Exploring genomic inbreeding and selection signatures in a commercial Brangus herd through functional annotation

Composite breeds, including Brangus, are widely utilized in subtropical and tropical regions to harness the advantages of both Bos t. taurus and Bos t. indicus breeds. The formation and subsequent selection of composite breeds may result in discernible signatures of selection and shifts in genomic population structure. The objectives of this study were to 1) assess genomic inbreeding, 2) identify signatures of selection, 3) assign functional roles to these signatures in a commercial Brangus herd, and 4) contrast signatures of selection between selected and non-selected cattle from the same year. A total of 4035 commercial Brangus cattle were genotyped using the GGP-F250K array. Runs of Homozygosity (ROH) were used to identify signatures of selection and calculate genomic inbreeding. Quantitative trait loci (QTL) enrichment analysis and literature search identified phenotypic traits linked to ROH islands. Genomic inbreeding averaged 5%, primarily stemming from ancestors five or more generations back. A total of nine ROH islands were identified, QTL enrichment analysis revealed traits related to growth, milk composition, carcass, reproductive, and meat quality traits. Notably, the ROH island on BTA14 encompasses the pleiomorphic adenoma (PLAG1) gene, which has been linked to growth, carcass, and reproductive traits. Moreover, ROH islands associated with milk yield and composition were more pronounced in selected replacement heifers of the population, underscoring the importance of milk traits in cow-calf production. In summary, our research sheds light on the changing genetic landscape of the Brangus breed due to selection pressures and reveals key genomic regions impacting production traits.

Antecedents to and outcomes associated with teacher-child relationship perceptions in early childhood: Further evidence for child-driven effects

Preschool teachers' perceptions about relationships with students (teacher-child relationships [TCRs]) predict children's subsequent social competence (SC) and academic progress. Why this is so remains unclear. Do TCRs shape children's development, or do child attributes influence both TCRs and subsequent development? Relations between TCRs and other measures were examined for 185 preschoolers (107 girls, 89 longitudinal, and ~75% European American). Teachers rated TCRs and child social/affective behaviors. Teacher-child interactions (TCIs) and children's affect expressiveness were observed. Child SC and receptive vocabulary were assessed. TCRs were significantly correlated with each type of outcome. TCIs, SC, expressed affect, and teacher-rated behaviors also predicted TCRs longitudinally. Results suggest that TCR ratings predict subsequent adaptation because they summarize children's behavioral profiles rather than on TCR quality per se.

A variety-specific analysis of climate change effects on California winegrapes

California contains a broad geography over which climate conditions can be suitable for cultivating multiple varieties of winegrapes. However, climate change is projected to make winegrape cultivation more challenging across many of California's winegrowing regions. In order to understand the potential effects of climate change on winegrapes, this study models variety-specific phenology for six winegrape varieties and quantifies the change in phenology and viticulturally-important agroclimate metrics over 12 of California's American Viticultural Areas (AVAs) by the mid-21st century. Results show more rapid development for winegrapes with earlier budburst, flowering, veraison, and maturation across all varieties and AVAs. Cabernet Sauvignon shows the greatest change in phenology timing, while Chardonnay shows the least change. Likewise, the West Sonoma Coast AVA shows the greatest average change in phenology timing across varieties and development stages and Lodi AVA shows the least. Projected changes in agroclimatic metrics include an additional month of potentially damaging heat days (above 35 °C) in some AVAs, and decreases in frost days. These results have implications for numerous factors related to viticultural production, including water resources management and crop yield and quality, and underscore the need for California winegrape growers to improve their resilience to climate change by adopting strategies such as increasing soil health and water use efficiency and selecting cultivars suited for future climate conditions. By conducting climate effects analyses at the variety-specific and AVA scale, important information is provided to the winegrowing industry at a resolution that can support decision-making towards resilience.

Mental health profiles of depressive symptoms and personal well-being among active-duty military families

Although some research has examined the mental health of individual family members in military families, additional research is needed that considers mental health among multiple members of the family system simultaneously and that characterizes subsets of families with distinct patterns. Mental health patterns of depressive symptoms and well-being in and among families were identified using latent profile analysis with a community sample of 236 military families with a service member (SM) parent, civilian partner, and adolescent. Drawing from the Family Adjustment and Adaptation Response model, we examined several military-related family demands (e.g., relocations, deployments) and capabilities (e.g., family cohesion, social support outside the family) as correlates of the family profiles. Three profiles emerged: thriving families (62.3% of the sample where all three family members reported relatively low depressive symptoms and high personal well-being), families with a relatively distressed SM (24.2%), and families with a relatively distressed adolescent (13.5%). Overall, there were no differences between the groups of families regarding military-related demands, yet there were differences between the groups regarding their capabilities, namely family cohesion and social support. In general, families in the thriving profile tended to have higher family cohesion and social support as reported by multiple family members compared to the other two profiles. Findings can inform the development of family needs assessments and tailored interventions (and intervention points) based on family profiles and current capabilities.

On Protein Loops, Prior Molecular States and Common Ancestors of Life

The principle of continuity demands the existence of prior molecular states and common ancestors responsible for extant macromolecular structure. Here, we focus on the emergence and evolution of loop prototypes - the elemental architects of protein domain structure. Phylogenomic reconstruction spanning superkingdoms and viruses generated an evolutionary chronology of prototypes with six distinct evolutionary phases defining a most parsimonious evolutionary progression of cellular life. Each phase was marked by strategic prototype accumulation shaping the structures and functions of common ancestors. The last universal common ancestor (LUCA) of cells and viruses and the last universal cellular ancestor (LUCellA) defined stem lines that were structurally and functionally complex. The evolutionary saga highlighted transformative forces. LUCA lacked biosynthetic ribosomal machinery, while the pivotal LUCellA lacked essential DNA biosynthesis and modern transcription. Early proteins therefore relied on RNA for genetic information storage but appeared initially decoupled from it, hinting at transformative shifts of genetic processing. Urancestral loop types suggest advanced folding designs were present at an early evolutionary stage. An exploration of loop geometric properties revealed gradual replacement of prototypes with α-helix and β-strand bracing structures over time, paving the way for the dominance of other loop types. AlphFold2-generated atomic models of prototype accretion described patterns of fold emergence. Our findings favor a ‛processual' model of evolving stem lines aligned with Woese's vision of a communal world. This model prompts discussing the 'problem of ancestors' and the challenges that lie ahead for research in taxonomy, evolution and complexity.

Aphid-Induced Volatiles and Subsequent Attraction of Natural Enemies Varies among Sorghum Cultivars

The production of herbivore-induced plant volatiles (HIPVs) is a type of indirect defense used by plants to attract natural enemies and reduce herbivory by insect pests. In many crops little is known about genotypic variation in HIPV production or how this may affect natural enemy attraction. In this study, we identified and quantified HIPVs produced by 10 sorghum (Sorghum bicolor) cultivars infested with a prominent aphid pest, the sorghum aphid (Melanaphis sorghi Theobald). Volatiles were collected using dynamic headspace sampling techniques and identified and quantified using GC-MS. The total amounts of volatiles induced by the aphids did not differ among the 10 cultivars, but overall blends of volatiles differed significantly in composition. Most notably, aphid herbivory induced higher levels of methyl salicylate (MeSA) emission in two cultivars, whereas in four cultivars, the volatile emissions did not change in response to aphid infestation. Dual-choice olfactometer assays were used to determine preference of the aphid parasitoid, Aphelinus nigritus, and predator, Chrysoperla rufilabris, between plants of the same cultivar that were un-infested or infested with aphids. Two aphid-infested cultivars were preferred by natural enemies, while four other cultivars were more attractive to natural enemies when they were free of aphids. The remaining four cultivars elicited no response from parasitoids. Our work suggests that genetic variation in HIPV emissions greatly affects parasitoid and predator attraction to aphid-infested sorghum and that screening crop cultivars for specific predator and parasitoid attractants has the potential to improve the efficacy of biological control.

Gradients in embolism resistance within stems driven by secondary growth in herbs

The stems of some herbaceous species can undergo basal secondary growth, leading to a continuum in the degree of woodiness along the stem. Whether the formation of secondary growth in the stem base results in differences in embolism resistance between the base and the upper portions of stems is unknown. We assessed the embolism resistance of leaves and the basal and upper portions of stems simultaneously within the same individuals of two divergent herbaceous species that undergo secondary growth in the mature stem bases. The species were Solanum lycopersicum (tomato) and Senecio minimus (fireweed). Basal stem in mature plants of both species displayed advanced secondary growth and greater resistance to embolism than the upper stem. This also resulted in significant vulnerability segmentation between the basal stem and the leaves in both species. Greater embolism resistance in the woodier stem base was found alongside decreases in the pith-to-xylem ratio, increases in the proportion of secondary xylem, and increases in lignin content. We show that there can be considerable variation in embolism resistance across the stem in herbs and that this variation is linked to the degree of secondary growth present. A gradient in embolism resistance across the stem in herbaceous plants could be an adaptation to ensure reproduction or basal resprouting during episodes of drought late in the lifecycle.

