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Fulltext A modified method for genomic DNA extraction from the fish intestinal microflora

Han Z, Sun J, Lv A, Sung Y, Sun X, Shi H, et al.

AMB Express, 2018 Apr 02;8(1):52.
PMID: 29610998 DOI: 10.1186/s13568-018-0578-3

A modified genomic DNA extraction method named the combination of lysozyme and ultrasonic lysis (CLU) method was used to analyze the fish intestinal microflora. In this method, the physical disruption and chemical lysis steps were combined, and some parameters in the key steps were adjusted. In addition, the results obtained by this method were compared with the results obtained by the Zirmil-beating cell disruption method and the QIAamp Fast DNA Stool Mini Kit. The OD260/OD280ratio and concentration of the DNA extracted using the CLU method were 2.02 and 282.8 µg/µL, respectively; when the incubation temperatures for lysozyme and RNase were adjusted to 37 °C, those values were 2.08 and 309.8 µg/µL, respectively. On the agarose gel, a major high-intensity, discrete band of more than 10 kb was found for the CLU method. However, the smearing intensity of degraded DNA was lower when the incubation temperatures were 60 °C for lysozyme and 30 °C for RNase than when incubation temperatures of 37 °C for lysozyme and 37 °C for RNase were used. The V3 variable region of the prokaryotic 16S rDNA was amplified, and an approximately 600-bp fragment was observed when the DNA extracted using the CLU method was used as a template. The CLU method is simple and cost effective, and it yields high-quality, unsheared, high-molecular-weight DNA, which is comparable to that obtained with a commercially available kit. The extracted DNA has potential for applications in critical molecular biology techniques.

Matched MeSH terms: DNA, Ribosomal
Fulltext In Vitro Pro-apoptotic and Anti-migratory Effects of Ficus deltoidea L. Plant Extracts on the Human Prostate Cancer Cell Lines PC3

Hanafi MMM, Afzan A, Yaakob H, Aziz R, Sarmidi MR, Wolfender JL, et al.

Front Pharmacol, 2017;8:895.
PMID: 29326585 DOI: 10.3389/fphar.2017.00895

This study aims to evaluate the in vitro cytotoxic and anti-migratory effects of Ficus deltoidea L. on prostate cancer cells, identify the active compound/s and characterize their mechanism of actions. Two farmed varieties were studied, var. angustifolia (FD1) and var. deltoidea (FD2). Their crude methanolic extracts were partitioned into n-hexane (FD1h, FD2h) chloroform (FD1c, FD2c) and aqueous extracts (FD1a, FD2a). Antiproliferative fractions (IC50 < 30 μg/mL, SRB staining of PC3 cells) were further fractionated. Active compound/s were dereplicated using spectroscopic methods. In vitro mechanistic studies on PC3 and/or LNCaP cells included: annexin V-FITC staining, MMP depolarization measurements, activity of caspases 3 and 7, nuclear DNA fragmentation and cell cycle analysis, modulation of Bax, Bcl-2, Smac/Diablo, and Alox-5 mRNA gene expression by RT-PCR. Effects of cytotoxic fractions on 2D migration and 3D invasion were tested by exclusion assays and modified Boyden chamber, respectively. Their mechanisms of action on these tests were further studied by measuring the expression VEGF-A, CXCR4, and CXCL12 in PC3 cells by RT-PCR. FD1c and FD2c extracts induced cell death (P < 0.05) via apoptosis as evidenced by nuclear DNA fragmentation. This was accompanied by an increase in MMP depolarization (P < 0.05), activation of caspases 3 and 7 (P < 0.05) in both PC3 and LNCaP cell lines. All active plant extracts up-regulated Bax and Smac/DIABLO, down-regulated Bcl-2 (P < 0.05). Both FD1c and FD2c were not cytotoxic against normal human fibroblast cells (HDFa) at the tested concentrations. Both plant extracts inhibited both migration and invasion of PC3 cells (P < 0.05). These effects were accompanied by down-regulation of both VEGF-A and CXCL-12 gene expressions (P < 0.001). LC-MS dereplication using taxonomy filters and molecular networking databases identified isovitexin in FD1c; and oleanolic acid, moretenol, betulin, lupenone, and lupeol in FD2c. In conclusion, FD1c and FD2c were able to overcome three main hallmarks of cancer in PC3 cells: (1) apoptosis by activating of the intrinsic pathway, (2) inhibition of both migration and invasion by modulating the CXCL12-CXCR4 axis, and (3) inhibiting angiogenesis by modulating VEGF-A expression. Moreover, isovitexin is here reported for the first time as an antiproliferative principle (IC50 = 43 μg/mL, SRB staining of PC3 cells).

