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Article ; Online: Proteomic characterization of

Abu Bakar, Nurlizah / Chung, Benjamin Lau Yii / Smykla, Jerzy / Karsani, Saiful Anuar / Alias, Siti Aisyah

2024 Volume 116, Issue 3, Page(s) 449–463

Abstract: 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 ... ...

Abstract	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
MeSH term(s)	Ascomycota/classification ; Ascomycota/metabolism ; Ascomycota/genetics ; Ascomycota/chemistry ; Ascomycota/isolation & purification ; Proteomics ; Fungal Proteins/metabolism ; Fungal Proteins/genetics ; Soil Microbiology ; Proteome ; Tandem Mass Spectrometry ; Arctic Regions
Chemical Substances	Fungal Proteins ; Proteome
Language	English
Publishing date	2024-03-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	281335-x
ISSN	1557-2536 ; 0027-5514
ISSN (online)	1557-2536
ISSN	0027-5514
DOI	10.1080/00275514.2024.2313429
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Article ; Online: 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, Muhammad Azizan / Saiman, Mohd Zuwairi / Abdul Majid, Nazia / Karsani, Saiful Anuar / Yaacob, Jamilah Syafawati

Cell biochemistry and biophysics

2024 Volume 82, Issue 1, Page(s) 153–173

Abstract: 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 ... ...

Abstract	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 [H
MeSH term(s)	Male ; Humans ; Female ; Telomerase/genetics ; Telomerase/metabolism ; RNA Interference ; Berberine/pharmacology ; Hydrogen Peroxide ; RNA/genetics ; RNA/metabolism ; HCT116 Cells ; Colorectal Neoplasms/genetics ; Telomere/metabolism
Chemical Substances	telomerase RNA ; Telomerase (EC 2.7.7.49) ; Berberine (0I8Y3P32UF) ; Hydrogen Peroxide (BBX060AN9V) ; RNA (63231-63-0) ; TERT protein, human (EC 2.7.7.49)
Language	English
Publishing date	2024-01-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	1357904-6
ISSN	1559-0283 ; 1085-9195
ISSN (online)	1559-0283
ISSN	1085-9195
DOI	10.1007/s12013-023-01210-8
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Zs.A 1498: Show issues

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Article ; Online: Identification of Potential Biomarkers and Small Molecule Drugs for Bisphosphonate-Related Osteonecrosis of the Jaw (BRONJ): An Integrated Bioinformatics Study Using Big Data.

Balachandran, Kumarendran / Ramli, Roszalina / Karsani, Saiful Anuar / Abdul Rahman, Mariati

International journal of molecular sciences

2023 Volume 24, Issue 10

Abstract: This study aimed to identify potential molecular mechanisms and therapeutic targets for bisphosphonate-related osteonecrosis of the jaw (BRONJ), a rare but serious side effect of bisphosphonate therapy. This study analyzed a microarray dataset (GSE7116) ... ...

Abstract	This study aimed to identify potential molecular mechanisms and therapeutic targets for bisphosphonate-related osteonecrosis of the jaw (BRONJ), a rare but serious side effect of bisphosphonate therapy. This study analyzed a microarray dataset (GSE7116) of multiple myeloma patients with BRONJ
MeSH term(s)	Humans ; Bisphosphonate-Associated Osteonecrosis of the Jaw/diagnosis ; Bisphosphonate-Associated Osteonecrosis of the Jaw/drug therapy ; Bisphosphonate-Associated Osteonecrosis of the Jaw/etiology ; Big Data ; Molecular Docking Simulation ; Biomarkers ; Multiple Myeloma/drug therapy ; Diphosphonates/adverse effects ; Bone Density Conservation Agents/therapeutic use
Chemical Substances	Biomarkers ; Diphosphonates ; Bone Density Conservation Agents
Language	English
Publishing date	2023-05-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24108635
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Article ; Online: Environmental impact and human health effects of polycyclic aromatic hydrocarbons and remedial strategies: A detailed review.

