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Fulltext Effect of Plant Growth Regulators on Coloured Callus Formation and Accumulation of Azadirachtin, an Essential Biopesticide in Azadirachta indica

Ashokhan S, Othman R, Abd Rahim MH, Karsani SA, Yaacob JS

Plants (Basel), 2020 Mar 11;9(3).
PMID: 32168737 DOI: 10.3390/plants9030352

For centuries, Azadirachta indica or neem has been utilized as a primary source of medicine due to its antimicrobial, larvacidal, antimalarial and antifungal properties. Recently, its potential as an effective biopesticide has garnered attention, especially towards efficient and continuous production of its bioactive compounds. The present study investigated the effect of the plant growth regulators (PGRs) thiadiazuron (TDZ) and 2,4-dichlorophenoxyacetic acid (2,4-D) on the induction of colored callus formation and subsequent accumulation of azadirachtin (AZA) in A. indica. An efficient protocol was established for micropropagation and colored callus production of this species, followed by quantification of AZA (a mixture of azadirachtin A and B) and its safety assessment. For induction of the callus, leaf and petiole explants obtained from a young growing neem plant were excised and cultured on Murashige and Skoog (MS) medium supplemented with TDZ (0.2-0.6 mg L-1) and 2,4-D (0.2-0.6 mg L-1), either applied singly or in combination. Callus was successfully induced from both explant types at different rates, where media with 0.6 mg L-1 of TDZ resulted in the highest fresh weight (3.38 ± 0.08 g). In general, media with a single hormone (particularly TDZ) was more effective in producing a high mass of callus compared to combined PGRs. A culture duration of six weeks resulted in the production of green, brown and cream colored callus. The highest callus weight and accumulation of AZA was recorded in green callus (214.53 ± 33.63 mg g-1 dry weight (DW)) induced using TDZ. On the other hand, small amounts of AZA were detected in both brown and cream callus. Further experimentation indicated that the green callus with the highest AZA was found to be non-toxic (LC50 at 4606 µg mL-1) to the zebrafish animal model. These results suggested that the addition of different PGRs during in vitro culture could prominently affect callus and secondary metabolite production and can further be manipulated as a sustainable method for the production of a natural and environmentally friendly pesticide.
Geographical Diversity of Proteomic Responses to Cold Stress in the Fungal Genus Pseudogymnoascus

Abu Bakar N, Lau BYC, González-Aravena M, Smykla J, Krzewicka B, Karsani SA, et al.

Microb Ecol, 2023 Dec 07;87(1):11.
PMID: 38060022 DOI: 10.1007/s00248-023-02311-w

In understanding stress response mechanisms in fungi, cold stress has received less attention than heat stress. However, cold stress has shown its importance in various research fields. The following study examined the cold stress response of six Pseudogymnoascus spp. isolated from various biogeographical regions through a proteomic approach. In total, 2541 proteins were identified with high confidence. Gene Ontology enrichment analysis showed diversity in the cold stress response pathways for all six Pseudogymnoascus spp. isolates, with metabolic and translation-related processes being prominent in most isolates. 25.6% of the proteins with an increase in relative abundance were increased by more than 3.0-fold. There was no link between the geographical origin of the isolates and the cold stress response of Pseudogymnoascus spp. However, one Antarctic isolate, sp3, showed a distinctive cold stress response profile involving increased flavin/riboflavin biosynthesis and methane metabolism. This Antarctic isolate (sp3) was also the only one that showed decreased phospholipid metabolism in cold stress conditions. This work will improve our understanding of the mechanisms of cold stress response and adaptation in psychrotolerant soil microfungi, with specific attention to the fungal genus Pseudogymnoascus.
Berberine and RNAi-Targeting Telomerase Reverse Transcriptase (TERT) and/or Telomerase RNA Component (TERC) Caused Oxidation in Colorectal Cancer Cell Line, HCT 116: An Integrative Approach using Molecular and Metabolomic Studies

