bluuebunny/crossref_metadata_2025_split huggingface dataset:
The tectonic complex regulates membrane protein composition in the photoreceptor cilium
Authors: Truong Hanh M. , Cruz-Colón Kevin O. , Martínez-Márquez Jorge Y. , Willer Jason R. , Travis Amanda M. , Biswas Sondip K. , Lo Woo-Kuen , Bolz Hanno J. , Pearring Jillian N. 
Published: September 2023

AbstractThe primary cilium is a signaling organelle with a unique membrane composition maintained by a diffusional barrier residing at the transition zone. Many transition zone proteins, such as the tectonic complex, are linked to preserving ciliary composition but the mechanism remains unknown. To understand tectonic’s role, we generate a photoreceptor-specific Tctn1 knockout mouse. Loss of Tctn1 results in the absence of the entire tectonic complex and associated MKS proteins yet has minimal effects on the transition zone structure of rod photoreceptors. We find that the protein composition of the photoreceptor cilium is disrupted as non-resident membrane proteins accumulate in the cilium over time, ultimately resulting in photoreceptor degeneration. We further show that fluorescent rhodopsin moves faster through the transition zone in photoreceptors lacking tectonic, which suggests that the tectonic complex acts as a physical barrier to slow down membrane protein diffusion in the photoreceptor transition zone to ensure proper removal of non-resident membrane proteins.
Hyperactive learning for data-driven interatomic potentials
Authors: van der Oord Cas , Sachs Matthias , Kovács Dávid Péter , Ortner Christoph , Csányi Gábor 
Published: September 2023

AbstractData-driven interatomic potentials have emerged as a powerful tool for approximating ab initio potential energy surfaces. The most time-consuming step in creating these interatomic potentials is typically the generation of a suitable training database. To aid this process hyperactive learning (HAL), an accelerated active learning scheme, is presented as a method for rapid automated training database assembly. HAL adds a biasing term to a physically motivated sampler (e.g. molecular dynamics) driving atomic structures towards uncertainty in turn generating unseen or valuable training configurations. The proposed HAL framework is used to develop atomic cluster expansion (ACE) interatomic potentials for the AlSi10 alloy and polyethylene glycol (PEG) polymer starting from roughly a dozen initial configurations. The HAL generated ACE potentials are shown to be able to determine macroscopic properties, such as melting temperature and density, with close to experimental accuracy.
Bacterial pathogens deliver water- and solute-permeable channels to plant cells
Authors: Nomura Kinya , Andreazza Felipe , Cheng Jie , Dong Ke , Zhou Pei , He Sheng Yang 
Published: September 2023

AbstractMany animal- and plant-pathogenic bacteria use a type III secretion system to deliver effector proteins into host cells1,2. Elucidation of how these effector proteins function in host cells is critical for understanding infectious diseases in animals and plants3–5. The widely conserved AvrE-family effectors, including DspE in Erwinia amylovora and AvrE in Pseudomonas syringae, have a central role in the pathogenesis of diverse phytopathogenic bacteria6. These conserved effectors are involved in the induction of ‘water soaking’ and host cell death that are conducive to bacterial multiplication in infected tissues. However, the exact biochemical functions of AvrE-family effectors have been recalcitrant to mechanistic understanding for three decades. Here we show that AvrE-family effectors fold into a β-barrel structure that resembles bacterial porins. Expression of AvrE and DspE in Xenopus oocytes results in inward and outward currents, permeability to water and osmolarity-dependent oocyte swelling and bursting. Liposome reconstitution confirmed that the DspE channel alone is sufficient to allow the passage of small molecules such as fluorescein dye. Targeted screening of chemical blockers based on the predicted pore size (15–20 Å) of the DspE channel identified polyamidoamine dendrimers as inhibitors of the DspE/AvrE channels. Notably, polyamidoamines broadly inhibit AvrE and DspE virulence activities in Xenopus oocytes and during E. amylovora and P. syringae infections. Thus, we have unravelled the biochemical function of a centrally important family of bacterial effectors with broad conceptual and practical implications in the study of bacterial pathogenesis.
A framework for FAIR robotic datasets
Authors: Motta Corrado , Aracri Simona , Ferretti Roberta , Bibuli Marco , Bruzzone Gabriele , Caccia Massimo , Odetti Angelo , Ferreira Fausto , de Pascalis Francesca 
Published: September 2023