Venkatraman, Gopinath / Giribabu, Nelli / Mohan, Priyadarshini Sakthi / Muttiah, Barathan / Govindarajan, Venkat Kumar / Alagiri, Mani / Abdul Rahman, Puteri Shafinaz / Karsani, Saiful Anuar

Chemosphere

2024 Volume 351, Page(s) 141227

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Humans ; Polycyclic Aromatic Hydrocarbons/analysis ; Biodegradation, Environmental ; Soil ; Soil Pollutants/analysis ; Cities ; Environmental Monitoring/methods
Chemical Substances	Polycyclic Aromatic Hydrocarbons ; Soil ; Soil Pollutants
Language	English
Publishing date	2024-01-20
Publishing country	England
Document type	Review ; Journal Article
ZDB-ID	120089-6
ISSN	1879-1298 ; 0045-6535 ; 0366-7111
ISSN (online)	1879-1298
ISSN	0045-6535 ; 0366-7111
DOI	10.1016/j.chemosphere.2024.141227
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Article ; Online: Enhanced azadirachtin production in neem (Azadirachta indica) callus through NaCl elicitation: Insights into differential protein regulation via shotgun proteomics.

Omar, Siti Ainnsyah / Ashokhan, Sharmilla / Abdul Majid, Nazia / Karsani, Saiful Anuar / Lau, Benjamin Yii Chung / Yaacob, Jamilah Syafawati

Pesticide biochemistry and physiology

2024 Volume 199, Page(s) 105778

Abstract: With their remarkable bioactivity and evolving commercial importance, plant secondary metabolites (PSMs) have gained significant research interest in recent years. Plant tissue culture serves as a credible tool to examine how abiotic stresses modulate ... ...

Abstract	With their remarkable bioactivity and evolving commercial importance, plant secondary metabolites (PSMs) have gained significant research interest in recent years. Plant tissue culture serves as a credible tool to examine how abiotic stresses modulate the production of PSMs, enabling clear insights into plant stress responses and the prospects for controlled synthesis of bioactive compounds. Azadirachta indica, or neem has been recognized as a repository of secondary metabolites for centuries, particularly for the compound named azadirachtin, due to its bio-pesticidal and high antioxidant properties. Introducing salt stress as an elicitor makes it possible to enhance the synthesis of secondary metabolites, specifically azadirachtin. Thus, in this research, in vitro callus cultures of neem were micro-propagated and induced with salinity stress to explore their effects on the production of azadirachtin and identify potential proteins associated with salinity stress through comparative shotgun proteomics (LCMS/MS). To induce salinity stress, 2-month-old calli were subjected to various concentrations of NaCl (0.05-1.5%) for 4 weeks. The results showed that the callus cultures were able to adapt and survive in the salinity treatments, but displayed a reduction in fresh weight as the NaCl concentration increased. Notably, azadirachtin production was significantly enhanced in the salinity treatment compared to control, where 1.5% NaCl-treated calli produced the highest azadirachtin amount (10.847 ± 0.037 mg/g DW). The proteomics analysis showed that key proteins related to primary metabolism, such as defence, energy, cell structure, redox, transcriptional and photosynthesis, were predominantly differentially regulated (36 upregulated and 93 downregulated). While a few proteins were identified as being regulated in secondary metabolism, they were not directly involved in the synthesis of azadirachtin. In conjunction with azadirachtin elicitation, salinity stress treatment could therefore be successfully applied in commercial settings for the controlled synthesis of azadirachtin and other plant-based compounds. Further complementary omics approaches can be employed to enhance molecular-level modifications, to facilitate large-scale production of bioactive compounds in the future.
MeSH term(s)	Azadirachta/chemistry ; Azadirachta/metabolism ; Sodium Chloride/pharmacology ; Sodium Chloride/metabolism ; Proteomics ; Limonins/pharmacology
Chemical Substances	azadirachtin (O4U1SAF85H) ; Sodium Chloride (451W47IQ8X) ; Limonins
Language	English
Publishing date	2024-01-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	184819-7
ISSN	1095-9939 ; 0048-3583 ; 0048-3575
ISSN (online)	1095-9939
ISSN	0048-3583 ; 0048-3575
DOI	10.1016/j.pestbp.2024.105778
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Article: Fungal survival under temperature stress: a proteomic perspective.

Abu Bakar, Nurlizah / Karsani, Saiful Anuar / Alias, Siti Aisyah

PeerJ

2020 Volume 8, Page(s) e10423

Abstract: Background: Increases in knowledge of climate change generally, and its impact on agricultural industries specifically, have led to a greater research effort aimed at improving understanding of the role of fungi in various fields. Fungi play a key role ... ...