Samad MA, Saiman MZ, Abdul Majid N, Karsani SA, Yaacob JS

Cell Biochem Biophys, 2024 Mar;82(1):153-173.
PMID: 38198024 DOI: 10.1007/s12013-023-01210-8

Colorectal cancer (CRC) is the most common cancer in both men and women and is associated with increased telomerase levels and activity. The potential downstream effects of TERT and/or TERC downregulation by berberine (a telomerase inhibitor) or RNA interference (RNAi) on various target RNAs, proteins, relative telomerase activity (RTA), relative telomere length (RTL), hydrogen peroxide concentration [H2O2], percentage of cell cycle distribution, cell size and granularity as well as cellular metabolites were explored in HCT 116 cell line. Knockdown of TERT decreased TERC. The downregulation of TERT and/or TERC caused increment of [H2O2], G0/G1 phase arrest in addition to decreased S and G2/M phases, as well as diminished cell size. RTL was later reduced as a result of TERT, TERT and/or TERC downregulation which decreased RTA. It was discovered that xanthine oxidase (XO) was significantly and positively correlated at FDR-adjusted p value
Proteomic characterization of Pseudogymnoascus spp. isolates from polar and temperate regions

Abu Bakar N, Chung BLY, Smykla J, Karsani SA, Alias SA

Mycologia, 2024;116(3):449-463.
PMID: 38484286 DOI: 10.1080/00275514.2024.2313429

Proteomics has been used extensively in the field of mycology, mainly in trying to understand the complex network of protein-protein interactions that has been implicated in the molecular functions of fungi. It is also a useful tool to compare metabolic differences within a genus. Species of Pseudogymnoascus, a genus under the phyla Ascomycota, have been shown to play an important role in the soil environment. They have been found in both polar and temperate regions and are a known producer of many extracellular hydrolases that contribute to soil decomposition. Despite the apparent importance of Pseudogymnoascus spp. in the soil ecosystem, investigations into their molecular functions are still very limited. In the present study, proteomic characterization of six Pseudogymnoascus spp. isolated from three biogeographic regions (the Arctic, Antarctic, and temperate regions) was carried out using tandem mass spectrometry. Prior to proteomic analysis, the optimization for protein extraction was carried out. Trichloroacetic acid‑acetone‑phenol was found to be the best extraction method to be used for proteomic profiling of Pseudogymnoascus spp. The proteomic analysis identified 2003 proteins that were successfully mapped to the UniProtKB database. The identified proteins were clustered according to their biological processes and molecular functions. The shared proteins found in all Pseudogymnoascus spp. (1201 proteins) showed a significantly close relationship in their basic cellular functions, despite differences in morphological structures. Analysis of Pseudogymnoascus spp. proteome also identified proteins that were unique to each region. However, a high number of these proteins belonged to protein families of similar molecular functions, namely, transferases and hydrolases. Our proteomic data can be used as a reference for Pseudogymnoascus spp. across different global regions and a foundation for future soil ecosystem function research.
Comprehensive Study of Sperm Proteins and Metabolites Potentially Associated with Higher Fertility of Zebu Cattle (Bos indicus) in Tropical Areas

