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Fulltext Sponges from North Borneo and their bioactivity against human colorectal cancer cells

Yong, Yoong-Soon, Lim, Swee-Cheng, Lee, Ping-Chin, Ling, Yee-Soon

Borneo Journal of Marine Science and Aquaculture, 2018;2(1):40-47.
MyJurnal

Sponges are major source of numerous cytotoxic compounds that are used for defence as well as adaptation to the environment. Numerous studies have discovered compounds from sponge extracts that were effective against a wide range of cancer cells. In this study, a total of 23 sponges comprising of 19 species were collected from Northeast Borneo. Sponges were treated and extracted using modified Folch extraction method, followed by cytotoxicity assay to determine their effectiveness against different colorectal cancer cells. Our results demonstrate that Monanchora clathrata, Dysidea sp., and Jaspis sp. possess different degrees of cytotoxicity against a wide range of human colorectal cancer cells. Monanchora clathrata (KDT07), Dysidea sp. (KDT09), and Jaspis sp. (KDT18) are among the demosponges which possess significant cytotoxicity against colorectal cancer cell lines, including HCT116, LoVo, SW480, and SW620. KDT08 and KDT21 which fall under the same genus Dysidea, possess insignificant cytotoxicity against colorectal cancer cells suggested environmental factors (symbiotic organisms) play a role in biosynthesizing bioactive compounds. Presented results suggested the importance of intensifying research on isolating and purifying natural products from marine sponges for useful applications.
Fulltext Reassessment of the catalytic activity and substrate specificity of fkbp35 from plasmodium knowlesi using protease-free assay

Cahyo Budiman, Carlmond Goh Kah Wun, Lee, Ping Chin, Rafida Razali, Thean, Chor Leow

Borneo International Journal of Biotechnology, 2020;1(1):125-143.
MyJurnal

FK506-binding protein35 of Plasmodium knowlesi (Pk-FKBP35) is a member of peptidyl prolyl cis-trans isomerase (PPIase) and is considered as a promising avenue of antimalarial drug target development. This protein is organized into the N-terminal domain responsible for PPIase catalytic activity followed and the tetratricopeptide repeat domain for its dimerization. The protease-coupling and protease-free assays are known to be the common methods for investigating the catalytic properties of PPIase. Earlier, the protease-coupling assay was used to confirm the catalytic activity of Pk-FKBP35 in accelerating cis-trans isomerization of the peptide substrate. This report is aimed to re-assess the catalytic and substrate specificity of Pk-FKBP35 using an alternative method of a protease-free assay. The result indicated that while Pk-FKBP35 theoretically contained many possible cleavage sites of chymotrypsin, experimentally, the catalytic domain was relatively stable from chymotrypsin. Furthermore, under protease-free assay, Pk-FKBP35 also demonstrated remarkable PPIase catalytic activity with kcat/KM of 4.5 + 0.13 × 105 M−1 s−1, while the kcat/KM of active site mutant of D55A is 0.81 + 0.05 × 105 M−1 s−1. These values were considered comparable to kcat/KM obtained from the protease-coupling assay. Interestingly, the substrate specificities of Pk-FKBP35 obtained from both methods are also similar, with the preference of Pk-FKBP35 towards Xaa at P1 position was Leu>Phe>Lys>Trp>Val>Ile>His>Asp>Ala>Gln>Glu. Altogether, we proposed that protease-free and protease-coupling assays arereliable for Pk-FKBP35.
Fulltext Development of insulated isothermal PCR for rapid on-site malaria detection

Chua KH, Lee PC, Chai HC

Malar J, 2016;15:134.
PMID: 26931146 DOI: 10.1186/s12936-016-1183-z

Detection of Plasmodium spp. is sometimes inconvenient especially in rural areas that are distant from a laboratory. In this study a portable diagnostic test of Plasmodium spp. was developed using insulated isothermal polymerase chain reaction (iiPCR) as an alternative approach to improve this situation.
Analysis of polymorphisms and selective pressures on ama1 gene in Plasmodium knowlesi isolates from Sabah, Malaysia

