Foci-Xpress: Automated and Fast Nuclear Foci Counting Tool.

In the nucleus, distinct, discrete spots or regions called "foci" have been identified, each harboring a specific molecular function. Accurate and efficient quantification of these foci is essential for understanding cellular dynamics and signaling pathways. In this study, we present an innovative automated image analysis method designed to precisely quantify subcellular foci within the cell nucleus. Manual foci counting methods can be tedious and time-consuming. To address these challenges, we developed an open-source software that automatically counts the number of foci from the indicated image files. We compared the foci counting efficiency, velocity, accuracy, and convenience of Foci-Xpress with those of other conventional methods in foci-induced models. We can adjust the brightness of foci to establish a threshold. The Foci-Xpress method was significantly faster than other conventional methods. Its accuracy was similar to that of conventional methods. The most significant strength of Foci-Xpress is automation, which eliminates the need for analyzing equipment while counting. This enhanced throughput facilitates comprehensive statistical analyses and supports robust conclusions from experiments. Furthermore, automation completely rules out biases caused by researchers, such as manual errors or daily variations. Thus, Foci-Xpress is a convincing, convenient, and easily accessible focus-counting tool for cell biologists.

Peptidylarginine deiminase 2 plays a key role in osteogenesis by enhancing RUNX2 stability through citrullination.

Peptidylarginine deiminase (PADI) 2 catalyzes the post-translational conversion of peptidyl-arginine to peptidyl-citrulline in a process called citrullination. However, the precise functions of PADI2 in bone formation and homeostasis remain unknown. In this study, our objective was to elucidate the function and regulatory mechanisms of PADI2 in bone formation employing global and osteoblast-specific Padi2 knockout mice. Our findings demonstrate that Padi2 deficiency leads to the loss of bone mass and results in a cleidocranial dysplasia (CCD) phenotype with delayed calvarial ossification and clavicular hypoplasia, due to impaired osteoblast differentiation. Mechanistically, Padi2 depletion significantly reduces RUNX2 levels, as PADI2-dependent stabilization of RUNX2 protected it from ubiquitin-proteasomal degradation. Furthermore, we discovered that PADI2 binds to RUNX2 and citrullinates it, and identified ten PADI2-induced citrullination sites on RUNX2 through high-resolution LC-MS/MS analysis. Among these ten citrullination sites, the R381 mutation in mouse RUNX2 isoform 1 considerably reduces RUNX2 levels, underscoring the critical role of citrullination at this residue in maintaining RUNX2 protein stability. In conclusion, these results indicate that PADI2 plays a distinct role in bone formation and osteoblast differentiation by safeguarding RUNX2 against proteasomal degradation. In addition, we demonstrate that the loss-of-function of PADI2 is associated with CCD, thereby providing a new target for the treatment of bone diseases.

Nicotinamide enhances osteoblast differentiation through activation of the mitochondrial antioxidant defense system.

Although the normal physiological level of oxidative stress is beneficial for maintaining bone homeostasis, imbalance between reactive oxygen species (ROS) production and antioxidant defense can cause various bone diseases. The purpose of this study was to determine whether nicotinamide (NAM), an NAD+ precursor, can support the maintenance of bone homeostasis by regulating osteoblasts. Here, we found that NAM enhances osteoblast differentiation and mitochondrial metabolism. NAM increases the expression of antioxidant enzymes, which is due to increased FOXO3A transcriptional activity via SIRT3 activation. NAM has not only a preventive effect against weak and chronic oxidative stress but also a therapeutic effect against strong and acute exposure to H2O2 in osteoblast differentiation. Collectively, the results indicate that NAM increases mitochondrial biogenesis and antioxidant enzyme expression through activation of the SIRT3-FOXO3A axis, which consequently enhances osteoblast differentiation. These results suggest that NAM could be a potential preventive or therapeutic agent for bone diseases caused by ROS.

Optimal Energetic-Trap Distribution of Nano-Scaled Charge Trap Nitride for Wider Vth Window in 3D NAND Flash Using a Machine-Learning Method.

A machine-learning (ML) technique was used to optimize the energetic-trap distributions of nano-scaled charge trap nitride (CTN) in 3D NAND Flash to widen the threshold voltage (Vth) window, which is crucial for NAND operation. The energetic-trap distribution is a critical material property of the CTN that affects the Vth window between the erase and program Vth. An artificial neural network (ANN) was used to model the relationship between the energetic-trap distributions as an input parameter and the Vth window as an output parameter. A well-trained ANN was used with the gradient-descent method to determine the specific inputs that maximize the outputs. The trap densities (NTD and NTA) and their standard deviations (σTD and σTA) were found to most strongly impact the Vth window. As they increased, the Vth window increased because of the availability of a larger number of trap sites. Finally, when the ML-optimized energetic-trap distributions were simulated, the Vth window increased by 49% compared with the experimental value under the same bias condition. Therefore, the developed ML technique can be applied to optimize cell transistor processes by determining the material properties of the CTN in 3D NAND Flash.

