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  1. Mustapha Bala Abubakar, Aini Ideris, AbdulRahman Omar, Mohd Hair Bejo
    MyJurnal
    Avian Influenza viruses belonging to the Orthomyxoviridae family are enveloped viruses with segmented negative sense RNA genome surrounded by a helical symmetry capsid. Influenza viruses, especially the highly pathogenic avian influenza virus (HPAI) such as H5 or H7 subtype are the most important pathogens for the poultry industry in recent times. The haemagglutinin protein and neuraminidase, serves as the target for the immune response of the host. Due to recurrent genetic reassortments between avian and human influenza viruses, global pandemics may emerge and the naive human immunity could not withstand pressure by the novel hybrid virus. The emergence of genetic engineering technology provided the industry with new methods of manufacturing diagnostics tools and vaccines. After extraction of RNA from the cell culture of strain influenza A/Chicken/Malaysia/2004(H5N1) of AIV, the viral RNA was converted to cDNA by a specific primer. The cDNA was amplified by the polymerase chain reaction (PCR) and analyzed
    by agarose gel electrophoresis. The intact PCR product of full length haemagglutinin gene was cloned in TO POTM TA Cloning vector. The full-length HA-encoding gene of H5N1 AIV was subcloned into a pPICZA vector. After successful ligation, the constructed plasmid was transformed into E.coli.Top10, Plasmid DNA from transformed bacteria was extracted in white colony and positive clones were confirmed by restriction digestion with Sacl and Not1 restriction enzymes, colony PCR screening and nucleotide sequencing. Construction of a recombinant pPICZA/H5HA plasmid containing the full length haemagglutinin gene was achieved as a first step
    towards the expression in Pichia pastoris.
    Matched MeSH terms: DNA Primers; DNA, Complementary
  2. Suzana Shahar, Kim, Tiu Teng, Nor Fadilah Rajab, Fatimah Arshad
    MyJurnal
    A preliminary study was conducted to determine the level of oxidative DNA damage, fruits and vegetables intake among 50 breast cancer patients (cases) as compared to 50 healthy women (controls) with no known medical history of breast cancer in Klang Valley. Both groups were matched for age and ethnicity. Data on socio-demographic, health status and medical history, fruits and vegetables intake, and supplements intake were obtained through an interviewbased questionnaire. Anthropometry measurements included weight, height, and waist and hip circumference were also carried out on subjects. A total of 3mL fasting venous blood was drawn to assess lymphocytes oxidative DNA damage using Alkaline Comet Assay. Results indicated that the mean intake of fruits and vegetables was lower in cases (4.09 ± 1.17 servings/d) than controls (4.77 ± 0.90 servings/d)(p < 0.05) The intake of fruits and vegetables from family groups of solanaceae, myrtaceae, caricaceae, apiaceae, brinjal, rutaceae, broccoli, orange, carrot, watermelon were 0.5 - 1 servings/week significantly higher among controls as compared to cases (p < 0.05 for all parameters). However, the intake of fruits from rosaceae family and apple was higher among controls than cases (p < 0.05). The estimated intake of ß-carotene, carotenoids, vitamin A, vitamin C (p < 0.001), a-carotene and lycopene (p < 0.05) from fruits and vegetables were higher among controls than cases. Mean DNA damage level of cases (4.55 ± 1.78 % DNA in tail, %TD; 0.35 ± 0.21 tail moment, TM) were 3.5 and 3.9 times higher than the value of controls (1.3 ± 0.70% TD; 0.09 ± 0.09 TM) (p < 0.001) and the damage increased with higher values of waist hip ratio (% TD, r = 0.396, p < 0.05; TM, r = 0.349, p < 0.05) and waist circumference (% TD, r = 0.334, p < 0.05; TM, r = 0.360, p < 0.05). There was an inverse relationship between oxidative DNA damage with intake of total fruits and vegetables, cauliflowers and water convolvulus and also consumption from rutaceae and solanaceae families. Similar trend was noted for estimated intake of vitamin A, carotenoids, vitamin C, ß-carotene and lycopene. In conclusion, the intake of fruits and vegetables of five servings/d and the consumption of specific families and types of fruits and vegetables might protect against oxidative DNA damage and further reduce breast cancer risk.
