bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mature tubers of purple nutsedge (Cyperus rotundus) confer flooding tolerance by adopting a low-oxygen quiescence strategy that may contribute to its emergence in rice fields
Authors: Yi Shan-Chi , Wei Chen-Yang , Tong Yao , Xu Lin , Fan Dan-Li , Yu Shi-Xian , Liu Shu-Yu , Wu Ren-Hai , Liu Xiao-Liang , Tang Wen-Wei 
Published: October 2024

AbstractPurple nutsedge (Cyperus rotundus L.) is one of the world’s resilient upland weeds, primarily spreading through its tubers. Its emergence in rice (Oryza sativa L.) fields has been increasing, likely due to changing paddy-farming practices. This study aimed to investigate how C. rotundus, an upland weed, can withstand soil flooding and become a problematic weed in rice fields. The first comparative analysis focused on the survival and recovery characteristics of growing and mature tubers of C. rotundus exposed to soil-flooding conditions. Notably, mature tubers exhibited significant survival and recovery abilities in these environments. Based on this observation, further investigation was carried out to explore the morphological structure, nonstructural carbohydrates, and respiratory mechanisms of mature tubers in response to prolonged soil flooding. Over time, the mature tubers did not form aerenchyma but instead gradually accumulated lignified sclerenchymal fibers, with lignin content also increasing. After 90 d, the lignified sclerenchymal fibers and lignin contents were 4.0 and 1.1 times higher than those in the no soil-flooding treatment. Concurrently, soluble sugar content decreased while starch content increased, providing energy storage, and alcohol dehydrogenase activity rose to support anaerobic respiration via alcohol fermentation. These results indicated that mature tubers survived in soil-flooding conditions by adopting a low-oxygen quiescence strategy, which involves morphological adaptations through the development of lignified sclerenchymal fibers, increased starch reserves for energy storage, and enhanced anaerobic respiration. This mechanism likely underpins the flooding tolerance of mature C. rotundus tubers, allowing them to endure unfavorable conditions and subsequently germinate and grow once flooding subsides. This study provides a preliminary explanation of the mechanism by which mature tubers of C. rotundus from the upland areas confer flooding tolerance, shedding light on the reasons behind this weed’s increasing presence in rice fields.
Structured, inbred, and plastic: the genome and population genetics of the weed false cleavers (Galium spurium)
Authors: Martin Sara L. , Sears Elizabeth , James Tracey , Sharpe Shaun , Tidemann Breanne D. 
Published: October 2024

Abstract
False cleavers (Galium spurium L.) is an aggressive weed from the Rubiaceae. Here we assemble a chromosome-scale draft of its genome, laying the foundations for determining the genetic basis of auxinic herbicide resistance and for systematic research into its polyphyletic genus. We use the genome to examine the population genetics of material from the Canadian Prairies and, in concert with a common greenhouse experiment, to examine whether the phenotypic variation observed in the field results primarily from genetic or environmental factors. The genome assembly covers approximately 85% of G. spurium’s expected 360-Mbp genome size, with 94% of BUSCO (Benchmarking Universal Single-Copy Orthologs) genes complete and most single copy (89%). Approximately 37% of the genome is repetitive elements and 35,540 genes were annotated using RNA-seq data, including 100 homologues for genes involved in, or potentially involved in, herbicide resistance. The genome shows strong synteny with other members of the Rubiaceae, including smooth bedstraw (Cruciata laevipes Opiz) and robusta coffee [Coffea canephora (Pierre ex Froehner]. Double-digested RAD-seq data for the 19 populations from the Canadian Prairies indicated that G. spurium has high levels of population structure (FST = 0.54) and inbreeding (FIS = 0.86) with low levels of hetrozygosity (HO = 0.02) and nucleotide diversity (π = 0.0003). Variation in flowering time and seed weight largely overlapped among populations grown in the greenhouse. A redundancy analysis investigating genotype–phenotype associations showed few associations between single-nucleotide polymorphism (SNP) variation and these characteristics. In contrast, the majority of SNPs under selection were associated with mericarp hook density. This suggests that for most traits, environmental variation rather than genetic variation likely underlies phenotypic differences observed in the field. Several genes of interest, including several homologues involved in the assembly of the Skp1-Cullin-F-Box IR1/AFB E3 ubiquitin ligase complex (e.g., CAND1, ECR1), are located in areas of the genome with evidence of selection and are targets for further investigation.
Confirmation of glyphosate resistance in annual bluegrass (Poa annua) via EPSPS duplication in a soybean and rice rotation
Authors: Sudhakar Susee , Norsworthy Jason K. , Avent Tristan , González-Torralva Fidel , McElroy Scott , Butts Thomas R. 
Published: October 2024