DairyCoPilot-Automated data compilation and analysis tools for DairyComp data assets

Modern dairy farm management requires meaningful data and careful analysis to maximize profitability, cow health, and welfare. Current data platforms, such as DairyComp, lack robust integrated data analysis tools. Producers and consultants need dedicated tools to turn collected data sets into assets for informed decision-making processes. The DairyCoPilot app allows users to rapidly extract health and production data from DairyComp, then compile and analyze the data using a menu-driven point-and-click approach. Prospects for training consultants in applied data analysis skills make DairyCoPilot a tool to identify farm management bottlenecks with less time spent for data analysis, improving cow health, and dairy production. The DairyCoPilot Dashboard R Shiny application is published using RStudio Connect: https://connect.doit.wisc.edu/dairy-copilot/.

Assessing the impact of isochoric freezing as a preservation method on the quality attributes of orange juice

Isochoric (constant volume) freezing is a novel food preservation technology that has demonstrated the ability to preserve food products at subfreezing temperatures in an unfrozen state, thereby avoiding the detrimental effects of ice formation. It minimizes the quality loss of fresh fruits and juices, increases their nutrient content, and reduces microbial counts. Orange juice (OJ) samples were subjected to conventional freezing (CF) and isochoric freezing (IF) for 7 days and then stored at 4°C for an additional 7 days. We evaluated the microbiological and physicochemical quality of CF and IF OJ before and after storage. The IF was performed at three different conditions: -5°C/73 MPa, -10°C/93 MPa, and -15°C/143 MPa. The results indicate that the total aerobic count of OJ remained below the detection limit after heat treatment, 7 days of CF and 7 days of IF. Yeast and mold counts increased in fresh and CF OJ after 7 days of storage at 4°C, whereas IF OJ remained below the detection limit. Less color difference was observed in IF (-15°C/143 MPa) OJ compared to heat-treated and CF OJ. Heat treatment inactivated 42% of pectin methylesterase (PME), whereas 7-day long IF increased PME activity up to 150%. Additionally, IF (-15°C/143 MPa) OJ showed reduced pulp sedimentation, which can be advantageous, as sedimentation in juices has been a recognized technological issue in the juice industry. Ascorbic acid level was significantly higher in IF (-15°C/143 MPa) OJ compared to fresh and CF OJ after storage.

Distinct growth patterns in seedling and tillering wheat plants suggests a developmentally restricted role of HYD2 in salt-stress response

KEY MESSAGE

Mutants lacking functional HYD2 homoeologs showed improved seedling growth, but comparable or increased susceptibility to salt stress in tillering plants, suggesting a developmentally restricted role of HYD2 in salt response. Salinity stress threatens global food security by reducing the yield of staple crops such as wheat (Triticum ssp.). Understanding how wheat responds to salinity stress is crucial for developing climate resilient varieties. In this study, we examined the interplay between carotenoid metabolism and the response to salt (NaCl) stress, a specific form of salinity stress, in tetraploid wheat plants with mutations in carotenoid β-hydroxylase 1 (HYD1) and HYD2. Our investigation encompassed both the vulnerable seedling stage and the more developed tillering stage of wheat plant growth. Mutant combinations lacking functional HYD2 homoeologs, including hyd-A2 hyd-B2, hyd-A1 hyd-A2 hyd-B2, hyd-B1 hyd-A2 hyd-B2, and hyd-A1 hyd-B1 hyd-A2 hyd-B2, had longer first true leaves and slightly enhanced root growth during germination under salt stress compared to the segregate wild-type (control) plants. Interestingly, these mutant seedlings also showed decreased levels of neoxanthin and violaxanthin (xanthophylls derived from β-carotene) and an increase in β-carotene in roots. However, tillering hyd mutant and segregate wild-type plants generally did not differ in their height, tiller count, and biomass production under acute or prolonged salt stress, except for decreases in these parameters observed in the hyd-A1 hyd-B1 hyd-A2 hyd-B2 mutant that indicate its heightened susceptibility to salt stress. Taken together, these findings suggest a significant, yet developmentally restricted role of HYD2 homoeologs in salt-stress response in tetraploid wheat. They also show that hyd-A2 hyd-B2 mutant plants, previously demonstrated for possessing enriched nutritional (β-carotene) content, maintain an unimpaired ability to withstand salt stress.

Clodronate disodium does not produce measurable effects on bone metabolism in an exercising, juvenile, large animal model

Bisphosphonates are commonly used to treat and prevent bone loss, but their effects in active, juvenile populations are unknown. This study examined the effects of intramuscular clodronate disodium (CLO) on bone turnover, serum bone biomarkers (SBB), bone mineral density (BMD), bone microstructure, biomechanical testing (BT), and cartilage glycosaminoglycan content (GAG) over 165 days. Forty juvenile sheep (253 ± 6 days of age) were divided into four groups: Control (saline), T0 (0.6 mg/kg CLO on day 0), T84 (0.6 mg/kg CLO on day 84), and T0+84 (0.6 mg/kg CLO on days 0 and 84). Sheep were exercised 4 days/week and underwent physical and lameness examinations every 14 days. Blood samples were collected for SBB every 28 days. Microstructure and BMD were calculated from tuber coxae (TC) biopsies (days 84 and 165) and bone healing was assessed by examining the prior biopsy site. BT and GAG were evaluated postmortem. Data, except lameness data, were analyzed using a mixed-effects model; lameness data were analyzed as ordinal data using a cumulative logistic model. CLO did not have any measurable effects on the skeleton of sheep. SBB showed changes over time (p ≤ 0.03), with increases in bone formation and decreases in some bone resorption markers. TC biopsies showed increasing bone volume fraction, trabecular spacing and thickness, and reduced trabecular number on day 165 versus day 84 (p ≤ 0.04). These changes may be attributed to exercise or growth. The absence of a treatment effect may be explained by the lower CLO dose used in large animals compared to humans. Further research is needed to examine whether low doses of bisphosphonates may be used in active juvenile populations for analgesia without evidence of bone changes.

From buds to shoots: insights into grapevine development from the Witch's Broom bud sport

BACKGROUND

Bud sports occur spontaneously in plants when new growth exhibits a distinct phenotype from the rest of the parent plant. The Witch's Broom bud sport occurs occasionally in various grapevine (Vitis vinifera) varieties and displays a suite of developmental defects, including dwarf features and reduced fertility. While it is highly detrimental for grapevine growers, it also serves as a useful tool for studying grapevine development. We used the Witch's Broom bud sport in grapevine to understand the developmental trajectories of the bud sports, as well as the potential genetic basis. We analyzed the phenotypes of two independent cases of the Witch's Broom bud sport, in the Dakapo and Merlot varieties of grapevine, alongside wild type counterparts. To do so, we quantified various shoot traits, performed 3D X-ray Computed Tomography on dormant buds, and landmarked leaves from the samples. We also performed Illumina and Oxford Nanopore sequencing on the samples and called genetic variants using these sequencing datasets.

RESULTS

The Dakapo and Merlot cases of Witch's Broom displayed severe developmental defects, with no fruit/clusters formed and dwarf vegetative features. However, the Dakapo and Merlot cases of Witch's Broom studied were also phenotypically different from one another, with distinct differences in bud and leaf development. We identified 968-974 unique genetic mutations in our two Witch's Broom cases that are potential causal variants of the bud sports. Examining gene function and validating these genetic candidates through PCR and Sanger-sequencing revealed one strong candidate mutation in Merlot Witch's Broom impacting the gene GSVIVG01008260001.

CONCLUSIONS

The Witch's Broom bud sports in both varieties studied had dwarf phenotypes, but the two instances studied were also vastly different from one another and likely have distinct genetic bases. Future work on Witch's Broom bud sports in grapevine could provide more insight into development and the genetic pathways involved in grapevine.

Characterisation and mapping of a Globodera pallida resistance derived from the wild potato species Solanum spegazzinii

KEY MESSAGE

A new resistance locus acting against the potato cyst nematode Globodera pallida was mapped to chromosome VI in the diploid wild potato species Solanum spegazzinii CPC 7195. The potato cyst nematodes (PCN) Globodera pallida and Globodera rostochiensis are economically important potato pests in almost all regions where potato is grown. One important management strategy involves deployment through introgression breeding into modern cultivars of new sources of naturally occurring resistance from wild potato species. We describe a new source of resistance to G. pallida from wild potato germplasm. The diploid species Solanum spegazzinii Bitter accession CPC 7195 shows resistance to G. pallida pathotypes Pa1 and Pa2/3. A cross and first backcross of S. spegazzinii with Solanum tuberosum Group Phureja cultivar Mayan Gold were performed, and the level of resistance to G. pallida Pa2/3 was determined in progeny clones. Bulk-segregant analysis (BSA) using generic mapping enrichment sequencing (GenSeq) and genotyping-by-sequencing were performed to identify single-nucleotide polymorphisms (SNPs) that are genetically linked to the resistance, using S. tuberosum Group Phureja clone DM1-3 516 R44 as a reference genome. These SNPs were converted into allele-specific PCR assays, and the resistance was mapped to an interval of roughly 118 kb on chromosome VI. This newly identified resistance, which we call Gpa VIlspg, can be used in future efforts to produce modern cultivars with enhanced and broad-spectrum resistances to the major pests and pathogens of potato.

