bluuebunny/crossref_metadata_2025_split huggingface dataset:
A fungal NRPS-PKS enzyme catalyses the formation of the flavonoid naringenin
Authors: Zhang Hongjiao , Li Zixin , Zhou Shuang , Li Shu-Ming , Ran Huomiao , Song Zili , Yu Tao , Yin Wen-Bing 
Published: October 2022

AbstractBiosynthesis of the flavonoid naringenin in plants and bacteria is commonly catalysed by a type III polyketide synthase (PKS) using onep-coumaroyl-CoA and three malonyl-CoA molecules as substrates. Here, we report a fungal non-ribosomal peptide synthetase -polyketide synthase (NRPS-PKS) hybrid FnsA for the naringenin formation. Feeding experiments with isotope-labelled precursors demonstrate that FnsA accepts not onlyp-coumaric acid (p-CA), but alsop-hydroxybenzoic acid (p-HBA) as starter units, with three or four malonyl-CoA molecules for elongation, respectively. In vitro assays and MS/MS analysis prove that bothp-CA andp-HBA are firstly activated by the adenylation domain of FnsA. Phylogenetic analysis reveals that the PKS portion of FnsA shares high sequence homology with type I PKSs. Refactoring the biosynthetic pathway in yeast with the involvement offnsAprovides an alternative approach for the production of flavonoids such as isorhamnetin and acacetin.
Rapid and comprehensive diagnostic method for repeat expansion diseases using nanopore sequencing
Authors: Miyatake Satoko , Koshimizu Eriko , Fujita Atsushi , Doi Hiroshi , Okubo Masaki , Wada Taishi , Hamanaka Kohei , Ueda Naohisa , Kishida Hitaru , Minase Gaku , Matsuno Atsuhiro , Kodaira Minori , Ogata Katsuhisa , Kato Rumiko , Sugiyama Atsuhiko , Sasaki Ayako , Miyama Takabumi , Satoh Mai , Uchiyama Yuri , Tsuchida Naomi , Hamanoue Haruka , Misawa Kazuharu , Hayasaka Kiyoshi , Sekijima Yoshiki , Adachi Hiroaki , Yoshida Kunihiro , Tanaka Fumiaki , Mizuguchi Takeshi , Matsumoto Naomichi 
Published: October 2022

AbstractWe developed a diagnostic method for repeat expansion diseases using a long-read sequencer to improve currently available, low throughput diagnostic methods. We employed the real-time target enrichment system of the nanopore GridION sequencer using the adaptive sampling option, in which software-based target assignment is available without prior sample enrichment, and built an analysis pipeline that prioritized the disease-causing loci. Twenty-two patients with various neurological and neuromuscular diseases, including 12 with genetically diagnosed repeat expansion diseases and 10 manifesting cerebellar ataxia, but without genetic diagnosis, were analyzed. We first sequenced the 12 molecularly diagnosed patients and accurately confirmed expanded repeats in all with uniform depth of coverage across the loci. Next, we applied our method and a conventional method to 10 molecularly undiagnosed patients. Our method corrected inaccurate diagnoses of two patients by the conventional method. Our method is superior to conventional diagnostic methods in terms of speed, accuracy, and comprehensiveness.
On the growth dynamics of the cyanobacterium Anabaena sp. PCC 7938 in Martian regolith
Authors: Ramalho Tiago P. , Chopin Guillaume , Salman Lina , Baumgartner Vincent , Heinicke Christiane , Verseux Cyprien 
Published: October 2022

AbstractThe sustainability of crewed infrastructures on Mars will depend on their abilities to produce consumables on site. These abilities may be supported by diazotrophic, rock-leaching cyanobacteria: from resources naturally available on Mars, they could feed downstream biological processes and lead to the production of oxygen, food, fuels, structural materials, pharmaceuticals and more. The relevance of such a system will be dictated largely by the efficiency of regolith utilization by cyanobacteria. We therefore describe the growth dynamics of Anabaena sp. PCC 7938 as a function of MGS-1 concentration (a simulant of a widespread type of Martian regolith), of perchlorate concentration, and of their combination. To help devise improvement strategies and predict dynamics in regolith of differing composition, we identify the limiting element in MGS-1 – phosphorus – and its concentration-dependent effect on growth. Finally, we show that, while maintaining cyanobacteria and regolith in a single compartment can make the design of cultivation processes challenging, preventing direct physical contact between cells and grains may reduce growth. Overall, we hope for the knowledge gained here to support both the design of cultivation hardware and the modeling of cyanobacterium growth within.
Single-mode quantum non-Gaussian light from warm atoms
Authors: Mika Jaromír , Lachman Lukáš , Lamich Tomáš , Filip Radim , Slodička Lukáš 
Published: October 2022

