bluuebunny/crossref_metadata_2025_split huggingface dataset:
The lactonase BxdA mediates metabolic specialisation of maize root bacteria to benzoxazinoids
Authors: Thoenen Lisa , Kreuzer Marco , Pestalozzi Christine , Florean Matilde , Mateo Pierre , Züst Tobias , Wei Anlun , Giroud Caitlin , Rouyer Liza , Gfeller Valentin , Notter Matheus D. , Knoch Eva , Hapfelmeier Siegfried , Becker Claude , Schandry Niklas , Robert Christelle A. M. , Köllner Tobias G. , Bruggmann Rémy , Erb Matthias , Schlaeppi Klaus 
Published: August 2024

AbstractRoot exudates contain specialised metabolites that shape the plant’s root microbiome. How host-specific microbes cope with these bioactive compounds, and how this ability affects root microbiomes, remains largely unknown. We investigated how maize root bacteria metabolise benzoxazinoids, the main specialised metabolites of maize. Diverse and abundant bacteria metabolised the major compound in the maize rhizosphere MBOA (6-methoxybenzoxazolin-2(3H)-one) and formed AMPO (2-amino-7-methoxy-phenoxazin-3-one). AMPO forming bacteria were enriched in the rhizosphere of benzoxazinoid-producing maize and could use MBOA as carbon source. We identified a gene cluster associated with AMPO formation in microbacteria. The first gene in this cluster, bxdA encodes a lactonase that converts MBOA to AMPO in vitro. A deletion mutant of the homologous bxdA genes in the genus Sphingobium, did not form AMPO nor was it able to use MBOA as a carbon source. BxdA was identified in different genera of maize root bacteria. Here we show that plant-specialised metabolites select for metabolisation-competent root bacteria. BxdA represents a benzoxazinoid metabolisation gene whose carriers successfully colonize the maize rhizosphere and thereby shape the plant’s chemical environmental footprint.
The unique allosteric property of crocodilian haemoglobin elucidated by cryo-EM
Authors: Takahashi Katsuya , Lee Yongchan , Fago Angela , Bautista Naim M. , Storz Jay F. , Kawamoto Akihiro , Kurisu Genji , Nishizawa Tomohiro , Tame Jeremy R. H. 
Published: August 2024

AbstractThe principal effect controlling the oxygen affinity of vertebrate haemoglobins (Hbs) is the allosteric switch between R and T forms with relatively high and low oxygen affinity respectively. Uniquely among jawed vertebrates, crocodilians possess Hb that shows a profound drop in oxygen affinity in the presence of bicarbonate ions. This allows them to stay underwater for extended periods by consuming almost all the oxygen present in the blood-stream, as metabolism releases carbon dioxide, whose conversion to bicarbonate and hydrogen ions is catalysed by carbonic anhydrase. Despite the apparent universal utility of bicarbonate as an allosteric regulator of Hb, this property evolved only in crocodilians. We report here the molecular structures of both human and a crocodilian Hb in the deoxy and liganded states, solved by cryo-electron microscopy. We reveal the precise interactions between two bicarbonate ions and the crocodilian protein at symmetry-related sites found only in the T state. No other known effector of vertebrate Hbs binds anywhere near these sites.
Climate change is associated with higher phytoplankton biomass and longer blooms in the West Antarctic Peninsula
Authors: Ferreira Afonso , Mendes Carlos R. B. , Costa Raul R. , Brotas Vanda , Tavano Virginia M. , Guerreiro Catarina V. , Secchi Eduardo R. , Brito Ana C. 
Published: August 2024

AbstractThe Antarctic Peninsula (West Antarctica) marine ecosystem has undergone substantial changes due to climate-induced shifts in atmospheric and oceanic temperatures since the 1950s. Using 25 years of satellite data (1998-2022), this study presents evidence that phytoplankton biomass and bloom phenology in the West Antarctic Peninsula are significantly changing as a response to anthropogenic climate change. Enhanced phytoplankton biomass was observed along the West Antarctic Peninsula, particularly in the early austral autumn, resulting in longer blooms. Long-term sea ice decline was identified as the main driver enabling phytoplankton growth in early spring and autumn, in parallel with a recent intensification of the Southern Annular Mode (2010-ongoing), which was observed to influence regional variability. Our findings contribute to the understanding of the complex interplay between environmental changes and phytoplankton responses in this climatically key region of the Southern Ocean and raise important questions regarding the far-reaching consequences that these ecological changes may have on global carbon sequestration and Antarctic food webs in the future.
Phenotypic heterogeneity follows a growth-viability tradeoff in response to amino acid identity
Authors: Shabestary Kiyan , Klemm Cinzia , Carling Benedict , Marshall James , Savigny Juline , Storch Marko , Ledesma-Amaro Rodrigo 
Published: August 2024