Abstract
Annual bluegrass (Poa annua L.) populations in turfgrass have evolved resistance to several herbicides in the United States, but there has been no confirmed resistance from an agricultural field. Recently, glyphosate failed to control a P. annua population found in a field in a soybean [Glycine max (L.) Merr.] and rice (Oryza sativa L.) rotation in Poinsett County, AR. The present study focused on determining the sensitivity of a putatively resistant accession (R1) to glyphosate compared with two susceptible accessions (S1 and S2). The experiments included a dose–response study, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene copy number and expression analysis, and assessment of mutations in EPSPS. Based on the dose–response analysis, R1 required 1,038 g ae ha−1 of glyphosate to cause 50% biomass reduction, whereas S1 and S2 only required 148.2 and 145.5 g ae ha−1, respectively. The resistance index (RI) was approximately 7-fold relative to the susceptible accessions. Real-time polymerase chain reaction data revealed at least a 15-fold increase in the EPSPS copy number in R1, along with a higher gene expression. No mutations in EPSPS were found. Gene duplication was identified as the main mechanism conferring resistance in R1. The research presented here reports the first incidence of glyphosate resistance in P. annua from an agronomic field crop situation in the United States.
Setting Up Methane Mitigation Measures for Indian Rice Fields: Representative Emissions and New Interpretations
Authors: Sahil Fida Mohammad , Narayanan Mukund , Ilampooranan Idhayachandhiran 
Published: October 2024

AbstractRice cultivation produces methane (CH4) due to anaerobic conditions induced by flood irrigation, significantly contributing to global warming. While most studies use national emission factors (EFs), our study synthesized 726 published measurements across India (the second largest methane emitter after China) to develop district‐level water regime‐specific EFs for estimating district‐scale emissions and warming potential. CH4 emissions from Indian rice fields increased from 3.7 (3.4–4.1) Tg to 4.8 (4.4–5.3) Tg during 1966–2017, driven by rice area and water‐regime variations. Meanwhile, district‐level emissions increased by ∼930%, influenced by management practices such as animal manure, fertilizer application, and water input, accurately reflecting regional variations compared to previous estimates. Employing a novel muti‐output random forest mitigation model (R2 ∼ 0.9), we found that a 25% warming reduction at the district‐level requires curtailing animal manure, nitrogen fertilizer, and water input by 8.5%, 12.9%, and 10.9%, respectively. These curtailments nearly double for a 50% mitigation scenario. Comparing our emissions with previous bottom‐up studies (used as inputs in global climate models) revealed discrepancies in prior national figures. With top‐down estimates, our emissions correlated positively, suggesting higher reliability. Including our new regionally validated data in global climate models may provide more accurate climate projections at the Indian and global scales.
Agricultural Irrigation Exacerbates Humid Heat Stress in the Mid‐Lower Reaches of the Yangtze River
Authors: Zou Liangfeng , Shao Dongguo , Zha Yuanyuan , Diao Yuqing , Chen Shu , Gu Wenquan 
Published: October 2024

AbstractMassive irrigation across eastern China (EC) could reduce extreme heat by altering energy and water budgets. However, the irrigation effect on increasing humidity has often been missed, especially in humid regions, leaving its effect and mechanism on extreme humid heat (EHH) poorly characterized. We analyzed assemblies of observations and performed regional simulations with more detailed irrigation scheme to explore the irrigation impacts and potential mechanisms on EHH. We find that irrigation in EC, despite having a cooling effect of about 0.2–0.6C, leads to an increase of about 0.4–0.8C in EHH, with a more intense impact on the Middle‐Lower Yangtze Plain (MLYP) by 0.9C. Cooling effect induced by increased latent heat fluxes through irrigation contributes to air deposition, which lowers boundary layer height, raises near‐surface moist enthalpy, and ultimately exacerbates the EHH. Results mechanistically emphasized irrigation impacts on EHH and highlighted the necessity of improving irrigation modeling reality.
Observations of the Near‐Field Yellow River Plume, Multiple Fronts and Their Biogeochemical Effects
Authors: Chen Zhixing , Wang Tao , Xu Dan , Jiang Wensheng , Bian Changwei 
Published: October 2024