Ashrafzadeh A, Yajit NLM, Nathan S, Othman I, Karsani SA

J Proteome Res, 2024 Nov 26.
PMID: 39591502 DOI: 10.1021/acs.jproteome.4c00926

Crossbreeding of zebu cattle (Bos indicus) with European breeds (Bos taurus) producing crossbred cattle was performed to overcome the low growth rates and milk production of indigenous tropical cattle breeds. However, zebu cattle fertility is higher than those of crossbred cattle and European breeds under warm conditions. Combination study of proteomics and metabolomics toward Malaysian indigenous breed Kedah × Kelantan-KK (B. indicus) and crossbreed Mafriwal-M (B. taurus × B. indicus) to understand physiological reasons for higher thermotolerance and fertility in Zebu cattle sperm. 161 regulated metabolites and 96 regulated proteins in KK and M (p < 0.05) showed more efficient carbohydrate and energy metabolism, higher integrity of the DNA and plasma membrane, a lower level of reactive oxygen species, and higher levels of phospholipids, which confirmed higher sperm plasma membrane integrity in KK. A stronger antioxidant system and lower polyunsaturated fatty acids help KK sperm cope with oxidative stress under warm conditions. The higher abundance of flagella structural proteins in KK provides a stronger structure that supports sperm motility. Abnormality of flagella, plasma membrane disruption, and DNA fragmentation were higher in M. These findings provide selective molecular markers for developing high-producing and more thermotolerant cattle breeds in tropical areas (197 words).
Effects of blend of canola oil and palm oil on nutrient intake and digestibility, growth performance, rumen fermentation and fatty acids in goats

Adeyemi KD, Sazili AQ, Ebrahimi M, Samsudin AA, Alimon AR, Karim R, et al.

Anim Sci J, 2016 Sep;87(9):1137-47.
PMID: 26582150 DOI: 10.1111/asj.12549

The study examined the effects of blend of 80% canola oil and 20% palm oil (BCPO) on nutrient intake and digestibility, growth performance, rumen fermentation and fatty acids (FA) in goats. Twenty-four Boer bucks were randomly assigned to diets containing 0, 4 and 8% BCPO on a dry matter basis, fed for 100 days and slaughtered. Diet did not affect feed efficiency, growth performance, intake and digestibility of all nutrients except ether extract. Intakes and digestibilities of ether extract, unsaturated fatty acids (FA) and total FA were higher (P
Plasma proteome analysis of cervical intraepithelial neoplasia and cervical squamous cell carcinoma

Looi ML, Karsani SA, Rahman MA, Dali AZ, Ali SA, Ngah WZ, et al.

J Biosci, 2009 Dec;34(6):917-25.
PMID: 20093745

Although cervical cancer is preventable with early detection, it remains the second most common malignancy among women. An understanding of how proteins change in their expression during a particular diseased state such as cervical cancer will contribute to an understanding of how the disease develops and progresses. Potentially, it may also lead to the ability to predict the occurrence of the disease. With this in mind, we aimed to identify differentially expressed proteins in the plasma of cervical cancer patients. Plasma from control, cervical intraepithelial neoplasia (CIN) grade 3 and squamous cell carcinoma (SCC) stage IV subjects was resolved by two-dimensional gel electrophoresis and the resulting proteome profiles compared. Differentially expressed protein spots were then identified by mass spectrometry. Eighteen proteins were found to be differentially expressed in the plasma of CIN 3 and SCC stage IV samples when compared with that of controls. Competitive ELISA further validated the expression of cytokeratin 19 and tetranectin. Functional analyses of these differentially expressed proteins will provide further insight into their potential role(s) in cervical cancer-specific monitoring and therapeutics.
Genetic and phenotype recovery of Ananas comosus var. MD2 in response to ionizing radiation

Ma S, Mohd Raffi AN, Rosli MA, Mohd Zain NA, Ibrahim MH, Karsani SA, et al.

Sci Rep, 2023 Jan 05;13(1):182.
PMID: 36604574 DOI: 10.1038/s41598-022-26745-3

Due to their sessile nature, plants are exposed to various environmental stressors such as exposure to high levels of harmful ultraviolet (UV), ionizing, and non-ionizing radiations. This exposure may result in various damages, ranging from DNA and chromosomal aberrations to phenotypic abnormalities. As an adaptation, plants have evolved efficient DNA repair mechanisms to detect and repair any damage caused by exposure to these harmful stressors to ensure their survival. In this study, the effects of gamma radiation (as a source of ionizing radiation) on clonal Ananas comosus var. MD2 was evaluated. The morphology and physiology of the clonal plantlets before and after exposure to gamma radiation were monitored at specific time intervals. The degree of genetic variation between the samples pre- and post-irradiation was also analyzed by using inter-simple sequence repeat (ISSR) markers. The resulting data revealed that the heights of the irradiated plantlets were significantly reduced (compared to control), but improved with the recovery period. Irradiated samples also exhibited relatively good photosynthetic efficiency that further improved as the plantlets recover. These observations were supported by the ISSR analysis, where the genetic dissimilarities between the irradiated samples and control were reduced by 0.1017, after 4 weeks of recovery. Overall, our findings suggested that the phenotype recovery of the clonal A. comosus var. MD2 plantlets was contributed by their ability to detect and repair the DNA lesions (as exemplified by the reduction in genetic dissimilarity after 4 weeks) and hence allow the plantlets to undergo phenotype reversion to normal plant stature.
Environmental impact and human health effects of polycyclic aromatic hydrocarbons and remedial strategies: A detailed review

