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Genomic, metabolomic, and functional characterisation of beneficial properties of Pediococcus pentosaceus ST58, isolated from human oral cavity

Favaro L, Campanaro S, Fugaban JII, Treu L, Jung ES, d'Ovidio L, et al.

Benef Microbes, 2023 Mar 14;14(1):57-72.
PMID: 36815495 DOI: 10.3920/BM2022.0067

Bacteriocins produced by lactic acid bacteria are proteinaceous antibacterial metabolites that normally exhibit bactericidal or bacteriostatic activity against genetically closely related bacteria. In this work, the bacteriocinogenic potential of Pediococcus pentosaceus strain ST58, isolated from oral cavity of a healthy volunteer was evaluated. To better understand the biological role of this strain, its technological and safety traits were deeply investigated through a combined approach considering physiological, metabolomic and genomic properties. Three out of 14 colonies generating inhibition zones were confirmed to be bacteriocin producers and, according to repPCR and RAPD-PCR, differentiation assays, and 16S rRNA sequencing it was confirmed to be replicates of the same strain, identified as P. pentosaceus, named ST58. Based on multiple isolation of the same strain (P. pentosaceus ST58) over the 26 weeks in screening process for the potential bacteriocinogenic strains from the oral cavity of the same volunteer, strain ST58 can be considered a persistent component of oral cavity microbiota. Genomic analysis of P. pentosaceus ST58 revealed the presence of operons encoding for bacteriocins pediocin PA-1 and penocin A. The produced bacteriocin(s) inhibited the growth of Listeria monocytogenes, Enterococcus spp. and some Lactobacillus spp. used to determine the activity spectrum. The highest levels of production (6400 AU/ml) were recorded against L. monocytogenes strains after 24 h of incubation and the antimicrobial activity was inhibited after treatment of the cell-free supernatants with proteolytic enzymes. Noteworthy, P. pentosaceus ST58 also presented antifungal activity and key metabolites potentially involved in these properties were identified. Overall, this strain can be of great biotechnological interest towards the development of effective bio-preservation cultures as well as potential health promoting microbes.

Matched MeSH terms: Random Amplified Polymorphic DNA Technique
Fulltext Antibodies against citrullinated proteins in relation to periodontitis with or without rheumatoid arthritis: a cross-sectional study

Lew PH, Rahman MT, Safii SH, Baharuddin NA, Bartold PM, Sockalingam S, et al.

BMC Oral Health, 2021 07 20;21(1):360.
PMID: 34284769 DOI: 10.1186/s12903-021-01712-y

BACKGROUND: Previous studies have reported conflicting findings between serum anti-citrullinated protein antibodies (ACPA) levels in rheumatoid arthritis (RA) participants with and without periodontitis (Pd). This study aimed to analyse possible correlations between serum ACPA levels and clinical parameters in Pd and RA participants.
METHODS: Full mouth periodontal examination (probing pocket depth, clinical attachment levels, gingival bleeding index, visual plaque index) was conducted and serum samples obtained from 80 participants comprising RA, Pd, both RA and Pd (RAPd) and healthy individuals (HC). Erythrocyte sedimentation rates (ESR) and periodontal inflamed surface area (PISA) were obtained. Serum samples were analysed for ACPA quantification using enzyme-linked immunosorbent assay (ELISA).
RESULTS: Median levels (IU/mL) of ACPA (interquartile range, IQR) in RAPd, RA, Pd and HC groups were 118.58(274.51), 102.02(252.89), 78.48(132.6) and 51.67(91.31) respectively. ACPA levels were significantly higher in RAPd and RA as compared to HC group (p RA > Pd > HC. However, lack of any significant correlation between the serum ACPA levels with the clinical Pd and RA parameters warrants further studies to investigate the causal link between RA and Pd for such a trend. Further studies involving more inflammatory biomarkers might be useful to establish the causal link between Pd in the development and progression of RA or vice versa.

Matched MeSH terms: Random Amplified Polymorphic DNA Technique
Oecophyllibacter saccharovorans gen. nov. sp. nov., a bacterial symbiont of the weaver ant Oecophylla smaragdina

Chua KO, See-Too WS, Tan JY, Song SL, Yong HS, Yin WF, et al.

