Influence of Graphene-Based Nanocomposites in Neurogenesis and Neuritogenesis: A Brief Summary.

Graphene is a prospective candidate for various biomedical applications, including drug transporters, bioimaging agents, and scaffolds for tissue engineering, thanks to its superior electrical conductivity and biocompatibility. The clinical issue of nerve regeneration and rehabilitation still has a major influence on people's lives. Nanomaterials based on graphene have been exploited extensively to promote nerve cell differentiation and proliferation. Their high electrical conductivity and mechanical robustness make them appropriate for nerve tissue engineering. Combining graphene with other substances, such as biopolymers, may transmit biochemical signals that support brain cell division, proliferation, and regeneration. The utilization of nanocomposites based on graphene in neurogenesis and neuritogenesis is the primary emphasis of this review. Here are some examples of the many synthetic strategies used. For neuritogenesis and neurogenesis, it has also been explored to combine electrical stimulation with graphene-based materials.

Potential of Zinc Oxide-Graphene Quantum Dots and Zinc Oxide-Nitrogen-Doped Graphene Quantum Dot Nanocomposites as Neurotrophic Agents.

Over the past few decades, zinc oxide nanoparticles have also proven to be essential to a variety of scientific research sectors, including antimicrobial therapy, tissue engineering, bioimaging, biosensors, drug delivery, gene delivery, and bioimaging. There is an urgent need to establish and develop unique alternative treatment modalities to treat neurodegenerative disorders due to the shortcomings of the existing drugs. As a possible therapy for brain diseases and disorders, the ability of the nanoparticles to cross the blood-brain barrier (BBB) as well as their reduced toxicity, solubility, and biodegradability has lately attracted attention. Scientists are quietly turning their attention to develop green synthesis of nanoparticles as an alternative to the physical and chemical techniques of producing the same. Existing literature has emphasized the use of ZnO for the potential treatment of cerebral ischemia and its neuroprotective properties. This work discusses the potential of ZnO prepared using Gynura cusimba extract and its nanocomposites with graphene quantum dots (GQDs) and its nitrogen doped variant, N-GQDs as neurotrophic agents, in accordance with our previous report on the use of GQDs and N-GQDs as neurotrophic agents. Pristine ZnO nanoparticles as well as composites were duly characterized by using several techniques to confirm the formation of the nanocomposites. Biological evaluation using the neurite outgrowth assay following the cell viability assay revealed that incorporation of GQDs and N-GQDs enhanced the neurite length in comparison to that of pristine ZnO with the nanocomposites of N-GQDs showing comparatively better results, corroborated by the real-time PCR studies as well.

Highly coherent hybrid dual-comb spectrometer.

Dual comb spectroscopy (DCS) is a broadband technique offering high resolution and fast data acquisition. Current state-of-the-art designs are based on a pair of fiber or solid-state lasers, which allow broadband spectroscopy but require a complicated stabilization setup. Semiconductor lasers are tunable, cost-effective, and easily integrable while limited by a narrow bandwidth. This motivates a hybrid design combining the advantages of both systems. However, establishing sufficiently long mutual coherence time remains challenging. This work describes a hybrid dual-comb spectrometer comprising a broadband fiber laser (FC) and an actively mode-locked semiconductor laser (MLL) with a narrow but tunable spectrum. A high mutual coherence time of around 100 seconds has been achieved by injection locking the MLL to a continuous laser (CW), which is locked on a single line of the FC. We have also devised a method to directly stabilize the entire spectrum of FC to a high finesse cavity. This results in a long term stability of 5 × 10-12 at 1 second and 5 × 10-14 at 350 seconds. Additionally, we have addressed the effect of cavity dispersion on the locking quality, which is important for broadband comb lasers.

Biological Evaluation of Graphene Quantum Dots and Nitrogen-Doped Graphene Quantum Dots as Neurotrophic Agents.

Over time, developments in nano-biomedical research have led to the creation of a number of systems to cure serious illnesses. Tandem use of nano-theragnostics such as diagnostic and therapeutic approaches tailored to the individual disease treatment is crucial for further development in the field of biomedical advancements. Graphene has garnered attention in the recent times as a potential nanomaterial for tissue engineering and regenerative medicines owing to its biocompatibility among the several other unique properties it possesses. The zero-dimensional graphene quantum dots (GQDs) and their nitrogen-doped variant, nitrogen-doped GQDs (N-GQDs), have good biocompatibility, and optical and physicochemical properties. GQDs have been extensively researched owing to several factors such as their size, surface charge, and interactions with other molecules found in biological media. This work briefly elucidates the potential of electroactive GQDs as well as N-GQDs as neurotrophic agents. In vitro investigations employing the N2A cell line were used to evaluate the effectiveness of GQDs and N-GQDs as neurotrophic agents, wherein basic investigations such as SRB assay and neurite outgrowth assay were performed. The results inferred from immunohistochemistry followed by confocal imaging studies as well as quantitative real-time PCR (qPCR) studies corroborated those obtained from neurite outgrowth assay. We have also conducted a preliminary investigation of the pattern of gene expression for neurotrophic and gliotrophic growth factors using ex vivo neuronal and mixed glial cultures taken from the brains of postnatal day 2 mice pups. Overall, the studies indicated that GQDs and N-GQDs hold prospect as a framework for further development of neuroactive compounds for relevant central nervous system (CNS) purposes.

