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At least 19 records

GhBZR3 suppresses cotton fiber elongation by inhibiting very‐long‐chain fatty acid biosynthesis

SUMMARY The BRASSINAZOLE‐RESISTANT (BZR) transcription factor is a core component of brassinosteroid (BR) signaling and is involved in the development of many plant species. BR is essential for the initiation and elongation of cotton fibers. However, the mechanism of BR‐regulating fiber development and the function of BZR is poorly understood in Gossypium hirsutum L. (cotton). Here, we identified a BZR family transcription factor protein referred to as GhBZR3 in cotton. Overexpression of GhBZR3 in Arabidopsis caused shorter root hair length, hypocotyl length, and hypocotyl cell length, indicating that GhBZR3 negatively regulates cell elongation. Pathway enrichment analysis from VIGS ‐GhBZR3 cotton plants found that fatty acid metabolism and degradation might be the regulatory pathway that is primarily controlled by GhBZR3. Silencing GhBZR3 expression in cotton resulted in taller plant height as well as longer fibers. The very‐long‐chain fatty acid (VLCFA) content was also significantly increased in silenced GhBZR3 plants compared with the wild type. The GhKCS13 promoter, a key gene for VLCFA biosynthesis, contains two GhBZR3 binding sites. The results of yeast one‐hybrid, electrophoretic mobility shift, and luciferase assays revealed that GhBZR3 directly interacted with the GhKCS13 promoter to suppress gene expression. Taken together, these results indicate that GhBZR3 negatively regulates cotton fiber development by reducing VLCFA biosynthesis. This study not only deepens our understanding of GhBZR3 function in cotton fiber development, but also highlights the potential of improving cotton fiber length and plant growth using GhBZR3 and its related genes in future cotton breeding programs.

Shi, Zemin↗

Genome resources for three modern cotton lines guide future breeding efforts

Cotton ( Gossypium hirsutum L.) is the key renewable fibre crop worldwide, yet its yield and fibre quality show high variability due to genotype-specific traits and complex interactions among cultivars, management practices and environmental factors. Modern breeding practices may limit future yield gains due to a narrow founding gene pool. Precision breeding and biotechnological approaches offer potential solutions, contingent on accurate cultivar-specific data. Here we address this need by generating high-quality reference genomes for three modern cotton cultivars (‘UGA230’, ‘UA48’ and ‘CSX8308’) and updating the ‘TM-1’ cotton genetic standard reference. Despite hypothesized genetic uniformity, considerable sequence and structural variation was observed among the four genomes, which overlap with ancient and ongoing genomic introgressions from ‘Pima’ cotton, gene regulatory mechanisms and phenotypic trait divergence. Differentially expressed genes across fibre development correlate with fibre production, potentially contributing to the distinctive fibre quality traits observed in modern cotton cultivars. These genomes and comparative analyses provide a valuable foundation for future genetic endeavours to enhance global cotton yield and sustainability.

59 BASIC BIOLOGICAL SCIENCES↗

Filtration Performance of Layering Masks and Face Coverings and the Reusability of Cotton Masks after Repeated Washing and Drying

In this study, filtration efficiency of different respirators, face masks, and a 2-ply cotton handkerchief bandana was compared for particles in the size range of 60 nm-4 um under a "perfect fit" condition. The filtration efficiency at the most penetrating particle size of 0.3 um on average ranged from 83-99% for N95 and KN95 respirators, 42-88% for surgical masks, 16-23% for cloth masks, and 9% for bandana. We also investigated the effects of using double surgical masks or layering a cloth mask over various surgical masks in terms of their filtration characteristics. In most of these combinations, the filtration efficiency improved by ~25% for particles 0.3-1 um in diameter without any substantial change in the filter quality factor when compared to the highest of the individual mask results. To investigate the reusability of cotton cloth masks, 2-layer cotton fabric sample coupons were machine washed and dried for 52 cycles leading to an increase in inhalation resistance (~20 Pa) without affecting size-resolved filtration efficiency. Scanning electron microscopy revealed that washing and drying led to the gradual deconstruction of cotton fibers at the scale of several micrometers to hundreds of nanometers in the form of delamination of the fiber wall and fibrillation of the nanofiber constituents. Results indicate that cloth masks may be layered over surgical masks for additional benefits, and that cloth masks made out of cotton fabric can be washed and reused numerous times without a significant loss in filtration efficiency.