Bacterial community shifts of commercial apples, oranges, and peaches at different harvest points across multiple growing seasons

Assessing the microbes present on tree fruit carpospheres as the fruit enters postharvest processing could have useful applications, as these microbes could have a major influence on spoilage, food safety, verification of packing process controls, or other aspects of processing. The goal of this study was to establish a baseline profile of bacterial communities associated with apple (pome fruit), peach (stone fruit), and Navel orange (citrus fruit) at harvest. We found that commercial peaches had the greatest bacterial richness followed by oranges then apples. Time of harvest significantly changed bacterial diversity in oranges and peaches, but not apples. Shifts in diversity varied by fruit type, where 70% of the variability in beta diversity on the apple carposphere was driven by the gain and loss of species (i.e., nestedness). The peach and orange carposphere bacterial community shifts were driven by nearly an even split between turnover (species replacement) and nestedness. We identified a small core microbiome for apples across and between growing seasons that included only Methylobacteriaceae and Sphingomonadaceae among the samples, while peaches had a larger core microbiome composed of five bacterial families: Bacillaceae, Geodermtophilaceae, Nocardioidaceae, Micrococcaeceae, and Trueperaceae. There was a relatively diverse core microbiome for oranges that shared all the families present on apples and peaches, except for Trueperaceae, but also included an additional nine bacterial families not shared including Oxalobacteraceae, Cytophagaceae, and Comamonadaceae. Overall, our findings illustrate the important temporal dynamics of bacterial communities found on major commercial tree fruit, but also the core bacterial families that constantly remain with both implications being important entering postharvest packing and processing.

Evaluating the role of social context and environmental factors in mediating overwintering physiology in honey bees (Apis mellifera)

In temperate climates, honey bees show strong phenotypic plasticity associated with seasonal changes. In summer, worker bees typically only survive for about a month and can be further classified as young nurse bees (which feed the developing brood) and older forager bees. In winter, brood production and foraging halt and the worker bees live for several months. These differences in task and longevity are reflected in their physiology, with summer nurses and long-lived winter bees typically having large fat bodies, high expression levels of vitellogenin (a longevity-, nutrition- and immune-related gene), and large provisioning glands in their head. The environmental factors (both within the colony and within the surrounding environment) that trigger this transition to long-lived winter bees are poorly understood. One theory is that winter bees are an extended nurse bee state, brought on by a reduction in nursing duties in autumn (i.e. lower brood area). We examined that theory here by assessing nurse bee physiology in both the summer and autumn, in colonies with varying levels of brood. We found that season is a better predictor of nurse bee physiology than brood area. This suggests that seasonal factors beyond brood area, such as pollen availability and colony demography, may be necessary for inducing the winter bee phenotype. This finding furthers our understanding of winter bee biology, which could have important implications for colony management for winter, a critical period for colony survival.

Mutual Effects and Uptake of Organic Contaminants and Nanoplastics by Lettuce in Co-Exposure

Organic contaminants, such as pesticides and pharmaceuticals, are commonly found in agricultural systems. With the growing use of plastic products, micro- and nanoplastics (MNPs) are increasingly detected in these agricultural systems, necessitating research into their interactions and joint effects to truly understand their impact. Unfortunately, while there has been a long history of research into the uptake of organic pollutants by plants, similar research with MNPs is only beginning, and studies on their mutual effects and plant uptake are extremely rare. In this study, we examined the effects of three agriculturally relevant organic pollutants with distinctive hydrophobicity as measured by log KOW (trimethoprim: 0.91, atrazine: 2.61, and ibuprofen: 3.97) and 500 nm polystyrene nanoplastics on their uptake and accumulation by lettuce at two different salinity levels. Our results showed that nanoplastics increased the shoot concentration of ibuprofen by 77.4 and 309% in nonsaline and saline conditions, respectively. Alternatively, organic co-contaminants slightly lowered the PS NPs uptake in lettuce with a more pronounced decrease in saline water. These results underscore the impactful interactions of hydrophobic organic pollutants and increasing MNPs on a dynamic global environment.

Delayed spinetoram application is useful in managing Scirtothrips dorsalis Hood (Thysanoptera: Thripidae) in Florida strawberry

Scirtothrips dorsalis Hood (Thysanoptera: Thripidae) is an invasive, early-season pest of strawberry in Florida, causing feeding injury to young foliage that results in stunted plant growth and yield loss. Spinetoram, an effective insecticide for thrips pests with up to 3 applications per season permitted in strawberry, is often applied repeatedly during the early-season (Oct-Nov) to manage S. dorsalis, leaving few or no applications for flower thrips pests later in the season (Dec-Mar). Therefore, new strategies are needed to manage S. dorsalis with less insecticide, with the hypothesis that the first insecticide application can be delayed because young strawberry plants can compensate for minor feeding injury without compromising strawberry yield. Experiments conducted in strawberry field plots in Balm, FL, during 2018 and 2019 showed that delaying a spinetoram application for 14 days after infesting a plant with zero, 5, 10, or 20 S. dorsalis adults did not reduce the plant vigor and yield compared to spinetoram application after 4 days. Furthermore, young plants recovered from injury (10-30% bronzing injury on leaf veins and petioles) due to 1 or 2 S. dorsalis adults or larvae per trifoliate. A strategy of delaying the first spinetoram application when plants have 4-5 trifoliates should help reduce the number of insecticide applications needed for S. dorsalis management and reserve spinetoram applications for later in the season. Lower input costs in Florida strawberry without compromising yields due to thrips damage will improve the economics and sustainability of production systems.

Chemical Composition and Optical Properties of Secondary Organic Aerosol from Photooxidation of Volatile Organic Compound Mixtures

The chemical and optical properties of secondary organic aerosols (SOA) have been widely studied through environmental chamber experiments, and some of the results have been parametrized in atmospheric models to help understand their radiative effects and climate influence. While most chamber studies investigate the aerosol formed from a single volatile organic compound (VOC), the potential interactions between reactive intermediates derived from VOC mixtures are not well understood. In this study, we investigated the SOA formed from pure and mixtures of anthropogenic (phenol and 1-methylnaphthalene) and/or biogenic (longifolene) VOCs using continuous-flow, high-NOx photooxidation chamber experiments to better mimic ambient conditions. SOA optical properties, including single scattering albedo (SSA), mass absorption coefficient (MAC), and refractive index (RI) at 375 nm, and chemical composition, including the formation of oxygenated organic compounds, organic-nitrogen compounds (including organonitrates and nitro-organics), and the molecular structure of the major chromophores, were explored. Additionally, the imaginary refractive index values of SOA in the multi-VOC system were predicted using a linear-combination assumption and compared with the measured values. When two VOCs were oxidized simultaneously, we found evidence for changes in SOA chemical composition compared to SOA formed from single-VOC systems, and this change led to nonlinear effects on SOA optical properties. The nonlinear effects were found to vary between different systems.

Endosymbiont diversity across native and invasive brown widow spider populations

The invasive brown widow spider, Latrodectus geometricus (Araneae: Theridiidae), has spread in multiple locations around the world and, along with it, brought associated organisms such as endosymbionts. We investigated endosymbiont diversity and prevalence across putative native and invasive populations of this spider, predicting lower endosymbiont diversity across the invasive range compared to the native range. First, we characterized the microbial community in the putative native (South Africa) and invasive (Israel and the United States) ranges via high throughput 16S sequencing of 103 adult females. All specimens were dominated by reads from only 1-3 amplicon sequence variants (ASV), and most individuals were infected with an apparently uniform strain of Rhabdochlamydia. We also found Rhabdochlamydia in spider eggs, indicating that it is a maternally-inherited endosymbiont. Relatively few other ASV were detected, but included two variant Rhabdochlamydia strains and several Wolbachia, Spiroplasma and Enterobacteriaceae strains. We then diagnostically screened 118 adult female spiders from native and invasive populations specifically for Rhabdochlamydia and Wolbachia. We found Rhabdochlamydia in 86% of individuals and represented in all populations, which suggests that it is a consistent and potentially important associate of L. geometricus. Wolbachia was found at lower overall prevalence (14%) and was represented in all countries, but not all populations. In addition, we found evidence for geographic variation in endosymbiont prevalence: spiders from Israel were more likely to carry Rhabdochlamydia than those from the US and South Africa, and Wolbachia was geographically clustered in both Israel and South Africa. Characterizing endosymbiont prevalence and diversity is a first step in understanding their function inside the host and may shed light on the process of spread and population variability in cosmopolitan invasive species.

A network of transcription factors in complex with a regulating cell cycle cyclin orchestrates fungal oxidative stress responses

BACKGROUND

Response to oxidative stress is universal in almost all organisms and the mitochondrial membrane protein, BbOhmm, negatively affects oxidative stress responses and virulence in the insect fungal pathogen, Beauveria bassiana. Nothing further, however, is known concerning how BbOhmm and this phenomenon is regulated.

