bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physiological adaptive traits are a potential allele reservoir for maize genetic progress under challenging conditions
Authors: Welcker Claude , Spencer Nadir Abusamra , Turc Olivier , Granato Italo , Chapuis Romain , Madur Delphine , Beauchene Katia , Gouesnard Brigitte , Draye Xavier , Palaffre Carine , Lorgeou Josiane , Melkior Stephane , Guillaume Colin , Presterl Thomas , Murigneux Alain , Wisser Randall J. , Millet Emilie J. , van Eeuwijk Fred , Charcosset Alain , Tardieu François 
Published: June 2022

AbstractCombined phenomic and genomic approaches are required to evaluate the margin of progress of breeding strategies. Here, we analyze 65 years of genetic progress in maize yield, which was similar (101 kg ha−1 year−1) across most frequent environmental scenarios in the European growing area. Yield gains were linked to physiologically simple traits (plant phenology and architecture) which indirectly affected reproductive development and light interception in all studied environments, marked by significant genomic signatures of selection. Conversely, studied physiological processes involved in stress adaptation remained phenotypically unchanged (e.g. stomatal conductance and growth sensitivity to drought) and showed no signatures of selection. By selecting for yield, breeders indirectly selected traits with stable effects on yield, but not physiological traits whose effects on yield can be positive or negative depending on environmental conditions. Because yield stability under climate change is desirable, novel breeding strategies may be needed for exploiting alleles governing physiological adaptive traits.
Evolutionary action of mutations reveals antimicrobial resistance genes in Escherichia coli
Authors: Marciano David C. , Wang Chen , Hsu Teng-Kuei , Bourquard Thomas , Atri Benu , Nehring Ralf B. , Abel Nicholas S. , Bowling Elizabeth A. , Chen Taylor J. , Lurie Pamela D. , Katsonis Panagiotis , Rosenberg Susan M. , Herman Christophe , Lichtarge Olivier 
Published: June 2022

AbstractSince antibiotic development lags, we search for potential drug targets through directed evolution experiments. A challenge is that many resistance genes hide in a noisy mutational background as mutator clones emerge in the adaptive population. Here, to overcome this noise, we quantify the impact of mutations through evolutionary action (EA). After sequencing ciprofloxacin or colistin resistance strains grown under different mutational regimes, we find that an elevated sum of the evolutionary action of mutations in a gene identifies known resistance drivers. This EA integration approach also suggests new antibiotic resistance genes which are then shown to provide a fitness advantage in competition experiments. Moreover, EA integration analysis of clinical and environmental isolates of antibiotic resistant of E. coli identifies gene drivers of resistance where a standard approach fails. Together these results inform the genetic basis of de novo colistin resistance and support the robust discovery of phenotype-driving genes via the evolutionary action of genetic perturbations in fitness landscapes.
Dual phase patterning during a congruent grain boundary phase transition in elemental copper
Authors: Langenohl Lena , Brink Tobias , Freitas Rodrigo , Frolov Timofey , Dehm Gerhard , Liebscher Christian H. 
Published: June 2022

AbstractThe phase behavior of grain boundaries can have a strong influence on interfacial properties. Little is known about the emergence of grain boundary phases in elemental metal systems and how they transform. Here, we observe the nanoscale patterning of a grain boundary by two alternating grain boundary phases with distinct atomic structures in elemental copper by atomic resolution imaging. The same grain boundary phases are found by computational grain boundary structure search indicating a first-order transformation. Finite temperature atomistic simulations reveal a congruent, diffusionless transition between these phases under ambient pressure. The patterning of the grain boundary at room temperature is dominated by the grain boundary phase junctions separating the phase segments. Our analysis suggests that the reduced mobility of the phase junctions at low temperatures kinetically limits the transformation, but repulsive elastic interactions between them and disconnections could additionally stabilize the pattern formation.
Dynamic mRNA degradome analyses indicate a role of histone H3K4 trimethylation in association with meiosis-coupled mRNA decay in oocyte aging
Authors: Wu Yun-Wen , Li Sen , Zheng Wei , Li Yan-Chu , Chen Lu , Zhou Yong , Deng Zuo-Qi , Lin Ge , Fan Heng-Yu , Sha Qian-Qian 
Published: June 2022