99 GENERAL AND MISCELLANEOUS↗

The preparation and characterization of chemically deuterium incorporated cotton fibers

Preparation of deuterium incorporated cellulose is a vital tool to investigate cellulose internal structure and to expand the application fields of cellulose materials. In this study, cellulosic cotton fibers with anti-rehydration (exchange-resistant) deuterium incorporated in cellulose were prepared by chemical hydrogen–deuterium exchange treatment. The chemical hydrogen–deuterium exchange process, along with exchange time, were characterized by nuclear magnetic resonance hydrogen spectroscopy (1H-NMR). The anti-rehydration deuterium incorporation was determined by Fourier Transform infrared spectroscopy (FTIR) and Stable Isotope Ratio Mass Spectrometer (IRSM). Here, the effect of the deuterium hydroxyl substitution on cotton fiber’s spectral data, microstructure, crystalline information, degree of polymerization, as well as it’s thermogravimetric analysis (charcoalization and combustion) are explored. Analysis of the chemical exchange process indicated that the hydrogen–deuterium exchange occurred preferentially in the amorphous cellulose component over the first several minutes. Deuterium exchange in the anti-rehydration crystalline phase took several hours. Increasing the treatment time, enhanced exchange-resistant deuterium incorporation to as high as about 60% of the cotton fibers’ cellulose hydroxyl groups was achieved. The characterization of FTIR, Fourier transform Raman (FT-Raman), and near-infrared spectra (NIR) all exhibited the deuterium spectral isotope effect on cellulose hydroxl groups. While, apart from the effect of reaction temperature, deuterium incorporation isotope effect did not affect the cellulose microstructure, crystalline index and the degree of polymerization properties. Furthermore, the thermogravimetric analysis of deuterated cotton fibers under N 2 and air atmosphere were both altered due to the thermodynamic isotope effect. These observations revealed the hydrogen–deuterium exchange treatment process and impacts on cellulose fiber properties, which helped us to better understand the cellulose internal structure and may facilitate the potential utilization of deuterated cellulosic materials.

59 BASIC BIOLOGICAL SCIENCES↗

Lignin-first biorefining of Nordic poplar to produce cellulose fibers could displace cotton production on agricultural lands

Here, we show that lignin-first biorefining of poplar can enable the production of dissolving cellulose pulp that can produce regenerated cellulose, which could substitute cotton. These results in turn indicate that agricultural land dedicated to cotton could be reclaimed for food production by extending poplar plantations to produce textile fibers. Based on climate-adapted poplar clones capable of growth on marginal lands in the Nordic region, we estimate an environmentally sustainable annual biomass production of ~11 tonnes/ha. At scale, lignin-first biorefining of this poplar could annually generate 2.4 tonnes/ha of dissolving pulp for textiles and 1.1 m 3 biofuels. Life cycle assessment indicates that, relative to cotton production, this approach could substantially reduce water consumption and identifies certain areas for further improvement. Overall, this work highlights a new value chain to reduce the environmental footprint of textiles, chemicals, and biofuels while enabling land reclamation and water savings from cotton back to food production.

09 BIOMASS FUELS↗

AmeriFlux FLUXNET-1F US-NSb NASA HAQ - SJV West Irrigated Cotton

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-NSb NASA HAQ - SJV West Irrigated Cotton. This is the FLUXNET version of the carbon flux data for the site US-NSb NASA HAQ - SJV West Irrigated Cotton produced by applying the standard ONEFlux (1F) software. Site Description - Irrigated cotton field loated on the west side of the San Joaquin Valley, utilizing furrow irrigation. The flux tower is situated in the southeastern corner of a 200 * 300 m field densely planted with Egyptian cotton. Surrounding land is primarily cultivated with other crops.