J Microbiol, 2020 Dec;58(12):988-997.
PMID: 33095388 DOI: 10.1007/s12275-020-0325-8

In this study, bacterial strains Ha5T, Ta1, and Jb2 were isolated from different colonies of weaver ant Oecophylla smaragdina. They were identified as bacterial symbionts of the ant belonging to family Acetobacteraceae and were distinguished as different strains based on distinctive random-amplified polymorphic DNA (RAPD) fingerprints. Cells of these bacterial strains were Gram-negative, rod-shaped, aerobic, non-motile, catalase-positive and oxidase-negative. They were able to grow at 15-37°C (optimum, 28-30°C) and in the presence of 0-1.5% (w/v) NaCl (optimum 0%). Their predominant cellular fatty acids were C18:1ω7c, C16:0, C19:0ω8c cyclo, C14:0, and C16:0 2-OH. Strains Ha5T, Ta1, and Jb2 shared highest 16S rRNA gene sequence similarity (94.56-94.63%) with Neokomagataea tanensis NBRC106556T of family Acetobacteraceae. Both 16S rRNA gene sequence-based phylogenetic analysis and core gene-based phylogenomic analysis placed them in a distinct lineage in family Acetobacteraceae. These bacterial strains shared higher than species level thresholds in multiple overall genome-relatedness indices which indicated that they belonged to the same species. In addition, they did not belong to any of the current taxa of Acetobacteraceae as they had low pairwise average nucleotide identity (< 71%), in silico DNA-DNA hybridization (< 38%) and average amino acid identity (< 67%) values with all the type members of the family. Based on these results, bacterial strains Ha5T, Ta1, and Jb2 represent a novel species of a novel genus in family Acetobacteaceae, for which we propose the name Oecophyllibacter saccharovorans gen. nov. sp. nov., and strain Ha5T as the type strain.

Matched MeSH terms: Random Amplified Polymorphic DNA Technique
Fulltext Genetic diversity of Sabah rice cultivars using random amplified polymorphic dna (rapd) markers

Alvina Simon, Vijay Kumar Subbiah, Chee, Fong Tyng, Noor Hydayaty Md Yusuf

Borneo International Journal of Biotechnology, 2020;1(1):35-43.
MyJurnal

Rice is the most important staple crop in Malaysia and is cultivated all over the country, including the state of Sabah. The uniqueness of rice cultivation in Sabah lies in the type of rice itself, deriving mainly from local or non-commercial cultivars but with distinctive characteristics including long grains, aromatic properties, and drought tolerance. However, despite having these important agricultural traits, information on the genetic diversity of Sabah rice remains limited. Hence, the purpose of this study was to determine the genetic polymorphisms of Sabah rice using random amplification of polymorphic DNA (RAPD) markers. A total of 101 alleles were profiled, from which 94% were identified as polymorphic. Phylogenetic analysis grouped the rice samples into three clusters, with two clusters classifying the ability of rice to grow under different planting conditions, suitable for growth irrigate and upland condition. The first cluster was dominated by cultivars that could survive in wet (irrigated) areas, while the other featured those that were found in dry (upland) areas. Furthermore, two alleles, OPA-05-B2 and OPA-01-B11, were found to be unique to cultivars within the upland cluster and were thus proposed to be involved in dry environmental adaptation. The results of the present study provide an insight into the genetic relationships and diversity of Sabah rice.

Matched MeSH terms: Random Amplified Polymorphic DNA Technique
Fulltext Development of species-specific SCAR markers for identification and authentication of three rare Peninsular Malaysian endemic Coelogyne (Orchidaceae) orchids

Kok Hon Y, Yong CS, Abdullah JO, Go R

F1000Res, 2020;9:1161.
PMID: 33299554 DOI: 10.12688/f1000research.26170.2

Background:Coelogyne kaliana, Coelogyne stenochila and Coelogyne tiomanensis are three valuable rare orchid species endemic to Peninsular Malaysia, currently rampantly traded illegally via the internet and through local nurseries, which label them as hybrids to avoid enforcement detection. Drastic measures to ensure the continued existence of their populations in the wild should be introduced as they are rapidly diminishing into extinction, including the development of rapid and accurate species-specific identification tools. These three orchid species are highly similar morphologically and currently it is impossible to distinguish among them without their reproductive structures. Methods: RAPD-based species-specific SCAR markers were developed to distinguish and authenticate the identity of these three endemic Peninsular Malaysian Coelogyne species. Results: Three SCAR markers were successfully developed in this study. SCAR marker primer pair , CKL_f / CKL_r was specific to C. kaliana as it produced a unique single band of 271 bp but not in C. stenochila and C. tiomanensis. SCAR marker primer pair CST_f / CST_r amplified a single band of 854 bp in C. stenochila and two bands of different sizes (372 bp and 858 bp) in C. tiomanensis, but no amplification in C. kaliana. The third SCAR marker primer pair, CTI_f / CTI_r produced a single band (about 500 bp) for both C. stenochila and C. tiomanensis, but showed no amplification in C. kaliana. Conclusions: Although not all these SCAR markers were species amplification specific, they could be used to discriminate among the three Coelogyne species effectively. Accurate species identification is one of the most important steps to allow a proper management plan to be established in the effort to conserve these three endangered orchid species of Peninsular Malaysia. Besides, it could effectively put a stop to the illegal trading of these rare endangered orchid species worldwide.

