Biology subjects

Dehghani, M.

Publications and source records attributed to Dehghani, M..

10 recordsLinked to original sources

bioRxiv2025

Over-Reliance on Prior Expectations in Relapsing-Remitting Multiple Sclerosis

Cognitive impairment is a common and disabling feature of multiple sclerosis (MS). Bayesian models of perception and action provide a powerful framework to better understand how cognitive processes are altered in MS. In this case-control study, we employed a time reproduction paradigm within a Bayesian framework to investigate the underlying mechanisms of cognitive dysfunction in patients with relapsing-remitting MS. We applied a modified Bayesian observer model, which partitions time reproduction into three stages: sensory measurement, time estimation, and motor response. We found that both MS and control groups showed a systematic bias in reproducing time, overestimating short intervals and underestimating long intervals. This bias was significantly larger in patients with MS compared with controls, reflecting an over-reliance on prior expectations relative to sensory-motor information. Computational modeling indicated that this increased bias in the MS group was driven by greater measurement noise during the sensory stage. Moreover, central tendency bias increases with age in healthy participants as reliance on prior expectations becomes stronger than sensory-motor evidence. Interestingly, we found that this age-related effect on bias was absent in patients with MS. Further analysis showed both younger and older patients performed equally biased, and their performance was similar to older healthy participants.

neuroscience↗

bioRxiv2025

ΔCt-Informed, Calibrated Logistic Regression Accurately Attributes mecA in Staphylococcus aureus-Positive Wound Specimens.

In wound specimens, co-detection of mecA and Staphylococcus aureus by PCR does not necessarily indicate MRSA because coagulase-negative staphylococci (CoNS) frequently harbor mecA. We evaluated a {Delta}Ct-informed, biologically gated, calibrated logistic regression to attribute mecA to S. aureus versus CoNS. Using paired culture/AST and multiplex real-time PCR Ct values (internal n=93; external n=47), we trained 5-fold cross-validated models in the culture-positive S. aureus subset (n=36) and applied an S. aureus PCR gate (no attribution when S. aureus PCR is negative). The primary model achieved sensitivity 90.9% and specificity 92.0% for MRSA attribution with AUC 0.931 (out-of-fold). Decision curve analysis showed positive net benefit across clinically relevant thresholds; at the prespecified 50% cutoff, the model achieved a net benefit of 0.222 compared with negative benefit for a treat-all strategy. In an external cohort, S. aureus detection by PCR versus culture showed 92.3% sensitivity and 97.1% specificity; within S. aureus PCR-positives (n=12), MRSA attribution reached 100% sensitivity and 87.5% specificity (accuracy = 91.7%). This framework improves mecA interpretability in polymicrobial specimens and can reduce unnecessary MRSA-directed antibiotics.

microbiology↗

bioRxiv2025

Orthogonal and Robust Analytics Enable Reproducible and Scalable Manufacturing of High Purity Extracellular Vesicles Derived from Mesenchymal Stromal Cells

The development of extracellular vesicle (EV) based therapeutics requires robust analytical assays and scalable downstream processing (DSP) strategies to ensure product quality and reproducibility. In this study, we established an analytical toolbox comprising scattering and fluorescence mode nanoparticle tracking analysis (NTA), fluorescence-based flow cytometry (Fl-FC), and multi-detector analytical size exclusion chromatography. Liposomes, selected for their physicochemical similarity to EVs, were used as reference materials to optimize assay parameters, fluorescence labeling conditions, and dynamic range, minimizing artifacts such as photobleaching and masking effects. Using these optimized analytical tools, we designed a scalable DSP workflow for human bone marrow mesenchymal stromal cell (hBM-MSC) derived EVs, incorporating clarification, tangential flow filtration (TFF), ion exchange chromatography (IEX), buffer exchange, and sterile filtration. IEX chromatography resulted in the elution of two cell-secreted populations, with similar scattering signals while eluate 1 showed approximately 30 times higher absorbance signal compared to eluate 2. Transmission electron microscopy revealed that eluate 1 contained non-vesicular extracellular particles (NVEPs), and eluate 2 was enriched in EVs and showed higher expression of positive markers such as CD81 and CD73 using Simple Western. Additionally, the two IEX eluates showed different proteomic and lipidomic profiles. Then the analytical toolbox was utilized to monitor the DSP process in terms of particle recovery and impurity removal throughout the process determining the high purity level of the final EV preparation. Together, these results demonstrate that orthogonal analytics coupled to a scalable DSP yield reproducible MSC-EV preparations while depleting commonly co-isolated NVEPs. This practical framework advances process analytics of MSC-EV manufacturing and supports reporting of identity, purity, and function aligned with existing guidelines in the field. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=91 SRC="FIGDIR/small/672476v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@142ff8aorg.highwire.dtl.DTLVardef@196c0bforg.highwire.dtl.DTLVardef@485c36org.highwire.dtl.DTLVardef@9dff39_HPS_FORMAT_FIGEXP M_FIG C_FIG Liposomes were used as reference materials to optimize single particle analytics as well as multi detector analytical chromatography to assess particle recovery and impurity removal. This optimized analytical toolbox enabled accurate monitoring of downstream processing steps, establishing a robust workflow for reproducible and scalable mesenchymal stromal derived extracellular vesicles bioprocessing.