    Matched MeSH terms: DNA; DNA Damage
  3. Ismail NF, Rani AQ, Nik Abdul Malik NM, Boon Hock C, Mohd Azlan SN, Abdul Razak S, et al.
    J Mol Diagn, 2017 03;19(2):265-276.
    PMID: 28087349 DOI: 10.1016/j.jmoldx.2016.10.009
    Tuberous sclerosis complex (TSC) is an autosomal dominant neurocutaneous disorder characterized by tumor growth in multiple organs and caused by mutations in either TSC1 or TSC2 genes. Because of their relatively large genomic sizes, absence of hotspots, and common type of mutations, mutation detection in TSC1 and TSC2 genes has been challenging. We devised a combination of multiple ligation-dependent probe amplification (MLPA) and amplicon sequencing (AS) to simplify the detection strategy, yet we come up with reasonably high detection rate. Thirty-four Malaysian patients diagnosed with TSC were referred to Human Genome Center, Universiti Sains Malaysia. We used a combination of MLPA to detect large copy number changes and AS to detect smaller mutations. TSC1 pathogenic or likely pathogenic mutations were found in 6 patients (18%) and TSC2 in 21 patients (62%), whereas 6 patients (18%) show no mutations and 1 patient (2%) showed only TSC2 missense variant with uncertain significance. Six of the mutations are novel. Our detection strategy costs 81% less and require 1 working week less than the conventional strategy. Confirmatory sequencing using Sanger method on a few representative mutations showed agreement with results of the AS. Combination of MLPA and Illumina MiSeq AS provides a simplified strategy and reasonably high detection rate for TSC1/TSC2 mutation, which suggested application of the strategies into clinical molecular diagnostics.
    Matched MeSH terms: DNA Mutational Analysis/methods
  4. Goh KM, Liew KJ, Chai KP, Illias RM
    Methods Mol Biol, 2017;1498:385-396.
    PMID: 27709591
    Protein engineering is a very useful tool for probing structure-function relationships in proteins. Specifically, site-directed mutagenized proteins can provide useful insights into structural, binding and catalytic mechanisms of a protein, particularly when coupled with crystallization. In this chapter, we describe two protocols for performing site-directed mutagenesis of any protein-coding sequence, namely, megaprimer PCR and overlapping extension PCR (OE-PCR). We use as an example how these two SDM methods enhanced the function of a cyclodextrin glucosyltransferase (CGTase) from Bacillus lehensis strain G1.
    Matched MeSH terms: DNA Primers/genetics*
  5. Hancock SJ, Phan MD, Peters KM, Forde BM, Chong TM, Yin WF, et al.
    PMID: 27872077 DOI: 10.1128/AAC.01740-16
    Plasmids of incompatibility group A/C (IncA/C) are becoming increasingly prevalent within pathogenic Enterobacteriaceae They are associated with the dissemination of multiple clinically relevant resistance genes, including blaCMY and blaNDM Current typing methods for IncA/C plasmids offer limited resolution. In this study, we present the complete sequence of a blaNDM-1-positive IncA/C plasmid, pMS6198A, isolated from a multidrug-resistant uropathogenic Escherichia coli strain. Hypersaturated transposon mutagenesis, coupled with transposon-directed insertion site sequencing (TraDIS), was employed to identify conserved genetic elements required for replication and maintenance of pMS6198A. Our analysis of TraDIS data identified roles for the replicon, including repA, a toxin-antitoxin system; two putative partitioning genes, parAB; and a putative gene, 053 Construction of mini-IncA/C plasmids and examination of their stability within E. coli confirmed that the region encompassing 053 contributes to the stable maintenance of IncA/C plasmids. Subsequently, the four major maintenance genes (repA, parAB, and 053) were used to construct a new plasmid multilocus sequence typing (PMLST) scheme for IncA/C plasmids. Application of this scheme to a database of 82 IncA/C plasmids identified 11 unique sequence types (STs), with two dominant STs. The majority of blaNDM-positive plasmids examined (15/17; 88%) fall into ST1, suggesting acquisition and subsequent expansion of this blaNDM-containing plasmid lineage. The IncA/C PMLST scheme represents a standardized tool to identify, track, and analyze the dissemination of important IncA/C plasmid lineages, particularly in the context of epidemiological studies.
