Biology subjects

Ibrahim, Z.

Publications and source records attributed to Ibrahim, Z..

6 recordsLinked to original sources

bioRxiv2026

Early-Stage Cultures of Acidithiobacillus ferrooxidans Enable Efficient Bioleaching of Li-ion Battery Cathode Material

In response to the growing need to recycle E-waste, specifically that of lithium-ion batteries (LIBs), the development of sustainable recycling methodologies will be vital. As one of the most sustainable and low-cost options, biohydrometallurgy (BioHM) uses biological organisms to facilitate the recovery of critical metals from spent LIBs. Despite the advantages of BioHM, its slow kinetics, due to the reliance on the metabolic activity of microorganisms, limit its large-scale application for the closed-loop recycling of LIBs. In this work, we investigate the correlation between the incubation time of Acidithiobacillus ferrooxidans (Atf) and its leaching efficiency of four common elements in LIBs: Li, Ni, Mn, and Co. We assess how specific incubation times along the biological growth curve affect the leaching efficiency of Li[Ni0.6Mn0.2Co0.2]O2 (NMC622), a model electrode material. Our results show that pH alone is not an accurate descriptor of the leaching efficiency of Atf cultures used at different growth stages. The addition of NMC622 during the bacterial lag phase reaches similar or even improved extraction compared to cultures used after reaching the exponential or stationary phases. A simple model of leaching dynamics shows predictions consistent with our experimental observations under the condition that the inhibition of bacterial growth by NMC is not severe. Our findings indicate that early-stage cultures can alleviate the kinetic bottleneck and improve the throughput of recovering critical materials from spent batteries.

microbiology↗

bioRxiv2026

Bioelectricity Generation from Acidogenic Palm Oil Mill Effluents using Microbial Fuel Cells

Microbial fuel cell offers a promising approach to improve wastewater quality and generate bioenergy from dark fermented effluents. In this study, the use of dark-fermented palm oil mill effluent as an electron donor for bioelectricity generation was investigated using a double-chambered microbial fuel cell (MFC). The MFCs were operated at room temperature (29 {+/-} 2{degrees}C), anode electrolytes adjusted to pH 7, and a chemical catholyte as the oxidizing agent. The maximum power {+/-} 8.07 mW/m2 and 155.16 {+/-} 12.88 mA/m2, respectively, were generated from the MFCs inoculated with sludge, which was 5.9 times higher than control without inoculum. Microbial community analysis revealed the enrichment of fermentative and electrogenic representative taxa from the phyla Bacillota, Bacteroidota and Pseudomonadota on the anode electrodes. Optimizations of the running conditions were carried out, suggesting the optimum parameters of 0.5 k{Omega} external resistance, anolyte initial pH 9, and 75% DFPOME substrate concentration. Operation under the optimized conditions increased current production, wastewater treatment, and Coulombic efficiency compared to the non-optimized conditions. Multiple configurations were also evaluated, showing higher cumulative voltage, power, and current densities with the stacked MFC connections, compared to single MFC units. Parallel circuit connection produced higher power and current density than serial connection. This study demonstrated the feasibility of MFC as a promising downstream treatment for biohydrogen production processes, towards higher treatment efficiency and resource recovery.

microbiology↗

bioRxiv2025

Targeting and combating drug resistance in triple-negative breast cancer using nano polymer: Efficacy of A6 peptide-PLGA-PEG nanoparticle loaded with doxorubicin and anti-miR-21 in in vitro and vivo model.

Triple-negative breast cancer (TNBC) poses a significant challenge in treatment due to the emergence of drug resistance to standard chemotherapeutics, along with associated risks to non-targeted tissues. This study is dedicated to developing a nanoparticle drug delivery system utilizing PLGA-PEG nanoparticles (NP) with the integration of A6 peptide (NPA6) as a specific targeting ligand for TNBC. Encapsulating Doxorubicin (DOX) and antisense-miR-21 (AM21), these nanoparticles are designed to counter drug resistance in vitro and in vivo. Characterized by an average size of 103.5 ({+/-}8.1) nm and remarkable DOX encapsulation efficiency, these nanoparticles have been successfully engineered. Results demonstrate that NPA6.DOX.AM21 effectively mitigates drug resistance, displaying a significantly decreased doxorubicin IC50 as opposed to free DOX (2.5 {micro}M vs 25.7{micro}Mrespectively, p<0.01). In mice models, the A6 peptide-incorporated formulation (NPA6.DOX, NPA6.DOX.AM21) exhibits substantial tumour size reduction and increased doxorubicin concentration within tumours, all while minimizing non-specific doxorubicin exposure compared to non-A6 formulations (NPDOX, FREE DOX) treatments. This innovative PLGA-PEG-A6 peptide complex loaded with DOX and AM21 showcases superior efficacy in surmounting cell resistance in breast cancer cell line, targeting tumour progression, and decreasing drug distribution in non-targeted organs in mice. These results hold promise for enhanced combat against drug resistance and precise chemotherapy, hence potentially improving patient outcomes and survival rates. Graphical abstact O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/631287v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@283f0forg.highwire.dtl.DTLVardef@43fa12org.highwire.dtl.DTLVardef@d6d5baorg.highwire.dtl.DTLVardef@69e65d_HPS_FORMAT_FIGEXP M_FIG C_FIG Figure Graphical abstract of the study. Fron left to right, development of nanoparticles formulation a followed by characterization and efficacy of the nanoparticle formulation in in vitro and in vivo to reduce drug resistance and target triple negative breast cancer (TNBC). PLGA: polylactic-co-glycolic acid, PEG: polyethylene glycol, A6: A6 peptide, DOX: Doxorubicin, AM21: antisense-microRNA -21 HighlightsO_LIThe nanoparticle of A6 conjugated PLGA-PEG co-loaded Doxorubicin with anti-miRNA21 (NPA6.DOX.AM21) was successfully fabricated with the size of 99.8 - 103.5 nm diameter and PDI 0.2 with high drugs encapsulation efficiency. C_LIO_LINPA6.DOX.AM21 increased cell death, reduced drug resistance in MDA MB-231 resistant cells, and reduced IC50 of doxorubicin dose. C_LIO_LINPA6.DOX.AM21 targeted and reduced TNBC tumour size, with high doxorubicin distribution in tumor and less accumulation in off-target organs, in comparison to the control in mice model. C_LI

