bluuebunny/crossref_metadata_2025_split huggingface dataset:
His-tag based supramolecular biopolymerization
Authors: Lal Mitra , Kesselman Ellina , Wachtel Ellen , Kleinerman Olga , Peleg Yoav , Albeck Shira , Majhi Koushik , Sheves Mordechai , Patchornik Guy 
Published: November 2024

AbstractThe term supramolecular polymer has been applied to polymeric materials in which the individual units, i.e., building blocks—are bound to each other via noncovalent interactions, including electrostatic or hydrogen bonding, as well as metal–ligand conjugation. The building blocks are generally low molecular weight amphiphiles. Methods for preparing biopolymers based on non-toxic, metal–ligand conjugation have been little studied; however, they offer significant potential for tuning the response of biologically relevant macromolecules. In this communication, we characterize the assembly and morphology of supramolecular biopolymers in which the building blocks are low- or medium-molecular weight globular proteins—ubiquitin and Cas9-interacting via metal–ligand conjugation. In each case, the protein gene was expressed in cell culture with the addition of hexa-His/linkers at both the N and C termini. Divalent cations investigated were Zn2+ and Ni2+. We observe in cryo-TEM imaging an absolute requirement for divalent cations for the formation of supramolecular biopolymers. In the presence of Ni2+, 1D assembled fibers are predominant, while with Zn2+, the more frequently detected structures are sheet-like. We use gel electrophoresis and CD spectroscopy to monitor possible secondary and tertiary structural changes in the protein building blocks during conjugation.
Fabrication of novel PVA loaded ZnO nanoparticles for anti-renal failure
Authors: Hassan Shawky M. , Tarek Mahmoud , Samra Salem , El-Dafrawy Shady M. 
Published: November 2024

AbstractX-ray diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were used to investigate the structural, surface and particles properties of a series of zinc oxides (ZnO) doped with polyvinyl alcohol (PVA) that were prepared using the sol-gel method. The results demonstrated that the crystallinity of the catalysts decreased as the PVA content increased beyond 5 PVA/ZnO. However, on raising the calcination temperature up to 500 °C, the average crystal size of the PVA/ZnO nanoparticles increased. Next Pyridine adsorption was used to measure the surface acidity of the catalysts, and the results showed that doping ZnO with PVA and raising the calcination temperature to 500 °C increased the catalyst’s surface acidity. Furthermore, the data indicates that raising the ratio of the Brønsted to Lewis acid sites enhanced the catalytic activity for the synthesis of coumarin derivatives. We concluded that the structural and acidity characteristics of the catalysts under study had a significant impact on the catalytic activity. Furthermore, a study examining the biological activity of ZnO/PVA and pure ZnO revealed that 5PVA/ZnO performed the best in terms of improving the kidney functions of diabetic rats.
Starvation-induced metabolic rewiring affects mTORC1 composition in vivo
Authors: Kaade Edgar , Mausbach Simone , Erps Nina , Sylvester Marc , Shakeri Farhad , Jachimowicz Ron D. , Gieselmann Volkmar , Thelen Melanie 
Published: November 2024

Abstract
Lysosomes play a crucial role in metabolic adaptation to starvation, but detailed in vivo studies are scarce. Therefore, we investigated the changes of the proteome of liver lysosomes in mice starved short-term for 6h or long-term for 24h. We verified starvation-induced catabolism by weight loss, ketone body production, drop in blood glucose and an increase of 3-methylhistidine. Deactivation of mTORC1 in vivo after short-term starvation causes a depletion of mTORC1 and the associated Ragulator complex in hepatic lysosomes, resulting in diminished phosphorylation of mTORC1 target proteins. While mTORC1 lysosomal protein levels and activity in liver were restored after long-term starvation, the lysosomal levels of Ragulator remained constantly reduced. To determine whether this mTORC1 activity pattern may be organ-specific, we further investigated the key metabolic organs muscle and brain. mTORC1 inactivation, but not re-activation, occurred in muscle after a starvation of 12 h or longer. In brain, mTORC1 activity remained unchanged during starvation. As mTORC1 deactivation is known to induce autophagy, we further investigated the more than 150 non-lysosomal proteins enriched in the lysosomal fraction upon starvation. Proteasomal, cytosolic and peroxisomal proteins dominated after short-term starvation, while after long-term starvation, mainly proteasomal and mitochondrial proteins accumulated, indicating ordered autophagic protein degradation.
Biological control of nosemosis in Apis mellifera L. with Acacia nilotica extract
Authors: El-Sayed Ashraf S. A. , Fathy Nahla A. M. , Labib Mai , El-Baz Ashraf F. , El-Sheikh Aly A. , Moustafa Ahmed H. 
Published: November 2024