Matched MeSH terms: DNA Fragmentation
Fulltext Data on partial polyhydroxyalkanoate synthase genes (phaC) mined from Aaptos aaptos marine sponge-associated bacteria metagenome

Amelia TSM, Amirul AA, Bhubalan K

Data Brief, 2018 Feb;16:75-80.
PMID: 29188224 DOI: 10.1016/j.dib.2017.11.011

We report data associated with the identification of three polyhydroxyalkanoate synthase genes (phaC) isolated from the marine bacteria metagenome of Aaptos aaptos marine sponge in the waters of Bidong Island, Terengganu, Malaysia. Our data describe the extraction of bacterial metagenome from sponge tissue, measurement of purity and concentration of extracted metagenome, polymerase chain reaction (PCR)-mediated amplification using degenerate primers targeting Class I and II phaC genes, sequencing at First BASE Laboratories Sdn Bhd, and phylogenetic analysis of identified and known phaC genes. The partial nucleotide sequences were aligned, refined, compared with the Basic Local Alignment Search Tool (BLAST) databases, and released online in GenBank. The data include the identified partial putative phaC and their GenBank accession numbers, which are Rhodocista sp. phaC (MF457754), Pseudomonas sp. phaC (MF437016), and an uncultured bacterium AR5-9d_16 phaC (MF457753).

Matched MeSH terms: DNA Primers
Mytilus galloprovincialis (Lamarck, 1819) spermatozoa: hsp70 expression and protamine-like protein property studies

Piscopo M, Notariale R, Rabbito D, Ausió J, Olanrewaju OS, Guerriero G

Environ Sci Pollut Res Int, 2018 May;25(13):12957-12966.
PMID: 29478169 DOI: 10.1007/s11356-018-1570-9

In this work, we describe results of the reproductive health monitoring studies in Mytilus galloprovincialis following spermatozoa hsp70 expression and protamine-like protein properties. Mussels control (ctr) were released within cages for 30 days in three different marine sites near Naples (Campania, Italy): Bagnoli south (BAs) and Bagnoli north (BAn), both close to a disposal metallurgical factory and in Capo Miseno (CM). Studies of hsp70 gene expression carried out, by RT-qPCR, in mussel spermatozoa have shown varied expression levels, particularly 5, 13, and 15-fold more than ctr in CM, BAs, and BAn, respectively, indicating highest involvement of stress proteins in spermatozoa of mussels in Bagnoli. In order to evaluate the possible risk on Mytilus galloprovincialis sustainability loss, electrophoretic analyses were performed on protamine-like proteins (PL) of collected spermatozoa. The results showed that CM PL were apparently unaltered with respect to ctr PL, while BAs and BAn PL appeared in part in the form of peptides and in part as bands with low mobility. Further, CM and BAs PL showed, by electrophoretic mobility shift assay, a decrease in DNA binding ability and a change in their DNA binding mode. The results of this investigation show the usefulness of the study of alterations of spermatozoa hsp70 expression and protamine-like protein properties for eco-toxicological evaluation using Mytilus galloprovincialis as a bioindicator.

