bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative genetics of breeding coloration in sand lizards; genic capture unlikely to maintain additive genetic variance
Authors: Lindsay Willow R. , Bererhi Badreddine , Ljungström Gabriella , Wapstra Erik , Olsson Mats 
Published: March 2023

AbstractSexual selection on fitness-determining traits should theoretically erode genetic variance and lead to low heritability. However, many sexually selected traits maintain significant phenotypic and additive genetic variance, with explanations for this “lek paradox” including genic capture due to condition-dependence, and breaks on directional selection due to environmental sources of variance including maternal effects. Here we investigate genetic and environmental sources of variance in the intrasexually selected green badge of the sand lizard (Lacerta agilis). The badge functions as a cue to male fighting ability in this species, and male–male interactions determine mate acquisition. Using animal models on a pedigree including three generations of males measured over an extensive 9-year field study, we partition phenotypic variance in both badge size and body condition into additive genetic, maternal, and permanent environmental effects experienced by an individual over its lifespan. Heritability of badge size was 0.33 with a significant estimate of underlying additive genetic variance. Body condition was strongly environmentally determined in this species and did not show either significant additive genetic variance or heritability. Neither badge size nor body condition was responsive to maternal effects. We propose that the lack of additive genetic variance and heritability of body condition makes it unlikely that genic capture mechanisms maintain additive genetic variance for badge size. That said, genic capture was originally proposed for male traits under female choice, not agonistic selection. If developmental pathways generating variance in body condition, and/or the covarying secondary sex trait, differ between inter- and intrasexual selection, or the rate at which their additive genetic variance or covariance is depleted, future work may show whether genic capture is largely restricted to intersexual selection processes.
Tyrosyl-tRNA synthetase has a noncanonical function in actin bundling
Authors: Ermanoska Biljana , Asselbergh Bob , Morant Laura , Petrovic-Erfurth Maria-Luise , Hosseinibarkooie Seyyedmohsen , Leitão-Gonçalves Ricardo , Almeida-Souza Leonardo , Bervoets Sven , Sun Litao , Lee LaTasha , Atkinson Derek , Khanghahi Akram , Tournev Ivaylo , Callaerts Patrick , Verstreken Patrik , Yang Xiang-Lei , Wirth Brunhilde , Rodal Avital A. , Timmerman Vincent , Goode Bruce L. , Godenschwege Tanja A. , Jordanova Albena 
Published: March 2023

AbstractDominant mutations in tyrosyl-tRNA synthetase (YARS1) and six other tRNA ligases cause Charcot-Marie-Tooth peripheral neuropathy (CMT). Loss of aminoacylation is not required for their pathogenicity, suggesting a gain-of-function disease mechanism. By an unbiased genetic screen inDrosophila, we link YARS1 dysfunction to actin cytoskeleton organization. Biochemical studies uncover yet unknown actin-bundling property of YARS1 to be enhanced by a CMT mutation, leading to actin disorganization in theDrosophilanervous system, human SH-SY5Y neuroblastoma cells, and patient-derived fibroblasts. Genetic modulation of F-actin organization improves hallmark electrophysiological and morphological features in neurons of flies expressing CMT-causing YARS1 mutations. Similar beneficial effects are observed in flies expressing a neuropathy-causing glycyl-tRNA synthetase. Hence, in this work, we show that YARS1 is an evolutionary-conserved F-actin organizer which links the actin cytoskeleton to tRNA-synthetase-induced neurodegeneration.
Genomic diversity of non-diarrheagenic fecal Escherichia coli from children in sub-Saharan Africa and south Asia and their relatedness to diarrheagenic E. coli
Authors: Hazen Tracy H. , Michalski Jane M. , Tennant Sharon M. , Rasko David. A. 
Published: March 2023