AbstractNosemosis is one of the most devastating diseases of Apis mellifera (Honey bees) caused by the single-celled spore-forming fungi Nosema apis, N. ceranae and N. neumanii, causing a severe loss on the colony vitality and productivity. Fumagillin, a MetAP2 inhibitor, was a certified treatment for controlling nosemosis, nevertheless, due to its deleterious effects on honey bees and humans, it is prohibited. So, searching for novel biological agents with affordable selectivity to target Nosema species infecting Apis mellifera, with nil toxicity to bees and humans is the main objective of this study. Nosema species were isolated from naturally infected honey bees. The methanolic extracts of Acacia nilotica, Elaeis guineensis, and Catharanthus roseus were tested to selectively control the growth of Nosema spp of honeybees. The spores of Nosema species were molecularly and morphologically identified. Among the tested plant extracts, the methanolic extracts (0.1%) of A. nilotica had the most activity towards Nosema spp causing about 37.8 and 32.5% reduction in the spores’ load at 5- and 9-days post-infection, respectively, compared to the untreated control. At 0.1%, the A. nilotica methanolic extract exhibited the highest inhibitory effect for Nosema spores, without any obvious bee mortality. Catharanthus roseus displayed a reduction of spores by 27.02%, with bee mortality rate of 27.02%. At 1% for 5 dpi, the A. nilotica extracts led to 18.18% bee mortality, while the C. roseus extracts resulted in 100% mortality, as revealed from the toxicity and quantification bioassays. So, the extracts of A. nilotica and C. roseus had a significant effect in controlling the N. apis and N. ceranae titer compared to the infected untreated control at both time points. The titer of N. apis and N. ceranae was noticeably decreased by more than 80% and 90%, in response to A. nilotica, compared to the control. From the metabolic profiling by GC–MS analysis, the most frequent active compounds of A. nilotica were 2,4,6-trihy-droxybenzoic acid, 1,2-dihydroxybenzene, myristic acid, and linoleic acid. These compounds were analyzed in silico to assess their binding affinity to the ATP binding protein, methionine aminopeptidase and polar tube protein of Nosema species as target enzymes. The compound 2,4,6-trihydroxybenzoic acid had the lowest energy to bind with ATP binding protein, methionine aminopeptidase and polar tube protein of Nosema, followed by 1,2-dihydroxybenzene and myristic acid, compared to fumagilin. So, from the experimental and molecular docking analysis, the extracts of A. nilotica had the highest activity to attack the cellular growth machinery of Nosema species without an obvious effect to the honeybees, ensuring their prospective promising application.
ZnO doped PAMAM for asphalt improvement as anti-corrosive coatings
Authors: Al-Gamal Abdalrahman G. , Gado Walaa S. , Abo El-Khair Muhammad A. , Zakaria Khaled , Ragab A. A. , Kabel Khalid I. 
Published: November 2024

AbstractAsphalt is widely used as a coating resin due to its excellent adhesion strength and cost-effectiveness; however, its limited corrosion protection necessitates enhancement. In this study, poly(amidoamine) (PAMAM), combined with zinc oxide (ZnO) nanoparticles, was incorporated into the asphalt matrix to improve its anticorrosive properties. Various ratios of PAMAM-ZnO nanocomposite (1, 2, 4, and 6% by weight) were added to the asphalt binder, with the materials characterized using XRD, ¹H-NMR, and SEM techniques. The 2% PAMAM-ZnO/asphalt ratio exhibited the most significant improvement, achieving a corrosion protection efficiency (η%) of 97.93%, as confirmed by Tafel analysis, and a charge transport resistance (RCT) of 75.91 Ω cm² according to electrochemical impedance spectroscopy (EIS) data. A combination of barrier formation and sacrificial protection drives the corrosion inhibition mechanism. The PAMAM-ZnO nanocomposite forms a highly uniform layer on the carbon steel surface, creating an effective physical barrier that prevents the penetration of corrosive agents, thereby minimizing defects like pinholes. This barrier effect is complemented by the sacrificial protection provided by the ZnO nanoparticles, which are more reactive than the underlying steel and preferentially interact with corrosive ions (e.g., chloride ions). This interaction leads to the formation of stable ZnO corrosion products, which enhance the barrier and reduce the likelihood of corrosion on the steel surface. Additionally, PAMAM facilitates the even distribution and strong adhesion of ZnO within the asphalt matrix, ensuring a durable protective layer. The synergic impact between the polymer barrier and sacrificial ZnO protection results in the exceptional corrosion resistance observed in the 2% PAMAM-ZnO/asphalt formulation, offering a promising approach for advanced anticorrosive coatings.
Antibacterial efficacy of berry juices against Bacillus cereus relative to their phytochemical composition and antioxidant properties
Authors: Królak Kamil , Ścieszka Sylwia , Kordialik-Bogacka Edyta , Oracz Joanna , Ditrych Maciej , Szczygieł Tomasz , Dybka-Stępień Katarzyna , Otlewska Anna , Żyżelewicz Dorota 
Published: November 2024