AbstractRiver plumes transport fresh water into the ocean, and exhibit intense convergent and turbulent processes in the frontal regions, ultimately influencing coastal ecosystems. Satellite images show multiple fronts can be generated in river plumes. Although some efforts have been done to study the generation of multiple fronts inside river plumes by theoretical, numerical modeling and laboratory methods, their generation mechanisms and effects on biogeochemical processes remain to be clarified through in situ observational evidence. In the present study, the near‐field Yellow River plume, multiple fronts and their biogeochemical effects are investigated through moored, shipboard, and remote sensing observations. Numerical model simulations are conducted to help study the tidal movement of the Yellow River plume. The results show that the near‐field Yellow River plume is generally advected back and forth in the east‒west direction under the effects of tidal currents. Following the plume leading front, a turbulent bore is observed to be generated and mix near‐surface water with low turbidity and high concentration of dissolved oxygen into the water column. Behind the turbulent bore, a series of subfronts with distances of O (∼100 m) are formed. The generation mechanisms of these subfronts are found to be associated with internal shear instabilities. Under the effects of cross‐front shear currents and vertical mixing near the subfronts, a three‐layer structure of turbidity and surface low‐turbidity stripes form inside the plume. Multiple fronts also have significant effects on the accumulation of surface materials.
Monthly and Interannual Variations in Upwelling and Chlorophyll off the Vietnam Coast in Summer Based on Deep Learning
Authors: Lian Qiang , Lin Haiyuan , Huang Yawen , Zhang Shuwen , Chen Zhaoyun 
Published: October 2024

AbstractThe deep learning technique is used to automatically identify upwelling regions off the Vietnam coast using Sea Surface Temperature (SST) data from satellite imagery. After delineating these upwelling areas, this study is pioneering in deriving the upwelling probability off the Vietnam coast, pinpointing two significant upwelling hotspots. To deepen the understanding of the individual impacts of wind and sea surface height anomalies on monthly and spatial variations in upwelling probability and chlorophyll distribution, the Empirical Orthogonal Function method was employed to analyze this data set. The upwelling probability demonstrates a close relationship with wind and sea surface height anomalies, while chlorophyll concentration correlates with the strength of the southwesterly wind. The southwesterly wind, Ekman pumping, eddy dipole, and northeastward jet have been identified as key drivers of the formation and spatial variability of upwelling in summer, albeit with varying contributions to different parts of the coastal region. The distribution of upwelling probability correlates with chlorophyll variation off the northern Vietnam coast. High chlorophyll concentration off the southern Vietnam coast is primarily influenced by the southwesterly wind that carries the Mekong River plume eastward. Furthermore, two abnormal scenarios in upwelling and chlorophyll concentration during 2010 and 2018 were analyzed, attributed to the abnormal southwesterly monsoon and coastal circulation influenced by an El Niño event and a weak La Niña event with a positive Indian Ocean Dipole, respectively. This study elucidates the dynamic processes underlying the intricate chlorophyll distribution over the continental shelf, which is influenced by both the river plume and upwelling.
Vertical Carbon Export During a Phytoplankton Bloom in the Chukchi Sea: Physical Setting and Frontal Subduction
Authors: Pickart Robert S. , Spall Michael A. , Bahr Frank , Lago Loreley , Lin Peigen , Pacini Astrid , Mills Matthew , Huang Jie , Arrigo Kevin R. , van Dijken Gert , McRaven Leah T. , Roberts Steven 
Published: October 2024

