Naturally colored cotton for wearable applications

Naturally colored cotton (NCC) offers an environmentally friendly fiber for textile applications. Processing white cotton fiber into textiles requires extensive energy, water, and chemicals, whereas processing of NCC skips the most polluting activity, scouring-bleaching and dyeing; therefore, NCC provides an avenue to minimize the harmful impacts of textile production. NCC varieties are suitable for organic agriculture since they are naturally insect and disease-resistant, salt and drought-tolerant. Various fiber shades, ranging from light green to tan and brown, are available in the cultivated NCC (Gossypium hirsutum L.) species. The pigments responsible for the color of brown cotton fiber are proanthocyanidins or their derivatives synthesized by the flavonoid pathway. Due to pigments, the NCC has excellent ultraviolet protection properties. Some brown cotton varieties exhibited superior thermal resistance of fiber that can be used to make fabrics with enhanced flame retardancy. Here, we review molecular mechanisms involved in the pigment production of brown cotton and challenges in breeding NCC varieties with a wide range of colors but without penalty in fiber quality. Also, we discuss opportunities for NCC with flame-retarding properties in textile applications.

Environmental parameters factors exploration on lettuce seed germination with hydrogel

Lettuce (Lactuca sativa) germination is sensitive to environmental conditions. Recently, hydrogel has received increased attention as an alternative media to soil for seed germination. Compared to soil seeding, hydrogel-aided germination provides more controlled seeding environments. However, there are still challenges preventing hydrogel-aided seed germination from being widely used in industry production or academic studies, such as hydrogel formulation variations, seeding operation standardization, and germination evaluation. In this study, we tested how the combination of multiple environmental conditions affect lettuce seed germination time, which is measured as the time needed for the first pair of leaves to appear (leaf emergence) or, alternatively, the third leaf to appear (leaf development). We found that germination time and success rate of two lettuce varieties (Iceberg A and Butter Crunch) showed different sensitivities to pH, Hoagland formulations and concentrations, light intensity, and hydrogel content. We have conducted statistical analysis on the correlation between germination time and these environmental conditions.

Weight history of individuals with and without physical disability in the International Weight Control Registry

Background

People with physical disabilities (PWD) have an increased risk of obesity and related comorbidities compared with people without physical disabilities (PWoD). Previously identified contributors to weight loss maintenance pose challenges to PWD. However, it is not known if PWD experience less success in weight management.

Methods

Six hundred and nine participants in the International Weight Control Registry (IWCR) were eligible for this analysis (PWD, n = 174; PWoD, n = 435). Self-reported weight history metrics were compared using general linear models. Perceived weight history category was compared using Chi-squared tests. Importance of diet and physical activity strategies for weight management were compared using Wilcoxon rank-signed tests.

Results

PWD reported higher current body mass index (BMI) (36.1 ± 0.7 vs. 31.0 ± 0.5; p < 0.0001) and more weight loss attempts (9.1 ± 0.7 vs. 7.1 ± 0.4; p = 0.01) than PWoD. Current weight loss percentage (PWD 13.0 ± 1.0; PWoD, 13.0 ± 0.6; p = 0.97) and weight loss category (χ 2 [3, N = 609] = 2.9057, p = 0.41) did not differ between the groups. There were no differences in any weight strategy between PWD who were successful and those who regained.

Conclusions

PWD and PWoD in the IWCR achieved similar levels of weight maintenance success. However, higher BMI and more weight loss attempts suggest that PWD may face challenges with weight management. More research is needed to identify strategies leading to success for PWD.

Genome size variation and evolution during invasive range expansion in an introduced plant

Plants demonstrate exceptional variation in genome size across species, and their genome sizes can also vary dramatically across individuals and populations within species. This aspect of genetic variation can have consequences for traits and fitness, but few studies attributed genome size differentiation to ecological and evolutionary processes. Biological invasions present particularly useful natural laboratories to infer selective agents that might drive genome size shifts across environments and population histories. Here, we test hypotheses for the evolutionary causes of genome size variation across 14 invading populations of yellow starthistle, Centaurea solstitialis, in California, United States. We use a survey of genome sizes and trait variation to ask: (1) Is variation in genome size associated with developmental trait variation? (2) Are genome sizes smaller toward the leading edge of the expansion, consistent with selection for "colonizer" traits? Or alternatively, does genome size increase toward the leading edge of the expansion, consistent with predicted consequences of founder effects and drift? (3) Finally, are genome sizes smaller at higher elevations, consistent with selection for shorter development times? We found that 2C DNA content varied 1.21-fold among all samples, and was associated with flowering time variation, such that plants with larger genomes reproduced later, with lower lifetime capitula production. Genome sizes increased toward the leading edge of the invasion, but tended to decrease at higher elevations, consistent with genetic drift during range expansion but potentially strong selection for smaller genomes and faster development time at higher elevations. These results demonstrate how genome size variation can contribute to traits directly tied to reproductive success, and how selection and drift can shape that variation. We highlight the influence of genome size on dynamics underlying a rapid range expansion in a highly problematic invasive plant.

Streptomyces spp. as biocatalyst sources in pulp and paper and textile industries: Biodegradation, bioconversion and valorization of waste

Complex polymers represent a challenge for remediating environmental pollution and an opportunity for microbial-catalysed conversion to generate valorized chemicals. Members of the genus Streptomyces are of interest because of their potential use in biotechnological applications. Their versatility makes them excellent sources of biocatalysts for environmentally responsible bioconversion, as they have a broad substrate range and are active over a wide range of pH and temperature. Most Streptomyces studies have focused on the isolation of strains, recombinant work and enzyme characterization for evaluating their potential for biotechnological application. This review discusses reports of Streptomyces-based technologies for use in the textile and pulp-milling industry and describes the challenges and recent advances aimed at achieving better biodegradation methods featuring these microbial catalysts. The principal points to be discussed are (1) Streptomyces' enzymes for use in dye decolorization and lignocellulosic biodegradation, (2) biotechnological processes for textile and pulp and paper waste treatment and (3) challenges and advances for textile and pulp and paper effluent treatment.

Maternal upbringing and selective breeding for voluntary exercise behavior modify patterns of DNA methylation and expression of genes in the mouse brain

Selective breeding has been utilized to study the genetic basis of exercise behavior, but research suggests that epigenetic mechanisms, such as DNA methylation, also contribute to this behavior. In a previous study, we demonstrated that the brains of mice from a genetically selected high runner (HR) line have sex-specific changes in DNA methylation patterns in genes known to be genomically imprinted compared to those from a non-selected control (C) line. Through cross-fostering, we also found that maternal upbringing can modify the DNA methylation patterns of additional genes. Here, we identify an additional set of genes in which DNA methylation patterns and gene expression may be altered by selection for increased wheel-running activity and maternal upbringing. We performed bisulfite sequencing and gene expression assays of 14 genes in the brain and found alterations in DNA methylation and gene expression for Bdnf, Pde4d and Grin2b. Decreases in Bdnf methylation correlated with significant increases in Bdnf gene expression in the hippocampus of HR compared to C mice. Cross-fostering also influenced the DNA methylation patterns for Pde4d in the cortex and Grin2b in the hippocampus, with associated changes in gene expression. We also found that the DNA methylation patterns for Atrx and Oxtr in the cortex and Atrx and Bdnf in the hippocampus were further modified by sex. Together with our previous study, these results suggest that DNA methylation and the resulting change in gene expression may interact with early-life influences to shape adult exercise behavior.

