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Isolation of Wheat Genomic DNA for Gene Mapping and Cloning

Yu G, Hatta A, Periyannan S, Lagudah E, Wulff BBH

Methods Mol Biol, 2017;1659:207-213.
PMID: 28856653 DOI: 10.1007/978-1-4939-7249-4_18

DNA is widely used in plant genetic and molecular biology studies. In this chapter, we describe how to extract DNA from wheat tissues. The tissue samples are ground to disrupt the cell wall. Then cetyltrimethylammonium bromide (CTAB) or sodium dodecyl sulfate (SDS) is used to disrupt the cell and nuclear membranes to release the DNA into solution. A reducing agent, β-mercaptoethanol, is added to break the disulfide bonds between the cysteine residues and to help remove the tanins and polyphenols. A high concentration of salt is employed to remove polysaccharides. Ethylenediaminetetraacetic acid (EDTA) stops DNase activity by chelating the magnesium ions. The nucleic acid solution is extracted with chloroform-isoamyl alcohol (24:1) or 6 M ammonium acetate. The DNA in aqueous phase is precipated with ethanol or isopropanol, which makes DNA less hydrophilic in the presence of sodium ions (Na+).
Fulltext Prevalence of human papillomavirus in abnormal cervical smears in Malaysian patients

Sharifah NA, Seeni A, Nurismah MI, Clarence-Ko CH, Hatta AZ, Ho NP, et al.

Asian Pac J Cancer Prev, 2009 Apr-Jun;10(2):303-6.
PMID: 19537900

Cervical cancer is the second most common female malignancy in Malaysia. Despite advances in treatment, the overall survival for this disease has not changed in the last decade. Infection by certain types of HPV is recognized as a causal and necessary factor for its development. This study was carried out to determine the prevalence of HPV infection in abnormal cervical smears in Malaysian patients using archival cervical smears retrieved from the Cytopathology Unit, Universiti Kebangsaan Malaysia Medical Centre (UKMMC) between the years 1992-1995. DNA was extracted from 38 abnormal smears comprising 25 intraepithelial lesions and 13 cervical carcinomas and 10 normal smears. Amplification of HPV genes was carried out using the polymerase chain reaction (PCR) technique. HPV genotypes were determined using direct sequencing and the results were compared to the database from Genebank. DNA was successfully extracted from all 48 cervical smears. High-risk HPV (HR-HPV) genotypes were detected in 95% of the abnormal smears. Eight high-risk oncogenic types were identified: 16, 18, 31, 51, 52, 56, 58 and 66. All (100%) cervical cancer smears showed presence of HR-HPV compared to 92% of the cervical intraepithelial lesions. Among the eight HR-HPV genotypes identified, HPV 16 and 52 were the commonest (23.7% each) HPV genotypes encountered and among the CIN lesions, HPV 16 (28%) was the most frequent. We conclude that HPV 16 is the most prevalent HPV genotype present in abnormal cervical smears in Malaysian patients, and that the use of archival material to assess the presence of HPV is potentially worthwhile, and can be utilized for longitudinal studies of HPV presence and persistence.
Fulltext Immunohistochemical study of p16 INK4A and survivin expressions in cervical squamous neoplasm

Tan GC, Norlatiffah S, Sharifah NA, Razmin G, Shiran MS, Hatta AZ, et al.

Indian J Pathol Microbiol, 2010 Jan-Mar;53(1):1-6.
PMID: 20090212 DOI: 10.4103/0377-4929.59173

Cervical cancer is the second most common cancer affecting Malaysian women. Despite the implementation of pap smear screening, many women are still diagnosed only in the advanced stage of cervical cancer. This could partly be due to failure of detection of its precursor lesions; hence the need to search for novel biomarkers to assist in the screening and diagnosis of cervical neoplasia. This study aims to determine the expression of p16INK4A and survivin as possible predictive biomarkers in cervical squamous neoplasm.
Environmental remediation of hazardous pollutants using MXene-perovskite-based photocatalysts: A review

Sharaf Aldeen EM, Jalil AA, Mim RS, Hatta AH, Hazril NIH, Chowdhury A, et al.

Environ Res, 2023 Oct 01;234:116576.
PMID: 37423362 DOI: 10.1016/j.envres.2023.116576

Photocatalysis utilizing semiconductors offer a cost-effective and promising solution for the removal of pollutants. MXene and perovskites, which possess desirable properties such as a suitable bandgap, stability, and affordability, have emerged as a highly promising material for photocatalytic activity. However, the efficiency of MXene and perovskites is limited by their fast recombination rates and inadequate light harvesting abilities. Nonetheless, several additional modifications have been shown to enhance their performance, thereby warranting further exploration. This study delves into the fundamental principles of reactive species for MXene-perovskites. Various methods of modification of MXene-perovskite-based photocatalysts, including Schottky junction, Z-scheme and S-scheme are analyzed with regard to their operation, differences, identification techniques and reusability. The assemblance of heterojunctions is demonstrated to enhance photocatalytic activity while also suppressing charge carrier recombination. Furthermore, the separation of photocatalysts through magnetic-based methods is also investigated. Consequently, MXene-perovskite-based photocatalysts are seen as an exciting emerging technology that necessitates further research and development.
Characterization, molecular identification, and antimicrobial activity of lactic acid bacteria isolated from selected fermented foods and beverages in Malaysia

Haryani Y, Halid NA, Guat GS, Nor-Khaizura MAR, Hatta A, Sabri S, et al.

