Analysis of Coconut cadang-cadang viroid variants on field samples exhibiting variation in orange spotting symptom expression and severity

BACKGROUND

Sequence variation has been attributed to symptom variations but has not been investigated in Orange Spotting-Coconut cadang-cadang viroid (OS-CCCVd) infected palms. Likewise, the relationship between Coconut cadang-cadang viroid (CCCVd) variants, Orange Spotting (OS) severity and the accumulation of the viroid in the palms have not been elucidated. This paper describes the characterization of CCCVd variants by cloning and sequencing, followed by correlation with symptom expression.

METHODS AND RESULTS

Total nucleic acids were extracted from leaf samples harvested from frond 20 of seven Dura × Pisifera (D × P) African oil palm (Elaeis guineensis Jacq.) aged between 13 and 21 years old collected from local plantations. The nucleic acids were fractionated using 5% non-denaturing polyacrylamide gel electrophoresis (PAGE) before being subjected to detection by reverse transcribed polymerase chain reaction (RT-PCR). The PCR products were cloned into a plasmid vector and the sequence of the clones was analyzed. CCCVd variants were quantified using real-time qPCR assay with CCCVd specific primers. Sixteen randomly selected clones of (OP246) had an arbitrary 100% identity with CCCVdOP246 (GeneBank Accession No: HQ608513). Meanwhile, four clones had >93% similarity with several minor sequence variations forming variants of OP234, OP235, OP251 and OP279.

CONCLUSION

The OS symptoms observed in the field were characterized into three categories based on the size and morphology of the orange spots on the affected fronds. In addition, there was no direct correlation between disease severity and the accumulation of CCCVd variants in oil palm. This finding is the first report describing the sequence variation of the CCCVd RNA and symptom variation in OS oil palm field samples.

Genomics and Transcriptomics Reveal Genetic Contribution to Population Diversity and Specific Traits in Coconut

Coconut is an economically important palm species with a long history of human use. It has applications in various food, nutraceuticals, and cosmetic products, and there has been renewed interest in coconut in recent years due to its unique nutritional and medicinal properties. Unfortunately, the sustainable growth of the coconut industry has been hampered due to a shortage of good quality seedlings. Genetic improvement through the traditional breeding approach faced considerable obstacles due to its perennial nature, protracted juvenile period, and high heterozygosity. Molecular biotechnological tools, including molecular markers and next-generation sequencing (NGS), could expedite genetic improvement efforts in coconut. Researchers have employed various molecular markers to reveal genetic diversity among coconut populations and for the construction of a genetic map for exploitation in coconut breeding programs worldwide. Whole genome sequencing and transcriptomics on the different varieties have generated a massive amount of publicly accessible sequence data, substantially improving the ability to analyze and understand molecular mechanisms affecting crop performance. The production of high-yielding and disease-resilient coconuts and the deciphering of the complex coconut genome's structure can profit tremendously from these technologies. This paper aims to provide a comprehensive review of the progress of coconut research, using genomics, transcriptomics, and molecular markers initiatives.

Alterations in Mycelial Morphology and Flow Cytometry Assessment of Membrane Integrity of Ganoderma boninense Stressed by Phenolic Compounds

Global increase in demand for palm oil has caused an intensification in oil palm plantation; however, production is greatly hindered by Basal Stem Rot (BSR) disease caused by Ganoderma boninense. There are many approaches to controlling BSR, although, there is no accurate, sustainable and effective method to suppress G. boninense completely. Hence, four phenolic compounds [Gallic acid (GA), Thymol (THY), Propolis (PRO) and Carvacrol (CARV)] were selected to evaluate their antifungal effect, ability to alter the mycelium morphology, and fungal cell integrity against G. boninense. Significant differences (p < 0.05) were observed and 94% of inhibition was exerted by GA on G. boninense growth. Scanning Electron Microscopy and High-Resolution Transmission Electron Microscopy observations revealed that GA and THY treatment caused severe damage to the mycelium and recorded the highest amount of sugar and electrolyte leakage. The study of cell integrity and morphological disruption has elucidated the reduction of G. boninense cell viability. Generally, our findings confirm the fungistatic effects of GA and THY. The evolution of phenolic compounds during the phytopathology studies indicated their coherence in eradicating the G. boninense. It is proposed that GA and THY had the potential to be developed further as a natural antifungal treatment to suppress G. boninense.

