Antibiotic resistance and Nanotechnology: A narrative review.

The rise of antibiotic resistance poses a significant threat to public health worldwide, leading researchers to explore novel solutions to combat this growing problem. Nanotechnology, which involves manipulating materials at the nanoscale, has emerged as a promising avenue for developing novel strategies to combat antibiotic resistance. This cutting-edge technology has gained momentum in the medical field by offering a new approach to combating infectious diseases. Nanomaterial-based therapies hold significant potential in treating difficult bacterial infections by circumventing established drug resistance mechanisms. Moreover, their small size and unique physical properties enable them to effectively target biofilms, which are commonly linked to resistance development. By leveraging these advantages, nanomaterials present a viable solution to enhance the effectiveness of existing antibiotics or even create entirely new antibacterial mechanisms. This review article explores the current landscape of antibiotic resistance and underscores the pivotal role that nanotechnology plays in augmenting the efficacy of traditional antibiotics. Furthermore, it addresses the challenges and opportunities within the realm of nanotechnology for combating antibiotic resistance, while also outlining future research directions in this critical area. Overall, this comprehensive review articulates the potential of nanotechnology in addressing the urgent public health concern of antibiotic resistance, highlighting its transformative capabilities in healthcare.

Non-coding RNAs and exosomal non-coding RNAs in lung cancer: insights into their functions.

Lung cancer is the second most common form of cancer worldwide Research points to the pivotal role of non-coding RNAs (ncRNAs) in controlling and managing the pathology by controlling essential pathways. ncRNAs have all been identified as being either up- or downregulated among individuals suffering from lung cancer thus hinting that they may play a role in either promoting or suppressing the spread of the disease. Several ncRNAs could be effective non-invasive biomarkers to diagnose or even serve as effective treatment options for those with lung cancer, and several molecules have emerged as potential targets of interest. Given that ncRNAs are contained in exosomes and are implicated in the development and progression of the malady. Herein, we have summarized the role of ncRNAs in lung cancer. Moreover, we highlight the role of exosomal ncRNAs in lung cancer.

Epigenetic regulation of autophagy by non-coding RNAs and exosomal non-coding RNAs in colorectal cancer: A narrative review.

One of the major diseases affecting people globally is colorectal cancer (CRC), which is primarily caused by a lack of effective medical treatment and a limited understanding of its underlying mechanisms. Cellular autophagy functions to break down and eliminate superfluous proteins and substances, thereby facilitating the continual replacement of cellular elements and generating vital energy for cell processes. Non-coding RNAs and exosomal ncRNAs have a crucial impact on regulating gene expression and essential cellular functions such as autophagy, metastasis, and treatment resistance. The latest research has indicated that specific ncRNAs and exosomal ncRNA to influence the process of autophagy in CRC cells, which could have significant consequences for the advancement and treatment of this disease. It has been determined that a variety of ncRNAs have a vital function in regulating the genes essential for the formation and maturation of autophagosomes. Furthermore, it has been confirmed that ncRNAs have a considerable influence on the signaling pathways associated with autophagy, such as those involving AMPK, AKT, and mTOR. Additionally, numerous ncRNAs have the potential to affect specific genes involved in autophagy. This study delves into the control mechanisms of ncRNAs and exosomal ncRNAs and examines how they simultaneously influence autophagy in CRC.

The effects of exercise on epigenetic modifications: focus on DNA methylation, histone modifications and non-coding RNAs.

Physical activity on a regular basis has been shown to bolster the overall wellness of an individual; research is now revealing that these changes are accompanied by epigenetic modifications. Regular exercise has been proven to make intervention plans more successful and prolong adherence to them. When it comes to epigenetic changes, there are four primary components. This includes changes to the DNA, histones, expression of particular non-coding RNAs and DNA methylation. External triggers, such as physical activity, can lead to modifications in the epigenetic components, resulting in changes in the transcription process. This report pays attention to the current knowledge that pertains to the epigenetic alterations that occur after exercise, the genes affected and the resulting characteristics.

DL_POLY Quantum 2.0: A modular general-purpose software for advanced path integral simulations.