AbstractEnsuring the safety and stability of minimally processed foods using natural preservatives is of great scientific and commercial interest in modern biotechnology. Berry juice supplementation is increasingly recognized within this field. This study investigated the effectiveness of juices from four berry species Aronia melanocarpa, Ribes nigrum, Vaccinium macrocarpon, and Sambucus nigra, against the food pathogen Bacillus cereus. Overall, the antibacterial potency of juice supplements (up to 10% v/v in tryptic soy broth) followed the order of chokeberry > blackcurrant > cranberry > elderberry, with the latter showing no inhibitory effects. Notably, chokeberry and elderberry juices presented lower acidity and significantly greater phenolic contents (p < 0.05) than blackcurrant and cranberry juices did, suggesting that B. cereus susceptibility is not strictly dependent upon low extracellular pH or elevated anthocyanin levels. Instead, it is inferred to correlate with pro-oxidative effects induced directly at the intracellular level. Accordingly, this paper discusses the antioxidative, acidic, and lipophilic attributes of juices and their constituent fractions, including anthocyanins, to elucidate their biopreservative potential. The results of this study increase our understanding of the antibacterial susceptibility of B. cereus.
Bidirectional Mendelian randomization links gut microbiota to primary biliary cholangitis
Authors: Zhou Zhijia , Li Wenxuan , Wu Yuelan , Wang Tao , Zhang Jinghao , You Liping , Li Haoran , Zheng Chao , Gao Yueqiu , Sun Xuehua 
Published: November 2024

AbstractPrimary biliary cholangitis (PBC) and gut microbiota (GM) are epidemiologically correlated but the causal inter-relationships remain poorly understood. We aim to explore the causal relationships between GM and PBC. Using the MiBioGen consortium, GWAS data for GM at the species level and the largest publicly available PBC GWAS data to date, we performed a bidirectional two-sample Mendelian randomization by the inverse variance weighted, MR-Egger, weighted median, weighted model and MR-PRESSO to elucidate the potential causal role of GM in PBC. To measure the heterogeneity of instrumental variables (IV), Cochran’s Q statistic and MR-Egger intercept test were used. Genetically instrumented order Coriobacteriales (odds ratio [OR] = 2.18, 95% confidence interval [CI] 1.30–3.66, P = 0.004) significantly increased the risk for PBC, while genetically driven class Deltaproteobacteria (OR = 0.52, 95% CI 0.36–0.74, P = 0.002) causally decrease the NAFLD risk. Reverse MR analysis showed no significant association between PBC and the two specific GM. However, it indicated that PBC progression significantly increases the abundance of the class Bacteroidia, order Bacteroidales, and phylum Bacteroidetes (OR = 1.02, 95% CI 1.002–1.03, P = 0.026), while decreasing the abundance of the genus Lachnospiraceae UCG010 (OR = 0.98, 95% CI 0.96–0.995, P = 0.026). Our study demonstrated that genetically driven order Coriobacteriales and class Deltaproteobacteria were causally related to PBC risk. This causality provided a new perspective on ameliorating PBC by modulating GM. Our study demonstrated that genetically driven order Coriobacteriales and class Deltaproteobacteria were causally related to PBC risk. PBC was causally related to the abundance of four GM taxa(class Bacteroidia, order Bacteroidales, phylum Bacteroidetes and genus Lachnospiraceae UCG010). This causality provided a new perspective on ameliorating PBC by modulating GM.
Generating and validating renewable affimer protein binding reagents targeting SH2 domains
Authors: Heseltine Sophie J. , Billenness Gregory J. , Martin Heather L , Tiede Christian , Tang Anna A.S. , Foy Eleanor , Reddy Grace , Gibson Naomi , Johnson Matt , Webb Michael E. , McPherson Michael J. , Tomlinson Darren C. 
Published: November 2024