AbstractEscherichia coli is a frequent member of the healthy human gastrointestinal microbiota, as well as an important human pathogen. Previous studies have focused on the genomic diversity of the pathogenic E. coli and much remains unknown about the non-diarrheagenic E. coli residing in the human gut, particularly among young children in low and middle income countries. Also, gaining additional insight into non-diarrheagenic E. coli is important for understanding gut health as non-diarrheagenic E. coli can prevent infection by diarrheagenic bacteria. In this study we examine the genomic diversity of non-diarrheagenic fecal E. coli from male and female children with or without diarrhea from countries in sub-Saharan Africa and south Asia as part of the Global Enteric Multicenter Study (GEMS). We find that these E. coli exhibit considerable genetic diversity as they were identified in all E. coli phylogroups and an Escherichia cryptic clade. Although these fecal E. coli lack the characteristic virulence factors of diarrheagenic E. coli pathotypes, many exhibit remarkable genomic similarity to previously described diarrheagenic isolates with differences attributed to mobile elements. This raises an important question of whether these non-diarrheagenic fecal E. coli may have at one time possessed the mobile element-encoded virulence factors of diarrheagenic pathotypes or may have the potential to acquire these virulence factors.
Ozone exposure disrupts insect sexual communication
Authors: Jiang Nan-Ji , Chang Hetan , Weißflog Jerrit , Eberl Franziska , Veit Daniel , Weniger Kerstin , Hansson Bill S. , Knaden Markus 
Published: March 2023

AbstractInsect sexual communication often relies upon sex pheromones. Most insect pheromones, however, contain carbon-carbon double bonds and potentially degrade by oxidation. Here, we show that frequently reported increased levels of Anthropocenic ozone can oxidize all described male-specific pheromones of Drosophila melanogaster, resulting in reduced amounts of pheromones such as cis-Vaccenyl Acetate and (Z)−7-Tricosene. At the same time female acceptance of ozone-exposed males is significantly delayed. Interestingly, groups of ozone-exposed males also exhibit significantly increased levels of male-male courtship behaviour. When repeating similar experiments with nine other drosophilid species, we observe pheromone degradation and/or disrupted sex recognition in eight of them. Our data suggest that Anthropocenic levels of ozone can extensively oxidize double bonds in a variety of insect pheromones, thereby leading to deviations in sexual recognition.
Contribution of tree community structure to forest productivity across a thermal gradient in eastern Asia
Authors: Kohyama Tetsuo I. , Sheil Douglas , Sun I-Fang , Niiyama Kaoru , Suzuki Eizi , Hiura Tsutom , Nishimura Naoyuki , Hoshizaki Kazuhiko , Wu Shu-Hui , Chao Wei-Chun , Nur Hajar Zamah S. , Rahajoe Joeni S. , Kohyama Takashi S. 
Published: March 2023

AbstractDespite their fundamental importance the links between forest productivity, diversity and climate remain contentious. We consider whether variation in productivity across climates reflects adjustment among tree species and individuals, or changes in tree community structure. We analysed data from 60 plots of humid old-growth forests spanning mean annual temperatures (MAT) from 2.0 to 26.6 °C. Comparing forests at equivalent aboveground biomass (160 Mg C ha–1), tropical forests ≥24 °C MAT averaged more than double the aboveground woody productivity of forests <12 °C (3.7 ± 0.3 versus 1.6 ± 0.1 Mg C ha–1 yr–1). Nonetheless, species with similar standing biomass and maximum stature had similar productivity across plots regardless of temperature. We find that differences in the relative contribution of smaller- and larger-biomass species explained 86% of the observed productivity differences. Species-rich tropical forests are more productive than other forests due to the high relative productivity of many short-stature, small-biomass species.
Snapshots of the second-step self-splicing of Tetrahymena ribozyme revealed by cryo-EM
Authors: Li Shanshan , Palo Michael Z. , Zhang Xiaojing , Pintilie Grigore , Zhang Kaiming 
Published: March 2023

AbstractGroup I introns are catalytic RNAs that coordinate two consecutive transesterification reactions for self-splicing. To understand how the group I intron promotes catalysis and coordinates self-splicing reactions, we determine the structures of L-16 Tetrahymena ribozyme in complex with a 5′-splice site analog product and a 3′-splice site analog substrate using cryo-EM. We solve six conformations from a single specimen, corresponding to different splicing intermediates after the first ester-transfer reaction. The structures reveal dynamics during self-splicing, including large conformational changes of the internal guide sequence and the J5/4 junction as well as subtle rearrangements of active-site metals and the hydrogen bond formed between the 2′-OH group of A261 and the N2 group of guanosine substrate. These results help complete a detailed structural and mechanistic view of this paradigmatic group I intron undergoing the second step of self-splicing.
MicroRNA156 conditions auxin sensitivity to enable growth plasticity in response to environmental changes in Arabidopsis
Authors: Sang Qing , Fan Lusheng , Liu Tianxiang , Qiu Yongjian , Du Juan , Mo Beixin , Chen Meng , Chen Xuemei 
Published: March 2023

