bluuebunny/crossref_metadata_2025_split huggingface dataset:
Upcycling fish scales through heating for steganography and Rhodamine B adsorption application
Authors: Sow Malcolm Miao Geng , Zhang Zheng , Sow Chorng Haur , Lim Sharon Xiaodai 
Published: October 2023

AbstractWith increasing population and limited resources, a potential route for improving sustainability is increased reuse of waste materials. By re-looking at wastes, interesting properties and multifunctionalities can be discovered in materials previously explored. Despite years of research on bio-compatible fish scales, there is limited study on the fluorescence property of this abundant waste material. Controlled denaturation of collagen and introduction of defects can serve as a means to transform the fluorescence property of these fish scale wastes while providing more adsorption sites for pollutant removal, turning multifunctional fish scales into a natural steganographic material for transmitting text and images at both the macroscopic and microscopic levels and effectively removing Rhodamine B pollutants (91 % removal) within a short contact time (10 minutes). Our work offers a glimpse into the realm of engineering defects-induced fluorescence in natural material with potential as bio-compatible fluorescence probes while encouraging multidimensional applicability to be established in otherwise overlooked waste resources.
Structural basis of dimerization of chemokine receptors CCR5 and CXCR4
Authors: Di Marino Daniele , Conflitti Paolo , Motta Stefano , Limongelli Vittorio 
Published: October 2023

AbstractG protein-coupled receptors (GPCRs) are prominent drug targets responsible for extracellular-to-intracellular signal transduction. GPCRs can form functional dimers that have been poorly characterized so far. Here, we show the dimerization mechanism of the chemokine receptors CCR5 and CXCR4 by means of an advanced free-energy technique named coarse-grained metadynamics. Our results reproduce binding events between the GPCRs occurring in the minute timescale, revealing a symmetric and an asymmetric dimeric structure for each of the three investigated systems, CCR5/CCR5, CXCR4/CXCR4, and CCR5/CXCR4. The transmembrane helices TM4-TM5 and TM6-TM7 are the preferred binding interfaces for CCR5 and CXCR4, respectively. The identified dimeric states differ in the access to the binding sites of the ligand and G protein, indicating that dimerization may represent a fine allosteric mechanism to regulate receptor activity. Our study offers structural basis for the design of ligands able to modulate the formation of CCR5 and CXCR4 dimers and in turn their activity, with therapeutic potential against HIV, cancer, and immune-inflammatory diseases.
Redundancy and the role of protein copy numbers in the cell polarization machinery of budding yeast
Authors: Brauns Fridtjof , Iñigo de la Cruz Leila , Daalman Werner K.-G. , de Bruin Ilse , Halatek Jacob , Laan Liedewij , Frey Erwin 
Published: October 2023

AbstractHow can a self-organized cellular function evolve, adapt to perturbations, and acquire new sub-functions? To make progress in answering these basic questions of evolutionary cell biology, we analyze, as a concrete example, the cell polarity machinery of Saccharomyces cerevisiae. This cellular module exhibits an intriguing resilience: it remains operational under genetic perturbations and recovers quickly and reproducibly from the deletion of one of its key components. Using a combination of modeling, conceptual theory, and experiments, we propose that multiple, redundant self-organization mechanisms coexist within the protein network underlying cell polarization and are responsible for the module’s resilience and adaptability. Based on our mechanistic understanding of polarity establishment, we hypothesize that scaffold proteins, by introducing new connections in the existing network, can increase the redundancy of mechanisms and thus increase the evolvability of other network components. Moreover, our work gives a perspective on how a complex, redundant cellular module might have evolved from a more rudimental ancestral form.
A single nanobody neutralizes multiple epochally evolving human noroviruses by modulating capsid plasticity
Authors: Salmen Wilhelm , Hu Liya , Bok Marina , Chaimongkol Natthawan , Ettayebi Khalil , Sosnovtsev Stanislav V. , Soni Kaundal , Ayyar B. Vijayalakshmi , Shanker Sreejesh , Neill Frederick H. , Sankaran Banumathi , Atmar Robert L. , Estes Mary K. , Green Kim Y. , Parreño Viviana , Prasad B. V. Venkataram 
Published: October 2023