RESULTS

Three oxidative stress response regulating Zn2Cys6 transcription factors (BbOsrR1, 2, and 3) were identified and verified via chromatin immunoprecipitation (ChIP)-qPCR analysis as binding to the BbOhmm promoter region, with BbOsrR2 showing the strongest binding. Targeted gene knockout of BbOsrR1 or BbOsrR3 led to decreased BbOhmm expression and consequently increased tolerances to free radical generating compounds (H2O2 and menadione), whereas the ΔBbOsrR2 strain showed increased BbOhmm expression with concomitant decreased tolerances to these compounds. RNA and ChIP sequencing analysis revealed that BbOsrR1 directly regulated a wide range of antioxidation and transcription-associated genes, negatively affecting the expression of the BbClp1 cyclin and BbOsrR2. BbClp1 was shown to localize to the cell nucleus and negatively mediate oxidative stress responses. BbOsrR2 and BbOsrR3 were shown to feed into the Fus3-MAPK pathway in addition to regulating antioxidation and detoxification genes. Binding motifs for the three transcription factors were found to partially overlap in the promoter region of BbOhmm and other target genes. Whereas BbOsrR1 appeared to function independently, co-immunoprecipitation revealed complex formation between BbClp1, BbOsrR2, and BbOsrR3, with BbClp1 partially regulating BbOsrR2 phosphorylation.

CONCLUSIONS

These findings reveal a regulatory network mediated by BbOsrR1 and the formation of a BbClp1-BbOsrR2-BbOsrR3 complex that orchestrates fungal oxidative stress responses.

Urbanization exacerbates climate sensitivity of eastern United States broadleaf trees

Tree growth is a key mechanism driving carbon sequestration in forest ecosystems. Environmental conditions are important regulators of tree growth that can vary considerably between nearby urban and rural forests. For example, trees growing in cities often experience hotter and drier conditions than their rural counterparts while also being exposed to higher levels of light, pollution, and nutrient inputs. However, the extent to which these intrinsic differences in the growing conditions of trees in urban versus rural forests influence tree growth response to climate is not well known. In this study, we tested for differences in the climate sensitivity of tree growth between urban and rural forests along a latitudinal transect in the eastern United States that included Boston, Massachusetts, New York City, New York, and Baltimore, Maryland. Using dendrochronology analyses of tree cores from 55 white oak trees (Quercus alba), 55 red maple trees (Acer rubrum), and 41 red oak trees (Quercus rubra) we investigated the impacts of heat stress and water stress on the radial growth of individual trees. Across our three-city study, we found that tree growth was more closely correlated with climate stress in the cooler climate cities of Boston and New York than in Baltimore. Furthermore, heat stress was a significant hindrance to tree growth in higher latitudes while the impacts of water stress appeared to be more evenly distributed across latitudes. We also found that the growth of oak trees, but not red maple trees, in the urban sites of Boston and New York City was more adversely impacted by heat stress than their rural counterparts, but we did not see these urban-rural differences in Maryland. Trees provide a wide range of important ecosystem services and increasing tree canopy cover was typically an important component of urban sustainability strategies. In light of our findings that urbanization can influence how tree growth responds to a warming climate, we suggest that municipalities consider these interactions when developing their tree-planting palettes and when estimating the capacity of urban forests to contribute to broader sustainability goals in the future.

Overwintering site selection and associated microclimates for the redbanded stink bug (Hemiptera: Pentatomidae), a non-native pest of soybean

Cold winter temperatures govern the distribution and abundance of many insect species, but refugia that provide microclimates can moderate temperature-driven mortality. Winter temperatures have been implicated in limiting the survival and range of Piezodorus guildinii (Westwood) (Hemiptera: Pentatomidae; redbanded stink bug), an economically damaging invasive pest in the southeastern United States, but the role of refugia in overwintering survival of this pest is poorly understood. We conducted 2 studies in successive years to evaluate how leaf litter from hardwoods, pines, and soybeans modulate overwintering site selection and survival of P. guildinii. In the second-year study, we also quantified the buffering effect of the 3 leaf litter types compared to ambient conditions and assessed diapause. In the first-year study, we found that stink bugs preferentially dispersed into leaf litter compared with remaining unsheltered on bare soil; no clear preference among leaf litter types was found. In the second year, however, no clear differences were found among leaf litter types and bare soil. Means of daily minimum temperatures under leaf litter were at least 3.0 ± 0.9 °C (SE) warmer and generally less variable than ambient conditions. While high mortality in both studies illustrates that more work must be done to fully understand overwintering survival, limited survival through potentially lethal conditions in the first-year study nonetheless emphasizes the possibility of populations persisting and rebounding in the following spring. Furthermore, our study highlights the potential for stink bugs to persist in areas with lethal ambient temperatures by dispersing into widely available substrates.

Bacterial diversity and composition on the rinds of specific melon cultivars and hybrids from across different growing regions in the United States

The goal of this study was to characterize the bacterial diversity on different melon varieties grown in different regions of the US, and determine the influence that region, rind netting, and variety of melon has on the composition of the melon microbiome. Assessing the bacterial diversity of the microbiome on the melon rind can identify antagonistic and protagonistic bacteria for foodborne pathogens and spoilage organisms to improve melon safety, prolong shelf-life, and/or improve overall plant health. Bacterial community composition of melons (n = 603) grown in seven locations over a four-year period were used for 16S rRNA gene amplicon sequencing and analysis to identify bacterial diversity and constituents. Statistically significant differences in alpha diversity based on the rind netting and growing region (p < 0.01) were found among the melon samples. Principal Coordinate Analysis based on the Bray-Curtis dissimilarity distance matrix found that the melon bacterial communities clustered more by region rather than melon variety (R2 value: 0.09 & R2 value: 0.02 respectively). Taxonomic profiling among the growing regions found Enterobacteriaceae, Bacillaceae, Microbacteriaceae, and Pseudomonadaceae present on the different melon rinds at an abundance of ≥ 0.1%, but no specific core microbiome was found for netted melons. However, a core of Pseudomonadaceae, Bacillaceae, and Exiguobacteraceae were found for non-netted melons. The results of this study indicate that bacterial diversity is driven more by the region that the melons were grown in compared to rind netting or melon type. Establishing the foundation for regional differences could improve melon safety, shelf-life, and quality as well as the consumers' health.

A profile of urban agricultural growers, organizations, their needs, and challenges in the Northeastern United States

Urban agriculture is increasingly valued as a strategy for improving quality of life in cities, but urban growers face challenges and often lack coordinated support from governments and the agricultural industry. We surveyed urban growers through an online survey, primarily in the Northeastern United States, to develop a profile of growers and associated organizations, assess the current state of urban agriculture, and determine how universities could help meet their needs. A total of 394 respondents completed the survey and most urban growers were white (non-Hispanic) and younger than 45 years old. Women and men were in almost equal proportion. Urban growers were well-educated, but most did not receive a degree in agriculture. Urban agriculture in our study area was dominated by relatively small non-profit organizations and home and community gardens were the most common types of organizations. Urban agricultural organizations want to improve environmental sustainability and socio-cultural conditions through food access and security, regardless of their tax status. Urban growers face diverse barriers and challenges and the most ubiquitous barriers and challenges reported by respondents were related to availability of land and long-term access in urban areas. Many respondents received low revenue or were operating at a net loss even though they reported diverse income streams. Respondents need a wide range of training, including in traditional agricultural topics as well as financial management and business trainings. Universities can play a key role in promoting urban agriculture by offering training and research. Workforce development is a large priority among universities, so urban growers should regularly be consulted, and the results shared with career and workforce development professionals and researchers in urban areas to identify training and research that meets the needs of stakeholders.

Bioinspired Superhydrophobic Nanocoating Based on Polydopamine and Nanodiamonds to Mitigate Bacterial Attachment to Polyvinyl Chloride Surfaces in Food Industry Environments

Polyvinyl chloride (PVC) is commonly utilized as a food-contact surface by the food industry for processing and storage purposes due to its durability, ease of fabrication, and cost-effectiveness. Herein, we report a composite coating for the superhydrophobization of PVC without the use of polyfluoroalkyl chemistry. This coating rendered the PVC superhydrophobic, exhibiting a static water contact angle of 151.9 ± 0.7° and a contact angle hysteresis of only 3.1 ± 1.0°. The structure of this composite coating, consisting of polydopamine, nanodiamonds, and an alkyl silane, was investigated by utilizing both scanning electron microscopy and atomic force microscopy. Surface chemistry was probed using attenuated total reflectance-Fourier transform infrared, and the surface wetting behavior was thoroughly characterized using both static and dynamic water contact angle measurements. It was demonstrated that the superhydrophobic PVC was cleanable using a food-grade surfactant, becoming wet in contact with high concentration surfactant solutions, but regaining its nonwetting property upon rinsing with water. It was demonstrated that the coating produced a 2.1 ± 0.1 log10 reduction (99.2%) in the number of Escherichia coli O157:H7 cells and a 2.2 ± 0.1 log10 reduction (99.3%) in the number of Salmonella enterica Typhimurium cells that were able to adsorb onto PVC surfaces over a 24 h period. The use of this fluorine-free superhydrophobic coating on PVC equipment, such as conveyor belts within food production facilities, may help to mitigate bacterial cross-contamination and curb the spread of foodborne illnesses.