AbstractIn their natural environments, microorganisms mainly operate at suboptimal growth conditions with fluctuations in nutrient abundance. The resulting cellular adaptation is subject to conflicting tasks: growth or survival maximisation. Here, we study this adaptation by systematically measuring the impact of a nitrogen downshift to 24 nitrogen sources on cellular metabolism at the single-cell level. Saccharomyces lineages grown in rich media and exposed to a nitrogen downshift gradually differentiate to form two subpopulations of different cell sizes where one favours growth while the other favours viability with an extended chronological lifespan. This differentiation is asymmetrical with daughter cells representing the new differentiated state with increased viability. We characterise the metabolic response of the subpopulations using RNA sequencing, metabolic biosensors and a transcription factor-tagged GFP library coupled to high-throughput microscopy, imaging more than 800,000 cells. We find that the subpopulation with increased viability is associated with a dormant quiescent state displaying differences in MAPK signalling. Depending on the identity of the nitrogen source present, differentiation into the quiescent state can be actively maintained, attenuated, or aborted. These results establish amino acids as important signalling molecules for the formation of genetically identical subpopulations, involved in chronological lifespan and growth rate determination.
Evaluating batch correction methods for image-based cell profiling
Authors: Arevalo John , Su Ellen , Ewald Jessica D. , van Dijk Robert , Carpenter Anne E. , Singh Shantanu 
Published: August 2024

AbstractHigh-throughput image-based profiling platforms are powerful technologies capable of collecting data from billions of cells exposed to thousands of perturbations in a time- and cost-effective manner. Therefore, image-based profiling data has been increasingly used for diverse biological applications, such as predicting drug mechanism of action or gene function. However, batch effects severely limit community-wide efforts to integrate and interpret image-based profiling data collected across different laboratories and equipment. To address this problem, we benchmark ten high-performing single-cell RNA sequencing (scRNA-seq) batch correction techniques, representing diverse approaches, using a newly released Cell Painting dataset, JUMP. We focus on five scenarios with varying complexity, ranging from batches prepared in a single lab over time to batches imaged using different microscopes in multiple labs. We find that Harmony and Seurat RPCA are noteworthy, consistently ranking among the top three methods for all tested scenarios while maintaining computational efficiency. Our proposed framework, benchmark, and metrics can be used to assess new batch correction methods in the future. This work paves the way for improvements that enable the community to make the best use of public Cell Painting data for scientific discovery.
Going beyond gadgets: the importance of scalability for analogue quantum simulators
Authors: Harley Dylan , Datta Ishaun , Klausen Frederik Ravn , Bluhm Andreas , França Daniel Stilck , Werner Albert H. , Christandl Matthias 
Published: August 2024

AbstractQuantum hardware has the potential to efficiently solve computationally difficult problems in physics and chemistry to reap enormous practical rewards. Analogue quantum simulation accomplishes this by using the dynamics of a controlled many-body system to mimic those of another system; such a method is feasible on near-term devices. We show that previous theoretical approaches to analogue quantum simulation suffer from fundamental barriers which prohibit scalable experimental implementation. By introducing a new mathematical framework and going beyond the usual toolbox of Hamiltonian complexity theory with an additional resource of engineered dissipation, we show that these barriers can be overcome. This provides a powerful new perspective for the rigorous study of analogue quantum simulators.
Quantum advantage and stability to errors in analogue quantum simulators
Authors: Trivedi Rahul , Franco Rubio Adrian , Cirac J. Ignacio 
Published: August 2024