Davis, Kenneth [The Pennsylvania State University]↗

Direct isotopic analysis of solid uranium particulates on cotton swipes by microextraction-ICP-MS

Direct isotope ratio analysis of solid uranium particulates on cotton swipes was achieved using a solution-based microextraction technique, coupled to a quadrupole inductively coupled plasma - mass spectrometer (ICP-MS). This microextraction-ICP-MS methodology provides rapid isotopic analysis which could be applicable to nuclear safeguards measurements. Particulates of uranyl nitrate hexahydrate (UO 2 (NO 3 ) 2 ·6H 2 O) and uranyl fluoride (UO 2 F 2 ) ranging from 6 μm to 40 μm in length were transferred to cotton swipes with a particle manipulator. The microextraction probe then delivers a 5% nitric acid (HNO3) solvent onto the swipe surface to extract the uranium species. The extracted sample is then delivered to the ICP-MS for isotopic determination. The majority of uranium signal (~99% and ~94% for UO2(NO3)2·6H2O and UO 2 F 2 , respectively) was detected in the first 15 s extraction, while subsequent extractions on the same location had low or no U signal, suggesting near complete removal of the solid uranium compounds from the swipe surface. Ten samples (for each of the uranium compounds), were analyzed for their isotopic composition. For UO 2 (NO 3 ) 2 ·6H 2 O, the determined isotope ratios resulted in a % relative difference (% RD) from the referenced isotope ratios of 0.97, 1.0, and 7.3% for 234 U/ 238 U, 235 U/ 238 U, and 236 U/ 238 U, respectively. The % RD of the UO 2 F 2 isotope ratios were 1.9 and 0.60% for 234 U/ 238 U and 235 U/ 238 U, respectively. The preliminary limits of detection were determined to be 0.002, 0.4, and 60 pg for 234 U, 235 U and 238 U, respectively This work demonstrates that microextraction ICP-MS is a rapid and sensitive method that could directly determine uranium isotope ratios of UO 2 (NO 3 ) 2 ·6H 2 O and UO 2 F 2 particulates on cotton swipes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Microextraction–TQ–ICP–MS for the Direct Analysis of U and Pu from Cotton Swipes

Here, the microextraction sampling technique was integrated with triple quadrupole–inductively coupled plasma–mass spectrometry (TQ–ICP–MS) to directly sample and measure the isotopic compositions of uranium (U) and plutonium (Pu) from cotton swipes. Once extracted, the U/Pu were directed into the TQ–ICP–MS instrument for isotopic determination. Carbon dioxide (CO 2 ) and helium (He) gases were delivered to a collision reaction cell within the ICP–MS system for ion separation. The CO 2 reacts with the U + forming UO + which is ultimately separated from the Pu + ions of interest in the third quadrupole. This study demonstrates direct liquid extraction of U/Pu from a solid surface and subsequent measurement by TQ–ICP–MS in <60 s. Flow rates were optimized (0.3 mL min –1 CO 2 and 5 mL min –1 He) in the reaction cell of the ICP–MS system to maximize the Pu signal while minimizing U interferences (i.e., 238 U + tail and 238 UH + ) at m/z 239. Low levels of Pu (~2 pg) were deposited on a cotton swipe along with U at concentrations ranging from 20 to 200 ng. The 240 Pu/ 239 Pu ratio was measured with <7% relative difference from the certified value at all U concentrations. Major and minor U isotope ratios were also measured with <4% relative difference. This highlights that the microextraction–TQ–ICP–MS method can extract a mixed U/Pu sample directly from a cotton swipe and measure both isotopic systems without chemical separation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

Abstract Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection and domestication remains elusive. Here we analyze genome evolution and diversification for all five allopolyploid cotton species, including economically important Upland and Pima cottons. Although these polyploid genomes are conserved in gene content and synteny, they have diversified by subgenomic transposon exchanges that equilibrate genome size, evolutionary rate heterogeneities and positive selection between homoeologs within and among lineages. These differential evolutionary trajectories are accompanied by gene-family diversification and homoeolog expression divergence among polyploid lineages. Selection and domestication drive parallel gene expression similarities in fibers of two cultivated cottons, involving coexpression networks and N 6 -methyladenosine RNA modifications. Furthermore, polyploidy induces recombination suppression, which correlates with altered epigenetic landscapes and can be overcome by wild introgression. These genomic insights will empower efforts to manipulate genetic recombination and modify epigenetic landscapes and target genes for crop improvement.