bioengineering↗

bioRxiv2025

Development of a PEGylated Parylene Nanopocket Membrane for the Capture and Release of Lipid Vesicles

Membranes are commonly used for the separation and purification of a variety of biological species. In this study, we developed a nanopocket membrane that can capture nanoparticles and extracellular vesicles in tangential flow filtration by pulling the species of interest into a nanopocket, while tangential flow washes away particles too large to be captured. We developed the pores using a four-step lithography process. By optimizing photolithography parameters, particularly exposure dose, we achieved well-defined pore shapes with the desired wall tilt, forming nanopocket geometries. We validated membrane performance using bead mixtures of varying diameters (50 nm -10 {micro}m), demonstrating its ability to pass small particles, capture mid-sized particles, and exclude larger ones. Surface modification with poly(l-lysine)- grafted poly(ethylene glycol) enhanced this performance by reducing pore size and improving particle release. Additionally, we demonstrated selective capture and release of liposomes as well as EVs in the presence of fluorescently labeled BSA (f-BSA) protein. During this process, EVs were retained and later released, while f-BSA passed through, confirming selective capture and reduced protein contamination. These PEGylated nanopocket membranes constitute a low-pressure platform for gentle, size-selective isolation of nanoscale bioparticles, laying the groundwork for improved extracellular-vesicle analytics and point-of-care diagnostic applications.

bioengineering↗

bioRxiv2024

An inappropriate decline in ribosome levels drives a diverse set of neurodevelopmental disorders

Many neurodevelopmental defects are linked to perturbations in genes involved in housekeeping functions, such as those encoding ribosome biogenesis factors. However, how reductions in ribosome biogenesis can result in tissue and developmental specific defects remains a mystery. Here we describe new allelic variants in the ribosome biogenesis factor AIRIM primarily associated with neurodevelopmental disorders. Using human cerebral organoids in combination with proteomic analysis, single-cell transcriptome analysis across multiple developmental stages, and single organoid translatome analysis, we identify a previously unappreciated mechanism linking changes in ribosome levels and the timing of cell fate specification during early brain development. We find ribosome levels decrease during neuroepithelial differentiation, making differentiating cells particularly vulnerable to perturbations in ribosome biogenesis during this time. Reduced ribosome availability more profoundly impacts the translation of specific transcripts, disrupting both survival and cell fate commitment of transitioning neuroepithelia. Enhancing mTOR activity by both genetic and pharmacologic approaches ameliorates the growth and developmental defects associated with intellectual disability linked variants, identifying potential treatment options for specific brain ribosomopathies. This work reveals the cellular and molecular origins of protein synthesis defect-related disorders of human brain development. HighlightsO_LIAIRIM variants reduce ribosome levels specifically in neural progenitor cells. C_LIO_LIInappropriately low ribosome levels cause a transient delay in radial glia fate commitment. C_LIO_LIReduced ribosome levels impair translation of a selected subset of mRNAs. C_LIO_LIGenetic and pharmacologic activation of mTORC1 suppresses AIRIM-linked phenotypes. C_LI

developmental biology↗

bioRxiv2022

mRNA-based vaccine candidate COReNAPCIN(R) induces robust humoral and cellular immunity in mice and non-human primates

At the forefront of biopharmaceutical industry, the messenger RNA (mRNA) technology offers a flexible and scalable platform to address the urgent need for world-wide immunization in pandemic situations. This strategic powerful platform has recently been used to immunize millions of people proving both of safety and highest level of clinical efficacy against infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here we provide preclinical report of COReNAPCIN(R); a vaccine candidate against SARS-CoV-2 infection. COReNAPCIN(R) is a nucleoside modified mRNA-based vaccine formulated in lipid nanoparticles (LNPs) for encoding the full-length prefusion stabilized SARS-CoV-2 spike glycoprotein on the cell surface. Vaccination of C57BL/6 and BALB/c mice and rhesus macaque with COReNAPCIN(R) induced strong humoral responses with high titers of virus-binding and neutralizing antibodies. Upon vaccination, a robust SARS-CoV-2 specific cellular immunity was also observed in both mice and non-human primate models. Additionally, vaccination protected rhesus macaques from symptomatic SARS-CoV-2 infection and pathological damage to the lung upon challenging the animals with high viral loads of up to 2x108 live viral particles. Overall, our data provide supporting evidence for COReNAPCIN(R) as a potent vaccine candidate against SARS-CoV-2 infection for clinical studies.

immunology↗

bioRxiv2020

Longitudinal Quantification of Metabolites and Macromolecules Reveals Age- and Sex-Related Changes in the Healthy Fischer 344 Rat Brain