Fabrication of cylindrical 3D cellulose nanofibril(CNF) aerogel for continuous removal of copper(Cu2+) from wastewater.

Heavy metal contamination in wastewater is a serious problem due to its high toxicity. In this study, three-dimensional porous and flexible polyethylene imine grafted cellulose nanofibril aerogel (PEI@CNF aerogel) is synthesized as a highly efficient biosorbent for continuous treatment of wastewater containing copper (Cu2+). The synthesized PEI@CNF aerogel efficiently separates Cu2+ from wastewater and exhibits outstanding selectivity for Cu2+ in the presence of other metal ions. The amine groups in polyethylene imine (PEI) grafted onto the porous cellulose nanofibrils (CNFs) scaffold form chelates with Cu2+ thereby effectively adsorbing Cu2+. The combination of a flexible CNF scaffold and rigid PEI results in a durable elastic matrix of the aerogel providing excellent wet stability, shape recovery property and recycle ability of PEI@CNF aerogel. Finally, in the column test, the PEI@CNF aerogel treats 88 bed volumes of wastewater containing Cu2+(∼20 mg/L). This result demonstrates that PEI@CNF aerogels are practically viable and highly efficient bio-sorbents for the treatment of wastewater containing Cu2+.

Modified tunicate nanocellulose liquid crystalline fiber as closed loop for recycling platinum-group metals.

Rising demand and elemental rarity requires the recycling of precious metals such as platinum group elements (PGMs). Recently, biosorption has been focused on the capability of recovering precious metals, but in practice, recycling is inefficient or far away from a closed-loop material system. Here we use a polyethylenimine (PEI)-grafted spun-fiber made of cellulose nanofibril (CNF) extracted from a tunicate as a biosorbent for PGMs. Liquid crystallinity (LC) of TCNF suspension appears to contribute the generation of well-developed open porous structure in the fiber. We show the fiber has the selectivity and high capacity of Pt (120.2 mg/g, 86%) and Pd (26.5 mg/g, 74.2%) adsorption under the presence of other metals in simulated automobile waste. The adsorbed Pt and Pd with nano-scale clusters were uniformly distributed on the porous surface, which were directly applied as a catalyst. These results propose an easy approach to recover precious metals and reuse them directly, thereby closing loops of metal recycling.

Tailoring of Aqueous-Based Carbon Nanotube⁻Nanocellulose Films as Self-Standing Flexible Anodes for Lithium-Ion Storage.

An easy and environmentally friendly method was developed for the preparation of a stabilized carbon nanotube-crystalline nanocellulose (CNT-CNC) dispersion and for its deposition to generate self-standing CNT-CNC composite films. The composite films were carbonized at different temperatures of 70 °C, 800 °C, and 1300 °C. Structural and morphological characteristics of the CNT-CNC films were investigated by X-ray diffraction (XRD), Raman spectroscopy, and scanning electron microscopy (SEM), which revealed that the sample annealed at 800 °C (CNT-CNC800) formed nano-tree networks of CNTs with a high surface area (1180 m2·g-1) and generated a conductive CNC matrix due to the effective carbonization. The carbonized composite films were applied as anodes for lithium-ion batteries, and the battery performance was evaluated in terms of initial voltage profile, cyclic voltammetry, capacity, cycling stability, and current rate efficiency. Among them, the CNT-CNC800 anode exhibited impressive electrochemical performance by showing a reversible capacity of 443 mAh·g-1 at a current density of 232 mA·g-1 after 120 cycles with the capacity retention of 89% and high rate capability.

Carboxymethlyated cellulose nanofibrils(CMCNFs) embedded in polyurethane foam as a modular adsorbent of heavy metal ions.

Polyurethane (PU) foam was utilized as an efficient and durable template to immobilize surface-functionalized nanocellulose, carboxymethylated cellulose nanofibrils (CMCNFs), to address some of the challenges for the application of nanocellulose to industrial water purification, such as its agglomeration, difficulties in separation from effluent, and regeneration. The composite foams exhibited well dispersed CMCNFs in PU matrices with open pore structure; the hydrogen bonds result in the enhancement of mechanical strength, which is another requirement of ideal adsorbents for wastewater treatment. The composite foams show high adsorption capacity and the potential for recyclability. The combination of optimal surface modification of nanocellulose with isolation and immobilization in durable PU foam achieved an efficient and cost-competitive bio-sorbent for heavy metal ions.

Raman scattering study of phase biaxiality in a thermotropic bent-core nematic liquid crystal.

Polarized Raman spectroscopy was used to investigate the development of orientational order and the degree of phase biaxiality in a bent-core mesogenic system. The values of the uniaxial order parameters and , and biaxial order parameters , , and , and their evolution with temperature were determined. The temperature dependence of almost all order parameters reveals a second order transition from the uniaxial to biaxial nematic phase with increasing to ∼0.22 before a first order transition to the smectic-C phase, upon cooling.