Matched MeSH terms: Random Amplified Polymorphic DNA Technique
Fulltext Analysis of Salmonella enterica Serovar Typhi by Outer Membrane Protein (OMP) Profiling, Random Amplification of Polymorphic DNA (RAPD) and Pulsed Field Gel Electrophoresis (PFGE)

Kumar Y, Mani KR, Tahlan AK

Trop Life Sci Res, 2019 Jan;30(1):57-71.
PMID: 30847033 DOI: 10.21315/tlsr2019.30.1.4

A number of countries, including developed countries, still have typhoid fever as a major problem resulting in frequent outbreaks. The importance of controlling spread of typhoid fever is well known and necessitates periodic studies to delineate epidemiological relationships. Although phage typing remains to be the preferred conventional method for characterisation of typhoid bacilli, it is of limited use due to prevalence of few predominant phage types in the country like India. Therefore, an effort has been made to assess three molecular methods [Outer Membrane Protein (OMP) Profiling, Random Amplification of Polymorphic DNA (RAPD) and Pulsed Field Gel Electrophoresis (PFGE)] for typing of Salmonella enterica serovar Typhi. 128 Salmonella enterica serovar Typhi isolates were identified using biotyping and serotyping followed by antimicrobial susceptibility testing. These isolates were further subjected to OMP analysis, RAPD and PFGE. PFGE (114 unique clusters) was found to be the most discriminatory method followed by RAPD (94 unique clusters) and OMP profiling (50 unique clusters). Multidrug resistant strains were well discriminated by all three methods used in the study. PFGE still remains the most preferred method for detailed epidemiological investigations. However, random amplification of polymorphic DNA and outer membrane protein profiling can also be considered for molecular discrimination of the isolates in the laboratories lacking high-end facilities.

Matched MeSH terms: Random Amplified Polymorphic DNA Technique
Fulltext Salivary and serum levels of Ca and Zn in periodontitis with or without rheumatoid arthritis

Jazli Aziz, Zamri Radzi, Rathna Devi Vaithilingam, Mohammad Tariqur Rahman

Malaysian Journal of Medicine and Health Sciences, 2019;15(108):32-32.
MyJurnal

Introduction: While sharing a common causal link, both rheumatoid arthritis (RA) and periodontitis (PD) manifest similar inflammatory responses. With the progression of severity, both diseases result in bone loss. Hence, Ca and Zn, as structural components of the bones, are expected to be altered in saliva and serum in PD and RA respectively. Zinc and calcium concentrations have been studied previously in patients with PD or RA, with PD patients exhibiting increased salivary Ca and decreased Zn concentrations in serum, while RA patients have been reported to express low plasma concentrations of both Zn and Ca. The aim of this study is to evaluate the saliva and serum levels of Ca and Zn in PD patients with or without RA. Methods: Serum and saliva samples were collected from 82 patients from the Faculty of Dentistry, University of Malaya and the University Malaya Medical Centre rheumatoid clinic. Patients were grouped according to their periodontal health and RA status (healthy n=21; PD n=21; RA n=21; RAPD n=19). Results: Zinc concentration in serum was significantly higher (p

Matched MeSH terms: Random Amplified Polymorphic DNA Technique
Genetic diversity, antifungal susceptibility and enzymatic characterisation of Malaysian clinical isolates of Candida glabrata