An averaging model for analysis and interpretation of high-order genetic interactions

While combinatorial genetic data collection from biological systems in which quantitative phenotypes are controlled by active and inactive alleles of multiple genes (multi-gene systems) is becoming common, a standard analysis method for such data has not been established. The currently common approaches have three major drawbacks. First, although it is a long tradition in genetics, modeling the effect of an inactive allele (a null mutant allele) contrasted against that of the active allele (the wild-type allele) is not suitable for mechanistic understanding of multi-gene systems. Second, a commonly-used additive model (ANOVA with interaction) mathematically fails in estimation of interactions among more than two genes when the phenotypic response is not linear. Third, interpretation of higher-order interactions defined by an additive model is not intuitive. I derived an averaging model based on algebraic principles to solve all these problems within the framework of a general linear model. In the averaging model: the effect of the active allele is contrasted against the effect of the inactive allele for easier mechanistic interpretations; there is mathematical stability in estimation of higher-order interactions even when the phenotypic response is not linear; and interpretations of higher-order interactions are intuitive and consistent-interactions are defined as the mean effects of the last active genes added to the system. Thus, the key outcomes of this study are development of the averaging model, which is suitable for analysis of multi-gene systems, and a new, intuitive, and mathematically and interpretationally consistent definition of a genetic interaction, which is central to the averaging model.

Cover crop residue decomposition triggered soil oxygen depletion and promoted nitrous oxide emissions

Cover cropping is a promising strategy to improve soil health, but it may also trigger greenhouse gas emissions, especially nitrous oxide (N2O). Beyond nitrogen (N) availability, cover crop residue decomposition may accelerate heterotrophic respiration to limit soil O2 availability, hence promote N2O emissions from denitrification under sub-optimal water-filled pore space (WFPS) conditions that are typically not conducive to large N2O production. We conducted a 21-day incubation experiment to examine the effects of contrasting cover crop residue (grass vs legume) decomposition on soil O2 and biogeochemical changes to influence N2O and CO2 emissions from 15N labeled fertilized soils under 50% and 80% WFPS levels. Irrespective of cover crop type, mixing cover crop residue with N fertilizer resulted in high cumulative N2O emissions under both WFPS conditions. In the absence of cover crop residues, the N fertilizer effect of N2O was only realized under 80% WFPS, whereas it was comparable to the control under 50% WFPS. The N2O peaks under 50% WFPS coincided with soil O2 depletion and concomitant high CO2 emissions when cover crop residues were mixed with N fertilizer. While N fertilizer largely contributed to the total N2O emissions from the cover crop treatments, soil organic matter and/or cover crop residue derived N2O had a greater contribution under 50% than 80% WFPS. Our results underscore the importance of N2O emissions from cover crop-based fertilized systems under relatively lower WFPS via a mechanism of respiration-induced anoxia and highlight potential risks of underestimating N2O emissions under sole reliance on WFPS.

Genotype-by-environment interactions and local adaptation shape selection in the US National Chip Processing Trial

KEY MESSAGE

We find evidence of selection for local adaptation and extensive genotype-by-environment interaction in the potato National Chip Processing Trial (NCPT). We present a novel method for dissecting the interplay between selection, local adaptation and environmental response in plant breeding schemes. Balancing local adaptation and the desire for widely adapted cultivars is challenging for plant breeders and makes genotype-by-environment interactions (GxE) an important target of selection. Selecting for GxE requires plant breeders to evaluate plants across multiple environments. One way breeders have accomplished this is to test advanced materials across many locations. Public potato breeders test advanced breeding material in the National Chip Processing Trial (NCPT), a public-private partnership where breeders from ten institutions submit advanced chip lines to be evaluated in up to ten locations across the country. These clones are genotyped and phenotyped for important agronomic traits. We used these data to interrogate the NCPT for GxE. Further, because breeders submitting clones to the NCPT select in a relatively small geographic range for the first 3 years of selection, we examined these data for evidence of incidental selection for local adaptation, and the alleles underlying it, using an environmental genome-wide association study (envGWAS). We found genomic regions associated with continuous environmental variables and discrete breeding programs, as well as regions of the genome potentially underlying GxE for yield.

Genetic linkage mapping and quantitative trait locus (QTL) analysis of sweet basil (Ocimum basilicum L.) to identify genomic regions associated with cold tolerance and major volatiles

Chilling sensitivity is one of the greatest challenges affecting the marketability and profitability of sweet basil (Ocimum basilicum L.) in the US and worldwide. Currently, there are no sweet basils commercially available with significant chilling tolerance and traditional aroma profiles. This study was conducted to identify quantitative trait loci (QTLs) responsible for chilling tolerance and aroma compounds in a biparental mapping population, including the Rutgers advanced breeding line that served as a chilling tolerant parent, 'CB15', the chilling sensitive parent, 'Rutgers Obsession DMR' and 200 F2 individuals. Chilling tolerance was assessed by percent necrosis using machine learning and aroma profiling was evaluated using gas chromatography (GC) mass spectrometry (MS). Single nucleotide polymorphism (SNP) markers were generated from genomic sequences derived from double digestion restriction-site associated DNA sequencing (ddRADseq) and converted to genotype data using a reference genome alignment. A genetic linkage map was constructed and five statistically significant QTLs were identified in response to chilling temperatures with possible interactions between QTLs. The QTL on LG24 (qCH24) demonstrated the largest effect for chilling response and was significant in all three replicates. No QTLs were identified for linalool, as the population did not segregate sufficiently to detect this trait. Two significant QTLs were identified for estragole (also known as methyl chavicol) with only qEST1 on LG1 being significant in the multiple-QTL model (MQM). QEUC26 was identified as a significant QTL for eucalyptol (also known as 1,8-cineole) on LG26. These QTLs may represent key mechanisms for chilling tolerance and aroma in basil, providing critical knowledge for future investigation of these phenotypic traits and molecular breeding.

A Multidrug-Resistant Extended-Spectrum Beta-Lactamase (ESBL)-Producing Enterobacter hormaechei Strain from Mixed Sprouts

Fresh vegetables can harbor antibiotic-resistant bacteria, including extended-spectrum β-lactamase (ESBL)-producing Enterobacterales. Enterobacter hormaechei is a bacterium belonging to the Enterobacterales order and the most commonly identified nosocomial pathogen of Enterobacter cloacae complex. The purpose of this study was to characterize a multi-drug resistant ESBL-producing E. hormaechei strain isolated from a sample of mixed sprouts. Vegetable samples were pre-enriched in buffered peptone water, followed by enrichment in Enterobacteria Enrichment Broth, and isolation on Chromagar™ ESBL plates. One isolate from a sprout sample was confirmed to produce both ESBL and AmpC β-lactamases through the combination disk diffusion assay using antibiotic disks containing cefotaxime and ceftazidime with or without clavulanate, and with or without cloxacillin, respectively. The isolate was also resistant to multiple antibiotics, including cefotaxime, ceftazidime, chloramphenicol, trimethoprim-sulfamethoxazole, tetracycline, gentamicin, ampicillin, and amoxicillin-clavulanate, as determined by antimicrobial susceptibility testing. Through whole genome sequencing, the isolate was identified as E. hormaechei 057-E1, which carried multiple antibiotic resistance (AR) genes and a sul2-aph(3″)-Ib-aph(6)-Id-blaTEM-1-ISEcp1 -blaCTX-M-15 gene cluster. Our results further demonstrate the important role of fresh vegetables in AR and highlight the need to develop strategies for AR mitigation in fresh vegetables.

Properties of APTES-Modified CNC Films

Sulfated cellulose nanocrystals' (CNCs') facile aqueous dispersibility enables producing films, fibers, and other materials using only water as a solvent but prevents using sulfated CNCs in applications that require water immersion. We report that modifying CNCs with 3-aminopropyl-triethoxysilane (APTES) via a simple, single-pot reaction scheme dramatically improves the hydrolytic stability of CNC films. The effects of APTES modification on CNCs' properties were studied using attenuated total reflectance Fourier transform infrared spectroscopy, atomic force and optical microscopy, thermogravimetric analysis, dynamic light scattering, and ultimate analysis. Substituting a mere 12.6% of the CNCs' available hydroxyl groups with APTES dramatically increased the hydrolytic stability of shear cast films while only having minor impacts on their mechanical properties. In addition, quartz crystal microbalance with dissipation monitoring (QCMD) and multiparametric surface plasmon resonance (MP-SPR) studies showed that the CNC-APTES films also had a greater irreversible binding with carbofuran, a pesticide and emerging contaminant. These results highlight that APTES modification is a promising method for increasing the utility of sulfated CNCs in sensors, adsorbents, and other applications requiring water immersion.

Application of Artificial Intelligence and Sensor Fusion for Soil Organic Matter Prediction

Soil organic matter (SOM) is one of the best indicators to assess soil health and understand soil productivity and fertility. Therefore, measuring SOM content is a fundamental practice in soil science and agricultural research. The traditional approach (oven-dry) of measuring SOM is a costly, arduous, and time-consuming process. However, the integration of cutting-edge technology can significantly aid in the prediction of SOM, presenting a promising alternative to traditional methods. In this study, we tested the hypothesis that an accurate estimate of SOM might be obtained by combining the ground-based sensor-captured soil parameters and soil analysis data along with drone images of the farm. The data are gathered using three different methods: ground-based sensors detect soil parameters such as temperature, pH, humidity, nitrogen, phosphorous, and potassium of the soil; aerial photos taken by UAVs display the vegetative index (NDVI); and the Haney test of soil analysis reports measured in a lab from collected samples. Our datasets combined the soil parameters collected using ground-based sensors, soil analysis reports, and NDVI content of farms to perform the data analysis to predict SOM using different machine learning algorithms. We incorporated regression and ANOVA for analyzing the dataset and explored seven different machine learning algorithms, such as linear regression, Ridge regression, Lasso regression, random forest regression, Elastic Net regression, support vector machine, and Stochastic Gradient Descent regression to predict the soil organic matter content using other parameters as predictors.

