jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Zheng Ser
Source: QRB Discovery (review, 2024-12-27)
Field: Chemistry — Spectroscopy

Filling in missing puzzle pieces in protein structural biology with cross-linking mass spectrometry High resolution structures of protein complexes provide a wealth of information on protein structure and function. Databases of these protein structures are also used for artificial-intelligence (AI)-based methods of structural modelling. Despite the wealth of protein structures that have been determined by structural biologists, there are still gaps, or missing pieces in the puzzle of protein structural biology. Highly flexible regions may be missing from protein structures and conformational changes of different protein complex states may not be captured by current databases. In this perspective, I sketch out several ways that cross-linking mass spectrometry can contribute to filling in some of these missing pieces: Identification of cross-linked interactions in highly flexible protein regions not captured by other structural techniques; capturing conformational changes of protein complexes in different functional states; serving as distance constraints in integrative structural modelling and providing structural information of <i>in cellulo</i> proteins. The myriad ways in which cross-linking mass spectrometry contributes to filling in missing pieces in structural biology makes it a powerful technique in structural biology. Mass spectrometry ; Computational biology ; Biology ; Chemistry ; Chromatography Mass Spectrometry Techniques and Applications ; Enzyme Structure and Function ; Advanced Proteomics Techniques and Applications
Authors: Loushambam Samananda Singh | Peter De Roux Sumer | Waibiangki Lyngdoh | Akash Sharma | Phaibiang Lapasam | Bimal Debbarma
Source: International Journal of Zoological Investigations (article, 2024-01-01)
Field: Materials Science — Biomaterials

Targeting Lymph Nodes with a Nanoparticle-Based Drug Delivery System The lymphatic system is essential for moving substances from tissues in the body's outer regions to lymph nodes, producing immune responses before circulating throughout the body.Numerous lymph nodes, which also serve as sites for lymphocyte accumulation, activation, and proliferation, house a significant portion of the body's immune cells.The ability to deliver drugs directly to lymphocytes and cells residing in lymph nodes offers the chance to modify the adaptive immune response.The lymphatic system can be effectively targeted to greatly aid in the treatment of disease and boost the efficacy of vaccination.Recently, interest has increased in creating drug delivery systems that specifically target lymph nodes using nanotechnologies and novel biomaterials.Nanoparticles have several benefits that make effective lymphatic system delivery possible.The lymphatics offer a promising pathway for delivering immune-modulatory therapies to lymph nodes, where immunotherapies can be improved, and they also function as an alternative route to general circulation.In this review, we concentrate on materials moving from peripheral tissues to lymph nodes and nanomaterial-based delivery strategies that make use of the potential of lymphatic transport to either deliver therapeutics to lymph nodes or the bloodstream. Drug delivery ; Lymph ; Targeted drug delivery ; Drug ; Nanoparticle ; Computer science ; Medicine ; Nanotechnology ; Pharmacology ; Materials science ; Pathology Nanoparticle-Based Drug Delivery ; Advanced Drug Delivery Systems ; Inhalation and Respiratory Drug Delivery
Authors: Omid Sabzevari Joopari | Amir Eghbal Khajerahimi | Reza Kazempoor | Bahareh Nowruzi
Source: Journal of Microbiology Biotechnology and Food Sciences (article, 2024-10-16)
Field: Materials Science — Materials Chemistry

