Biology subjects

Rahmani, M.

Publications and source records attributed to Rahmani, M..

7 recordsLinked to original sources

bioRxiv2026

In Vitro Detection of Breast Cancer Cell Types Using Machine Learning-Assisted Spectral Fingerprinting of SWCNTs

The early detection of breast cancer currently relies on expensive mammography, followed by pathology that uses biopsied, fixed, and immunohistochemically stained tissues. A live-cell detection approach could be highly beneficial as a supportive diagnostic and research tool to better understand and resolve the dynamic nature of breast cancer cells and their response to treatment in real time. Here, we present a single-walled carbon nanotube (SWCNT) near-infrared fluorescence spectral fingerprinting approach combined with machine learning to precisely detect the heterogeneity of breast cancer cells in live culture. We introduced DNA-functionalized SWCNTs to MCF-10A (a non-tumorigenic healthy control) and cancer cell lines spanning known extrinsic disease subtypes: MCF-7 (luminal A), HCC1954 (HER2+), MDA-MB-231, and MDA-MB-468 (both triple-negative). The NIR fluorescence spectra of DNA-SWCNTs across 600 individual cells within each type showed significant differences in emission peak intensities, center wavelengths, and peak intensity ratios, attributable to variations in cellular uptake and biomolecular interactions. These spectral changes likely arise from complex SWCNT-cellular interaction "fingerprint" that includes redox-mediated modulation of the local nanotube environment, rather than from a single biomarker response. The extracted spectral features were used to train an ensemble machine learning model. The model achieved 98% classification accuracy for breast cancer detection and 95% classification accuracy for breast cancer cell subtyping. Moreover, Raman microscopy further showed that MDA-MB-468 cells exhibited the highest SWCNT uptake, whereas MCF-10A cells showed greater SWCNT aggregation, consistent with their lower broadband NIR fluorescence intensity. These results demonstrate that SWCNT NIR fluorescence fingerprints can capture cell line-specific optical signatures. This platform provides a foundation for nanomaterial-enabled biosensing strategies aimed at real-time monitoring of cancer-associated cellular states.

bioengineering↗

bioRxiv2025

Enhancing Optical Properties and Stability of DNA-Functionalized Carbon Nanotubes with Cryoprotectant Mediated Lyophilization

The long-term optical performance and stability of single-walled carbon nanotubes (SWCNTs) functionalized with single-stranded DNA are critical for their application in near-infrared (NIR) fluorescence biological sensing and imaging. However, the aggregation of such DNA-SWCNTs during storage presents a significant challenge. Here, we explored the use of lyophilization combined with various cryoprotectants to enhance the long-term stability and reconstitution of DNA-SWCNTs at room temperature. Five conventionally used cryoprotectants, including glucose, sucrose, mannitol, polyethylene glycol (PEG), and polyvinyl alcohol (PVA), were evaluated for their ability to maintain desired optical properties and prevent aggregation of SWCNTs through the process of lyophilization and reconstitution. Our results indicated that glucose and PEG, particularly in an 80:20 ratio by weight, provided the best performance, preserving NIR fluorescence and ensuring consistent reconstitution without significant aggregation. Further, in vitro studies using murine macrophages demonstrated that lyophilized SWCNTs with glucose-PEG protectants and then held at room temperature before subsequent reconstitution maintained stable intracellular optical performance, supporting their potential for long-term storage, ease of transport, and use in biomedical applications. These findings suggest that the optimized lyophilization protocol with specific cryoprotectant combinations can significantly improve the shelf life and reproducibility of SWCNT-based sensors, paving the way for their broader application in biological and clinical settings.

bioengineering↗

bioRxiv2025

Direct observation of single intrinsically disordered proteins in solution

Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) in structured proteins are integral to many biological processes including neurotransmitter regulation, microtubule regulation, and transcription. IDP/IDRs are heterogenous, existing in a conformational ensemble of various interconnected states without a definitive tertiary structure. The high dynamicity of IDPs/IDRs limits ensemble protein characterisation techniques from capturing their properties, and measurements at the single-molecule level are hampered by the necessity to label the protein or modify its microenvironment, affecting their biophysics. Consequently, our understanding of IDPs/IDRs is limited, translating to a lack of knowledge of their roles in related diseases including Alzheimers disease, Parkinsons disease, and various cancers. This work presents the first experimental observation of unmodified IDP/IDR conformational dynamics in vitro, at the single-molecule level in real time, achieved by trapping individual IDPs/IDRs in a nanoscale volume using nanoaperture optical tweezers. Our results reveal that IDPs/IDRs exhibit significantly larger conformational variations in solution compared to globular proteins of similar size, as expected. We demonstrate that phosphorylation of native tau-441 by glycogen synthase kinase 3-beta (GSK3{beta}-tau) induces compaction and reduced conformational dynamics. We further observed a disorder-to-order transition during binding of an IDR, the N-terminal region of Src-associated protein in mitosis of 68 kDa (Sam68), to G8.5 RNA. The capability of nanoaperture optical tweezers to monitor the dynamic behaviours of single, unmodified IDPs/IDRs provides a powerful approach to advance our understanding of their elusive behaviours and further decode their roles in associated diseases.

biophysics↗

bioRxiv2023

Structural Flexibility and Disassembly Kinetics of Single Ferritins using Optical Nanotweezers

