Chemistry & Biochemistry Research Works

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Quantifying modeling uncertainties in seismic analysis of dams: Insights from an international benchmark study
(Wiley, 2023-12-19) Hariri-Ardebili, Mohammad Amin
Advances in nonlinear dynamic analysis of dams have not completely resolved concerns over modeling confidence and analysis accuracy. Verification and validation offer accuracy assessment, but uncertainties persist during performance evaluation due to both epistemic (modeling) and aleatory (parametric) sources. Epistemic uncertainties arise from simplifications and modeling techniques. This paper addresses epistemic uncertainties in a gravity dam seismic analysis using data from the International Comnission on Large Dams (ICOLD) benchmark study. While the benchmark formulation included the finite element model of the dam, mechanical material properties, and dynamic loads, participants retained the flexibility to opt for best-practice modeling assumptions, simplifications, and other specifics. Notable response variability emerged, particularly in crack profiles and damage predictions. This study examines sources of variability, quantifying modeling uncertainty for the benchmark problem. More specifically, the modeling variability is quantified using the logarithmic standard deviation, also known as dispersion. This metric enables its incorporation into other seismic risk assessment and fragility studies. Under relatively low-intensity motion (peak ground acceleration [PGA] of 0.18 g in this case), modeling dispersion of 0.45, 0.30, 0.32, and 0.30 were calculated for the maximum dynamic crest displacement, maximum hydrodynamic pressure at the heel, heel and crest maximum acceleration, respectively. Additionally, the dispersion of the failure PGA was determined to be 0.7. Findings underscore the need for systematic seismic response modeling in dam engineering to enhance prediction accuracy. A better understanding of the sources and magnitudes of modeling uncertainties can help improve the reliability of dam seismic analysis and contribute to the development of more effective risk assessment and mitigation strategies.
Comments regarding “Seismic damage analysis due to near-fault multipulse ground motion” by Guan Chen, Jiashu Yang, Ruohan Wang, Kaiqi Li, Yong Liu, Michael Beer; Earthquake Engineering & Structural Dynamics, 2023
(Wiley, 2023-11-27) Hariri-Ardebili, Mohammad Amin
This discussion is based on the paper by Chen et al. in 2023 (hereafter referred to as “the original paper/authors”). In their study, the original authors conducted a series of analyses using nonpulse, single-pulse, and multipulse ground motion records, evaluating their impact on a frame structure, a slope, and a gravity dam. Their key finding suggests that multipulse ground motion leads to more severe structural damage compared to nonpulse and single-pulse ground motions. However, it is important to note that the seismic damage analysis of the gravity dam in this paper does not adhere to state-of-the-practice recommendations. Consequently, drawing a definitive conclusion regarding the influence and importance of multipulse ground motion records on the seismic response of concrete dams requires further justification. This necessitates the incorporation of high-fidelity numerical models and probabilistic performance evaluation. We will discuss the significance of modeling assumptions, specifically addressing the dam–rock dynamic interaction in crack propagation and failure in dams.
Mechanism of selective recognition of Lys48-linked polyubiquitin by macrocyclic peptide inhibitors of proteasomal degradation
(Springer Nature, 2023-11-08) Lemma, Betsegaw; Zhang, Di; Vamisetti, Ganga B.; Wentz, Bryan G.; Suga, Hiroaki; Brik, Ashraf; Lubkowski, Jacek; Fushman, David
Post-translational modification of proteins with polyubiquitin chains is a critical cellular signaling mechanism in eukaryotes with implications in various cellular states and processes. Unregulated ubiquitin-mediated protein degradation can be detrimental to cellular homeostasis, causing numerous diseases including cancers. Recently, macrocyclic peptides were developed that selectively target long Lysine-48-linked polyubiquitin chains (tetra-ubiquitin) to inhibit ubiquitin-proteasome system, leading to attenuation of tumor growth in vivo. However, structural determinants of the chain length and linkage selectivity by these cyclic peptides remained unclear. Here, we uncover the mechanism underlying cyclic peptide's affinity and binding selectivity by combining X-ray crystallography, solution NMR, and biochemical studies. We found that the peptide engages three consecutive ubiquitins that form a ring around the peptide and determined requirements for preferential selection of a specific trimer moiety in longer polyubiquitin chains. The structural insights gained from this work will guide the development of next-generation cyclic peptides with enhanced anti-cancer activity.