EVALUATING THE BIOLOGICAL ACTIVITIES OF SILVER AND ZINC OXIDE NANOPARTICLES BIOSYNTHESIZED BY NEOWESTIELLOPSIS PERSICA A1387 In this research, the antimicrobial properties of zinc oxide (ZnO NPs) and silver (AgNPs) nanoparticles, synthesized biologically using Neowestiellopsis persica through various methods (such as wet biomass, boiling biomass, supernatant, extracellular polysaccharides, and phycocyanin), were examined against fish pathogens including Aeromonas hydrophila, Edwardsiella tarda, Yersinia enterocolitica, and Pseudomonas putida. The nanoparticles were successfully created using all methods and characterized employing techniques like UV-visible spectroscopy, scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and dynamic light scattering (DLS). The antibacterial activity of the nanoparticles was assessed using agar-well diffusion assays, while transmission electron microscopy (TEM) was utilized to analyze the ultrastructural interactions between the nanoparticles and the pathogens. Cytotoxicity was evaluated via the trypan blue exclusion method. Notably, nanoparticles generated through the boiling-biomass method demonstrated significantly enhanced characteristics. The analysis revealed two distinct populations of AgNPs measuring 78.82 nm (41.2%) and 91.28 nm (45.5%), along with a pronounced absorption peak at 68.6 nm (80.1%) for ZnO NPs. AgNPs exhibited the strongest growth inhibition against Pseudomonas putida and Edwardsiella tarda, whereas ZnO NPs showed the largest inhibition zone against Yersinia enterocolitica, Pseudomonas aeruginosa, and Aeromonas hydrophila. TEM imagery illustrated the binding of nanoparticles to the outer membranes of Yersinia enterocolitica, compromising their structural integrity. The application of 25 µg/ml of AgNPs and 6.25 µg/ml of ZnO did not lead to significant cell death, but higher concentrations resulted in a dose-dependent cytotoxic effect. Ultimately, the findings of this study confirm that the antibacterial and cytotoxic attributes of silver and zinc oxide nanoparticles, produced through the biosynthesis of Neowestiellopsis persica A1387, can be leveraged to meet future needs in aquaculture. Zinc ; Silver nanoparticle ; Nanoparticle ; Nuclear chemistry ; Chemistry ; Silver oxide ; Materials science ; Nanotechnology ; Metallurgy ; Organic chemistry Nanoparticles: synthesis and applications
Authors: Abiola Grace Femi-Adepoju
Source: International Journal of Agriculture and Biology (review, 2024-09-25)
Field: Materials Science — Materials Chemistry

Nanotechnology and Crop Protection: A Review of Principles and Prospects Nanoparticles have numerous applications in agriculture, because of their great mobility in plant and animal cells and high penetrability. It has the ability to close the gap between farming that is sustainable and farming that is not. A significant issue in agricultural systems is post-harvest losses, which have been demonstrated to be decreased using nanomaterials. Ultra-small particles, known as nanoparticles, have distinct physical, chemical and biological characteristics. It has been discovered that nanopesticides and nanoinsecticides have improved pesticidal and insecticidal characteristics, can supplement traditional pesticides and are anticipated to completely transform pest management in the near future. Specific antibacterial potentials exist in nanoemulsions, nanoliposomes, edible coatings and other forms of nanoparticles like nanosensors that are used to facilitate the measurement and monitoring of crop production as well as the control of pests, diseases, insect attacks and environmental contaminants. The agricultural system makes extensive use of nanoparticles, particularly for plant infection prevention. Due to their small sizes, nanoparticles interact with plant pathogens more effectively and display their antibacterial properties when exposed to various bacteria that have developed resistance to antibiotics. Agricultural research using nanotechnology has recently focused on diagnosing plants, boosting output and developing new disease-resistant varieties. It has the potential to improve agricultural productivity, reduce disease tolerance, speed up the identification of plant illnesses and reduce input costs. In this review paper, the fundamentals, practices and future possibilities of nanotechnology in crop protection have been discussed. Biology ; Nanotechnology ; Crop protection ; Crop ; Biotechnology ; Agronomy ; Materials science Nanoparticles: synthesis and applications
Authors: Tongtong Zhang | Fuqiang Sun | Yaorong Wang | Yang Li | Jing Wang | Zhongqiang Wang | Kwai Hei Li | Ye Zhu | Qi Wang | Lei Shao | Ngai Wong | Dangyuan Lei | Yuan Lin | Zhiqin Chu
Source: ACS Nano (preprint, 2024-12-19)
Field: Materials Science — Materials Chemistry