Helicobacter pylori infection is unlikely to be transmitted between partners: evidence from genotypic study in partners of infected patients

INTRODUCTION

We postulated that the oro-oral route of transmission between spouses could be an important route of transmission of Helicobacter pylori.

AIMS

To estimate the prevalence of different genotypes of H. pylori as distinguished by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method in our local population, and to compare the genotypes of H. pylori isolated from patients and their spouses.

METHODS

Gastric biopsies were obtained from 183 dyspeptic patients during endoscopy. PCR for H. pylori was carried out using the uceC gene for amplification, and PCR products were digested further for RFLP analysis using the enzyme MboI. Spouses of H. pylori-positive index cases were screened for the infection using serological testing; if found to be positive serologically, endoscopy and gastric biopsies were performed for genotypic study of the micro-organism. For couples with indistinguishable H. pylori strain on RFLP with restriction endonuclease MboI, the process of RFLP was repeated with digestion of the PCR products using restriction endonuclease HhaI.

RESULTS

We established our PCR technique to be 89.5% sensitive and 95.5% specific. Eighty-nine subjects were found to be H. pylori positive by PCR, and eight different genotypic strains were found according to our RFLP analysis. Two genotypes accounted for 80.8% of the cases. Sixteen of 31 spouses tested serologically for H. pylori were positive. All 13 spouses who agreed to undergo endoscopy were PCR positive for H. pylori. Five couples shared indistinguishable H. pylori genotypes, but this strain was also the commonest genotype in our local population, as based on RFLP with restriction endonuclease MboI. Further RFLP on the PCR products on these five couples using restriction endonucleases HhaI showed that the H. pylori isolated from these five couples were of different strains.

CONCLUSION

The oro-oral route of transmission between spouses is unlikely to be an important mode for H. pylori infection.

Efficacy of a nitroimidazole containing tripletherapy regime in Singapore

BACKGROUND

There has been a gradual increase in the proportion of Singapore patients with metronidazole resistant strains of Helicobacter pylori. We studied the efficacy of a nitroimidazole containing regime in eradicating H. pylori.

METHODS

Consecutive treatment naive patients with peptic ulcer disease and culture proven H. pylori were recruited. From each patient, two antral biopsies were taken for rapid urease test and two for histology. Two biopsies each from the gastric antrum and corpus were taken for H. pylori culture. Antibiotic sensitivity to amoxycillin, metronidazole, clarithromycin and tetracycline were tested using the disc diffusion method. Patients were treated with lansoprazole 30 mg bd, tinidazole 500 mg bd and clarithromycin 500 mg bd for seven days. Successful eradication was defined as either negative urea breath tests 4 and 12 weeks after treatment, or negative histology and culture at least four weeks after the end of treatment.

RESULTS

A total of 64 patients were culture positive (51 males, 13 females). Forty-two patients had duodenal ulcers (DU), 17 gastric ulcers (GU), and 5 DU and GU. Metronidazole resistance was detected in 16 patients (25%). Three of the 16 patients (19%) had a mixed population of resistant and sensitive strains of H. pylori. None of the H. pylori isolates were resistant to amoxycillin, tetracycline or clarithromycin. Overall, eradication was achieved in 51/64 patients (80%). Eradication rate was 88% (42/48) among those with metronidazole sensitive strains, and 56% (9/16) among those with metronidazole resistant strains (p < 0.02).

CONCLUSION

A high proportion of our patients with metronidazole resistant strains of H. pylori failed eradication therapy when a nitroimidazole containing regime was used. It may not be appropriate to use a nitroimidazole containing without prior knowledge of the antibiotic sensitivity pattern of the H. pylori isolate.

Lipid hydroperoxide and markers of renal disease susceptibility in African-Caribbean and Caucasian patients with Type 2 diabetes mellitus

AIMS

The reasons for the increased incidence of diabetic nephropathy in African-Caribbean compared with Caucasian subjects are poorly understood. Increased oxidative stress is linked to the development of endothelial dysfunction and histological abnormalities associated with diabetic renal disease. Therefore, it was assessed whether a marker of oxidative stress, lipid hydroperoxide (LOOH) and endothelial damage, von Willebrand factor (vWF) varied according to ethnic origin in the presence or absence of early diabetic nephropathy.