AbstractThe distributed quantum information processing and hybridization of quantum platforms raises increasing demands on the quality of light-matter interaction and realization of efficient quantum interfaces. This becomes particularly challenging for needed states possessing fundamental quantum non-Gaussian (QNG) aspects. They correspond to paramount resources in most potent applications of quantum technologies. We demonstrate the generation of light with provably QNG features from a warm atomic ensemble in a single-mode regime. The light is generated in a spontaneous four-wave mixing process in the presence of decoherence effects caused by a large atomic thermal motion. Despite its high sensitivity to any excess noise, direct observability of heralded QNG light could be achieved due to a combination of a fast resonant excitation, large spectral bandwidth, and a low absorption loss of resonant photons guaranteed by the source geometry.
Enterotoxin tilimycin from gut-resident Klebsiella promotes mutational evolution and antibiotic resistance in mice
Authors: Kienesberger Sabine , Cosic Amar , Kitsera Maksym , Raffl Sandra , Hiesinger Marlene , Leitner Eva , Halwachs Bettina , Gorkiewicz Gregor , Glabonjat Ronald A. , Raber Georg , Lembacher-Fadum Christian , Breinbauer Rolf , Schild Stefan , Zechner Ellen L. 
Published: October 2022

AbstractKlebsiella spp. that secrete the DNA-alkylating enterotoxin tilimycin colonize the human intestinal tract. Numbers of toxigenic bacteria increase during antibiotic use, and the resulting accumulation of tilimycin in the intestinal lumen damages the epithelium via genetic instability and apoptosis. Here we examine the impact of this genotoxin on the gut ecosystem. 16S rRNA sequencing of faecal samples from mice colonized with Klebsiella oxytoca strains and mechanistic analyses show that tilimycin is a pro-mutagenic antibiotic affecting multiple phyla. Transient synthesis of tilimycin in the murine gut antagonized niche competitors, reduced microbial richness and altered taxonomic composition of the microbiota both during and following exposure. Moreover, tilimycin secretion increased rates of mutagenesis in co-resident opportunistic pathogens such as Klebsiella pneumoniae and Escherichia coli, as shown by de novo acquisition of antibiotic resistance. We conclude that tilimycin is a bacterial mutagen, and flares of genotoxic Klebsiella have the potential to drive the emergence of resistance, destabilize the gut microbiota and shape its evolutionary trajectory.
Cryo-EM structure of the SEA complex
Authors: Tafur Lucas , Hinterndorfer Kerstin , Gabus Caroline , Lamanna Chiara , Bergmann Ariane , Sadian Yashar , Hamdi Farzad , Kyrilis Fotis L. , Kastritis Panagiotis L. , Loewith Robbie 
Published: October 2022

AbstractThe SEA complex (SEAC) is a growth regulator that acts as a GTPase-activating protein (GAP) towards Gtr1, a Rag GTPase that relays nutrient status to the Target of Rapamycin Complex 1 (TORC1) in yeast1. Functionally, the SEAC has been divided into two subcomplexes: SEACIT, which has GAP activity and inhibits TORC1, and SEACAT, which regulates SEACIT2. This system is conserved in mammals: the GATOR complex, consisting of GATOR1 (SEACIT) and GATOR2 (SEACAT), transmits amino acid3 and glucose4 signals to mTORC1. Despite its importance, the structure of SEAC/GATOR, and thus molecular understanding of its function, is lacking. Here, we solve the cryo-EM structure of the native eight-subunit SEAC. The SEAC has a modular structure in which a COPII-like cage corresponding to SEACAT binds two flexible wings, which correspond to SEACIT. The wings are tethered to the core via Sea3, which forms part of both modules. The GAP mechanism of GATOR1 is conserved in SEACIT, and GAP activity is unaffected by SEACAT in vitro. In vivo, the wings are essential for recruitment of the SEAC to the vacuole, primarily via the EGO complex. Our results indicate that rather than being a direct inhibitor of SEACIT, SEACAT acts as a scaffold for the binding of TORC1 regulators.
Database of SARS-CoV-2 and coronaviruses kinetics relevant for assessing persistence in food processing plants
Authors: Luong Ngoc-Du Martin , Guillier Laurent , Martin-Latil Sandra , Batejat Christophe , Leclercq India , Druesne Christine , Sanaa Moez , Chaix Estelle 
Published: October 2022

AbstractSARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2), a virus causing severe acute respiratory disease in humans, emerged in late 2019. This respiratory virus can spread via aerosols, fomites, contaminated hands or surfaces as for other coronaviruses. Studying their persistence under different environmental conditions represents a key step for better understanding the virus transmission. This work aimed to present a reproducible procedure for collecting data of stability and inactivation kinetics from the scientific literature. The aim was to identify data useful for characterizing the persistence of viruses in the food production plants. As a result, a large dataset related to persistence on matrices or in liquid media under different environmental conditions is presented. This procedure, combining bibliographic survey, data digitalization techniques and predictive microbiological modelling, identified 65 research articles providing 455 coronaviruses kinetics. A ranking step as well as a technical validation with a Gage Repeatability & Reproducibility process were performed to check the quality of the kinetics. All data were deposited in public repositories for future uses by other researchers.
Histoarchitecture of the fibrillary matrix of human fetal posterior tibial tendons
Authors: Macedo Rodrigo Sousa , Teodoro Walcy Rosolia , Capellozzi Vera Luiza , Rosemberg Dov Lagus , Sposeto Rafael Barban , de Cesar Netto Cesar , Deland Jonathan T. , Maffulli Nicola , Ellis Scott J. , Godoy-Santos Alexandre Leme 
Published: October 2022

AbstractAdult tendons are highly differentiated. In mature individuals, tendon healing after an injury occurs through fibrotic tissue formation. Understanding the intrinsic reparative properties of fetal tendons would help to understand the maturation tissue process and tendon tissue repair. The present study evaluated the evolution of histoarchitecture, cellularity and the distribution of collagens I, III and V in the posterior tibial tendon in human fetuses at different gestational ages. Morphological profiles were assessed in nine fresh spontaneously aborted fetuses (Group I: five fetuses aged between 22 and 28 weeks of gestation; Group II: four fetuses aged between 32 and 38 weeks of gestation), characterized by a combination of histology, fluorescence and immunohistochemistry. In Group I, the posterior tibial tendon showed statistically significant greater cellularity and presence of collagen III and V than in Group II tendon, which showed a predominance of collagenous I and a better organization of the extracellular matrix compared with Group I tendons. In addition, a statistically significant higher rate of CD90, a marker of mesenchymal cells, was found in Group I tendons. In fetuses with gestational age between 22 and 28 weeks, the posterior tibialis tendons showed a thin and disorganized fibrillar structure, with an increase in collagen III and V fibers and mesenchymal cells. In the posterior tibialis tendons of fetuses with gestational age between 32 and 38 weeks, the fibrillar structure was thicker with a statistically significant increase in type I collagen and decreased cellularity.
ACSL1 promotes imatinib-induced chronic myeloid leukemia cell senescence by regulating SIRT1/p53/p21 pathway
Authors: Liu Wen , Zhu Xiaoying , Tang Ling , Shen Na , Cheng Fanjun , Zou Ping , You Yong , Yuan Guolin , Li Qing , Zhu Xiaojian 
Published: October 2022

AbstractAlthough tyrosine kinase inhibitors (TKIs) improve the prognosis of chronic myeloid leukemia (CML) patients, resistance to TKIs and residual leukemia stem cells (LSCs) inevitably become the bottleneck of cure. Therefore, we need to explore novel treatment strategies based on conventional treatment strategies. Our previous study found that CML cell senescence may be one of the main factors to achieve clinical cure of CML. Studies have shown that lipid metabolism plays a key role in cellular senescence. Here, we found that long-chain acyl-CoA synthetase 1 (ACSL1) was significantly up-regulated in senescent CML cells. Furthermore, we demonstrated that overexpression of ACSL1 induces senescence and inhibits cell growth in K562 cells by altering cell cycle progression, and enhances the proliferation-inhibiting effect of imatinib. Overexpression of ACSL1 enhances imatinib-induced tumorigenic decline in K562 cells in vivo. Knockdown of ACSL1 reverses imatinib-induced senescence in K562 cells. Mechanistically, overexpression of ACSL1 induced senescence in K562 cells via the SIRT1/p53/p21 axis. Collectively, our study showed that ACSL1 promotes imatinib-induced K562 cells senescence and tumor growth by regulating SIRT1/p53/p21 pathway. The ACSL1/SIRT1/p53 signal axis is a novel mechanism of cell senescence in CML and a new potential target for eradication of CML LSCs.
Transcriptome analysis and prediction of the metabolic state of stress-induced viable but non-culturable Bacillus subtilis cells
Authors: Morawska Luiza P. , Kuipers Oscar P. 
Published: October 2022