Lotfalikhani A, Khosravi Y, Sabet NS, Na SL, Ng KP, Tay ST

Trop Biomed, 2018 Dec 01;35(4):1123-1130.
PMID: 33601859

Candida glabrata has been reported as the second or third most common yeast species isolated from patients with vaginitis and invasive candidiasis. This study was aimed to determine the genetic diversity, antifungal susceptibility and enzymatic profiles of C. glabrata isolated from vaginal and blood samples in the Medical Microbiology Diagnostic Laboratory, University Malaya Medical Centre. A random amplified polymorphic DNA (RAPD) analysis method, using M13 and (GTG)5 primers, was used for strain differentiation of C. glabrata isolates. Antifungal susceptibility testing of C. glabrata isolates was determined using E-test against amphotericin B, caspofungin, fluconazole and voriconazole and microbroth dilution method against clotrimazole. The enzymic profiles of C. glabrata were determined using APIZYM semi-quantitation kit and egg-yolk agar method. A total of 14 RAPD patterns were identified amongst C. glabrata isolates investigated this study. Susceptibility to amphotericin B, caspofungin, fluconazole and voriconazole was noted. Approximately one third of the isolates demonstrated resistance to clotrimazole (MIC>=1 µg/ml). A single isolate of C. glabrata was resistant to caspofungin (MIC:1.5 µg/ml). Enzymatic activities of acid and alkaline phosphatase, aminopeptidases, esterase and lipase and phospholipase were detected in the C. glabrata isolates. The genetic diversity and antifungal susceptibility profiles of C. glabrata isolates were presented in this study. Continued surveillance and monitoring of the incidence and antifungal resistance in C. glabrata isolates is necessary.

Matched MeSH terms: Random Amplified Polymorphic DNA Technique
Fulltext Acute ophthalmic artery occlusion in decompression illness with underlying anterior cerebral artery A1 segment hypoplasia

Omar AR, Ibrahim M, Hussein A

Diving Hyperb Med, 2018 Jun 30;48(2):112-113.
PMID: 29888385 DOI: 10.28920/dhm48.2.112-113

A diver presented with total loss of vision in the left eye and right hemiparesis following a routine no-stop scuba dive to 20 metres' depth. A diagnosis of decompression illness (DCI) with acute ophthalmic artery air embolism and left carotid artery insult causing acute anterior circulatory ischaemia was made. He underwent seven hyperbaric treatments leading to a full recovery. Magnetic resonance angiography revealed an underlying left anterior cerebral artery A1 segment hypoplasia. Making a prompt diagnosis and early hyperbaric oxygen treatment are crucial to halt further tissue damage from ischaemia in central nervous system DCI. In this case, the finding of a left A1 anterior cerebral artery segment hypoplasia variant may have increased the severity of DCI due to deficient collateral circulation.

Matched MeSH terms: Random Amplified Polymorphic DNA Technique
Fulltext Severe orbital cellulitis secondary to chronic sinusitis: challenges in saving the eye

Diymitra, K. G., Mushawiahti, M., Aida Zairani, M. Z.

Journal of Surgical Academia, 2018;8(1):47-50.
MyJurnal

Orbital cellulitis is a relatively common disease affecting predominantly the paediatric population. Most cases occur as a result of spread from the nearby sinuses. Other causes include penetrating trauma or extension from infected adjacent structures.If left untreated, this condition may result in devastating sequelae such as orbital apex syndrome, cavernous sinus thrombosis, meningitis, cranial nerve palsies, intracranial abscess formation and even death. A 47 year old immunocompetent Burmese lady presented with left eyelid swelling of 2 days duration associated with eye redness, blurring of vision and diplopia. Previously, there was history of right maxillary sinusitis and parapharyngeal abscess 9 months prior to presentation. On examination, she was afebrile with vision of 1/60 for the left eye with positiverelative afferent pupillary defect (RAPD). The eye was proptosed and swollen with restricted extraocular movements in all gazes. Conjunctiva was injected with chemosis and there was corneal epithelial bedewing. Otherwise anterior chamber was quiet and intraocular pressure was 51mmHg. Bilateral fundus examination was normal. Computed tomography (CT) scan of the orbit and paranasal sinus showed dense sinusitis and periosteal abscess at the lateral orbital wall.She was started on intravenous (IV) Cefuroxime and Metronidazole and underwent Functional Endoscopic Sinus Surgery (FESS) and orbital decompression. Intra-operatively there was pus and debris at the left anterior ethmoid, maxillary and sphenoid air sinuses and cultures revealed Klebsiella pneumoniae which was sensitive to Cefuroxime. Despite medical and surgical treatment, left orbital swelling only reduced minimally. However after starting intravenous Dexamethasone the swelling dramatically improved. She completed 10 days of intravenous Dexamethasone. Upon discharge, she was given oral Dexamethasone 2mg daily for 2 weeks and completed 2 weeks of oral Cefuroxime and Metronidazole. Intraocular pressure normalised and vision recovered to 6/9. A repeat CT orbit 3 weeks later showed resolving preseptal and periorbital collection.