    Matched MeSH terms: DNA Transposable Elements; DNA Replication
  6. Norbäck D, Hashim JH, Hashim Z, Sooria V, Ismail SA, Wieslander G
    Int J Hyg Environ Health, 2017 06;220(4):697-703.
    PMID: 28254266 DOI: 10.1016/j.ijheh.2017.01.016
    BACKGROUND: There are few studies on ocular effects of indoor mould exposure in schools, especially in the tropics OBJECTIVE: To study associations between eye symptoms and tear film break up time (BUT) in students and demographic data and fungal DNA in schools.

    METHODS: A school environment study was performed among randomly selected students in eight randomly selected secondary schools in Penang, Malaysia. Information on eye symptoms and demographic data was collected by a standardised questionnaire. BUT was measured by two methods, self-reported BUT (SBUT) and by the non-invasive Tearscope (NIBUT). Dust was collected by vacuuming in 32 classrooms and analysed for five fungal DNA sequences. Geometric mean (GM) for total fungal DNA was 7.31*104 target copies per gram dust and for Aspergillus/Penicillium DNA 3.34*104 target copies per gram dust. Linear mixed models and 3-level multiple logistic regression were applied adjusting for demographic factors.

    RESULTS: A total of 368 students (58%) participated and 17.4% reported weekly eye symptoms the last 3 months. The median SBUT and TBUT were 15 and 12s, respectively. Students wearing glasses (OR 2.41, p=0.01) and with a history of atopy (OR=2.67; p=0.008) had more eye symptoms. Girls had less eye symptoms than boys (OR=0.34; p=0.006) Indoor carbon dioxide in the classrooms was low (range 380-720ppm), temperature was 25-30°C and relative air humidity 70-88%. Total fungal DNA in vacuumed dust was associated with shorter SBUT (4s shorter per 105 target copies per gram dust; p=0.04) and NIBUT (4s shorter per 105 target copies per gram dust; p<0.001). Aspergillus/Penicillium DNA was associated with shorter NIBUT (5s shorter per 105 target copies per gram dust; p=0.01).

    CONCLUSION: Fungal contamination in schools in a tropical country can be a risk factor for impaired tear film stability among students.

    Matched MeSH terms: DNA, Fungal/analysis*
  7. Radu S, Yuherman, Rusul G, Yeang LK, Nishibuchi M
    PMID: 11414409
    A total of 57 Vibrio vulnificus isolates from coastal water were characterized for their antimicrobial resistance, plasmid profiles and were typed by the PCR-based techniques: a random amplification of polymorphic DNA (RAPD) method and the enterobacterial repetitive intergenic consensus sequence (ERIC) method. All isolates were susceptible to chloramphenicol, nalidixic acid, tetracycline and trimethoprim-sulfamethoxazole. Fifty-one isolates were resistant to one or more of the other antibiotics tested. Plasmid analysis indicated that only 18 isolates carried small plasmids of 1.6 to 16 megadaltons. Analysis of the RAPD and ERIC DNA fingerprints of the V. vulnificus isolates with Gel Compare and cluster analysis software revealed significant genetic heterogeneity among these isolates. The combination of RAPD and ERIC analysis allowed us to distinguish all isolates. Thus, the combination of the two techniques is recommended for epidemiological investigation.
    Matched MeSH terms: DNA Primers; Random Amplified Polymorphic DNA Technique
  8. Cabauatan PQ, Melcher U, Ishikawa K, Omura T, Hibino H, Koganezawa H, et al.
    J Gen Virol, 1999 Aug;80 ( Pt 8):2229-37.