DL_POLY Quantum 2.0, a vastly expanded software based on DL_POLY Classic 1.10, is a highly parallelized computational suite written in FORTRAN77 with a modular structure for incorporating nuclear quantum effects into large-scale/long-time molecular dynamics simulations. This is achieved by presenting users with a wide selection of state-of-the-art dynamics methods that utilize the isomorphism between a classical ring polymer and Feynman's path integral formalism of quantum mechanics. The flexible and user-friendly input/output handling system allows the control of methodology, integration schemes, and thermostatting. DL_POLY Quantum is equipped with a module specifically assigned for calculating correlation functions and printing out the values for sought-after quantities, such as dipole moments and center-of-mass velocities, with packaged tools for calculating infrared absorption spectra and diffusion coefficients.

Spinal Cord Injury: From MicroRNAs to Exosomal MicroRNAs.

Spinal cord injury (SCI) is an unfortunate experience that may generate extensive sensory and motor disabilities due to the destruction and passing of nerve cells. MicroRNAs are small RNA molecules that do not code for proteins but instead serve to regulate protein synthesis by targeting messenger RNA's expression. After SCI, secondary damage like apoptosis, oxidative stress, inflammation, and autophagy occurs, and differentially expressed microRNAs show a function in these procedures. Almost all animal and plant cells release exosomes, which are sophisticated formations of lipid membranes. These exosomes have the capacity to deliver significant materials, such as proteins, RNAs and lipids, to cells in need, regulating their functions and serving as a way of communication. This new method offers a fresh approach to treating spinal cord injury. Obviously, the exosome has the benefit of conveying the transported material across performing regulatory activities and the blood-brain barrier. Among the exosome cargoes, microRNAs, which modulate their mRNA targets, show considerable promise in the pathogenic diagnosis, process, and therapy of SCI. Herein, we describe the roles of microRNAs in SCI. Furthermore, we emphasize the importance of exosomal microRNAs in this disease.

Non-coding RNAs and exosomal non-coding RNAs in diabetic retinopathy: A narrative review.

Diabetic retinopathy (DR) is a devastating complication of diabetes, having extensive and resilient effects on those who suffer from it. As yet, the underlying cell mechanisms of this microvascular disorder are largely unclear. Recently, growing evidence suggests that epigenetic mechanisms can be responsible for gene deregulation leading to the alteration of key processes in the development and progression of DR, in addition to the widely recognized pathological mechanisms. It is noteworthy that seemingly unending epigenetic modifications, caused by a prolonged period of hyperglycemia, may be a prominent factor that leads to metabolic memory, and brings epigenetic entities such as non-coding RNA into the equation. Consequently, further investigation is necessary to truly understand this mechanism. Exosomes are responsible for carrying signals from cells close to the vasculature that are participating in abnormal signal transduction to faraway organs and cells by sailing through the bloodstream. These signs indicate metabolic disorders. With the aid of their encased structure, they can store diverse signaling molecules, which then can be dispersed into the blood, urine, and tears. Herein, we summarized various non-coding RNAs (ncRNAs) that are related to DR pathogenesis. Moreover, we highlighted the role of exosomal ncRNAs in this disease.

Evaluation of the relationship between serum BDNF concentration and indicators of oxidative stress and inflammation in COVID-19 patients with neurological disorders - a pilot study.

INTRODUCTION: The aim of this study was to determine the effect of serum level of brain-derived neurotrophic factor (BDNF) on the development of neurological disorders in COVID-19 patients and the probable role of oxidative stress and inflammation in this phenomenon. METHODS: The present case-control study included 42 COVID-19 patients referring to Golestan and Sina hospitals of Ahvaz, Iran, for treatment. Patients with (n = 18) and without (n = 24) neurological disorders were allocated into test and control groups, respectively. Following blood sampling, serum isolation was done, and the serum was stored at -80°C until biochemical assessment for measuring BDNF, oxidative stress indices, and inflammatory factors. RESULTS: Although no significant brain damage was observed in the COVID-19 patients with neurological disorders, the results showed that the serum level of BDNF in the test group increased compared to that in the control group, and this increment was accompanied with increased Tumor Necrosis Factor-alpha (TNF-α) and decreased Interferon gamma (IFN-γ) levels in the serum. Moreover, compared to the control group, patients in the test group had a decreased level of Thiol and an increased level of Malondialdehyde (MDA) in the serum. Furthermore, there was a significant positive correlation between the serum concentration of BDNF and nitric oxide (NO) in the test group. CONCLUSION: Using over-the-counter (OTC) medicines which include thiol-group-related agents or any other antioxidants can alleviate oxidative stress and the associated increased inflammation in COVID-19 patients with neurological symptoms.

