jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Trishant R. Umrekar | Yvonne B. Winterborn | Shamphavi Sivabalasarma | Julian Brantl | Sonja‐Verena Albers | Morgan Beeby
Source: Frontiers in Microbiology (article, 2021-11-29)
Field: Materials Science — Materials Chemistry

Evolution of Archaellum Rotation Involved Invention of a Stator Complex by Duplicating and Modifying a Core Component Novelty in biology can arise from opportunistic repurposing of nascent characteristics of existing features. Understanding how this process happens at the molecular scale, however, suffers from a lack of case studies. The evolutionary emergence of rotary motors is a particularly clear example of evolution of a new function. The simplest of rotary motors is the archaellum, a molecular motor that spins a helical propeller for archaeal motility analogous to the bacterial flagellum. Curiously, emergence of archaellar rotation may have pivoted on the simple duplication and repurposing of a pre-existing component to produce a stator complex that anchors to the cell superstructure to enable productive rotation of the rotor component. This putative stator complex is composed of ArlF and ArlG, gene duplications of the filament component ArlB, providing an opportunity to study how gene duplication and neofunctionalization contributed to the radical innovation of rotary function. Toward understanding how this happened, we used electron cryomicroscopy to determine the structure of isolated ArlG filaments, the major component of the stator complex. Using a hybrid modeling approach incorporating structure prediction and validation, we show that ArlG filaments are open helices distinct to the closed helical filaments of ArlB. Curiously, further analysis reveals that ArlG retains a subset of the inter-protomer interactions of homologous ArlB, resulting in a superficially different assembly that nevertheless reflects the common ancestry of the two structures. This relatively simple mechanism to change quaternary structure was likely associated with the evolutionary neofunctionalization of the archaellar stator complex, and we speculate that the relative deformable elasticity of an open helix may facilitate elastic energy storage during the transmission of the discrete bursts of energy released by ATP hydrolysis to continuous archaellar rotation, allowing the inherent properties of a duplicated ArlB to be co-opted to fulfill a new role. Furthermore, agreement of diverse experimental evidence in our work supports recent claims to the power of new structure prediction techniques. Neofunctionalization ; Stator ; Flagellum ; Protein filament ; Component (thermodynamics) ; Molecular machine ; Biology ; Molecular motor ; Biological system ; Physics ; Gene duplication ; Genetics ; Biophysics ; Gene Enzyme Structure and Function ; Protein Structure and Dynamics ; Photosynthetic Processes and Mechanisms
Authors: Soraya Chebib | Wilfried Schwab
Source: Foods (article, 2021-11-11)
Field: Chemistry — Physical and Theoretical Chemistry

Microscale Thermophoresis Reveals Oxidized Glutathione as High-Affinity Ligand of Mal d 1 Pathogenesis-related (PR)-10 proteins, due to their particular secondary structure, can bind various ligands which could be important for their biological function. Accordingly, the PR-10 protein Mal d 1, the major apple allergen, probably also binds molecules in the hydrophobic cavity of its secondary structure, but it has not yet been investigated in this respect. In this study, various natural products found in apples such as flavonoids, glutathione (GSH), and glutathione disulfide (GSSG) were investigated as possible ligands of Mal d 1 using microscale thermophoresis. Dissociation constants of 16.39 µM, 29.51 µM, 35.79 µM, and 0.157 µM were determined for catechin, quercetin-3-<i>O</i>-rhamnoside, GSH, and GSSG, respectively. Molecular docking was performed to better understand the underlying binding mechanism and revealed hydrophobic interactions that stabilize the ligands within the pocket while hydrophilic interactions determine the binding of both GSH derivatives. The binding of these ligands could be important for the allergenicity of the PR-10 protein and provide further insights into its physiological role. Microscale thermophoresis ; Glutathione ; Chemistry ; Dissociation constant ; Microscale chemistry ; Thermophoresis ; Catechin ; Hydrophobic effect ; Stereochemistry ; Biophysics ; Biochemistry ; Receptor ; Antioxidant ; Polyphenol ; Nanoparticle ; Enzyme ; Nanotechnology ; Biology thermodynamics and calorimetric analyses ; Allergic Rhinitis and Sensitization ; Essential Oils and Antimicrobial Activity
Authors: Rebecca Brendel | Sascha Rohn | Philipp Weller
Source: Analytical and Bioanalytical Chemistry (article, 2021-04-10)
Field: Chemistry — Spectroscopy