Scalable Reshaping of Diamond Particles via Programmable Nanosculpting Diamond particles have many interesting properties and possible applications. However, producing diamond particles with well-defined shapes on a large scale is challenging because diamonds are chemically inert and extremely hard. Here, we show that air oxidation, a routine method for purifying diamonds, can be used to precisely shape diamond particles at scale. By exploiting the distinct reactivities of different crystal facets and defects inside the diamond, layer-by-layer outward-to-inward and inward-to-outward oxidation produced diverse diamond shapes including spheres, twisted surfaces, pyramidal islands, inverted pyramids, nanoflowers, and porous polygons. The nanosculpted diamonds had more and finer features that enabled them to outperform the original raw diamonds in various applications. Using experimental observations and Monte Carlo simulations, we built a shape library that guides the design and fabrication of diamond particles with well-defined features that could be critical for anticounterfeiting, optical, and other practical applications. Our study presents a simple, economical, and scalable way to produce shape-customized diamonds for various potential technologies. Diamond ; Nanotechnology ; Materials science ; Fabrication ; Scalability ; Layer (electronics) ; Nanometre ; Computer science ; Composite material Diamond and Carbon-based Materials Research ; Advanced Surface Polishing Techniques ; Pickering emulsions and particle stabilization
Authors: Jogirdas Vainauskas | Alexander Wahrhaftig‐Lewis | Tomislav Friščić
Source: Angewandte Chemie (article, 2024-05-23)
Field: Chemistry — Physical and Theoretical Chemistry

Utilizing “Latent” Carbon: Repositioning Hydrogen‐Bonded Synthons and Assemblies via Halogen Bonding to π‐Systems Abstract Molecules bearing carboxylic acid, amide, and hydroxyl groups are ubiquitous in crystal engineering, where robust hydrogen‐bonded synthons centred on these functionalities enable reliable crystal structure design. We now show that halogen bonding to the carbon π‐system of such molecules, traditionally ignored in crystal engineering, permits the recognition and directional assembly of the resulting hydrogen‐bonded structural subunits, leaving the archetypal hydrogen‐bonded ring, ladder, and chain homosynthons intact, but repositioned in space. When applied to heteromolecular synthons, this enables rearranging more complex hydrogen‐bonded motifs and the evolution of binary cocrystals into ternary ones through “latent” carbon‐based recognition sites, demonstrating a rational approach to build higher‐order solid‐state supramolecular assemblies. Synthon ; Halogen bond ; Hydrogen bond ; Chemistry ; Carbon fibers ; Halogen ; Crystal engineering ; Nanotechnology ; Combinatorial chemistry ; Materials science ; Organic chemistry ; Molecule ; Composite material ; Composite number Crystallography and molecular interactions ; Fluorine in Organic Chemistry ; Coordination Chemistry and Organometallics
Authors: Niklas Hellmer | Jan Spaliński
Source: arXiv (Cornell University) (preprint, 2024-05-24)
Field: Chemistry — Inorganic Chemistry

Density Sensitive Bifiltered Dowker Complexes via Total Weight In this paper, we introduce new density-sensitive bifiltrations for data using the framework of Dowker complexes. Previously, Dowker complexes were studied to address directional or bivariate data whereas density-sensitive bifiltrations on Čech and Vietoris--Rips complexes were suggested to make them more robust, while increasing computational complexity. We combine these two lines of research, noting that the superlevels of the total weight function of a Dowker complex can be identified as an instance of Sheehy's multicover filtration. We prove a version of Dowker duality that is compatible with this filtration and show that it corresponds to the multicover nerve theorem. As a consequence, we find that the subdivision intrinsic Čech complex admits a smaller model. Moreover, regarding the total weight function as a counting measure, we generalize it to arbitrary measures and prove a density-sensitive stability theorem for the case of probability measures. As an application, we propose a robust landmark-based bifiltration which approximates the multicover bifiltration. Additionally, we provide an algorithm to calculate the appearances of simplices in our bifiltration and present computational examples. Chemistry Metal-Organic Frameworks: Synthesis and Applications
Authors: Christine Lim | Michele Vendruscolo
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2024-12-23)
Field: Chemistry — Spectroscopy