Effect of standard and physiological cell culture temperatures on in vitro proliferation and differentiation of primary broiler chicken pectoralis major muscle satellite cells

Culture temperatures for broiler chicken cells are largely based on those optimized for mammalian species, although normal broiler body temperature is typically more than 3°C higher. The objective was to evaluate the effects of simulating broiler peripheral muscle temperature, 41°C, compared with standard temperature, 38°C, on the in vitro proliferation and differentiation of primary muscle-specific stem cells (satellite cells; SC) from the pectoralis major (PM) of broiler chickens. Primary SC cultures were isolated from the PM of 18-day-old Ross 708 × Yield Plus male broilers. SC were plated in triplicate, 1.8-cm2, gelatin-coated wells at 40,000 cells per well. Parallel plates were cultured at either 38°C or 41°C in separate incubators. At 48, 72, and 96 h post-plating, the culture wells were fixed and immunofluorescence-stained to determine the expression of the myogenic regulatory factors Pax7 and MyoD as well as evaluated for apoptosis using a TUNEL assay. After 168 h in culture, plates were immunofluorescence-stained to visualize myosin heavy chain and Pax7 expression and determine myotube characteristics and SC fusion. Population doubling times were not impacted by temperature (p ≥ 0.1148), but culturing broiler SC at 41°C for 96 h promoted a more rapid progression through myogenesis, while 38°C maintained primitive populations (p ≤ 0.0029). The proportion of apoptotic cells increased in primary SC cultured at 41°C (p ≤ 0.0273). Culturing at 41°C appeared to negatively impact fusion percentage (p < 0.0001) and tended to result in the formation of thinner myotubes (p = 0.061) without impacting the density of differentiated cells (p = 0.7551). These results indicate that culture temperature alters primary broiler PM SC myogenic kinetics and has important implications for future in vitro work as well as improving our understanding of how thermal manipulation can alter myogenesis patterns during broiler embryonic and post-hatch muscle growth.

A membrane protein of the rice pathogen Burkholderia glumae required for oxalic acid secretion and quorum sensing

Bacterial panicle blight is caused by Burkholderia glumae and results in damage to rice crops worldwide. Virulence of B. glumae requires quorum sensing (QS)-dependent synthesis and export of toxoflavin, responsible for much of the damage to rice. The DedA family is a conserved membrane protein family found in all bacterial species. B. glumae possesses a member of the DedA family, named DbcA, which we previously showed is required for toxoflavin secretion and virulence in a rice model of infection. B. glumae secretes oxalic acid as a "common good" in a QS-dependent manner to combat toxic alkalinization of the growth medium during the stationary phase. Here, we show that B. glumae ΔdbcA fails to secrete oxalic acid, leading to alkaline toxicity and sensitivity to divalent cations, suggesting a role for DbcA in oxalic acid secretion. B. glumae ΔdbcA accumulated less acyl-homoserine lactone (AHL) QS signalling molecules as the bacteria entered the stationary phase, probably due to nonenzymatic inactivation of AHL at alkaline pH. Transcription of toxoflavin and oxalic acid operons was down-regulated in ΔdbcA. Alteration of the proton motive force with sodium bicarbonate also reduced oxalic acid secretion and expression of QS-dependent genes. Overall, the data show that DbcA is required for oxalic acid secretion in a proton motive force-dependent manner, which is critical for QS of B. glumae. Moreover, this study supports the idea that sodium bicarbonate may serve as a chemical for treatment of bacterial panicle blight.

Genetic analysis of basal stalk rot resistance introgressed from wild Helianthus petiolaris into cultivated sunflower (Helianthus annuus L.) using an advanced backcross population

Introduction

Sclerotinia sclerotiorum is a serious pathogen causing severe basal stalk rot (BSR) disease on cultivated sunflower (Helianthus annuus L.) that leads to significant yield losses due to insufficient resistance. The wild annual sunflower species H. petiolaris, commonly known as prairie sunflower is known for its resistance against this pathogen. Sunflower resistance to BSR is quantitative and determined by many genes with small effects on the resistance phenotype. The objective of this study was to identify loci governing BSR resistance derived from H. petiolaris using a quantitative trait loci (QTL) mapping approach.

Methods

BSR resistance among lines of an advanced backcross population (AB-QTL) with 174 lines developed from a cross of inbred line HA 89 with H. petiolaris PI 435843 was determined in the field during 2017-2019, and in the greenhouse in 2019. AB-QTL lines and the HA 89 parent were genotyped using genotyping-by-sequencing and a genetic linkage map was developed spanning 997.51 cM and using 1,150 SNP markers mapped on 17 sunflower chromosomes.

Results and discussion

Highly significant differences (p<0.001) for BSR response among AB-QTL lines were observed disease incidence (DI) in all field seasons, as well as disease rating (DR) and area under the disease progress curve (AUDPC) in the greenhouse with a moderately high broad-sense heritability (H 2) of 0.61 for the tested resistance parameters. A total of 14 QTL associated with BSR resistance were identified on nine chromosomes, each explaining a proportion of the phenotypic variation ranging from 3.5% to 28.1%. Of the 14 QTL, eight were detected for BSR resistance in the field and six were detected under greenhouse conditions. Alleles conferring increased BSR resistance were contributed by the H. petiolaris parent at 11 of the 14 QTL.

Genomic and transcriptomic analyses reveal polygenic architecture for ecologically important traits in aspen (Populus tremuloides Michx.)

Intraspecific genetic variation in foundation species such as aspen (Populus tremuloides Michx.) shapes their impact on forest structure and function. Identifying genes underlying ecologically important traits is key to understanding that impact. Previous studies, using single-locus genome-wide association (GWA) analyses to identify candidate genes, have identified fewer genes than anticipated for highly heritable quantitative traits. Mounting evidence suggests that polygenic control of quantitative traits is largely responsible for this "missing heritability" phenomenon. Our research characterized the genetic architecture of 30 ecologically important traits using a common garden of aspen through genomic and transcriptomic analyses. A multilocus association model revealed that most traits displayed a highly polygenic architecture, with most variation explained by loci with small effects (likely below the detection levels of single-locus GWA methods). Consistent with a polygenic architecture, our single-locus GWA analyses found only 38 significant SNPs in 22 genes across 15 traits. Next, we used differential expression analysis on a subset of aspen genets with divergent concentrations of salicinoid phenolic glycosides (key defense traits). This complementary method to traditional GWA discovered 1243 differentially expressed genes for a polygenic trait. Soft clustering analysis revealed three gene clusters (241 candidate genes) involved in secondary metabolite biosynthesis and regulation. Our work reveals that ecologically important traits governing higher-order community- and ecosystem-level attributes of a foundation forest tree species have complex underlying genetic structures and will require methods beyond traditional GWA analyses to unravel.

Bioactive fatty acids from non-conventional lipid sources and their potential application in functional food development

There is growing evidence that bioactive fatty acids (BFAs), including eicosapentaenoic acid (EPA; 20:5-3), docosahexaenoic acid (DHA; 22:6-3), and conjugated fatty acids offer multiple biological benefits and constitute ingredients in functional food development. Despite their potential, novel and alternative/nonconventional sources with unique bioactive properties to meet growing demand remain largely unexplored, poorly characterized, and their effects are not well understood. We systematically reviewed the literature to identify studies on alternative sources of BFAs, their functions, extraction, and application in the food and nutraceutical industry. Twenty studies delved into alternate sources such as plants, bacteria, and algae. Six studies found EPA and DHA as the dominant FA in algal sources, while ten studies reported several BFAs from plant sources. Five studies assessed the health benefits of docosapentaenoic acid (DPA), arachidonic acid (ARA), EPA, γ-linolenic acid (GLA), and linoleic acid (LA). Eleven studies compared the quality of oil recovered by green solvents, pressurized liquid, supercritical fluid, and assisted extraction methods. Three studies assessed the effects of assisted extraction methods and reported that these approaches improved oil yield and quality, but the findings may have limited applicability to other lipid sources. The quality of nonconventional lipids largely depends on extraction techniques. Four studies suggested methods like 1D and 2D NMR spectroscopy, LC-MS/MS; however, their analytical differences make accurate comparison inadequate. Five studies found that the incorporation of algal and seafood biolipids during product development increased EHA and DHA contents.