Polysaccharide Aldehydes and Ketones: Synthesis and Reactivity

Polysaccharides are biodegradable, abundant, sustainable, and often benign natural polymers. The achievement of selective modification of polysaccharides is important for targeting specific properties and structures and will benefit future development of highly functional, sustainable materials. The synthesis of polysaccharides containing aldehyde or ketone moieties is a promising tool for achieving this goal because of the rich chemistry of aldehyde or ketone groups, including Schiff base formation, nucleophilic addition, and reductive amination. The obtained polysaccharide aldehydes or ketones themselves have rich potential for making useful materials, such as self-healing hydrogels, polysaccharide-protein therapeutic conjugates, or drug delivery vehicles. Herein, we review recent advances in synthesizing polysaccharides containing aldehyde or ketone moieties and briefly introduce their reactivity and corresponding applications.

Mo than meets the eye: genomic insights into molybdoenzyme diversity of Seleniivibrio woodruffii strain S4T

Seleniivibrio woodruffii strain S4T is an obligate anaerobe belonging to the phylum Deferribacterota. It was isolated for its ability to respire selenate and was also found to respire arsenate. The high-quality draft genome of this bacterium is 2.9 Mbp, has a G+C content of 48%, 2762 predicted genes of which 2709 are protein-coding, and 53 RNA genes. An analysis of the genome focusing on the genes encoding for molybdenum-containing enzymes (molybdoenzymes) uncovered a remarkable number of genes encoding for members of the dimethylsulfoxide reductase family of proteins (DMSOR), including putative reductases for selenate and arsenate respiration, as well as genes for nitrogen fixation. Respiratory molybdoenzymes catalyze redox reactions that transfer electrons to a variety of substrates that can act as terminal electron acceptors for energy generation. Seleniivibrio woodruffii strain S4T also has essential genes for molybdate transporters and the biosynthesis of the molybdopterin guanine dinucleotide cofactors characteristic of the active centers of DMSORs. Phylogenetic analysis revealed candidate respiratory DMSORs spanning nine subfamilies encoded within the genome. Our analysis revealed the untapped potential of this interesting microorganism and expanded our knowledge of molybdoenzyme co-occurrence.

Endotoxin-induced alterations of adipose tissue function: a pathway to bovine metabolic stress

During the periparturient period, dairy cows exhibit negative energy balance due to limited appetite and increased energy requirements for lactogenesis. The delicate equilibrium between energy availability and expenditure puts cows in a state of metabolic stress characterized by excessive lipolysis in white adipose tissues (AT), increased production of reactive oxygen species, and immune cell dysfunction. Metabolic stress, especially in AT, increases the risk for metabolic and inflammatory diseases. Around parturition, cows are also susceptible to endotoxemia. Bacterial-derived toxins cause endotoxemia by promoting inflammatory processes and immune cell infiltration in different organs and systems while impacting metabolic function by altering lipolysis, mitochondrial activity, and insulin sensitivity. In dairy cows, endotoxins enter the bloodstream after overcoming the defense mechanisms of the epithelial barriers, particularly during common periparturient conditions such as mastitis, metritis, and pneumonia, or after abrupt changes in the gut microbiome. In the bovine AT, endotoxins induce a pro-inflammatory response and stimulate lipolysis in AT, leading to the release of free fatty acids into the bloodstream. When excessive and protracted, endotoxin-induced lipolysis can impair adipocyte's insulin signaling pathways and lipid synthesis. Endotoxin exposure can also induce oxidative stress in AT through the production of reactive oxygen species by inflammatory cells and other cellular components. This review provides insights into endotoxins' impact on AT function, highlighting the gaps in our knowledge of the mechanisms underlying AT dysfunction, its connection with periparturient cows' disease risk, and the need to develop effective interventions to prevent and treat endotoxemia-related inflammatory conditions in dairy cattle.

Evaluating Bacterial Nanocellulose Interfaces for Recording Surface Biopotentials from Plants

The study of plant electrophysiology offers promising techniques to track plant health and stress in vivo for both agricultural and environmental monitoring applications. Use of superficial electrodes on the plant body to record surface potentials may provide new phenotyping insights. Bacterial nanocellulose (BNC) is a flexible, optically translucent, and water-vapor-permeable material with low manufacturing costs, making it an ideal substrate for non-invasive and non-destructive plant electrodes. This work presents BNC electrodes with screen-printed carbon (graphite) ink-based conductive traces and pads. It investigates the potential of these electrodes for plant surface electrophysiology measurements in comparison to commercially available standard wet gel and needle electrodes. The electrochemically active surface area and impedance of the BNC electrodes varied based on the annealing temperature and time over the ranges of 50 °C to 90 °C and 5 to 60 min, respectively. The water vapor transfer rate and optical transmittance of the BNC substrate were measured to estimate the level of occlusion caused by these surface electrodes on the plant tissue. The total reduction in chlorophyll content under the electrodes was measured after the electrodes were placed on maize leaves for up to 300 h, showing that the BNC caused only a 16% reduction. Maize leaf transpiration was reduced by only 20% under the BNC electrodes after 72 h compared to a 60% reduction under wet gel electrodes in 48 h. On three different model plants, BNC-carbon ink surface electrodes and standard invasive needle electrodes were shown to have a comparable signal quality, with a correlation coefficient of >0.9, when measuring surface biopotentials induced by acute environmental stressors. These are strong indications of the superior performance of the BNC substrate with screen-printed graphite ink as an electrode material for plant surface biopotential recordings.

The massive 340 megabase genome of Anisogramma anomala, a biotrophic ascomycete that causes eastern filbert blight of hazelnut

BACKGROUND

The ascomycete fungus Anisogramma anomala causes Eastern Filbert Blight (EFB) on hazelnut (Corylus spp.) trees. It is a minor disease on its native host, the American hazelnut (C. americana), but is highly destructive on the commercially important European hazelnut (C. avellana). In North America, EFB has historically limited commercial production of hazelnut to west of the Rocky Mountains. A. anomala is an obligately biotrophic fungus that has not been grown in continuous culture, rendering its study challenging. There is a 15-month latency before symptoms appear on infected hazelnut trees, and only a sexual reproductive stage has been observed. Here we report the sequencing, annotation, and characterization of its genome.

RESULTS

The genome of A. anomala was assembled into 108 scaffolds totaling 342,498,352 nt with a GC content of 34.46%. Scaffold N50 was 33.3 Mb and L50 was 5. Nineteen scaffolds with lengths over 1 Mb constituted 99% of the assembly. Telomere sequences were identified on both ends of two scaffolds and on one end of another 10 scaffolds. Flow cytometry estimated the genome size of A. anomala at 370 Mb. The genome exhibits two-speed evolution, with 93% of the assembly as AT-rich regions (32.9% GC) and the other 7% as GC-rich (57.1% GC). The AT-rich regions consist predominantly of repeats with low gene content, while 90% of predicted protein coding genes were identified in GC-rich regions. Copia-like retrotransposons accounted for more than half of the genome. Evidence of repeat-induced point mutation (RIP) was identified throughout the AT-rich regions, and two copies of the rid gene and one of dim-2, the key genes in the RIP mutation pathway, were identified in the genome. Consistent with its homothallic sexual reproduction cycle, both MAT1-1 and MAT1-2 idiomorphs were found. We identified a large suite of genes likely involved in pathogenicity, including 614 carbohydrate active enzymes, 762 secreted proteins and 165 effectors.

CONCLUSIONS

This study reveals the genomic structure, composition, and putative gene function of the important pathogen A. anomala. It provides insight into the molecular basis of the pathogen's life cycle and a solid foundation for studying EFB.

Efficacy and residual toxicity of chitosan for Rhagoletis pomonella (Diptera: Tephritidae)

Chitosan is a naturally derived polymer that has significant potential for use as a bioinsecticide. Despite this, there is a lack of research as to the efficacy of chitosan for many insect pest species. The apple maggot fly, Rhagoletis pomonella (Walsh) (Diptera: Tephritidae), is one such pest for which chitosan toxicity has not been explored. In this study, the toxicity of chitosan for R. pomonella adults was tested via no-choice feeding assays. An aging trial was further used to test the mortality of flies provided dried chitosan-sucrose treatments (CST), which were aged for 0 or 3 days in greenhouse conditions. This study found that the CST is toxic for R. pomonella adults when ingested, leading to a significant increase in the rate of mortality compared to control groups. The use of dried chitosan, however, did not change the mortality of flies, suggesting this will not be an effective delivery mechanism. Effective biopesticide delivery systems have not been defined for chitosan use outside of a laboratory, indicating the need for further research testing delivery mechanisms. It is suggested that an effective method of delivery can be as a food-based bait in attract-and-kill traps, as chitosan must be ingested to kill flies. Forming a viscous solution, chitosan may be best suited to these lure systems.