Structural modulation and spin glassiness upon oxidation in oxygen storage material LnFeMnO4+x for Ln = Y, Lu, and Yb
(AIP, 2023-06-12) Li, Tianyu; Liou, Sz-Chian; Hong, Stephanie J.; Zhang, Qiang; Mandujano, H. Cein; Rodriguez, Efrain E.
The mixed valence multiferroic LnFe2+Fe3+O4 (where Ln = Y, Lu, and Yb) can reversibly uptake oxygen into its lattice, which is evidenced by a crystallographic phase transition along with the appearance of structural modulations. In this study, we show that the Mn-substituted version of this multiferroic can also be readily oxidized to LnFe3+Mn3+O4.5 revealing similar oxygen storage behavior. Through neutron, electron, and synchrotron x-ray diffraction studies, we observe a structural modulation that we attribute to a displacement wave in the fully oxidized compound. This wave exhibits commensurability with a wavevector q = (−2/7, 1/7, 0). Bond valence summation analysis of plausible interstitial oxygen positions suggests that oxygen insertion likely occurs at the middle of the Fe/Mn–O bipyramid layers. The structural modulation of LnFeMnO4.5 is two-dimensional, propagates along the ab-plane, and is highly symmetric as 12 identical modulation vectors are observed in the diffraction patterns. The nature of the lanthanide, Ln3+, does not seem to influence such modulations since we observe identical satellite reflections for all three samples of Ln = Y, Lu, and Yb. Both LnFeMnO4 and LnFeMnO4.5 display spin glassy behavior with 2D short-range magnetic ordering being observed in LnFeMnO4. Analysis of the neutron diffraction data reveals a correlation length of ∼10 nm. Upon oxidation to LnFeMnO4.5, the short-range magnetic order is significantly suppressed.
A Pro-Drug Approach for Selective Modulation of AI-2-Mediated Bacterial Cell-to-Cell Communication
(MDPI, 2012-03-21) Guo, Min; Gamby, Sonja; Nakayama, Shizuka; Smith, Jacqueline; Sintim, Herman O.
The universal quorum sensing autoinducer, AI-2, is utilized by several bacteria. Analogs of AI-2 have the potential to modulate bacterial behavior. Selectively quenching the communication of a few bacteria, in the presence of several others in an ecosystem, using analogs of AI-2 is non-trivial due to the ubiquity of AI-2 processing receptors in many bacteria that co-exist. Herein, we demonstrate that when an AI-2 analog, isobutyl DPD (which has been previously shown to be a quorum sensing, QS, quencher in both Escherichia coli and Salmonella typhimurium) is modified with ester groups, which get hydrolyzed once inside the bacterial cells, only QS in E. coli, but not in S. typhimurium, is inhibited. The origin of this differential QS inhibition could be due to differences in analog permeation of the bacterial membranes or ester hydrolysis rates. Such differences could be utilized to selectively target QS in specific bacteria amongst a consortium of other species that also use AI-2 signaling.
Endo-S-c-di-GMP Analogues-Polymorphism and Binding Studies with Class I Riboswitch
(MDPI, 2012-11-09) Zhou, Jie; Sayre, David A.; Wang, Jingxin; Pahadi, Nirmal; Sintim, Herman O.
