Biology subjects

Gholizadeh, S.

Publications and source records attributed to Gholizadeh, S..

8 recordsLinked to original sources

bioRxiv2025

Heat Stress and Soil Microbial Disturbance Influence Soybean Root Metabolite, Microbiome Profiles, and Nodulation

Heat stress is a major limiting factor for soybean productivity worldwide. Recent studies have highlighted the critical role of the plant microbiome in enhancing plant resilience to heat stress. However, our understanding of the molecular and physiological mechanisms underlying root-microbiome interactions under heat stress remains limited. To elucidate the role of native soil microbes in the heat tolerance of soybean genotypes, we analyzed rhizosphere bacterial and fungal communities via 16S rRNA and ITS sequencing, and characterized root metabolites and anatomical traits in response to microbiome composition and heat stress. Soybean plants were grown under controlled conditions in either natural soil containing native microbiota or in microbiome-disturbed soil (via 3-hour autoclaving), under both optimal and elevated temperature regimes. Alpha and beta diversity analyses revealed significant microbial shifts between treatments. Distinct clustering of bacterial, fungal, and metabolite profiles was observed under high temperature and microbial disturbance. Nodule-forming bacteria such as Rhizobium and Janthinobacterium were markedly suppressed, and belowground traits exhibited sensitivity, with significantly reduced nodule numbers and nodulation efficiency under high temperature and soil microbial perturbation. Non-targeted root metabolomics identified 372 differentially accumulated metabolites. Integrative multi-omics analysis revealed associations between metagenomic profiles, metabolite levels, and nitrogen-fixation traits, implying a coordinated modulation of root physiological processes. These findings contribute to a growing understanding of how heat stress interacts with rhizosphere microbial communities and may support future efforts in breeding climate-resilient soybean cultivars.

plant biology↗

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↗

bioRxiv2022

Effects of Oxygen Plasma Treatment on Parylene C and Parylene N Membrane Biocompatibility for Tissue Barrier Models

Porous membranes are integral components of in vitro tissue barrier and co-culture models and their interaction with cells and tissues directly affects the performance and credibility of these models. Plasma-treated Parylene C and Parylene N are two biocompatible Parylene variants with perceived potential for use in these models but their biocompatibility and biological interactions at their interface with cells are not well understood. Here, we use a simple approach for benchtop oxygen plasma treatment and investigate the changes in cell spreading and extracellular matrix deposition as well as the changes in material surface properties. Our results support the previous findings on the persistent effects of plasma treatment on Parylene biocompatibility while showing a more pronounced improvement for Parylene C over Parylene N. It is observed that although both increased surface roughness and persistent increases in oxygen species govern the plasma-driven improvement, the changes in oxygen concentration at the interface are the dominant factor. Overall, the results of this study provide a clear picture of potential mechanisms of plasma-induced changes in synthetic polymers which have implications for their use in in vitro model systems and other BioMEMS applications.

bioengineering↗

bioRxiv2021

Disrupted Surfaces of Porous Membranes Reduce Nuclear YAP Localization through Diminished Cell Spreading and Enhance Adipogenesis

The disrupted surface of porous membranes, commonly used in tissue-chip and cellular co-culture systems, is known to weaken cell-substrate interactions. Here, we investigated whether disrupted surfaces of membranes with micron and sub-micron scale pores affect YAP localization and differentiation of adipose-derived stem cells (ADSCs). We found that these substrates reduce YAP nuclear localization through decreased cell spreading, consistent with reduced cell-substrate interactions, and in turn enhance adipogenesis, while decreasing osteogenesis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/429012v3_ufig1.gif" ALT="Figure 1"> View larger version (82K): org.highwire.dtl.DTLVardef@5fa0daorg.highwire.dtl.DTLVardef@3981d9org.highwire.dtl.DTLVardef@17bd8f5org.highwire.dtl.DTLVardef@1e0c9e5_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2020

Microengineered three-dimensional collagen landscapes with independently tunable fiber anisotropy and directionality

Fibrillar collagens are structural proteins in the extracellular matrix (ECM), and cellular processes, including differentiation, proliferation, and migration, have been linked to the orientation (directionality) and alignment (anisotropy) of collagen fibers. Given the importance of cell-substrate interactions in driving biological functions, several microfluidic approaches have demonstrated three-dimensional (3D) collagen gels with defined fiber properties that enable quantitative correlations between structural cues and observed cell responses. Although existing methods provide excellent definition over collagen fiber anisotropy, independent control over both anisotropy and directionality (that we collectively refer to as the collagen landscape) has not been demonstrated. Therefore, to advance collagen microengineering capabilities, we present a user-friendly approach that uses controlled fluid flows within a non-uniform microfluidic channel network to create well-defined collagen landscapes. We demonstrate capabilities including i) control over fiber anisotropy, ii) spatial gradients in fiber anisotropy, iii) defined fiber directionality, and iv) multi-material interfaces. We then show that cells respond to the microengineered topographic cues by aligning along the anisotropy domains and following fiber directionality. Finally, this platforms modular capability is demonstrated by integrating an ultrathin porous parylene (UPP) membrane on the microengineered collagen as a mask to control cell-substrate interactions.