Matched MeSH terms: DNA
Fulltext Inclusion of 2-Mercaptoethanol in Lysis Buffer Could Interfere with Isolation of High Molecular Weight DNA from Freshwater Microalgae

Yee W, Kumar JN, Muthusamy PD

Indian J Microbiol, 2018 Mar;58(1):109-113.
PMID: 29434405 DOI: 10.1007/s12088-017-0698-5

2-mercaptoethanol (2-ME), alongside polyvinylpyrrolidone is commonly used in plant DNA extractions to deal with polyphenols, which could interfere with extraction and downstream applications. 2-ME is also commonly used to denature proteins and nucleases, especially RNAses. On the contrary, we found that the presence of 2-ME in lysis buffer interfered with DNA extraction from 12 strains of freshwater microalgae, resulting in DNA with poor integrity. We also found that the TNES-urea buffer, commonly used for preservation and DNA extraction from fish, appears as effective as the SDS and CTAB buffer for some microalgae strains. Results from our study suggests that the inclusion of 2-ME in DNA extraction protocols may be detrimental for isolation of good quality DNA from freshwater microalgae, and therefore recommend eliminating it or testing varying concentrations of 2-ME when developing species-specific extraction protocols for microalgae.

Matched MeSH terms: DNA, Plant
Fulltext Identification and Preliminary Evaluation of a Novel Recombinant Protein for Serodiagnosis of Strongyloidiasis

Arifin N, Yunus MH, Nolan TJ, Lok JB, Noordin R

Am J Trop Med Hyg, 2018 04;98(4):1165-1170.
PMID: 29436335 DOI: 10.4269/ajtmh.17-0697

Strongyloides stercoralis is a human parasite that can cause a long-term infection. In immunosuppressed patients, strongyloidiasis may be fatal when there is overwhelming autoinfection resulting in the migration of large numbers of larvae through many organs. Definitive diagnosis is still a challenge, and a combination of symptoms, microscopic identification, and serology test results are often used to arrive at a clinical decision. However, intermittent larval excretion, low parasite burden, and occult infections are challenges with parasitological diagnosis of infection with S. stercoralis. Meanwhile, serologic tests using immunoglobulin G and parasite antigen extract have problems of cross-reactivity with other helminthic infections. Recombinant antigen-based serodiagnosis is a good alternative to overcome the laboratory diagnostic issues. Herein, we report on the isolation of cDNA clone encoding an antigen of potential diagnostic value identified from immunoscreening of a S. stercoralis cDNA library. The translated protein had highest similarity to Strongyloides ratti immunoglobulin-binding protein 1. The recombinant antigen produced, rSs1a, was assessed using western blot and enzyme-linked immunosorbent assay. The latter showed 96% diagnostic sensitivity and 93% specificity; thus, rSs1a has good potential for use in serodiagnosis of human strongyloidiasis.

Matched MeSH terms: DNA, Complementary
Genome Organization of Escherichia Phage YD-2008.s: A New Entry to Siphoviridae Family

Sellvam D, Lau NS, Arip YM

Trop Life Sci Res, 2018 Mar;29(1):37-50.
PMID: 29644014 DOI: 10.21315/tlsr2018.29.1.3

Malaysia is one of the countries that are loaded with mega biodiversity which includes microbial communities. Phages constitute the major component in the microbial communities and yet the numbers of discovered phages are just a minute fraction of its population in the biosphere. Taking into account of a huge numbers of waiting to be discovered phages, a new bacteriophage designated as Escherichia phage YD-2008.s was successfully isolated using Escherichia coli ATCC 11303 as the host. Phage YD-2008.s poses icosahedral head measured at 57nm in diameter with a long non-contractile flexible tail measured at 107nm; proving the phage as one of the members of Siphoviridae family under the order of Caudovirales. Genomic sequence analyses revealed phage YD-2008.s genome as linear dsDNA of 44,613 base pairs with 54.6% G+C content. Sixty-two open reading frames (ORFs) were identified on phage YD-2008.s full genome, using bioinformatics annotation software; Rapid Annotation using Subsystem Technology (RAST). Among the ORFs, twenty-eight of them code for functional proteins. Thirty two are classified as hypothetical proteins and there are two unidentified proteins. Even though majority of the coded putative proteins have high amino acids similarities to phages from the genus Hk578likevirus of the Siphoviridae family, yet phage YD-2008.s stands with its' own distinctiveness. Therefore, this is another new finding to Siphoviridae family as well as to the growing list of viruses in International Committee on Taxonomy of Viruses (ICTV) database.