AbstractMicroRNAs (miRNAs) play diverse roles in plant development, but whether and how miRNAs participate in thermomorphogenesis remain ambiguous. Here we show that HYPONASTIC LEAVES 1 (HYL1)—a key component of miRNA biogenesis—acts downstream of the thermal regulator PHYTOCHROME INTERACTING FACTOR 4 in the temperature-dependent plasticity of hypocotyl growth inArabidopsis. Ahyl1-2suppressor screen identified a dominantdicer-like1allele that rescueshyl1-2’s defects in miRNA biogenesis and thermoresponsive hypocotyl elongation. Genome-wide miRNA and transcriptome analysis revealed microRNA156 (miR156) and its targetSQUAMOSA PROMOTER-BINDING-PROTEIN-LIKE 9(SPL9) to be critical regulators of thermomorphogenesis. Surprisingly, perturbation of the miR156/SPL9module disengages seedling responsiveness to warm temperatures by impeding auxin sensitivity. Moreover, miR156-dependent auxin sensitivity also operates in the shade avoidance response at lower temperatures. Thus, these results unveil the miR156/SPL9module as a previously uncharacterized genetic circuit that enables plant growth plasticity in response to environmental temperature and light changes.
SAPS3 subunit of protein phosphatase 6 is an AMPK inhibitor and controls metabolic homeostasis upon dietary challenge in male mice
Authors: Yang Ying , Reid Michael A. , Hanse Eric A. , Li Haiqing , Li Yuanding , Ruiz Bryan I. , Fan Qi , Kong Mei 
Published: March 2023

AbstractInhibition of AMPK is tightly associated with metabolic perturbations upon over nutrition, yet the molecular mechanisms underlying are not clear. Here, we demonstrate the serine/threonine-protein phosphatase 6 regulatory subunit 3, SAPS3, is a negative regulator of AMPK. SAPS3 is induced under high fat diet (HFD) and recruits the PP6 catalytic subunit to deactivate phosphorylated-AMPK, thereby inhibiting AMPK-controlled metabolic pathways. Either whole-body or liver-specific deletion of SAPS3 protects male mice against HFD-induced detrimental consequences and reverses HFD-induced metabolic and transcriptional alterations while loss of SAPS3 has no effects on mice under balanced diets. Furthermore, genetic inhibition of AMPK is sufficient to block the protective phenotype in SAPS3 knockout mice under HFD. Together, our results reveal that SAPS3 is a negative regulator of AMPK and suppression of SAPS3 functions as a guardian when metabolism is perturbed and represents a potential therapeutic strategy to treat metabolic syndromes.
2019 M7.1 Ridgecrest earthquake slip distribution controlled by fault geometry inherited from Independence dike swarm
Authors: Nevitt Johanna M. , Brooks Benjamin A. , Hardebeck Jeanne L. , Aagaard Brad T. 
Published: March 2023

AbstractFaults often form through reactivation of pre-existing structures, developing geometries and mechanical properties specific to the system’s geologic inheritance. Competition between fault geometry and other factors (e.g., lithology) to control slip at Earth’s surface is an open question that is central to our knowledge of fault processes and seismic hazards. Here we use remote sensing data and field observations to investigate the origin of the 2019 M7.1 Ridgecrest, California, earthquake rupture geometry and test its impact on the slip distribution observed at Earth’s surface. Common geometries suggest the fault system evolved through reactivation of structures within the surrounding Independence dike swarm (IDS). Mechanical models testing a range of fault geometries and stress fields indicate that the inherited rupture geometry strongly controlled the M7.1 earthquake slip distribution. These results motivate revisiting the development of other large-magnitude earthquake ruptures (1992 M7.3 Landers, 1999 M7.1 Hector Mine) and tectonic provinces within the IDS.
Creating complex protocells and prototissues using simple DNA building blocks
Authors: Arulkumaran Nishkantha , Singer Mervyn , Howorka Stefan , Burns Jonathan R. 
Published: March 2023