A plant virus protein, NIa-pro, interacts with Indole-3-acetic acid-amido synthetase, whose levels positively correlate with disease severity

Potato virus Y (PVY) is an economically important plant pathogen that reduces the productivity of several host plants. To develop PVY-resistant cultivars, it is essential to identify the plant-PVY interactome and decipher the biological significance of those molecular interactions. We performed a yeast two-hybrid (Y2H) screen of Nicotiana benthamiana cDNA library using PVY-encoded NIa-pro as the bait. The N. benthamiana Indole-3-acetic acid-amido synthetase (IAAS) was identified as an interactor of NIa-pro protein. The interaction was confirmed via targeted Y2H and bimolecular fluorescence complementation (BiFC) assays. NIa-pro interacts with IAAS protein and consequently increasing the stability of IAAS protein. Also, the subcellular localization of both NIa-pro and IAAS protein in the nucleus and cytosol was demonstrated. By converting free IAA (active form) to conjugated IAA (inactive form), IAAS plays a crucial regulatory role in auxin signaling. Transient silencing of IAAS in N. benthamiana plants reduced the PVY-mediated symptom induction and virus accumulation. Conversely, overexpression of IAAS enhanced symptom induction and virus accumulation in infected plants. In addition, the expression of auxin-responsive genes was found to be downregulated during PVY infection. Our findings demonstrate that PVY NIa-pro protein potentially promotes disease development via modulating auxin homeostasis.

Dams and tribal land loss in the United States

Indigenous peoples in the United States have faced continued land dispossession for centuries. Through the reservation system as well as policies including forced removal and allotment, colonial settlers and later the federal government acquired over two billion acres from Native Nations. We argue that another important, yet understudied and unquantified, contributor to tribal land loss is through the construction of dams. By restricting water flow in rivers or lakes, dams submerge land under reservoirs and disrupt aquatic and terrestrial ecosystems. This impacts livelihoods of local communities, destroys culturally important places and resources, and displaces people from their homes and land. To quantify the amount of tribal land lost as a result of dam construction, we engage in an innovative data linkage project. We use geospatial data on the boundaries of federal Indian reservations and Oklahoma Tribal Statistical Areas (OTSAs) and overlay these data with the locations of approximately 7,900 dams in the continental US. We estimate that 139 dams have submerged over 619 000 acres of land on 56 federal reservations and that 287 dams have inundated over 511 000 acres of land on 19 OTSAs. Taken together, our lower-bound estimate is that over 1.13 million acres of tribal land have been flooded under the reservoirs of 424 dams, which amounts to an area larger than Great Smokey Mountains National Park, Grand Teton National Park, and Rocky Mountain National Park combined. In light of recent federal legislation to address aging infrastructure in the US as well as the increasing risks to dam function and safety caused by climate change, dams that impact tribal land should be prioritized for removal. In cases where removal is not a preferred or viable option, alternatives include tribal ownership or funding for repairs and improvements.

Filter sterilized carcass rinsate for recovery of Salmonella species with various concentrations of cetylpyridinium chloride

Controlling Salmonella in poultry processing continues to be important to processors and consumers. Cetylpyridinium chloride (CPC) has proven to be effective in vitro in controlling Salmonella. This study evaluated the recovery of Salmonella after overnight storage in 4°C filter-sterilized carcass rinsate containing CPC from 0.44 to 909 ppm (μg/mL). Ten Salmonella serotypes (18 strains), of which 6 serotypes are commonly isolated from poultry products, were grown in Bacto-Tryptic Soy Broth overnight at 37°C. Serial dilutions of a CPC/propylene glycol solution were prepared in 24-well tissue culture plates containing filter-sterilized carcass rinsate. Approximately 107 cfu/mL of each Salmonella serotype was added to the appropriate wells. Inoculated plates were stored overnight at 4°C. After storage, triplicate plates of brilliant green agar with sulfapyridine (BGS) were surface inoculated with 10 μL of the contents for each well, streaked for isolation, and incubated at 37°C for 24 h. Three replications were conducted. The presence of typical colonies on BGS plates was recorded as growth and verified through biochemical and serological testing. Of the serotypes chosen, Salmonella Kentucky, Dublin, and Enteritidis were the least resistant to CPC with a median minimum inhibitory concentration (MIC) of 14.22 μg/mL (range from 3.55 to 56.88 μg/mL); S. Typhimurium demonstrated a median MIC of 114.00 μg/mL (range from 28.44 to 114.00 μg/mL). Residual CPC potentially remaining attached to a carcass or in the weep after processing could potentially alter which Salmonella serotype is recovered from a carcass rinse due to different growth patterns during regulatory testing, with a potential for more virulent strains not to be recovered.

QTL discovery for resistance to black spot and cercospora leaf spot, and defoliation in two interconnected F1 bi-parental tetraploid garden rose populations

Garden roses are an economically important horticultural crop worldwide, and two major fungal pathogens, black spot (Diplocarpon rosae F.A. Wolf) and cercospora leaf spot of rose (Rosisphaerella rosicola Pass.), affect both the health and ornamental value of the plant. Most studies on black spot disease resistance have focused on diploid germplasm, and little work has been performed on cercospora leaf spot resistance. With the use of newly developed software tools for autopolyploid genetics, two interconnected tetraploid garden rose F1 populations (phenotyped over the course of 3 years) were used for quantitative trait locus (QTL) analysis of black spot and cercospora leaf spot resistance as well as plant defoliation. QTLs for black spot resistance were mapped to linkage groups (LGs) 1-6. QTLs for cercospora resistance and susceptibility were found in LGs 1, 4, and 5 and for defoliation in LGs 1, 3, and 5. The major locus on LG 5 for black spot resistance coincides with the previously discovered Rdr4 locus inherited from Rosa L. 'Radbrite' (Brite Eyes™), the common parent used in these mapping populations. This work is the first report of any QTL for cercospora resistance/susceptibility in tetraploid rose germplasm and the first report of defoliation QTL in roses. A major QTL for cercospora susceptibility coincides with the black spot resistance QTL on LG 5 (Rdr4). A major cercospora resistance QTL was found on LG 1. These populations provide a genetic resource that will further the knowledge base of rose genetics as more traits are studied. Studying more traits from these populations will allow for the stacking of various QTLs for desirable traits.

Comprehensive meta-analysis of QTL and gene expression studies identify candidate genes associated with Aspergillus flavus resistance in maize

Aflatoxin (AF) contamination, caused by Aspergillus flavus, compromises the food safety and marketability of commodities, such as maize, cotton, peanuts, and tree nuts. Multigenic inheritance of AF resistance impedes conventional introgression of resistance traits into high-yielding commercial maize varieties. Several AF resistance-associated quantitative trait loci (QTLs) and markers have been reported from multiple biparental mapping and genome-wide association studies (GWAS) in maize. However, QTLs with large confidence intervals (CI) explaining inconsistent phenotypic variance limit their use in marker-assisted selection. Meta-analysis of published QTLs can identify significant meta-QTLs (MQTLs) with a narrower CI for reliable identification of genes and linked markers for AF resistance. Using 276 out of 356 reported QTLs controlling resistance to A. flavus infection and AF contamination in maize, we identified 58 MQTLs on all 10 chromosomes with a 66.5% reduction in the average CI. Similarly, a meta-analysis of maize genes differentially expressed in response to (a)biotic stresses from the to-date published literature identified 591 genes putatively responding to only A. flavus infection, of which 14 were significantly differentially expressed (-1.0 ≤ Log2Fc ≥ 1.0; p ≤ 0.05). Eight MQTLs were validated by their colocalization with 14 A. flavus resistance-associated SNPs identified from GWAS in maize. A total of 15 genes were physically close between the MQTL intervals and SNPs. Assessment of 12 MQTL-linked SSR markers identified three markers that could discriminate 14 and eight cultivars with resistance and susceptible responses, respectively. A comprehensive meta-analysis of QTLs and differentially expressed genes led to the identification of genes and makers for their potential application in marker-assisted breeding of A. flavus-resistant maize varieties.