Nitrogen monoxide as dopant for enhanced selectivity of isomeric monoterpenes in drift tube ion mobility spectrometry with 3H ionization The ion mobility spectra of the isomeric monoterpenes α-pinene, β-pinene, myrcene, and limonene in drift tube ion mobility spectrometry (IMS) with <sup>3</sup>H radioactive ionization are highly similar and difficult to distinguish. The aim of this work was to enhance the selectivity of IMS by the addition of nitrogen monoxide (NO) as dopant and to investigate the underlying changes in ion formation responsible for the modified ion signals observed in the ion mobility spectra. Even though <sup>3</sup>H-based-IMS systems have been used in hyphenation with gas chromatography (GC) for profiling of volatile organic compounds (VOCs), the investigation of ion formation still remains challenging and was exemplified by the investigated monoterpenes. Nonetheless, the formation of monomeric, dimeric, and trimeric ion clusters could be tentatively confirmed by a mass-to-mobility correlation and the highly similar pattern of ion signals in the monomer region was attributed to isomerization mechanisms potentially occurring after proton transfer reactions. The addition of NO as dopant could finally lead to the formation of additional product ions and increased the selectivity of IMS for the investigated monoterpenes as confirmed by principal component analysis (PCA). The discrimination of monoterpenes in the volatile profile is highly relevant in the quality control of hops and was given as the example for application. The results indicate that additional product ions were obtained by the formation of NO<sup>+</sup> adduct ions, next to hydride abstraction, charge transfer, or fragmentation reactions. This approach can potentially leverage selectivity issues in VOC profiling of complex matrices, such as food matrices or raw materials in combination with chemometric pattern recognition techniques. Chemistry ; Ion-mobility spectrometry ; Selectivity ; Mass spectrometry ; Ion ; Analytical Chemistry (journal) ; Dopant ; Chromatography ; Organic chemistry ; Catalysis Analytical Chemistry and Chromatography ; Plant biochemistry and biosynthesis ; Advanced Chemical Sensor Technologies
Authors: Han Ye | Yanrong Wang | Shuhe Zhang | Danshi Wang | Yumin Liu | Mingchao Wang | Qiming Zhang
Source: Nanoscale Advances (article, 2021-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Topology design of digital metamaterials for ultra-compact integrated photonic devices based on mode manipulation Precise manipulation of mode order in silicon waveguides plays a fundamental role in the on-chip all-optical interconnections and is still a tough task in design when the functional region is confined to a subwavelength footprint. In this paper, digital metamaterials consisting of silicon and air pixels are topologically designed by an efficient method combining 2D finite element method for optical simulations, density method for material description and method of moving asymptotes for optimization. Only around 150 iterations are required for searching satisfactory solutions. Six high-quality and efficient conversions between four TE-polarized modes are achieved in a functional region with footprint 0.645<i>λ</i> <sup>2</sup> (center wavelength <i>λ</i> = 1550 nm). Based on asymmetric mode conversion, a reciprocal optical diode with high contrast ratio is further obtained with the optimization starting from TE0-to-TE1 mode converter. Moreover, we successfully design a 1 × 2 demultiplexer with footprint 1.0<i>λ</i> <sup>2</sup> and demonstrate a simple mode division multiplexing system with satisfactory performances. Finally, by changing the refractive index to an equivalent value, quasi-3D designs are obtained and the functionalities are validated in 3D simulations for both free-standing and SOI configurations. Metamaterial ; Mode (computer interface) ; Photonics ; Optoelectronics ; Topology (electrical circuits) ; Computer science ; Physics ; Materials science ; Electronic engineering ; Engineering ; Electrical engineering ; Human–computer interaction Metamaterials and Metasurfaces Applications ; Photonic Crystals and Applications ; Photonic and Optical Devices
Authors: Falah M. Fakhree | Ibrahim F. Waheed | Kamal M. Mahmoud
Source: Egyptian Journal of Chemistry (article, 2021-03-15)
Field: Materials Science — Materials Chemistry