AbstractA decrease in oocyte developmental potential is a major obstacle for successful pregnancy in women of advanced age. However, the age-related epigenetic modifications associated with dynamic transcriptome changes, particularly meiotic maturation-coupled mRNA clearance, have not been adequately characterized in human oocytes. This study demonstrates a decreased storage of transcripts encoding key factors regulating the maternal mRNA degradome in fully grown oocytes of women of advanced age. A similar defect in meiotic maturation-triggered mRNA clearance is also detected in aged mouse oocytes. Mechanistically, the epigenetic and cytoplasmic aspects of oocyte maturation are synchronized in both the normal development and aging processes. The level of histone H3K4 trimethylation (H3K4me3) is high in fully grown mouse and human oocytes derived from young females but decreased during aging due to the decreased expression of epigenetic factors responsible for H3K4me3 accumulation. Oocyte-specific knockout of the gene encoding CxxC-finger protein 1 (CXXC1), a DNA-binding subunit of SETD1 methyltransferase, causes ooplasm changes associated with accelerated aging and impaired maternal mRNA translation and degradation. These results suggest that a network of CXXC1-maintained H3K4me3, in association with mRNA decay competence, sets a timer for oocyte deterioration and plays a role in oocyte aging in both mouse and human oocytes.
Observation of non-Hermitian topological Anderson insulator in quantum dynamics
Authors: Lin Quan , Li Tianyu , Xiao Lei , Wang Kunkun , Yi Wei , Xue Peng 
Published: June 2022

AbstractDisorder and non-Hermiticity dramatically impact the topological and localization properties of a quantum system, giving rise to intriguing quantum states of matter. The rich interplay of disorder, non-Hermiticity, and topology is epitomized by the recently proposed non-Hermitian topological Anderson insulator that hosts a plethora of exotic phenomena. Here we experimentally simulate the non-Hermitian topological Anderson insulator using disordered photonic quantum walks, and characterize its localization and topological properties. In particular, we focus on the competition between Anderson localization induced by random disorder, and the non-Hermitian skin effect under which all eigenstates are squeezed toward the boundary. The two distinct localization mechanisms prompt a non-monotonous change in profile of the Lyapunov exponent, which we experimentally reveal through dynamic observables. We then probe the disorder-induced topological phase transitions, and demonstrate their biorthogonal criticality. Our experiment further advances the frontier of synthetic topology in open systems.
Profiling Fusobacterium infection at high taxonomic resolution reveals lineage-specific correlations in colorectal cancer
Authors: Bi Dexi , Zhu Yin , Gao Yaohui , Li Hao , Zhu Xingchen , Wei Rong , Xie Ruting , Cai Chunmiao , Wei Qing , Qin Huanlong 
Published: June 2022

AbstractThe bacterial genus Fusobacterium promotes colorectal cancer (CRC) development, but an understanding of its precise composition at the species level in the human gut and the relevant association with CRC is lacking. Herein, we devise a Fusobacterium rpoB amplicon sequencing (FrpoB-seq) method that enables the differentiation of Fusobacterium species and certain subspecies in the microbiota. By applying this method to clinical tissue and faecal samples from CRC patients, we detect 62 Fusobacterium species, including 45 that were previously undescribed. We additionally reveal that Fusobacterium species may display different lineage-dependent functions in CRC. Specifically, a lineage (designated L1) including F. nucleatum, F. hwasookii, F. periodonticum and their relatives (rather than any particular species alone) is overabundant in tumour samples and faeces from CRC patients, whereas a non-enriched lineage (designated L5) represented by F. varium and F. ulcerans in tumours has a positive association with lymphovascular invasion.
Light-activated photodeformable supramolecular dissipative self-assemblies
Authors: Chen Xu-Man , Feng Wei-Jie , Bisoyi Hari Krishna , Zhang Shu , Chen Xiao , Yang Hong , Li Quan 
Published: June 2022