AbstractSeveral quantum hardware platforms, while being unable to perform fully fault-tolerant quantum computation, can still be operated as analogue quantum simulators for addressing many-body problems. However, due to the presence of errors, it is not clear to what extent those devices can provide us with an advantage with respect to classical computers. In this work, we make progress on this problem for noisy analogue quantum simulators computing physically relevant properties of many-body systems both in equilibrium and undergoing dynamics. We first formulate a system-size independent notion of stability against extensive errors, which we prove for Gaussian fermion models, as well as for a restricted class of spin systems. Remarkably, for the Gaussian fermion models, our analysis shows the stability of critical models which have long-range correlations. Furthermore, we analyze how this stability may lead to a quantum advantage, for the problem of computing the thermodynamic limit of many-body models, in the presence of a constant error rate and without any explicit error correction.
Accelerated discovery of perovskite solid solutions through automated materials synthesis and characterization
Authors: Omidvar Mojan , Zhang Hangfeng , Ihalage Achintha Avin , Saunders Theo Graves , Giddens Henry , Forrester Michael , Haq Sajad , Hao Yang 
Published: August 2024

AbstractAccelerating perovskite solid solution discovery and sustainable synthesis is crucial for addressing challenges in wireless communication and biosensors. However, the vast array of chemical compositions and their dependence on factors such as crystal structure, and sintering temperature require time-consuming manual processes. To overcome these constraints, we introduce an automated materials discovery approach encompassing machine learning (ML) assisted material screening, robotic synthesis, and high-throughput characterization. Our proposed platform for rapid sintering and dielectric analysis streamlines the characterization of perovskites and the discovery of disordered materials. The setup has been successfully validated, demonstrating processing materials within minutes, in stark contrast to conventional procedures that can take hours or days. Following setup validation with established samples, we showcase synthesizing single-phase solid solutions within the barium family, such as (BaxSr1-x)CeO3, identified through ML-guided chemistry.
The 4.2 ka event is not remarkable in the context of Holocene climate variability
Authors: McKay Nicholas P. , Kaufman Darrell S. , Arcusa Stéphanie H. , Kolus Hannah R. , Edge David C. , Erb Michael P. , Hancock Chris L. , Routson Cody C. , Żarczyński Maurycy , Marshall Leah P. , Roberts Georgia K. , Telles Frank 
Published: August 2024

AbstractThe “4.2 ka event” is a commonly described abrupt climate excursion that occurred about 4200 years ago. However, the extent to which this event is coherent across regional and larger scales is unclear. To objectively assess climate excursions in the Holocene we compile 1142 paleoclimate datasets that span all continents and oceans and include a wide variety of archive and proxy types. We analyze these data to determine the timing, significance and spatial imprint of climate excursions using an objective method that quantifies local, regional and global significance. Site-level excursions in temperature and hydroclimate are common throughout the Holocene, but significant global-scale excursions are rare. The most prominent excursion occurred 8200 years ago, when cold and dry conditions formed a large, significant excursion centered in the North Atlantic. We find additional significant excursions between 1600 and 1000 years ago, which agree with tree-ring data and annual-scale paleoclimate reconstructions, adding confidence and context to our findings. In contrast, although some datasets show significant climate excursions 4200 years ago, they do not occur in large, coherent spatial regions. Consequently, like most other periods in the Holocene, the “4.2 ka event” is not a globally significant climate excursion.
Single-cell RNA sequencing reveals placental response under environmental stress
Authors: Van Buren Eric , Azzara David , Rangel-Moreno Javier , Garcia-Hernandez Maria de la Luz , Murphy Shawn P. , Cohen Ethan D. , Lewis Ethan , Lin Xihong , Park Hae-Ryung 
Published: August 2024