Normal aging is associated with numerous biological changes including altered brain metabolism and tissue chemistry. In vivo characterization of the neurochemical profile during aging is possible using magnetic resonance spectroscopy, a powerful non-invasive technique capable of quantifying brain metabolites involved in physiological processes that become impaired with age. A prominent macromolecular signal underlies those of brain metabolites and is particularly visible at high fields; parameterization of this signal into components improves quantification and expands the number of biomarkers comprising the neurochemical profile. The present study reports, for the first time, the simultaneous absolute quantification of brain metabolites and individual macromolecules in aging male and female Fischer 344 rats, measured longitudinally using proton magnetic resonance spectroscopy at 7T. We identified age- and sex-related changes in neurochemistry, with prominent differences in metabolites implicated in anaerobic energy metabolism, antioxidant capacity, and neuroprotection, as well as numerous macromolecule changes. These findings contribute to our understanding of the neurobiological processes associated with healthy aging, critical for the proper identification and management of pathological aging trajectories. HIGHLIGHTS[->] Magnetic resonance spectroscopy reveals altered chemistry in the aging rat brain [->]Age- and sex-dependent differences in metabolites and macromolecules are present [->]Metabolites and macromolecules are markers of processes involved in healthy aging [->]This study clarifies normative progression of brain chemistry and metabolism in vivo [->]Improved understanding will inform future studies in pathological aging

neuroscience↗

bioRxiv2019

Use of Nanosphere Self-Assembly to Pattern Nanoporous Membranes for the Study of Extracellular Vesicles

Nanoscale biocomponents naturally released by cells, such as extracellular vesicles (EVs), have recently gained interest due to their therapeutic and diagnostic potential. Membrane based isolation and co-culture systems have been utilized in an effort to study EVs and their effects. Nevertheless, improved platforms for the study of small EVs are still needed. Suitable membranes, for isolation and co-culture systems, require pore sizes to reach into the nanoscale. These pore sizes cannot be achieved through traditional lithographic techniques and conventional thick nanoporous membranes commonly exhibit low permeability. Here we utilized nanospheres, similar in size and shape to the targeted small EVs, as patterning features for the fabrication of freestanding SiN membranes (120 nm thick) released in minutes through a sacrificial ZnO layer. We evaluated the feasibility of separating subpopulation of EVs based on size using these membranes. The membrane used here showed an effective size cut-off of 300 nm with the majority of the EVs [≤]200 nm. This work provides a convenient platform with great potential for studying subpopulations of EVs.

bioengineering↗

bioRxiv2019

Tangential flow microfluidics for the capture and release of nanoparticles and extracellular vesicles on conventional and ultrathin membranes

Membranes have been used extensively for the purification and separation of biological species. A persistent challenge is the purification of species from concentrated feed solutions such as extracellular vesicles (EVs) from biological fluids. We investigated a new method to isolate micro- and nano-scale species termed tangential flow for analyte capture (TFAC), which is an extension of traditional tangential flow filtration (TFF). Initially, EV purification from plasma on ultrathin nanomembranes was compared between both normal flow filtration (NFF) and TFF. NFF resulted in rapid formation of a protein cake which completely obscured any captured EVs and also prevented further transport across the membrane. On the other hand, TFF showed capture of CD63 positive EVs with minimal contamination. We explored the use of TFF to capture target species over membrane pores, wash and then release in a physical process that does not rely upon affinity or chemical interactions. This process of TFAC was studied with model particles on both ultrathin nanomembranes and conventional thickness membranes (polycarbonate track-etch). Successful capture and release of model particles was observed using both membranes. Ultrathin nanomembranes showed higher efficiency of capture and release with significantly lower pressures indicating that ultrathin nanomembranes are well-suited for TFAC of delicate nanoscale particles such as EVs.

bioengineering↗

bioRxiv2019

Exosome labeling by lipophilic dye PKH26 results in significant increase in vesicle size

Exosomes are membrane vesicles secreted by cells and distributed widely in all biofluids. Exosomes can modulate the biological activities of cells in a paracrine or endocrine manner, in part by transferring their content, such as miRNA, following uptake in recipient cells. Fluorescent labelling of exosomes is a commonly used technique for understanding their cellular targeting and biodistribution. Lipophilic fluorescent dyes such as those in the PKH family have been widely used for exosome labelling. One concern with the use of lipophilic dyes is an increase in the exosome size due to membrane fusion or intercalation. This size shift alone may undermine the validity of exosomes tracing studies as small changes in the size of inorganic nanoparticles are known to affect their cellular uptake and biodistribution. Here, the possibility of minimizing the size shift of PKH labelled exosomes was systematically studied by changing the labelling condition. Unfortunately, the size shift towards larger particles was observed in all the PKH labelling conditions, including those where the labelled exosomes were below the fluorescent detection limit. As opposed to lipophilic dyes, no significant shift in the size of labelled exosomes was detected with protein binding dyes. Since the size shifts identified in all the PKH labelling conditions are likely to affect the cellular uptake and biodistribution, PKH may not be a reliable technique for exosomes tracking.

biochemistry↗