Matched MeSH terms: Random Amplified Polymorphic DNA Technique
Fulltext Characterization of a Group B Streptococcus infection based on the demographics, serotypes, antimicrobial susceptibility and genotypes of selected isolates from sterile and non-sterile isolation sites in three major hospitals in Malaysia

Suhaimi MES, Desa MNM, Eskandarian N, Pillay SG, Ismail Z, Neela VK, et al.

J Infect Public Health, 2017 Jan-Feb;10(1):14-21.
PMID: 27095302 DOI: 10.1016/j.jiph.2016.01.009

BACKGROUND/PURPOSE: The purpose of this study is to characterize GBS isolates that were collected from three major hospitals in a densely populated area of Klang Valley for their demographics, serotypes, antibiotic susceptibility patterns and genetic background.

METHODS: Sixty GBS isolates from sterile and non-sterile samples in three major hospitals in the Klang Valley area of Malaysia were collected by convenience sampling from 2012 until March 2014. These isolates were studied for their antimicrobial susceptibilities, serotypes and genotypes. Patients' demographic data and clinical information were collected from lab request forms.

RESULTS: Diabetes mellitus was the only underlying condition (7 patients, 23.3%); the remaining samples were from patients who were immunocompromised due to medications. Fifty-nine (98%) isolates were sensitive to penicillin, while 78.3% and 88.3% of the isolates were sensitive to erythromycin and clindamycin, respectively. Serotype Ia was the most common serotype (n=27, 45%), followed by serotype III (n=10, 16.7%), V (n=9, 15%), VI (n=8, 13.3%), VIII (n=2, 3.3%) and VII (n=1, 1.7%). Random Amplified Polymorphic DNA (RAPD) typing showed a diverse genetic pedigree for all isolates, including four major groups that clustered according to geographical location.

CONCLUSION: This preliminary study determines the prevalence of limited common serotypes and antimicrobial resistance in distinct GBS isolates. Nonetheless, the RAPD clustering pattern suggests a close genetic lineage of the GBS isolates based on their isolation sites and location of hospitals.

Matched MeSH terms: Random Amplified Polymorphic DNA Technique
Fulltext Assessment of the genetic variability and fibre composition of Gamma Ray induced mutant lines of Ginger (Zingiber Officinale Roscoe)

Nor Yusliza Kamaruddin, Shamsiah Abdullah

Pertanika Journal of Science & Technology, 2017;25(103):325-334.
MyJurnal

This study looked at mutagenic effectiveness of gamma rays d on two varieties of Zingiber officinale Roscoe: Bentong and Tanjung Sepat. The rhizomes were exposed to different doses (0, 5, 7, 9, 11, 13 and 15 Gy) using Caesium-137 as source of the gamma rays. The effect of different gamma doses on the crude fibre composition of irradiated ginger was studied and genetic variability was assessed using molecular marker technique, RAPD. Findings showed different doses of gamma rays could induce variability in these two ginger varieties and the effect was found to be variety-dependent. Bentong variety irradiated with 9 Gy recorded 8.53% of crude fibre composition while Tanjung Sepat irradiated ginger with 5 Gy recorded 8.70% of crude fibre which gave the lowest composition compared with other irradiated ginger. A total of nine different arbitrary decamers were used as primers to amplify DNA from mutant plant material to assess their polymorphism level of ginger mutant lines. Polymorphism of all mutant lines was 97.62% indicating that there were significant changes in genetic sequences in irradiated ginger genotypes.

Matched MeSH terms: Random Amplified Polymorphic DNA Technique
Evaluation of genetic diversity of Clinacanthus nutans (Acanthaceaea) using RAPD, ISSR and RAMP markers