Mitigation Potential of Herbal Extracts and Constituent Bioactive Compounds on Salmonella in Meat-Type Poultry

Herbal extracts have been widely evaluated in poultry production for their beneficial effects and potential substitute for antibiotics, which contribute to AMR and risks to human health through the consumption of infected meat. Salmonellosis is a systemic infection caused by Salmonella, an intracellular bacterium with the ability to cause systemic infections with significant implications for both the health and safety of farmers and consumers. The excessive use of antibiotics has escalated the incidence of antibiotic resistance bacteria in the poultry and livestock industry, highlighting the urgent need for alternatives especially in meat-type poultry. Both in vivo usage and in vitro studies of bioactive compounds from herbal extracts have demonstrated the effective antimicrobial activities against pathogenic bacteria, showing promise in managing Salmonella infections and enhancing poultry performance. Phytobiotic feed additives have shown promising results in improving poultry output due to their pharmacological properties, such as stimulating consumption, and enhancing antioxidant properties and preventing the increasing antimicrobial resistance threats. Despite potential for synergistic effects from plant-derived compounds, a further investigation into is essential to fully understand their role and mechanisms of action, for developing effective delivery systems, and for assessing environmental sustainability in controlling Salmonella in poultry production.

Effect of Ginger Root Extract on Intestinal Oxidative Status and Mucosal Morphometrics in Broiler Chickens

This study was designed to assess the effect of ginger root extract (GRE) supplementation on the oxidative status and intestinal mucosal development in broiler chickens for 6 weeks. Day-old chicks (Ross 708 strain, n = 432) were distributed into six treatments with six replicate of twelve birds each: Negative CON (basal), MX (basal diet + bacitracin methylene disalicylate (BMD) 0.055 g/kg diet), GRE-1 (basal diet + 0.375% GRE), GRE-2 (basal diet + 0.75% GRE), GRE-3 (basal diet + 1.5% GRE), GRE-4 (basal diet + 3% GRE). Growth indices, goblets cell count, mucin (MUC2) in ileum tissue, antioxidant (SOD, CAT, and GPX) in ileum and liver, biological antioxidant potential (BAP), and reactive oxygen metabolite level in blood and intestinal villi measurement were determined. Body weight (BW) was highest (p < 0.05) in all groups except GRE-4, body weight gain (BWG) was best in GRE-1, while FCR was least in all groups except GRE-4. Optimum MUC2 gene expression, SOD, CAT, blood antioxidants, and intestinal morphometric values were observed in GRE-3. The inclusion of ginger root extract up to 1.5% improved growth and reduced oxidative stress while enhancing mucosal development in broiler chicks.

Risk Factor Analysis and Genetic Parameter Estimation for Pre-Weaning Mortality Traits in Boer, Spanish, and Crossbred Goat Kids

The objectives of this study were to evaluate fixed risk factors associated with PWM and to estimate genetic parameters for PWM. A total of 927 birth records from a mixed population of purebred and crossbred Boer and Spanish goats born between 2016 and 2023 at the International Goat Research Center (IGRC) were used for this study. Four binary traits were studied: D0-3 (death within 3 days after birth), D4-60 (death between 4 and 60 days), D61-90 (death between 61 and 90 days), and D0-90 (death within 90 days). Logistic regression models were used to evaluate the risk factors associated with PWM traits. Bayesian threshold models and Gibbs sampling were used to estimate the genetic parameters. Birth weight, season, litter size, sex, dam age, breed, and heterosis were found to be significantly associated with at least one of the PWM traits. Heritability estimates were 0.263, 0.124, 0.080, and 0.207, for D0-3, D4-60, D61-90, and D0-90, respectively. The genetic correlations between the studied traits ranged from 0.892 (D0-3 and D0-90) to 0.999 (D0-3 and D61-90). These results suggest that PWM in goats is influenced by both non-genetic and genetic factors and can be reduced by management, genetic selection, and crossbreeding approaches.

Integrating plant morphological traits with remote-sensed multispectral imageries for accurate corn grain yield prediction

Sustainable crop production requires adequate and efficient management practices to reduce the negative environmental impacts of excessive nitrogen (N) fertilization. Remote sensing has gained traction as a low-cost and time-efficient tool for monitoring and managing cropping systems. In this study, vegetation indices (VIs) obtained from an unmanned aerial vehicle (UAV) were used to detect corn (Zea mays L.) response to varying N rates (ranging from 0 to 208 kg N ha-1) and fertilizer application methods (liquid urea ammonium nitrate (UAN), urea side-dressing and slow-release fertilizer). Four VIs were evaluated at three different growth stages of corn (V6, R3, and physiological maturity) along with morphological traits including plant height and leaf chlorophyll content (SPAD) to determine their predictive capability for corn yield. Our results show no differences in grain yield (average 13.2 Mg ha-1) between furrow-applied slow-release fertilizer at ≥156 kg N ha-1 and 208 kg N ha-1 side-dressed urea. Early season remote-sensed VIs and morphological data collected at V6 were least effective for grain yield prediction. Moreover, multivariate grain yield prediction was more accurate than univariate. Late-season measurements at the R3 and mature growth stages using a combination of normalized difference vegetation index (NDVI) and green normalized difference vegetation index (GNDVI) in a multilinear regression model showed effective prediction for corn yield. Additionally, a combination of NDVI and normalized difference red edge index (NDRE) in a multi-exponential regression model also demonstrated good prediction capabilities.

Pneumatic spray delivery-based fixed spray system configuration optimization for efficient agrochemical application in modern vineyards

BACKGROUND

The hydraulic spray delivery (HSD)-based solid set canopy delivery system (SSCDS) emitter configuration has been optimized for agrochemical applications in vertical shoot position (VSP) vineyards. It uses cost-prohibitive emitters, and their placement restricts the mechanical pruning activities. Therefore, this study focused on optimizing the spray performance of a pneumatic spray delivery (PSD)-based SSCDS variant that addresses the earlier issues. Three PSD-SSCDS emitter configurations (C1-C3) were designed using modified low-cost emitters (E1: modified flat fan, E2: 90° modular flat fan) for agrochemical applications in VSP vineyards. C1 had an E1 installed on trellis posts at 1.67 m above ground level. C2 had a pair of E2 installed per vine at 0.3 m below the cordon, while C3 combined the emitter placement of C1 and C2. The spray deposition (ng cm-2) and coverage (%) were quantified (mean ± standard error) using mylar cards and water-sensitive paper samplers placed within the canopy, respectively.

RESULTS

Spray deposition for C1, C2, and C3 was 301.12 ± 63.30, 347.9 ± 66.29, and 837.6 ± 92.53 ng cm-2, respectively. Whereas spray coverage for corresponding configurations was 18.02 ± 2.63, 8.98 ± 1.84, and 28.84 ± 2.46%, respectively.

CONCLUSIONS

Overall, configuration C3 provided significantly higher spray deposition and coverage than C1 and C2. Substantially reduced system installation cost and emitter density per hectare with improved spray performance were achieved by C3 compared to earlier optimized HSD-SSCDS configuration in the VSP vineyards. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

The effect of repeated hurricanes on the age of organic carbon in humid tropical forest soil

Increasing hurricane frequency and intensity with climate change is likely to affect soil organic carbon (C) stocks in tropical forests. We examined the cycling of C between soil pools and with depth at the Luquillo Experimental Forest in Puerto Rico in soils over a 30-year period that spanned repeated hurricanes. We used a nonlinear matrix model of soil C pools and fluxes ("soilR") and constrained the parameters with soil and litter survey data. Soil chemistry and stable and radiocarbon isotopes were measured from three soil depths across a topographic gradient in 1988 and 2018. Our results suggest that pulses and subsequent reduction of inputs caused by severe hurricanes in 1989, 1998, and two in 2017 led to faster mean transit times of soil C in 0-10 cm and 35-60 cm depths relative to a modeled control soil with constant inputs over the 30-year period. Between 1988 and 2018, the occluded C stock increased and δ13C in all pools decreased, while changes in particulate and mineral-associated C were undetectable. The differences between 1988 and 2018 suggest that hurricane disturbance results in a dilution of the occluded light C pool with an influx of young, debris-deposited C, and possible microbial scavenging of old and young C in the particulate and mineral-associated pools. These effects led to a younger total soil C pool with faster mean transit times. Our results suggest that the increasing frequency of intense hurricanes will speed up rates of C cycling in tropical forests, making soil C more sensitive to future tropical forest stressors.