Matched MeSH terms: DNA
Fulltext Integrative taxonomy of a new and highly-diverse genus of onchidiid slugs from the Coral Triangle (Gastropoda, Pulmonata, Onchidiidae)

Goulding TC, Khalil M, Tan SH, Dayrat B

Zookeys, 2018.
PMID: 29896045 DOI: 10.3897/zookeys.763.21252

A new genus of onchidiid slugs, Wallaconchis Goulding & Dayrat, gen. n., is described, including ten species. Five species were previously described but known only from the type material: Wallaconchis ater (Lesson, 1830), W. graniferum (Semper, 1880), W. nangkauriense (Plate, 1893), W. buetschlii (Stantschinsky, 1907), and W. gracile (Stantschinsky, 1907), all of which were originally classified in Onchidium Buchannan, 1800. Many new records are provided for these five species, which greatly expand their known geographic distributions. Five species are new: Wallaconchis achleitneri Goulding, sp. n., W. comendadori Goulding & Dayrat, sp. n., W. melanesiensis Goulding & Dayrat, sp. n., W. sinanui Goulding & Dayrat, sp. n., and W. uncinus Goulding & Dayrat, sp. n. Nine of the ten Wallaconchis species are found in the Coral Triangle (eastern Indonesia and the Philippines). Sympatry is high, with up to six species found on the island of Bohol (Philippines) and eight species overlapping in northern Sulawesi (Indonesia). Wallaconchis is distinguished from other onchidiids by its bright dorsal colors (red, yellow, orange) but those are extremely variable and not useful for specific identification. Internally, the reproductive system can be used to identify all Wallaconchis species. The copulatory organs of Wallaconchis species are especially diverse compared to other onchidiid genera, and the possible role of reproductive incompatibility in species diversification is discussed. All specimens examined were freshly collected for the purpose of a worldwide revision of the Onchidiidae Rafinesque, 1815. The species are well delineated using DNA sequences and comparative anatomy. Mitochondrial DNA analysis yields thirteen molecular units separated by a large barcode gap, while nuclear DNA yields nine units. By integrating nuclear DNA and mitochondrial DNA with morphology, ten species are recognized. The natural history of each species (e.g., the microhabitat where they are found) is also documented. Nomenclature is addressed thoroughly (the types of all onchidiid species were examined, lectotypes were designated when needed, nomina dubia are discussed). Morphological characters, transitions to new microhabitats, and diversification processes are discussed in the context of a robust molecular phylogeny.

Matched MeSH terms: DNA, Mitochondrial
Fulltext Identification of pathogenic bacteria isolated from raw and after sand filtration water at Lubok Buntar Water Treatment Plant

Nur Hafizah Zakaria, Husnul Azan Tajarudin, Mohd Sharizal Mohd Sapingi, Mohamad Fared Murshed

Scientific Research Journal, 2017;14(1):42-52.
MyJurnal

This study focused on the identification of pathogenic bacteria in raw water intake and after sand filtration for drinking water treatment plant during flood event in 2014. The samples was collected from the Lubok Buntar Water Treatment Plant (WTP) and processed through bacterial isolation using chocolate agar as a media. The isolation process conducted based on serial samples dilution and streaking method prior to DNA extraction. Deoxyribonucleic acid (DNA) extraction kit was used to get selected bacteria DNA and further analysis using Polymerase Chain Reaction (PCR) test and electrophoresis to get DNA sequences. The Basic Local Alignment Search Tool (BLAST) analysis was employed to identify the species of the isolated bacteria. As a result, Pantoeaagglomerans and Enterobacter sp. were found in raw and filtered water sample and indicating the same family types. It was concluded that bacteria of the same species were found before and after sand filtration and need to be removed by disinfectant process. The findings also indicated that all the physicochemical parameters measured were within the values prescribed by the Interim National Water Quality Standard (INWQS).