AbstractDissipative self-assembly, one of fundamentally important out-of-equilibrium self-assembly systems, can serve as a controllable platform to exhibit temporal processes for various non-stimulus responsive properties. However, construction of light-fueled dissipative self-assembly structures with transformable morphology to modulate non-photoresponsive properties remains a great challenge. Here, we report a light-activated photodeformable dissipative self-assembly system in aqueous solution as metastable fluorescent palette. Zwitterionic sulfonato-merocyanine is employed as a light-induced amphiphile to co-assemble with polyethyleneimine after light irradiation. The formed spherical nanoparticles spontaneously transform into cuboid ones in the dark with simultaneous variation of the particle sizes. Then the two kinds of nanoparticles can reversibly interconvert to each other by periodical light irradiation and thermal relaxation. Furthermore, after loading different fluorophores exhibiting red, green, blue emissions and their mixtures, all these fluorescent dissipative deformable nanoparticles display time-dependent fluorescence variation with wide range of colors. Owing to the excellent performance of photodeformable dissipative assembly platform, the light-controlled fluorescence has achieved a 358-fold enhancement. Therefore, exposing the nanoparticles loaded with fluorophores to light in a spatially controlled manner allows us to draw multicolored fluorescent images that spontaneously disappeared after a specific period of time.
Direct investigation of the atomic structure and decreased magnetism of antiphase boundaries in garnet
Authors: Xu Kun , Lin Ting , Rao Yiheng , Wang Ziqiang , Yang Qinghui , Zhang Huaiwu , Zhu Jing 
Published: June 2022

AbstractThe ferrimagnetic insulator iron garnets, tailored artificially with specific compositions, have been widely utilized in magneto-optical (MO) devices. The adjustment on synthesis always induces structural variation, which is underestimated due to the limited knowledge of the local structures. Here, by analyzing the structure and magnetic properties, two different antiphase boundaries (APBs) with individual interfacial structure are investigated in substituted iron garnet film. We reveal that magnetic signals decrease in the regions close to APBs, which implies degraded MO performance. In particular, the segregation of oxygen deficiencies across the APBs directly leads to reduced magnetic elements, further decreases the magnetic moment of Fe and results in a higher absorption coefficient close to the APBs. Furthermore, the formation of APBs can be eliminated by optimizing the growth rate, thus contributing to the enhanced MO performance. These analyses at the atomic scale provide important guidance for optimizing MO functional materials.
Climate and hydraulic traits interact to set thresholds for liana viability
Authors: Willson Alyssa M. , Trugman Anna T. , Powers Jennifer S. , Smith-Martin Chris M. , Medvigy David 
Published: June 2022

AbstractLianas, or woody vines, and trees dominate the canopy of tropical forests and comprise the majority of tropical aboveground carbon storage. These growth forms respond differently to contemporary variation in climate and resource availability, but their responses to future climate change are poorly understood because there are very few predictive ecosystem models representing lianas. We compile a database of liana functional traits (846 species) and use it to parameterize a mechanistic model of liana-tree competition. The substantial difference between liana and tree hydraulic conductivity represents a critical source of inter-growth form variation. Here, we show that lianas are many times more sensitive to drying atmospheric conditions than trees as a result of this trait difference. Further, we use our competition model and projections of tropical hydroclimate based on Representative Concentration Pathway 4.5 to show that lianas are more susceptible to reaching a hydraulic threshold for viability by 2100.
Diamagnetically levitated nanopositioners with large-range and multiple degrees of freedom
Authors: Vikrant K. S. , Jayanth G. R. 
Published: June 2022

AbstractPrecision positioning stages are often central to science and technology at the micrometer and nanometer length scales. Compact, multi-degree-of-freedom stages with large dynamic range are especially desirable, since they help to improve the throughput and versatility in manipulation without introducing spatial constraints. Here, we report compact diamagnetically levitated stages, which employ dual-sided actuation to achieve large-range, six degrees-of-freedom positioning. Dual-sided actuation is demonstrated to enable trapping a magnet array in 3D, with independent control of the trap stiffness about two axes, independent control of forces in 3D and torque about 2 axes. A simplified model is proposed to directly relate these physical quantities to the necessary actuation currents. Experimentally, we demonstrate six degrees-of-freedom positioning with low cross-axis motion, large range and nanometer-scale resolution. In particular, here we show linear motion range of 5 mm with positioning precision better than 1.88 nm, and angular motion range of 1.1 radian with a resolution of 50 micro-radian. With the volume of the stage being between 10-20 cm3, its utility as a compact nano-positioner is showcased by using it to automatically replace the tip of an atomic force microscope probe.
Rapid syntheses of N-fused heterocycles via acyl-transfer in heteroaryl ketones
Authors: Ye Dan , Lu Hong , He Yi , Zheng Zhaojing , Wu Jinghao , Wei Hao 
Published: June 2022