Epigallocatechin-3-gallate and its nanoformulation in cervical cancer therapy: the role of genes, MicroRNA and DNA methylation patterns.

Green tea, a popular and healthy nonalcoholic drink consumed globally, is abundant in natural polyphenols. One of these polyphenols is epigallocatechin-3-gallate (EGCG), which offers a range of health benefits, such as metabolic regulation, antioxidant properties, anti-inflammatory effects, and potential anticancer properties. Clinical research has shown that EGCG can inhibit cancers in the male and female reproductive systems, including ovarian, cervical, endometrial, breast, testicular, and prostate cancers. Further research on cervical cancer has revealed the crucial role of epigenetic mechanisms in the initiation and progression of this type of cancer. These include changes to the DNA, histones, and non-coding RNAs, such as microRNAs. These changes are reversible and can occur even before genetic mutations, making them a potential target for intervention therapies. One promising approach to cancer prevention and treatment is the use of specific agents (known as epi-drugs) that target the cancer epigenome or epigenetic dysregulation. Phytochemicals, a group of diverse molecules, have shown potential in modulating cancer processes through their interaction with the epigenetic machinery. Among these, green tea and its main polyphenol EGCG have been extensively studied. This review highlights the therapeutic effects of EGCG and its nanoformulations on cervical cancer. It also discusses the epigenetic events involved in cervical cancer, such as DNA methylation and microRNA dysregulation, which may be affected by EGCG.

Effects of Defects and Presence of Open-Metal Sites on the Structure and Dynamics of Water in Hydrophobic Zeolitic Imidazolate Frameworks.

Most of the chemistry in nanoporous materials with small pore sizes and windows takes place on the outer surface, which is in direct contact with the substrate/solvent, rather than within the pores and channels. Here, we report the results of our comprehensive atomistic molecular dynamics (MD) simulations to decipher the interaction of water with a realistic finite ∼5.1 nm nanoparticle (NP) model of ZIF-8, with edges containing undercoordinated Zn metal sites, vs a conventionally employed pristine crystalline bulk (CB) model. The hydrophobic interior surface of the CB model imparts significant dynamical behavior on water molecules with (i) increasing diffusivity from the surface toward the center of the pores and (ii) confined water, at low concentration, showing similar diffusivity to that of the bulk water. On the other hand, water molecules adsorbed on the surface of the NP model exhibit a range of characteristics, including "coordinated", "confined", and "bulk-like" behavior. Some of the water molecules form coordinative bonds with the undercoordinated Zn metal centers and act as nucleation sites for the water droplets to form, facilitating diffusion into the pores. However, diffusion of water molecules is limited to the areas near the surface and not all the way to the core of the NP model. Our atomistic MD simulations provide insights into the stability of ZIFs in aqueous solutions despite hydrolysis of their outer surface. Such insights are helpful in designing more robust nanoporous materials for applications in humid environments.

In Silico High-Throughput Design and Prediction of Structural and Electronic Properties of Low-Dimensional Metal-Organic Frameworks.