Feeding the fever: Complex host-pathogen dynamics along continuous resource gradients

Food has long been known to perform dual functions of nutrition and medicine, but mounting evidence suggests that complex host-pathogen dynamics can emerge along continuous resource gradients. Empirical examples of nonmonotonic responses of infection with increasing host resources (e.g., low prevalence at low and high resource supply but high prevalence at intermediate resources) have been documented across the tree of life, but these dynamics, when observed, often are interpreted as nonintuitive, idiosyncratic features of pathogen and host biology. Here, by developing generalized versions of existing models of resource dependence for within- and among-host infection dynamics, we provide a synthetic view of nonmonotonic infection dynamics. We demonstrate that where resources jointly impact two (or more) processes (e.g., growth, defense, transmission, mortality, predation), nonmonotonic infection dynamics, including alternative states, can emerge across a continuous resource supply gradient. We review the few empirical examples that concurrently measured resource effects on multiple rates and pair this with a wide range of examples in which resource dependence of multiple rates could generate nonmonotonic infection outcomes under realistic conditions. This review and generalized framework highlight the likely generality of such resource effects in natural systems and point to opportunities ripe for future empirical and theoretical work.

Cryptic genetic diversity and associated ecological differences of Anastatus orientalis, an egg parasitoid of the spotted lanternfly

Anastatus orientalis, native to northern China, is an egg parasitoid wasp of the spotted lanternfly (Lycorma delicatula) and is being tested as a potential biological control agent for invasive L. delicatula in the United States. As a component of these evaluations, live A. orientalis collected from Beijing and Yantai in China were reared in containment in the U.S. These specimens showed different responses in diapause behaviors to rearing conditions used previously by other researchers. To understand the primary mechanism potentially driving discrepancies in important life history traits, we used molecular tools to examine the genetic composition of A. orientalis from China and from South Korea, where the parasitoid has been introduced to aid in the population management of invasive L. delicatula. Molecular analysis of mitochondrial DNA recovered six haplotype groups, which exhibit biased frequency of abundance between collection sites. Some haplotypes are widespread, and others only occur in certain locations. No apparent pattern is observed between wasps collected from different years or emergence seasons. Uncorrected genetic distances between haplotype groups range from 0.44% to 1.44% after controlling for within-group variation. Genetic variance of A. orientalis is characterized by high levels of local diversity that contrasts with a lack of a broad-scale population structure. The introduced Korean population exhibits lower genetic diversity compared to native populations. Additionally, we created iso-female lines for major haplotype groups through laboratory rearing. Differences in diapause behavior were correlated with mitochondrial haplotype. Our results indicate that the observed life history traits in A. orientalis have a genetic base.

Transcriptomics reveal the genetic coordination of early defense to Armillaria root rot (ARR) in Prunus spp

Armillaria root rot (ARR) poses a significant threat to the long-term productivity of stone-fruit and nut crops in the predominant production area of the United States. To mitigate this issue, the development of ARR-resistant and horticulturally-acceptable rootstocks is a crucial step towards the maintenance of production sustainability. To date, genetic resistance to ARR has been found in exotic plum germplasm and a peach/plum hybrid rootstock, 'MP-29'. However, the widely-used peach rootstock Guardian® is susceptible to the pathogen. To understand the molecular defense mechanisms involved in ARR resistance in Prunus rootstocks, transcriptomic analyses of one susceptible and two resistant Prunus spp. were performed using two causal agents of ARR, including Armillaria mellea and Desarmillaria tabescens. The results of in vitro co-culture experiments revealed that the two resistant genotypes showed different temporal response dynamics and fungus-specific responses, as seen in the genetic response. Gene expression analysis over time indicated an enrichment of defense-related ontologies, including glucosyltransferase activity, monooxygenase activity, glutathione transferase activity, and peroxidase activity. Differential gene expression and co-expression network analysis highlighted key hub genes involved in the sensing and enzymatic degradation of chitin, GSTs, oxidoreductases, transcription factors, and biochemical pathways likely involved in Armillaria resistance. These data provide valuable resources for the improvement of ARR resistance in Prunus rootstocks through breeding.

Interactions between large-scale and local factors influence seed predation rates and seed loss

Herbivores often have highly variable impacts on plant fecundity. The relative contribution of different environmental factors operating at varying spatial scales in affecting this variability is often unclear. We examined how density-dependent seed predation at local scales and regional differences in primary productivity are associated with variation in the magnitude of pre-dispersal seed predation on Monarda fistulosa (Lamiaceae). Within M. fistulosa populations growing in a low-productivity region (LPR), Montana, USA, and a high-productivity region (HPR), Wisconsin, USA, we quantified the magnitude of pre-dispersal seed predation among individual plants differing in seed head densities. Out of a total of 303 M. fistulosa plants that were surveyed, we found half as many herbivores in seed heads in the LPR (n = 133 herbivores) compared to the HPR (n = 316). In the LPR, 30% of the seed heads were damaged in plants with low seed head density, while 61% of seed heads were damaged in plants with high seed head density. Seed head damage was consistently high in the HPR (about 49% across the range of seed head density) compared to the LPR (45% across a range of seed head density). However, the proportion of seeds per seed head that were destroyed by herbivores was nearly two times higher (~38% loss) in the LPR compared to HPR (22% loss). Considering the combined effects of probability of damage and seed loss per seed head, the proportion seed loss per plant was consistently higher in the HPR regardless of seed head density. Nevertheless, because of greater seed head production, the total number of viable seeds produced per plant was higher in HPR and high-density plants, despite being exposed to greater herbivore pressure. These findings show how large-scale factors can interact with local-scale factors to influence how strongly herbivores suppress plant fecundity.

Cotton leafroll dwarf disease: An enigmatic viral disease in cotton

TAXONOMY

Cotton leafroll dwarf virus (CLRDV) is a member of the genus Polerovirus, family Solemoviridae. Geographical Distribution: CLRDV is present in most cotton-producing regions worldwide, prominently in North and South America.

PHYSICAL PROPERTIES

The virion is a nonenveloped icosahedron with T = 3 icosahedral lattice symmetry that has a diameter of 26-34 nm and comprises 180 molecules of the capsid protein. The CsCl buoyant density of the virion is 1.39-1.42 g/cm3 and S20w is 115-127S. Genome: CLRDV shares genomic features with other poleroviruses; its genome consists of monopartite, single-stranded, positive-sense RNA, is approximately 5.7-5.8 kb in length, and is composed of seven open reading frames (ORFs) with an intergenic region between ORF2 and ORF3a.

TRANSMISSION

CLRDV is transmitted efficiently by the cotton aphid (Aphis gossypii Glover) in a circulative and nonpropagative manner. Host: CLRDV has a limited host range. Cotton is the primary host, and it has also been detected in different weeds in and around commercial cotton fields in Georgia, USA.

SYMPTOMS

Cotton plants infected early in the growth stage exhibit reddening or bronzing of foliage, maroon stems and petioles, and drooping. Plants infected in later growth stages exhibit intense green foliage with leaf rugosity, moderate to severe stunting, shortened internodes, and increased boll shedding/abortion, resulting in poor boll retention. These symptoms are variable and are probably influenced by the time of infection, plant growth stage, varieties, soil health, and geographical location. CLRDV is also often detected in symptomless plants.

CONTROL

Vector management with the application of chemical insecticides is ineffective. Some host plant varieties grown in South America are resistant, but all varieties grown in the United States are susceptible. Integrated disease management strategies, including weed management and removal of volunteer stalks, could reduce the abundance of virus inoculum in the field.