Proteostasis Signatures in Human Diseases Abstract The protein homeostasis (proteostasis) system maintains the proteome in a healthy state. Although this system has been comprehensively mapped, its perturbations in disease remain incompletely characterised. To address this problem, here we define the proteostasis signatures, which represent the characteristic patterns of change in the proteostasis system associated with disease. We performed a large-scale, pandisease analysis across 32 human diseases spanning 7 disease types. We first identified unique proteostasis perturbations in specific disease states. We then uncovered distinctive signatures differentiating disease types, pointing to a range of proteostasis mechanisms in disease development. Next, we tracked the temporal evolution of proteostasis signatures, revealing shifts in proteostasis disruption over the course of disease progression. Finally, we demonstrated how smoking, a major risk factor of many diseases, impairs proteostasis in a manner similar to disease, potentially creating a predisposed environment for disease onset. These results illustrate the opportunities offered by the study of human diseases from the perspective of proteostasis signatures. Proteostasis ; Disease ; Biology ; Proteome ; Bioinformatics ; Medicine ; Genetics ; Internal medicine Advanced Proteomics Techniques and Applications ; Bioinformatics and Genomic Networks ; Metabolomics and Mass Spectrometry Studies
Source: Angewandte Chemie International Edition (article, 2024-07-09)
Field: Chemistry — Spectroscopy

Jonathan S. Ward "The best advice I have ever been given is, if you ever find yourself disagreeing with something, to take a moment to step back and think about why that might be and consider alternative viewpoints before solidifying your opinion… I'm always in a good mood when I successfully synthesise a new compound and get a clean NMR spectrum…" Find out more about Jonathan Ward in his Introducing… Profile. Chemistry ; Philosophy Molecular spectroscopy and chirality ; Chemistry and Chemical Engineering ; Advanced NMR Techniques and Applications
Authors: Maomao Li | Wenjie Zhu | Dongdong Song | Zuo‐Qin Liang | Changqing Ye
Source: Research Square (preprint, 2024-01-24)
Field: Materials Science — Materials Chemistry

An AIEE-active triphenylethylene derivative with photoresponsive character for latent fingerprints detection via a simple soaking method Abstract Latent fingerprints (LFPs) is one of the most important physical evidence in the criminal scene, playing an important role in forensic investigations. Therefore, developing highly sensitive and convenient materials for the visualization of LFP is of great significance. We designed and synthesized an organic fluorescent molecule TP-PH with aggregation-induced enhanced emission (AIEE) activity. By simply soaking, blue fluorescent images with high contrast and resolution are readily developed on surfaces including tinfoil, steel, glass and plastic. Remarkably, LFPs can be visualized within 5 minutes including the first-, second- and tertiary-level details. In addition, TP-PH exhibits interesting photoactivated fluorescence enhancement properties. Under irradiation by 365 nm UV light with a power density of 382 mW/cm 2 , the fluorescence quantum yield displays approximately 21.5-fold enhancement. Mechanism studies reveals that the photoactivated fluorescence is attributed to the irreversible cyclodehydrogenation reactions under UV irradiation. This work provides a guideline for the design of multifunctional AIE fluorescent materials. Simple (philosophy) ; Character (mathematics) ; Derivative (finance) ; Chemistry ; Biological system ; Chromatography ; Combinatorial chemistry ; Computer science ; Mathematics ; Business ; Biology ; Philosophy Luminescence and Fluorescent Materials ; Forensic Fingerprint Detection Methods ; Nicotinic Acetylcholine Receptors Study
Authors: Jiaqi Guo | Weiyi Tan | Bing Xu
Source: Journal of Materials Chemistry B (article, 2024-01-01)
Field: Materials Science — Biomaterials