59 BASIC BIOLOGICAL SCIENCES↗

Round Robin Analysis of Uranium Isotopics on Cotton Swipes Measured Using Microextraction-Based Sampling Versus Conventional Bulk Analysis

A comparison of microextraction sampling methods to directly analyze uranium isotopics on cotton swipes was performed concurrently with traditional bulk-processing methods. For the microextraction sampling approach, two different detection platforms were evaluated, a quadrupole-based inductively coupled plasma mass spectrometer (ICP-MS) and the liquid sampling-atmospheric pressure glow discharge (LS-APGD) coupled to an Orbitrap mass spectrometer. Results presented from this innovative sampling approach (i.e., microextraction) are compared with a more traditional approach employed for analysis of cotton-based environmental swipes, namely bulk ashing/digestion, separation, and subsequent analysis by high-precision multi-collector ICP-MS. Overall, the microextraction approach proved to be a reliable and accurate means to determine isotopic ratios of uranium collected on cotton swipes. The ICP-MS-based detection had relative standard deviations of <0.65% for the major isotopic determinations, whereas the LS-APGD-Orbitrap method had relative standard deviations of <3%. The percent relative difference for the 235 U/ 238 U ratios, in comparison to the expected values, was <1% for ICP-MS and <4% for the microplasma-Orbitrap method. Additionally, the microextraction ICP-MS accurately (<2%) and precisely (<5%) determined the minor isotopic compositions (i.e., 234 U/ 238 U and 236 U/ 238 U).

ICP-MS↗

Spatial Study 2022: Surface Water Samples, Cotton Strip Degradation, and Hydrologic Sensor Data across the Yakima River Basin, Washington, USA (v3)

This dataset supports a broader study examining the drivers of spatial variability in sediment respiration rates in the Yakima River Basin. The dataset provides data and photos generated from sample collection during the same one-week period at 48 sites within multiple rivers throughout the Yakima River Basin in Washington, USA. The contents include surface water geochemistry data; river substrate grain size photos; stream depth data; manual chamber open channel respiration data; and field metadata (including qualitative information on instream and river corridor characteristics). Grain size photos can be used to improve estimates of channel substrate D50 data. The dataset also includes tensile strength and photos from cotton strip field degradation experiments; five-week sensor time series temperature, dissolved oxygen, pressure, pH, specific conductance, chlorophyll A, and turbidity data; plots of the sensor data; and R scripts used to generate the plots. Samples collected during this study were labeled as “Second Spatial Study” or “SSS.” A subset of data from the SSS samples were published in the contiguous United States (CONUS)-Scale Model-Sample (CM) study data package available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1923689 that presents data from across the CONUS. SSS data published in the CM data package were not included in this data package. They include dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC), total nitrogen (TN), grain size, aerobic sediment respiration, dissolved oxygen (DO), and temperature. Parent IDs and Site IDs are consistent between the SSS and CM data packages, and they can be mapped directly so data across packages can be used together. Additionally, sensor data from a similar 2021 spatial study can be found at https://data.ess-dive.lbl.gov/view/doi:10.15485/1892052 and 2021 sample data can be found at https://data.ess-dive.lbl.gov/view/doi:10.15485/1898914. The 2021 spatial study had some sites in common with this 2022 spatial study. This dataset is comprised of three photo folders and one main data folder with six subfolders. The photo folders contain photographs and videos of cotton strip retrieval and sediment quadrats. The main data folder consists of (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) total suspended solids (TSS) data and cotton strip tensile strength data and averages; (5) field protocol; (6) readme; (7) methods codes; (8) international generic sample number (IGSN) mapping file; (9) sensor installation methods summary; (10) stream depth and averages; and (11) Ultrameter data and averages. The Sonar subfolder consists of Sonar time-series depth data and a processing script. The BarotrollAtm, DepthHOBO, MantaRiver, miniDOT, and miniDOTManualChamber subfolders contain time-series data, plots, and summary files. All files are .csv, .pdf, .txt, .R, .Rmd, .jpg, .jpeg, .AVI, .mp4, or .mov. The data package was originally published in April 2023. It was updated in August 2023 (v2; modified files) and September 2024 (v3; modified files). See the change history section in the readme for details. We acknowledge the Yakama Nation as owners and caretakers of the lands where we collected these data. We thank the Confederated Tribes and Bands of the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗

AmeriFlux US-NSb NASA HAQ - SJV West Irrigated Cotton

This is the AmeriFlux version of the carbon flux data for the site US-NSb NASA HAQ - SJV West Irrigated Cotton. Site Description - Irrigated cotton field loated on the west side of the San Joaquin Valley, utilizing furrow irrigation. The flux tower is situated in the southeastern corner of a 200 * 300 m field densely planted with Egyptian cotton. Surrounding land is primarily cultivated with other crops.

Davis, Kenneth [The Pennsylvania State University]↗

AmeriFlux FLUXNET-1F US-WT1 Kress, TX no-till cotton and grain sorghum production

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-WT1 Kress, TX no-till cotton and grain sorghum production. This is the FLUXNET version of the carbon flux data for the site US-WT1 Kress, TX no-till cotton and grain sorghum production produced by applying the standard ONEFlux (1F) software. Site Description - Non irrigated cotton and gain sorghum production

Bednarz, Craig [West Texas A&M University]↗

Depth-dependent links between microbial taxa and nitrous oxide emissions in a long-term cotton cropping system employing soil health practices

Long-term management practices can shape soil microbial communities in ways that influence nitrogen (N) dynamics and nitrous oxide (N 2 O) emissions. We leverage a 41-year continuous cotton cropping experiment with contrasting tillage, cover cropping, and N fertilization regimes to investigate how these long-term strategies influence soil microbial communities and their associations with N 2 O fluxes during the cotton growing season. Using 16S rRNA gene metabarcoding, we assessed microbial composition in surface and subsurface soils and evaluated its relationship with temporal N 2 O emissions. Among the management practices, N fertilization – a known driver of N 2 O emissions – had the strongest effect on microbial community composition and was linked to a greater number of taxa correlated to N 2 O emissions, particularly in surface soils. Soil pH emerged as a key variable influencing microbial structure across depth and was negatively associated with both N 2 O emissions and microbial composition in the surface layers of fertilized soils. In total, 57 archaeal/bacterial taxa were correlated with N 2 O fluxes, but only seven were shared across depths, suggesting distinct microbial contributors in surface and subsurface soils. Several of these taxa have been previously reported to be associated with N and C cycling processes such as nitrate respiration or carbon turnover, indicating functional context to their correlation with N 2 O fluxes. Temporal shifts in the abundance of key taxa aligned with seasonal peaks in N 2 O emissions, notably in early and late August, and were most pronounced under conventional tillage, hairy vetch cover cropping, and N fertilization. While 16S-based associations cannot confirm functional gene presence or activity, these findings demonstrate that long-term fertilization and associated soil acidification are dominant drivers of microbial shifts linked to N 2 O emissions and highlight the importance of accounting for depth-specific and seasonal microbial dynamics when evaluating management impacts on greenhouse gas emissions.