    PMID: 10466823
    The DNA of three biological variants, G1, Ic and G2, which originated from the same greenhouse isolate of rice tungro bacilliform virus (RTBV) at the International Rice Research Institute (IRRI), was cloned and sequenced. Comparison of the sequences revealed small differences in genome sizes. The variants were between 95 and 99% identical at the nucleotide and amino acid levels. Alignment of the three genome sequences with those of three published RTBV sequences (Phi-1, Phi-2 and Phi-3) revealed numerous nucleotide substitutions and some insertions and deletions. The published RTBV sequences originated from the same greenhouse isolate at IRRI 20, 11 and 9 years ago. All open reading frames (ORFs) and known functional domains were conserved across the six variants. The cysteine-rich region of ORF3 showed the greatest variation. When the six DNA sequences from IRRI were compared with that of an isolate from Malaysia (Serdang), similar changes were observed in the cysteine-rich region in addition to other nucleotide substitutions and deletions across the genome. The aligned nucleotide sequences of the IRRI variants and Serdang were used to analyse phylogenetic relationships by the bootstrapped parsimony, distance and maximum-likelihood methods. The isolates clustered in three groups: Serdang alone; Ic and G1; and Phi-1, Phi-2, Phi-3 and G2. The distribution of phylogenetically informative residues in the IRRI sequences shared with the Serdang sequence and the differing tree topologies for segments of the genome suggested that recombination, as well as substitutions and insertions or deletions, has played a role in the evolution of RTBV variants. The significance and implications of these evolutionary forces are discussed in comparison with badnaviruses and caulimoviruses.
    Matched MeSH terms: DNA, Bacterial; Sequence Analysis, DNA
  9. Cox-Singh J, Pomrehn AS, Rahman HA, Zakaria R, Miller AO, Singh B
    Int J Parasitol, 1999 May;29(5):717-21.
    PMID: 10404266
    In the absence of a suitable Brugia malayi antigen detection assay, PCR remains one of the more sensitive alternatives to Giemsa-stained thick blood films for B. malayi detection. The need for refrigerated storage and transportation of blood has limited the use of PCR for large-scale epidemiology studies in remote endemic areas. Here we report simple finger-prick blood-spot collection, a one-tube DNA template extraction method and the development of a B. malayi-specific nested PCR assay. The assay was tested on 145 field samples and was positive for all 30 microscopy-positive samples and for an additional 13 samples which were microscopy-negative.
    Matched MeSH terms: DNA, Helminth/isolation & purification*
  10. Choong ML, Koay ES, Khaw MC, Aw TC
    Hum Hered, 1999 Jan;49(1):31-40.
    PMID: 9858855
    The allele frequencies for the apolipoprotein B (apo B) 5'-Ins/Del and 3'-VNTR polymorphisms varied significantly (p < 0.01) among Singaporeans of Chinese, Malay and Indian descent. We calculated the unbiased expected heterozygosities for the 5'-Ins/Del polymorphism as 0.3357, 0.1984 and 0.2418, and for the 3'-VNTR as 0.5980, 0.5260 and 0.6749, respectively, in the Chinese, Malays and Indians. Compared to heterozygosities reported for other populations, the Singaporeans differed from most Caucasians in having significantly lower values but were closely related to other non-Caucasians. Thirteen alleles, with a bimodal distribution, were observed at the 3'-VNTR polymorphic locus; the alleles occurring most frequently among the Chinese and Malays were of 35 or 53 repeats, and among the Indians, of 37 or 47 repeats. The Del allele was associated with elevated serum cholesterol (p = 0.023), LDL-cholesterol (LDL-C) (p = 0.001) in the Chinese, and apo B (p = 0.007) in the Indians. Likewise, the larger 3'-VNTR alleles (> 41 repeats) were associated with raised cholesterol (p = 0.018), LDL-C (p = 0.025), and triglyceride (p = 0.001) in the Chinese. The two polymorphisms were not in significant linkage disequilibrium (D = -0.0029, p = 0.494) in the three ethnic groups.
    Matched MeSH terms: DNA Transposable Elements/genetics
  11. Leisner JJ, Pot B, Christensen H, Rusul G, Olsen JE, Wee BW, et al.
    Appl Environ Microbiol, 1999 Feb;65(2):599-605.