Molecular mapping of quantitative trait loci for resistance to early blight in tomatoes

Early blight (EB), caused by Alternaria linariae (Neerg.) (syn. A. tomatophila) Simmons, is a disease that affects tomatoes (Solanum lycopersicum L.) throughout the world, with tremendous economic implications. The objective of the present study was to map the quantitative trait loci (QTL) associated with EB resistance in tomatoes. The F₂ and F_2:3 mapping populations consisting of 174 lines derived from NC 1CELBR (resistant) × Fla. 7775 (susceptible) were evaluated under natural conditions in the field in 2011 and in the greenhouse in 2015 by artificial inoculation. In all, 375 Kompetitive Allele Specific PCR (KASP) assays were used for genotyping parents and the F₂ population. The broad-sense heritability estimate for phenotypic data was 28.3%, and 25.3% for 2011, and 2015 disease evaluations, respectively. QTL analysis revealed six QTLs associated with EB resistance on chromosomes 2, 8, and 11 (LOD 4.0 to 9.1), explaining phenotypic variation ranging from 3.8 to 21.0%. These results demonstrate that genetic control of EB resistance in NC 1CELBR is polygenic. This study may facilitate further fine mapping of the EB-resistant QTL and marker-assisted selection (MAS) to transfer EB resistance genes into elite tomato varieties, including broadening the genetic diversity of EB resistance in tomatoes.

Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils

Neutrophils are vital components of the immune system for limiting the invasion and proliferation of pathogens in the body. Surprisingly, the functional annotation of porcine neutrophils is still limited. The transcriptomic and epigenetic assessment of porcine neutrophils from healthy pigs was performed by bulk RNA sequencing and transposase accessible chromatin sequencing (ATAC-seq). First, we sequenced and compared the transcriptome of porcine neutrophils with eight other immune cell transcriptomes to identify a neutrophil-enriched gene list within a detected neutrophil co-expression module. Second, we used ATAC-seq analysis to report for the first time the genome-wide chromatin accessible regions of porcine neutrophils. A combined analysis using both transcriptomic and chromatin accessibility data further defined the neutrophil co-expression network controlled by transcription factors likely important for neutrophil lineage commitment and function. We identified chromatin accessible regions around promoters of neutrophil-specific genes that were predicted to be bound by neutrophil-specific transcription factors. Additionally, published DNA methylation data from porcine immune cells including neutrophils were used to link low DNA methylation patterns to accessible chromatin regions and genes with highly enriched expression in porcine neutrophils. In summary, our data provides the first integrative analysis of the accessible chromatin regions and transcriptional status of porcine neutrophils, contributing to the Functional Annotation of Animal Genomes (FAANG) project, and demonstrates the utility of chromatin accessible regions to identify and enrich our understanding of transcriptional networks in a cell type such as neutrophils.

Gene silencing in adult Popillia japonica through feeding of double-stranded RNA (dsRNA) complexed with branched amphiphilic peptide capsules (BAPCs)

Gene silencing by feeding double-stranded (dsRNA) holds promise as a novel pest management strategy. Nonetheless, degradation of dsRNA in the environment and within the insect gut, as well as inefficient systemic delivery are major limitations to applying this strategy. Branched amphiphilic peptide capsules (BAPCs) complexed with dsRNA have been used to successfully target genes outside and inside the gut epithelium upon ingestion. This suggests that BAPCs can protect dsRNA from degradation in the gut environment and successfully shuttle it across gut epithelium. In this study, our objectives were to 1) Determine whether feeding on BAPC-dsRNA complexes targeting a putative peritrophin gene of P. japonica would result in the suppression of gut peritrophin synthesis, and 2) gain insight into the cellular uptake mechanisms and transport of BAPC-dsRNA complexes across the larval midgut of P. japonica. Our results suggest that BAPC-dsRNA complexes are readily taken up by the midgut epithelium, and treatment of the tissue with endocytosis inhibitors effectively suppresses intracellular transport. Further, assessment of gene expression in BAPC- peritrophin dsRNA fed beetles demonstrated significant downregulation in mRNA levels relative to control and/or dsRNA alone. Our results demonstrated that BAPCs increase the efficacy of gene knockdown relative to dsRNA alone in P. japonica adults. To our knowledge, this is the first report on nanoparticle-mediated dsRNA delivery through feeding in P. japonica.

Habitat and climatic associations of climate-sensitive species along a southern range boundary

Climate change and habitat loss are recognized as important drivers of shifts in wildlife species' geographic distributions. While often considered independently, there is considerable overlap between these drivers, and understanding how they contribute to range shifts can predict future species assemblages and inform effective management. Our objective was to evaluate the impacts of habitat, climatic, and anthropogenic effects on the distributions of climate-sensitive vertebrates along a southern range boundary in Northern Michigan, USA. We combined multiple sources of occurrence data, including harvest and citizen-science data, then used hierarchical Bayesian spatial models to determine habitat and climatic associations for four climate-sensitive vertebrate species (American marten [Martes americana], snowshoe hare [Lepus americanus], ruffed grouse [Bonasa umbellus] and moose [Alces alces]). We used total basal area of at-risk forest types to represent habitat, and temperature and winter habitat indices to represent climate. Marten associated with upland spruce-fir and lowland riparian forest types, hares with lowland conifer and aspen-birch, grouse with lowland riparian hardwoods, and moose with upland spruce-fir. Species differed in climatic drivers with hares positively associated with cooler annual temperatures, moose with cooler summer temperatures and grouse with colder winter temperatures. Contrary to expectations, temperature variables outperformed winter habitat indices. Model performance varied greatly among species, as did predicted distributions along the southern edge of the Northwoods region. As multiple species were associated with lowland riparian and upland spruce-fir habitats, these results provide potential for efficient prioritization of habitat management. Both direct and indirect effects from climate change are likely to impact the distribution of climate-sensitive species in the future and the use of multiple data types and sources in the modelling of species distributions can result in more accurate predictions resulting in improved management at policy-relevant scales.

Cry1Ba1-mediated toxicity of transgenic Bergera koenigii and Citrus sinensis to the Asian citrus psyllid Diaphorina citri

The Asian citrus psyllid, Diaphorina citri, vectors the bacterial causative agent of citrus greening disease, which has severely impacted citrus production on a global scale. As the current repeated application of chemical insecticides is unsustainable for management of this insect and subsequent protection of groves, we investigated the potential use of the bacteria-derived pesticidal protein, Cry1Ba1, when delivered via transgenic citrus plants. Having demonstrated transformation of the Indian curry leaf tree, Bergera koenigii, for Cry1Ba1 expression for use as a trap plant, we produced transgenic plants of Duncan grapefruit, Citrus paridisi, Valencia sweet orange, Citrus sinensis, and Carrizo citrange, C. sinensis x Poncirus trifoliata, for expression of Cry1Ba1. The presence of the cry1ba1 gene, and cry1ba1 transcription were confirmed. Western blot detection of Cry1Ba1 was confirmed in most cases. When compared to those from wild-type plants, leaf discs from transgenic Duncan and Valencia expressing Cry1Ba1 exhibited a "delayed senescence" phenotype, similar to observations made for transgenic B. koenigii. In bioassays, significant reductions in the survival of adult psyllids were noted on transgenic B. koenigii and Valencia sweet orange plants expressing Cry1Ba1, but not on transgenic Duncan grapefruit or Carrizo citrange. In contrast to psyllids fed on wild type plants, the gut epithelium of psyllids fed on transgenic plants was damaged, consistent with the mode of action of Cry1Ba1. These results indicate that the transgenic expression of a bacterial pesticidal protein in B. koenigii and Valencia sweet orange offers a viable option for management of D. citri, that may contribute to solutions that counter citrus greening disease.