FEMS Microbiol Lett, 2023 Jan 17;370.
PMID: 37002414 DOI: 10.1093/femsle/fnad023

The present work investigated the profile and biodiversity of lactic acid bacteria (LAB) isolated from selected manufactured and homemade fermented foods in Malaysia. A total of 55 LAB were isolated from 20 samples, and identified based on the sequencing of 16S rRNA gene. The LAB isolates were identified as Lacticaseibacillus rhamnosus (34.5%), Lactiplantibacillus plantarum (20%), Limosilactobacillus fermentum (20%), Lacticaseibacillus paracasei (12.7%), Lacticaseibacillus casei (3.6%), Lactobacillus sp. (1.8%), Enterococcus faecalis (3.6%), Enterococcus faecium (1.8%), and Enterococcus durans (1.8%). Majority (94%) of the LAB isolates exhibited broad-spectrum antimicrobial activity against selected foodborne pathogens, and four isolates (L. fermentum SC1001, L. paracasei K2003, and L. rhamnosus KF1002 and MK2003) could produce bacteriocin-like inhibitory substance (BLIS). Lacticaseibacillus paracasei M1001 (homemade mozzarella) exhibited high-temperature tolerance and acid resistance, was homofermentative, and generated good antimicrobial activity, which strongly implied its potential for industrial applications. The present work results would potentially widen our knowledge of LAB diversity in Malaysian fermented foods and provide a potential for their applications in the food industry or other purposes.
Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture

Steuernagel B, Periyannan SK, Hernández-Pinzón I, Witek K, Rouse MN, Yu G, et al.

Nat Biotechnol, 2016 Jun;34(6):652-5.
PMID: 27111722 DOI: 10.1038/nbt.3543

Wild relatives of domesticated crop species harbor multiple, diverse, disease resistance (R) genes that could be used to engineer sustainable disease control. However, breeding R genes into crop lines often requires long breeding timelines of 5-15 years to break linkage between R genes and deleterious alleles (linkage drag). Further, when R genes are bred one at a time into crop lines, the protection that they confer is often overcome within a few seasons by pathogen evolution. If several cloned R genes were available, it would be possible to pyramid R genes in a crop, which might provide more durable resistance. We describe a three-step method (MutRenSeq)-that combines chemical mutagenesis with exome capture and sequencing for rapid R gene cloning. We applied MutRenSeq to clone stem rust resistance genes Sr22 and Sr45 from hexaploid bread wheat. MutRenSeq can be applied to other commercially relevant crops and their relatives, including, for example, pea, bean, barley, oat, rye, rice and maize.
Humoral response to SARS-CoV-2 vaccines among healthcare workers in a tertiary hospital in Malaysia

Amrina MA, Shahidah M, Sofiah HR, Mirlia SCM, Thilakaveni R, Chong ZL, et al.

Med J Malaysia, 2023 Jan;78(1):20-24.
PMID: 36715186

INTRODUCTION: Healthcare workers (HCWs) were among the first to be fully vaccinated against SARS-CoV-2. However, the antibody responses to the vaccines and potential decline among Malaysian HCW are still unclear. The objective of this study is to follow-up anti-S antibody levels among HCW vaccinated with mRNA vaccine (BTN162b2) and inactivated vaccine (CoronaVac).
MATERIALS AND METHODS: Plasma samples were collected prevaccination, 2 weeks and 6 months post-vaccination and tested for total immunoglobulin levels using ELISA method.
RESULTS: A small percentage of HCW (2.2%, 15/677) had elevated anti-S antibody levels in their pre-vaccination plasma samples (median 20.4, IQR 5.8), indicating that they were exposed to SARS-CoV-2 infection prior to vaccination. The mRNA vaccine significantly increased anti-S levels of both previously infected and uninfected individuals to saturation levels (median 21.88, IQR.0.88) at 2 weeks postsecond dose of the vaccine. At 6 months post-vaccination, the antibody levels appeared to be maintained among the recipients of the mRNA vaccine. However, at this time point, anti-S antibody levels were lower in individuals given inactivated vaccine (median 20.39, IQR 7.31, n=28), and interestingly, their antibody levels were similar to anti-S levels in pre-vaccination exposed individuals. Antibody levels were not different between the sexes.
CONCLUSION: Anti-S levels differ in individuals given the different vaccines. While further study is required to determine the threshold level for protection against SARSCoV- 2, individuals with low antibody levels may be considered for boosters.