AbstractThe placenta is crucial for fetal development, yet the impact of environmental stressors such as arsenic exposure remains poorly understood. We apply single-cell RNA sequencing to analyze the response of the mouse placenta to arsenic, revealing cell-type-specific gene expression, function, and pathological changes. Notably, the Prap1 gene, which encodes proline-rich acidic protein 1 (PRAP1), is significantly upregulated in 26 placental cell types including various trophoblast cells. Our study shows a female-biased increase in PRAP1 in response to arsenic and localizes it in the placenta. In vitro and ex vivo experiments confirm PRAP1 upregulation following arsenic treatment and demonstrate that recombinant PRAP1 protein reduces arsenic-induced cytotoxicity and downregulates cell cycle pathways in human trophoblast cells. Moreover, PRAP1 knockdown differentially affects cell cycle processes, proliferation, and cell death depending on the presence of arsenic. Our findings provide insights into the placental response to environmental stress, offering potential preventative and therapeutic approaches for environment-related adverse outcomes in mothers and children.
MEILB2-BRME1 forms a V-shaped DNA clamp upon BRCA2-binding in meiotic recombination
Authors: Gurusaran Manickam , Zhang Jingjing , Zhang Kexin , Shibuya Hiroki , Davies Owen R. 
Published: August 2024

AbstractDNA double-strand break repair by homologous recombination has a specialised role in meiosis by generating crossovers that enable the formation of haploid germ cells. This requires meiosis-specific MEILB2-BRME1, which interacts with BRCA2 to facilitate loading of recombinases onto resected DNA ends. Here, we report the crystal structure of the MEILB2-BRME1 2:2 core complex, revealing a parallel four-helical assembly that recruits BRME1 to meiotic double-strand breaks in vivo. It forms an N-terminal β-cap that binds to DNA, and a MEILB2 coiled-coil that bridges to C-terminal ARM domains. Upon BRCA2-binding, MEILB2-BRME1 2:2 complexes dimerize into a V-shaped 2:4:4 complex, with rod-like MEILB2-BRME1 components arranged at right-angles. The β-caps located at the tips of the MEILB2-BRME1 limbs are separated by 25 nm, allowing them to bridge between DNA molecules. Thus, we propose that BRCA2 induces MEILB2-BRME1 to function as a DNA clamp, connecting resected DNA ends or homologous chromosomes to facilitate meiotic recombination.
Engineering of a mammalian VMAT2 for cryo-EM analysis results in non-canonical protein folding
Authors: Lyu Ying , Fu Chunting , Ma Haiyun , Su Zhaoming , Sun Ziyi , Zhou Xiaoming 
Published: August 2024

AbstractVesicular monoamine transporter 2 (VMAT2) belongs to the major facilitator superfamily (MFS), and mediates cytoplasmic monoamine packaging into presynaptic vesicles. Here, we present two cryo-EM structures of VMAT2, with a frog VMAT2 adopting a canonical MFS fold and an engineered sheep VMAT2 adopting a non-canonical fold. Both VMAT2 proteins mediate uptake of a selective fluorescent VMAT2 substrate into cells. Molecular docking, substrate binding and transport analysis reveal potential substrate binding mechanism in VMAT2. Meanwhile, caution is advised when interpreting engineered membrane protein structures.
Regio‐ and enantioselective nickel-alkyl catalyzed hydroalkylation of alkynes
Authors: Gao Qian , Xu Wei-Cheng , Nie Xuan , Bian Kang-Jie , Yuan Hong-Rui , Zhang Wen , Wu Bing-Bing , Wang Xi-Sheng 
Published: August 2024

AbstractThe migratory insertion of metal-hydride into alkene has allowed regioselective access to organometallics, readily participating in subsequent functionalization as one conventional pathway of hydroalkylation, whereas analogous process with feedstock alkyne is drastically less explored. Among few examples, the regioselectivity of metal-hydride insertion is mostly governed by electronic bias of alkynes. To alter the regioselectivity and drastically expand the intermediate pools that we can access, one aspirational design is through alternative nickel-alkyl insertion, providing opposite regioselectivity induced by steric demand. Leveraging in situ formed nickel-alkyl species, we herein report the regio- and enantioselective hydroalkylation of alkynes with broad functional group tolerance, excellent regio- and enantioselectivity, enabling efficient route to diverse valuable chiral allylic amines motifs. Preliminary mechanistic studies indicate the aminoalkyl radical species can participate in metal-capture and lead to formation of nickel-alkyl, of which the migratory insertion is key to reverse regioselectivity observed in metal-hydride insertion.
Atomic resolution coherent x-ray imaging with physics-based phase retrieval
Authors: Meziere Jason , Carpenter Abigail Hardy , Pateras Anastasios , Harder Ross , Sandberg Richard L. 
Published: August 2024