AbstractIt is essential to publish and make available environmental data gathered by emerging robotic platforms to contribute to the Global Ocean Observing System (GOOS), supported by the United Nations - Decade of Ocean Science for Sustainable Development (2021–2030). The transparency of these unique observational datasets needs to be supported by the corresponding robotic records. The data describing the observational platform behaviour and its performance are necessary to validate the environmental data and repeat consistently the in-situ robotic deployment. The Free and Open Source Software (FOSS), proposed in this manuscript, describes how, using the established approach in Earth Sciences, the data characterising marine robotic missions can be formatted and shared following the FAIR (Findable, Accessible, Interoperable, Reusable) principles. The manuscript is a step-by-step guide to render marine robotic telemetry FAIR and publishable. State-of-the-art protocols for metadata and data formatting are proposed, applied and integrated automatically using Jupyter Notebooks to maximise visibility and ease of use. The method outlined here aims to be a first fundamental step towards FAIR interdisciplinary observational science.
Viral-like TLR3 induction of cytokine networks and α-synuclein are reduced by complement C3 blockade in mouse brain
Authors: Thomas Ria , Connolly Kyle J. , Brekk Oeystein R. , Hinrich Anthony J. , Hastings Michelle L. , Isacson Ole , Hallett Penelope J. 
Published: September 2023

AbstractInflammatory processes and mechanisms are of central importance in neurodegenerative diseases. In the brain, α-synucleinopathies such as Parkinson’s disease (PD) and Lewy body dementia (LBD) show immune cytokine network activation and increased toll like receptor 3 (TLR3) levels for viral double-stranded RNA (dsRNA). Brain inflammatory reactions caused by TLR3 activation are also relevant to understand pathogenic cascades by viral SARS-CoV-2 infection causing post- COVID-19 brain-related syndromes. In the current study, following regional brain TLR3 activation induced by dsRNA in mice, an acute complement C3 response was seen at 2 days. A C3 splice-switching antisense oligonucleotide (ASO) that promotes the splicing of a non-productive C3 mRNA, prevented downstream cytokines, such as IL-6, and α-synuclein changes. This report is the first demonstration that α-synuclein increases occur downstream of complement C3 activation. Relevant to brain dysfunction, post-COVID-19 syndromes and pathological changes leading to PD and LBD, viral dsRNA TLR3 activation in the presence of C3 complement blockade further revealed significant interactions between complement systems, inflammatory cytokine networks and α-synuclein changes.
Antimicrobial and anticarcinogenic activity of bioactive peptides derived from abalone viscera (Haliotis fulgens and Haliotis corrugata)
Authors: Rivera-Pérez Crisalejandra , Ponce González Xolotl Paloma , Hernández-Savedra Norma Yolanda 
Published: September 2023

AbstractBioactive peptides have been studied in several sources due to their valuable potential in the pharmaceutical and food industries. Abalone viscera, which are normally discarded as byproducts, are a rich source of protein. Thus, the aim of this study was to explore the potential bioactivity of peptides derived from abalone viscera (Haliotis fulgens and Haliotis corrugata) after hydrolysis with a commercial mixture of enzymes. The hydrolysates obtained were fractionated using gel filtration chromatography. The resulting hydrolysate fractions were investigated for their antimicrobial and cytotoxic activities, including the expression of gelatinases mmp-2 and mmp-9 in human prostate cancer cell lines (PC3). Results showed antimicrobial activity for protein fractions of H. corrugata against Proteus mirabilis and Pseudomona aeuroginosa (66.2–116.25 kDa), Bacillus subtilis (6.5–21.5 kDa), and Aspergillus niger (97.4–116.25 kDa), while H. fulgens peptide fractions (200–31 kDa) displayed activity against six bacterial strains, and fractions from 116.25 to 21.5 kDa had effects on the fungus A. niger, Alternaria alternata, and Aspergillus flavus. Additionally, protein fractions displayed cytotoxic activity, inhibiting 30.4–53.8% of PC3 cellular growth. Selected fractions decreased the PMA-induced and not-induced expressions of mmp-2 and mmp-9 in PC3 cells. Abalone viscera, as byproducts, can be used as a potential source of antimicrobial and anticancer peptides.
Soil water dynamics and biomass production of young rooibos (Aspalathus linearis) plants
Authors: van Schalkwyk Roeline , Hoffman J. Eduard , Hardie Ailsa G. , van Zyl Johan L. 
Published: September 2023

