Biology subjects

Attar, A.

Publications and source records attributed to Attar, A..

4 recordsLinked to original sources

bioRxiv2026

Discovering Novel PETase Enzymes for Enhanced PET Plastic Degradation Using in Silico Approaches

Accounting for 12% of global solid waste, Poly (ethylene terephthalate) (PET) is one of the most abundantly produced synthetic polymers. While PET offers substantial commercial benefits, its widespread use has led to disproportionate environmental hazards due to its resistance to degradation. To address this problem, several solutions have been proposed, including enzymatic degradation via PETase, MHETase, and Cutinase. Among these, PETase exhibited significant PET-degrading activity. However, the application of PETase has been hampered by its lack of robustness to pH, temperature ranges, and slow reaction rates. Hence, it has become novel enzymes that can overcome these limitations and function efficiently. In this study, we utilised an integrated in silico bioinformatics pipeline to identify and characterise novel PETase candidates from the Thermophilic actinobacteria Thermobifida cellulosilytica and Thermobifida halotolerans species. The PlasticDB database contains 228 plastic-degrading enzyme sequences. In which PETase (00188) is significantly homologous with two putative proteins, Hydrolase (ALF00495.1) and hypothetical protein (WOZ56011.1). The discrete optimized protein energy (DOPE) scores, stereochemical assessments, and homology modeling results closely mirrored our findings for both proteins, supporting their structural stability. The molecular dynamics simulations revealed that the putative ALF00495 variant exhibited more extensive and robust hydrogen-bonding networks, enhanced conformational stability, and increased structural compactness compared to the reference enzyme. The present in silico investigation underscores the potential of putative ALF00495 as a highly effective PETase biocatalyst for polyethylene terephthalate (PET) degradation. Collectively, these findings illustrate the utility of computational approaches of novel PET-degrading enzymes, thereby facilitating the development of sustainable biotechnological strategies to mitigate global plastic pollution.

bioinformatics↗

bioRxiv2026

Establishment of the Saudi Bank of Induced Pluripotent Stem Cells (SBiPSCs): A National Platform for iPSC-Based Research and Therapy

BackgroundThe global landscape of induced pluripotent stem cell (iPSC) resources remains heavily skewed toward European, North American, and East Asian populations, leaving the Middle East and North Africa (MENA) region critically underrepresented. This disparity hinders the application of precision medicine in populations with unique genetic backgrounds, particularly those with high rates of consanguinity and distinctive rare disease profiles. To address this gap, we established the Saudi Bank of Induced Pluripotent Stem Cells (SBiPSCs), at King Abdullah International Medical Research Centre (KAIMRC). The bank comprises two major complementary arms: one dedicated to the derivation and biobanking of iPSCs from individuals with rare and common genetic disorders, and a second focused on Human Leukocyte Antigen (HLA)-based iPSC banking to support the development of immunocompatible cell therapies. MethodsSBiPSCs operates within King Abdulaziz Medical City in Jeddah under the Ministry of National Guard for Health Affairs (MNGHA)s ethical and clinical framework. To establish the repository, we implemented a clinic-guided enrolment strategy in which treating physicians, briefed on the banks objectives, recruited patients with confirmed genetic diagnoses. Peripheral blood samples were collected, processed, and cells were reprogrammed using non-integrating episomal plasmids. All derived lines underwent rigorous quality control in accordance with International Society for Stem Cell Research (ISSCR) standards, including assessment of pluripotency markers, genomic integrity, and trilineage differentiation potential. To demonstrate our iPS characterization workflow and translational utility, iPSCs from a Saudi patient with familial Long QT Syndrome (LQTS) and a healthy sibling were differentiated into functional cardiac organoids. Simultaneously, for the HLA-based banking arm, the Saudi Stem Cell Donor Registry (SSCDR) database was leveraged to identify donors predicted to provide maximal coverage for the Saudi population. ResultsTo date, SBiPSCs has successfully generated 37 iPSC lines derived from 19 Saudi patients and healthy donors. All lines exhibit robust expression of pluripotency markers, maintain normal karyotypes, and demonstrate differentiation capacity. To demonstrate our characterization pipeline and translational utility, iPSCs from an LQTS patient and a healthy sibling were generated, validated, and differentiated into beating cardiac organoids that recapitulated the disease phenotype, with microelectrode array analysis confirming prolonged field potential durations mirroring the clinical QT prolongation. Furthermore, the HLA-based banking arm has expanded to include two homozygous iPSC lines, which together provide immunological compatibility for approximately 9% of the Saudi population. ConclusionsSBiPSCs represents the first centralized iPSC repository in the MENA region. The SBiPSCs is well-positioned to accelerate the translation of stem cell research into scalable, immunocompatible cell therapies and precision medicine applications aligned with national and regional healthcare priorities.