AbstractIn order to quantify pelagic‐benthic coupling on high‐latitude shelves, it is imperative to identify the different physical mechanisms by which phytoplankton are exported to the sediments. In June–July 2023, a field program documented the evolution of an under‐ice phytoplankton bloom on the northeast Chukchi shelf. Here, we use in situ data from the cruise, a simple numerical model, historical water column data, and ocean reanalysis fields to characterize the physical setting and describe the dynamically driven vertical export of chlorophyll associated with the bloom. A water mass front separating cold, high‐nutrient winter water in the north and warmer summer waters to the south—roughly coincident with the ice edge—supported a baroclinic jet which is part of the Central Channel flow branch that veers eastward toward Barrow Canyon. A plume of high chlorophyll fluorescence extending from the near‐surface bloom in the winter water downwards along the front was measured throughout the cruise. Using a passive tracer to represent phytoplankton in the model, it was demonstrated that the plume is the result of subduction due to baroclinic instability of the frontal jet. This process, in concert with the gravitational sinking, pumps the chlorophyll downwards an order of magnitude faster than gravitational sinking alone. Particle tracking using the ocean reanalysis fields reveals that a substantial portion of the chlorophyll away from the front is advected off of the northeast Chukchi shelf before reaching the bottom. This highlights the importance of the frontal subduction process for delivering carbon to the sea floor.
Global Temperature Dependency of Biogenic HCHO Columns Observed From Space: Interpretation of TROPOMI Results Using GEOS‐Chem Model
Authors: Li Xicheng , Zhu Lei , De Smedt Isabelle , Sun Wenfu , Chen Yuyang , Shu Lei , Wang Dakang , Liu Song , Pu Dongchuan , Li Juan , Zuo Xiaoxing , Fu Weitao , Li Yali , Zhang Peng , Yan Zhuoxian , Fu Tzung‐May , Shen Huizhong , Wang Chen , Ye Jianhuai , Yang Xin 
Published: October 2024

AbstractTemperature is the principal driver of global atmospheric formaldehyde (HCHO) and its primary oxidation precursor biogenic volatile organic compounds (BVOCs). We revisit such a temperature (T‐) dependency globally, leveraging TROPOMI HCHO column data. We find substantial variations in the T‐dependency of biogenic HCHO across plant functional types (PFTs), with the highest over Broadleaf Evergreen Tropical Trees (doubling every 6.0 K ± 4.1 K) and lowest over Arctic C3 Grass (doubling every 30.8 K ± 9.6 K). The GEOS‐Chem model interprets HCHO columns' T‐dependency at the PFT level (r = 0.87), with a 16% discrepancy on average. The discrepancy can be explained by BVOC emissions T‐dependency for Broadleaf Evergreen Tropical Trees and Warm C4 Grass and can be attributed to the insensitivity of HCHO columns to BVOC emissions for other PFTs. Our findings underscore a potentially magnified variation of BVOC emissions by GEOS‐Chem and MEGAN therein, particularly in regions experiencing greater temperature variations.
Divergent Responses of Organic Carbon to Sedimentary Environment Transformation in a River‐Dominated Marginal Sea
Authors: Zhang Zhuoyue , Lu Ming , Wang Chenglong , Zhang Chuchu , Lin Bingying , Liao Qihang , Qiu Penghua , Zou Xinqing 
Published: October 2024

AbstractThe fate of organic carbon (OC) in most river‐dominated ocean margins (RiOMars) has undergone a noticeable transformation with the increased sediment retention engineering in watersheds. In the East China Sea (ECS), transformation in sediment and the influence of bulk OC have been broadly studied. However, the response of different mechanisms of OC protection under transformation has not been investigated, hindering our understanding of the factors that control OC deposition. In this study, we isolated different OC fractions, analyzed the basic parameters of the sediments, and compared the previous study's data to reveal how OC deposition responded to transformation. Our research indicates that transformation leads to the reduction of OC associated with minerals and sorting of OC occluded by plant debris and OC associated with minerals resulting in increased decomposition and mineralization of OC. The transformation affects the mechanism of OC binding with reactive iron (FeR), increasing FeR‐protected OC content. Still, the co‐precipitation mechanism and the intense redox environment in the mud deposit decrease the FeR‐protected OC stability. Taken together, the impact of transformation is to increase the risk of OC decomposition and to weaken the OC preservation ability in RiOMars as carbon sinks. This study has implications for river‐dominated passive margins subject to increased sediment retention engineering in watersheds worldwide and deserves more attention.
Dynamic Responses of Outer Radiation Belt Electron Phase Space Densities to Geomagnetic Storms: A Statistical Analysis Based on Van Allen Probes Observations
Authors: Wang Xiaoyu , Ni Binbin , Cao Xing , Ma Xin , Lei Yuan , Dou Xiankang 
Published: October 2024