Matched MeSH terms: DNA
Fulltext Avian polyomavirus: a recent update

Padzil, F., Mariatulqabtiah, A. R., Abu, J.

Jurnal Veterinar Malaysia, 2017;29(2):9-13.
MyJurnal

Avian polyomavirus disease is among the most common viral diseases of domesticated exotic birds as such in psittacine families. Caused by avian polyomavirus (APV) which possess a circular, double-stranded DNA which encodes for major structural virus protein 1 (VP1) and minor structural proteins VP2, VP3 and VP4, the disease is also known as Budgerigar fledgling disease polyomavirus (BFPyV), Papovavirus, and Psittacine polyomavirus. Infections from APV may lead to cutaneous haemorrhage, abdominal distension, feather abnormalities and even death. The APV virus has a broad avian host range and is known to cause acute chronic disease in several psittacine birds such as parrot, cockatoo, macaw, and budgerigar. The current status of APV epidemiology globally has not been fully recorded. Only the studies of the virus and disease caused within several countries are used as references, and few were done together with detection of beak and feather disease virus. Despite the common occurrence of APV among bird breeders in Malaysia, a very limited study has been done to evaluate the prevalence status of APV in Malaysia. In this review, we wish to disseminate knowledge, particularly to pet owners and bird breeders, on APV characterisations, its updated occurrence worldwide and prevention strategies. This information may be useful to trigger in depth study on the epidemiology of disease and better management practises among breeders.

Matched MeSH terms: DNA
Fulltext Pyrosequencing-based quantitative evaluation of P16 methylation in diffuse large b-cell lymphoma

Mohd. Ridah L.J., Ismail A., A. Talib N., Muhammad N., Hussain F.A., Zainuddin N.

Journal of Biomedical and Clinical Sciences, 2016;1(1):12-17.
MyJurnal

Introduction: Methylation of promoter region of p16 leading to gene silencing has been implicated ina wide range of malignancies including lymphomas. In diffuse large B cell lymphoma (DLBCL) particularly, a varying percentage of epigenetic inactivation of p16 promoter region was observed ranging from 16 -54%. However, quantitative analysis of p16 promoter methylation in DLBCL has not been extensively studied in Malaysia. Objective: This study aims to quantitatively analyse p16 methylation in DLBCL samples using pyrosequencing technique. Methods: Genomic DNA was extracted from 16 formalin-fixed paraffin-embedded lymphoma tissue blocks from patients diagnosed with DLBCL. Samples were retrieved from Hospital Tengku Ampuan Afzan, Pahang and Hospital Universiti Sains Malaysia, Kelantan. Primers were designed to amplify bisulfite-treated DNA targeting p16 promoter region. Methylation status of 7 CpG sites was determined by pyrosequencing. Results: All the 16 samples studied showed promoter methylation of p16. The range of mean methylation percentage was between 18 to 81%. Conclusion: The present study has successfully measured the level of methylation of p16 in all 7 CpG sites despite the limitation in sample size. Since p16 methylation is a common event in our series of DLBCL cases, it is worth including a larger sample size in future studies to increase the chance of finding a significant correlation with clinical parameters.

