Biology subjects

Abbasi, S.

Publications and source records attributed to Abbasi, S..

8 recordsLinked to original sources

bioRxiv2025

Vertical distribution and migration of microplastics in soils from Fars Province, southwest Iran

Microplastics (MPs) in soils have recently emerged as a significant environmental concern because of their potential impacts on ecosystems and human health. In this study, MPs have been determined in genetic soil horizons to a maximum depth of 140 cm along four transects that encompass various land uses (managed and unmanaged) in Fars Province, southwest Iran. Soils have also been characterised in terms of texture and chemistry using established methods. With little contemporary or historical application through agricultural practices, MPs were dominated by fibres of various colours and sizes and polymeric construction (mainly polyamides, polyesters and polyolefins), with remaining particles largely consisting of sheet-like fragments. MP abundance (up to about 200 per kg of dry soil) and size were heterogeneously distributed throughout the region and with respect to soil depth, regardless of land use, with inverse correlations with soil particle size observed at two locations. We infer that atmospheric deposition is the principal source at the soil surface and that MPs that evade erosion are able to readily migrate downwards to depths extending to at least that of the lowest horizon sampled. Migration appears to be independent of particle size or density and is likely driven by percolating precipitation but facilitated through bioturbation and soil cracking during dry periods. The persistence and vertical migration of MPs in soils may have adverse impacts on subterranean ecosystems and ground water quality. HighlightsO_LIMicroplastics (MPs) determined in soil horizons covering different land uses in Fars Province C_LIO_LIMPs dominated by fibres and derived largely from atmospheric deposition C_LIO_LIMPs distributed heterogeneously with depth, land use, soil texture C_LIO_LIRegardless of size and density, MPs able to migrate to at least 140 cm C_LIO_LIMigration may have adverse impacts on subterranean ecosystems and ground water C_LI

biochemistry↗

bioRxiv2025

Assessing the efficiency and the side effects of atrazine-degrading biocomposites amended to atrazine-contaminated soil

Even decades after being banned in Europe, atrazine and its main metabolites can still be found in soils. While bioaugmentation using pesticide-degrading bacteria is already employed as a strategy for remediating polluted soils, there is still a need to improve its efficiency. Therefore, investigating the application of carrier materials to deliver and stabilize pesticide-degrading microorganisms in situ emerges as an interesting approach for further exploration. Here, we generated atrazine-degrading biocomposites by cultivating either a single strain or a 4-species bacterial consortium as biofilms on zeolite, which serves as the carrier material. Using a microcosm experiment, we then evaluated their efficiency to mineralize 14C-atrazine in an agricultural soil comparing to free-living cells, and assessed the side effects of the two inoculation methods on the native soil bacterial community using 16S rDNA amplicon sequencing. We showed that, right after inoculation, the atrazine mineralization potential of the free-living cells was higher than that of the biocomposites. However, microcosms inoculated with the biocomposites displayed significantly higher atrazine mineralization potential than the ones inoculated with free-living cells after 15 and 45 days of incubation, not only indicating a higher efficiency but also a better stability in the soil environment, further confirmed by qPCR of the atz genes. We also showed that the inoculation of free-living cells and biocomposites differently influences the diversity and composition of the native microbial community, and that these effects are modulated by the scenario of atrazine contamination during soil inoculation. Altogether, our results provide a thorough evaluation of the efficiency and the ecotoxicological impact of atrazine-degrading biocomposites in soil.

microbiology↗

bioRxiv2025

Differential Roles of Broadly Expressed Transcription Factors in Early Cardiac Cell Specification

