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Fulltext Transcriptome Profiling of Haloxylon persicum (Bunge ex Boiss and Buhse) an Endangered Plant Species under PEG-Induced Drought Stress

Thayale Purayil F, Rajashekar B, S Kurup S, Cheruth AJ, Subramaniam S, Hassan Tawfik N, et al.

Genes (Basel), 2020 06 10;11(6).
PMID: 32531994 DOI: 10.3390/genes11060640

Haloxylon persicum is an endangered western Asiatic desert plant species, which survives under extreme environmental conditions. In this study, we focused on transcriptome analysis of H. persicum to understand the molecular mechanisms associated with drought tolerance. Two different periods of polyethylene glycol (PEG)-induced drought stress (48 h and 72 h) were imposed on H. persicum under in vitro conditions, which resulted in 18 million reads, subsequently assembled by de novo method with more than 8000 transcripts in each treatment. The N50 values were 1437, 1467, and 1524 for the control sample, 48 h samples, and 72 h samples, respectively. The gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis resulted in enrichment of mitogen-activated protein kinase (MAPK) and plant hormone signal transduction pathways under PEG-induced drought conditions. The differential gene expression analysis (DGEs) revealed significant changes in the expression pattern between the control and the treated samples. The KEGG analysis resulted in mapping transcripts with 138 different pathways reported in plants. The differential expression of drought-responsive transcription factors depicts the possible signaling cascades involved in drought tolerance. The present study provides greater insight into the fundamental transcriptome reprogramming of desert plants under drought.
Effect of graphene oxide nanoparticles on in vitro growth of Fragaria x ananassa (Cameron Highlands white Strawberry) and evaluation of genetic stability using DAMD and ISSR markers

Pang WQ, Lai CS, Mad' Atari MF, Pandian BR, Mohamad Ibrahim MN, Tan ST, et al.

Plant Physiol Biochem, 2023 Nov;204:108104.
PMID: 37862933 DOI: 10.1016/j.plaphy.2023.108104

Graphene oxide (GO) is a novel nanomaterial with distinct physical properties and significant biological applications. The use of GO in plant tissue culture offers several new properties and potential applications. This research is vital due to the growing need for innovative techniques to promote plant growth, improve plant productivity and mitigate challenges posed by environmental stressors. This study focused on the rare Cameron Highlands white strawberry plants (Fragaria x ananassa) and addressed issues such as callus production during direct shoot induction and hyperhydricity. The research aimed to investigate the effects of GO on the regeneration process and genetic stability of white strawberry plants and to use molecular markers to ensure that plants propagated in vitro are true to type. For this purpose, shoot tip explants were used and different concentrations of GO (0, 2.5, 5.0, 7.5, 10 mg/L) were added to the Murashige and Skoog (MS) medium for six weeks. The results showed that the optimum concentration for promoting the development of white strawberry seedlings was 7.5 mg/L of GO. The study also revealed that the addition of 7.5 mg/L GO in combination with 8 μM TDZ to the MS medium facilitated the induction of multiple shoots. Moreover, the clonal fidelity of the in vitro plants treated with GO showed a genetic similarity of over 97%. These results confirm that lower GO concentrations improve plant development and stability. Consequently, this nanomaterial has a positive effect on the growth of strawberry plants and is therefore well suited for strawberry tissue culture.
The antioxidant and antimicrobial activity of ethanolic extract in roots, stems, and leaves of three commercial Cymbopogon species

Wahyuni DK, Kharisma VD, Murtadlo AAA, Rahmawati CT, Syukriya AJ, Prasongsuk S, et al.

BMC Complement Med Ther, 2024 Jul 18;24(1):272.
PMID: 39026301 DOI: 10.1186/s12906-024-04573-4