AbstractMany bacteria adapt their physiology and enter the viable but non-culturable state to survive prolonged exposure to adverse environmental conditions. The VBNC cells maintain active metabolism, membrane integrity and gene transcription. However, they lose the ability to form colonies on a conventional culture media. Thus, standard colony counting methods cannot detect these alive but dormant cells. The Gram-positive bacterium Bacillus subtilis was found to enter the VBNC state when pre-exposed to osmotic stress and treated with a lethal dose of kanamycin. These cells reduced their metabolic activity, ceased growth and division and became kanamycin-tolerant. Interestingly, despite active metabolism, the majority of the kanamycin tolerant cells could not be revived on LB agar. In this study, we use a robust RNA-Seq technique to elucidate the differences in transcriptional profiles of B. subtilis VBNC cells. A comparative analysis of differently expressed genes and operons performed in this study indicates high similarities in transcriptional responses of VBNC and kanamycin-sensitive cells to antibiotic treatment. Moreover, this work reveals that VBNC cells strongly upregulate genes involved in proline uptake and catabolism, suggesting a putative role of proline as nutrient in VBNC cells.
MicroRNA-25-5p negatively regulates TXNIP expression and relieves inflammatory responses of brain induced by lipopolysaccharide
Authors: Wang Jiabing , Ye Zhinan , Chen Yuan , Qiao Xinyu , Jin Yong 
Published: October 2022

AbstractSepsis is one of the most common causes of death in patients suffering from severe infection or injury. Currently, a specific effective therapy remains to be established. In the present study, miR-25-5p, miR-105, miR-106b-5p, miR-154-3p, miR-20b-5p, miR-295-3p, miR-291-3p, miR-301b, miR-352, and miR-93-5p were predicted to target TXNIP mRNA from the databases of miRDB, Targetscan, and microT-CDS. The luciferase reporter assay confirmed that miR-25-5p negatively regulates TXNIP expression. The ELISA analyses and western blotting demonstrated that miR-25-5p downregulated the production of IL-1β, IL-6, IL-8, and TNF-α in lipopolysaccharide (LPS)-stimulated cells or rats, as well as the protein levels of TXNIP, NLRP3, and cleaved caspase-1. In addition, miR-25-5p increased the cell viability and decreased the apoptosis in LPS-stimulated CTX TNA2 cells and reduced the abnormal morphology of the brain in LPS-stimulated rats. Besides, miR-25-5p decreased the relative mean fluorescence intensity of DCF in LPS-stimulated CTX TNA2 cell, apoptosis, and protein levels of MnSOD and catalase in LPS-stimulated brains. These findings indicate that miR-25-5p downregulated LPS-induced inflammatory responses, reactive oxygen species production, and brain damage, suggesting that miR-25-5p is a candidate treatment for septic encephalopathy.
Feasibility of transthoracic esophagectomy with a next-generation surgical robot
Authors: Puntambekar Shailesh , Bharambe Suyog , Pawar Swapnil , Chitale Mihir , Panse Mangesh 
Published: October 2022

AbstractRobot-assisted minimal access surgery (MAS), compared with conventional MAS, has shown a number of benefits across several therapeutic indications but its use for transthoracic esophagectomy (TTE) requires further evaluation. Here, we report the first-in-human series of major esophageal resections performed using a next-generation tele-operated robotic surgical system in a single center. Robot-assisted TTE was performed using the Versius Surgical System by a single surgeon to assess the robotic system’s ability to achieve tumor clearance (measured by R0 resection rates) whilst reducing anastomotic leakage rates. Intra- and post-operative outcomes such as median operative time, length of hospitalization, intra-operative blood loss, and the number of complications were also assessed. Fifty-seven patients underwent robot-assisted TTE between August 2019 and June 2021. All procedures were completed successfully with no unplanned conversions to alternative surgical methods. Estimated blood loss was minimal, and no adverse events, complications or deaths were reported. Our experience with the Versius Surgical System demonstrates its safe adoption and implementation for TTE.
Plant growth acceleration using a transparent Eu3+-painted UV-to-red conversion film
Authors: Shoji Sunao , Saito Hideyuki , Jitsuyama Yutaka , Tomita Kotono , Haoyang Qiang , Sakurai Yukiho , Okazaki Yuhei , Aikawa Kota , Konishi Yuki , Sasaki Kensei , Fushimi Koji , Kitagawa Yuichi , Suzuki Takashi , Hasegawa Yasuchika 
Published: October 2022