Consistent physiological, ecological and evolutionary effects of fire regime on conservative leaf economics strategies in plant communities

The functional response of plant communities to disturbance is hypothesised to be controlled by changes in environmental conditions and evolutionary history of species within the community. However, separating these influences using direct manipulations of repeated disturbances within ecosystems is rare. We evaluated how 41 years of manipulated fire affected plant leaf economics by sampling 89 plant species across a savanna-forest ecotone. Greater fire frequencies created a high-light and low-nitrogen environment, with more diverse communities that contained denser leaves and lower foliar nitrogen content. Strong trait-fire coupling resulted from the combination of significant intraspecific trait-fire correlations being in the same direction as interspecific trait differences arising through the turnover in functional composition along the fire-frequency gradient. Turnover among specific clades helped explain trait-fire trends, but traits were relatively labile. Overall, repeated burning led to reinforcing selective pressures that produced diverse plant communities dominated by conservative resource-use strategies and slow soil nitrogen cycling.

Spatiotemporal variation in the competitive environment, with implications for how climate change may affect a species with parental care

Burying beetles of the genus Nicrophorus have become a model for studying the evolution of complex parental care in laboratory studies. Nicrophorus species depend on small vertebrate carcasses to breed, which they process and provision to their begging offspring. However, vertebrate carcasses are highly sought after by a wide variety of species and so competition is expected to be critical to the evolution of parental care. Despite this, the competitive environment for Nicrophorus is rarely characterized in the wild and remains a missing factor in laboratory studies. Here, we performed a systematic sampling of Nicrophorus orbicollis living near the southern extent of their range at Whitehall Forest in Clarke County, Georgia, USA. We determined the density of N. orbicollis and other necrophilous species that may affect the availability of this breeding resource through interference or exploitation competition. In addition, we characterize body size, a key trait involved in competitive ability, for all Nicrophorus species at Whitehall Forest throughout the season. Finally, we compare our findings to other published natural history data for Nicrophorines. We document a significantly longer active season than was observed 20 years previously at Whitehall Forest for both N. orbicollis and Nicrophorus tomentosus, potentially due to climate change. As expected, the adult body size of N. orbicollis was larger than N. tomentosus, the only other Nicrophorus species that was captured in 2022 at Whitehall Forest. The other most prevalent insects captured included species in the families Staphylinidae, Histeridae, Scarabaeidae, and Elateridae, which may act as competitors or predators of Nicrophorus young. Together, our results indicate significant variation in intra- and interspecific competition relative to populations within the N. orbicollis range. These findings suggest that the competitive environment shows extensive spatiotemporal variation, providing the basis to make predictions for how ecology may influence parenting in this species.

Monitoring for a new I3 resistance gene-breaking race of F. oxysporum f. sp. lycopersici (Fusarium wilt) in California processing tomatoes following recent widespread adoption of resistant (F3) cultivars: Challenges with race 3 and 4 differentiation methods

Fusarium wilt, caused by Fusarium oxysporum f. sp. lycopersici (Fol), causes losses in tomato production worldwide, with major impacts on Californian tomato processing. Single-gene resistance is the primary management tool, but its efficacy has been compromised following the emergence of two successive resistance-breaking races, which, in California, emerged within 12 years of resistance deployment. Fol race 3-resistant (F3) processing tomato cultivars (containing the I3 resistance gene) were deployed in the state starting in approximately 2009. The emergence of a new resistance-breaking race (which would be called race 4) is imminent, and early detection will be critical to delay the spread while new resistance is sought. The detection of Fol race 4 is challenged by the lack of validated, rapid, and accurate diagnostic tools. In evaluating in planta phenotyping methods, this study found that rapid seedling phenotyping is not reliable and generates false positives for nonpathogens. Longer (10 weeks) mature plant assays are the most reliable, but may not be sufficiently timely. As an additional challenge, based on field and greenhouse studies, Fol race 3 can cause symptoms in resistant F3 cultivars at frequencies greater (30%) than expected for off-types (<2%). We developed a three-F3 cultivar in planta assay to overcome the challenges this posed to differentiating Fol race 3 and Fol race 4. Using the assay, we determined that all putative resistance-breaking cases were Fol race 3; Fol race 4 was not detected in these early survey efforts. These results highlight the need for developing rapid Fol race 4 detection tools and a better understanding of the factors underlying inconsistent I3 gene expression in Fol race 3.

Unhealthy herds and the predator–spreader: Understanding when predation increases disease incidence and prevalence

Disease ecologists now recognize the limitation behind examining host–parasite interactions in isolation: community members—especially predators—dramatically affect host–parasite dynamics. Although the initial paradigm was that predation should reduce disease in prey populations (“healthy herds hypothesis”), researchers have realized that predators sometimes increase disease in their prey. These “predator–spreaders” are now recognized as critical to disease dynamics, but empirical research on the topic remains fragmented. In a narrow sense, a “predator–spreader” would be defined as a predator that mechanically spreads parasites via feeding. However, predators affect their prey and, subsequently, disease transmission in many other ways such as altering prey population structure, behavior, and physiology. We review the existing evidence for these mechanisms and provide heuristics that incorporate features of the host, predator, parasite, and environment to understand whether or not a predator is likely to be a predator–spreader. We also provide guidance for targeted study of each mechanism and quantifying the effects of predators on parasitism in a way that yields more general insights into the factors that promote predator spreading. We aim to offer a better understanding of this important and underappreciated interaction and a path toward being able to predict how changes in predation will influence parasite dynamics.

Differentiation of Andean and Mesoamerican accessions in a proposed core collection of grain amaranths

Grain amaranths are made up of three New World species of pseudo-cereals with C4 photosynthesis from the dicotyledonous family Amaranthaceae and the genus Amaranthus. They originate in two ecoregions of the Americas, namely, the inter-Andean valleys of South America and the volcanic axis and lowlands of Mexico and Central America. These correspond to two centers of domestications for Andean and Mesoamerican crops, with one cultivated species found in the first region and two found in the latter region. To date, no core collection has been made for the grain amaranths in the United States Department of Agriculture (USDA) germplasm system. In this study, our objective was to create a core for the 2,899 gene bank accessions with collection site data by town or farm site of which 1,090 have current geo-referencing of latitude and longitude coordinates. We constituted the core with 260 genotypes of Amaranthus, which we evaluated with 90 single-nucleotide polymorphism markers. Our goal was to distinguish between Andean and Mesoamerican gene pools of amaranths, including the cultivated species and three possible progenitor or wild relative ancestors along with two more species in an outgroup. Population structure, clustering, and discriminant analysis for principal components showed that Andean species Amaranthus caudatus and Amaranthus quitensis shared fewer alleles with Mesoamerican species Amaranthus cruentus and Amaranthus hypochondriacus, compared to each group individually. Amaranthus hybridus was a bridge species that shared alleles with both regions. Molecular markers have the advantage over morphological traits at quickly distinguishing the Andean and Mesoamerican cultivars and have the added benefit of being useful for following inter-species crosses and introgression.

Understanding protein import in diverse non-green plastids

The spectacular diversity of plastids in non-green organs such as flowers, fruits, roots, tubers, and senescing leaves represents a Universe of metabolic processes in higher plants that remain to be completely characterized. The endosymbiosis of the plastid and the subsequent export of the ancestral cyanobacterial genome to the nuclear genome, and adaptation of the plants to all types of environments has resulted in the emergence of diverse and a highly orchestrated metabolism across the plant kingdom that is entirely reliant on a complex protein import and translocation system. The TOC and TIC translocons, critical for importing nuclear-encoded proteins into the plastid stroma, remain poorly resolved, especially in the case of TIC. From the stroma, three core pathways (cpTat, cpSec, and cpSRP) may localize imported proteins to the thylakoid. Non-canonical routes only utilizing TOC also exist for the insertion of many inner and outer membrane proteins, or in the case of some modified proteins, a vesicular import route. Understanding this complex protein import system is further compounded by the highly heterogeneous nature of transit peptides, and the varying transit peptide specificity of plastids depending on species and the developmental and trophic stage of the plant organs. Computational tools provide an increasingly sophisticated means of predicting protein import into highly diverse non-green plastids across higher plants, which need to be validated using proteomics and metabolic approaches. The myriad plastid functions enable higher plants to interact and respond to all kinds of environments. Unraveling the diversity of non-green plastid functions across the higher plants has the potential to provide knowledge that will help in developing climate resilient crops.