    PMID: 9925588
    Ninety-two strains of lactic acid bacteria (LAB) were isolated from a Malaysian food ingredient, chili bo, stored for up to 25 days at 28 degreesC with no benzoic acid (product A) or with 7,000 mg of benzoic acid kg-1 (product B). The strains were divided into eight groups by traditional phenotypic tests. A total of 43 strains were selected for comparison of their sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) whole-cell protein patterns with a SDS-PAGE database of LAB. Isolates from product A were identified as Lactobacillus plantarum, Lactobacillus fermentum, Lactobacillus farciminis, Pediococcus acidilactici, Enterococcus faecalis, and Weissella confusa. Five strains belonging to clusters which could not be allocated to existing species by SDS-PAGE were further identified by 16S rRNA sequence comparison. One strain was distantly related to the Lactobacillus casei/Pediococcus group. Two strains were related to Weissella at the genus or species level. Two other strains did not belong to any previously described 16S rRNA group of LAB and occupied an intermediate position between the L. casei/Pediococcus group and the Weissella group and species of Carnobacterium. The latter two strains belong to the cluster of LAB that predominated in product B. The incidence of new species and subspecies of LAB in chili bo indicate the high probability of isolation of new LAB from certain Southeast Asian foods. None of the isolates exhibited bacteriocin activity against L. plantarum ATCC 14917 and LMG 17682.
    Matched MeSH terms: DNA, Bacterial/chemistry
  12. Salemi S, Besson A, Eblé A, Gallati S, Pfäffle RW, Mullis PE
    Growth Horm. IGF Res., 2003 Oct;13(5):264-8.
    PMID: 12932747
    OBJECTIVE: Growth is an inherent property of life. About 10% of the congenital forms of growth retardation and short stature are genetically caused. Beside the gene involved in direct GH-production, there are different candidate genes important for appropriate pituitary development causing combined pituitary hormone deficiency (CPHD). However, severe growth retardation and failure to thrive remain the leading reason for medical assessment in these patients.

    PATIENTS AND METHODS: We report two siblings of a healthy but consanguineous Malaysian family presenting with severe short stature caused by CPHD with a variable phenotype. Importantly, at the beginning the girl presented with isolated GHD, whereas the boy was hypothyroid. As the most common gene alterations responsible for CPHD are within either the PROP-1- or the POU1F1- (PIT-1)-gene these two genes were further studied.

    RESULTS: Subsequent sequencing of the six exons of the POU1F1-gene allowed the identification of a new N-terminal mutation (Q4ter) in these two children. A substitution of C to T induced a change from a glutamine (CAA) to a stop codon (TAA) in exon 1 of the PIT-1 protein. Both affected children were homozygous for the mutation, whereas the mother and father were heterozygous.

    CONCLUSION: We describe two children with autosomal recessive inherited CPHD caused by a new N-terminal located mutation within the PUO1F1-gene. The clinical history of these two children underline the phenotypic variability and support the fact that children with any isolated and/or combined PHD need to be closely followed as at an any time other hormonal deficiencies may occur. In addition, molecular analysis of the possible genes involved might be most helpful for the future follow-up.

    Matched MeSH terms: DNA-Binding Proteins/genetics*
  13. Norazah A, Lim VK, Rohani MY, Alfizah H, Koh YT, Kamel AG
    Epidemiol Infect, 2003 Jun;130(3):407-11.
    PMID: 12825724
    This study was conducted to determine the molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in Malaysian hospitals. A total of 264 MRSA isolates from eight hospitals were subjected to typing by pulsed-field gel electrophoresis (PFGE) of SmaI restricted DNA. Antibiotic disk susceptibility testing was also carried out to determine their resistance patterns. Thirty-one PFGE pattern types were identified. Three major pattern types A, ZC and K were found with type A the predominant profile in c. 80% of strains and present in all hospitals. Unlike type A, other DNA pattern types were unique to the hospitals in which they were isolated. PFGE type A also consisted of strains that were multiply antibiotic resistant. The presence of a single predominant PFGE type in Malaysian hospitals is an important finding which suggests that inter-hospital spread of MRSA had occurred frequently and regularly.
    Matched MeSH terms: DNA, Bacterial/genetics
  14. Yu H, Wang W, Fang S, Zhang YP, Lin FJ, Geng ZC
    Mol Phylogenet Evol, 1999 Dec;13(3):556-65.