Abstract	Background: Increases in knowledge of climate change generally, and its impact on agricultural industries specifically, have led to a greater research effort aimed at improving understanding of the role of fungi in various fields. Fungi play a key role in soil ecosystems as the primary agent of decomposition, recycling of organic nutrients. Fungi also include important pathogens of plants, insects, bacteria, domestic animals and humans, thus highlighting their importance in many contexts. Temperature directly affects fungal growth and protein dynamics, which ultimately will cascade through to affect crop performance. To study changes in the global protein complement of fungi, proteomic approaches have been used to examine links between temperature stress and fungal proteomic profiles. Survey methodology and objectives: A traditional rather than a systematic review approach was taken to focus on fungal responses to temperature stress elucidated using proteomic approaches. The effects of temperature stress on fungal metabolic pathways and, in particular, heat shock proteins (HSPs) are discussed. The objective of this review is to provide an overview of the effects of temperature stress on fungal proteomes. Concluding remarks: Elucidating fungal proteomic response under temperature stress is useful in the context of increasing understanding of fungal sensitivity and resilience to the challenges posed by contemporary climate change processes. Although useful, a more thorough work is needed such as combining data from multiple -omics platforms in order to develop deeper understanding of the factor influencing and controlling cell physiology. This information can be beneficial to identify potential biomarkers for monitoring environmental changes in soil, including the agricultural ecosystems vital to human society and economy.
Language	English
Publishing date	2020-12-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.10423
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Article ; Online: Flavokawain C exhibits anti-tumor effects on in vivo HCT 116 xenograft and identification of its apoptosis-linked serum biomarkers via proteomic analysis.

Phang, Chung-Weng / Abd Malek, Sri Nurestri / Karsani, Saiful Anuar

Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie

2021 Volume 137, Page(s) 110846

Abstract: Chalcones and their derivatives belong to the flavonoid family. They have been extensively studied for their anticancer properties and some have been approved for clinical use. In this study, the in vivo anti-tumor activity of flavokawain C (FKC), a ... ...

Abstract	Chalcones and their derivatives belong to the flavonoid family. They have been extensively studied for their anticancer properties and some have been approved for clinical use. In this study, the in vivo anti-tumor activity of flavokawain C (FKC), a naturally occurring chalcone found in Kava (Piper methysticum Forst) was evaluated in HCT 116 cells (colon carcinoma). We also attempted to identify potential biomarkers and/or molecular targets in serum with applicability in predicting treatment outcome. The anti-tumor effects and toxicity of FKC were assessed using the xenograft nude mice model. Cisplatin was used as positive control. The anti-proliferative and apoptotic activities were then evaluated in tumor tissues treated with FKC. Furthermore, two-dimensional electrophoresis (2-DE) followed by protein identification using MALDI-TOF/TOF-MS/MS was performed to compare the serum proteome profiles between healthy nude mice and nude mice bearing HCT 116 tumor treated with vehicle solution and FKC, respectively. Our results showed that FKC treatment significantly inhibited HCT 116 tumor growth. In vivo toxicity studies showed that administration of FKC did not cause damage to major organs and had no significant effect on body weight. FKC was found to induce apoptosis in tumor, and this was associated with increased expression of cleaved caspase-3 and decreased expression of Ki67 in tumor tissues. Our proteomic analysis identified five proteins that changed in abundance - Ig mu chain C region (secreted form), GRP78, hemopexin, kininogen-1 and apolipoprotein E. Overall, our findings demonstrated the potential of FKC as an anti-cancer agent for the treatment of colon carcinoma.
MeSH term(s)	Animals ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents, Phytogenic/adverse effects ; Antineoplastic Agents, Phytogenic/pharmacology ; Antineoplastic Agents, Phytogenic/therapeutic use ; Apoptosis/drug effects ; Apoptosis/genetics ; Apoptosis Regulatory Proteins/genetics ; Biomarkers/blood ; Body Weight/drug effects ; Caspase 3/metabolism ; Cell Proliferation/drug effects ; Chalcones/adverse effects ; Chalcones/pharmacology ; Chalcones/therapeutic use ; Cisplatin/pharmacology ; Colonic Neoplasms/drug therapy ; Female ; HCT116 Cells ; Humans ; Kava/chemistry ; Mice ; Mice, Inbred BALB C ; Mice, Nude ; Proteomics/methods ; Xenograft Model Antitumor Assays
Chemical Substances	Antineoplastic Agents ; Antineoplastic Agents, Phytogenic ; Apoptosis Regulatory Proteins ; Biomarkers ; Chalcones ; flavokawain C ; CASP3 protein, human (EC 3.4.22.-) ; Caspase 3 (EC 3.4.22.-) ; Cisplatin (Q20Q21Q62J)
Language	English
Publishing date	2021-02-20
Publishing country	France
Document type	Journal Article
ZDB-ID	392415-4
ISSN	1950-6007 ; 0753-3322 ; 0300-0893
ISSN (online)	1950-6007
ISSN	0753-3322 ; 0300-0893
DOI	10.1016/j.biopha.2020.110846
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Article ; Online: Protein homeostasis, regulation of energy production and activation of DNA damage-repair pathways are involved in the heat stress response of Pseudogymnoascus spp.