Parasitic nematode secreted phospholipase A2 suppresses cellular and humoral immunity by targeting hemocytes in Drosophila melanogaster

A key aspect of parasitic nematode infection is the nematodes' ability to evade and/or suppress host immunity. This immunomodulatory ability is likely driven by the release of hundreds of excretory/secretory proteins (ESPs) during infection. While ESPs have been shown to display immunosuppressive effects on various hosts, our understanding of the molecular interactions between individual proteins released and host immunity requires further study. We have recently identified a secreted phospholipase A2 (sPLA2) released from the entomopathogenic nematode (EPN) Steinernema carpocapsae we have named Sc-sPLA2. We report that Sc-sPLA2 increased mortality of Drosophila melanogaster infected with Streptococcus pneumoniae and promoted increased bacterial growth. Furthermore, our data showed that Sc-sPLA2 was able to downregulate both Toll and Imd pathway-associated antimicrobial peptides (AMPs) including drosomycin and defensin, in addition to suppressing phagocytosis in the hemolymph. Sc-sPLA2 was also found to be toxic to D. melanogaster with the severity being both dose- and time-dependent. Collectively, our data highlighted that Sc-sPLA2 possessed both toxic and immunosuppressive capabilities.

Biological insights from multi-omics analysis strategies: Complex pleotropic effects associated with autophagy

Research strategies that combine molecular data from multiple levels of genome expression (i.e., multi-omics data), often referred to as a systems biology strategy, has been advocated as a route to discovering gene functions. In this study we conducted an evaluation of this strategy by combining lipidomics, metabolite mass-spectral imaging and transcriptomics data from leaves and roots in response to mutations in two AuTophaGy-related (ATG) genes of Arabidopsis. Autophagy is an essential cellular process that degrades and recycles macromolecules and organelles, and this process is blocked in the atg7 and atg9 mutants that were the focus of this study. Specifically, we quantified abundances of ~100 lipids and imaged the cellular locations of ~15 lipid molecular species and the relative abundance of ~26,000 transcripts from leaf and root tissues of WT, atg7 and atg9 mutant plants, grown either in normal (nitrogen-replete) and autophagy-inducing conditions (nitrogen-deficient). The multi-omics data enabled detailed molecular depiction of the effect of each mutation, and a comprehensive physiological model to explain the consequence of these genetic and environmental changes in autophagy is greatly facilitated by the a priori knowledge of the exact biochemical function of the ATG7 and ATG9 proteins.

Gene expression in Verson's glands of the fall armyworm suggests their role in molting and immunity

Verson's glands are segmental pairs of dermal glands attached to the epidermis in lepidopteran larvae. They produce macromolecules during intermolt period and empty them during each molt. Morphological, histochemical, developmental, and protein analysis studies have been conducted to determine the functions of Verson's glands. However, the exact role of Verson's glands remains unclear. In our previous study, a strain of transgenic fall armyworm, Spdoptera frugiperda expressing green fluorescence protein (GFP) and Systemic RNA interference defective protein 1 (SID1) from Caenorhabditis elegans was established to improve RNA interference (RNAi) efficiency. Unexpectedly, we found that GFP fluorescence was significantly brighter in Verson's glands than in other tissues. Also, RNAi efficiency improved more in Verson's glands than in other tissues. We took advantage of improved RNAi efficiency to explore the function of Verson's glands. RNA-seq analysis revealed that genes highly expressed in Verson's glands code for cuticular proteins, molting fluid proteins, hemolymph proteins, and antimicrobial peptides. Injection of dsRNA targeting essential genes, inhibitor of apoptosis (IAP), Actin, and vacuolar-type ATPase (VATPase) interfered with Verson's glands growth. These results revealed that Verson's glands may contribute to hemolymph, cuticle, molting fluid, and immune response during molting. This study also provide useful tools for future research in identifying the physiological role of Verson's glands in lepidopteran insects.

Spotted! Computer-aided individual photo-identification allows for mark-recapture of invasive spotted lanternfly (Lycorma delicatula)

The spotted lanternfly is an invasive pest for which we lack individual movement data due in part to the difficulty posed by individual identification. We developed a computer-aided method to identify individual adult spotted lanternfly using wing spot patterns from photos processed in the software I3S and demonstrated the method's accuracy with lab and field validations. Based on 176 individuals in the lab, we showed that digitizing the spots of one wing allowed a 100% reliable individual identification. The errors due to user input and the variation in the angle of the image were largely negligible compared to inter-individual variations. We applied this method in the context of a mark-recapture experiment to assess the feasibility of this method in the field. We initially identified a total of 84 unique spotted lanternflies, 31 of which were recaptured after four hours along with 49 new individuals. We established that the analysis of recaptures can possibly be automated based on scores and may not require systematic visual pairwise comparison. The demonstration of the effectiveness of this method on relatively small sample sizes makes it a promising tool for field experimentation as well as lab manipulations. Once validated on larger datasets and in different contexts, it will provide ample opportunity to collect useful data on spotted lanternfly ecology that can greatly inform management.

Genome-wide association analysis of sucrose and alanine contents in edamame beans

The sucrose and Alanine (Ala) content in edamame beans significantly impacts the sweetness flavor of edamame-derived products as an important attribute to consumers' acceptance. Unlike grain-type soybeans, edamame beans are harvested as fresh beans at the R6 to R7 growth stages when beans are filled 80-90% of the pod capacity. The genetic basis of sucrose and Ala contents in fresh edamame beans may differ from those in dry seeds. To date, there is no report on the genetic basis of sucrose and Ala contents in the edamame beans. In this study, a genome-wide association study was conducted to identify single nucleotide polymorphisms (SNPs) related to sucrose and Ala levels in edamame beans using an association mapping panel of 189 edamame accessions genotyped with a SoySNP50K BeadChip. A total of 43 and 25 SNPs was associated with sucrose content and Ala content in the edamame beans, respectively. Four genes (Glyma.10g270800, Glyma.08g137500, Glyma.10g268500, and Glyma.18g193600) with known effects on the process of sucrose biosynthesis and 37 novel sucrose-related genes were characterized. Three genes (Gm17g070500, Glyma.14g201100 and Glyma.18g269600) with likely relevant effects in regulating Ala content and 22 novel Ala-related genes were identified. In addition, by summarizing the phenotypic data of edamame beans from three locations in two years, three PI accessions (PI 532469, PI 243551, and PI 407748) were selected as the high sucrose and high Ala parental lines for the perspective breeding of sweet edamame varieties. Thus, the beneficial alleles, candidate genes, and selected PI accessions identified in this study will be fundamental to develop edamame varieties with improved consumers' acceptance, and eventually promote edamame production as a specialty crop in the United States.

Global transcriptome and gene co-expression network analyses reveal regulatory and non-additive effects of drought and heat stress in grapevine

Despite frequent co-occurrence of drought and heat stress, the molecular mechanisms governing plant responses to these stresses in combination have not often been studied. This is particularly evident in non-model, perennial plants. We conducted large scale physiological and transcriptome analyses to identify genes and pathways associated with grapevine response to drought and/or heat stress during stress progression and recovery. We identified gene clusters with expression correlated to leaf temperature and water stress and five hub genes for the combined stress co-expression network. Several differentially expressed genes were common to the individual and combined stresses, but the majority were unique to the individual or combined stress treatments. These included heat-shock proteins, mitogen-activated kinases, sugar metabolizing enzymes, and transcription factors, while phenylpropanoid biosynthesis and histone modifying genes were unique to the combined stress treatment. Following physiological recovery, differentially expressed genes were found only in plants under heat stress, both alone and combined with drought. Taken collectively, our results suggest that the effect of the combined stress on physiology and gene expression is more severe than that of individual stresses, but not simply additive, and that epigenetic chromatin modifications may play an important role in grapevine responses to combined drought and heat stress.