C-di-GMP, a cyclic guanine dinucleotide, has been shown to regulate biofilm formation as well as virulence gene expression in a variety of bacteria. Analogues of c-di-GMP have the potential to be used as chemical probes to study c-di-GMP signaling and could even become drug leads for the development of anti-biofilm compounds. Herein we report the synthesis and biophysical studies of a series of c-di-GMP analogues, which have both phosphate and sugar moieties simultaneously modified (called endo-S-c-di-GMP analogues). We used computational methods to predict the relative orientation of the guanine nucleobases in c-di-GMP and analogues. DOSY NMR of the endo-S-c-di-GMP series showed that the polymorphism of c-di-GMP can be tuned with conservative modifications to the phosphate and sugar moieties (conformational steering). Binding studies with Vc2 RNA (a class I c-di-GMP riboswitch) revealed that conservative modifications to the phosphate and 2'-positions of c-di-GMP dramatically affected binding to class I riboswitch.
Small Molecule Inhibitors of AI-2 Signaling in Bacteria: State-of-the-Art and Future Perspectives for Anti-Quorum Sensing Agents
(MDPI, 2013-08-29) Guo, Min; Gamby, Sonja; Zheng, Yue; Sintim, Herman O.
Bacteria respond to different small molecules that are produced by other neighboring bacteria. These molecules, called autoinducers, are classified as intraspecies (i.e., molecules produced and perceived by the same bacterial species) or interspecies (molecules that are produced and sensed between different bacterial species). AI-2 has been proposed as an interspecies autoinducer and has been shown to regulate different bacterial physiology as well as affect virulence factor production and biofilm formation in some bacteria, including bacteria of clinical relevance. Several groups have embarked on the development of small molecules that could be used to perturb AI-2 signaling in bacteria, with the ultimate goal that these molecules could be used to inhibit bacterial virulence and biofilm formation. Additionally, these molecules have the potential to be used in synthetic biology applications whereby these small molecules are used as inputs to switch on and off AI-2 receptors. In this review, we highlight the state-of-the-art in the development of small molecules that perturb AI-2 signaling in bacteria and offer our perspective on the future development and applications of these classes of molecules.
3D DNA Crystals and Nanotechnology
(MDPI, 2016-08-18) Paukstelis, Paul J.; Seeman, Nadrian C.
DNA’s molecular recognition properties have made it one of the most widely used biomacromolecular construction materials. The programmed assembly of DNA oligonucleotides has been used to create complex 2D and 3D self-assembled architectures and to guide the assembly of other molecules. The origins of DNA nanotechnology are rooted in the goal of assembling DNA molecules into designed periodic arrays, i.e., crystals. Here, we highlight several DNA crystal structures, the progress made in designing DNA crystals, and look at the current prospects and future directions of DNA crystals in nanotechnology.
Implementation of Glycan Remodeling to Plant-Made Therapeutic Antibodies
(MDPI, 2018-01-31) Bennett, Lindsay D.; Yang, Qiang; Berquist, Brian R.; Giddens, John P.; Ren, Zhongjie; Kommineni, Vally; Murray, Ryan P.; White, Earl L.; Holtz, Barry R.; Wang, Lai-Xi; Marcel, Sylvain
N-glycosylation profoundly affects the biological stability and function of therapeutic proteins, which explains the recent interest in glycoengineering technologies as methods to develop biobetter therapeutics. In current manufacturing processes, N-glycosylation is host-specific and remains difficult to control in a production environment that changes with scale and production batches leading to glycosylation heterogeneity and inconsistency. On the other hand, in vitro chemoenzymatic glycan remodeling has been successful in producing homogeneous pre-defined protein glycoforms, but needs to be combined with a cost-effective and scalable production method. An efficient chemoenzymatic glycan remodeling technology using a plant expression system that combines in vivo deglycosylation with an in vitro chemoenzymatic glycosylation is described. Using the monoclonal antibody rituximab as a model therapeutic protein, a uniform Gal2GlcNAc2Man3GlcNAc2 (A2G2) glycoform without α-1,6-fucose, plant-specific α-1,3-fucose or β-1,2-xylose residues was produced. When compared with the innovator product Rituxan®, the plant-made remodeled afucosylated antibody showed similar binding affinity to the CD20 antigen but significantly enhanced cell cytotoxicity in vitro. Using a scalable plant expression system and reducing the in vitro deglycosylation burden creates the potential to eliminate glycan heterogeneity and provide affordable customization of therapeutics’ glycosylation for maximal and targeted biological activity. This feature can reduce cost and provide an affordable platform to manufacture biobetter antibodies.
Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level
(MDPI, 2019-02-22) Lin, Xingcheng; Kulkarni, Prakash; Bocci, Federico; Schafer, Nicholas P.; Roy, Susmita; Tsai, Min-Yeh; He, Yanan; Chen, Yihong; Rajagopalan, Krithika; Mooney, Steven M.; Zeng, Yu; Weninger, Keith; Grishaev, Alex; Onuchic, José N.; Levine, Herbert; Wolynes, Peter G.; Salgia, Ravi; Rangarajan, Govindan; Uversky, Vladimir; Orban, John; Jolly, Mohit Kumar
Folded proteins show a high degree of structural order and undergo (fairly constrained) collective motions related to their functions. On the other hand, intrinsically disordered proteins (IDPs), while lacking a well-defined three-dimensional structure, do exhibit some structural and dynamical ordering, but are less constrained in their motions than folded proteins. The larger structural plasticity of IDPs emphasizes the importance of entropically driven motions. Many IDPs undergo function-related disorder-to-order transitions driven by their interaction with specific binding partners. As experimental techniques become more sensitive and become better integrated with computational simulations, we are beginning to see how the modest structural ordering and large amplitude collective motions of IDPs endow them with an ability to mediate multiple interactions with different partners in the cell. To illustrate these points, here, we use Prostate-associated gene 4 (PAGE4), an IDP implicated in prostate cancer (PCa) as an example. We first review our previous efforts using molecular dynamics simulations based on atomistic AWSEM to study the conformational dynamics of PAGE4 and how its motions change in its different physiologically relevant phosphorylated forms. Our simulations quantitatively reproduced experimental observations and revealed how structural and dynamical ordering are encoded in the sequence of PAGE4 and can be modulated by different extents of phosphorylation by the kinases HIPK1 and CLK2. This ordering is reflected in changing populations of certain secondary structural elements as well as in the regularity of its collective motions. These ordered features are directly correlated with the functional interactions of WT-PAGE4, HIPK1-PAGE4 and CLK2-PAGE4 with the AP-1 signaling axis. These interactions give rise to repeated transitions between (high HIPK1-PAGE4, low CLK2-PAGE4) and (low HIPK1-PAGE4, high CLK2-PAGE4) cell phenotypes, which possess differing sensitivities to the standard PCa therapies, such as androgen deprivation therapy (ADT). We argue that, although the structural plasticity of an IDP is important in promoting promiscuous interactions, the modulation of the structural ordering is important for sculpting its interactions so as to rewire with agility biomolecular interaction networks with significant functional consequences.
Solid-Phase Chemical Synthesis of Stable Isotope-Labeled RNA to Aid Structure and Dynamics Studies by NMR Spectroscopy
(MDPI, 2019-09-25) Becette, Owen; Olenginski, Lukasz T.; Dayie, Theodore K.
RNA structure and dynamic studies by NMR spectroscopy suffer from chemical shift overlap and line broadening, both of which become worse as RNA size increases. Incorporation of stable isotope labels into RNA has provided several solutions to these limitations. Nevertheless, the only method to circumvent the problem of spectral overlap completely is the solid-phase chemical synthesis of RNA with labeled RNA phosphoramidites. In this review, we summarize the practical aspects of this methodology for NMR spectroscopy studies of RNA. These types of investigations lie at the intersection of chemistry and biophysics and highlight the need for collaborative efforts to tackle the integrative structural biology problems that exist in the RNA world. Finally, examples of RNA structure and dynamic studies using labeled phosphoramidites are highlighted.