Chua CY, Lee PC, Lau TY

J Genet, 2017 Sep;96(4):653-663.
PMID: 28947714

The apical membrane antigen-1 (AMA-1) of Plasmodium spp. is a merozoite surface antigen that is essential for the recognition and invasion of erythrocytes. Polymorphisms occurring in this surface antigen will cause major obstacles in developing effective malaria vaccines based on AMA-1. The objective of this study was to characterize ama1 gene in Plasmodium knowlesi isolates from Sabah. DNA was extracted from blood samples collected from Keningau, Kota Kinabalu and Kudat. The Pkama1 gene was amplified using nested PCR and subjected to bidirectional sequencing. Analysis of DNA sequence revealed that most of the nucleotide polymorphisms were synonymous and concentrated in domain I of PkAMA-1. Forteen haplotypes were identified based on amino acid variations and haplotype K5 was the most common haplotype. dN/dS ratios implied that purifying selection was prevalent in Pkama1 gene. Fu and Li's D and F values further provided evidence of negative selection acting on domain II of Pkama1. Lownucleotide diversitywas also detected for the Pkama1 sequences,which is similar to reports on Pkama1 from Peninsular Malaysia and Sarawak. The presence of purifying selection and low nucleotide diversity indicated that domain II of Pkama1 can be used as a target for vaccine development.
Fulltext Draft genome sequence data of Streptomyces sp. FH025

Goh LPW, Mahmud F, Lee PC

Data Brief, 2021 Jun;36:107128.
PMID: 34095378 DOI: 10.1016/j.dib.2021.107128

The genome data of Streptomyces sp. FH025 comprised of 8,381,474 bp with a high GC content of 72.51%. The genome contains 7035 coding sequences spanning 1261 contigs. Streptomyces sp. FH025 contains 57 secondary metabolite gene clusters including polyketide synthase, nonribosomal polyketide synthase and other biosynthetic pathways such as amglyccycl, butyrolactone, terpenes, siderophores, lanthipeptide-class-iv, and ladderane. 16S rRNA analysis of Streptomyces sp. FH025 is similar to the Streptomyces genus. This whole genome project has been deposited at NCBI under the accession JAFLNG000000000.
Anti-malarial and anti-inflammatory effects of gynura procumbens are mediated by kaempferol via inhibition of glycogen synthase kinase-3β (gsk3β)

Hasidah Mohd Sidek, Sok Kuan Wong, Michelle Lee Sue Jann, Suhaini Sudi, Wan Rozianoor bt Mohd Hassan, Noor Embi, et al.

Sains Malaysiana, 2015;44:1489-1500.

Gynura procumbens is a medicinal plant, traditionally used to treat inflammation and fever. A yeast-based assay detected GSK3β-inhibitory activity in the aqueous extract of G. procumbens. GSK3β is now known to have a central role in the modulation of host inflammatory response during bacterial infections. In this study, we investigated the involvement of GSK3β in the anti-malarial and anti-inflammatory effects of an aqueous extract of G. procumbens. Our results showed that G. procumbens inhibited growth of P. falciparum 3D7. Consecutive four-day administration of 250 mg/kg body weight (b.w.) G. procumbens resulted in strong chemosuppression and improved survivability in P. berghei-infected mice. B. pseudomallei-infected mice treated with G. procumbens (50 mg/kg b.w.) showed increased survivability. TNF-α and IFN-γ levels in liver and serum of B. pseudomallei-infected mice were lowered by G. procumbens treatment. IL-10 level was higher in serum of G. procumbens-administered infected mice. G. procumbens treatment of P. berghei- and B. pseudomallei-infected animals each resulted in increased hepatic GSK3β (Ser9) phosphorylation. It is noteworthy that kaempferol (one of the compounds in G. procumbens) also inhibited the growth of P. falciparum 3D7; showed strong chemosuppression and improved survivability in P. berghei-infected mice at 5 mg/kg b.w. B. pseudomallei-infected mice treated with kaempferol (10 mg/kg b.w.) showed improved survivability. Concomitantly, the described effects due to kaempferol also involved enhanced GSK3β (Ser9) phosphorylation as observed with G. procumbens. In summary, the observed anti-malarial and anti-inflammatory effects of G. procumbens involved inhibition of GSK3β and kaempferol may in part be responsible for the pharmacological effects.
Fulltext Prevalence of Alpha(α)-Thalassemia in Southeast Asia (2010-2020): A Meta-Analysis Involving 83,674 Subjects

