Esterase-mediated degradation of dibutyl and diethylhexyl phthalates in aqueous and soil systems.

Phthalate esters (PAEs), widely used as plasticizers, pose severe environmental and health risks. This study investigated the enzymatic hydrolysis of PAE congeners (dibutyl phthalate (DBP) and diethylhexyl phthalate (DEHP)) in aqueous and soil systems using Bacillus subtilis esterase and a new thermoalkaliphilic Geobacillus sp. esterase.

Quantifying hydrogen bonding using electrically tunable nanoconfined water.

Hydrogen bonding plays a crucial role in biology and technology, yet it remains poorly understood and quantified despite its fundamental importance. Traditional models, which describe hydrogen bonds as electrostatic interactions between electropositive hydrogen and electronegative acceptors, fail to quantitatively capture bond strength, directionality, or cooperativity, and cannot predict the properties of complex hydrogen-bonded materials. Here, we introduce a concept of hydrogen bonds as elastic dipoles in an electric field, which captures a wide range of hydrogen bonding phenomena in various water systems.

Phase-dependent optical, photocatalytic and capacitive properties of tungsten oxide nanowires.

Transition metal oxides hold great promise across a wide range of applications due to favorable properties such as high abundance, low toxicity, and excellent stability. Nanoengineering approaches are essential for controlling the structural, optical, and electronic properties of these materials, enabling the achievement of desired characteristics in a cost-effective and environmentally friendly manner. In this study, we synthesize stoichiometric (WO) and sub-stoichiometric (WO) tungsten oxide nanowires by controlling their phases and morphologies through the hydrothermal method.

The Role of tRNA Fragments on Neurogenesis Alteration by H₂O₂-induced Oxidative Stress.

Transfer RNAs (tRNAs) are small non-coding RNA molecules transcribed from tRNA genes. tRNAs cleaved into a diverse population tRNA fragments (tRFs) ranging in length from 18 to 40 nucleotides, they interact with RNA binding proteins and influence the stability and translation. Stress is one of the reasons for tRFs cleavage.

Surface sediments as a sink and risk source for legacy POPs during waste management practices.

Persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) are globally recognized contaminants due to their persistence, bioaccumulative properties, and toxicity. Despite regulatory efforts, these compounds continue to enter the environment through improper waste management practices, including shipbreaking activities. This study investigates the PCB and PBDE contamination of marine sediments along a 30 km coastline in Aliağa, Türkiye, involving one of the world's largest shipbreaking yards.

Unveiling Bone and Dental Regeneration Potential of Quince Seed Mucilage-Nanohydroxyapatite Scaffolds in Rabbit Mandibles.

Donor-side morbidity of autografting for maxillofacial region defect regeneration has directed attention to bioengineered scaffolds. Composite scaffolds that mimic the bone extracellular matrix (ECM) are the potential candidates for defect reconstruction. Herein, a plant-based regenerative hydrogel, quince seed mucilage (QSM), was enriched with the nanohydroxyapatite (nHAp) particles to construct composite scaffolds (QSM/nHAp).

Improved Isolation of Ultra-High-Molecular-Weight Genomic DNA Suitable for Third-Generation Sequencing.

Although a variety of protocols to isolate high-molecular-weight genomic DNA exist, the isolation and preservation of ultra-high-molecular-weight genomic DNA of sufficient quality and length for error-free third-generation sequencing remains challenging. Inspired by the isolation of high-molecular-weight DNA in agarose plugs suitable to be separated by pulsed-field gel electrophoresis, we report the construction of an incubation chamber for DNA isolation. The chamber is flanked by semi-permeable polycarbonate membranes of variable pore size for the selective diffusion of compounds and components, which allows efficient cell lysis and the subsequent isolation of ultra-high-molecular-weight genomic DNA without shearing.

Magnetic Levitational Assembly of Differentiated SH-SY5Y Cells for Aβ-Induced 3D Alzheimer's Disease Modeling and Curcumin Screening.

Alzheimer's disease is one of the prevalent neurodegenerative diseases and is characterized by amyloid beta aggregate (Aβ) accumulation. This study reports an Aβ 1-42 induced 3D Alzheimer's disease modeling utilizing differentiated SH-SY5Y spheroids, which is carried out by Magnetic levitation approach, and the neuroprotective effect of Curcumin is further investigated on this model. For this purpose, SH-SY5Y spheroids are differentiated using Retinoic acid-Brain-derived neurotrophic factor sequentially during 3D cell culture.

MagSity platform: a hybrid magnetic levitation-based lensless holographic microscope platform for liquid density and viscosity measurements.