AbstractThe wide-ranging potencies of bioactive N-fused heterocycles inspire the development of synthetic transformations that simplify preparation of their complex, diverse structural motifs. Heteroaryl ketones are ubiquitous, readily available, and inexpensive molecular scaffolds, and are thus synthetically appealing as precursors in preparing N-fused heterocycles via intramolecular acyl-transfer. To best of our knowledge, acyl-transfer of unstrained heteroaryl ketones remains to be demonstrated. Here, we show an acyl transfer-annulation to convert heteroaryl ketones to N-fused heterocycles. Driven via aromatisation, the acyl of a heteroaryl ketone can be transferred from the carbon to the nitrogen of the corresponding heterocycle. The reaction commences with the spiroannulation of a heteroaryl ketone and an alkyl bromide, with the resulting spirocyclic intermediate undergoing aromatisation-driven intramolecular acyl transfer. The reaction conditions are optimised, with the reaction exhibiting a broad substrate scope in terms of the ketone and alkyl bromide. The utility of this protocol is further demonstrated via application to complex natural products and drug derivatives to yield heavily functionalised N-fused heterocycles.
Donor-dependent fecal microbiota transplantation efficacy against necrotizing enterocolitis in preterm pigs
Authors: Hui Yan , Vestergaard Gisle , Deng Ling , Kot Witold Piotr , Thymann Thomas , Brunse Anders , Nielsen Dennis Sandris 
Published: June 2022

AbstractThe development of necrotizing enterocolitis (NEC), a life-threatening inflammatory bowel disease affecting preterm infants, is connected with gut microbiota dysbiosis. Using preterm piglets as a model for preterm infants we recently showed that fecal microbiota transplantation (FMT) from healthy suckling piglet donors to newborn preterm piglets decreased the NEC risk. However, in a follow-up study using donor stool from piglets recruited from another farm, this finding could not be replicated. This allowed us to study donor-recipient microbiota dynamics in a controlled model system with a clear difference in NEC phenotype. Preterm piglets (n = 38) were randomly allocated to receive control saline (CON), or rectal FMT using either the ineffective (FMT1) or the effective donor stool (FMT2). All animals were followed for four days before necropsy and gut pathological evaluation. Donor and recipient colonic gut microbiota (GM) were analyzed by 16 S rRNA gene amplicon sequencing and shotgun metagenomics. As expected, only FMT2 recipients were protected against NEC. Both FMT groups had shifted GM composition relative to CON, but FMT2 recipients had a higher lactobacilli relative abundance compared to FMT1. Limosilactobacillus reuteri and Lactobacillus crispatus strains of FMT recipients showed high phylogenetic similarity with their respective donors, indicating engraftment. Moreover, the FMT2 group had a higher lactobacilli replication rate and harbored specific glycosaminoglycan-degrading Bacteroides. In conclusion, subtle species-level donor differences translate to major changes in engraftment dynamics and the ability to prevent NEC. This could have implications for proper donor selection in future FMT trials for NEC prevention.
Lysosome lipid signalling from the periphery to neurons regulates longevity
Authors: Savini Marzia , Folick Andrew , Lee Yi-Tang , Jin Feng , Cuevas André , Tillman Matthew C. , Duffy Jonathon D. , Zhao Qian , Neve Isaiah A. , Hu Pei-Wen , Yu Yong , Zhang Qinghao , Ye Youqiong , Mair William B. , Wang Jin , Han Leng , Ortlund Eric A. , Wang Meng C. 
Published: June 2022