- Invited Review - Pig production in Latin America

Latin America is a culturally, geographically, politically, and economically diverse region. Agriculture in Latin America is marked by a remarkable diversity of production systems, reflecting various agroecological zones, farm sizes, and technological levels. In the last decade, the swine industry increased by 30.6%, emerging as a great contributor to food security and economic development in Latin America. Brazil and Mexico dominate the pig production landscape, together accounting for 70% of sow inventory in the region. The swine industry in Latin America is predominantly comprised of small and medium-sized farms, however, in the past 30 years, the number of pig producers in Brazil dropped by 78%, whereas pork production increased by 326%. Similar to the global pork industry, the growing demand for pork, driven by population growth and changing dietary habits, presents an opportunity for the industry with an expected growth of 16% over the next decade. The export prospects are promising, however subject to potential disruptions from global market conditions and shifts in trade policies. Among the challenges faced by the swine industry, disease outbreaks, particularly African Swine Fever (ASF), present significant threats, necessitating enhanced biosecurity and surveillance systems. In 2023, ASF was reported to the Dominican Republic and Haiti, Porcine Reproductive and Respiratory Syndrome (PRRS) in Mexico, Costa Rica, the Dominican Republic, Colombia, and Venezuela, and Porcine Epidemic Diarrhea (PED) in Mexico, Peru, the Dominican Republic, Colombia, and Ecuador. Additionally, feed costs, supply chain disruptions, and energy expenses have affected mainly the smaller and less efficient producers. The swine industry is also transitioning towards more sustainable and environmentally friendly practices, including efficient feed usage, and precision farming. Ensuring long-term success in the swine industry in Latin America requires a holistic approach that prioritizes sustainability, animal welfare, and consumer preferences, ultimately positioning the industry to thrive in the evolving global market.

Incidence of eriophyid mites (Acariformes: Eriophyidae) and predatory mites (Parasitiformes: Phytoseiidae) in Florida citrus orchards under three different pest management programs

The abundance and diversity of eriophyid and phytoseiid mites in south and central Florida were assessed in six citrus orchards under three different pest management systems, conventional, organic, and untreated. Tree canopy, ground cover, and leaf litter were sampled every two months in two groves for each of the three pest management systems from April 2019 to February 2021. The citrus rust mite, Phyllocoptruta oleivora (Ashmead) represented 95 to 99% of the rust mites sampled in each grove except in one untreated orchard where it accounted for 45% of the samples (n = 938 total P. oleivora mounted specimens). The pink citrus rust mite, Aculops pelekassi (Keifer) was present in organic and untreated orchards at 5% and 28%, respectively, but absent from conventional orchards (n = 134 total A. pelekassi mounted specimens). Twenty-nine species of phytoseiid mites were identified from 1778 specimens. Thirteen species were present in the canopy, fifteen in the ground cover, and eighteen in the leaf litter with some common species among these habitats. In the tree canopy, Typhlodromalus peregrinus (39%), Euseius spp. (25%), and Iphiseiodes quadripilis (19%) were the dominant species. Typhlodromalus peregrinus (43%), Typhlodromips dentilis (25%), and Proprioseiopsis mexicanus (13%) were the major species in the ground cover. Species richness was lower in organic orchards (3.0) compared to conventional and untreated orchards (5.0 and 4.7, respectively). In the leaf litter, Amblyseius curiosus (26%), Proprioseiopsis carolinianus (15%), Chelaseius floridanus (14%), and Amblyseius tamatavensis (12%) were the most common species. Shannon index was significantly higher in conventional orchards (1.45) compared to organic and untreated orchards (1.02 and 1.05, respectively). Evenness was also higher in conventional orchards (0.86) compared to organic and untreated (0.72 and 0.68, respectively). Finding of several phytoseiids in abundance across pest management programs suggest the need for identifying their role in pest suppression particularly mites.

Accelerating Biodegradation: Enhancing Poly(lactic acid) Breakdown at Mesophilic Environmental Conditions with Biostimulants

Poly(lactic acid) (PLA) has garnered interest due to its low environmental footprint and ability to replace conventional polymers and be disposed of in industrial composting environments. Although PLA is compostable when subjected to a suitable set of conditions, its broader acceptance in industrial composting facilities has been affected adversely due to longer degradation timeframes than the readily biodegradable organic waste fraction. PLA must be fully exposed to thermophilic conditions for prolonged periods to biodegrade, which has restricted its adoption and hindered its acceptance in industrial composting facilities, negating its home composting potential. Thus, enhancing PLA biodegradation is crucial to expand its acceptance. PLA's biodegradability is investigated in a compost matrix under mesophilic conditions at 37 °C for 180 days by biostimulating the compost environment with skim milk, gelatin, and ethyl lactate to enhance the different stages of PLA biodegradation. The evolved CO2, number average molecular weight (Mn), and crystallinity evolution are tracked. To achieve a Mn ≲ 10 kDa for PLA, the biodegradation rate is accelerated by 15% by adding skim milk, 25% by adding gelatin, and 22% by adding ethyl lactate. This work shows potential techniques to help biodegrade PLA in home composting setting by adding biostimulants.

Genome-wide association identifies a BAHD acyltransferase activity that assembles an ester of glucuronosylglycerol and phenylacetic acid

Genome-wide association studies (GWAS) are an effective approach to identify new specialized metabolites and the genes involved in their biosynthesis and regulation. In this study, GWAS of Arabidopsis thaliana soluble leaf and stem metabolites identified alleles of an uncharacterized BAHD-family acyltransferase (AT5G57840) associated with natural variation in three structurally related metabolites. These metabolites were esters of glucuronosylglycerol, with one metabolite containing phenylacetic acid as the acyl component of the ester. Knockout and overexpression of AT5G57840 in Arabidopsis and heterologous overexpression in Nicotiana benthamiana and Escherichia coli demonstrated that it is capable of utilizing phenylacetyl-CoA as an acyl donor and glucuronosylglycerol as an acyl acceptor. We, thus, named the protein Glucuronosylglycerol Ester Synthase (GGES). Additionally, phenylacetyl glucuronosylglycerol increased in Arabidopsis CYP79A2 mutants that overproduce phenylacetic acid and was lost in knockout mutants of UDP-sulfoquinovosyl: diacylglycerol sulfoquinovosyl transferase, an enzyme required for glucuronosylglycerol biosynthesis and associated with glycerolipid metabolism under phosphate-starvation stress. GGES is a member of a well-supported clade of BAHD family acyltransferases that arose by duplication and neofunctionalized during the evolution of the Brassicales within a larger clade that includes HCT as well as enzymes that synthesize other plant-specialized metabolites. Together, this work extends our understanding of the catalytic diversity of BAHD acyltransferases and uncovers a pathway that involves contributions from both phenylalanine and lipid metabolism.

Specifically targeting antimicrobial peptides for inhibition of Candidatus Liberibacter asiaticus

AIMS

Huanglongbing (citrus greening) is a plant disease putatively caused by the unculturable Gram-negative bacterium Candidatus Liberibacter asiaticus (CLas), and it has caused severe damage to citrus plantations worldwide. There are no definitive treatments for this disease, and conventional disease control techniques have shown limited efficacy. This work presents an in silico evaluation of using specifically targeting anti-microbial peptides (STAMPs) consisting of a targeting segment and an antimicrobial segment to inhibit citrus greening by inhibiting the BamA protein of CLas, which is an outer membrane protein crucial for bacterial viability.

METHODS AND RESULTS

Initially, a set of peptides with a high affinity toward BamA protein were screened and evaluated via molecular docking and molecular dynamics simulations and were verified in vitro via bio-layer interferometry (BLI). In silico studies and BLI experiments indicated that two peptides, HASP2 and HASP3, showed stable binding to BamA. Protein structures for STAMPs were created by fusing known anti-microbial peptides (AMPs) with the selected short peptides. The binding of STAMPs to BamA was assessed using molecular docking and binding energy calculations. The attachment of high-affinity short peptides significantly reduced the free energy of binding for AMPs, suggesting that it would make it easier for the STAMPs to bind to BamA. Efficacy testing in vitro using a closely related CLas surrogate bacterium showed that STAMPs had greater inhibitory activity than AMP alone.

CONCLUSIONS

In silico and in vitro results indicate that the STAMPs can inhibit CLas surrogate Rhizobium grahamii more effectively compared to AMPs, suggesting that STAMPs can achieve better inhibition of CLas, potentially via enhancing the site specificity of AMPs.

Facile synthesis of gold nanostars for the duplex detection of pesticide residues in grapes using SERS

In recent years, concerns have been raised regarding the contamination of grapes with pesticide residues. As consumer demand for safer food products grows, regular monitoring of pesticide residues in food has become essential. This study sought to develop a rapid and sensitive technique for detecting two specific pesticides (phosmet and paraquat) present on the grape surface using the surface-enhanced Raman spectroscopy (SERS) method. Gold nanostars (AuNS) particles were synthesized, featuring spiky tips that act as hot spots for localized surface plasmon resonance, thereby enhancing Raman signals. Additionally, the roughened surface of AuNS increases the surface area, resulting in improved interactions between the substrate and analyte molecules. Prominent Raman peaks of mixed contaminants were acquired and used to characterize and quantify the pesticides. It was observed that the SERS intensity of the Raman peaks changed in proportion to the concentration ratio of phosmet and paraquat. Moreover, AuNS exhibited superior SERS enhancement compared to gold nanoparticles. The results demonstrate that the lowest detectable concentration for both pesticides on grape surfaces is 0.5 mg/kg. These findings suggest that SERS coupled with AuNS constitutes a practical and promising approach for detecting and quantifying trace contaminants in food. PRACTICAL APPLICATION: This research established a novel surface-enhanced Raman spectroscopy (SERS) method coupled with a simplified extraction protocol and gold nanostar substrates to detect trace levels of pesticides in fresh produce. The detection limits meet the maximum residue limits set by the EPA. This substrate has great potential for rapid measurements of chemical contaminants in foods.