The viscosity and density of liquids are the most extensively studied material properties, as their accurate measurement is critical in various industries. Although developments in micro-viscometers have overcome the limitations of traditional bulky methods, more accessible technologies are required. Here, we introduce a novel magnetic levitation-based method to measure the viscosity and density of solutions in a microcapillary channel.

Tuning toxicity profiles of graphene oxide through imidazole-oxime modification: zebrafish as a model system.

The increasing use of nanotechnology, especially in agriculture and the food industry, has raised concerns about the possible adverse effects of nanomaterials (NMs) on human health and the environment. This study investigates the effects of synthesized graphene oxide (GO) and its derivatives on zebrafish exposed for 96 hr, focusing on morphological changes in brain tissue, histopathology, and immunofluorescent markers such as 8-hydroxy-2'-deoxyguanosine (8-OHdG) and nucleolar protein 10 (NOP10). Exposure to GO resulted in malformations, DNA damage, and increased NOP10 expression, and it reduced hatching and survival rates.

Recent Advances in Hydrogel-Based 3D Disease Modeling and Drug Screening Platforms.

Three-dimensional (3D) disease modeling and drug screening systems have become important in tissue engineering, drug screening, and development. The newly developed systems support cell and extracellular matrix (ECM) interactions, which are necessary for the formation of the tissue or an accurate model of a disease. Hydrogels are favorable biomaterials due to their properties: biocompatibility, high swelling capacity, tunable viscosity, mechanical properties, and their ability to biomimic the structure and function of ECM.

TurkMedNLI: a Turkish medical natural language inference dataset through large language model based translation.

Natural language inference (NLI) is a subfield of natural language processing (NLP) that aims to identify the contextual relationship between premise and hypothesis sentences. While high-resource languages like English benefit from robust and rich NLI datasets, creating similar datasets for low-resource languages is challenging due to the cost and complexity of manual annotation. Although translation of existing datasets offers a practical solution, direct translation of domain-specific datasets presents unique challenges, particularly in handling abbreviations, metric conversions, and cultural alignment.

Sulfonated Cellulose: A Strategy for Effective Methylene Blue Sequestration.

This study investigates the sulfonation modification of cellulose for the removal of methylene blue (MB) from aqueous solutions. The prepared biosorbent was characterized, and its sorption capacity, kinetics, and thermodynamics were systematically evaluated. Fourier-transform infrared (FTIR) spectroscopy analyzed structural modifications, while scanning electron microscopy (SEM) examined the surface properties.

Imbalance in redox homeostasis is associated with neurodegeneration in the murine model of Tay-Sachs disease.

Background: Tay-Sachs disease is a neurodegenerative disorder characterized by a build-up of GM2 ganglioside in the brain, which results in progressive central nervous system dysfunction. Our group recently generated Hexa-/-Neu3-/- mice, a murine model with neuropathological abnormalities similar to the infantile form of Tay-Sachs disease. Previously, we reported progressive neurodegeneration with neuronal loss in the brain sections of Hexa-/-Neu3-/- mice.

TCGEx: a powerful visual interface for exploring and analyzing cancer gene expression data.

Analyzing gene expression data from the Cancer Genome Atlas (TCGA) and similar repositories often requires advanced coding skills, creating a barrier for many researchers. To address this challenge, we developed The Cancer Genome Explorer (TCGEx), a user-friendly, web-based platform for conducting sophisticated analyses such as survival modeling, gene set enrichment analysis, unsupervised clustering, and linear regression-based machine learning. TCGEx provides access to preprocessed TCGA data and immune checkpoint inhibition studies while allowing integration of user-uploaded data sets.

Radially Aligned Carbon Nanotube Glass Fiber Composites as Ion-Selective Microelectrodes.

Detection of ions is challenging due to their small size, rapid diffusion, and high mobility, especially for assaying in samples of low volumes. Among the traditional analytical methods, potentiometric ion-selective electrodes (ISE) have become a popular choice for detecting ions as they are cost-effective, user-friendly and can be miniaturized, making them useful for on-site analysis. In this context, radially aligned carbon nanotubes (RACNT) directly grown on glass fibers (GF) via the chemical vapor deposition method is investigated as a solid contact material for the fabrication of ion-selective microelectrodes (μISE) upon incorporating specific ionophores within a polymeric encapsulation membrane.

Nanoarchitectonics approach to graphite/starch-supported bioelectrode for enhanced supercapacitor performance.

There has been an increasing interest in finding suitable materials for supercapacitor applications in response to the growing need for energy, to use alternative energy sources to fossil fuels in addition to energy storage. In this regard, bio-based carbon-loaded materials can be a promising option for high-performance supercapacitors because of their abundance, diversity, and reproducibility with waste management strategies. In this study, a new graphite-loaded bioelectrode is synthesized for supercapacitor application.