AbstractCoherent x-ray imaging and scattering from accelerator based sources such as synchrotrons continue to impact biology, medicine, technology, and materials science. Many synchrotrons around the world are currently undergoing major upgrades to increase their available coherent x-ray flux by approximately two orders of magnitude. The improvement of synchrotrons may enable imaging of materials in operando at the atomic scale which may revolutionize battery and catalysis technologies. Current algorithms used for phase retrieval in coherent x-ray imaging are based on the projection onto sets method. These traditional iterative phase retrieval methods will become more computationally expensive as they push towards atomic resolution and may struggle to converge. Additionally, these methods do not incorporate physical information that may additionally constrain the solution. In this work, we present an algorithm which incorporates molecular dynamics into Bragg coherent diffraction imaging (BCDI). This algorithm, which we call PRAMMol (Phase Retrieval with Atomic Modeling and Molecular Dynamics) combines statistical techniques with molecular dynamics to solve the phase retrieval problem. We present several examples where our algorithm is applied to simulated coherent diffraction from 3D crystals and show convergence to the correct solution at the atomic scale.
‘Candidatus Liberibacter brunswickensis’ colonization has no effect to the early development of Solanum melongena
Authors: Morris Jacqueline , Mann Rachel , Perera Angage Sanka , Frampton Rebekah , Malipatil Mallik , Norng Sorn , Yen Alan , Smith Grant , Rodoni Brendan 
Published: August 2024

AbstractThis study is the first to investigate the presence and movement of the novel Liberibacter species ‘Candidatus Liberibacter brunswickensis’ (CLbr) in eggplant, Solanum melongena. The psyllid, Acizzia solanicola can transmit CLbr to eggplant and CLbr can be acquired by CLbr-negative A. solanicola individuals from CLbr-positive eggplants. In planta, CLbr can replicate, move and persist. Investigation into the early development of eggplants showed that CLbr titres had increased at the inoculation site at 14 days post inoculation access period (DPIAP). CLbr had become systemic in the majority of plants tested by 28 DPIAP. The highest bacterial titres were recorded at 35 DPIAP in all samples of the inoculated leaf, the roots, stems and the midrib and petiole samples of the newest leaf (the top leaf). This finding strongly suggests that CLbr movement in planta follows the source to sink relationship as previously described for ‘Ca. Liberibacter asiaticus’ (CLas) and ‘Ca. Liberibacter solanacearum’ (CLso). No symptoms consistent with Liberibacter-associated diseases were noted for plants colonised by CLbr during this study, consistent with the hypothesis that CLbr does not cause disease of eggplant during the early stages of host colonisation. In addition, no significant differences in biomass were found between eggplant colonised with CLbr, compared to those that were exposed to CLbr-negative A. solanicola, and to control plants.
The latest shallow-sea isocrinids from the Miocene of Paratethys and implications to the Mesozoic marine revolution
Authors: Salamon Mariusz A. , Radwańska Urszula , Paszcza Karolina , Krajewski Marcin , Brachaniec Tomasz , Niedźwiedzki Robert , Gorzelak Przemysław 
Published: August 2024

AbstractThe predation-driven Mesozoic marine revolution (MMR) is believed to have induced a dramatic change in the bathymetric distribution of many shallow marine invertebrates since the late Mesozoic. For instance, stalked crinoids – isocrinids (Isocrinida) have undergone a striking decline in shallow-sea environments and today they are restricted to deep-sea settings (below 100 m depth). However, the timing and synchronicity of this shift are a matter of debate. A delayed onset of MMR and/or shifts to a retrograde, low-predation community structure during the Paleogene in the Southern Ocean were invoked. In particular, recent data from the Southern Hemisphere suggest that the environmental restriction of isocrinids to the deep-sea settings may have occurred at the end of the Eocene around Antarctica and Australia, and later in the early Miocene in New Zealand. Here, we report the anomalous occurrence of the isocrinids in shallow nearshore marine facies from the middle Miocene of Poland (Northern Hemisphere, Central Paratethys). Thus, globally, this is the youngest record of shallow-sea stalked crinoids. This finding suggests that some relict stalked crinoids may have been able to live in the shallow-water environments by the middle Miocene, and further confirms that the depth restriction of isocrinids to offshore environments was not synchronous on a global scale.