The advent of π-stacked layered metal-organic frameworks (MOFs), which offer electrical conductivity on top of permanent porosity and high surface area, opened up new horizons for designing compact MOF-based devices such as battery electrodes, supercapacitors, and spintronics. Permutation of structural building blocks, including metal nodes and organic linkers, in these electrically conductive (EC) materials, results in new systems with unprecedented and unexplored physical and chemical properties. With the ultimate goal of providing a platform for accelerated material design and discovery, here we lay the foundations for the creation of the first comprehensive database of EC-MOFs with an experimentally guided approach. The first phase of this database, coined EC-MOF/Phase-I, is composed of 1,057 bulk and monolayer structures built by all possible combinations of experimentally reported organic linkers, functional groups, and metal nodes. A high-throughput screening (HTS) workflow is constructed to implement density functional theory calculations with periodic boundary conditions to optimize the structures and calculate some of their most relevant properties. Because research and development in the area of EC-MOFs has long been suffering from the lack of appropriate initial crystal structures, all of the geometries and property data have been made available for the use of the community through an online platform that was developed during the course of this work. This database provides comprehensive physical and chemical data of EC-MOFs as well as the convenience of selecting appropriate materials for specific applications, thus accelerating the design and discovery of EC-MOF-based compact devices.

Correction: Gauging van der Waals interactions in aqueous solutions of 2D MOFs: when water likes organic linkers more than open-metal sites.

Correction for 'Gauging van der Waals interactions in aqueous solutions of 2D MOFs: when water likes organic linkers more than open-metal sites' by Mohammad R. Momeni et al., Phys. Chem. Chem. Phys., 2021, 23, 3135-3143, https://doi.org/10.1039/D0CP05923D.

Short-term celecoxib (celebrex) adjuvant therapy: a clinical trial study on COVID-19 patients.

BACKGROUND: It is known that severe acute respiratory coronavirus 2 (SARS-CoV-2) is the viral strain responsible for the recent coronavirus disease 2019 (COVID-19) pandemic. Current documents have demonstrated that the virus causes a PGE2 storm in a substantial proportion of patients via upregulating cyclooxygenase-2 (COX-2) and downregulating prostaglandin E2 (PGE2)-degrading enzymes within the host cell. AIM: Herein, we aimed to study how short-term treatment with celecoxib (Celebrex), a selective COX-2 inhibitor, affects demographic features, early symptoms, O2 saturation, and hematological indices of cases with COVID-19. METHODS: A total of 67 confirmed COVID-19 cases with a mild or moderate disease, who had been referred to an institutional hospital in south-eastern Iran from October 2020 to September 2021, were enrolled. Demographic characteristics, symptoms, and hematological indices of the patients were recorded within different time periods. One-way ANOVA or Kruskal-Wallis tests were used to determine differences between data sets based on normal data distribution. RESULTS: O2 saturation was statistically different between the control group and patients receiving celecoxib (p = 0.039). There was no marked difference between the groups in terms of the symptoms they experienced (p > 0.05). On the first days following Celebrex therapy, analysis of complete blood counts showed that white blood cell (WBC) counts were markedly lower in patients treated with a high dose of celecoxib (0.4 g/day) than in controls (p = 0.026). However, mean lymphocyte levels in patients receiving a high dose of celecoxib (0.4 g/day) were markedly higher than in patients receiving celecoxib with half of the dose (0.2 g/day) for one week or the untreated subjects (p = 0.004). Changes in platelet count also followed the WBC alteration pattern. CONCLUSION: Celecoxib is a relatively safe, inexpensive, and widely available drug with non-steroidal anti-inflammatory properties. The therapeutic efficacy of celecoxib depends on the administrated dose. Celecoxib might improve disease-free survival in patients with COVID-19.

Modeling energy transfer and absorption spectra in layered metal-organic frameworks based on a Frenkel-Holstein Hamiltonian.

Optimizing energy and charge transfer is key in design and implementation of efficient layered conductive metal-organic frameworks (MOFs) for practical applications. In this work, for the first time, we investigate the role of both long-range excitonic and short-range charge transfer coupling as well as their dependency on reorganization energy on through-space charge transfer in layered MOFs. A π-stacked model system is built based on the archetypal Ni3(HITP)2, HITP = 2,3,6,7,10,11-hexaiminotriphenylene, layered MOF, and a Frenkel/charge transfer Holstein Hamiltonian is developed that takes into account both electronic coupling and intramolecular vibrations. The dependency of the long- and short-range couplings of secondary building units (SBUs) on the stacking geometry is evaluated, which predicts that photophysical properties of layered MOFs critically depend on the degree of ordering between layers. We show that the impact of the two coupling sources in these materials can be discerned or enhanced by the displacement of the SBUs along the long or short molecular axes. The effects of vibronic spectral signatures are examined in both perturbative and resonance regimes. Although, to the best of our knowledge, displacement engineering in layered MOFs currently remains beyond reach, the findings reported here offer new details on the photophysical structure-property relationships in layered MOFs and provide suggestions on how to combine elements of molecular design and engineering to achieve desirable properties and functions for nano- and mesoscale optoelectronic applications.