AbstractRooibos (Aspalathus linearis) is endemic to certain regions of the Western- and Northern Cape of South Africa, where it is also commercially grown. Being low-rainfall regions, information on the soil water balance of rooibos is essential, but such data is limited. Consequently, the effect of inorganic fertilisation and soil depth on soil water dynamics in a young rooibos plantation at Nardouwsberg, Western Cape were studied. Soil water content of plots planted to unfertilised and fertilised plants as well as that of bare soil were determined over the duration of the 2016/17 season. All treatments were replicated on shallow and deep soils sites and plant growth was determined at the end of the season. At the end of the study, the profile soil water content and evapotranspiration of the bare and planted plots were similar which prove that fallowing (water harvesting) is not an option in the sandy soils of this region. With the exception of the 20−30 cm root zone of the planted plots at the deep site, the water content decreased to levels below the permanent wilting point in the soil profile during summer. It was concluded that rooibos plants could survive through an adapted root system. A further survival method was proposed, involving moisture moved through evaporation from the deeper soil layers into the drying-front in the ~ 10−30 cm soil layer where a condensation-evaporation cycle enables rooibos to harvest small amounts of water. The highest shoot biomass with the longest taproot resulted from the unfertilised treatment on the deep soil thanks to higher soil water content, whereas the shoot and root biomass of the fertilised treatment at both sites were low due to high P soil concentration. This study revealed that unfertilised plants on deeper soils result in higher rooibos production under drought conditions.
Rapid cold plasma synthesis of cobalt metal–organic framework/reduced graphene oxide nanocomposites for use as supercapacitor electrodes
Authors: Karimzadeh Zeinab , Shokri Babak , Morsali Ali 
Published: September 2023

AbstractMetal–organic frameworks (MOFs) are recognized as a desirable class of porous materials for energy storage applications, despite their limited conductivity. In the present study, Co-MOF-71 was fabricated as a high-performance supercapacitor electrode at ambient temperature using a fast and straightforward, one-pot cold plasma method. A supercapacitor electrode based on Co-MOF@rGO was also synthesized by adding reduced graphene oxide (rGO) during processing to increase the capacitance retention and stability after 4000 cycles from 80 to 95.4%. The Co-MOF-71 electrode provided a specific capacitance (Cs) of 651.7 Fg−1 at 1 Ag−1, whereas the Co-MOF@rGO electrode produced a Cs value of 967.68 Fg−1 at 1 Ag−1. In addition, we fabricated an asymmetric device (Co-MOF@rGO||AC) using Co-MOF-rGO as a high-rate positive electrode and activated carbon (AC) as a negative electrode. This hybrid device has a remarkable specific energy and power density. The combination of MOFs with reduced graphene oxide (rGO) in a cold plasma environment resulted in the formation of a three-dimensional nanostructure composed of nanosheets. This nanostructure exhibited an increased number of electroactive sites, providing benefits for energy storage applications.
Comparison of sampling methods for the determination of volatile organic compounds in consumer aerosol sprays
Authors: Jung Sungyo , Lee Myoungho , Do Geonho , kim Boowook , Lee Kiyoung , Zoh Kyung-Duk , Yoon Chungsik 
Published: September 2023