AbstractThe stimulation of photosynthesis is a strategy for achieving sustainable plant production. Red light is useful for plant growth because it is absorbed by chlorophyll pigments, which initiate natural photosynthetic processes. Ultraviolet (UV)-to-red wavelength-converting materials are promising candidates for eco-friendly plant cultures that do not require electric power. In this study, transparent films equipped with a UV-to-red wavelength-converting luminophore, the Eu3+ complex, were prepared on commercially available plastic films for plant growth experiments. The present Eu3+-based films absorb UV light and exhibit strong red luminescence under sunlight. Eu3+-painted films provide significant growth acceleration with size increment and biomass production for vegetal crops and trees in a northern region. The plants cultured with Eu3+-painted films had a 1.2-fold height and 1.4-fold total body biomass than those cultures without the Eu3+ luminophores. The present film can promote the plant production in fields of agriculture and forestry.
Hetastarch induced volume changes of starving adenoma and suggested mechanism of action
Authors: Jakabčin P. , Kello M. , Záň J. , Kolář J. , Uličný Jozef 
Published: October 2022

AbstractSubmucosal injection is often required step during endoscopic mucosal resection (EMR). In clinical practice we have observed that the EMR injection solution containing hetastarch (HES) lead to selective increase of the neoplasms volume, facilitating their resection. The aim of this study was to explore the possible mechanisms of such behaviour, which was not reported elsewhere. The HCT116 cell line of human colon cancer was exposed to the same EMR solution in vitro. The significant volume increase of HCT116 cells was observed, but only for starving cell culture, suggesting that the starving is essential for the neoplasms-specific volume change. We suggest, that for the iso-oncotic composition of the EMR submucosa injection solution the HES component is crucial, as it can be subject of the starch hydrolysis followed by facilitated transport of resulting monosaccharides from the submucosa into the neoplastic tissue.
The language of opinion change on social media under the lens of communicative action
Authors: Monti Corrado , Aiello Luca Maria , De Francisci Morales Gianmarco , Bonchi Francesco 
Published: October 2022

AbstractWhich messages are more effective at inducing a change of opinion in the listener? We approach this question within the frame of Habermas’ theory of communicative action, which posits that theillocutionary intentof the message (its pragmatic meaning) is the key. Thanks to recent advances in natural language processing, we are able to operationalize this theory by extracting the latent social dimensions of a message, namely archetypes of social intent of language, that come from social exchange theory. We identify key ingredients to opinion change by looking at more than 46k posts and more than 3.5M comments on Reddit’s , a debate forum where people try to change each other’s opinion and explicitly mark opinion-changing comments with a special flag calleddelta. Comments that express no intent are about 77% less likely to change the mind of the recipient, compared to comments that convey at least one social dimension. Among the various social dimensions, the ones that are most likely to produce an opinion change are knowledge, similarity, and trust, which resonates with Habermas’ theory of communicative action. We also find other new important dimensions, such as appeals to power or empathetic expressions of support. Finally, in line with theories of constructive conflict, yet contrary to the popular characterization of conflict as the bane of modern social media, our findings show that voicing conflict in the context of a structured public debate can promote integration, especially when it is used to counter another conflictive stance. By leveraging recent advances in natural language processing, our work provides an empirical framework for Habermas’ theory, finds concrete examples of its effects in the wild, and suggests its possible extension with a more faceted understanding of intent interpreted as social dimensions of language.
Bond-specific fragmentation of oligopeptides via electronic stopping of swift heavy ions in molecular films
Authors: Schneider P. , Keller P. , Schubert I. , Bender M. , Trautmann C. , Dürr M. 
Published: October 2022

AbstractHighly bond-specific fragmentation of oligopeptides induced by swift heavy ion (SHI) irradiation was investigated by means of mass spectrometry. In pronounced contrast to measurements of samples irradiated with keV ions, oligopeptides which were exposed to 946 MeV Au ions show a high abundance of specific fragments. The highly bond-specific nature of SHI-induced fragmentation is attributed to electronic stopping as the most relevant energy loss mechanism for SHI in the oligopeptide samples in combination with the subsequent coupling between the excited electronic and the atomic subsystem. Fragmentation induced by SHI is observed to be further influenced by the structure of the oligopeptides, suggesting that electronic excitation and/or the electronic-vibrational coupling depend on the details of the molecular structure.