Recent progress in polyaniline-based composites as electrode materials for pliable supercapacitors.

Significant contributions have been made towards the development of flexible energy storage devices to meet the ever-growing energy demand. Flexibility, mechanical stability, and electrical conductivity are three critical qualities that distinguish conducting polymers from other materials. Polyaniline (PANI) has drawn considerable attention among the various conducting polymers for use in flexible supercapacitors. PANI offers several desirable properties including high porosity, a large surface area, and high conductivity. Despite its merits, it also suffers from poor cyclic stability, low mechanical strength, and notable discrepancy between theoretical and actual capacitance. These shortcomings have been addressed by creating composites of PANI with structurally sturdy elements such as graphene, carbon nanotubes (CNTs), metal-organic framework (MOFs), MXenes, etc., thus enhancing the performance of supercapacitors. This review outlines the several schemes adopted to prepare diverse binary and ternary composites of PANI as the electrode material for flexible supercapacitors and the significant impact of composite formation on the flexibility and electrochemical performance of the fabricated pliable supercapacitors.

RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a 'living data resource.' Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.

An idea to explore: How an interdisciplinary undergraduate course exploring a global health challenge in molecular detail enabled science communication and collaboration in diverse audiences.

Communication and collaboration are key science competencies that support sharing of scientific knowledge with experts and non-experts alike. On the one hand, they facilitate interdisciplinary conversations between students, educators, and researchers, while on the other they improve public awareness, enable informed choices, and impact policy decisions. Herein, we describe an interdisciplinary undergraduate course focused on using data from various bioinformatics data resources to explore the molecular underpinnings of diabetes mellitus (Types 1 and 2) and introducing students to science communication. Building on course materials and original student-generated artifacts, a series of collaborative activities engaged students, educators, researchers, healthcare professionals and community members in exploring, learning about, and discussing the molecular bases of diabetes. These collaborations generated novel educational materials and approaches to learning and presenting complex ideas about major global health challenges in formats accessible to diverse audiences.

RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D.

Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open-access global archive housing three-dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is funded by the National Science Foundation, National Institutes of Health, and US Department of Energy and serves as the US data center for the wwPDB. RCSB PDB is also responsible for the security of PDB data in its role as wwPDB-designated Archive Keeper. Every year, RCSB PDB serves tens of thousands of depositors of 3D macromolecular structure data (coming from macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction). The RCSB PDB research-focused web portal (RCSB.org) makes PDB data available at no charge and without usage restrictions to many millions of PDB data consumers around the world. The RCSB PDB training, outreach, and education web portal (PDB101.RCSB.org) serves nearly 700 K educators, students, and members of the public worldwide. This invited Tools Issue contribution describes how RCSB PDB (i) is organized; (ii) works with wwPDB partners to process new depositions; (iii) serves as the wwPDB-designated Archive Keeper; (iv) enables exploration and 3D visualization of PDB data via RCSB.org; and (v) supports training, outreach, and education via PDB101.RCSB.org. New tools and features at RCSB.org are presented using examples drawn from high-resolution structural studies of proteins relevant to treatment of human cancers by targeting immune checkpoints.

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.

Creating heralded hyper-entangled photons using Rydberg atoms.

Entangled photon pairs are a fundamental component for testing the foundations of quantum mechanics, and for modern quantum technologies such as teleportation and secured communication. Current state-of-the-art sources are based on nonlinear processes that are limited in their efficiency and wavelength tunability. This motivates the exploration of physical mechanisms for entangled photon generation, with a special interest in mechanisms that can be heralded, preferably at telecommunications wavelengths. Here we present a mechanism for the generation of heralded entangled photons from Rydberg atom cavity quantum electrodynamics (cavity QED). We propose a scheme to demonstrate the mechanism and quantify its expected performance. The heralding of the process enables non-destructive detection of the photon pairs. The entangled photons are produced by exciting a rubidium atom to a Rydberg state, from where the atom decays via two-photon emission (TPE). A Rydberg blockade helps to excite a single Rydberg excitation while the input light field is more efficiently collectively absorbed by all the atoms. The TPE rate is significantly enhanced by a designed photonic cavity, whose many resonances also translate into high-dimensional entanglement. The resulting high-dimensionally entangled photons are entangled in more than one degree of freedom: in all of their spectral components, in addition to the polarization-forming a hyper-entangled state, which is particularly interesting in high information capacity quantum communication. We characterize the photon comb states by analyzing the Hong-Ou-Mandel interference and propose proof-of-concept experiments.

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including >660 000 educators, students and members of the curious public using PDB101.RCSB.org. PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators and students studying fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. During the past 2 years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with >40 external biodata resources. New features and resources are described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic.