Venkatraman G, Giribabu N, Mohan PS, Muttiah B, Govindarajan VK, Alagiri M, et al.

Chemosphere, 2024 Mar;351:141227.
PMID: 38253087 DOI: 10.1016/j.chemosphere.2024.141227

Polycyclic Aromatic Hydrocarbons (PAHs) profoundly impact public and environmental health. Gaining a comprehensive understanding of their intricate functions, exposure pathways, and potential health implications is imperative to implement remedial strategies and legislation effectively. This review seeks to explore PAH mobility, direct exposure pathways, and cutting-edge bioremediation technologies essential for combating the pervasive contamination of environments by PAHs, thereby expanding our foundational knowledge. PAHs, characterised by their toxicity and possession of two or more aromatic rings, exhibit diverse configurations. Their lipophilicity and remarkable persistence contribute to their widespread prevalence as hazardous environmental contaminants and byproducts. Primary sources of PAHs include contaminated food, water, and soil, which enter the human body through inhalation, ingestion, and dermal exposure. While short-term consequences encompass eye irritation, nausea, and vomiting, long-term exposure poses risks of kidney and liver damage, difficulty breathing, and asthma-like symptoms. Notably, cities with elevated PAH levels may witness exacerbation of bronchial asthma and chronic obstructive pulmonary disease (COPD). Bioremediation techniques utilising microorganisms emerge as a promising avenue to mitigate PAH-related health risks by facilitating the breakdown of these compounds in polluted environments. Furthermore, this review delves into the global concern of antimicrobial resistance associated with PAHs, highlighting its implications. The environmental effects and applications of genetically altered microbes in addressing this challenge warrant further exploration, emphasising the dynamic nature of ongoing research in this field.
Fulltext Profiling lysophosphatidic acid levels in plasma from head and neck cancer patients

Abdul Rahman M, Mohamad Haron DE, Hollows RJ, Abdul Ghani ZDF, Ali Mohd M, Chai WL, et al.

PeerJ, 2020;8:e9304.
PMID: 32547888 DOI: 10.7717/peerj.9304

Head and neck squamous cell carcinoma (HNSCC) represents a significant world health problem, with approximately 600,000 new cases being diagnosed annually. The prognosis for patients with HNSCC is poor and, therefore, the identification of biomarkers for screening, diagnosis and prognostication would be clinically beneficial. A limited number of studies have used lipidomics to profile lipid species in the plasma of cancer patients. However, the profile and levels of lysophosphatidic acid (LPA) species have not been examined in HNSCC. In this study, a targeted lipidomics approach using liquid chromatography triple quadrupole mass spectrometry (LCMS/MS) was used to analyse the concentration of LPA (16:0 LPA, 18:0 LPA, 18:1 LPA, 18:2 LPA and 20:4 LPA) in the plasma of patients with oral squamous cell carcinoma (OSCC) and nasopharyngeal carcinoma (NPC), together with healthy controls. The levels of three LPA species (18:1 LPA, 18:2 LPA and 20:4 LPA) were significantly lower in the plasma of OSCC patients, whilst the concentrations of all five LPA species tested were significantly lower in plasma from NPC patients. Furthermore, the order of abundance of LPA species in plasma was different between the control and cancer groups, with 16:0 LPA, 18:0 LPA levels being more abundant in OSCC and NPC patients. Medium to strong correlations were observed using all pairs of LPA species and a clear separation of the normal and tumour groups was observed using PCA analysis. In summary, the results of this study showed that the levels of several LPA species in the plasma of patients with OSCC and NPC were lower than those from healthy individuals. Understanding these variations may provide novel insights into the role of LPA in these cancers.
Label-free Quantitative Proteomic Analysis of Ascorbic Acid-induced Differentially Expressed Osteoblast-related Proteins in Dental Pulp Stem Cells from Deciduous and Permanent Teeth