Goh LPW, Chong ETJ, Lee PC

Int J Environ Res Public Health, 2020 10 09;17(20).
PMID: 33050119 DOI: 10.3390/ijerph17207354

Alpha(α)-thalassemia is a blood disorder caused by many types of inheritable α-globin gene mutations which causes no-to-severe clinical symptoms, such as Hb Bart's hydrops fetalis that leads to early foetal death. Therefore, the aim of this meta-analysis was to provide an update from year 2010 to 2020 on the prevalence of α-thalassemia in Southeast Asia. A systematic literature search was performed using PubMed and SCOPUS databases for related studies published from 2010 to 2020, based on specified inclusion and exclusion criteria. Heterogeneity of included studies was examined with the I2 index and Q-test. Funnel plots and Egger's tests were performed in order to determine publication bias in this meta-analysis. Twenty-nine studies with 83,674 subjects were included and pooled prevalence rates in this meta-analysis were calculated using random effect models based on high observed heterogeneity (I2 > 99.5, p-value < 0.1). Overall, the prevalence of α-thalassemia is 22.6%. The highest α-thalassemia prevalence was observed in Vietnam (51.5%) followed by Cambodia (39.5%), Laos (26.8%), Thailand (20.1%), and Malaysia (17.3%). No publication bias was detected. Conclusions: This meta-analysis suggested that a high prevalence of α-thalassemia occurred in selected Southeast Asia countries. This meta-analysis data are useful for designing thalassemia screening programs and improve the disease management.
Risk association, linkage disequilibrium and haplotype analyses of FASN rs4246445, rs2229425, rs2228305 and rs2229422 polymorphisms in overweight and obesity

Chong ETJ, Kuok SSE, Lee PC

Bioimpacts, 2018;8(3):159-165.
PMID: 30211075 DOI: 10.15171/bi.2018.18

Introduction:
Obesity is commonly linked up with several life-threatening diseases. This study aims to investigate the association of fatty acid synthase (FASN) rs4246445, rs2229425, rs2228305, and rs2229422 single nucleotide polymorphisms (SNPs) with the risk of overweight and obesity in the Malaysian population.
Methods:
Blood samples were collected from 1030 individuals who were grouped into normal, overweight, and obese categories. Blood biochemistry test and lipid profiling were performed and genomic DNA was extracted. Genotyping was performed using hydrolysis probes and odd ratio with 95% CI was calculated for risk association analysis. Linkage disequilibrium and haplotypes analyses were carried out using SHEsis software.
Results:
We found that the hemoglobin and white blood cell counts were significantly high in the obese subjects. There is a lack of evidence to link the FASN SNPs with the risk of overweight and obesity in the population. All 4 SNPs were seemed to be in linkage equilibrium. Five common haplotypes were identified in this study but none of them was significantly associated with overweight and obesity in the population.
Conclusion:
Our findings suggest a lack of evidence to associate the FASN rs4246445, rs2229425, rs2228305, and rs2229422 SNPs with the risk of overweight and obesity in the Malaysian population. All 4 SNPs were independent of each other and not all identified haplotypes were significantly associated with overweight and obesity in this study.
Fulltext Effects of 12-week rowing training on resting cardiac output, stroke volume, and heart rate of stroke survivors

Chong, Melvina Marvin, Jesus, Jonatan, Mollyanna, Peter, Lajangan, Florence J. E., Liong, Kum Peik, Zuliana Bacho, et al.