Ismail NZ, Arsad H, Samian MR, Ab Majid AH, Hamdan MR

Physiol Mol Biol Plants, 2016 Oct;22(4):523-534.
PMID: 27924125

Three polymerase chain reaction (PCR) techniques were compared to analyse the genetic diversity of Clinacanthus nutans eight populations in the northern region of Peninsular Malaysia. The PCR techniques were random amplified polymorphic deoxyribonucleic acids (RAPD), inter-simple sequence repeats (ISSR) and random amplified microsatellite polymorphisms (RAMP). Leaf genomic DNA was PCR amplified using 17 RAPD, 8 ISSR and 136 RAMP primers . However, only 10 RAPD primers, 5 ISSR primers and 37 RAMP primers produced reproducible bands. The results were evaluated for polymorphic information content (PIC), marker index (MI) and resolving power (RP). The RAMP marker was the most useful marker compared to RAPD and ISSR markers because it showed the highest average value of PIC (0.25), MI (11.36) and RP (2.86). The genetic diversity showed a high percentage of polymorphism at the species level compared to the population level. Furthermore, analysis of molecular variance revealed that the genetic diversity was higher within populations, as compared to among populations of C. nutans. From the results, the RAMP technique was recommended for the analysis of genetic diversity of C. nutans.

Matched MeSH terms: Random Amplified Polymorphic DNA Technique
Effects of fusaric acid treatment on the protocorm-like bodies of Dendrobium sonia-28

Dehgahi R, Zakaria L, Mohamad A, Joniyas A, Subramaniam S

Protoplasma, 2016 Sep;253(5):1373-83.
PMID: 26471909 DOI: 10.1007/s00709-015-0895-1

Dendrobium sonia-28 is a popular orchid hybrid due to its flowering recurrence and dense inflorescences. Unfortunately, it is being decimated by fungal diseases, especially those caused by Fusarium proliferatum. In this study, selection of F. proliferatum-tolerant protocorm-like bodies (PLBs) was carried out by assessing the effects of differing concentrations of fusaric acid (FA). PLBs were cultured on Murashige and Skoog (MS) medium supplemented with 0.05 to 0.2 millimolar (mM) concentrations of FA. Higher concentrations of FA increased mortality of PLBs and reduced their growth. The survival rate for 0.05 mM FA was 20 % but only 1 % at the highest dose of 0.2 mM. Additionally, two different size ranges of PLBs were investigated, and growth increased more at lower FA concentrations for larger PLBs, whilst the growth rate of smaller PLBs was inhibited at an FA concentration of 0.2 mM. Histological examination using transmission electron microscopy (TEM) and scanning electron microscopy (SEM) analyses disclosed severe cell wall and organelle damage, as well as stomatal closure in PLBs treated with the high FA concentrations. Reductions in plantlet growth were much greater at the highest concentrations of FA. Some randomly amplified polymorphic DNA (RAPD) markers clearly discriminated between selected and non-selected variants of Dendrobium sonia-28, showing different banding patterns for each FA concentration and specific bands for selected and control plants.

Matched MeSH terms: Random Amplified Polymorphic DNA Technique
Fulltext Genetic Relatedness of Salmonella Serovars Isolated from Catfish (Clarias gariepinus) and Tilapia (Tilapia mossambica) Obtained from Wet Markets and Ponds in Penang, Malaysia

Budiati T, Rusul G, Wan-Abdullah WN, Chuah LO, Ahmad R, Thong KL

J Food Prot, 2016 Apr;79(4):659-65.
PMID: 27052872 DOI: 10.4315/0362-028X.JFP-15-372

A total of 43 Salmonella enterica isolates belonging to different serovars (Salmonella Albany, Salmonella Agona, Salmonella Corvallis, Salmonella Stanley, Salmonella Typhimurium, Salmonella Mikawasima, and Salmonella Bovismorbificans) were isolated from catfish (Clarias gariepinus) and tilapia (Tilapia mossambica) obtained from nine wet markets and eight ponds in Penang, Malaysia. Thirteen, 19, and 11 isolates were isolated from 9 of 32 catfish, 14 of 32 tilapia, and 11 of 44 water samples, respectively. Fish reared in ponds were fed chicken offal, spoiled eggs, and commercial fish feed. The genetic relatedness of these Salmonella isolates was determined by random amplified polymorphic DNA PCR (RAPD-PCR) using primer OPC2, repetitive extragenic palindromic PCR (REP-PCR), and pulsed-field gel electrophoresis (PFGE). Composite analysis of the RAPD-PCR, REP-PCR, and PFGE results showed that the Salmonella serovars could be differentiated into six clusters and 15 singletons. RAPD-PCR differentiated the Salmonella isolates into 11 clusters and 10 singletons, while REP-PCR differentiated them into 4 clusters and 1 singleton. PFGE differentiated the Salmonella isolates into seven clusters and seven singletons. The close genetic relationship of Salmonella isolates from catfish or tilapia obtained from different ponds, irrespective of the type of feed given, may be caused by several factors, such as the quality of the water, density of fish, and size of ponds.