Matched MeSH terms: DNA
Characterization of Simulium (Simulium) hackeri Edwards (Diptera: Simuliidae) from Malaysia: Morphological description of the pupa and larva, and DNA barcoding

Ya'cob Z, Takaoka H, Low VL, Sofian-Azirun M

Acta Trop, 2018 Sep;185:110-114.
PMID: 29709632 DOI: 10.1016/j.actatropica.2018.04.029

Simulium (Simulium) hackeri Edwards, 1928 of the Simulium variegatum species-group from Malaysia was described initially based on the female specimen from Cameron Highlands, Pahang. In the present study, the pupa and larva of this species are described for the first time. Their morphological characters resemble those of the Simulium variegatum species-group by having six gill filaments per side, abdomen with dorsal spine-combs at least on segments 7 and 8, cocoon with wall-pocket shaped and with or without an anterodorsal projection. Postgenal cleft of the larva medium-sized, rarely small, ventral papillae small or absent. The DNA barcode of this species is also reported herein.

Matched MeSH terms: DNA Barcoding, Taxonomic
Fulltext Developing new primers for molecular identification of plasmodium spp. recorded in Sabah

Chua, T.H., Stanis, C.S., Song, B.K., Lau, Y.L., Jelip, P., Lau, T.Y.

Borneo Journal of Medical Sciences, 2015;9(1):3-10.
MyJurnal

Malaria is a major public health problem in tropical and subtropical areas, caused by five
species of Plasmodium (P. falciparum, P. vivax, P. malariae, P. ovale andP. knowlesi) and is the leading cause of morbidity and mortality worldwide. We have developed molecular markers for three genes viz, Cytb, dhfr and Msp-1 gene and designed a protocol for rapid molecular diagnostics of the four malaria parasites prevalent in Southeast Asia. The new primers were used on the blood
samples containing Plasmodium parasites by conventional PCR. The result was compared with
the nested PCR of Singh et al. (2004) and the microscopy method. The result shows that the new
set of primers had successfully amplified all four human malaria parasite species. These primers
were 100% sensitive and more specific than microscopy and PCR identification using these
primers was faster than the nested PCR. These alternative primers should provide powerful and
rapid molecular diagnostic method for detecting Plasmodium species as well as providing reliable
data for epidemiology study. These primers have the potential to be combined and used in
multiplex PCR.

Matched MeSH terms: DNA Primers
Metal-Polydopamine Framework as an Effective Fluorescent Quencher for Highly Sensitive Detection of Hg(II) and Ag(I) Ions through Exonuclease III Activity

Ravikumar A, Panneerselvam P, Morad N

ACS Appl Mater Interfaces, 2018 Jun 20;10(24):20550-20558.
PMID: 29792319 DOI: 10.1021/acsami.8b05041

In this paper, we propose a metal-polydopamine (MPDA) framework with a specific molecular probe which appears to be the most promising approach to a strong fluorescence quencher. The MPDA framework quenching ability toward various organic fluorophore such as aminoethylcoumarin acetate, 6-carboxyfluorescein (FAM), carboxyteramethylrhodamine, and Cy5 are used to establish a fluorescent biosensor that can selectively recognize Hg2+ and Ag+ ions. The fluorescent quenching efficiency was sufficient to achieve more than 96%. The MPDA framework also exhibits different affinities with ssDNA and dsDNA. In addition, the FAM-labeled ssDNA was adsorbed onto the MPDA framework, based on their interaction with the complex formed between MPDA frameworks/ssDNA taken as a sensing platform. By taking advantage of this sensor, highly sensitive and selective determination of Hg2+ and Ag+ ions is achieved through exonuclease III signal amplification activity. The detection limits of Hg2+ and Ag+ achieved to be 1.3 and 34 pM, respectively, were compared to co-existing metal ions and graphene oxide-based sensors. Furthermore, the potential applications of this study establish the highly sensitive fluorescence detection targets in environmental and biological fields.