AbstractDespite SH2 domains, being pivotal in protein interactions linked to various diseases like cancer, we lack specific research tools for intracellular assays. Understanding SH2-mediated interactions and creating effective inhibitors requires tools which target individual protein domains. Affimer reagents exhibit promise, yet their potential against the extensive SH2 domain family remains largely unexplored. Our study aimed to bridge this gap by identifying Affimer reagents that selectively bind to 22 out of 41 SH2 domains. These reagents enabled a medium-throughput screening approach resembling siRNA studies, shedding light on their functionality. Notably, select Affimers demonstrated the ability to curtail the nuclear translocation of pERK, with Grb2 being a prominent target. Further analyses revealed that these Grb2-specific Affimer reagents displayed competitive inhibition with impressive metrics: IC50s ranging from 270.9 nM to 1.22 µM, together with low nanomolar binding affinities. Moreover, they exhibited the ability to pull down endogenous Grb2 from cell lysates, illustrating their efficacy in binding the Grb2 SH2 domain. This comprehensive assessment underscores the potential of Affimer reagents as domain-specific inhibitors. Their viability for medium/high-throughput phenotypic screening presents a promising avenue via which to identify and characterize potential drug targets within the SH2 domain family.
Microfluidic qPCR for detection of 21 common respiratory viruses in children with influenza-like illness
Authors: Saville Thomas J. , Colton Hayley , Jarju Sheikh , Armitage Edwin P. , Drammeh Sainabou , Tazzyman Simon , Jagne Ya Jankey , Sallah Hadijatou J. , Senghore Elina , Evans Cariad M. , Darton Thomas C. , de Silva Thushan I. 
Published: November 2024

AbstractMultiple respiratory viruses lead to high morbidity and mortality, yet global surveillance platforms focus primarily on seasonal influenza viruses. The COVID-19 pandemic and new RSV vaccines highlight the importance of a broader approach. Upper respiratory tract swabs from children aged 24–59 months presenting with influenza-like illness in The Gambia were collected during follow-up of a live-attenuated influenza vaccine randomised controlled trial in 2017–18. A microfluidic quantitative polymerase chain reaction (qPCR) assay was established and used to detect 21 respiratory viruses. 76.6% of samples had one or more viruses detected (n = 121/158). The viruses detected most frequently were rhinovirus (n = 37/158, 23.4%) and adenovirus (n = 34/158, 21.5%), followed by parainfluenza virus 3, influenza B and human metapneumovirus B. A third of positive samples had multiple viruses detected (two n = 31/121, 25.6%; three n = 9/121, 7.4%). Our data demonstrates how microfluidic qPCR is a useful tool for high-throughput, comprehensive detection of multiple respiratory viruses in surveillance platforms. Rapidly changing epidemiology exemplifies the need for new, broader approaches to virus surveillance in low-resource settings to respond to future epidemics and to guide the need for and use of new prevention and therapeutic measures.
Impact of molecular configuration on the photoluminescence and electrical characteristics of poly-pyrrol-thiazol-imine polymers films
Authors: Ghazy Ahmed R. , Kenawy El-Refaie , Darwesh Nourhan , Shendy S. , El-Shaer Abdelhamid , Ghazy R. 
Published: November 2024

AbstractThe optical, photoluminescence, and electrical properties of Poly(Z)-PTI and Poly(E)-PTI, two Poly-Pyrrol-Thiazol-Imine polymers with comparable chemical structures but distinct configurations, were examined. Using the dip-casting method, polymer films were deposited on ITO substrates. UV-VIS spectroscopy revealed that both polymers diverged between 500 and 800 nm, showing the impact of molecular arrangement, but showed similar absorption behavior for wavelengths shorter than 500 nm. For Poly(Z)-PTI, the direct optical energy gaps were 2.06 eV, while for Poly(E)-PTI, they were 1.78 eV. Poly(Z)-PTI displayed an emission peak at 610 nm (red) according to laser photoluminescence spectra, while Poly(E)-PTI peaked at 563 nm (green-yellow). The capacitance behavior was revealed by electrochemical impedance spectroscopy. Nyquist plots suggested an equivalent circuit model of Rs (CRct)(QR)(CR) for both polymers, and the relaxation times were 15.9 ns for Poly(Z)-PTI and 89.5 ns for Poly(E)-PTI. The Mott-Schottky analysis verified the n-type conductivity, revealing 2.18 × 1016 cm− 3 carrier densities for Poly(Z)-PTI and 1.78 × 1016 cm− 3 for Poly(E)-PTI. At lower frequencies, both polymers exhibited limited conductivity and large dielectric constants. Insights into the possible uses of Poly-Pyrrol-Thiazol-Imine polymers in electrical and optoelectronic devices are provided by this study, which emphasizes the influence of molecular configuration on these polymers’ characteristics.
Potential biological applications of environment friendly synthesized iron oxide nanoparticles using Sageretia thea root extract
Authors: Israeel Muhammad , Iqbal Javed , Abbasi Banzeer Ahsan , Ijaz Shumaila , Ullah Rafi , Zarshan Farishta , Yaseen Tabassum , Khan Gul , Murtaza Ghulam , Ali Iftikhar , Alarjani Khaloud Mohammed , Elshikh Mohamed S , Rizwan Muhammad , Khan Shoaib , Iqbal Rashid 
Published: November 2024