Matched MeSH terms: Random Amplified Polymorphic DNA Technique
Fulltext Molecular confirmation and characterization of Vibrio parahaemolyticus from retailed fish

Vincent, M., Chan, C. S. W., Apun, K.

International Food Research Journal, 2015;22(4):1705-1710.
MyJurnal

The present study was conducted to assess the rapid molecular identification and characterization of 45 Vibrio parahaemolyticus isolates from 15 samples of 3 different types of fish (Kembung, Bawal and Sangeh) in the Kuching-Samarahan district. Polymerase chain reaction (PCR) based confirmation was done targeting the 450 bp fragment of the thermolabile (tl) gene, while DNA fingerprinting was performed using Randomly Amplified Polymorphic DNA (RAPD) PCR with the primer GEN15008. All the 45 V. parahaemolyticus isolates were positive for the tl gene, however, only 34 were typable via RAPD-PCR with bands sizes ranging from slightly over 250 bp to 2.5 kbp. The degree of diversity was then determined via the Simpson Index which showed a value of 0.891, indicating high diversity among the isolates. Data from the RAPD-PCR fingerprints were later used to construct a dendrogram for clustal analysis. From the dendrogram, the 34 isolates were grouped into 2 major clusters containing 26 and 8 isolates, respectively. Further analyses of the dendrogram also indicated that the 34 isolated were clustered according to the period of sampling. This is an interesting observation as it shows the high discriminatory capability of RAPD-PCR to be used as molecular epidemiological tool to study the temporal distribution of V. parahaemolyticus.

Matched MeSH terms: Random Amplified Polymorphic DNA Technique
Morpho-molecular analysis as a prognostic model for repulsive feedback of the medicinal plant "Andrographis paniculata" to allogamy

Valdiani A, Talei D, Javanmard A, Tan SG, Kadir MA, Maziah M

Gene, 2014 Jun 1;542(2):156-67.
PMID: 24680780 DOI: 10.1016/j.gene.2014.03.039

Andrographis paniculata Nees. (AP) is a self-pollinated medicinal herb with a wide range of pharmaceutical properties, facing a low diversity in Malaysia. Cross-pollination of AP accessions leads to considerable rates of heterosis in the agro-morphological characteristics and anticancer phytochemicals of this eminent medicinal herb. However, the poor crossability of the plant at the interpopulation or intraspecific levels is an obstacle from the evolutionary and breeding points of view as an average of 4.56% crossability was recorded for AP in this study. Hence, this research aimed to elicit the impact of parental genetic distances (GDs) on the rate of crossability of AP using seven accessions in 21 possible cross combinations. To this end, a set of 55 randomly amplified polymorphic DNA (RAPD) primers and a total of 13 agro-morphological markers were employed to test the hypothesis. Twenty-two out of the 55 RAPD primers amplified a total of 257 bands of which 107 bands were found to be polymorphic. The principal component analysis (PCA) based on the RAPD markers revealed that the studied AP accessions were distributed to three distinct groups. Furthermore, it was noticed that even a minor increase in GD between two parents can cause a decline in their crossability. Unlike, the morphological-based GDs acted neutrally to crossability. This finding suggests that, despite the low genetic diversity among the Malaysian APs, a population prescreening using RAPD markers would be useful to enhance the rate of fruit set through selecting the genetically adjacent parents.

Matched MeSH terms: Random Amplified Polymorphic DNA Technique
Phylogeography and molecular diversity analysis of Jatropha curcas L. and the dispersal route revealed by RAPD, AFLP and nrDNA-ITS analysis

Sudheer Pamidimarri DV, Reddy MP

Mol Biol Rep, 2014 May;41(5):3225-34.
PMID: 24469734 DOI: 10.1007/s11033-014-3185-7