AbstractBuilding synthetic protocells and prototissues hinges on the formation of biomimetic skeletal frameworks. Recreating the complexity of cytoskeletal and exoskeletal fibers, with their widely varying dimensions, cellular locations and functions, represents a major material hurdle and intellectual challenge which is compounded by the additional demand of using simple building blocks to ease fabrication and control. Here we harness simplicity to create complexity by assembling structural frameworks from subunits that can support membrane-based protocells and prototissues. We show that five oligonucleotides can anneal into nanotubes or fibers whose tunable thicknesses and lengths spans four orders of magnitude. We demonstrate that the assemblies’ location inside protocells is controllable to enhance their mechanical, functional and osmolar stability. Furthermore, the macrostructures can coat the outside of protocells to mimic exoskeletons and support the formation of millimeter-scale prototissues. Our strategy could be exploited in the bottom-up design of synthetic cells and tissues, to the generation of smart material devices in medicine.
Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization
Authors: Amselem Elias , Broadwater Bo , Hävermark Tora , Johansson Magnus , Elf Johan 
Published: March 2023

AbstractReaching sub-millisecond 3D tracking of individual molecules in living cells would enable direct measurements of diffusion-limited macromolecular interactions under physiological conditions. Here, we present a 3D tracking principle that approaches the relevant regime. The method is based on the true excitation point spread function and cross-entropy minimization for position localization of moving fluorescent reporters. Tests on beads moving on a stage reaches 67 nm lateral and 109 nm axial precision with a time resolution of 0.84 ms at a photon count rate of 60 kHz; the measurements agree with the theoretical and simulated predictions. Our implementation also features a method for microsecond 3D PSF positioning and an estimator for diffusion analysis of tracking data. Finally, we successfully apply these methods to track the Trigger Factor protein in living bacterial cells. Overall, our results show that while it is possible to reach sub-millisecond live-cell single-molecule tracking, it is still hard to resolve state transitions based on diffusivity at this time scale.
Higher productivity in forests with mixed mycorrhizal strategies
Authors: Luo Shan , Phillips Richard P. , Jo Insu , Fei Songlin , Liang Jingjing , Schmid Bernhard , Eisenhauer Nico 
Published: March 2023

AbstractDecades of theory and empirical studies have demonstrated links between biodiversity and ecosystem functioning, yet the putative processes that underlie these patterns remain elusive. This is especially true for forest ecosystems, where the functional traits of plant species are challenging to quantify. We analyzed 74,563 forest inventory plots that span 35 ecoregions in the contiguous USA and found that in ~77% of the ecoregions mixed mycorrhizal plots were more productive than plots where either arbuscular or ectomycorrhizal fungal-associated tree species were dominant. Moreover, the positive effects of mixing mycorrhizal strategies on forest productivity were more pronounced at low than high tree species richness. We conclude that at low richness different mycorrhizal strategies may allow tree species to partition nutrient uptake and thus can increase community productivity, whereas at high richness other dimensions of functional diversity can enhance resource partitioning and community productivity. Our findings highlight the importance of mixed mycorrhizal strategies, in addition to that of taxonomic diversity in general, for maintaining ecosystem functioning in forests.
Biased IL-2 signals induce Foxp3-rich pulmonary lymphoid structures and facilitate long-term lung allograft acceptance in mice
Authors: Yamada Yoshito , Nguyen Tuan Thanh , Impellizzieri Daniela , Mineura Katsutaka , Shibuya Rintaro , Gomariz Alvaro , Haberecker Martina , Nilsson Jakob , Nombela-Arrieta César , Jungraithmayr Wolfgang , Boyman Onur 
Published: March 2023

AbstractTransplantation of solid organs can be life-saving in patients with end-stage organ failure, however, graft rejection remains a major challenge. In this study, by pre-conditioning with interleukin-2 (IL-2)/anti-IL-2 antibody complex treatment biased toward IL-2 receptor α, we achieved acceptance of fully mismatched orthotopic lung allografts that remained morphologically and functionally intact for more than 90 days in immunocompetent mice. These allografts are tolerated by the actions of forkhead box p3 (Foxp3)+ regulatory T (Treg) cells that home to the lung allografts. Although counts of circulating Treg cells rapidly return to baseline following cessation of IL-2 treatment, Foxp3+ Treg cells persist in peribronchial and peribronchiolar areas of the grafted lungs, forming organized clusters reminiscent of inducible tertiary lymphoid structures (iTLS). These iTLS in lung allografts are made of Foxp3+ Treg cells, conventional T cells, and B cells, as evidenced by using microscopy-based distribution and neighborhood analyses. Foxp3-transgenic mice with inducible and selective deletion of Foxp3+ cells are unable to form iTLS in lung allografts, and these mice acutely reject lung allografts. Collectively, we report that short-term, high-intensity and biased IL-2 pre-conditioning facilitates acceptance of vascularized and ventilated lung allografts without the need of immunosuppression, by inducing Foxp3-controlled iTLS formation within allografts.
A phase I open-label clinical trial to study drug-drug interactions of Dorzagliatin and Sitagliptin in patients with type 2 diabetes and obesity
Authors: Chen Li , Zhang Jiayi , Sun Yu , Zhao Yu , Liu Xiang , Fang Zhiyin , Feng Lingge , He Bin , Zou Quanfei , Tracey Gregory J. 
Published: March 2023