cancer biology↗

bioRxiv2022

Structural insights into the regulation of acetylation-dependent genome condensation

Histone modifications are deposited by chromatin modifying enzymes and read out by proteins that recognize the modified state. BRD4-NUT is an oncogenic fusion protein of the acetyl lysine reader BRD4 that binds to the acetylase p300 and enables formation of long-range intra- and interchromosomal interactions. We here examine how acetylation reading and writing enable formation of such interactions. We show that NUT contains an acidic transcriptional activation domain that binds to the TAZ2 domain of p300. We use NMR to investigate the structure of the complex and found that the TAZ2 domain has an autoinhibitory role for p300. NUT-TAZ2 interaction or mutations found in cancer that interfere with autoinhibition by TAZ2 allosterically activate p300. p300 activation results in a self-organizing, acetylation-dependent feed-forward reaction that enables long-range interactions by bromodomain multivalent acetyl-lysine binding. We discuss the implications for chromatin organisation, gene regulation and dysregulation in disease.

biochemistry↗

bioRxiv2022

Topology of connective tissues: a key parameter in cellular heterogeneity, beyond composition and stiffness

Cellular plasticity is essential in physiological contexts, including pathological ones. It is the basis of morphogenesis and organogenesis, as well as tumorigenesis and metastasis. The extracellular matrix (ECM) is a key player in the generation of cellular heterogeneity. Advances in our understanding of cell plasticity rely on our ability to provide relevant in vitro models. This requires to catch the characteristics of the tissues that are essential for controlling cell fate. To do this, we must consider the diversity of tissues, the diversity of physiological contexts, and the constant remodeling of ECM along these processes. To this aim, we have fabricated a library of ECM models for reproducing the scaffold of connective tissues and basement membrane with different biofabrication routes based on the electrospining and drop casting of biopolymers. Using a combination of multiphoton imaging and nanoindentation, we show that we can vary independently protein composition, topology of connective tissues and stiffness of ECM models. Reproducing the features of a tissue and physiological context in turns allows to generate the complexity of the phenotypic landscape associated with the epithelial-to-mesenchymal transition (EMT) in human ovarian cancer. We show that EMT shift cannot be directly correlated with a unique ECM feature, which reflects the multidimensionality of living environments. Very importantly, our combinatorial approach allows us to provide in vitro models, where the impact of the topological cues on cellular phenotypes can be revealed, beyond protein composition and stiffness of the ECM matrix. On this line, this work is a further step towards the development of ECM models recapitulating the constantly remodeled scaffolding environment that cells face and provides new insights for the development of cell-free matrices.

bioengineering↗

bioRxiv2017

SemEHR: A General-purpose Semantic Search System to Surface Semantic Data from Clinical Notes for Tailored Care, Trial Recruitment and Clinical Research

ObjectiveUnlocking the data contained within both structured and unstructured components of Electronic Health Records (EHRs) has the potential to provide a step change in data available forsecondary research use, generation of actionable medical insights, hospital management and trial recruitment. To achieve this, we implemented SemEHR - a semantic search and analytics, open source tool for EHRs.\n\nMethodsSemEHR implements a generic information extraction (IE) and retrieval infrastructure by identifying contextualised mentions of a wide range of biomedical concepts within EHRs. Natural Language Processing (NLP) annotations are further assembled at patient level and extended with EHR-specific knowledge to generate a timeline for each patient. The semantic data is serviced via ontology-based search and analytics interfaces.\n\nResultsSemEHR has been deployed to a number of UK hospitals including the Clinical Record Interactive Search (CRIS), an anonymised replica of the EHR of the UK South London and Maudsley (SLaM) NHS Foundation Trust, one of Europes largest providers of mental health services. In two CRIS-based studies, SemEHR achieved 93% (Hepatitis C case) and 99% (HIV case) F-Measure results in identifying true positive patients. At Kings College Hospital in London, as part of the CogStack programme (github.com/cogstack), SemEHR is being used to recruit patients into the UK Dept of Health 100k Genome Project (genomicsengland.co.uk). The validation study suggests that the tool can validate previously recruited cases and is very fast in searching phenotypes - time for recruitment criteria checking reduced from days to minutes. Validated on an open intensive care EHR data - MIMICIII, the vital signs extracted by SemEHR can achieve around 97% accuracy.\n\nConclusionResults from the multiple case studies demonstrate SemEHRs efficiency - weeks or months of work can be done within hours or minutes in some cases. SemEHR provides a more comprehensive view of a patient, bringing in more and unexpected insight compared to study-oriented bespoke information extraction systems.\n\nSemEHR is open source available at https://github.com/CogStack/SemEHR.

bioinformatics↗