AbstractAcute gastroenteritis caused by human noroviruses (HuNoVs) is a significant global health and economic burden and is without licensed vaccines or antiviral drugs. The GII.4 HuNoV causes most epidemics worldwide. This virus undergoes epochal evolution with periodic emergence of variants with new antigenic profiles and altered specificity for histo-blood group antigens (HBGA), the determinants of cell attachment and susceptibility, hampering the development of immunotherapeutics. Here, we show that a llama-derived nanobody M4 neutralizes multiple GII.4 variants with high potency in human intestinal enteroids. The crystal structure of M4 complexed with the protruding domain of the GII.4 capsid protein VP1 revealed a conserved epitope, away from the HBGA binding site, fully accessible only when VP1 transitions to a “raised” conformation in the capsid. Together with dynamic light scattering and electron microscopy of the GII.4 VLPs, our studies suggest a mechanism in which M4 accesses the epitope by altering the conformational dynamics of the capsid and triggering its disassembly to neutralize GII.4 infection.
MANF stimulates autophagy and restores mitochondrial homeostasis to treat autosomal dominant tubulointerstitial kidney disease in mice
Authors: Kim Yeawon , Li Chuang , Gu Chenjian , Fang Yili , Tycksen Eric , Puri Anuradhika , Pietka Terri A. , Sivapackiam Jothilingam , Kidd Kendrah , Park Sun-Ji , Johnson Bryce G. , Kmoch Stanislav , Duffield Jeremy S. , Bleyer Anthony J. , Jackrel Meredith E. , Urano Fumihiko , Sharma Vijay , Lindahl Maria , Chen Ying Maggie 
Published: October 2023

AbstractMisfolded protein aggregates may cause toxic proteinopathy, including autosomal dominant tubulointerstitial kidney disease due to uromodulin mutations (ADTKD-UMOD), a leading hereditary kidney disease. There are no targeted therapies. In our generated mouse model recapitulating human ADTKD-UMOD carrying a leading UMOD mutation, we show that autophagy/mitophagy and mitochondrial biogenesis are impaired, leading to cGAS-STING activation and tubular injury. Moreover, we demonstrate that inducible tubular overexpression of mesencephalic astrocyte-derived neurotrophic factor (MANF), a secreted endoplasmic reticulum protein, after the onset of disease stimulates autophagy/mitophagy, clears mutant UMOD, and promotes mitochondrial biogenesis through p-AMPK enhancement, thus protecting kidney function in our ADTKD mouse model. Conversely, genetic ablation of MANF in the mutant thick ascending limb tubular cells worsens autophagy suppression and kidney fibrosis. Together, we have discovered MANF as a biotherapeutic protein and elucidated previously unknown mechanisms of MANF in the regulation of organelle homeostasis, which may have broad therapeutic applications to treat various proteinopathies.
A human lung alveolus-on-a-chip model of acute radiation-induced lung injury
Authors: Dasgupta Queeny , Jiang Amanda , Wen Amy M. , Mannix Robert J. , Man Yuncheng , Hall Sean , Javorsky Emilia , Ingber Donald E. 
Published: October 2023

AbstractAcute exposure to high-dose gamma radiation due to radiological disasters or cancer radiotherapy can result in radiation-induced lung injury (RILI), characterized by acute pneumonitis and subsequent lung fibrosis. A microfluidic organ-on-a-chip lined by human lung alveolar epithelium interfaced with pulmonary endothelium (Lung Alveolus Chip) is used to model acute RILI in vitro. Both lung epithelium and endothelium exhibit DNA damage, cellular hypertrophy, upregulation of inflammatory cytokines, and loss of barrier function within 6 h of radiation exposure, although greater damage is observed in the endothelium. The radiation dose sensitivity observed on-chip is more like the human lung than animal preclinical models. The Alveolus Chip is also used to evaluate the potential ability of two drugs - lovastatin and prednisolone - to suppress the effects of acute RILI. These data demonstrate that the Lung Alveolus Chip provides a human relevant alternative for studying the molecular basis of acute RILI and may be useful for evaluation of new radiation countermeasure therapeutics.
Spatial and temporal dynamics of West Nile virus between Africa and Europe
Authors: Mencattelli Giulia , Ndione Marie Henriette Dior , Silverj Andrea , Diagne Moussa Moise , Curini Valentina , Teodori Liana , Di Domenico Marco , Mbaye Rassoul , Leone Alessandra , Marcacci Maurilia , Gaye Alioune , Ndiaye ElHadji , Diallo Diawo , Ancora Massimo , Secondini Barbara , Di Lollo Valeria , Mangone Iolanda , Bucciacchio Andrea , Polci Andrea , Marini Giovanni , Rosà Roberto , Segata Nicola , Fall Gamou , Cammà Cesare , Monaco Federica , Diallo Mawlouth , Rota-Stabelli Omar , Faye Oumar , Rizzoli Annapaola , Savini Giovanni 
Published: October 2023