METHODS

Eighty-eight patients with Type 2 diabetes mellitus of African-Caribbean or Caucasian origin without a history of cardiovascular disease or clinical proteinuria were studied. Patients were classified as having microalbuminuria or normal albumin excretion. Fasting plasma vWF and LOOH were measured by an inhouse enzyme-linked immunoassay and ferrous oxidation with xylenol orange (FOX) assay, respectively. The relationship of LOOH to urinary albumin status, the metabolic disturbances of diabetes, blood pressure and ethnic origin were assessed using multivariate analysis.

RESULTS

Compared with Caucasian patients those of African-Caribbean origin had higher systolic blood pressure and HDL-cholesterol (157.8 +/- 17.0 vs. 147.8 +/- 24.4, P = 0.041 and 1.6 +/- 0.4 vs. 1.3 +/- 0.5, P = 0.018) but lower total triglycerides (1.3 +/- 0.8 vs. 1.9 +/- 1.1, P = 0.008). LOOH was significantly higher in the African-Caribbean patients compared with Caucasians (5.98 +/- 2.49 vs. 4.49 +/- 2.19, P = 0.006). vWF tended to be higher in microalbuminuric patients but showed no variation with ethnicity. In logistic regression analysis, LOOH was the only independent predictor of a raised albumin excretion rate (P = 0.008). In multiple regression analysis, African-Caribbean ethnicity (P = 0.020) HDL-cholesterol (P = 0.036), total triglycerides (P = 0.002) and a raised albumin excretion rate (P = 0.002) were independent predictors of LOOH.

CONCLUSIONS

In this group of Type 2 diabetic patients an increase in LOOH is associated with abnormal urinary albumin excretion. African-Caribbean origin was a determinant of LOOH independently of microalbuminuria. It is postulated that increased oxidative stress is of pathophysiological significance in accelerating the development of renal disease in African-Caribbean patients.

Isolation of a single strain of Helicobacter pylori from the antrum and body of individual patients

OBJECTIVES

This study aimed to determine intra-patient colonization patterns of Helicobacter pylori strains based on DNA fingerprinting and antibiotic susceptibility.

METHODS

Two biopsies, one from the antrum and one from the body of the stomach, were taken from 97 patients. Prior informed consent was obtained. The status of cagA gene of H. pylori strains was analysed by using the polymerase chain reaction (PCR) technique, while DNA fingerprints were generated by PCR-based, random amplified polymorphic DNA (RAPD) fingerprinting. The antibiotic susceptibility of the H. pylori isolates was examined by the disk diffusion method.

RESULTS

A total of 51 pairs of H. pylori strains were isolated from both antrum and body specimens of 51 patients. This included two patients who were endoscoped twice because of treatment failure. All strains were positive for cagA gene by PCR. These 51 patients were found to harbour a single strain of H. pylori with identical or highly similar DNA profiles by PCR-based RAPD fingerprinting. In four of the 51 pairs, the DNA patterns of H. pylori from antrum and body showed minor differences, while three pairs of strains with different metronidazole sensitivities showed identical DNA fingerprints. Interestingly, the two treatment failure patients remained colonized with the strains that had the same RAPD fingerprinting patterns before and after treatment.

CONCLUSION

The present study demonstrates that a single H. pylori strain colonizes a single stomach. However, this single genotypic strain may exhibit different metronidazole susceptibility in different parts of stomach.

One week triple therapy for Helicobacter pylori associated duodenal ulcer disease

INTRODUCTION

Eradication of Helicobacter pylori (H. pylori) cures and prevents the relapse of duodenal ulceration. Different treatment regimes for the eradication of H. pylori have been used and the most successful eradication regimens have been one week treatments with a proton pump inhibitor and two antibiotics.

AIM OF STUDY

To examine the eradication rate of H. pylori with a one week regimen consisting of OCT (Omeprazole 20 mg BD, Clarithromycin 250 mg BD, Tinidazole 500 mg BD). This treatment regimen has been used for H. pylori eradication in our department since the end of 1996.

METHODS

Patients diagnosed to have duodenal ulcer in 1997 were retrospectively reviewed. Infection with H. pylori must be documented either by gastric biopsy or by a positive CLO test. Eradication of H. pylori was confirmed by negative 14C urea breath test or by histology at least four weeks after cessation of therapy.

RESULTS

The review was performed on 251 patients. There were 177 males, 74 females. The median age was 51 (18-77) years. H. pylori infection was confirmed by CLO test in 170 patients and by histology in 72 patients. Thirty patients did not undergo further investigation after therapy to confirm the eradication. Of the remaining 221 patients, H. pylori was successfully eradicated in 198 patients (89.6%) as confirmed by 14C urea breath test (190 patients) or repeat gastroscopy and gastric biopsy (31 patients). There were no serious adverse events documented.

