Meta-aligner: long-read alignment based on genome statistics.

BACKGROUND: Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment of these reads play an important role in any downstream analysis. Similarly, reducing the overall cost of sequencing is related to the time consumption of the aligner. The tradeoff between accuracy and speed is the main challenge in designing long read aligners. RESULTS: We propose Meta-aligner which aligns long and very long reads to the reference genome very efficiently and accurately. Meta-aligner incorporates available short/long aligners as subcomponents and uses statistics from the reference genome to increase the performance. Meta-aligner estimates statistics from reads and the reference genome automatically. Meta-aligner is implemented in C++ and runs in popular POSIX-like operating systems such as Linux. CONCLUSIONS: Meta-aligner achieves high recall rates and precisions especially for long reads and high error rates. Also, it improves performance of alignment in the case of PacBio long-reads in comparison with traditional schemes.

Dual-mode optical biocompatible-sensor enabled by enzyme-like activity of UiO-66 (Zr) for ultra-sensitive ROS detection in vitro.

The simple, effective and highly sensitive detection of hydrogen peroxide (H2O2), which belongs to the reactive oxygen species (ROS), at low concentrations plays an indispensable role in the field of environmental protection, biological research and safety. In this study, a dual-mode optical biosensor, UiO-66@OPD, was developed based on the inherent peroxidase mimicking activity of UiO-66 (Zr) and the optical reaction of ortho-phenylenediamine (OPD) by extending the π-system through oxidative coupling, prototropism and elimination to form OPDox, thereby exhibiting strong orangish absorbance and greenish fluorescence. The catalase-mimicking activity of UiO-66 (Zr) was demonstrated by the catalytic oxidation of methylene blue in the presence of H2O2. Moreover, the Michaelis-Menten kinetic model confirmed the intrinsic peroxidase-like activity of UiO-66@OPD as a modified MOFzyme. The synthesized UiO-66 (Zr) facilitated the oxidation of OPD to OPDox by degrading H2O2 to the hydroxyl radicals. During the oxidation process, the absorption peak at 415 nm and the fluorescence peak at 565 nm of the synthesized probe were significantly enhanced by increasing the H2O2 concentration. Moreover, a colorimetric and fluorometric ultrasensitive sensor shows a good linear relationship between the intensity enhancement and H2O2 concentration in the range of 0-600 nM for absorption and fluorescence spectra with R2 = 0.9772, and R2 = 0.9948, respectively. To demonstrate the biological performance and biocompatibility of UiO-66@OPD as a biosensor, MTT evaluation was performed for the three cell lines MCF-10 A, HEK293 and A549, indicating high biocompatibility and good cell viability for biological applications. Ultimately, this convenient, environmentally friendly, biocompatible and cost-effective catalase-mimicking-based sensor system will open a new perspective for the development of portable kite-based biosensors In vitro.

Comparative study of synthesis methods and pH-dependent adsorption of methylene blue dye on UiO-66 and NH2-UiO-66.

Metal-organic frameworks (MOFs) are highly promising adsorbents with notable properties such as elevated adsorption capacities and versatile surface design capabilities. This study introduces two distinct synthesis methods, one lasting 1 h and the other 24 h, for UiO-66 and NH2-UiO-66. While both methods yield structures with comparable crystallinity and morphology, the adsorption performance of the cationic methylene blue dye varies at different pH levels. Despite the 24 h synthesis time being optimal for maximum adsorption in both MOFs, the relative difference in NH2-UiO-66 adsorption percentage at different times suggests reduced dependency on synthesis time for this property. Notably, NH2-UiO-66 exhibits consistent and effective performance across three pH levels, warranting further investigation into its adsorption kinetics and isotherm. The achievement of high adsorption efficiency coupled with a significantly reduced synthesis time underscores the importance of developing simplified synthetic methods, essential for enhancing the practical applicability of MOFs in diverse applications.

In Situ Nanoencapsulation of Curcumin in Soy Protein Isolate Amyloid-like Aggregates for Enhanced Wound Healing.

The importance of amyloid nanofibrils made from food proteins is rising in diverse fields, such as biomedicine and food science. These protein nanofibrils (PNFs) serve as versatile and sustainable building blocks for biomaterials, characterized by their high ß-sheet content and an ordered hydrogen bond network. These properties offer both stability and flexibility, along with an extreme aspect ratio and reactive functional groups. Plant-derived amyloid nanofibrils, such as soy protein isolate (SPI) PNFs, are increasingly favored due to their affordability and sustainability compared with animal proteins. This study aimed to explore the formation and application of SPI amyloid-like aggregates (SPIA) and their nanoencapsulation of curcumin (Cur) for biomedical purposes, particularly in wound healing. Under specific conditions of low pH and high temperature, SPIA formed, exhibited an amyloid nature, and successfully encapsulated Cur, thereby enhancing its stability and availability. Spectroscopic and microscopic analyses confirmed structural changes in SPIA upon the incorporation of Cur and the fabrication of SPIA@Cur. The obtained results indicate that in the presence of Cur, SPIA forms faster, attributed to accelerated SPI denaturation, an increased nucleation rate, and enhanced self-assembly facilitated by Cur's hydrophobic interactions and π-π stacking with SPI peptides. In vitro studies demonstrated the biocompatibility, biodegradability, and antioxidant properties of SPIA@Cur along with controlled release behavior. In vivo experiments in male Wistar rats revealed that both SPIA and SPIA@Cur significantly accelerate wound closure compared with untreated wounds, with SPIA@Cur showing slightly better efficacy. The histological analysis supported enhanced wound healing, indicating the potential of SPIA@Cur for biomedical applications.