AbstractIt is unclear whether West Nile virus (WNV) circulates between Africa and Europe, despite numerous studies supporting an African origin and high transmission in Europe. We integrated genomic data with geographic observations and phylogenetic and phylogeographic inferences to uncover the spatial and temporal viral dynamics of WNV between these two continents. We focused our analysis towards WNV lineages 1 (L1) and 2 (L2), the most spatially widespread and pathogenic WNV lineages. Our study shows a Northern-Western African origin of L1, with back-and-forth exchanges between West Africa and Southern-Western Europe; and a Southern African origin of L2, with one main introduction from South Africa to Europe, and no back introductions observed. We also noticed a potential overlap between L1 and L2 Eastern and Western phylogeography and two Afro-Palearctic bird migratory flyways. Future studies linking avian and mosquito species susceptibility, migratory connectivity patterns, and phylogeographic inference are suggested to elucidate the dynamics of emerging viruses.
Fibrocystin/Polyductin releases a C-terminal fragment that translocates into mitochondria and suppresses cystogenesis
Authors: Walker Rebecca V , Yao Qin , Xu Hangxue , Maranto Anthony , Swaney Kristen F , Ramachandran Sreekumar , Li Rong , Cassina Laura , Polster Brian M , Outeda Patricia , Boletta Alessandra , Watnick Terry , Qian Feng 
Published: October 2023

AbstractFibrocystin/Polyductin (FPC), encoded by PKHD1, is associated with autosomal recessive polycystic kidney disease (ARPKD), yet its precise role in cystogenesis remains unclear. Here we show that FPC undergoes complex proteolytic processing in developing kidneys, generating three soluble C-terminal fragments (ICDs). Notably, ICD15, contains a novel mitochondrial targeting sequence at its N-terminus, facilitating its translocation into mitochondria. This enhances mitochondrial respiration in renal epithelial cells, partially restoring impaired mitochondrial function caused by FPC loss. FPC inactivation leads to abnormal ultrastructural morphology of mitochondria in kidney tubules without cyst formation. Moreover, FPC inactivation significantly exacerbates renal cystogenesis and triggers severe pancreatic cystogenesis in a Pkd1 mouse mutant Pkd1V/V in which cleavage of Pkd1-encoded Polycystin-1 at the GPCR Proteolysis Site is blocked. Deleting ICD15 enhances renal cystogenesis without inducing pancreatic cysts in Pkd1V/V mice. These findings reveal a direct link between FPC and a mitochondrial pathway through ICD15 cleavage, crucial for cystogenesis mechanisms.
Expanding PROTACtable genome universe of E3 ligases
Authors: Liu Yuan , Yang Jingwen , Wang Tianlu , Luo Mei , Chen Yamei , Chen Chengxuan , Ronai Ze’ev , Zhou Yubin , Ruppin Eytan , Han Leng 
Published: October 2023

AbstractProteolysis-targeting chimera (PROTAC) and other targeted protein degradation (TPD) molecules that induce degradation by the ubiquitin-proteasome system (UPS) offer new opportunities to engage targets that remain challenging to be inhibited by conventional small molecules. One fundamental element in the degradation process is the E3 ligase. However, less than 2% amongst hundreds of E3 ligases in the human genome have been engaged in current studies in the TPD field, calling for the recruiting of additional ones to further enhance the therapeutic potential of TPD. To accelerate the development of PROTACs utilizing under-explored E3 ligases, we systematically characterize E3 ligases from seven different aspects, including chemical ligandability, expression patterns, protein-protein interactions (PPI), structure availability, functional essentiality, cellular location, and PPI interface by analyzing 30 large-scale data sets. Our analysis uncovers several E3 ligases as promising extant PROTACs. In total, combining confidence score, ligandability, expression pattern, and PPI, we identified 76 E3 ligases as PROTAC-interacting candidates. We develop a user-friendly and flexible web portal (https://hanlaboratory.com/E3Atlas/) aimed at assisting researchers to rapidly identify E3 ligases with promising TPD activities against specifically desired targets, facilitating the development of these therapies in cancer and beyond.
Controlling the selectivity of the hydrogenolysis of polyamides catalysed by ceria-supported metal nanoparticles
Authors: Wu XinBang , Lee Wei-Tse , Turnell-Ritson Roland C. , Delannoi Pauline C. L. , Lin Kun-Han , Dyson Paul J. 
Published: October 2023