CONCLUSIONS

Our retrospective study showed that the one week regimen used in our department is effective for the eradication of H. pylon in nearly 90% of infected cases.

Statistical modelling reveals demography and time are the main contributing factors in global sperm count changes between 1938 and 1996

Declining sperm count reports have caused enormous concern to both the scientific community and to society. We reproduced the linear regression analysis and the quadratic model analysis using the 50 year sperm count data published in Carlsen's report and found that neither model adequately described the data. The reported decline in sperm count could be due to observational bias and overinterpretation of linear regression. In fact only 36% of the total variability in sperm count was explained by the linear model and 42% by the quadratic model. The linear model was no longer valid when three new European reports on sperm counts were included in the analysis. The quadratic model, however, suggested an upward trend of sperm count after 1975 (R2 = 0.48, P < 0.0001). Factors other than the 'passage of time' may have contributed to the initial decline of sperm count. An immediate candidate was demography. Our analysis showed that sperm counts in USA were significantly higher in 1938-1956 compared with those in 1957-1974 and 1975-1988, but not in the European or Asian/African/South American countries. The variability of the USA sperm count (1938-1988) explained by the linear and quadratic models was found to be 71 and 70% respectively. The quadratic model importantly indicated that the sperm count in USA decreases asymptotically towards a limiting value and global sperm counts could be increasing since 1970. The non-uniform nature of the global sperm count change suggested that local variations in pollution, diet but not global warming were important determinants of reproductive health.

Low-density lipoprotein is the major carrier of lipid hydroperoxides in plasma. Relevance to determination of total plasma lipid hydroperoxide concentrations

High-density lipoprotein (HDL) has been proposed as the principal carrier of hydroperoxides in plasma, based upon data gathered with an HPLC-chemiluminescence technique. To test this hypothesis we have measured total lipid hydroperoxides in native plasma using the ferrous oxidation in Xylenol Orange (FOX) assay and then fractionated plasma into very-low-density lipoprotein (LDL) and HDL fractions. Hydroperoxides were found to accumulate principally (more than 65%) in LDL, as judged by hydroperoxide content per amount of protein or cholesterol, or expressed as a proportion of total hydroperoxide in plasma. Plasma was also incubated at 37 degrees C in the presence and absence of 2,2'-azo-bis-(2-amidinopropane) hydrochloride (AAPH), an azo-initiator of lipid peroxidation. The majority of hydroperoxides generated in plasma were recovered in the LDL fraction. Furthermore, when isolated lipoproteins were subject to oxidation initiated by AAPH, very-low-density lipoprotein and LDL showed the greatest propensity for hydroperoxide accumulation, whereas HDL seemed relatively resistant. Estimates for plasma and LDL peroxidation based upon techniques which measure total lipid hydroperoxides suggest that levels of hydroperoxides in plasma and LDL are far higher than that those estimates generated by ostensibly more selective techniques. Higher levels of hydroperoxides in LDL than those reported by HPLC-chemiluminescence also seem in greater accordance with other available data concerning LDL oxidation.

Fasting and postprandial determinants for the occurrence of small dense LDL species in non-insulin-dependent diabetic patients with and without hypertriglyceridaemia: the involvement of insulin, insulin precursor species and insulin resistance

We have studied low density lipoprotein (LDL) subclass distribution in a group of male patients with non-insulin-dependent diabetes mellitus (NIDDM) and investigated its relationships to fasting and postprandial triglyceride (TG)-rich lipoproteins, insulin resistance, lipoprotein lipase (EC 3.1.1.3; LPL), hepatic lipase (EC 3.1.1.34; HL), lecithin:cholesterol acyl transferase (EC 2.3.1.43; LCAT) and cholesteryl ester transfer protein (CETP) activities. LDL was subfractionated by density gradient ultracentrifugation. Postprandial lipoproteins were measured after an oral fat load using retinyl palmitate as a marker for intestinal TG-rich lipoproteins. Hypertriglyceridaemic NIDDMs (HTG) had a preponderance of small dense LDL particles present in the plasma and reduced amounts of large buoyant species when compared to normotriglyceridaemic patients (NTG) and controls. Both groups of diabetics were more insulin resistant than the controls (P < 0.05) and had raised concentrations of proinsulin (P < 0.05), although insulin content did not differ significantly. 32-33 split proinsulin (SPI) was the major insulin-like molecule present in HTG and was present in significantly higher amounts in these patients (P < 0.05) than either NTG or control subjects and correlated significantly with the presence of small dense LDL particles. After a test meal, the postprandial chylomicron response was greater in HTG than either NTG diabetics or controls (P < 0.05). Chylomicron remnants were present to a greater extent in HTG than in NTG and controls (P < 0.05), although in this case NTG also contained more chylomicron remnants than control subjects (P < 0.05). There was no difference in the LPL activity, CETP and LCAT between diabetics and controls, whereas an increase in hepatic lipase activity was seen in the HTG diabetics (P < 0.05). Both CETP and LCAT activities increased postprandially. Multivariate analysis showed that TG, HDL content and HL activity were the most important determinants of small dense LDL concentration in the fasting state (R2 = 67%). Postprandially, chylomicron remnant clearance, HL and insulin resistance were the major determinants (R2 = 61%) of LDL-III.