    PMID: 10620413
    The sequences of the mitochondrial ND4 gene (1339 bp) and the ND4L gene (290 bp) were determined for all the 14 extant taxa of the Drosophila nasuta subgroup. The average A + T content of ND4 genes is 76.5% and that of ND4L genes is 83.5%. A total of 114 variable sites were scored. The ND4 gene sequence divergence ranged from 0 to 5.4% within the subgroup. The substitution rate of the ND4 gene is about 1.25% per million years. The base substitution of the genes is strongly transition biased. Neighbor-joining and parsimony were used to construct a phylogeny based on the resultant sequence data set. According to these trees, five distinct mtDNA clades can be identified. D. niveifrons represents the most diverged lineage. D. sulfurigaster bilimbata and D. kepulauana form two independent lineages. The other two clades are the kohkoa complex and the albomicans complex. The kohkoa complex consists of D. sulfurigaster sulfurigaster, D. pulaua, D. kohkoa, and Taxon-F. The albomicans complex can be divided into two groups: D. nasuta, D. sulfurigaster neonasuta, D. sulfurigaster albostrigata, and D. albomicans from Chiangmai form one group; and D. pallidifrons, Taxon-I, Taxon-J, and D. albomicans from China form the other group. High genetic differentiation was found among D. albomicans populations. Based on our phylogenetic results, we hypothesize that D. niveifrons diverged first from the D. nasuta subgroup in Papua New Guinea about 3.5 Mya. The ancestral population spread to the north and when it reached Borneo, it diversified sequentially into the kohkoa complex, D. s. bilimbata, and D. kepulauana. About 1 Mya, another radiation occurred when the ancestral populations reached the Indo-China Peninsula, forming the albomicans complex. Discrepancy between morphological groupings and phylogenetic results suggests that the male morphological traits may not be orthologous.
    Matched MeSH terms: DNA, Mitochondrial/genetics*
  15. Poniah P, Mohd Zain S, Abdul Razack AH, Kuppusamy S, Karuppayah S, Sian Eng H, et al.
    Urol Oncol, 2017 09;35(9):545.e1-545.e11.
    PMID: 28527622 DOI: 10.1016/j.urolonc.2017.04.017
    BACKGROUND: Two key issues in prostate cancer (PCa) that demand attention currently are the need for a more precise and minimally invasive screening test owing to the inaccuracy of prostate-specific antigen and differential diagnosis to distinguish advanced vs. indolent cancers. This continues to pose a tremendous challenge in diagnosis and prognosis of PCa and could potentially lead to overdiagnosis and overtreatment complications. Copy number variations (CNVs) in the human genome have been linked to various carcinomas including PCa. Detection of these variants may improve clinical treatment as well as an understanding of the pathobiology underlying this complex disease.

    METHODS: To this end, we undertook a pilot genome-wide CNV analysis approach in 36 subjects (18 patients with high-grade PCa and 18 controls that were matched by age and ethnicity) in search of more accurate biomarkers that could potentially explain susceptibility toward high-grade PCa. We conducted this study using the array comparative genomic hybridization technique. Array results were validated in 92 independent samples (46 high-grade PCa, 23 benign prostatic hyperplasia, and 23 healthy controls) using polymerase chain reaction-based copy number counting method.

    RESULTS: A total of 314 CNV regions were found to be unique to PCa subjects in this cohort (P<0.05). A log2 ratio-based copy number analysis revealed 5 putative rare or novel CNV loci or both associated with susceptibility to PCa. The CNV gain regions were 1q21.3, 15q15, 7p12.1, and a novel CNV in PCa 12q23.1, harboring ARNT, THBS1, SLC5A8, and DDC genes that are crucial in the p53 and cancer pathways. A CNV loss and deletion event was observed at 8p11.21, which contains the SFRP1 gene from the Wnt signaling pathway. Cross-comparison analysis with genes associated to PCa revealed significant CNVs involved in biological processes that elicit cancer pathogenesis via cytokine production and endothelial cell proliferation.

    CONCLUSION: In conclusion, we postulated that the CNVs identified in this study could provide an insight into the development of advanced PCa.

    Matched MeSH terms: DNA Copy Number Variations/genetics*
  16. Asis A, Shahriar SA, Naher L, Saallah S, Fatihah HNN, Kumar V, et al.
    Mol Biol Rep, 2021 Apr;48(4):3285-3301.