AbstractCatalytic hydrogenolysis is a promising approach to transform waste plastic into valuable chemicals. However, the transformation of N-containing polymers, such as polyamides (i.e. nylon), remains under-investigated, particularly by heterogeneous catalysis. Here, we demonstrate the hydrogenolysis of various polyamides catalysed by platinum-group metal nanoparticles supported on CeO2. Ru/CeO2 and Pt/CeO2 are both highly active but display different selectivity; Ru/CeO2 is selective for the conversion of all polyamides into water, ammonia, and methane, whereas Pt/CeO2 yields hydrocarbons retaining the carbon backbone of the parent polyamide. Density functional theory computations illustrate that Pt nanoparticles require higher activation energy for carbon−carbon bond cleavage than Ru nanoparticles, rationalising the observed selectivity. The high activity and product selectivity of both catalysts was maintained when converting real-world polyamide products, such as fishing net. This study provides a mechanistic basis for heterogeneously catalysed polyamide hydrogenolysis, and a new approach to the valorisation of polyamide containing waste.
Controls of thermal response of temperate lakes to atmospheric warming
Authors: Zhou Jian , Leavitt Peter R. , Rose Kevin C. , Wang Xiwen , Zhang Yibo , Shi Kun , Qin Boqiang 
Published: October 2023

AbstractAtmospheric warming heats lakes, but the causes of variation among basins are poorly understood. Here, multi-decadal profiles of water temperatures, trophic state, and local climate from 345 temperate lakes are combined with data on lake geomorphology and watershed characteristics to identify controls of the relative rates of temperature change in water (WT) and air (AT) during summer. We show that differences in local climate (AT, wind speed, humidity, irradiance), land cover (forest, urban, agriculture), geomorphology (elevation, area/depth ratio), and water transparency explain >30% of the difference in rate of lake heating compared to that of the atmosphere. Importantly, the rate of lake heating slows as air warms (P < 0.001). Clear, cold, and deep lakes, especially at high elevation and in undisturbed catchments, are particularly responsive to changes in atmospheric temperature. We suggest that rates of surface water warming may decline relative to the atmosphere in a warmer future, particularly in sites already experiencing terrestrial development or eutrophication.
Photoelectrochemical oxidative C(sp3)−H borylation of unactivated hydrocarbons
Authors: Zhong Ping-Fu , Tu Jia-Lin , Zhao Yating , Zhong Nan , Yang Chao , Guo Lin , Xia Wujiong 
Published: October 2023

AbstractOrganoboron compounds are of high significance in organic synthesis due to the unique versatility of boryl substituents to access further modifications. The high demand for the incorporation of boryl moieties into molecular structures has witnessed significant progress, particularly in the C(sp3)−H borylation of hydrocarbons. Taking advantage of special characteristics of photo/electrochemistry, we herein describe the development of an oxidative C(sp3)−H borylation reaction under metal- and oxidant-free conditions, enabled by photoelectrochemical strategy. The reaction exhibits broad substrate scope (>57 examples), and includes the use of simple alkanes, halides, silanes, ketones, esters and nitriles as viable substrates. Notably, unconventional regioselectivity of C(sp3)−H borylation is achieved, with the coupling site of C(sp3)−H borylation selectively located in the distal methyl group. Our method is operationally simple and easily scalable, and offers a feasible approach for the one-step synthesis of high-value organoboron building blocks from simple hydrocarbons, which would provide ample opportunities for drug discovery.
Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells
Authors: Calandrelli Riccardo , Wen Xingzhao , Charles Richard John Lalith , Luo Zhifei , Nguyen Tri C. , Chen Chien-Ju , Qi Zhijie , Xue Shuanghong , Chen Weizhong , Yan Zhangming , Wu Weixin , Zaleta-Rivera Kathia , Hu Rong , Yu Miao , Wang Yuchuan , Li Wenbo , Ma Jian , Ren Bing , Zhong Sheng 
Published: October 2023

AbstractThe interphase genome is dynamically organized in the nucleus and decorated with chromatin-associated RNA (caRNA). It remains unclear whether the genome architecture modulates the spatial distribution of caRNA and vice versa. Here, we generate a resource of genome-wide RNA-DNA and DNA-DNA contact maps in human cells. These maps reveal the chromosomal domains demarcated by locally transcribed RNA, hereafter termed RNA-defined chromosomal domains. Further, the spreading of caRNA is constrained by the boundaries of topologically associating domains (TADs), demonstrating the role of the 3D genome structure in modulating the spatial distribution of RNA. Conversely, stopping transcription or acute depletion of RNA induces thousands of chromatin loops genome-wide. Activation or suppression of the transcription of specific genes suppresses or creates chromatin loops straddling these genes. Deletion of a specific caRNA-producing genomic sequence promotes chromatin loops that straddle the interchromosomal target sequences of this caRNA. These data suggest a feedback loop where the 3D genome modulates the spatial distribution of RNA, which in turn affects the dynamic 3D genome organization.
Methylphosphonate-driven methane formation and its link to primary production in the oligotrophic North Atlantic
Authors: von Arx Jan N. , Kidane Abiel T. , Philippi Miriam , Mohr Wiebke , Lavik Gaute , Schorn Sina , Kuypers Marcel M. M. , Milucka Jana 
Published: October 2023