Abu Bakar, Nurlizah / Lau, Benjamin Yii Chung / Smykla, Jerzy / Karsani, Saiful Anuar / Alias, Siti Aisyah

Environmental microbiology

2022 Volume 24, Issue 4, Page(s) 1849–1864

Abstract: Proteome changes can be used as an instrument to measure the effects of climate change, predict the possible future state of an ecosystem and the direction in which is headed. In this study, proteomic and gene ontology functional enrichment analysis of ... ...

Abstract	Proteome changes can be used as an instrument to measure the effects of climate change, predict the possible future state of an ecosystem and the direction in which is headed. In this study, proteomic and gene ontology functional enrichment analysis of six Pseudogymnoascus spp. isolated from various global biogeographical regions were carried out to determine their response to heat stress. In total, 2122 proteins were identified with high confidence. Comparative quantitative analysis showed that changes in proteome profiles varied greatly between isolates from different biogeographical regions. Although the identities of the proteins that changed varied between the different regions, the functions they governed were similar. Gene ontology analysis showed enrichment of proteins involved in multiple protective mechanisms, including the modulation of protein homeostasis, regulation of energy production and activation of DNA damage and repair pathways. Our proteomic analysis did not show any clear relationship between protein changes and the strains' biogeographical origins.
MeSH term(s)	DNA Damage ; Ecosystem ; Heat-Shock Response/genetics ; Proteome/genetics ; Proteome/metabolism ; Proteomics ; Proteostasis
Chemical Substances	Proteome
Language	English
Publishing date	2022-01-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.15776
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Article ; Online: Avian Influenza Virus Tropism in Humans.

AbuBakar, Umarqayum / Amrani, Lina / Kamarulzaman, Farah Ayuni / Karsani, Saiful Anuar / Hassandarvish, Pouya / Khairat, Jasmine Elanie

Viruses

2023 Volume 15, Issue 4

Abstract: An influenza pandemic happens when a novel influenza A virus is able to infect and transmit efficiently to a new, distinct host species. Although the exact timing of pandemics is uncertain, it is known that both viral and host factors play a role in ... ...

Abstract	An influenza pandemic happens when a novel influenza A virus is able to infect and transmit efficiently to a new, distinct host species. Although the exact timing of pandemics is uncertain, it is known that both viral and host factors play a role in their emergence. Species-specific interactions between the virus and the host cell determine the virus tropism, including binding and entering cells, replicating the viral RNA genome within the host cell nucleus, assembling, maturing and releasing the virus to neighboring cells, tissues or organs before transmitting it between individuals. The influenza A virus has a vast and antigenically varied reservoir. In wild aquatic birds, the infection is typically asymptomatic. Avian influenza virus (AIV) can cross into new species, and occasionally it can acquire the ability to transmit from human to human. A pandemic might occur if a new influenza virus acquires enough adaptive mutations to maintain transmission between people. This review highlights the key determinants AIV must achieve to initiate a human pandemic and describes how AIV mutates to establish tropism and stable human adaptation. Understanding the tropism of AIV may be crucial in preventing virus transmission in humans and may help the design of vaccines, antivirals and therapeutic agents against the virus.
MeSH term(s)	Animals ; Humans ; Influenza in Birds ; Influenza A virus/genetics ; Influenza A virus/metabolism ; Influenza, Human ; Birds ; Tropism
Language	English
Publishing date	2023-03-24
Publishing country	Switzerland
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15040833
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Article ; Online: Genetic and phenotype recovery of Ananas comosus var. MD2 in response to ionizing radiation.

Ma, Siyuan / Mohd Raffi, Anis Norsyahira / Rosli, Muhamad Afiq / Mohd Zain, Nurul Amalina / Ibrahim, Mohd Hafiz / Karsani, Saiful Anuar / Yaacob, Jamilah Syafawati

Scientific reports

2023 Volume 13, Issue 1, Page(s) 182

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Ananas/genetics ; Radiation, Ionizing ; Gamma Rays/adverse effects ; DNA Repair/genetics ; Phenotype ; Plants
Language	English
Publishing date	2023-01-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-26745-3
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