BACKGROUND: Cymbopogon is a member of the family Poaceae and has been explored for its phytochemicals and bioactivities. Although the antimicrobial activities of Cymbopogon spp. extracts have been extensively studied, comprehensive analyses are required to identify promising compounds for the treatment of antimicrobial resistance. Therefore, this study investigated the antioxidant and antimicrobial properties of Cymbopogon spp. ethanolic extracts in every single organ.
METHODS: Ethanolic extracts were obtained from three Indonesian commercial species of Cymbopogon spp., namely Cymbopogon citratus (L.) Rendle, Cymbopogon nardus (DC.) Spatf., and Cymbopogon winterianus Jowitt. The leaf, stem, and root extracts were evaluated via metabolite profiling using gas chromatography-mass spectrometry (GC-MS). In silico and in vitro analyses were used to evaluate the antioxidant and antimicrobial properties of the Cymbopogon spp. ethanolic extracts. In addition, bioactivity was measured using cytotoxicity assays. Antioxidant assays were performed using 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2-azino-bis [3-ethylbenzothiazoline-6-sulfonic acid (ABTS) to determine toxicity to Huh7it-1 cells using a tetrazolium bromide (MTT) assay. Finally, the antimicrobial activity of these extracts was evaluated against Candida albicans, Bacillus subtilis, Staphylococcus aureus, and Escherichia coli using a well diffusion assay.
RESULTS: GC-MS analysis revealed 53 metabolites. Of these, 2,5-bis(1,1-dimethylethyl)- phenol (27.87%), alpha-cadinol (26.76%), and 1,2-dimethoxy-4-(1-propenyl)-benzene (20.56%) were the predominant compounds. C. winterianus and C. nardus leaves exhibited the highest antioxidant activity against DPPH and ABTS, respectively. Contrastingly, the MTT assay showed low cytotoxicity. C. nardus leaf extract exhibited the highest antimicrobial activity against E. coli and S. aureus, whereas C. winterianus stem extract showed the highest activity against B. substilis. Furthermore, computational pathway analysis predicted that antimicrobial activity mechanisms were related to antioxidant activity.
CONCLUSIONS: These findings demonstrate that the leaves had strong antioxidant activity, whereas both the leaves and stems showed great antimicrobial activity. Furthermore, all Cymbopogon spp. ethanolic extracts showed low toxicity. These findings provide a foundation for future studies that assess the clinical safety of Cymbopogon spp. as novel drug candidates.
Selective detection of alpha synuclein amyloid fibrils by faradaic and non-faradaic electrochemical impedance spectroscopic approaches

Adam H, Gopinath SCB, Krishnan H, Adam T, Fakhri MA, Salim ET, et al.

Bioelectrochemistry, 2024 Aug 30;161:108800.
PMID: 39241513 DOI: 10.1016/j.bioelechem.2024.108800

This study utilized faradaic and non-faradaic electrochemical impedance spectroscopy to detect alpha synuclein amyloid fibrils on gold interdigitated tetraelectrodes (AuIDTE), providing valuable insights into electrochemical reactions for clinical use. AuIDE was purchased, modified with zinc oxide for increased hydrophobicity. Functionalization was conducted with hexacyanidoferrate and carbonyldiimidazole. Faradaic electrochemical impedance spectroscopy has been extensively explored in clinical diagnostics and biomedical research, providing information on the performance and stability of electrochemical biosensors. This understanding can help develop more sensitive, selective, and reliable biosensing platforms for the detection of clinically relevant analytes like biomarkers, proteins, and nucleic acids. Non-faradaic electrochemical impedance spectroscopy measures the interfacial capacitance at the electrode-electrolyte interface, eliminating the need for redox-active species and simplifying experimental setups. It has practical implications in clinical settings, like real-time detection and monitoring of biomolecules and biomarkers by tracking changes in interfacial capacitance. The limit of detection (LOD) for normal alpha synuclein in faradaic mode is 2.39-fM, The LOD for aggregated alpha synuclein detection is 1.82-fM. The LOD for non-faradaic detection of normal alpha synuclein is 2.22-fM, and the LOD for nonfaradaic detection of aggregated alpha synuclein is 2.40-fM. The proposed EIS-based AuIDTEs sensor detects alpha synuclein amyloid fibrils and it is highly sensitive.
Fulltext In silico analysis of angiotensin-converting enzyme inhibitory compounds obtained from soybean [Glycine max (L.) Merr.]

Ramlal A, Bhat I, Nautiyal A, Baweja P, Mehta S, Kumar V, et al.