Jatropha curcas L. (Euphorbiaceae) has acquired a great importance as a renewable source of energy with a number of environmental benefits. Very few attempts were made to understand the extent of genetic diversity and its distribution. This study was aimed to study the diversity and deduce the phylogeography of Jatropha curcas L. which is said to be the most primitive species of the genus Jatropha. Here we studied the intraspecific genetic diversity of the species distributed in different parts of the globe. The study also focused to understand the molecular diversity at reported probable center of origin (Mexico), and to reveal the dispersal route to other regions based on random amplified polymorphic DNA, amplified fragment length polymorphism and nrDNA-ITS sequences data. The overall genetic diversity of J. curcas found in the present study was narrow. The highest genetic diversity was observed in the germplasm collected from Mexico and supports the earlier hypothesis based on morphological data and natural distribution, it is the center for origin of the species. Least genetic diversity found in the Indian germplasm and clustering results revealed that the species was introduced simultaneously by two distinct germplasm and subsequently distributed in different parts of India. The present molecular data further revealed that J. curcas might have spread from the center of the origin to Cape Verde, than to Spain, Portuguese to other neighboring countries and simultaneously to Africa. The molecular evidence supports the Burkill et al. (A dictionary of the economic products of the Malay Peninsula, Governments of Malaysia and Singapore by the Ministry of Agriculture and Co-operatives. Kuala Lumpur, Malaysia, 1966) view of Portuguese might have introduced the species to India. The clustering pattern suggests that the distribution was interfered by human activity.

Matched MeSH terms: Random Amplified Polymorphic DNA Technique
Fulltext Genetic Diversity and Differentiation of Colletotrichum spp. Isolates Associated with Leguminosae Using Multigene Loci, RAPD and ISSR

Mahmodi F, Kadir JB, Puteh A, Pourdad SS, Nasehi A, Soleimani N

Plant Pathol J, 2014 Mar;30(1):10-24.
PMID: 25288981 DOI: 10.5423/PPJ.OA.05.2013.0054

Genetic diversity and differentiation of 50 Colletotrichum spp. isolates from legume crops studied through multigene loci, RAPD and ISSR analysis. DNA sequence comparisons by six genes (ITS, ACT, Tub2, CHS-1, GAPDH, and HIS3) verified species identity of C. truncatum, C. dematium and C. gloeosporiodes and identity C. capsici as a synonym of C. truncatum. Based on the matrix distance analysis of multigene sequences, the Colletotrichum species showed diverse degrees of intera and interspecific divergence (0.0 to 1.4%) and (15.5-19.9), respectively. A multilocus molecular phylogenetic analysis clustered Colletotrichum spp. isolates into 3 well-defined clades, representing three distinct species; C. truncatum, C. dematium and C. gloeosporioides. The ISSR and RAPD and cluster analysis exhibited a high degree of variability among different isolates and permitted the grouping of isolates of Colletotrichum spp. into three distinct clusters. Distinct populations of Colletotrichum spp. isolates were genetically in accordance with host specificity and inconsistent with geographical origins. The large population of C. truncatum showed greater amounts of genetic diversity than smaller populations of C. dematium and C. gloeosporioides species. Results of ISSR and RAPD markers were congruent, but the effective maker ratio and the number of private alleles were greater in ISSR markers.

Matched MeSH terms: Random Amplified Polymorphic DNA Technique
Identification and characterization of RAPD-SCAR markers linked to glyphosate-susceptible and -resistant biotypes of Eleusine indica (L.) Gaertn

Cha TS, Anne-Marie K, Chuah TS

Mol Biol Rep, 2014 Feb;41(2):823-31.
PMID: 24374894 DOI: 10.1007/s11033-013-2922-7

Eleusine indica is one of the most common weed species found in agricultural land worldwide. Although herbicide-glyphosate provides good control of the weed, its frequent uses has led to abundant reported cases of resistance. Hence, the development of genetic markers for quick detection of glyphosate-resistance in E. indica population is imperative for the control and management of the weed. In this study, a total of 14 specific random amplified polymorphic DNA (RAPD) markers were identified and two of the markers, namely S4R727 and S26R6976 were further sequence characterized. Sequence alignment revealed that marker S4R727 showing a 12-bp nucleotides deletion in resistant biotypes, while marker S26R6976 contained a 167-bp nucleotides insertion in the resistant biotypes. Based on these sequence differences, three pairs of new sequence characterized amplified region (SCAR) primers were developed. The specificity of these primer pairs were further validated with genomic DNA extracted from ten individual plants of one glyphosate-susceptible and five glyphosate-resistant (R2, R4, R6, R8 and R11) populations. The resulting RAPD-SCAR markers provided the basis for assessing genetic diversity between glyphosate-susceptible and -resistant E. indica biotypes, as well for the identification of genetic locus link to glyphosate-resistance event in the species.

Matched MeSH terms: Random Amplified Polymorphic DNA Technique/methods*

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