16S rRNA gene sequencing↗

Analysis of solid uranium particulates on cotton swipes with an automated microextraction-ICP-MS system

Here, an automated microextraction method coupled to an inductively coupled plasma – mass spectrometer (ICP-MS) was developed for the direct analysis of solid uranium particulates on the surface of cotton swipes. The microextraction probe extracts particulates from the sample surface, in a flowing solvent, and directs the removed analyte to an ICP-MS for isotopic determination. The automated system utilizes a mechanical XY stage that is software controlled with the capability of saving and returning to specific locations and a camera focused to the swipe surface for optimal viewing of the extracted locations (i.e., material present). Here, particulates (n = 135) were extracted and measured by ICP-MS, including 35 depleted uranyl nitrate hexahydrate (UN) (used for mass bias corrections), 50 uranyl fluoride (UO 2 F 2 ), and 50 uranyl acetate (UAc) particulates. Blank extractions were performed on the cotton swipes between triplicate sample analyses. Between each swipe extraction, the probe was sent between two wells containing 10% and 5% HNO 3 to clean the probe head and to eliminate any analyte carryover between particulates. The measured 235 U/ 238 U and 234 U/ 238 U isotope ratios for the UO 2 F 2 particulates were 0.00725(8) and 0.000054(4), a percent relative difference (% RD) of –0.041% and –1.7% from the reference isotope ratios determined in-lab through multi-collector ICP-MS analysis of dissolved aliquots of the U material. The UAc samples had a measured 235 U/ 238 U isotope ratio of 0.00206(7), a –0.96% relative difference from the reference value of 0.00208(1). The 234 U/ 238 U and 236 U/ 238 U isotope ratios were 0.000008(1) and 0.000031(4), –5.1% RD and –4.3% RD, respectively. The automated sample stage enabled seamless and rapid particle analysis, leading to a significant increase in throughput versus what was previously possible. Additionally, the saved location capability reduced user sampling error as sampling locations were easily stored and recalled. Analysis of U particles on the swipe surface – including blanks, mass bias, and triplicate extractions – was completed in less than an hour without any sample preparation necessary.

47 OTHER INSTRUMENTATION↗

Hyperspectral Reflectance-Based High Throughput Phenotyping to Assess Water-Use Efficiency in Cotton

Cotton is a pivotal global commodity underscored by its economic value and widespread use. In the face of climate change, breeding resilient cultivars for variable environmental conditions becomes increasingly essential. However, the process of phenotyping, crucial to breeding programs, is often viewed as a bottleneck due to the inefficiency of traditional, low-throughput methods. To address this limitation, this study utilizes hyperspectral remote sensing, a promising tool for assessing crucial crop traits across forty cotton varieties. The results from this study demonstrated the effectiveness of four vegetation indices (VIs) in evaluating these varieties for water-use efficiency (WUE). The prediction accuracy for WUE through VIs such as the simple ratio water index (SRWI) and normalized difference water index (NDWI) was higher (up to R2 = 0.66), enabling better detection of phenotypic variations (p < 0.05) among the varieties compared to physiological-related traits (from R2 = 0.21 to R2 = 0.42), with high repeatability and a low RMSE. These VIs also showed high Pearson correlations with WUE (up to r = 0.81) and yield-related traits (up to r = 0.63). We also selected high-performing varieties based on the VIs, WUE, and fiber quality traits. This study demonstrated that the hyperspectral-based proximal sensing approach helps rapidly assess the in-season performance of varieties for imperative traits and aids in precise breeding decisions.

Agriculture↗

Orbital Inverse Faraday and Cotton-Mouton Effects in Hall Fluids

We report two light-induced orbital magnetization effects in quantum Hall (QH) fluids, stemming from their transverse response. The first is a purely transverse contribution to the inverse Faraday effect (IFE), where circularly polarized light induces a dc magnetization by stirring the charged fluid. This contribution dominates the IFE in the QH regime. The second is the orbital inverse Cotton-Mouton effect (ICME), in which linearly polarized light generates a dc magnetization. Since the applied field in the ICME does not break time-reversal symmetry, the induced magnetization directly probes the chiral orbital response of the fluid at the driving frequency. We estimate that the resulting magnetization lies in the range of 0.5–10 Bohr magnetons per charge carrier in materials such as graphene and transition-metal dichalcogenides (TMDs) in the QH regime. Finally, we show that the induced magnetization is accompanied by a local correction to the static particle density, enabling optical quantum printing of density profiles into the QH fluid.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