Front Physiol, 2023;14:1172684.
PMID: 37324400 DOI: 10.3389/fphys.2023.1172684

Cardiovascular diseases (CVDs) are one of the major reasons for deaths globally. The renin-angiotensin-aldosterone system (RAAS) regulates body hypertension and fluid balance which causes CVD. Angiotensin-converting enzyme I (ACE I) is the central Zn-metallopeptidase component of the RAAS playing a crucial role in maintaining homeostasis of the cardiovascular system. The available drugs to treat CVD have many side effects, and thus, there is a need to explore phytocompounds and peptides to be utilized as alternative therapies. Soybean is a unique legume cum oilseed crop with an enriched source of proteins. Soybean extracts serve as a primary ingredient in many drug formulations against diabetes, obesity, and spinal cord-related disorders. Soy proteins and their products act against ACE I which may provide a new scope for the identification of potential scaffolds that can help in the design of safer and natural cardiovascular therapies. In this study, the molecular basis for selective inhibition of 34 soy phytomolecules (especially of beta-sitosterol, soyasaponin I, soyasaponin II, soyasaponin II methyl ester, dehydrosoyasaponin I, and phytic acid) was evaluated using in silico molecular docking approaches and dynamic simulations. Our results indicate that amongst the compounds, beta-sitosterol exhibited a potential inhibitory action against ACE I.
Fulltext Enhancing precision flood mapping: Pahang's vulnerability unveiled

Keya TA, Balakrishnan SS, Solayappan M, Dheena Dhayalan SS, Subramaniam S, An LJ, et al.

PLoS One, 2024;19(11):e0310435.
PMID: 39509412 DOI: 10.1371/journal.pone.0310435

Malaysia, particularly Pahang, experiences devastating floods annually, causing significant damage. The objective of the research was to create a flood susceptibility map for the designated area by employing an Ensemble Machine Learning (EML) algorithm based on geographic information system (GIS). By analyzing nine key factors from a geospatial database, flood susceptibility map was created with the ArcGIS software (ESRI ArcGIS Pro v3.0.1 x64). The Random Forest (RF) model was employed in this study to categorize the study area into distinct flood susceptibility classes. The Feature selection (FS) method was used to ranking the flood influencing factors. To validate the flood susceptibility models, standard statistical measures and the Area Under the Curve (AUC) were employed. The FS ranking demonstrated that the primary attributes to flooding in the study region are rainfall and elevation, with slope, geology, curvature, flow accumulation, flow direction, distance from the river, and land use/land cover (LULC) patterns ranking subsequently. The categories of 'very high' and 'high' class collectively made up 37.1% and 26.3% of the total area, respectively. The flood vulnerability assessment of Pahang found that the Eastern, Southern, and central regions were at high risk of flooding due to intense precipitation, low-lying topography with steep inclines, proximity to the shoreline and rivers, and abundant flooded vegetation, crops, urban areas, bare ground, and rangeland. Conversely, areas with dense tree canopies or forests were less susceptible to flooding in this research area. The ROC analysis demonstrated strong performance on the validation datasets, with an AUC value of >0.73 and accuracy scores exceeding 0.71. Research on flood susceptibility mapping can enhance risk reduction strategies and improve flood management in vulnerable areas. Technological advancements and expertise provide opportunities for more sophisticated methods, leading to better prepared and resilient communities.
Current Scenario in Associating Clinical COVID-19 Biomarkers for Developing Surveillance Platforms

Lakshmipriya T, Gopinath SCB, Chen Y, Sasidharan S, Subramaniam S, Gunny AAN, et al.

Curr Med Chem, 2025 Jan 09.
PMID: 39806951 DOI: 10.2174/0109298673331044241031100627

The novel coronavirus that caused the epidemic and pandemic resulting in the acute respiratory illness known as coronavirus disease 2019 (COVID-19) has plagued the world. This is unlike other coronavirus outbreaks that have occurred in the past, such as Middle East respiratory syndrome (MERS) or severe acute respiratory syndrome (SARS). COVID-19 has spread more quickly and posed special challenges due to the lack of appropriate treatments and vaccines. Real-time polymerase chain reaction (RTPCR) and rapid antibody tests (surveillance tests) are the two most used tests (confirmation tests). However, the latter takes hours to complete, and the former may produce false positives. Scientists have invested significant effort to create a COVID-19 diagnostic system that is both highly sensitive and reasonably priced. Early detection of COVID-19 is a major area of focus for sensing devices based on nanomaterials. This overview enhanced insights into potential coronavirus biomarkers and, compared to earlier studies, introduced new avenues. Further, it covers the development of COVID-19 diagnostic systems from an analytical point of view, including clinical markers and their subsequent applications with biosensors.