genetics↗

bioRxiv2025

Directing fratricide within T cell products using an anti-uPAR chimeric antigen receptor to drive the production of potent therapeutic cells

Cell therapy manufacturing of primary T cells often results in heterogeneous cell populations within a final product, with many cells lacking desired of receptor expression or those that have exhausted or other dysfunctional phenotypes. Here, we design a novel cell-intrinsic strategy to genetically reprogram primary human T cells to autonomously detect and eliminate dysfunctional cells. This integrated detection and elimination process, known as directed fratricide, is programmed via nonviral CRISPR genome-editing to eliminate the T cell receptor (TCR) alpha chain (TRAC gene knockout) and integrate a chimeric antigen receptor (CAR) against the urokinase-type plasminogen activator receptor (uPAR), also known as CD87. Within these cell products, strong T cell stimulation or activation during manufacturing causes a small subset of cells to express uPAR, which subsequently triggers CAR-mediated killing by a separate subset of cells within the product. This fratricide induces proliferation in the desired cells and destroys undesired cells, a process that could be modeled computationally and controlled robustly via supplements to the culture media. The strategy enabled enrichment of anti-uPAR and anti-GD2 CAR T cell products up to [≥]99% CAR+/TCR-, favoring a stem cell memory-like phenotype (CD45RAhigh/CD62Lhigh). Understanding growth dynamics among T cell subsets and reprogramming them via CRISPR could accelerate the biomanufacturing of potent cell products without extensive selection methods. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/684419v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@199d85forg.highwire.dtl.DTLVardef@14c638aorg.highwire.dtl.DTLVardef@1b3322org.highwire.dtl.DTLVardef@1ba253d_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2018

Modulatory effect of Syzygium aromaticum and Pelargonium graveolens on oxidative stress and inflammation

BackgroundTherapy combination is defined as disease treatment with two or more medication to acheive efficacy with lower doses or lower toxicity. Regarding its reported toxicities and efficacy, the Essential Oils (EOs) from Syzygium aromaticum (SA) and Pelargonium graveolens (PG) were combined for in vitro and in vivo assays and toxicities.\n\nMethodsThe Essential Oils and mixture were tested for in vivo/in vitro antioxidant and anti-inflammatory activities. The assays included the animal model of acute inflammation (carrageenan model), the protective effect on H2O2/Sodium nitroprissude induced stress in Tetrahymena pyriformis, and the in vitro antioxidant assays.\n\nResultsThe chemical analysis of the investigated Oils has lead to the identification of Eugenol (74.06%), Caryophyllene (11.52%) and Carvacrol acetate (7.82%) as the major element in SA; while PG was much higher in Citronellol (30.77%), 10-epi-{gamma}-Eudesmol (22.59%), and Geraniol (13.95%). In our pharmacological screening of samples, both Oils demonstrated good antioxidant effects. In vivo investigation of the antioxidant activity in the protozoa model (T. pyriformis) demonstrated a lesser toxic effect of EOs mixture with no significant differences when oxidative stress markers and antioxidant enzymes (MDA, SOD and CAT) were evaluated. On the other hand the in vivo model of inflammatory response to carrageenan demonstrated a good inhibitory potential of both EOs. The EOs Mixture demonstrated equivalent bioactivity with lower toxic effect and minimal risk for each compound.\n\nConclusionsThe results from this study indicate that EOs mixture from SA and PG demonstrated promising modulatory antioxidant/anti-inflammatory effect, which suggest an efficient association for therapy.

pharmacology and toxicology↗