Borneo Journal of Medical Sciences, 2018;12(3):19-27.
MyJurnal

Rowing exercise is one of the cardiorespiratory exercises that induce higher aerobic capacity. Cardiorespiratory parameters, cardiac output (CO), stroke volume (SV), and heart rate (HR) are indicators to measure one’s cardiorespiratory fitness. The aim was to study the effects of 12-week rowing training on resting cardiac output (RCO), resting stroke volume (RSV), and resting heart rate (RHR) of stroke survivors. Ten stroke survivors (6 males; 4 females), mean age of 43.6 ± 16.15 years, were subjected to a 12-week rowing training (Concept II Rowing Ergometer, Model C, USA). An individualised programme was prescribed based on %HRR for each of stroke individual. Rowing training was conducted twice per week (12 HIIT; 12 MR). Paired t-test and repeated measures ANOVA (RPM ANOVA) were used for statistical analyses using IBM® SPSS® Statistics 20 software. RPM ANOVA analysis showed no significant effect on RCO [F (5, 45) = 1.066, p = 0.392, RSV [F (2.188, 19.693) = 0.677, p = 0.532)], and RHR [F (5, 45) = 0.856, p = 0.518]. Paired t-test showed no significant difference between pre- and posttest despite the improved values of Mean ± Standard Deviation (RCO: 8129.50 ± 3916.31 to 8494.18 ± 6248.86 mL/min; RSV: 99.27 ± 33.98 to 121.84 ± 66.24 mL; RHR: 78.02 ± 17.39 to 77.17 ± 11.98 bpm) for all respective parameters. Twelve weeks rowing training did not improve resting cardiorespiratory parameters of stroke survivors statistically. Future studies are suggested to include gender difference and medication effect variables.
Fulltext Bacterial polysaccharides-A big source for prebiotics and therapeutics

Khan R, Shah MD, Shah L, Lee PC, Khan I

Front Nutr, 2022;9:1031935.
PMID: 36407542 DOI: 10.3389/fnut.2022.1031935

Bacterial polysaccharides are unique due to their higher purity, hydrophilic nature, and a finer three-dimensional fibrous structure. Primarily, these polymers provide protection, support, and energy to the microorganism, however, more recently several auxiliary properties of these biopolymers have been unmasked. Microbial polysaccharides have shown therapeutic abilities against various illnesses, augmented the healing abilities of the herbal and Western medicines, improved overall health of the host, and have exerted positive impact on the growth of gut dwelling beneficial bacteria. Specifically, the review is discussing the mechanism through which bacterial polysaccharides exert anti-inflammatory, antioxidant, anti-cancer, and anti-microbial properties. In addition, they are holding promising application in the 3D printing. The review is also discussing a perspective about the metagenome-based screening of polysaccharides, their integration with other cutting-edge tools, and synthetic microbiome base intervention of polysaccharides as a strategy for prebiotic intervention. This review has collected interesting information about the bacterial polysaccharides from Google Scholar, PubMed, Scopus, and Web of Science databases. Up to our knowledge, this is the first of its kind review article that is summarizing therapeutic, prebiotics, and commercial application of bacterial polysaccharides.
An Updated Review on the Role of Single Nucleotide Polymorphisms in COVID-19 Disease Severity: A Global Aspect

Ng JW, Chong ETJ, Lee PC

Curr Pharm Biotechnol, 2022 Jan 14.
PMID: 35034591 DOI: 10.2174/1389201023666220114162347

Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and recently has become a serious global pandemic. Age, gender, and comorbidities are known to be common risk factors for severe COVID-19 but are not enough to fully explain the magnitude of their effect on the risk of severity of the disease. Single nucleotide polymorphisms (SNPs) in several genes have been reported as a genetic factor contributing to COVID-19 severity. This comprehensive review focuses on the association between SNPs in four important genes and COVID-19 severity in a global aspect. We discuss a total of 39 SNPs in this review: five SNPs in the ABO gene, nine SNPs in the angiotensin-converting enzyme 2 (ACE2) gene, 19 SNPs in the transmembrane protease serine 2 (TMPRSS2) gene, and six SNPs in the toll-like receptor 7 (TLR7) gene. These SNPs data could assist in monitoring an individual's risk of severe COVID-19 disease, and therefore personalized management and pharmaceutical treatment could be planned in COVID-19 patients.
Significant genotype difference in the CYP2E1 PstI polymorphism of indigenous groups in Sabah, Malaysia with Asian and non-Asian populations

