen p18 as potential immobilized antigens in enzyme immunoassays for detection of nasopharyngeal carcinoma.

BACKGROUND: Development of indirect enzyme-linked immunosorbent assays (ELISAs) often utilizes synthetic peptides or recombinant proteins from Escherichia coli as immobilized antigens. Because inclusion bodies (IBs) formed during recombinant protein expression in E. coli are commonly thought as misfolded aggregates, only refolded proteins from IBs are used to develop new or in-house diagnostic assays. However, the promising utilities of IBs as nanomaterials and immobilized enzymes as shown in recent studies have led us to explore the potential use of IBs of recombinant Epstein-Barr virus viral capsid antigen p18 (VCA p18) as immobilized antigens in ELISAs for serologic detection of nasopharyngeal carcinoma (NPC). METHODS: Thioredoxin fusion VCA p18 (VCA-Trx) and IBs of VCA p18 without fusion tags (VCA-IBs) were purified from E. coli. The diagnostic performances of IgG/VCA-IBs, IgG/VCA-Denat-IBs (using VCA-IBs coated in 8mol/l urea), IgG/VCA-Trx, and IgG/VCA-Peptide assays were compared by screening 100 NPC case-control pairs. RESULTS: The IgG/VCA-Denat-IBs assay showed the best area under the receiver operating characteristic curve (AUC: 0.802; p<0.05), while the AUCs for the IgG/VCA-IBs, IgG/VCA-Trx, and IgG/VCA-Peptide assays were comparable (AUC: 0.740, 0.727, and 0.741, respectively). CONCLUSION: We improved the diagnostic performance of the ELISA significantly using IBs of recombinant VCA p18.

HLA-A SNPs and amino acid variants are associated with nasopharyngeal carcinoma in Malaysian Chinese.

Nasopharyngeal carcinoma (NPC) arises from the mucosal epithelium of the nasopharynx and is constantly associated with Epstein-Barr virus type 1 (EBV-1) infection. We carried out a genome-wide association study (GWAS) of 575,247 autosomal SNPs in 184 NPC patients and 236 healthy controls of Malaysian Chinese ethnicity. Potential association signals were replicated in a separate cohort of 260 NPC patients and 245 healthy controls. We confirmed the association of HLA-A to NPC with the strongest signal detected in rs3869062 (p = 1.73 × 10(-9)). HLA-A fine mapping revealed associations in the amino acid variants as well as its corresponding SNPs in the antigen peptide binding groove (p(HLA-A-aa-site-99) = 3.79 × 10(-8), p(rs1136697) = 3.79 × 10(-8)) and T-cell receptor binding site (p(HLA-A-aa-site-145) = 1.41 × 10(-4), p(rs1059520) = 1.41 × 10(-4)) of the HLA-A. We also detected strong association signals in the 5'-UTR region with predicted active promoter states (p(rs41545520) = 7.91 × 10(-8)). SNP rs41545520 is a potential binding site for repressor ATF3, with increased binding affinity for rs41545520-G correlated with reduced HLA-A expression. Multivariate logistic regression diminished the effects of HLA-A amino acid variants and SNPs, indicating a correlation with the effects of HLA-A*11:01, and to a lesser extent HLA-A*02:07. We report the strong genetic influence of HLA-A on NPC susceptibility in the Malaysian Chinese.

Recombinant production of Epstein-Barr virus BZLF1 trans-activator and characterization of its DNA-binding specificity.

This paper describes the recombinant production of a biologically active Epstein-Barr virus BZLF1 trans-activator, i.e., Z-encoded broadly reactive activator (ZEBRA), that recognized specific DNA motifs. We used auto-induction for histidine-tagged BZLF1 expression in Escherichia coli and immobilized cobalt affinity membrane chromatography for protein purification under native conditions. We obtained the purified BZLF1 at a yield of 5.4mg per gram of wet weight cells at 75% purity, in which 27% of the recombinant BZLF1 remained biologically active. The recombinant BZLF1 bound to oligonucleotides containing ZEBRA response elements, either AP-1 or ZIIIB, but not a ZIIIB mutant. The recombinant BZLF1 showed a specific DNA-binding activity which could be useful for functional studies.