Synthesis and characterization of CuO nanoparticles stabilized by quercetin and its application for anti-breast cancer activity The main idea in this research used quercetin (QT) as a stabilizing agent to prepare CuO nanoparticle (NPs). QT is a pigment which exists from plants, fruits, and in some medicines. It contains numerous hydroxyl groups, works as a complexing agent and a self-assembly agent. The prepared CuO-NPs were characterized by fourier transformed infrared (FT-IR), X-ray diffraction (XRD), scanning and transmission electron microscopy (SEM and TEM), and energy-dispersive X-ray analysis (EDX). The structure investigation confirm that the CuO-NPs were polycrystalline nature having a monoclinic crystalline form and showed (111̅) and (111) preferential orientations. The estimated particle sizes by XRD, TEM, and SEM ranged from 12.03 to 15.3 nm. Surface analysis displayed that homogeneously distributed CuO-NPs with a spherical shape. On the other hand, the synthesized CuO-NPs were tested for anticancer activity on the human Breast. The infected cell (MCF-7) uses MTT (3-(4,5-dimethyl-2-triazolyl)-2,5-diphenyl-2-tetrazolium bromide) test. The inferred CuO-NPs clarify high anticancer cytotoxicity of the (MCF-7) with an IC50 μM value of 57.6 and 42.8 µg/mL for 24 and 72 h respectively. Monoclinic crystal system ; Transmission electron microscopy ; Nanoparticle ; Bromide ; Crystallite ; Fourier transform infrared spectroscopy ; Powder diffraction ; Nuclear chemistry ; Scanning electron microscope ; Materials science ; Quercetin ; Cytotoxicity ; Particle size ; Nanotechnology ; Crystallography ; Chemical engineering ; Chemistry ; Organic chemistry ; In vitro ; Physical chemistry ; Crystal structure ; Antioxidant Nanoparticles: synthesis and applications ; Bioactive Compounds and Antitumor Agents ; Nanoparticle-Based Drug Delivery
Authors: Mikayla Shanafelt | Camille Larracas | Simmone Dyrness | Ryan Hekman | Coby La Mattina-Hawkins | Taylor Rabara | Wilson Wu | Craig Vierra
Source: Molecules (article, 2021-08-22)
Field: Materials Science — Biomaterials

Egg Case Protein 3: A Constituent of Black Widow Spider Tubuliform Silk Spider silk has outstanding mechanical properties, rivaling some of the best materials on the planet. Biochemical analyses of tubuliform silk have led to the identification of TuSp1, egg case protein 1, and egg case protein 2. TuSp1 belongs to the spidroin superfamily, containing a non-repetitive <i>N</i>- and <i>C</i>-terminal domain and internal block repeats. ECP1 and ECP2, which lack internal block repeats and sequence similarities to the highly conserved <i>N</i>- and <i>C</i>-terminal domains of spidroins, have cysteine-rich <i>N</i>-terminal domains. In this study, we performed an in-depth proteomic analysis of tubuliform glands, spinning dope, and egg sacs, which led to the identification of a novel molecular constituent of black widow tubuliform silk, referred to as egg case protein 3 or ECP3. Analysis of the translated ECP3 cDNA predicts a low molecular weight protein of 11.8 kDa. Real-time reverse transcription-quantitative PCR analysis performed with different silk-producing glands revealed ECP3 mRNA is predominantly expressed within tubuliform glands of spiders. Taken together, these findings reveal a novel protein that is secreted into black widow spider tubuliform silk. Spider silk ; SILK ; Complementary DNA ; Biology ; Spider ; Molecular biology ; Gene ; Genetics ; Zoology Silk-based biomaterials and applications ; Biochemical and Structural Characterization ; Antimicrobial Peptides and Activities
Authors: Shimon Rubin | Phuong H. L. Nguyen | Yeshaiahu Fainman
Source: Nanophotonics (article, 2021-02-14)
Field: Materials Science — Electronic, Optical and Magnetic Materials

The effect of DNA bases permutation on surface‐enhanced Raman scattering spectrum Abstract Surface‐enhanced Raman scattering (SERS) process results in a tremendous increase of Raman scattering cross section of molecules adsorbed to plasmonic metals and influenced by numerous physico‐chemical factors such as geometry and optical properties of the metal surface, orientation of chemisorbed molecules and chemical environment. While SERS holds promise for single molecule sensitivity and optical sensing of DNA sequences, more detailed understanding of the rich physico‐chemical interplay between various factors is needed to enhance predictive power of existing and future SERS‐based DNA sensing platforms. In this work, we report on experimental results indicating that SERS spectra of adsorbed single‐stranded DNA (ssDNA) isomers depend on the order on which individual bases appear in the 3‐base long ssDNA due to intramolecular interaction between DNA bases. Furthermore, we experimentally demonstrate that the effect holds under more general conditions when the molecules do not experience chemical enhancement due to resonant charge transfer effect and also under standard Raman scattering without electromagnetic or chemical enhancements. Our numerical simulations qualitatively support the experimental findings and indicate that base permutation results in modification of both Raman and chemically enhanced Raman spectra. Raman scattering ; Raman spectroscopy ; Molecule ; Plasmon ; Intramolecular force ; Nucleobase ; Scattering ; X-ray Raman scattering ; DNA Gold and Silver Nanoparticles Synthesis and Applications ; Advanced biosensing and bioanalysis techniques ; DNA and Nucleic Acid Chemistry
Authors: Florian N. Loch | Oliver Klein | Katharina Beyer | Frederick Klauschen | Christian Schineis | Johannes C. Lauscher | Georgios Antonios Margonis | Claudius E. Degro | Wael Rayya | Carsten Kamphues
Source: Biology (article, 2021-10-12)
Field: Chemistry — Spectroscopy