Goh LP, Chong ET, Chua KH, Chuah JA, Lee PC

Asian Pac J Cancer Prev, 2014;15(17):7377-81.
PMID: 25227845

CYP2E1 PstI polymorphism G-1259C (rs3813867) genotype distributions vary significantly among different populations and are associated with both diseases, like cancer, and adverse drug effects. To date, there have been limited genotype distributions and allele frequencies of this polymorphism reported in the three major indigenous ethnic groups (KadazanDusun, Bajau, and Rungus) in Sabah, also known as North Borneo. The aim of this study was to investigate the genotype distributions and allele frequencies of the CYP2E1 PstI polymorphism G-1259C in these three major indigenous peoples in Sabah. A total of 640 healthy individuals from the three dominant indigenous groups were recruited for this study. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) at G-1259C polymorphic site of CYP2E1 gene was performed using the Pst I restriction enzyme. Fragments were analyzed using agarose gel electrophoresis and confirmed by direct sequencing. Overall, the allele frequencies were 90.3% for c1 allele and 9.7% for c2 allele. The genotype frequencies for c1/c1, c1/c2 and c2/c2 were observed as 80.9%, 18.8%, and 0.3%, respectively. A highly statistical significant difference (p<0.001) was observed in the genotype distributions between indigenous groups in Sabah with all Asian and non-Asian populations. However, among these three indigenous groups, there was no statistical significant difference (p>0.001) in their genotype distributions. The three major indigenous ethnic groups in Sabah show unique genotype distributions when compared with other populations. This finding indicates the importance of establishing the genotype distributions of CYP2E1 PstI polymorphism in the indigenous populations.
Fulltext RsaI but not DraI polymorphism in CYP2E1 gene increases the risk of gastrointestinal cancer in Malaysians: a case-control study

Chong ET, Lee CC, Chua KH, Chuah JA, Lee PC

BMJ Open, 2014;4(1):e004109.
PMID: 24394801 DOI: 10.1136/bmjopen-2013-004109

Our study aimed to investigate the association of CYP2E1 C-1019T RsaI and T7678A DraI polymorphisms and factors such as age, gender and ethnicity to the risk of gastrointestinal cancer (GIC) in Malaysians.
Fulltext Development of High Resolution Melting Analysis for the Diagnosis of Human Malaria

Chua KH, Lim SC, Ng CC, Lee PC, Lim YA, Lau TP, et al.

Sci Rep, 2015;5:15671.
PMID: 26507008 DOI: 10.1038/srep15671

Molecular detection has overcome limitations of microscopic examination by providing greater sensitivity and specificity in Plasmodium species detection. The objective of the present study was to develop a quantitative real-time polymerase chain reaction coupled with high-resolution melting (qRT-PCR-HRM) assay for rapid, accurate and simultaneous detection of all five human Plasmodium spp. A pair of primers targeted the 18S SSU rRNA gene of the Plasmodium spp. was designed for qRT-PCR-HRM assay development. Analytical sensitivity and specificity of the assay were evaluated. Samples collected from 229 malaria suspected patients recruited from Sabah, Malaysia were screened using the assay and results were compared with data obtained using PlasmoNex(TM), a hexaplex PCR system. The qRT-PCR-HRM assay was able to detect and discriminate the five Plasmodium spp. with lowest detection limits of 1-100 copy numbers without nonspecific amplifications. The detection of Plasmodium spp. in clinical samples using this assay also achieved 100% concordance with that obtained using PlasmoNex(TM). This indicated that the diagnostic sensitivity and specificity of this assay in Plasmodium spp. detection is comparable with those of PlasmoNex(TM). The qRT-PCR-HRM assay is simple, produces results in two hours and enables high-throughput screening. Thus, it is an alternative method for rapid and accurate malaria diagnosis.
Association of CYP2E1, STK15 and XRCC1 Polymorphisms with Risk of Breast Cancer in Malaysian Women