Zainol Abidin IZ, Manogaran T, Abdul Wahab RM, Karsani SA, Yazid MD, Yazid F, et al.

Curr Stem Cell Res Ther, 2023;18(3):417-428.
PMID: 35762553 DOI: 10.2174/1574888X17666220627145424

BACKGROUND: Proteomic is capable of elucidating complex biological systems through protein expression, function, and interaction under a particular condition.
OBJECTIVE: This study aimed to determine the potential of ascorbic acid alone in inducing differentially expressed osteoblast-related proteins in dental stem cells via the liquid chromatography-mass spectrometry/ mass spectrometry (LC-MS/MS) approach.
METHODS: The cells were isolated from deciduous (SHED) and permanent teeth (DPSC) and induced with 10 μg/mL of ascorbic acid. Bone mineralisation and osteoblast gene expression were determined using von Kossa staining and reverse transcriptase-polymerase chain reaction. The label-free protein samples were harvested on days 7 and 21, followed by protein identification and quantification using LC-MS/MS. Based on the similar protein expressed throughout treatment and controls for SHED and DPSC, overall biological processes followed by osteoblast-related protein abundance were determined using the PANTHER database. STRING database was performed to determine differentially expressed proteins as candidates for SHED and DPSC during osteoblast development.
RESULTS: Both cells indicated brownish mineral stain and expression of osteoblast-related genes on day 21. Overall, a total of 700 proteins were similar among all treatments on days 7 and 21, with 482 proteins appearing in the PANTHER database. Osteoblast-related protein abundance indicated 31 and 14 proteins related to SHED and DPSC, respectively. Further analysis by the STRING database identified only 22 and 11 proteins from the respective group. Differential expressed analysis of similar proteins from these two groups revealed ACTN4 and ACTN1 as proteins involved in both SHED and DPSC. In addition, three (PSMD11/RPN11, PLS3, and CLIC1) and one (SYNCRIP) protein were differentially expressed specifically for SHED and DPSC, respectively.
CONCLUSION: Proteome differential expression showed that ascorbic acid alone could induce osteoblastrelated proteins in SHED and DPSC and generate specific differentially expressed protein markers.
Fulltext Boesenbergia rotunda: From Ethnomedicine to Drug Discovery

Eng-Chong T, Yean-Kee L, Chin-Fei C, Choon-Han H, Sher-Ming W, Li-Ping CT, et al.

Evid Based Complement Alternat Med, 2012;2012:473637.
PMID: 23243448 DOI: 10.1155/2012/473637

Boesenbergia rotunda is a herb from the Boesenbergia genera under the Zingiberaceae family. B. rotunda is widely found in Asian countries where it is commonly used as a food ingredient and in ethnomedicinal preparations. The popularity of its ethnomedicinal usage has drawn the attention of scientists worldwide to further investigate its medicinal properties. Advancement in drug design and discovery research has led to the development of synthetic drugs from B. rotunda metabolites via bioinformatics and medicinal chemistry studies. Furthermore, with the advent of genomics, transcriptomics, proteomics, and metabolomics, new insights on the biosynthetic pathways of B. rotunda metabolites can be elucidated, enabling researchers to predict the potential bioactive compounds responsible for the medicinal properties of the plant. The vast biological activities exhibited by the compounds obtained from B. rotunda warrant further investigation through studies such as drug discovery, polypharmacology, and drug delivery using nanotechnology.

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