AbstractMany studies have evaluated the hazardous substances contained in various household chemical products. However, for aerosol spray products there is currently no international standard sampling method for use in a component analysis. The aim of this study was to develop an appropriate sampling method for the analysis of volatile organic compounds (VOCs) in consumer aerosol sprays. Two different sampling methods, spraying (into a vial) and perforating (and transferring the contents into a vial), were used to evaluate the levels of 16 VOC components in eight different aerosol spray products. All eight products contained trace amounts of hazardous VOCs, and a quantitative analysis showed that, for the same product, VOC concentrations were higher when spraying than when perforating. Using the spraying method, average toluene, ethylbenzene, p-xylene, o-xylene, and styrene concentrations were 1.80-, 2.10- 2.25-, 2.03-fold, and 1.28-fold higher, respectively, than when using the perforating method. The spraying method may provide more realistic estimates of the user's exposure to harmful substances and the associated health risks when using spray products. Of the two representative methods widely used to analyze harmful substances in consumer aerosol sprays, the spraying method is recommended over the perforating method for the analysis of VOCs.
Migratory destinations and spatial structuring of humpback whales (Megaptera novaeangliae) wintering off Nicaragua
Authors: De Weerdt Joëlle , Pacheco Aldo S. , Calambokidis John , Castaneda Melvin , Cheeseman Ted , Frisch-Jordán Astrid , Garita Alpízar Frank , Hayslip Craig , Martínez-Loustalot Pamela , Palacios Daniel M. , Quintana-Rizzo Ester , Ransome Nicola , Urbán Ramírez Jorge , Clapham Phillip , Van der Stocken Tom 
Published: September 2023

AbstractUnderstanding the migratory patterns of large whales is of conservation importance, especially in identifying threats to specific populations. Migration ecology, including migratory destinations, movements and site fidelity for humpback whales (Megaptera novaeangliae) remain poorly studied in parts of the range of the Central America population, considered endangered under the United States Endangered Species Act. This study aimed to investigate the migratory destinations of humpback whales sighted at two study sites in Nicaragua, which are part of the Central America population. A ten-year photographic database of humpback whales observed off Nicaragua was combined with citizen science contributions and sightings from dedicated research programs. The resulting image collection was compared with available historical photo identifications and databases using an automated image recognition algorithm. This approach yielded 36 years of photographic identification totaling 431 recaptures in Nicaragua (2006–2008 and 2016–2021) and 2539 recaptures (1986–2020) in both feeding and breeding grounds of 176 unique individuals sighted in Nicaragua. Our results showed that photo-identified whales were recaptured between October and April in breeding grounds and year-round in feeding grounds between British Columbia and California, with peak recaptures between June and October. Our study provided first-time evidence on fine-scale site affinity of individual humpback whales within Nicaraguan waters and to other breeding and feeding grounds.
Short-term triphenyltin exposure alters microbial homeostasis in the silkworm (Bombyx mori) midgut
Authors: Zhou Wenlin , Zhang Xing , Chen Xuedong , Wu Xuehui , Ye Aihong , Cao Jinru , Hu Xiaolong 
Published: September 2023

AbstractTriphenyltin (TPT) is a widespread synthetic chemical used in many fields and its potential risk to organisms has been comprehensively investigated using different animal models and species. Currently, little is known about the effects of TPT exposure on microbial midgut diversity, therefore we explored these effects in the lepidopterous silkworm model using 16S rDNA sequencing. In total, 5273 and 5065 operational taxonomic units (OTUs) were identified in control and TPT-exposure group samples, ranging from 424 to 728 OTUs/sample. Alpha-diversity analyses revealed that TPT exposure induced the fluctuations of gut microbial diversity and abundance while beta-diversity analyses identified a distinct impact on major gut microbiota components. In our microbiome analyses, 23 phyla and 353 genera were recognized in the control group, while 20 phyla and 358 genera were recognized in the TPT exposure group. At the genus level, midgut microbiota were composed of several predominant bacterial genera, including Muribaculaceae, Lactobacillus, and UCG-010. In the TPT exposure group, o__Bacillales, f__Bacillaceae, and f__Caldicoprobacteraceae abundance was relatively high, while f__Oscillospiraceae, f__Fusobacteriaceae, and f__SC_I_84 abundance was relatively high in the control group. Gene function analyses in silkworm microbiota after TPT exposure showed that biosynthesis of ansamycins, fructose and mannose metabolism, glycerolipid metabolism, type II diabetes mellitus, glycolysis/gluconeogenesis, lipid metabolism, translation proteins, atrazine degradation, DNA repair and recombination proteins, nicotinate and nicotinamide metabolism were significantly increased. Collectively, our silkworm model identified gut microbial diversity risks and the adverse effects from TPT exposure, which were similar to other aquatic animals. Therefore, TPT levels in environmental samples must be monitored to prevent ecological harm.
Enhanced antibody-antigen structure prediction from molecular docking using AlphaFold2
Authors: Gaudreault Francis , Corbeil Christopher R. , Sulea Traian 
Published: September 2023