Peptide Signatures for Prognostic Markers of Pancreatic Cancer by MALDI Mass Spectrometry Imaging Despite the overall poor prognosis of pancreatic cancer there is heterogeneity in clinical courses of tumors not assessed by conventional risk stratification. This yields the need of additional markers for proper assessment of prognosis and multimodal clinical management. We provide a proof of concept study evaluating the feasibility of Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) to identify specific peptide signatures linked to prognostic parameters of pancreatic cancer. On 18 patients with exocrine pancreatic cancer after tumor resection, MALDI imaging analysis was performed additional to histopathological assessment. Principal component analysis (PCA) was used to explore discrimination of peptide signatures of prognostic histopathological features and receiver operator characteristic (ROC) to identify which specific <i>m</i>/<i>z</i> values are the most discriminative between the prognostic subgroups of patients. Out of 557 aligned <i>m</i>/<i>z</i> values discriminate peptide signatures for the prognostic histopathological features lymphatic vessel invasion (pL, 16 <i>m</i>/<i>z</i> values, eight proteins), nodal metastasis (pN, two <i>m</i>/<i>z</i> values, one protein) and angioinvasion (pV, 4 <i>m</i>/<i>z</i> values, two proteins) were identified. These results yield proof of concept that MALDI-MSI of pancreatic cancer tissue is feasible to identify peptide signatures of prognostic relevance and can augment risk assessment. Biology ; Pancreatic cancer ; Mass spectrometry imaging ; Mass spectrometry ; MALDI imaging ; Cancer ; Computational biology ; Matrix-assisted laser desorption/ionization ; Internal medicine ; Chromatography ; Genetics Mass Spectrometry Techniques and Applications ; Molecular Biology Techniques and Applications ; Advanced Proteomics Techniques and Applications
Authors: Joel R. Steele | Carly J. Italiano | Connor R. Phillips | Jake P. Violi | Lisa Pu | Kenneth J. Rodgers | Matthew P. Padula
Source: Proteomes (review, 2021-01-21)
Field: Chemistry — Spectroscopy

Misincorporation Proteomics Technologies: A Review Proteinopathies are diseases caused by factors that affect proteoform conformation. As such, a prevalent hypothesis is that the misincorporation of noncanonical amino acids into a proteoform results in detrimental structures. However, this hypothesis is missing proteomic evidence, specifically the detection of a noncanonical amino acid in a peptide sequence. This review aims to outline the current state of technology that can be used to investigate mistranslations and misincorporations whilst framing the pursuit as Misincorporation Proteomics (MiP). The current availability of technologies explored herein is mass spectrometry, sample enrichment/preparation, data analysis techniques, and the hyphenation of approaches. While many of these technologies show potential, our review reveals a need for further development and refinement of approaches is still required. Proteomics ; Computational biology ; Computer science ; Amino acid residue ; Data science ; Biology ; Bioinformatics ; Peptide sequence ; Biochemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; RNA and protein synthesis mechanisms
Authors: Fenfei Wei | Egidius W. F. Smeets | Johannes Voss | Geert–Jan Kroes | Sen Lin | Hua Guo
Source: Chinese Journal of Chemical Physics (article, 2021-12-01)
Field: Materials Science — Materials Chemistry