Matched MeSH terms: DNA, Single-Stranded
Enhanced phagocytosis of Aggregatibacter actinomycetemcomitans cells by macrophages activated by a probiotic Lactobacillus strain

Jaffar N, Okinaga T, Nishihara T, Maeda T

J Dairy Sci, 2018 Jul;101(7):5789-5798.
PMID: 29680655 DOI: 10.3168/jds.2017-14355

The activation of phagocytosis is one important approach to clearing pathogenic cells in a host. This study evaluated the ability of probiotic lactobacilli to induce phagocytic activity as well as the clearance of a periodontal pathogen, Aggregatibacter actinomycetemcomitans. First, the activation of phagocytosis was found by using lyophilized dead cells. Probiotic Lactobacillus strains significantly enhanced the phagocytic activity of macrophage cells, indicating that the probiotic lactobacilli have a remarkable ability to stimulate the macrophages. Essentially, 3 Lactobacillus strains tested did not have any critical toxic effect on the murine macrophage, and Lactobacillus johnsonii NBRC 13952 showed the least cytotoxic effect on the RAW264.7 macrophages. The expression of classically activated macrophage markers, IL-1β, and cluster of differentiation 80 increased by L. johnsonii NBRC 13952; however, there was no significant difference for IL-18. The highest phagocytic activity by macrophages was found in a condition in which the macrophage activated by L. johnsonii NBRC 13952 functions to kill the cells of A. actinomycetemcomitans. Correlating with the result, a high amount of hypodiploid DNA (SubG1) was detected from the macrophage cells stimulated by L. johnsonii NBRC 13952. Taken together, the results suggest that macrophages activated by the Lactobacillus strain can facilitate the phagocytosis of A. actinomycetemcomitans cells by linking with enhanced apoptotic activities. In conclusion, L. johnsonii NBRC 13952 has a certain role in activating the RAW264.7 macrophages, thereby counteracting the infection of A. actinomycetemcomitans.

Matched MeSH terms: DNA
Fulltext Evaluation of heterozygous Hb E and its interaction with deletional alpha thalassaemia in Kelantan

Nur Hidayah Muhamad Yasin, Majdan Ramli, Ilunihayati Ibrahim, Rosnah Bahar, Noraesah Mahmud, Siti Shahrum Muhamed Said, et al.

Journal of Biomedical and Clinical Sciences, 2017;2(202):35-37.
MyJurnal

Haemoglobin E (Hb E) is a variant of structurally abnormal haemoglobin that can be found very commonly in the Asian countries particularly the Southeast Asian [1]. [H1] Alpha thalassaemia is a red cell disorder which is caused by deletion or mutation of one or more of the four alpha globin genes leading to absence or decrease in production of alpha globin peptides [2]. This disorder is far more common in South East Asian regions and in Malaysia itself, and the gene frequency is about 4.1% [2]. The interactions of Hb E and alpha thalassaemia are evident in Kelantan which is bordered by southern Thailand. Using capillary electrophoresis (CE), a reduction of Hb E level is noticed as compared to Hb E heterozygotes. DNA analysis should be done to determine the presence of concurrent alpha thalassaemia variant. This study was done to evaluate haematological parameters using automated blood counters, morphology of red cells, Hb separation and quantitation of Hb fractions using CE and molecular analysis for alpha thalassemia. The study also aimed to discover cut off point of Hb E level in heterozygous Hb E patients with concurrent deletional alpha thalassaemia by CE.

Matched MeSH terms: DNA
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 DNA mismatch repair and CD133-marked cancer stem cells in colorectal carcinoma