Combined treatment of Ketogenic diet and propagermanium reduces neuroinflammation in Tay-Sachs disease mouse model.

Tay-Sachs disease is a rare lysosomal storage disorder caused by β-Hexosaminidase A enzyme deficiency causing abnormal GM2 ganglioside accumulation in the central nervous system. GM2 accumulation triggers chronic neuroinflammation due to neurodegeneration-based astrogliosis and macrophage activity with the increased expression level of Ccl2 in the cortex of a recently generated Tay-Sachs disease mouse model Hexa-/-Neu3-/-. Propagermanium blocks the neuroinflammatory response induced by Ccl2, which is highly expressed in astrocytes and microglia.

Fluorescent protein with environmentally-sensitive fluorescence lifetime for quantitative pH measurement.

Intracellular pH is a key factor in cell homeostasis, regulated within specific compartments, and changes in pH can result from or affect biochemical pathways. This study explores a yellow fluorescent protein EYFP-G65T as a core for a time-resolved pH-indicator. Among the tested designs-a circular permutant, a chimeric SypHer3s-like construct, and an unmodified protein-the unmodified EYFP-G65T performed best for live-cell imaging.

A selective BODIPY-based fluorescent sensor for the detection of Cu ions in biological and environmental samples.

In this study, we present the design, synthesis, and characterization of a 'turn-on' fluorescent probe, BOD-HDZ, for the selective detection of Cu ions in semi-aqueous solutions, environmental samples (water and soil), and MCF-7 cancer cells. BOD-HDZ was synthesized by functionalizing meso-formyl-BODIPY (BOD-ALD) with a 2-hydrazinopyridine, resulting in fluorescence quenching via a photoinduced electron transfer (PET) mechanism. The 1:1 coordination between Cu2 and the probe was confirmed through Job's plot analysis and 1H NMR spectroscopy, leading to a 210-fold fluorescence enhancement at 515 nm.

A microRNA-regulated transcriptional state defines intratumoral CD8 T cells that respond to immunotherapy.

The rising incidence of advanced-stage colorectal cancer (CRC) and poor survival outcomes necessitate new and effective therapies. Immune checkpoint inhibitors (ICIs), specifically anti-PD-1 therapy, show promise, yet clinical determinants of a positive response are suboptimal. Here, we identify microRNA-155 (miR-155) as necessary for CD8 T cell-infiltrated tumors through an unbiased in vivo CRISPR-Cas9 screen identifying functional tumor antigen-specific CD8 T cell-expressed microRNAs.

Periodate-Mediated Cross-Linking for the Preparation of Catechol Conjugated Albumin Nanoparticles Used for in Vitro Drug Delivery.

Conjugation of serum albumin protein with catechol-containing dopamine molecules provides an alternative method for the preparation of albumin nanoparticles (NPs). A commonly used desolvation method utilizes glutaraldehyde as a cross-linking agent. Here, the catechol cross-linking mechanism is used instead of glutaraldehyde providing advantages to prevent toxicity and an undesirable reaction of glutaraldehyde with cargo molecules.

Neolithic introgression of IL23R-related protection against chronic inflammatory bowel diseases in modern Europeans.

Background: The hypomorphic variant rs11209026-A in the IL23R gene provides significant protection against immune-related diseases in Europeans, notably inflammatory bowel diseases (IBD). Today, the A-allele occurs with an average frequency of 5% in Europe.

Methods: This study comprised 251 ancient genomes from Europe spanning over 14,000 years.

Assessment of thermal and solvent stable SPME fibers for metabolomics studies performed in living systems.

Solid phase microextraction (SPME), as a sampling/sample preparation technique, offers unique solutions for the most challenging applications, including metabolomics studies of living systems. However, for global metabolomics it is critical to use an SPME sampler facilitating the extraction of both volatiles and nonvolatiles, which at the same time is compatible with thermal and solvent-assisted desorption. As a promising universal coating, recently hydrophilic-lipophilic balanced (HLB) particles immobilized in PTFE have been introduced as a new SPME sampler to provide a wide-range of analyte coverage and compatibility with solvent and thermal desorption.

Dynamic fluidic manipulation in microfluidic chips with dead-end channels through spinning: the Spinochip technology for hematocrit measurement, white blood cell counting and plasma separation.

Centrifugation is crucial for size and density-based sample separation, but low-volume or delicate samples suffer from loss and impurity issues during repeated spins. We introduce the "Spinochip", a novel microfluidic system utilizing centrifugal forces for efficient filling of dead-end microfluidic channels. The Spinochip enables versatile fluid manipulation with a single reservoir for both inlet and outlet functions.