Assessing density functionals for describing methane dissociative chemisorption on Pt(110)-(2×1) surface In this work, we explore the suitability of several density functionals with the generalized gradient approximation (GGA) and beyond for describing the dissociative chemisorption of methane on the reconstructed Pt(110)-(2×1) surface. The bulk and surface structures of the metal, methane adsorption energy, and dissociation barrier are used to assess the functionals. A van der Waals corrected GGA functional (optPBE-vdW) and a meta-GGA functional with van der Waals correction (MS PBEl-rVV10) are selected for ab initio molecular dynamics calculations of the sticking probability. Our results suggest that the use of these two functionals may lead to a better agreement with existing experimental results, thus serving as a good starting point for future development of reliable machine-learned potential energy surfaces for the dissociation of methane on the Pt(110)-(2×1) surface. van der Waals force ; Dissociation (chemistry) ; Chemisorption ; Methane ; Density functional theory ; Adsorption ; Chemistry ; Ab initio ; Potential energy surface ; Chemical physics ; Sticking probability ; Thermodynamics ; Computational chemistry ; Atomic physics ; Physical chemistry ; Molecule ; Physics ; Desorption Machine Learning in Materials Science ; Advanced Chemical Physics Studies ; Catalytic Processes in Materials Science
Authors: Kirstie A. Goggin
Source: Journal of Oil Palm Research (article, 2021-04-08)
Field: Chemistry — Organic Chemistry

A PROOF-OF-CONCEPT STUDY: DETERMINING THE GEOGRAPHICAL ORIGIN OF CRUDE PALM OIL WITH THE COMBINED USE OF GC-IMS FINGERPRINTING AND CHEMOMETRICS Current administrative controls used to verify geographical provenance within palm oil supply chains require enhancement and strengthening by more robust analytical methods. In this study, the application of volatile organic compound fingerprinting, in combination with five different analytical classification models, has been used to verify the regional geographical provenance of crude palm oil (CPO) samples. For this purpose, 108 CPO samples were collected from two regions within Malaysia, namely Peninsular Malaysia (32) and Sabah (76). Samples were analysed by gas chromatography-ion mobility spectrometer (GC-IMS) and the five predictive models (Sparse Logistic Regression, Random Forests, Gaussian Processes, Support Vector Machines and Artificial Neural Networks) were built and applied. Models were validated using 10-fold cross-validation. The area under curve (AUC) measure was used as a summary indicator of the performance of each classifier. All models performed well (AUC 0.96) with the Sparse Logistic Regression model giving best performance (AUC = 0.98). This demonstrates that the verification of the geographical origin of CPO is feasible by volatile organic compound fingerprinting, using GC-IMS supported by chemometric analysis. Chemometrics ; Palm oil ; Proof of concept ; Crude oil ; Gas chromatography–mass spectrometry ; Chemistry ; Chromatography ; Botany ; Food science ; Biology ; Computer science ; Mass spectrometry ; Engineering ; Petroleum engineering Edible Oils Quality and Analysis ; Mass Spectrometry Techniques and Applications ; Petroleum Processing and Analysis
Authors: Mathias Walzer | David García‐Seisdedos | Ananth Prakash | Paul Brack | Peter Crowther | R. L. Graham | Nancy George | Suhaib Mohammed | Pablo Moreno | Irene Papathedourou | Simon J. Hubbard | Juan Antonio Vizcaíno
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2021-06-09)
Field: Chemistry — Spectroscopy

Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas ABSTRACT The number of mass spectrometry (MS)-based proteomics datasets in the public domain keeps increasing, particularly those generated by Data Independent Acquisition (DIA) approaches such as SWATH-MS. Unlike Data Dependent Acquisition datasets, the re-use of DIA datasets has been rather limited to date, despite its high potential, due to the technical challenges involved. We introduce a (re-)analysis pipeline for public SWATH-MS datasets which includes a combination of metadata annotation protocols, automated workflows for MS data analysis, statistical analysis, and the integration of the results into the Expression Atlas resource. Automation is orchestrated with Nextflow, using containerised open analysis software tools, rendering the pipeline readily available and reproducible. To demonstrate its utility, we reanalysed 10 public DIA datasets from the PRIDE database, comprising 1,278 SWATH-MS runs. The robustness of the analysis was evaluated, and the results compared to those obtained in the original publications. The final expression values were integrated into Expression Atlas, making SWATH-MS experiments more widely available and combining them with expression data originating from other proteomics and transcriptomics datasets. Computer science ; Metadata ; Workflow ; Annotation ; Pipeline (software) ; Human Protein Atlas ; Data mining ; Rendering (computer graphics) ; Database ; Information retrieval ; Data science ; Protein expression ; World Wide Web ; Artificial intelligence ; Biology Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Mass Spectrometry Techniques and Applications