On optimizing the blocking step of indirect enzyme-linked immunosorbent assay for Epstein-Barr virus serology.

BACKGROUND: Because blocking agent occupies most binding surface of a solid phase, its ability to prevent nonspecific binding determines the signal-to-noise ratio (SNR) and reliability of an enzyme-linked immunosorbent assay (ELISA). METHODS: We demonstrate a stepwise approach to seek a compatible blocking buffer for indirect ELISA, via a case-control study (n=176) of Epstein-Barr virus (EBV)-associated nasopharyngeal carcinoma (NPC). RESULTS: Regardless of case-control status, we found that synthetic polymer blocking agents, mainly Ficoll and poly(vinyl alcohol) (PVA) were able to provide homogeneous backgrounds among samples, as opposed to commonly used blocking agents, notably nonfat dry milk (NFDM). The SNRs for NPC samples that correspond to blocking using PVA were approximately 3-fold, on average, higher than those blocking using NFDM. Both intra- and inter-assay precisions of PVA-based assays were <14%. CONCLUSION: A blocking agent of choice should have tolerable sample backgrounds from both cases and controls to ensure the reliability of an immunoassay.

Clinical significance of plasma Epstein-Barr Virus DNA loads in a large cohort of Malaysian patients with nasopharyngeal carcinoma.

BACKGROUND: Nasopharyngeal carcinoma (NPC) is an Epstein-Barr Virus (EBV)-associated cancer that is the fifth most common cancer in Malaysia. Early and accurate diagnoses are critical for patient prognosis. Unfortunately, early detection of NPC is still a challenge and the cost of more accurate imaging protocols is prohibitive in developing countries like Malaysia. OBJECTIVES: To evaluate the clinical values of pre-treatment plasma EBV DNA levels in Malaysian NPC patients. STUDY DESIGN: Plasma EBV DNA levels were measured by quantitative PCR (Q-PCR) in a large and multi-ethnic cohort of Malaysian patients with NPC (n=459) and 72 control subjects. RESULTS: We show for the first time that, compared to controls, NPC patients with stage I disease had significantly higher levels of EBV DNA (p<0.001). Further, the median level of plasma EBV DNA in stage IV patients with distant metastasis was >9-fold higher than those without systemic spread (p=0.001), suggesting plasma EBV DNA measurement could aid in the diagnosis of metastatic disease in advanced cases. Further, using a cut-off value of 8000 copies/mL, we demonstrate that EBV DNA level is a strong predictor for overall survival of NPC patients. CONCLUSIONS: Our data show that pre-treatment plasma EBV DNA is a potential biomarker for early stage and metastatic NPC. We conclude that the quantification of plasma EBV DNA is a useful tool in developing countries to stratify patients for MRI or PET/CT scans where such imaging protocol is not routinely applied.

Phase II trial of capecitabine plus cisplatin as first-line therapy in patients with metastatic nasopharyngeal cancer.

BACKGROUND: Capecitabine is an oral fluoropyrimidine with single-agent activity in metastatic nasopharyngeal carcinoma (NPC). This multicenter phase II study was conducted to investigate the efficacy and safety of capecitabine plus cisplatin as a first-line treatment for metastatic NPC. METHODS: Patients with metastatic NPC received cisplatin 100 mg/m(2) day 1 plus capecitabine 1000 mg/m(2) twice daily on days 1 to 14 every 3 weeks for 6-8 cycles. The primary endpoint was overall response rate. RESULTS: Forty-four patients were enrolled; 39 patients were evaluable for efficacy. The overall response rate was 53.8% (95% confidence interval [CI], 37%-70%), including 1 complete response. Median time to tumor progression was 7.3 months (95% CI, 5.6-9.9 months) and median overall survival was 28.0 months (95% CI, 14.5 months-not reached). Common grade 3/4 adverse events were neutropenia (50%), vomiting (11%), thrombocytopenia (9%), and nausea (7%). CONCLUSIONS: Capecitabine plus cisplatin is an active first-line combination in metastatic NPC that requires a short hospital stay.