Chong ET, Goh LP, See EU, Chuah JA, Chua KH, Lee PC

Asian Pac J Cancer Prev, 2016;17(2):647-53.
PMID: 26925658

BACKGROUND: Breast cancer is the most common type of cancer affecting Malaysian women. Recent statistics revealed that the cumulative probability of breast cancer and related deaths in Malaysia is higher than in most of the countries of Southeast Asia. Single nucleotide polymorphisms (SNPs) in CYP2E1 (rs6413432 and rs3813867), STK15 (rs2273535 and rs1047972) and XRCC1 (rs1799782 and rs25487) have been associated with breast cancer risk in a meta-analysis but any link in Southeast Asia, including Malaysia, remained to be determined. Hence, we investigated the relationship between these SNPs and breast cancer risk among Malaysian women in the present case-control study.
MATERIALS AND METHODS: Genomic DNA was isolated from peripheral blood of 71 breast cancer patients and 260 healthy controls and subjected to polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis.
RESULTS: Our study showed that the c1/c2 genotype or subjects with at least one c2 allele in CYP2E1 rs3813867 SNP had significantly increased almost 1.8-fold higher breast cancer risk in Malaysian women overall. In addition, the variant Phe allele in STK15 rs2273535 SNP appeared to protect against breast cancer in Malaysian Chinese. No significance association was found between XRCC1 SNPs and breast cancer risk in the population.
CONCLUSIONS: This study provides additional knowledge on CYP2E1, STK15 and XRCC1 SNP impact of risk of breast cancer, particularly in the Malaysian population. From our findings, we also recommend Malaysian women to perform breast cancer screening before 50 years of age.
Fulltext Draft Genome Sequence of Flavobacterium sp. Strain PL002, Isolated from Antarctic Porphyra Algae

Teoh CP, Lavin P, Najimudin N, Lee PC, Iancu L, Purcarea C, et al.

Microbiol Resour Announc, 2021 Feb 25;10(8).
PMID: 33632855 DOI: 10.1128/MRA.00063-21

Here, we report the draft genome sequence of Flavobacterium sp. strain PL002, isolated from Antarctic Porphyra algae. The 4,299,965-bp genome sequence is assembled into 170 contigs, has 32.92% GC content, and 3,734 predicted genes.
Diversity and natural selection of Merozoite surface Protein-1 in three species of human malaria parasites: Contribution from South-East Asian isolates

Goh XT, Lim YAL, Lee PC, Nissapatorn V, Chua KH

Mol Biochem Parasitol, 2021 07;244:111390.
PMID: 34087264 DOI: 10.1016/j.molbiopara.2021.111390

The present study aimed to examine the genetic diversity of human malaria parasites (i.e., P. falciparum, P. vivax and P. knowlesi) in Malaysia and southern Thailand targeting the 19-kDa C-terminal region of Merozoite Surface Protein-1 (MSP-119). This region is essential for the recognition and invasion of erythrocytes and it is considered one of the leading candidates for asexual blood stage vaccines. However, the genetic data of MSP-119 among human malaria parasites in Malaysia is limited and there is also a need to update the current sequence diversity of this gene region among the Thailand isolates. In this study, genomic DNA was extracted from 384 microscopy-positive blood samples collected from patients who attended the hospitals or clinics in Malaysia and malaria clinics in Thailand from the year 2008 to 2016. The MSP-119 was amplified using PCR followed by bidirectional sequencing. DNA sequences identified in the present study were subjected to Median-joining network analysis with sequences of MSP-119 obtained from GenBank. DNA sequence analysis revealed that PfMSP-119 of Malaysian and Thailand isolates was not genetically conserved as high number of haplotypes were detected and positive selection was prevalent in PfMSP-119, hence questioning its suitability to be used as a vaccine candidate. A novel haplotype (Q/TNG/L) was also detected in Thailand P. falciparum isolate. In contrast, PvMSP-119 was highly conserved, however for the first time, a non-synonymous substitution (A1657S) was reported among Malaysian isolates. As for PkMSP-119, the presence of purifying selection and low nucleotide diversity indicated that it might be a potential vaccine target for P. knowlesi.
Fulltext Rapid identification of melioidosis agent by an insulated isothermal PCR on a field-deployable device