AbstractUsing Van Allen Probes observations from September 2012 to June 2019, we statistically investigate responses of the Earth's outer radiation belt electron phase space densities (PSDs) in the adiabatic invariant coordinates to isolated geomagnetic storms. Electron PSDs for μ = 50–5,000 MeV/G, covering energy range of seed, relativistic and ultra‐relativistic electrons, are calculated to evaluate three types of storm‐time PSD responses (i.e., enhancement, depletion, and no change). In statistics, the seed PSD variations are dominated by enhancement‐type events, the percentages of which increase from >50% for small storms (−50 nT < SYM‐Hmin ≤ −30 nT) to >70% for large storms (SYM‐Hmin ≤ −50 nT). The relativistic and ultra‐relativistic PSDs exhibit the three response types with comparable occurrence rates for small storms but present predominantly enhancement‐type variations (>50%) for large storms. Enhanced storm activity increases the enhancement‐type responses for seed PSDs at all L* and for relativistic and ultra‐relativistic PSDs at L* > 3.5. It also results in the increased depletion‐type response occurrence for relativistic and ultra‐relativistic PSDs at lower L*. Our results further indicate that the depletion‐type responses manifest evident dependence on the level of solar and geomagnetic activity and the μ‐value, implying complex physics accounting for outer zone electron losses. Improved knowledge of the storm‐time dynamics of outer radiation belt electron PSDs is valuable to in‐depth comprehension of various mechanisms responsible for the electron acceleration and loss. It has important implications for future simulations and forecasts of radiation belt electron variability, in particular, during geomagnetically disturbed periods.
Using Commercial Satellite Imagery to Reconstruct 3 m and Daily Spring Snow Water Equivalent
Authors: Pflug Justin M. , Yang Kehan , Cristea Nicoleta , Boudreau Emma T. , Vuyovich Carrie M. , Kumar Sujay V. 
Published: October 2024

AbstractSnow water equivalent (SWE) distribution at fine spatial scales (≤10 m) is difficult to estimate due to modeling and observational constraints. However, the distribution of SWE throughout the spring snowmelt season is often correlated to the timing of snow disappearance. Here, we show that snow cover maps generated from PlanetScope's constellation of Dove Satellites can resolve the 3 m date of snow disappearance across seven alpine domains in California and Colorado. Across a 5‐year period (2019–2023), the average uncertainty in the date of snow disappearance, or the period of time between the last date of observed snow cover and the first date of observed snow absence, was 3 days. Using a simple shortwave‐based snowmelt model calibrated at nearby snow pillows, the PlanetScope date of snow disappearance could be used to reconstruct spring SWE. Relative to lidar SWE estimates, the SWE reconstruction had a spatial coefficient of correlation of 0.75, and SWE spatial variability that was biased by 9%, on average. SWE reconstruction biases were then improved to within 0.04 m, on average, by calibrating snowmelt rates to track the spring temporal evolution of fractional snow cover observed by PlanetScope, including fractional snow cover over the full modeling domain, and across domain subsections where snowmelt rates may differ. This study demonstrates the utility of fine‐scale and high‐frequency optical observations of snow cover, and the simple and annually repeatable connections between snow cover and spring snow water resources in regions with seasonal snowpack.
GPA33 expression in colorectal cancer can be induced by WNT inhibition and targeted by cellular therapy
Authors: Börding Teresa , Janik Tobias , Bischoff Philip , Morkel Markus , Sers Christine , Horst David 
Published: October 2024

AbstractGPA33 is a promising surface antigen for targeted therapy in colorectal cancer (CRC). It is expressed almost exclusively in CRC and intestinal epithelia. However, previous clinical studies have not achieved expected response rates. We investigated GPA33 expression and regulation in CRC and developed a GPA33-targeted cellular therapy. We examined GPA33 expression in CRC cohorts using immunohistochemistry and immunofluorescence. We analyzed GPA33 regulation by interference with oncogenic signaling in vitro and in vivo using inhibitors and conditional inducible regulators. Furthermore, we engineered anti-GPA33-CAR T cells and assessed their activity in vitro and in vivo. GPA33 expression showed consistent intratumoral heterogeneity in CRC with antigen loss at the infiltrative tumor edge. This pattern was preserved at metastatic sites. GPA33-positive cells had a differentiated phenotype and low WNT activity. Low GPA33 expression levels were linked to tumor progression in patients with CRC. Downregulation of WNT activity induced GPA33 expression in vitro and in GPA33-negative tumor cell subpopulations in xenografts. GPA33-CAR T cells were activated in response to GPA33 and reduced xenograft growth in mice after intratumoral application. GPA33-targeted therapy may be improved by simultaneous WNT inhibition to enhance GPA33 expression. Furthermore, GPA33 is a promising target for cellular immunotherapy in CRC.