Cheah PL, Li J, Looi LM, Teoh KH, Ong DB, Arends MJ

PeerJ, 2018;6:e5530.
PMID: 30221090 DOI: 10.7717/peerj.5530

Background: Except for a few studies with contradictory observations, information is lacking on the possibility of association between DNA mismatch repair (MMR) status and the presence of cancer stem cells in colorectal carcinoma (CRC), two important aspects in colorectal carcinogenesis.
Methods: Eighty (40 right-sided and 40 left-sided) formalin-fixed, paraffin-embedded primary CRC were immunohistochemically studied for CD133, a putative CRC stem cell marker, and MMR proteins MLH1, MSH2, MSH6 and PMS2. CD133 expression was semi-quantitated for proportion of tumor immunopositivity on a scale of 0-5 and staining intensity on a scale of 0-3 with a final score (units) being the product of proportion and intensity of tumor staining. The tumor was considered immunopositive only when the tumor demonstrated moderate to strong intensity of CD133 staining (a decision made after analysis of CD133 expression in normal colon). Deficient MMR (dMMR) was interpreted as unequivocal loss of tumor nuclear staining for any MMR protein despite immunoreactivity in the internal positive controls.
Results: CD133 was expressed in 36 (90.0%) left-sided and 28 (70.0%) right-sided tumors (p 0.05).
Conclusion: Proficient MMR correlated with high levels of CD133-marked putative cancer stem cells in both right- and left-sided tumors, whereas significantly lower levels of CD133-marked putative cancer stem cells were associated with deficient MMR status in colorectal carcinomas found on the right.

Matched MeSH terms: DNA Mismatch Repair
Fulltext Feature selection methods: case of filter and wrapper approaches for maximising classification accuracy

Wah, Yap Bee, Nurain Ibrahim, Hamzah Abdul Hamid, Shuzlina Abdul-Rahman, Fong, Simon

Pertanika Journal of Science & Technology, 2018;26(1):329-340.
MyJurnal

Feature selection has been widely applied in many areas such as classification of spam emails, cancer cells, fraudulent claims, credit risk, text categorisation and DNA microarray analysis. Classification involves building predictive models to predict the target variable based on several input variables (features). This study compares filter and wrapper feature selection methods to maximise the classifier accuracy. The logistic regression was used as a classifier while the performance of the feature selection methods was based on the classification accuracy, Akaike information criteria (AIC), Bayesian information criteria (BIC), Area Under Receiver operator curve (AUC), as well as sensitivity and specificity of the classifier. The simulation study involves generating data for continuous features and one binary dependent variable for different sample sizes. The filter methods used are correlation based feature selection and information gain, while the wrapper methods are sequential forward and sequential backward elimination. The simulation was carried out using R, an open-source programming language. Simulation results showed that the wrapper method (sequential forward selection and sequential backward elimination) methods were better than the filter method in selecting the correct features.

Matched MeSH terms: DNA
Fulltext Zerumbone-Loaded Nanostructured Lipid Carrier Induces Apoptosis of Canine Mammary Adenocarcinoma Cells

Foong JN, Selvarajah GT, Rasedee A, Rahman HS, How CW, Beh CY, et al.

Biomed Res Int, 2018;2018:8691569.
PMID: 30410940 DOI: 10.1155/2018/8691569

Canine mammary gland tumor (CMT) is the most common tumor in intact female dog. Zerumbone (ZER) has promising anticancer properties, but plagued with poor water solubility, poor absorption, bioavailability, and delivery to target tissues. To solubilize, ZER was loaded into nanostructured lipid carrier (NLC) to produce ZER-loaded NLC (ZER-NLC). The objectives of this study were to determine the antiproliferative effect and the mode of cell death induced by ZER-NLC and ZER on a canine mammary gland tumor (CMT) adenocarcinoma primary cell line. There was no significant difference (p>0.05) between ZER-NLC and ZER treatments in the inhibition of CMT cell proliferation; thus, the loading of ZER into NLC did not compromise the cytotoxic effect of ZER. Microscopically, ZER-NLC- and ZER-treated CMT cells showed apoptotic cell morphology. ZER-NLC and ZER treatments significantly downregulated the antiapoptotic Bcl-2 and upregulated the proapoptotic Bax gene expressions in CMT cells. Both ZER-NLC and ZER-treated CMT cells showed significant (p<0.0001) increases in caspase-8, -9, and -3/7 protein activities. In conclusion, ZER-NLC induced CMT cell death via regulation of Bcl-2 and Bax gene expressions and caspase activations, indicating the involvement of both the intrinsic and extrinsic pathways of apoptosis. This study provided evidences for the potential of ZER-NLC as an anticanine mammary gland adenocarcinoma chemotherapy.

Matched MeSH terms: DNA-Binding Proteins

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