Ferritin, a spherical protein shell assembled from 24 subunits, functions as an efficient iron storage and release system through its channels. Understanding how various chemicals affect the structural behaviour of ferritin is crucial for unravelling the origins of iron-related diseases in living organisms including humans. In particular, the influence of chemicals on ferritins dynamics and iron release is barely explored at the single-protein level. Here, by employing optical nanotweezers using double nanohole (DNH) structures, we examined the effect of ascorbic acid (reducing reagent) and pH on ferritins conformational dynamics. The dynamics of ferritin increased as the concentration of ascorbic acid approached saturation. At pH 2.0 ferritin exhibited significant structural fluctuations and eventually underwent a stepwise disassembly into fragments. This work, for the first time, tracked the disassembly pathway and kinetics of single ferritins in solution. We identified four critical fragments during its disassembly pathway, which are 22-mer, 12-mer, tetramer, and dimer subunits. Moreover, we presented the first single-molecule evidence of the cooperative disassembly of ferritin. Interrogating ferritins structural change in response to different chemicals holds importance for understanding their roles in iron metabolism, hence facilitating further development of medical treatments for the associated diseases.

biophysics↗

bioRxiv2022

Brain aerobic glycolysis and resilience in Alzheimer disease

The distribution of brain aerobic glycolysis (AG) in normal young adults correlates spatially with amyloid-beta (A{beta}) deposition in individuals with dementia of the Alzheimer type (DAT) and asymptomatic individuals with brain amyloid deposition. Brain AG decreases with age but the functional significance of this decrease with regard to the development of DAT symptomatology is poorly understood. Using PET measurements of regional blood flow, oxygen consumption and glucose utilization--from which we derive AG--we find that cognitive impairment is strongly associated with loss of the typical youthful pattern of AG. In contrast, amyloid positivity without cognitive impairment was associated with preservation of youthful brain AG, which was even higher than that seen in typical, cognitively unimpaired, amyloid negative adults. Similar findings were not seen for blood flow nor oxygen consumption. Finally, in cognitively unimpaired adults, white matter hyperintensity burden was found to be specifically associated with decreased youthful brain AG. Our results implicate preserved AG as a factor in brain resilience to amyloid pathology and suggest that white matter disease may be a cause and/or consequence of this impaired resilience.

neuroscience↗

bioRxiv2022

D2BGAN: Dual Discriminator Bayesian Generative Adversarial Network for Deformable MR-Ultrasound Registration Applied to Brain Shift compensation

PurposeIn neurosurgery, image guidance is provided based on the patient to pre-operative data registration with a neuronavigation system. However, the brain shift phenomena invalidate the accuracy of the navigation system during neurosurgery. One of the most common approaches for brain shift compensation is using intra-operative ultrasound (iUS) imaging followed by registration of iUS with pre-operative magnetic resonance (MR) images. While, due to the unpredictable nature of brain deformation and the low quality of ultrasound images, finding a satisfactory multimodal image registration approach remains a challenging task. MethodsWe proposed a new automatic unsupervised end-to-end MR-iUS registration approach based on the Dual Discriminator Bayesian Generative Adversarial Network (D2BGAN). The proposed network consists of two discriminators and is optimized by introducing a Bayesian loss function to improve the generator functionality and adding a mutual information loss function to the discriminator for similarity measurement. An evaluation was performed using the RESECT training dataset based on the organizers manual landmarks. ResultsThe mean Target Registration Error (mTRE) after MR-iUS registration using D2BGAN reached 0.75{+/-}0.3 mm. The D2BGAN illustrated a clear advantage by 85% improvement in the mTRE of MR-iUS registration over the initial error. Also, the results confirmed that the proposed Bayesian loss function rather than the typical loss function outperforms the accuracy of MR-iUS registration by 23%. ConclusionThe D2BGAN improved the registration accuracy while allowing us to maintain the intensity and anatomical information of the input images in the registration process. It promotes the advancement of deep learning-based multi-modality registration techniques.

bioengineering↗

bioRxiv2018

Beneficial effects of Spirogyra Neglecta Extract on antioxidant and anti-inflammatory factors in streptozotocin-induced diabetic rats

ObjectivesThis study was conducted to evaluate the effects of oral supplementation of Spirogyra algae on oxidative damages and inflammatory responses in streptozotocin (STZ)-induced diabetic rats.\n\nMethodsDiabetes was induced by administration of 55 mg/kg of streptozotocin. A total of sixty-four rats were divided into eight groups of eight rats each as follows:1) non-diabetic control; 2, 3, and 4) non-diabetic rats treated with 15, 30, and 45 mg of Spirogyra algae/kg/d; 5) control diabetic; and 6, 7, and 8) diabetic rats treated with 15, 30, and 45 mg of Spirogyra algae extract. At the end of the trial, the serum concentrations of glucose, interleukin-6 (IL-6), tumor necrosis factor- (TNF-), malondialdehyde (MDA), glutathione (GSH), total antioxidant status (TAS), C-reactive protein (CRP), insulin, triglycerides, and cholesterol were examined by specified procedures.\n\nResultsOur findings indicated that the administration of STZ significantly increased the serum concentrations of glucose, triglycerides, cholesterol, CRP, IL-6, TNF-, and MDA and decreased the serum levels of GSH and TAS (P<0.05) in diabetic rats. Oral administration of Spirogyra alleviated adverse effects of diabetes on oxidative stress and inflammatory factors in diabetic rats (P<0.05).\n\nConclusionIt can be stated that Spirogyra algae extract can be used for treatment of diabetes likely due to prevention of oxidative stress and alleviation of inflammation in the rat model.

pharmacology and toxicology↗