AbstractMethylphosphonate is an organic phosphorus compound used by microorganisms when phosphate, a key nutrient limiting growth in most marine surface waters, becomes unavailable. Microbial methylphosphonate use can result in the formation of methane, a potent greenhouse gas, in oxic waters where methane production is traditionally unexpected. The extent and controlling factors of such aerobic methane formation remain underexplored. Here, we show high potential net rates of methylphosphonate-driven methane formation (median 0.4 nmol methane L−1 d−1) in the upper water column of the western tropical North Atlantic. The rates are repressed but still quantifiable in the presence of in-situ or added phosphate, suggesting that some methylphosphonate-driven methane formation persists in phosphate-replete waters. The genetic potential for methylphosphonate utilisation is present in and transcribed by key photo- and heterotrophic microbial taxa, such as Pelagibacterales, SAR116, and Trichodesmium. While the large cyanobacterial nitrogen-fixers dominate in the surface layer, phosphonate utilisation by Alphaproteobacteria appears to become more important in deeper depths. We estimate that at our study site, a substantial part (median 11%) of the measured surface carbon fixation can be sustained by phosphorus liberated from phosphonate utilisation, highlighting the ecological importance of phosphonates in the carbon cycle of the oligotrophic ocean.
Electrochemically induced crystalline-to-amorphization transformation in sodium samarium silicate solid electrolyte for long-lasting sodium metal batteries
Authors: Sun Ge , Lou Chenjie , Yi Boqian , Jia Wanqing , Wei Zhixuan , Yao Shiyu , Lu Ziheng , Chen Gang , Shen Zexiang , Tang Mingxue , Du Fei 
Published: October 2023

AbstractExploiting solid electrolyte (SE) materials with high ionic conductivity, good interfacial compatibility, and conformal contact with electrodes is essential for solid-state sodium metal batteries (SSBs). Here we report a crystalline Na5SmSi4O12 SE which features high room-temperature ionic conductivity of 2.9 × 10−3 S cm−1 and a low activation energy of 0.15 eV. All-solid-state symmetric cell with Na5SmSi4O12 delivers excellent cycling life over 800 h at 0.15 mA h cm−2 and a high critical current density of 1.4 mA cm−2. Such excellent electrochemical performance is attributed to an electrochemically induced in-situ crystalline-to-amorphous (CTA) transformation propagating from the interface to the bulk during repeated deposition and stripping of sodium, which leads to faster ionic transport and superior interfacial properties. Impressively, the Na|Na5SmSi4O12|Na3V2(PO4)3 sodium metal batteries achieve a remarkable cycling performance over 4000 cycles (6 months) with no capacity loss. These results not only identify Na5SmSi4O12 as a promising SE but also emphasize the potential of the CTA transition as a promising mechanism towards long-lasting SSBs.
A biocompatible electrolyte enables highly reversible Zn anode for zinc ion battery
Authors: Li Guanjie , Zhao Zihan , Zhang Shilin , Sun Liang , Li Mingnan , Yuwono Jodie A. , Mao Jianfeng , Hao Junnan , Vongsvivut Jitraporn , Xing Lidan , Zhao Chun-Xia , Guo Zaiping 
Published: October 2023

AbstractProgress towards the integration of technology into living organisms requires power devices that are biocompatible and mechanically flexible. Aqueous zinc ion batteries that use hydrogel biomaterials as electrolytes have emerged as a potential solution that operates within biological constraints; however, most of these batteries feature inferior electrochemical properties. Here, we propose a biocompatible hydrogel electrolyte by utilising hyaluronic acid, which contains ample hydrophilic functional groups. The gel-based electrolyte offers excellent anti-corrosion ability for zinc anodes and regulates zinc nucleation/growth. Also, the gel electrolyte provides high battery performance, including a 99.71% Coulombic efficiency, over 5500 hours of long-term stability, improved cycle life of 250 hours under a high zinc utilization rate of 80%, and high biocompatibility. Importantly, the Zn//LiMn2O4 pouch cell exhibits 82% capacity retention after 1000 cycles at 3 C. This work presents a promising gel chemistry that controls zinc behaviour, offering great potential in biocompatible energy-related applications and beyond.