AbstractThis is a phase 1, open-label, single-sequence, multiple-dose, single-center trial conducted in the US (NCT03790839), to evaluate the clinical pharmacokinetics, safety and pharmacodynamics of dorzagliatin co-administered with sitagliptin in patients with T2D and obesity. The trial has completed. 15 patients with T2D and obesity were recruited and treated with sitagliptin 100 mg QD on Day 1-5, followed by a combination of sitagliptin 100 mg QD with dorzagliatin 75 mg BID at second stage on Day 6-10 and the third stage of dorzagliatin 75 mg BID alone on Day 11-15. Primary outcomes include pharmacokinetic geometric mean ratio (GMR), safety and tolerability. Secondary outcomes include the incremental area under the curve for 4 hours post oral glucose tolerance test (iAUC) of pharmacodynamic biomarkers and glucose sensitivity. GMR for AUC0-24h and Cmax were 92.63 (90% CI, 85.61, 100.22) and 98.14 (90% CI, 83.73, 115.03) in combination/sitagliptin, and 100.34 (90% CI, 96.08, 104.79) and 102.34 (90% CI, 86.92, 120.50) in combination/dorzagliatin, respectively. Combination treatment did not increase the adverse events and well-tolerated in T2D patients. Lack of clinically meaningful pharmacokinetic interactions between dorzagliatin and sitagliptin, and an improvement of glycemic control under combination potentially support their co-administration for diabetes management.
Perovskite quantum dot one-dimensional topological laser
Authors: Tian Jingyi , Tan Qi Ying , Wang Yutao , Yang Yihao , Yuan Guanghui , Adamo Giorgio , Soci Cesare 
Published: March 2023

AbstractVarious topological laser concepts have recently enabled the demonstration of robust light-emitting devices that are immune to structural deformations and tolerant to fabrication imperfections. Current realizations of photonic cavities with topological boundaries are often limited by outcoupling issues or poor directionality and require complex design and fabrication that hinder operation at small wavelengths. Here we propose a topological cavity design based on interface states between two one-dimensional photonic crystals with distinct Zak phases. Using a few monolayers of solution-processed all-inorganic cesium lead halide perovskite quantum dots as the ultrathin gain medium, we demonstrate a lithography-free, vertical-emitting, low-threshold, and single-mode laser emitting in the green. We show that the topological laser, akin to vertical-cavity surface-emitting lasers (VCSELs), is robust against local perturbations of the multilayer structure. We argue that the design simplicity and reduction of the gain medium thickness enabled by the topological cavity make this architecture suitable for low-cost and efficient quantum dot vertical emitting lasers operating across the visible spectral region.
Evidence-based guidance on reflective pavement for urban heat mitigation in Arizona
Authors: Schneider Florian A. , Ortiz Johny Cordova , Vanos Jennifer K. , Sailor David J. , Middel Ariane 
Published: March 2023

AbstractUrban overheating is an increasing threat to people, infrastructure, and the environment. Common heat mitigation strategies, such as green infrastructure, confront space limitations in current car-centric cities. In 2020, the City of Phoenix, Arizona, piloted a “cool pavement” program using a solar reflective pavement seal on 58 km of residential streets. Comprehensive micrometeorological observations are used to evaluate the cooling potential of the reflective pavement based on three heat exposure metrics—surface, air, and mean radiant temperatures—across three residential reflective pavement-treated and untreated neighborhoods. In addition, the solar reflectivity of reflective pavement is observed over 7 months across eight residential neighborhoods. Results are synthesized with the literature to provide context-based reflective pavement implementation guidelines to mitigate urban overheating where common strategies cannot be applied. The three most important contextual factors to consider for effective implementation include urban location, background climate type, and heat exposure metric of interest.