Polymerization Reactions and Modifications of Polymers by Ionizing Radiation
(MDPI, 2020-11-30) Ashfaq, Aiysha; Clochard, Marie-Claude; Coqueret, Xavier; Dispenza, Clelia; Driscoll, Mark S.; Ulański, Piotr; Al-Sheikhly, Mohamad
Ionizing radiation has become the most effective way to modify natural and synthetic polymers through crosslinking, degradation, and graft polymerization. This review will include an in-depth analysis of radiation chemistry mechanisms and the kinetics of the radiation-induced C-centered free radical, anion, and cation polymerization, and grafting. It also presents sections on radiation modifications of synthetic and natural polymers. For decades, low linear energy transfer (LLET) ionizing radiation, such as gamma rays, X-rays, and up to 10 MeV electron beams, has been the primary tool to produce many products through polymerization reactions. Photons and electrons interaction with polymers display various mechanisms. While the interactions of gamma ray and X-ray photons are mainly through the photoelectric effect, Compton scattering, and pair-production, the interactions of the high-energy electrons take place through coulombic interactions. Despite the type of radiation used on materials, photons or high energy electrons, in both cases ions and electrons are produced. The interactions between electrons and monomers takes place within less than a nanosecond. Depending on the dose rate (dose is defined as the absorbed radiation energy per unit mass), the kinetic chain length of the propagation can be controlled, hence allowing for some control over the degree of polymerization. When polymers are submitted to high-energy radiation in the bulk, contrasting behaviors are observed with a dominant effect of cross-linking or chain scission, depending on the chemical nature and physical characteristics of the material. Polymers in solution are subject to indirect effects resulting from the radiolysis of the medium. Likewise, for radiation-induced polymerization, depending on the dose rate, the free radicals generated on polymer chains can undergo various reactions, such as inter/intramolecular combination or inter/intramolecular disproportionation, b-scission. These reactions lead to structural or functional polymer modifications. In the presence of oxygen, playing on irradiation dose-rates, one can favor crosslinking reactions or promotes degradations through oxidations. The competition between the crosslinking reactions of C-centered free radicals and their reactions with oxygen is described through fundamental mechanism formalisms. The fundamentals of polymerization reactions are herein presented to meet industrial needs for various polymer materials produced or degraded by irradiation. Notably, the medical and industrial applications of polymers are endless and thus it is vital to investigate the effects of sterilization dose and dose rate on various polymers and copolymers with different molecular structures and morphologies. The presence or absence of various functional groups, degree of crystallinity, irradiation temperature, etc. all greatly affect the radiation chemistry of the irradiated polymers. Over the past decade, grafting new chemical functionalities on solid polymers by radiation-induced polymerization (also called RIG for Radiation-Induced Grafting) has been widely exploited to develop innovative materials in coherence with actual societal expectations. These novel materials respond not only to health emergencies but also to carbon-free energy needs (e.g., hydrogen fuel cells, piezoelectricity, etc.) and environmental concerns with the development of numerous specific adsorbents of chemical hazards and pollutants. The modification of polymers through RIG is durable as it covalently bonds the functional monomers. As radiation penetration depths can be varied, this technique can be used to modify polymer surface or bulk. The many parameters influencing RIG that control the yield of the grafting process are discussed in this review. These include monomer reactivity, irradiation dose, solvent, presence of inhibitor of homopolymerization, grafting temperature, etc. Today, the general knowledge of RIG can be applied to any solid polymer and may predict, to some extent, the grafting location. A special focus is on how ionizing radiation sources (ion and electron beams, UVs) may be chosen or mixed to combine both solid polymer nanostructuration and RIG. LLET ionizing radiation has also been extensively used to synthesize hydrogel and nanogel for drug delivery systems and other advanced applications. In particular, nanogels can either be produced by radiation-induced polymerization and simultaneous crosslinking of hydrophilic monomers in “nanocompartments”, i.e., within the aqueous phase of inverse micelles, or by intramolecular crosslinking of suitable water-soluble polymers. The radiolytically produced oxidizing species from water, •OH radicals, can easily abstract H-atoms from the backbone of the dissolved polymers (or can add to the unsaturated bonds) leading to the formation of C-centered radicals. These C-centered free radicals can undergo two main competitive reactions; intramolecular and intermolecular crosslinking. When produced by electron beam irradiation, higher temperatures, dose rates within the pulse, and pulse repetition rates favour intramolecular crosslinking over intermolecular crosslinking, thus enabling a better control of particle size and size distribution. For other water-soluble biopolymers such as polysaccharides, proteins, DNA and RNA, the abstraction of H atoms or the addition to the unsaturation by •OH can lead to the direct scission of the backbone, double, or single strand breaks of these polymers.