Early embryogenesis is governed by intricate gene regulatory networks that orchestrate cell fate specification across all three germ layers. While the role of transcription factors (TFs) and pioneer factors (PFs) in shaping chromatin accessibility is well established, the mechanisms coordinating spatiotemporal gene expression before gastrulation remain poorly understood. Here, we investigate how a coordinated network of early-acting regulators, including the pioneer factors Zelda (Zld), GAGA factor (GAF), and the pioneer-like timing factor Odd-paired (Opa/ZIC3), along with Dorsal (Dl), Twist (Twi), the Polycomb subunit Enhancer of Zeste (E(z)), and the co-activator CBP, govern early transcriptional events in the Drosophila embryo. Using integrated chromatin accessibility, histone modification, TF binding, and transcriptomic data (bulk and single-cell), we identify two distinct classes of regulatory elements that govern early gene expression. The first class includes distal, PF-dependent enhancers that are inaccessible early and require PFs such as Opa and Zld to overcome Su(H) activities and H3K27me3-mediated repression and initiate transcription. The second class, enriched for PcG domains, comprises proximal enhancers that are accessible from the earliest nuclear cycles, despite being marked by H3K27me3 and bound by E(z). These regions are preloaded with RNA Polymerase II and positioned near promoters, suggesting a regulatory state primed for activation. While bound by multiple early TFs, these enhancers maintain accessibility independently of PF activity, functioning instead as autoregulatory elements that rely on PFs for maintenance rather than initiation. This study expands our understanding of how early TFs and PFs coordinate to balance transcriptional precision and developmental plasticity across germ layers, and redefines the role of PFs as both activators and stabilizers of gene regulatory architecture. Within this framework, Opa regulates key mesodermal and neuroectodermal genes such as slp1 and odd, and its activity is modulated by Suppressor of Hairless (Su(H)). At earlier stages, Su(H) represses Opa target genes, but rising Opa levels at later timepoints override this repression, enabling activation. Together, these findings support a dual-mode enhancer logic: one mode driven by PF-mediated chromatin opening at distal, repressed enhancers, and another where proximal, pre-accessible enhancers within PcG-marked regions are reinforced by PF binding. This study redefines the role of PFs in early development, emphasizing their maintenance and stabilizing roles at poised enhancers, and provides a framework for how embryos balance transcriptional plasticity with spatial precision across all germ layers.

developmental biology↗

bioRxiv2023

Intrinsic neural timescales attenuate information transfer along the uni-transmodal hierarchy

The brains intrinsic timescales are organized in a hierarchy with shorter timescales in sensory regions and longer ones in associative regions. This timescale hierarchy overlaps with the timing demands of sensory information. Our question was how does this timescale hierarchy affect information transfer. We used a model of the timescale hierarchy based on connected excitatory and inhibitory populations across the cortex. We found that a hierarchy of information transfer follows the hierarchy of timescales with higher information transfer in sensory areas while it is lower in associative regions. Probing the effect of changes in timescale hierarchy on information transfer, we changed various model parameters which all, through, the loss of hierarchy, induced increased information transfer. Finally, the steepness of the timescale hierarchy relates negatively to total information transfer. Human MEG data confirmed our results. In sum, we demonstrate a key role of the brains timescale hierarchy in mediating information transfer.

neuroscience↗

bioRxiv2023

Cutaneous jet-injection of naked mRNA vaccine induces robust immune responses without systemic vaccine spillage

Naked mRNA-based vaccines may reduce the reactogenicity associated with delivery carriers, but their effectiveness has been suboptimal against infectious diseases. Herein, we aimed to enhance their efficacy by using a pyro-drive liquid jet injector that precisely controls pressure to widely disperse mRNA solution in the skin. The jet injection boosted naked mRNA delivery efficiency in the mouse skin. Mechanistic analyses indicate that dendritic cells, upon uptake of antigen mRNA in the skin, migrate to the draining lymph nodes for antigen presentation. Additionally, the jet injector activated innate immune responses in the skin, presumably by inducing physical stress, thus serving as a physical adjuvant. From a safety perspective, our approach, utilizing naked mRNA, restricted mRNA distribution solely to the injection site, preventing systemic pro-inflammatory reactions following vaccination. Ultimately, the jet injection of naked mRNA encoding SARS-CoV-2 spike protein elicited robust humoral and cellular immunity, providing protection against SARS-CoV-2 infection in mice. Furthermore, our approach induced plasma activity of neutralizing SARS-CoV-2 in non-human primates, comparable to that observed in mice, with no detectable systemic reactogenicity.

bioengineering↗

bioRxiv2022

Cell-specific occupancy dynamics between the pioneer-like factor Opa/ZIC and Ocelliles/OTX regulate early head development in embryos