AbstractLysosomes are key cellular organelles that metabolize extra- and intracellular substrates. Alterations in lysosomal metabolism are implicated in ageing-associated metabolic and neurodegenerative diseases. However, how lysosomal metabolism actively coordinates the metabolic and nervous systems to regulate ageing remains unclear. Here we report a fat-to-neuron lipid signalling pathway induced by lysosomal metabolism and its longevity-promoting role in Caenorhabditis elegans. We discovered that induced lysosomal lipolysis in peripheral fat storage tissue upregulates the neuropeptide signalling pathway in the nervous system to promote longevity. This cell-non-autonomous regulation is mediated by a specific polyunsaturated fatty acid, dihomo-γ-linolenic acid, and LBP-3 lipid chaperone protein transported from the fat storage tissue to neurons. LBP-3 binds to dihomo-γ-linolenic acid, and acts through NHR-49 nuclear receptor and NLP-11 neuropeptide in neurons to extend lifespan. These results reveal lysosomes as a signalling hub to coordinate metabolism and ageing, and lysosomal signalling mediated inter-tissue communication in promoting longevity.
Genomic analysis defines clonal relationships of ductal carcinoma in situ and recurrent invasive breast cancer
Authors: Lips Esther H. , Kumar Tapsi , Megalios Anargyros , Visser Lindy L. , Sheinman Michael , Fortunato Angelo , Shah Vandna , Hoogstraat Marlous , Sei Emi , Mallo Diego , Roman-Escorza Maria , Ahmed Ahmed A. , Xu Mingchu , van den Belt-Dusebout Alexandra W. , Brugman Wim , Casasent Anna K. , Clements Karen , Davies Helen R. , Fu Liping , Grigoriadis Anita , Hardman Timothy M. , King Lorraine M. , Krete Marielle , Kristel Petra , de Maaker Michiel , Maley Carlo C. , Marks Jeffrey R. , Menegaz Brian A. , Mulder Lennart , Nieboer Frank , Nowinski Salpie , Pinder Sarah , Quist Jelmar , Salinas-Souza Carolina , Schaapveld Michael , Schmidt Marjanka K. , Shaaban Abeer M. , Shami Rana , Sridharan Mathini , Zhang John , Stobart Hilary , Collyar Deborah , Nik-Zainal Serena , Wessels Lodewyk F. A. , Hwang E. Shelley , Navin Nicholas E. , Futreal P. Andrew ,   Grand Challenge PRECISION consortium, Futreal P. Andrew , Hwang E. Shelley , Jonkers Jos , Jacco  , Behbod Fariba , Rea Daniel , Bhattacharjee Proteeti , Pinto Donna , Verschuur Ellen , van Oirsouw Marja , Thompson Alastair M. , Wesseling Jelle , Sawyer Elinor J. 
Published: June 2022

AbstractDuctal carcinoma in situ (DCIS) is the most common form of preinvasive breast cancer and, despite treatment, a small fraction (5–10%) of DCIS patients develop subsequent invasive disease. A fundamental biologic question is whether the invasive disease arises from tumor cells in the initial DCIS or represents new unrelated disease. To address this question, we performed genomic analyses on the initial DCIS lesion and paired invasive recurrent tumors in 95 patients together with single-cell DNA sequencing in a subset of cases. Our data show that in 75% of cases the invasive recurrence was clonally related to the initial DCIS, suggesting that tumor cells were not eliminated during the initial treatment. Surprisingly, however, 18% were clonally unrelated to the DCIS, representing new independent lineages and 7% of cases were ambiguous. This knowledge is essential for accurate risk evaluation of DCIS, treatment de-escalation strategies and the identification of predictive biomarkers.
Mendelian imputation of parental genotypes improves estimates of direct genetic effects
Authors: Young Alexander I. , Nehzati Seyed Moeen , Benonisdottir Stefania , Okbay Aysu , Jayashankar Hariharan , Lee Chanwook , Cesarini David , Benjamin Daniel J. , Turley Patrick , Kong Augustine 
Published: June 2022

AbstractEffects estimated by genome-wide association studies (GWASs) include effects of alleles in an individual on that individual (direct genetic effects), indirect genetic effects (for example, effects of alleles in parents on offspring through the environment) and bias from confounding. Within-family genetic variation is random, enabling unbiased estimation of direct genetic effects when parents are genotyped. However, parental genotypes are often missing. We introduce a method that imputes missing parental genotypes and estimates direct genetic effects. Our method, implemented in the software package snipar (single-nucleotide imputation of parents), gives more precise estimates of direct genetic effects than existing approaches. Using 39,614 individuals from the UK Biobank with at least one genotyped sibling/parent, we estimate the correlation between direct genetic effects and effects from standard GWASs for nine phenotypes, including educational attainment (r = 0.739, standard error (s.e.) = 0.086) and cognitive ability (r = 0.490, s.e. = 0.086). Our results demonstrate substantial confounding bias in standard GWASs for some phenotypes.