Potentiometric Carbon Quantum Dots-Based Screen-Printed Arrays for Nano-Tracing Gemifloxacin as a Model Fluoroquinolone Implicated in Antimicrobial Resistance
(MDPI, 2020-12-30) Ayad, Miriam F.; Trabik, Yossra A.; Abdelrahman, Mona H.; Fares, Nermine V.; Magdy, Nancy
Antimicrobial resistance (AMR) is a neglected issue that poses a serious global threat to public health, causing long-term negative consequences at both humanitarian and economic levels. Herein, we report an unprecedented economic fabrication method of seven potentiometric screen-printed sensors for the ultra-trace determination of gemifloxacin (GEMI) as a model of the fluoroquinolones antibiotics deeply involved in the growing AMR problem. Sensors were constructed by depositing homemade carbon ink on a recycled X-ray sheet, patterned using stencils printed with an office printer in simple, cost-effective steps requiring no sophisticated equipment. Four sensors were modified using carbon quantum dots (CQDs) synthesized from dextrose through a single-step method. Sensors exhibited a linear response in the concentration ranges 10−5–10−2 M (sensors 1, 3 and 4), 10−6–10−3 M (sensor 2) and 10−6–10−2 M (sensors 5, 6 and 7). LOD allowed tracing of the target drug at a nano-molar level down to 210 nM. GEMI was successfully determined in pharmaceutical formulations and different water samples without any pretreatment steps with satisfactory recovery (96.93–105.28% with SD values < 3). All sensors revealed a long lifetime of up to several months and are considered promising tools for monitoring water quality and efficiency of water treatment measures.
Intracellular Delivery of Active Proteins by Polyphosphazene Polymers
(MDPI, 2021-02-10) Qamar, Bareera; Solomon, Melani; Marin, Alexander; Fuerst, Thomas R.; Andrianov, Alexander K.; Muro, Silvia
Achieving intracellular delivery of protein therapeutics within cells remains a significant challenge. Although custom formulations are available for some protein therapeutics, the development of non-toxic delivery systems that can incorporate a variety of active protein cargo and maintain their stability, is a topic of great relevance. This study utilized ionic polyphosphazenes (PZ) that can assemble into supramolecular complexes through non-covalent interactions with different types of protein cargo. We tested a PEGylated graft copolymer (PZ-PEG) and a pyrrolidone containing linear derivative (PZ-PYR) for their ability to intracellularly deliver FITC-avidin, a model protein. In endothelial cells, PZ-PYR/protein exhibited both faster internalization and higher uptake levels than PZ-PEG/protein, while in cancer cells both polymers achieved similar uptake levels over time, although the internalization rate was slower for PZ-PYR/protein. Uptake was mediated by endocytosis through multiple mechanisms, PZ-PEG/avidin colocalized more profusely with endo-lysosomes, and PZ-PYR/avidin achieved greater cytosolic delivery. Consequently, a PZ-PYR-delivered anti-F-actin antibody was able to bind to cytosolic actin filaments without needing cell permeabilization. Similarly, a cell-impermeable Bax-BH3 peptide known to induce apoptosis, decreased cell viability when complexed with PZ-PYR, demonstrating endo-lysosomal escape. These biodegradable PZs were non-toxic to cells and represent a promising platform for drug delivery of protein therapeutics.