AbstractThe green synthesis of Iron oxide nanoparticles (IONPs) has shown numerous advantages over conventional physical and chemical synthesis methods as these methods non-ecofriendly and uses toxic chemicals and complicated equipments. In present study, Iron oxide nanoparticles (IONPs) were created using simple, sustainable, eco-friendly and green chemistry protocol. The roots of novel medicinal plant Sageretia thea was used as a bio-template for the preparation of IONPs. Further, the synthesis of IONPs was confirmed using different analytical tools like UV-Vis, FT-IR, XRD, EDX, and SEM. The average sizes of (NPs) were found to be 16.04 nm. Further, asynthesized IONPs were evaluated for several biological potentials including antibacterial, antifungal Anti-radical potentials (DPPH) and cytotoxicity assays. Antibacterial potencies were investigated using bacterial strains (in the concentration range of 1000–31.25 µg/mL) revealing significant antibacterial potentials. ABA and SAU was reported to be least susceptible while KPN was observed to be most susceptible strain in bactericidal studies. Further, different fungal strains were used to investigate the antifungal potentials of IONPs (in the concentration range of 1000–31.25 µg/mL) and revealed strong antifungal potencies against different pathogenic strains. Furthermore, MRA, FA and ANI were most susceptible and ABA was least susceptible in fungicidal examination. Significant cytotoxicity potential was examined using brine shrimps cytotoxicity assay, thus revealing the cytotoxic potential of asynthesized IONPs. The IC50 for S. thea based IONPs was recorded as 33.85 µg/mL. Strong anti-radical potentials (DPPH) assay was performed to evaluate the ROS scavenging potential of S.T@IONPs. The highest scavenging potential was noted as 78.06%, TRP as 81.92% and TAC as 84% on maximum concentration of 200 µg/mL. In summary, our experimental results concluded, that asynthesized IONPs have strong antibacterial, antifungal, DPPH scavenging and cytotoxic potentials and can be used in different biological applications. In nutshell, our as-prepared nanoparticles have shown potential bioactivities and we recommend, different other in vitro and in vivo biological and bioactivities to further analyze the biological potentials.
Water in peripheral TM-interfaces of Orai1-channels triggers pore opening
Authors: Hopl Valentina , Tiffner Adéla , Wutscher Armin , Sallinger Matthias , Grabmayr Herwig , Prantl Magdalena , Fröhlich Maximilian , Söllner Julia , Weiß Sarah , Najjar Hadil , Nazarenko Yuliia , Harant Selina , Kriško Natalia , Fahrner Marc , Humer Christina , Höglinger Carmen , Krobath Heinrich , Bonhenry Daniel , Derler Isabella 
Published: November 2024

AbstractThe activation of the Ca2+-channel Orai1 via the physiological activator stromal interaction molecule 1 (STIM1) requires structural rearrangements within the entire channel complex involving a series of gating checkpoints. Focusing on the gating mechanism operating along the peripheral transmembrane domain (TM) 3/TM4-interface, we report here that some charged substitutions close to the center of TM3 or TM4 lead to constitutively active Orai1 variants triggering nuclear factor of activated T-cell (NFAT) translocation into the nucleus. Molecular dynamics simulations unveil that this gain-of-function correlates with enhanced hydration at peripheral TM-interfaces, leading to increased local structural flexibility of the channel periphery and global conformational changes permitting pore opening. Our findings indicate that efficient dehydration of the peripheral TM-interfaces driven by the hydrophobic effect is critical for maintaining the closed state of Orai1. We conclude that a charge close to the center of TM3 or TM4 facilitates concomitant hydration and widening of peripheral TM interfaces to trigger constitutive Orai1 pore opening to a level comparable to or exceeding that of native activated Orai1.