AbstractPredicting the structure of antibody-antigen complexes has tremendous value in biomedical research but unfortunately suffers from a poor performance in real-life applications. AlphaFold2 (AF2) has provided renewed hope for improvements in the field of protein–protein docking but has shown limited success against antibody-antigen complexes due to the lack of co-evolutionary constraints. In this study, we used physics-based protein docking methods for building decoy sets consisting of low-energy docking solutions that were either geometrically close to the native structure (positives) or not (negatives). The docking models were then fed into AF2 to assess their confidence with a novel composite score based on normalized pLDDT and pTMscore metrics after AF2 structural refinement. We show benefits of the AF2 composite score for rescoring docking poses both in terms of (1) classification of positives/negatives and of (2) success rates with particular emphasis on early enrichment. Docking models of at least medium quality present in the decoy set, but not necessarily highly ranked by docking methods, benefitted most from AF2 rescoring by experiencing large advances towards the top of the reranked list of models. These improvements, obtained without any calibration or novel methodologies, led to a notable level of performance in antibody-antigen unbound docking that was never achieved previously.
A new fluorescence-based approach for direct visualization of coat formation during sporulation in Bacillus cereus
Authors: Lablaine Armand , Chamot Stéphanie , Serrano Mónica , Billaudeau Cyrille , Bornard Isabelle , Carballido-López Rut , Carlin Frédéric , Henriques Adriano O. , Broussolle Véronique 
Published: September 2023

AbstractThe human pathogenic bacteria Bacillus cereus, Bacillus anthracis and the entomopathogenic Bacillus thuringiensis form spores encased in a protein coat surrounded by a balloon-like exosporium. These structures mediate spore interactions with its environment, including the host immune system, control the transit of molecules that trigger germination and thus are essential for the spore life cycle. Formation of the coat and exosporium has been traditionally visualized by transmission electronic microscopy on fixed cells. Recently, we showed that assembly of the exosporium can be directly observed in live B. cereus cells by super resolution-structured illumination microscopy (SR-SIM) using the membrane MitoTrackerGreen (MTG) dye. Here, we demonstrate that the different steps of coat formation can also be visualized by SR-SIM using MTG and SNAP-cell TMR-star dyes during B. cereus sporulation. We used these markers to characterize a subpopulation of engulfment-defective B. cereus cells that develops at a suboptimal sporulation temperature. Importantly, we predicted and confirmed that synthesis and accumulation of coat material, as well as synthesis of the σK-dependent protein BxpB, occur in cells arrested during engulfment. These results suggest that, unlike the well-studied model organism Bacillus subtilis, the activity of σK is not strictly linked to the state of forespore development in B. cereus.
In-situ δ18O and 87Sr/86Sr proxies in an unconformable clastic unit at the Ordovician–Silurian transition
Authors: Park Chaewon , Song Yungoo , Kim Namsoo , Choi Sung-Ja , Chwae Ueechan , Jang Yirang , Kwon Sanghoon , Kim Jeongmin , Kim Ha , Jeong Youn-Joong 
Published: September 2023

AbstractClastic successions found in the carbonate platform of continental margin during the Ordovician–Silurian Transition (OST) period are archives for interpreting paleo-depositional systems. Here, we report in-situ δ18Oquartz and 87Sr/86Srcarbonate isotope chemo-stratigraphy for an unconformable clastic unit from the Cathaysia terrane that rifted off the Gondwana Supercontinent in the Early Paleozoic Era. Our results suggest a depositional proxy and model for geological events attributed to rapid changes in the sedimentary environment during the OST period. Importantly, these results present crucial clues that infer the influence of Paleo-Tethys Sea opening, global eustatic regression, and rapid sedimentary provenance change. Our study provides insight into paleo-tracer that could be a key method for interpreting depositional system of carbonate platform based on in-situ mineral isotope chemo-stratigraphy that preserves the original value of provenance and geochemical condition.