Chua KH, Tan EW, Chai HC, Puthucheary SD, Lee PC, Puah SM

PeerJ, 2020;8:e9238.
PMID: 32518734 DOI: 10.7717/peerj.9238

Background: Burkholderia pseudomallei causes melioidosis, a serious illness that can be fatal if untreated or misdiagnosed. Culture from clinical specimens remains the gold standard but has low diagnostic sensitivity.
Method: In this study, we developed a rapid, sensitive and specific insulated isothermal Polymerase Chain Reaction (iiPCR) targeting bimA gene (Burkholderia Intracellular Motility A; BPSS1492) for the identification of B. pseudomallei. A pair of novel primers: BimA(F) and BimA(R) together with a probe were designed and 121 clinical B. pseudomallei strains obtained from numerous clinical sources and 10 ATCC non-targeted strains were tested with iiPCR and qPCR in parallel.
Results: All 121 B. pseudomallei isolates were positive for qPCR while 118 isolates were positive for iiPCR, demonstrating satisfactory agreement (97.71%; 95% CI [93.45-99.53%]; k = 0.87). Sensitivity of the bimA iiPCR/POCKIT assay was 97.52% with the lower detection limit of 14 ng/µL of B. pseudomallei DNA. The developed iiPCR assay did not cross-react with 10 types of non-targeted strains, indicating good specificity.
Conclusion: This bimA iiPCR/POCKIT assay will undoubtedly complement other methodologies used in the clinical laboratory for the rapid identification of this pathogen.
Genetic and haplotype analyses targeting cytochrome b gene of Plasmodium knowlesi isolates of Malaysian Borneo and Peninsular Malaysia

Chong ETJ, Neoh JWF, Lau TY, Lim YA, Chua KH, Lee PC

Acta Trop, 2018 May;181:35-39.
PMID: 29409854 DOI: 10.1016/j.actatropica.2018.01.018

Malaria is a notorious disease which causes major global morbidity and mortality. This study aims to investigate the genetic and haplotype differences of Plasmodium knowlesi (P. knowlesi) isolates in Malaysian Borneo and Peninsular Malaysia based on the molecular analysis of the cytochrome b (cyt b) gene. The cyt b gene of 49 P. knowlesi isolates collected from Sabah, Malaysian Borneo and Peninsular Malaysia was amplified using PCR, cloned into a commercialized vector and sequenced. In addition, 45 cyt b sequences were retrieved from humans and macaques bringing to a total of 94 cyt b gene nucleotide sequences for phylogenetic analysis. Genetic and haplotype analyses of the cyt b were analyzed using MEGA6 and DnaSP ver. 5.10.01. The haplotype genealogical linkage of cyt b was generated using NETWORK ver. 4.6.1.3. Our phylogenetic tree revealed the conservation of the cyt b coding sequences with no distinct cluster across different geographic regions. Nucleotide analysis of cyt b showed that the P. knowlesi isolates underwent purifying selection with population expansion, which was further supported by extensive haplotype sharing between the macaques and humans from Malaysian Borneo and Peninsular Malaysia in the median-joining network analysis. This study expands knowledge on conservation of the zoonotic P. knowlesi cyt b gene between Malaysian Borneo and Peninsular Malaysia.
Fulltext Dataset of the complete genome of Streptomyces cavourensis strain 2BA6PGT isolated from sediment from the bottom of the salt lake Verkhnee Beloe (Buryatia, Russia)

Chong ETJ, Chiang C, Png KK, Abidueva E, Zaitseva S, Sun C, et al.

Data Brief, 2023 Feb;46:108877.
PMID: 36691562 DOI: 10.1016/j.dib.2022.108877

The Streptomyces cavourensis strain 2BA6PGT was isolated from sediment from the bottom of the salt lake Verkhnee Beloe (Buryatia, Russia). This strain's 7,651,223 bp complete genome has a high G + C content of 72.1% and consists of 7,069 coding sequences and 315 subsystems. The 16S ribosomal RNA of isolate 2BA6PGT was most closely related to Streptomyces cavourensis strain NBRC 13026T (98.91% identity), followed by Streptomyces bacillaris strain ATCC 15855T (95.36%), Streptomyces rhizosphaericola strain 1AS2cT (94.68%), and Streptomyces pluricolorescens strain JCM 4602T (86.75%). These comparisons were supported by pairwise comparisons using average nucleotide identity (ANI) and DNA-DNA hybridization analysis. This is the first complete genome reported on Streptomyces cavourensis isolated from sediment from the bottom of the salt lake Verkhnee Beloe. The complete genome sequence has been deposited at the NCBI GenBank with an accession number CP101140.

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