Enzymatic self-assembly of short peptides for cell spheroid formation Cell spheroids, including organoids, serve as a valuable link between <i>in vitro</i> systems and <i>in vivo</i> animal models, offering powerful tools for studying cell biology in a three-dimensional environment. However, existing methods for generating cell spheroids are time consuming or difficult to scale up for large-scale production. Our recent study has revealed that transcytotic peptide assemblies, which transform from nanoparticles to nanofibers by enzymatic reactions, can create an intercellular fibril/gel, accelerating cell spheroid formation from a 2D cell culture or a cell suspension. While this finding presents an alternative approach for generating cell spheroids, the specific structural features required for efficient cell spheroid formation remain unclear. Based on our observation that a phosphotetrapeptide with a biphenyl cap at its N-terminus enables cell spheroid formation, we produced 10 variants of the original peptide. The variants explored modifications to the peptide backbone, length, electronic properties of the biphenyl capping group, and the type of phosphorylated amino acid residue. We then evaluated their ability for inducing cell spheroid formation. Our analysis revealed that, among the tested molecules, peptides with C-terminal phosphotyrosine, low critical micelle concentration, and dephosphorylation-guided nanoparticle to nanofiber morphological transition were the most effective in inducing the formation of cell spheroids. This work represents the first example to correlate the thermodynamic properties (<i>e.g.</i>, self-assembling ability) and kinetic behavior (<i>e.g.</i>, enzymatic dephosphorylation) of peptides with the efficacy of controlling intercellular interaction, thus offering valuable insights into using enzymatic self-assembly to generate peptide assemblies for biological applications. Spheroid ; Enzyme ; Self-assembly ; Materials science ; Peptide ; Cell ; Biophysics ; Nanotechnology ; Chemistry ; Biochemistry ; Biology ; In vitro Supramolecular Self-Assembly in Materials ; Polydiacetylene-based materials and applications ; Silk-based biomaterials and applications
Authors: Masanobu Iwanaga
Source: Photonics (article, 2024-11-10)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Comprehensive Analysis of Optical Resonances and Sensing Performance in Metasurfaces of Silicon Nanogap Unit Metasurfaces composed of silicon nanogap units have a variety of optical resonances, including bound states in the continuum (BIC). We show comprehensive numerical results on metasurfaces of Si-nanogap units, analyze the optical resonances, and clarify optically prominent resonances as well as symmetry-forbidding resonances that are the BIC, based on the numerical analyses of optical spectra and resonant electromagnetic field distributions. Introducing asymmetry in the unit cell, the BIC become optically allowed, being identified as magnetic dipole, electric quadrupole, and magnetic quadrupole resonances. Moreover, the optical resonances are examined in terms of refractive index sensing performance. A pair of the resonances associated with electric field localization at the nanogap was found to be sensitive to the refractive index in contact with the metasurfaces. Consequently, the gap mode resonances are shown to be suitable for a wide range of refractive index sensing over 1.0–2.0. Silicon ; Optoelectronics ; Materials science ; Optics ; Unit (ring theory) ; Physics Metamaterials and Metasurfaces Applications ; Plasmonic and Surface Plasmon Research ; Photonic Crystals and Applications
Authors: Kanad Majumder | Soham Mukherjee | Jungjin Park | Woojae Kim | Andrew J. Musser | Satish Patil
Source: Angewandte Chemie (article, 2024-10-15)
Field: Materials Science — Materials Chemistry

The Acetylene Bridge in Intramolecular Singlet Fission: A Boon or A Nuisance? Abstract Various analogues of the alkylsilylacetylene group are frequently used as auxiliary groups to enhance the solubility and stability of the acene dimer core, widely used as platforms to investigate intramolecular singlet fission (iSF) mechanisms. However, while in the 2,2’‐linked dimers they are primarily auxiliary groups, these are essential fragments of the bridging units in 6,6’/5,5’‐linked dimers, the two preferred choices for dimerization. The starkly different iSF dynamics observed in the two variants raise the question of what role the acetylene bridges play. Here, we systematically designed a set of (oligo−) para ‐phenylene bridged 2,2’‐linked pentacene dimers with an additional acetylene fragment in the bridging unit to mimic the structure of 6,6’‐linked dimers. Contrasting the results with previously reported analogous 2,2’‐linked and 6,6’‐linked pentacene dimers reveals that the acetylene bridges contribute to significant conformational freedom. This effect provides a mechanism to promote spin evolution within the triplet pair to achieve free triplets but also offers new parasitic pathways for triplet‐pair recombination, revealing that this structural motif can be both a boon and a nuisance. Additionally, our analysis reveals that these bridges directly modify the electronic states, highlighting significant pitfalls of the standard chromophore‐bridge‐chromophore framework used to design and interpret photophysics of iSF materials. Intramolecular force ; Acetylene ; Fission ; Singlet fission ; Bridge (graph theory) ; Singlet state ; Nuisance ; Photochemistry ; Chemistry ; Computational chemistry ; Organic chemistry ; Excited state ; Physics ; Nuclear physics ; Law ; Neutron Porphyrin and Phthalocyanine Chemistry ; Photochemistry and Electron Transfer Studies ; Synthesis and Properties of Aromatic Compounds