Isotope-Labeled RNA Building Blocks for NMR Structure and Dynamics Studies
(MDPI, 2021-09-14) Olenginski, Lukasz T.; Taiwo, Kehinde M.; LeBlanc, Regan M.; Dayie, Theodore K.
RNA structural research lags behind that of proteins, preventing a robust understanding of RNA functions. NMR spectroscopy is an apt technique for probing the structures and dynamics of RNA molecules in solution at atomic resolution. Still, RNA analysis by NMR suffers from spectral overlap and line broadening, both of which worsen for larger RNAs. Incorporation of stable isotope labels into RNA has provided several solutions to these challenges. In this review, we summarize the benefits and limitations of various methods used to obtain isotope-labeled RNA building blocks and how they are used to prepare isotope-labeled RNA for NMR structure and dynamics studies.
On the Mechanism and Kinetics of Synthesizing Polymer Nanogels by Ionizing Radiation-Induced Intramolecular Crosslinking of Macromolecules
(MDPI, 2021-10-22) Ashfaq, Aiysha; An, Jung-Chul; Ulański, Piotr; Al-Sheikhly, Mohamad
Nanogels—internally crosslinked macromolecules—have a growing palette of potential applications, including as drug, gene or radioisotope nanocarriers and as in vivo signaling molecules in modern diagnostics and therapy. This has triggered considerable interest in developing new methods for their synthesis. The procedure based on intramolecular crosslinking of polymer radicals generated by pulses of ionizing radiation has many advantages. The substrates needed are usually simple biocompatible polymers and water. This eliminates the use of monomers, chemical crosslinking agents, initiators, surfactants, etc., thus limiting potential problems with the biocompatibility of products. This review summarizes the basics of this method, providing background information on relevant aspects of polymer solution thermodynamics, radiolysis of aqueous solutions, generation and reactions of polymer radicals, and the non-trivial kinetics and mechanism of crosslinking, focusing on the main factors influencing the outcomes of the radiation synthesis of nanogels: molecular weight of the starting polymer, its concentration, irradiation mode, absorbed dose of ionizing radiation and temperature. The most important techniques used to perform the synthesis, to study the kinetics and mechanism of the involved reactions, and to assess the physicochemical properties of the formed nanogels are presented. Two select important cases, the synthesis of nanogels based on polyvinylpyrrolidone (PVP) and/or poly(acrylic acid) (PAA), are discussed in more detail. Examples of recent application studies on radiation-synthesized PVP and PAA nanogels in transporting drugs across the blood–brain barrier and as targeted radioisotope carriers in nanoradiotherapy are briefly described.
Chemoenzymatic Synthesis and Antibody Binding of HIV-1 V1/V2 Glycopeptide-Bacteriophage Qβ Conjugates as a Vaccine Candidate
(MDPI, 2021-11-21) Zong, Guanghui; Toonstra, Christian; Yang, Qiang; Zhang, Roushu; Wang, Lai-Xi
The broadly neutralizing antibody PG9 recognizes a unique glycopeptide epitope in the V1V2 domain of HIV-1 gp120 envelope glycoprotein. The present study describes the design, synthesis, and antibody-binding analysis of HIV-1 V1V2 glycopeptide-Qβ conjugates as a mimic of the proposed neutralizing epitope of PG9. The glycopeptides were synthesized using a highly efficient chemoenzymatic method. The alkyne-tagged glycopeptides were then conjugated to the recombinant bacteriophage (Qβ), a virus-like nanoparticle, through a click reaction. Antibody-binding analysis indicated that the synthetic glycoconjugates showed significantly enhanced affinity for antibody PG9 compared with the monomeric glycopeptides. It was also shown that the affinity of the Qβ-conjugates for antibody PG9 was dependent on the density of the glycopeptide antigen display. The glycopeptide-Qβ conjugates synthesized represent a promising candidate of HIV-1 vaccine.