Combination treatment with cholestyramine and bezafibrate for heterozygous familial hypercholesterolaemia

Cholestyramine and bezafibrate were compared individually and in combination in the treatment of 18 patients with heterozygous familial hypercholesterolaemia. The study used a double blind, placebo controlled block design with a placebo run in period of two months followed by three phases of active treatment, each of two months' duration. Patients were randomly allocated to one of the six possible sequences of medication so that three patients would be treated with each sequence. Two patients withdrew from the study before completion. The median concentration of total cholesterol decreased from 9.65 mmol/l (interquartile range 8.62 to 8.72) to 7.24 mmol/l (6.70 to 7.52) with cholestyramine, to 8.09 mmol/l (7.18 to 8.68) with bezafibrate, and to 6.31 mmol/l (5.84 to 7.27) with the combination. This fall was due almost entirely to a decrease in the low density lipoprotein cholesterol concentration, and the combination was significantly more effective than either drug alone. The 98% confidence intervals for the median differences between the combination and cholestyramine and the combination and bezafibrate were 0.04 to 1.49 mmol/l and 0.51 to 2.18 mmol/l respectively. These results suggest that this combination is an effective and useful treatment in heterozygous familial hypercholesterolaemia.

Analysis of antimicrobial susceptibility results using microcomputers

A computer program has been developed on an IBM-PC-compatible microcomputer to analyze antimicrobial susceptibility results of large numbers of organisms tested against a variety of antimicrobial agents. For each species, the output includes the numbers, percentages, cumulative numbers, and cumulative percentages of organisms inhibited at different concentrations of each drug, the MICs for 50 and 90% of organisms tested, MIC ranges, and geometric mean MICs. The distributions of MICs are also plotted as histograms. The program was written in dBASE III command language, but a compiled version allows rapid program execution independently of the dBASE III package.

Mucosal surface pH of the large intestine of the rat and of normal and inflamed large intestine in man

The surface pH of rat distal colonic mucosa and human rectal mucosa was measured in vitro using first a small pH electrode with a flattened tip. In buffer with pH 7.56 the mean rat colonic surface pH was 6.72. Lowering the buffer pH in steps resulted in a small fall in surface pH, the values being buffer pH 7.06 surface pH 6.64, buffer pH 6.58 surface pH 6.61 and finally buffer pH 6.09 surface pH 6.39. Similar results were obtained with a buffer where butyrate, 30 mmol/l replaced chloride and when a CO2/bicarbonate buffer was used. During the time taken for the study transmural potential difference only changed by 1-2 mV. Serosal surface pH changed with buffer pH, suggesting that the maintained surface pH is a property of the mucosal surface only. The surface pH of human rectal mucosa was similar to that of rat distal colonic mucosa. As buffer pH fell from pH 7.51 to 5.96 mucosal surface pH only fell from pH 6.80 to 6.26. The values obtained in ulcerative proctitis did not differ from normal mucosa. Secondly pH microelectrodes were used to measure the juxta mucosal pH and the pH-microclimate thickness when luminal pH was controlled. The microclimate had a pH 6.63 adjacent to the mucosa with a thickness of 840 micron. The importance of mucus in maintaining the microclimate was shown by n-acetyl cysteine thinning and prostaglandin E2 thickening the layer. These results describe a surface microclimate in the large intestine of appreciable thickness and a constant juxta mucosal pH. Luminal pH changes produce only a small change in microclimate pH.