During development, embryonic patterning systems direct a set of initially uncommitted pluripotent cells to differentiate into a variety of cell types and tissues. A core network of transcription factors, such as Zelda/POU5F1, Odd-paired (Opa)/ZIC and Ocelliless (Oc)/OTX, are conserved across animals. While Opa is essential for a second wave of zygotic activation after Zelda, it is unclear whether Opa drives head cell specification past gastrulation onset, in the Drosophila embryo. Our hypothesis is that Opa and Oc are interacting with distinct cis-regulatory regions for shaping cell fates in the embryonic head. Using super-resolution microscopy and epigenomic meta-analysis of single cell RNAseq datasets we find that opas and ocs overlapping expression domains are dynamic in the head region, with both factors being simultaneously transcribed at the blastula stage. However, analysis of single-embryo RNAseq data reveals a subgroup of Opa-bound genes to be Opa-independent in the cellularized embryo. Interrogation of these genes against Oc ChIPseq combined with in situ data, suggests that Opa is competing with Oc for the regulation of a subgroup of genes later in gastrulation. Specifically, we find that Oc binds to late, head-specific enhancers independently and activates them in a head-specific wave of zygotic transcription, suggesting distinct roles for Oc in the blastula and gastrula stages.

developmental biology↗

bioRxiv2022

Tethering designer short double-stranded RNA to mRNA for co-delivery of molecularly-targeted adjuvants and antigens towards cancer vaccination

Integrating antigen-encoding mRNA and immunostimulatory adjuvant into a single formulation is a promising approach to potentiating the efficacy of mRNA vaccines. Here, we developed a scheme based on RNA engineering to integrate adjuvancy directly into antigen-encoding mRNA strands without hampering the ability to express antigen proteins. Short double-stranded RNA (dsRNA) was designed to target retinoic acid-inducible gene-I (RIG-I), an innate immune receptor, for effective cancer vaccination and then tethered onto mRNA strand via hybridization. Tuning the dsRNA structure and microenvironment by changing its length and sequence enabled the determination of the structure of dsRNA-tethered mRNA efficiently stimulating RIG-I. Eventually, the formulation loaded with dsRNA-tethered mRNA of the optimal structure effectively activated mouse and human dendritic cells and drove them to secrete a broad spectrum of proinflammatory cytokines without increasing the secretion of anti-inflammatory cytokines. Notably, the immunostimulating intensity was tunable by modulating the number of dsRNA along mRNA strand, which prevents excessive immunostimulation. Versatility in the applicable formulation is a practical advantage of the dsRNA-tethered mRNA. Its formulation with three existing systems, i.e., anionic lipoplex, ionizable lipid-based lipid nanoparticles, and polyplex micelles, induced appreciable cellular immunity in the mice model. Of particular interest, dsRNA-tethered mRNA encoding ovalbumin (OVA) formulated in anionic lipoplex used in clinical trials exerted a significant therapeutic effect in the mouse lymphoma (E.G7-OVA) model. In conclusion, the system developed here provides a simple and robust platform to supply the desired intensity of immunostimulation in various formulations of mRNA cancer vaccines.

bioengineering↗

bioRxiv2021

Synthetic repertoires derived from convalescent COVID-19 patients enable discovery of SARS-CoV-2 neutralizing antibodies and a novel quaternary binding modality

The ongoing evolution of SARS-CoV-2 into more easily transmissible and infectious variants has sparked concern over the continued effectiveness of existing therapeutic antibodies and vaccines. Hence, together with increased genomic surveillance, methods to rapidly develop and assess effective interventions are critically needed. Here we report the discovery of SARS-CoV-2 neutralizing antibodies isolated from COVID-19 patients using a high-throughput platform. Antibodies were identified from unpaired donor B-cell and serum repertoires using yeast surface display, proteomics, and public light chain screening. Cryo-EM and functional characterization of the antibodies identified N3-1, an antibody that binds avidly (Kd,app = 68 pM) to the receptor binding domain (RBD) of the spike protein and robustly neutralizes the virus in vitro. This antibody likely binds all three RBDs of the trimeric spike protein with a single IgG. Importantly, N3-1 equivalently binds spike proteins from emerging SARS-CoV-2 variants of concern, neutralizes UK variant B.1.1.7, and binds SARS-CoV spike with nanomolar affinity. Taken together, the strategies described herein will prove broadly applicable in interrogating adaptive immunity and developing rapid response biological countermeasures to emerging pathogens.

synthetic biology↗