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org), the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without usage restrictions to more than 1 million rcsb.org Users worldwide and 600 000 pdb101.rcsb.org education-focused Users around the globe. PDB Data Depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy and 3D electron microscopy. PDB Data Consumers include researchers, educators and students studying Fundamental Biology, Biomedicine, Biotechnology and Energy. Recent reorganization of RCSB PDB activities into four integrated, interdependent services is described in detail, together with tools and resources added over the past 2 years to RCSB PDB web portals in support of a 'Structural View of Biology.'

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.

Database URL: https://www.wwpdb.org/.

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.

OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the PDB archive, has been developed as a global collaboration by the worldwide PDB (wwPDB) partners. This new system was designed to ensure that the wwPDB could meet the evolving archiving requirements of the scientific community over the coming decades. OneDep unifies deposition, biocuration, and validation pipelines across all wwPDB, EMDB, and BMRB deposition sites with improved focus on data quality and completeness in these archives, while supporting growth in the number of depositions and increases in their average size and complexity. In this paper, we describe the design, functional operation, and supporting infrastructure of the OneDep system, and provide initial performance assessments.

Using the Tools and Resources of the RCSB Protein Data Bank.

The Protein Data Bank (PDB) archive is the worldwide repository of experimentally determined three-dimensional structures of large biological molecules found in all three kingdoms of life. Atomic-level structures of these proteins, nucleic acids, and complex assemblies thereof are central to research and education in molecular, cellular, and organismal biology, biochemistry, biophysics, materials science, bioengineering, ecology, and medicine. Several types of information are associated with each PDB archival entry, including atomic coordinates, primary experimental data, polymer sequence(s), and summary metadata. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves as the U.S. data center for the PDB, distributing archival data and supporting both simple and complex queries that return results. These data can be freely downloaded, analyzed, and visualized using RCSB PDB tools and resources to gain a deeper understanding of fundamental biological processes, molecular evolution, human health and disease, and drug discovery. © 2016 by John Wiley & Sons, Inc.

Graphene quantum dots from graphite by liquid exfoliation showing excitation-independent emission, fluorescence upconversion and delayed fluorescence.

Facile synthesis of 2-10 nm-sized graphene quantum dots (GQDs) from graphite powder by organic solvent-assisted liquid exfoliation using a sonochemical method is reported in this study. Synthesized GQDs are well dispersed in organic solvents like ethyl acetoacetate (EAA), dimethyl formamide (DMF) and also in water. MALDI-TOF mass spectrometry reveals its selective mass fragmentation. Detailed characterizations by various techniques like X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), Raman spectroscopy and high resolution transmission electron microscopy (HRTEM) confirm the formation of disordered, functional GQDs. Density functional theory (DFT) calculation confirms HOMO-LUMO energy gap variation with changing size and functionalities. Photoluminescence (PL) properties of as-prepared GQDs were studied in detail. The ensemble studies of GQDs showed excellent photoluminescence properties comprising normal and upconverted fluorescence, delayed fluorescence and room-temperature phosphorescence. PL decay dynamics of GQDs has been explored using time-correlated single-photon technique (TCSPC) as well as femtosecond fluorescence upconversion technique. In vitro cytotoxicity study reveals its biocompatibility and high cell viability (>91%) even at high concentration (400 µg mL(-1)) of GQDs in Chinese Hamster Ovary (CHO) cells.

Proliferation and differentiation potential of human adipose-derived stem cells grown on chitosan hydrogel.

Applied tissue engineering in regenerative medicine warrants our enhanced understanding of the biomaterials and its function. The aim of this study was to evaluate the proliferation and differentiation potential of human adipose-derived stem cells (hADSCs) grown on chitosan hydrogel. The stability of this hydrogel is pH-dependent and its swelling property is pivotal in providing a favorable matrix for cell growth. The study utilized an economical method of cross linking the chitosan with 0.5% glutaraldehyde. Following the isolation of hADSCs from omentum tissue, these cells were cultured and characterized on chitosan hydrogel. Subsequent assays that were performed included JC-1 staining for the mitochondrial integrity as a surrogate marker for viability, cell proliferation and growth kinetics by MTT assay, lineage specific differentiation under two-dimensional culture conditions. Confocal imaging, scanning electron microscopy (SEM), and flow cytometry were used to evaluate these assays. The study revealed that chitosan hydrogel promotes cell proliferation coupled with > 90% cell viability. Cytotoxicity assays demonstrated safety profile. Furthermore, glutaraldehyde cross linked chitosan showed < 5% cytotoxicity, thus serving as a scaffold and facilitating the expansion and differentiation of hADSCs across endoderm, ectoderm and mesoderm lineages. Additional functionalities can be added to this hydrogel, particularly those that regulate stem cell fate.

Small molecule annotation for the Protein Data Bank.

The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100,000 structures contain more than 20,000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors.

Trendspotting in the Protein Data Bank.

The Protein Data Bank (PDB) was established in 1971 as a repository for the three dimensional structures of biological macromolecules. Since then, more than 85000 biological macromolecule structures have been determined and made available in the PDB archive. Through analysis of the corpus of data, it is possible to identify trends that can be used to inform us abou the future of structural biology and to plan the best ways to improve the management of the ever-growing amount of PDB data.