bioengineering↗

bioRxiv2020

Robust and Gradient Thickness Porous Membranes for In Vitro Modeling of Physiological Barriers

Porous membranes are fundamental elements for tissue-chip barrier and co-culture models. However, the exaggerated thickness of commonly available membranes impedes an accurate in vitro reproduction of the biological multi-cellular continuum as it occurs in vivo. Existing techniques to fabricate membranes such as solvent cast, spin-coating, sputtering and PE-CVD result in uniform thickness films. To understand critical separation distances for various barrier and co-culture models, a gradient thickness membrane is needed. Here, we developed a robust method to generate ultrathin porous parylene C (UPP) membranes not just with precise thicknesses down to 300 nm, but with variable gradients in thicknesses, while at the same time having porosities up to 25%. We also show surface etching and increased roughness lead to improved cell attachment. Next, we examined the mechanical properties of UPP membranes with varying porosity and thickness and fit our data to previously published models, which can help determine practical upper limits of porosity and lower limits of thickness. Lastly, we validate a straightforward approach allowing the successful integration of the UPP membranes into a prototyped 3D-printed scaffold enabling in vitro barrier modeling and investigation of cell-cell interplay over variable distances using thickness gradients.

bioengineering↗

bioRxiv2020

Simple and Robust Fabrication and Characterization of Conductive Carbonized Nanofibers Loaded with Gold Nanoparticles for Bone Tissue Engineering Applications

Bone tissue engineering is a new and applicable emerging approach to repair the bone defects. Electrical conductive scaffolds through a physiologically relevant physical signaling, electrical stimulation, has shown a highly promise in this approach. In this paper, we fabricated carbon nanofiber/gold nanoparticle (CNF/GNP) conductive scaffolds using two distinct methods; blending electrospinning in which GNP were blended with electrospinning solution, and electrospinning/electrospraying in which GNP was electrosprayed simultaneously with electrospinning. The obtained electrospun mats underwent stabilization/carbonization process. The scaffolds were characterized by SEM, XRD, FT-IR and Raman spectroscopy. SEM characterizations showed improved morphology and a slight decrease in the diameter of the spinned and sprayed nanofibers (from 178.66 {+/-} 38.40 nm to 157.94 {+/-} 24.14 nm and 120.81 {+/-} 13.77 nm, respectively), while XRD analysis confirmed the crystal structure of the nanofibers. Raman spectroscopy revealed enhancement in the graphitization of the structure, and the electrical conductivity of the structure improved by up to 29.2% and 81% in electrospraying and blending electrospinning modes, respectively. Indirect MTT and LDH toxicity assays directly were performed to assess MG63 cell toxicity, but no significant toxicity was observed and the scaffolds did not adversely affect cell proliferation. It can be concluded this structure have potential for bone tissue engineering applications. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/013383v2_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1ac84f1org.highwire.dtl.DTLVardef@14bef2dorg.highwire.dtl.DTLVardef@438261org.highwire.dtl.DTLVardef@24e1b4_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2019

Altered Cell-Substrate Behavior on Microporous Membranes is a Result of Disruption and Grip

Porous membranes are ubiquitous in cell co-culture and tissue-on-a-chip studies. These materials are predominantly chosen for their semi-permeable and size exclusion properties to restrict or permit transmigration and cell-cell communication. However, previous studies have shown pore size, spacing and orientation affect cell behavior including extracellular matrix production and migration. The mechanism behind this behavior is not fully understood. In this study, we fabricated micropatterned non-fouling polyethylene glycol (PEG) islands to mimic pores in order to decouple the effect of surface discontinuity from grip provided by pore wall edges. Similar to porous membranes, we found that the PEG islands hindered fibronectin fibrillogenesis with cells on patterned substrates producing shorter fibrils. Additionally, cell migration speed over micropatterned PEG islands was greater than unpatterned controls, suggesting that disruption of cell-substrate interactions by PEG islands promoted a more dynamic and migratory behavior, similarly to cells migrating on microporous membranes. Preferred cellular directionality during migration was nearly identical between substrates with identically patterned PEG islands and micropores, further confirming disruption of cell-substrate interactions as a common mechanism behind the cellular responses on these substrates. Interestingly, cell spreading and the magnitude of migration speed was significantly greater on porous membranes compared to PEG islands with identical feature size and spacing, suggesting pore edges enhanced cellular grip. These results provide a more complete picture on how porous membranes affect cells which are grown on them in an increasing number of cellular barrier and co-culture studies.

bioengineering↗