Cryptococcus neoformans Infection in the Central Nervous System: The Battle between Host and Pathogen
(MDPI, 2022-10-12) Chen, Yanli; Shi, Zoe W.; Strickland, Ashley B.; Shi, Meiqing
Cryptococcus neoformans (C. neoformans) is a pathogenic fungus with a global distribution. Humans become infected by inhaling the fungus from the environment, and the fungus initially colonizes the lungs. If the immune system fails to contain C. neoformans in the lungs, the fungus can disseminate to the blood and invade the central nervous system, resulting in fatal meningoencephalitis particularly in immunocompromised individuals including HIV/AIDS patients. Following brain invasion, C. neoformans will encounter host defenses involving resident as well as recruited immune cells in the brain. To overcome host defenses, C. neoformans possesses multiple virulence factors capable of modulating immune responses. The outcome of the interactions between the host and C. neoformans will determine the disease progression. In this review, we describe the current understanding of how C. neoformans migrates to the brain across the blood–brain barrier, and how the host immune system responds to the invading organism in the brain. We will also discuss the virulence factors that C. neoformans uses to modulate host immune responses.
Cryptococcal Immune Reconstitution Inflammatory Syndrome: From Clinical Studies to Animal Experiments
(MDPI, 2022-12-07) Shi, Zoe W.; Chen, Yanli; Ogoke, Krystal M.; Strickland, Ashley B.; Shi, Meiqing
Cryptococcus neoformans is an encapsulated pathogenic fungus that initially infects the lung but can migrate to the central nervous system (CNS), resulting in meningoencephalitis. The organism causes the CNS infection primarily in immunocompromised individuals including HIV/AIDS patients, but also, rarely, in immunocompetent individuals. In HIV/AIDS patients, limited inflammation in the CNS, due to impaired cellular immunity, cannot efficiently clear a C. neoformans infection. Antiretroviral therapy (ART) can rapidly restore cellular immunity in HIV/AIDS patients. Paradoxically, ART induces an exaggerated inflammatory response, termed immune reconstitution inflammatory syndrome (IRIS), in some HIV/AIDS patients co-infected with C. neoformans. A similar excessive inflammation, referred to as post-infectious inflammatory response syndrome (PIIRS), is also frequently seen in previously healthy individuals suffering from cryptococcal meningoencephalitis. Cryptococcal IRIS and PIIRS are life-threatening complications that kill up to one-third of affected people. In this review, we summarize the inflammatory responses in the CNS during HIV-associated cryptococcal meningoencephalitis. We overview the current understanding of cryptococcal IRIS developed in HIV/AIDS patients and cryptococcal PIIRS occurring in HIV-uninfected individuals. We also describe currently available animal models that closely mimic aspects of cryptococcal IRIS observed in HIV/AIDS patients.
Localized Photoactuation of Polymer Pens for Nanolithography
(MDPI, 2023-01-25) Huang, Zhongjie; Li, Shaopeng; Zhang, Jiaqi; Pang, Huan; Ivankin, Andrey; Wang, Yuhuang
Localized actuation is an important goal of nanotechnology broadly impacting applications such as programmable materials, soft robotics, and nanolithography. Despite significant recent advances, actuation with high temporal and spatial resolution remains challenging to achieve. Herein, we demonstrate strongly localized photoactuation of polymer pens made of polydimethylsiloxane (PDMS) and surface-functionalized short carbon nanotubes based on a fundamental understanding of the nanocomposite chemistry and device innovations in directing intense light with digital micromirrors to microscale domains. We show that local illumination can drive a small group of pens (3 × 3 over 170 µm × 170 µm) within a massively two-dimensional array to attain an out-of-plane motion by more than 7 µm for active molecular printing. The observed effect marks a striking three-order-of-magnitude improvement over the state of the art and suggests new opportunities for active actuation.

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