A genome-wide association study identifies ITGA9 conferring risk of nasopharyngeal carcinoma.

To identify a gene(s) susceptible to nasopharyngeal carcinoma (NPC), we carried out a genome-wide association study (GWAS) through genotyping of more than 500,000 tag single-nucleotide polymorphisms (SNPs), using an initial sample set of 111 unrelated NPC patients and 260 controls of a Malaysian Chinese population. We further evaluated the top 200 SNPs showing the smallest P-values, using a replication sample set that consisted of 168 cases and 252 controls. The combined analysis of the two sets of samples found an SNP in intron 3 of the ITGA9 (integrin-alpha 9) gene, rs2212020, to be strongly associated with NPC (P=8.27 x 10(-7), odds ratio (OR)=2.24, 95% confidence intervals (CI)=1.59-3.15). The gene is located at 3p21 which is commonly deleted in NPC cells. We subsequently genotyped additional 19 tag SNPs within a 40-kb linkage disequilibrium (LD) block surrounding this landmark SNP. Among them, SNP rs189897 showed the strongest association with a P-value of 6.85 x 10(-8) (OR=3.18, 95% CI=1.94-5.21), suggesting that a genetic variation(s) in ITGA9 may influence susceptibility to NPC in the Malaysian Chinese population.

Silent sinus syndrome due to a maxillary mucocele.

Silent sinus syndrome is a rare clinical condition in which patients present with spontaneous enophthalmos and hypoglobus secondary to collapse of orbital floor due to chronic subclinical maxillary sinusitis. It is postulated that obstruction of the osteomeatal complex lead to negative antrum pressure which causes the maxillary sinus atelectasis.

Endoscopic coagulation of sphenopalatine artery for posterior epistaxis.

OBJECTIVE: To present our experience of endoscopic electrocoagulation of sphenopalatine artery for persistent posterior epistaxis despite conservative measures. METHODS: Seven endoscopic electrocoagulation of sphenopalatine artery was done for four patients from early 2001 till the present for recalcitrant epistaxis despite conservative treatment. The basic principle of this surgical method is to identify the sphenopalatine artery via endonasal endoscopy and to electrocoagulate the vessel. RESULTS: Seven procedures were carried out in four patients. Endoscopic coagulation of sphenopalatine artery was carried out unilaterally in one patient and bilaterally in three patients. The artery was identified in all cases with successful postoperative results. CONCLUSION: This method is an effective surgical technique for persistent posterior epistaxis with low morbidity.

Nasopharyngeal carcinoma and nasal allergy: any correlation?

Although it has been observed that nasal allergy is rarely seen in patients who have nasopharyngeal carcinoma, to our knowledge, no actual study of such a lack of association has been previously reported. To fill this void, we conducted a pilot study to investigate any such inverse relationship. We conducted skin-prick allergen tests on 22 patients with newly diagnosed but not-yet-treated nasopharyngeal carcinoma. Combining these test results with findings on the history and clinical examination, we concluded that only one of the 22 cancer patients (4.5%) had allergic rhinitis. Our study also confirmed the validity of using findings on the history, clinical examination, and skin-prick testing as a reliable means of diagnosing allergic rhinitis.

Papillary cystic type of acinic cell carcinoma of parotid: fine needle aspiration cytological features of a high grade variant with oncocytic metaplasia.

A 60-year-old female developed a right parotid swelling six months after surgery for intra-oral squamous cell carcinoma. Fine needle aspiration (FNA) cytological smears showed dissociated large and small pleomorphic tumour cells with abundant mitoses and oncocytic features. A cytological diagnosis of parotid acinic cell carcinoma (ACC) was made. Histological study of the subtotal parotidectomy specimen showed a papillary cystic variety of acinic cell carcinoma (ACC-PCV). FNA cytological features in this case of ACC-PCV differs from the two previously reported cases in that it showed prominent oncocytic and high grade features and absence of papillary pattern in the cytological smears. ACC-PCV is an uncommon tumour and knowledge of its varied FNA cytological features is important for the diagnosis of this neoplasm.