    PMID: 33880673 DOI: 10.1007/s11033-021-06321-0
    Trichoderma is a genus of soil-borne fungus with an abundance of reports of its economic importance in the agriculture industry. Thus, the correct identification of Trichoderma species is necessary for its commercial purposes. Globally, Trichoderma species are routinely identified from micro-morphological descriptions which can be tedious and prone to errors. Thus, we emphasize that the accurate identification of Trichoderma strains requires a three-pronged approach i.e. based on its morphological characteristics, multilocus gene sequences of the rDNA [internal transcribed spacer (ITS) 1 and 2 regions], translation elongation factor 1-α (TEF-1α), Calmodulin (CAL) and its lignocellulolytic activities. We used this approach to identify a total of 53 Trichoderma strains which were isolated from a wet paddy field located at Tuaran, Sabah, Malaysia. The 53 strains were positively identified as belonging to three Trichoderma species, namely T. asperellum (43 strains), T. harzianum (9 strains), and T. reesei (one strain) on the basis of its morphological characteristics and multilocus gene sequences. Phylogenetic trees constructed based on the UPGMA method of the ITS 1 and 2 regions of the rDNA, TEF-1α and CAL revealed three distinct groups with the T. asperellum, T. harzianum and T. reesei strains placed under the section of Trichoderma, Pachybasium and Longibrachiatum, respectively. In addition, the lignocellulolytic activities of the isolates were measured based on the diameters of the halo zones produced when degrading cellulose, lignin, and starch, respectively. This diagnostic assay can be used to identify Trichoderma as it produces polyphenol oxidase when Tannic Acid Media is used for the lignin test, endoglucanases when Jensen media is used for cellulose, and it hydrolyzes starch to glucose when the modified Melin-Nokrans media is used for the starch test. Accurate identification of Trichoderma species is needed as these strains can potentially be used as a biocontrol agent to prevent diseases and to increase yield in agriculture crops.
    Matched MeSH terms: DNA, Ribosomal/genetics
  17. Courage C, Oliver KL, Park EJ, Cameron JM, Grabińska KA, Muona M, et al.
    Am J Hum Genet, 2021 04 01;108(4):722-738.
    PMID: 33798445 DOI: 10.1016/j.ajhg.2021.03.013
    Progressive myoclonus epilepsies (PMEs) comprise a group of clinically and genetically heterogeneous rare diseases. Over 70% of PME cases can now be molecularly solved. Known PME genes encode a variety of proteins, many involved in lysosomal and endosomal function. We performed whole-exome sequencing (WES) in 84 (78 unrelated) unsolved PME-affected individuals, with or without additional family members, to discover novel causes. We identified likely disease-causing variants in 24 out of 78 (31%) unrelated individuals, despite previous genetic analyses. The diagnostic yield was significantly higher for individuals studied as trios or families (14/28) versus singletons (10/50) (OR = 3.9, p value = 0.01, Fisher's exact test). The 24 likely solved cases of PME involved 18 genes. First, we found and functionally validated five heterozygous variants in NUS1 and DHDDS and a homozygous variant in ALG10, with no previous disease associations. All three genes are involved in dolichol-dependent protein glycosylation, a pathway not previously implicated in PME. Second, we independently validate SEMA6B as a dominant PME gene in two unrelated individuals. Third, in five families, we identified variants in established PME genes; three with intronic or copy-number changes (CLN6, GBA, NEU1) and two very rare causes (ASAH1, CERS1). Fourth, we found a group of genes usually associated with developmental and epileptic encephalopathies, but here, remarkably, presenting as PME, with or without prior developmental delay. Our systematic analysis of these cases suggests that the small residuum of unsolved cases will most likely be a collection of very rare, genetically heterogeneous etiologies.
    Matched MeSH terms: DNA Copy Number Variations/genetics
  18. Alajmi RA, Ayaad TH, Al-Harbi HT, Shaurub EH, Al-Musawi ZM
    Trop Biomed, 2019 Sep 01;36(3):758-765.