Synthesis and characterization of Ag-ion-exchanged zeolite/TiO2 nanocomposites for antibacterial applications and photocatalytic degradation of antibiotics.

This paper investigates the synthesis, antibacterial, and photocatalytic properties of silver ion-exchanged natural zeolite/TiO2 photocatalyst nanocomposite. Zeolite is known to have a porous surface structure, making it an ideal substrate and framework in different nanocomposites. Moreover, natural zeolite has a superior thermal and chemical stability, with hardly any reactivity with chemicals. Finding an effective and low-cost method to remove both antibiotics and bacteria from water resources has become a vital global issue due to the worldwide excessive use of chemicals and antibiotics. This research aims to propose a facile method to synthesize Ag-ion-exchanged zeolite/TiO2 catalyst for anti-bacterial purposes and photocatalytic removal of atibiotics from wastewaters. TiO2 particles were deposited on the surface of natural zeolite. Ag ion exchanging was performed via a liquid ion-exchange method using 0.1 M AgNO3 solution. X-ray diffractometry (XRD), scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), and Fourier-transform infrared spectroscopy (FTIR) were used to evaluate the structure of synthesized powders. Antibacterial activities of samples were assessed, using Staphylococcus aureus ATCC 25923 and Escherichia coli ATCC 25922 by disc diffusion method. It was shown that Ag-containing nanocomposite samples have an improved antibacterial performance in both cases. Results showed that the synthesized catalyst has promising potentials in wastewater treatment.

Time perception impairment in multiple sclerosis patients: a survey on internal clock model.

Time perception is known as a mental ability to discern time. Although relative nature of time leaves its numerous aspects undefined, several models have been developed to describe temporal information processing in the brain as well as several areas of the brain have shown to be involved. Time perception alteration has been reported in several neurological conditions; however, the effect of multiple sclerosis (MS) on time perception has yet to be explained. In this study, we aimed to investigate the domains of temporal processing involved in patients with MS and the probable factors affecting it, such as the location of brain demyelinating plaques and gender. Two groups of participants (MS: n = 27 (8 men, 19 women), mean age = 33.85; control: n = 30 (10 men, 20 women), mean age = 28.46) were asked to perform quadruplet time perception tasks (prospective time estimation, duration discrimination, temporal reproduction, and paced motor timing) designed with a software program. Patients with MS had significantly higher scores in time estimation (p < 0.01) and duration discrimination (p < 0.001, in 100-ms interval; p < 0.05, in 1000-ms interval), indicating that MS patients overestimate the time. Since a slower internal clock for MS patients was expected as a result of axonal demyelination, these results suggest the time overestimation in patients with MS which is in contrast with the internal clock model. It means that a slow internal clock causes underestimating and perceiving the time slower.

Enhanced Drug Delivery to Solid Tumors via Drug-Loaded Nanocarriers: An Image-Based Computational Framework.