    PMID: 33597497
    The present work aimed to identify camel ticks Hyalomma dromedarii and Hyalomma marginatum using direct sequence of the mitochondrial 16S rRNA gene and the detection of their natural infection rate with Rickettsia and Borrelia using the PCR/ hybridization method for amplification of the citrate synthase (gltA) gene. The phylogenetic analysis showed 99% similarity between Hyalomma dromedarii and its reference with accession # L34306.1, as well as between Hyalomma marginatum and its reference with accession # KT391060.1 obtained from GenBank data base. The prevalence of H. dromedarii and H. marginatum was about 99% and 1%, respectively. The intraspecific variation among H. dromedarii ranged between 0.2-6.6%. The interspecific variation between H. dromedarii and H. marginatum was 18.3%. PCR/hybridization of the sampled H. dromedarii detected about 31%, 37% and 18% natural infection with Rickettsia, Borrelia and co-infection with both pathogens, respectively. In contrast, none of Rickettsia or Borrelia was detected in H. marginatum. The present study emphasizes the accuracy of the identification of camel ticks based on molecular techniques. The ability of H. dromedarii to spread more than one disease is an important issue from the epidemiological standpoint. Future epidemiological research should be carried out in Saudi Arabia to monitor the distribution of tick species and suggest effective control strategies.
    Matched MeSH terms: DNA, Bacterial/genetics
  19. Zafar MN, Butt AM, Chaudhry GE, Perveen F, Nazar MF, Masood S, et al.
    J Inorg Biochem, 2021 11;224:111590.
    PMID: 34507110 DOI: 10.1016/j.jinorgbio.2021.111590
    The bidentate N-(1-Alkylpyridin-4(1H)-ylidene)amide (PYA) pro-ligands [H2LBn][Cl]2 (2), and [H2LMe][TfO]2 (3) were prepared by simple alkylation reactions of the known compound, N,N-di(pyridin-4-yl)oxalamide (H2L, 1). The Pd(II) complexes, [Pd(LBn)2][Cl]2 (4), [Pd(LMe)2][Cl][TfO] (5), Pd(LBn)Cl2 (6) and Pd(LMe)Cl2 (7) were synthesized through reactions between these pro-ligands and suitable Pd(II) substrates in the presence of base. The molecular structures of 3 and 6 were obtained by single crystal X-ray structure determinations. Studies of the experimental and computational DNA binding interactions of the compounds 1-7 revealed that overall 4 and 6 have the largest values for the binding parameters Kb and ΔGbo. The results showed a good correlation with the steric and electronic parameters obtained by quantitative structure activity relationship (QSAR) studies. In-vitro cytotoxicity studies against four different cell lines showed that the human breast cancer cell lines MCF-7, T47D and cervical cancer cell line HeLa had either higher or similar sensitivities towards 4, 6 and 2, respectively, compared to cisplatin. In general, the cytotoxicity of the compounds, represented by IC50 values, decreased in the order 4 > 6 > 2 > 5 > 3 > 1 > 7 in cancer cell lines. Apoptosis contributed significantly to the cytotoxic effects of these anticancer agents as evaluated by apoptosis studies.
    Matched MeSH terms: DNA/chemistry
  20. Uddin SMK, Hossain MAM, Chowdhury ZZ, Johan MRB
    PMID: 34077338 DOI: 10.1080/19440049.2021.1925748
    Food fraud is a global problem raising increased concerns during the past decades and food authenticity is now a burning issue. Beef, buffalo, chicken, duck, goat, sheep, and pork are heavily consumed meats bearing nutritional, economic and cultural/religious importance and are often found to be adulterated in raw and processed states. To authenticate these species, we developed and validated a highly specific multiplex (heptaplex) PCR assay targeting short length amplicons (73-263 bp) using seven pairs of species-specific primer sets targeting mitochondrial cytochrome b (cytb) and NADH dehydrogenase subunit 5 (ND5) genes. Specificity checking (in silico and in vitro) against 25 non-target species revealed no cross-species amplification. The developed multiplex assay was validated with various adulterated and heat-treated (boiled, microwaved and autoclaved) meatball products and were found to show high sensitivity and stability under all processing conditions. The assay was sensitive enough to detect 0.01-0.005 ng of DNA from raw meat and 0.5% (w/w) adulterated meat in mixed matrices. A market survey revealed mislabelling of 95% beef and 15% chicken products while pork products were found pure. Given some advantageous features including short sizes of amplicons, exceptional stability and superior sensitivity, the developed assay could be conveniently used for discriminatory detection of target species with a variety of raw meat as well as processed meat products undergoing extreme processing treatments.
    Matched MeSH terms: DNA; DNA Primers
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