OBJECTIVE: Nano-sized drug delivery systems (NSDDSs) offer a promising therapeutic technology with sufficient biocompatibility, stability, and drug-loading rates towards efficient drug delivery to solid tumors. We aim to apply a multi-scale computational model for evaluating drug delivery to predict treatment efficacy. METHODOLOGY: Three strategies for drug delivery, namely conventional chemotherapy (one-stage), as well as chemotherapy through two- and three-stage NSDDSs, were simulated and compared. A geometric model of the tumor and the capillary network was obtained by processing a real image. Subsequently, equations related to intravascular and interstitial flows as well as drug transport in tissue were solved by considering real conditions as well as details such as drug binding to cells and cellular uptake. Finally, the role of periodic treatments was investigated considering tumor recurrence between treatments. The impact of different parameters, nanoparticle (NP) size, binding affinity of drug, and the kinetics of release rate, were additionally investigated to determine their therapeutic efficacy. RESULTS: Using NPs considerably increases the fraction of killed cells (FKCs) inside the tumor compared to conventional chemotherapy. Tumoral FKCs for two-stage DDS with smaller NP size (20nm) is higher than that of larger NPs (100nm), in all investigate release rates. Slower and continuous release of the chemotherapeutic agents from NPs have better treatment outcomes in comparison with faster release rate. In three-stage DDS, for intermediate and higher binding affinities, it is desirable for the secondary particle to be released at a faster rate, and the drug with slower rate. In lower binding affinities, high release rates have better performance. Results also demonstrate that after 5 treatments with three-stage DDS, 99.6% of tumor cells (TCs) are killed, while two-stage DDS and conventional chemotherapy kill 95.6% and 88.5% of tumor cells in the same period, respectively. CONCLUSION: The presented framework has the potential to enable decision making for new drugs via computational modeling of treatment responses and has the potential to aid oncologists with personalized treatment plans towards more optimal treatment outcomes.

Metal-to-Semiconductor Transition in Two-Dimensional Metal-Organic Frameworks: An Ab Initio Dynamics Perspective.

Two-dimensional (2D) π-stacked layered metal-organic frameworks (MOFs) are permanently porous and electrically conductive materials with easily tunable crystal structures. Here, we provide an accurate examination of the correlation between structural features and electronic properties of Ni3(HITP)2, HITP = 2,3,6,7,10,11-hexaiminotriphenylene, as an archetypical 2D MOF. The main objective of this work is to unravel the responsive nature of the layered architecture to external stimuli such as temperature and show how the layer flexibility translates to different conductive behaviors. To this end, we employ a combination of quantum mechanical tools, ab initio molecular dynamics (AIMD) simulations, and electronic band structure calculations. We compare the band structure and projected density of states of equilibrated system at 293 K to that of the 0 K optimized structure. Effect of interlayer π-π and intralayer d-π interactions on charge mobility is disentangled and studied by increasing the distance between layers of Ni3(HITP)2 and comparison to an exemplary case of Zn3(HITP)2 2D MOF. Our findings show how a structural change, which can be deformations along the layers, slipping of layers, or change of the interlayer distance, can induce metal-to-semiconductor or indirect-to-direct semiconductor transition, suggesting a way to adjust or even switch between the intralayer vs interlayer conductive anisotropy in Ni3(HITP)2, in particular, and 2D MOFs in general.

Gauging van der Waals interactions in aqueous solutions of 2D MOFs: when water likes organic linkers more than open-metal sites.

Molecular dynamics simulations combined with periodic electronic structure calculations are performed to decipher structural, thermodynamical and dynamical properties of the interfaced vs. confined water adsorbed in hexagonal 1D channels of the 2D layered electrically conductive Cu3(HHTP)2 and Cu3(HTTP)2 metal-organic frameworks (HHTP = 2,3,6,7,10,11-hexahydroxytriphenylene and HTTP = 2,3,6,7,10,11-hexathiotriphenylene). Comparing water adsorption in bulk vs. slab models of the studied 2D MOFs shows that water is preferentially adsorbed on the framework walls via forming hydrogen bonds to the organic linkers rather than by coordinating to the coordinatively unsaturated open-Cu2+ sites. Theory predicts that in Cu3(HTTP)2 the van der Waals interactions are stronger which helps the MOF maintain its layered morphology with allowing very little water molecules to diffuse into the interlayer space. Data presented in this work are general and helpful in implementing new strategies for preserving the integrity as well as electrical conductivity of porous materials in aqueous solutions.

Deterministic role of structural flexibility on catalytic activity of conductive 2D layered metal-organic frameworks.

A combined quantum mechanics and classical molecular dynamics approach is used to unravel the effects of structural deformations and heterogeneity on catalytic activity of 2D π-stacked layered metal-organic frameworks. Theory predicts that the flexible nature of these materials creates a complex array of catalytically active sites for oxidative dehydrogenation of propane. Using an ensemble approach and oxygen bond formation energy, as an excellent probe, we investigate the catalytic activity down to the single active site level.