Impact of volatility reduction agents on dicamba and glyphosate spray solution pH, droplet dynamics, and weed control

BACKGROUND

Regulations in 2021 required the addition of a volatility reduction agent (VRA) to dicamba spray mixtures for postemergence weed control. Understanding the impact of VRAs on weed control, droplet dynamics, and spray pH is essential.

RESULTS

Adding glyphosate to dicamba decreased the solution pH by 0.63 to 1.85 units. Across locations, potassium carbonate increased the tank-mixture pH by 0.85 to 1.65 units while potassium acetate raised the pH by 0.46 to 0.53 units. Glyphosate and dicamba in tank-mixture reduced Palmer amaranth control by 14 percentage points compared to dicamba alone and decreased barnyardgrass control by 12 percentage points compared to glyphosate alone 4 weeks after application (WAA). VRAs resulted in a 5-percentage point reduction in barnyardgrass control 4 WAA. Common ragweed, common lambsquarters, and giant ragweed control were unaffected by herbicide solution 4 WAA. Dicamba alone produced a larger average droplet size and had the fewest driftable fines (% volume < 200 μm). Potassium acetate produced a larger droplet size than potassium carbonate for D_v0.1 and D_v0.5 . The addition of glyphosate to dicamba decreased droplet size from the entire spray droplet spectrum (D_v0.1 , D_v0.5 , D_v0.9 ).

CONCLUSION

A reduction in spray pH, droplet size, and weed control was observed from mixing dicamba and glyphosate. It may be advisable to avoid tank-mixtures of these herbicides and instead, apply them sequentially to maximize effectiveness. VRAs differed in their impacts on spray solution pH and droplet dynamics, but resulted in a minimal negative to no impact on weed control. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Recent sarcopenia definitions-prevalence, agreement and mortality associations among men: Findings from population-based cohorts

BACKGROUND

The 2019 European Working Group on Sarcopenia in Older People (EWGSOP2) and the Sarcopenia Definitions and Outcomes Consortium (SDOC) have recently proposed sarcopenia definitions. However, comparisons of the performance of these approaches in terms of thresholds employed, concordance in individuals and prediction of important health-related outcomes such as death are limited. We addressed this in a large multinational assembly of cohort studies that included information on lean mass, muscle strength, physical performance and health outcomes.

METHODS

White men from the Health Aging and Body Composition (Health ABC) Study, Osteoporotic Fractures in Men (MrOS) Study cohorts (Sweden, USA), the Hertfordshire Cohort Study (HCS) and the Sarcopenia and Physical impairment with advancing Age (SarcoPhAge) Study were analysed. Appendicular lean mass (ALM) was ascertained using DXA; muscle strength by grip dynamometry; and usual gait speed over courses of 2.4-6 m. Deaths were recorded and verified. Definitions of sarcopenia were as follows: EWGSOP2 (grip strength <27 kg and ALM index <7.0 kg/m2 ), SDOC (grip strength <35.5 kg and gait speed <0.8 m/s) and Modified SDOC (grip strength <35.5 kg and gait speed <1.0 m/s). Cohen's kappa statistic was used to assess agreement between original definitions (EWGSOP2 and SDOC). Presence versus absence of sarcopenia according to each definition in relation to mortality risk was examined using Cox regression with adjustment for age and weight; estimates were combined across cohorts using random-effects meta-analysis.

RESULTS

Mean (SD) age of participants (n = 9170) was 74.3 (4.9) years; 5929 participants died during a mean (SD) follow-up of 12.1 (5.5) years. The proportion with sarcopenia according to each definition was EWGSOP2 (1.1%), SDOC (1.7%) and Modified SDOC (5.3%). Agreement was weak between EWGSOP2 and SDOC (κ = 0.17). Pooled hazard ratios (95% CI) for mortality for presence versus absence of each definition were EWGSOP2 [1.76 (1.42, 2.18), I2 : 0.0%]; SDOC [2.75 (2.28, 3.31), I2 : 0.0%]; and Modified SDOC [1.93 (1.54, 2.41), I2 : 58.3%].

CONCLUSIONS

There was low prevalence and poor agreement among recent sarcopenia definitions in community-dwelling cohorts of older white men. All indices of sarcopenia were associated with mortality. The strong relationship between sarcopenia and mortality, regardless of the definition, illustrates that identification of appropriate management and lifecourse intervention strategies for this condition is of paramount importance.

Leaf, plant, to canopy: A mechanistic study on aboveground plasticity and plant density within a maize-soybean intercrop system for the Midwest, USA

Plants have evolved to adapt to their neighbours through plastic trait responses. In intercrop systems, plant growth occurs at different spatial and temporal dimensions, creating a competitive light environment where aboveground plasticity may support complementarity in light-use efficiency, realizing yield gains per unit area compared with monoculture systems. Physiological and architectural plasticity including the consequences for light-use efficiency and yield in a maize-soybean solar corridor intercrop system was compared, empirically, with the standard monoculture systems of the Midwest, USA. The impact of reducing maize plant density on yield was investigated in the following year. Intercropped maize favoured physiological plasticity over architectural plasticity, which maintained harvest index (HI) but reduced light interception efficiency (ɛ_i ) and conversion efficiency (ɛ_c ). Intercropped soybean invested in both plasticity responses, which maintained ɛ_i , but HI and ɛ_c decreased. Reducing maize plant density within the solar corridor rows did not improve yields under monoculture and intercrop systems. Overall, the intercrop decreased land-use efficiency by 9%-19% and uncoordinated investment in aboveground plasticity by each crop under high maize plant density does not support complementarity in light-use efficiency. Nonetheless, the mechanistic understanding gained from this study may improve crop cultivars and intercrop designs for the Midwest to increase yield.

Meta-analysis of genetic diversity and intercolony relatedness among reproductives in commercial honey bee populations

Honey bee colonies are large kin groups, each with a single mother queen and thousands of female workers. Queen bees are highly polyandrous, each mating with an average of approximately 12 drones from other colonies. We used a meta-analysis approach to compare the pedigree relationships of honey bee reproductives (queens and their mates) across five different studies and to quantify the overall genetic diversity of breeding populations. We compared the inferred genotypes of queens and their mates from microsatellite analyses of worker offspring from a feral Africanized honey bee population (which served as a negative control for inbreeding), an experimentally derived population of sister queens (which served as a positive control for inbreeding), and three separate commercially managed populations. We then compared the relatedness of all drones mated to each queen (mate-mate), all queens within each population (queen-queen), each queen with each of her mates (queen-mate), and all drones within each population (drone-drone). We found, as expected, the lowest levels of genetic similarity in the outcrossed population and highest levels of genetic similarity in the inbred population. Levels of genetic similarity among the managed honey bee populations were intermediate but closer to that of the inbred population. Genetic structuring of the entire breeding population resulted in two major subpopulations, likely deriving from breeders on the east and west coast. The effects that these findings have on the overall population genetic diversity of managed honey bees is discussed.

The COVID-19 pandemic and trade in agricultural products

In this study, we develop a structural gravity model to analyse the effects of the ongoing COVID-19 pandemic on international trade in food and agriculture. Using detailed data on trade flows, we estimate the trade impacts of the pandemic for major sectors in food and agriculture. Supply-side impacts on trade caused by reductions in labour tend to be largest in labour-intensive sectors such as meat processing and processed fruit and vegetables. The supply-side export effects are dwarfed by the demand-side import effects, as the recessionary impact of the pandemic drives significant decreases in imports, largely in processed goods and labour-intensive commodities.

Transcriptome profiling, physiological, and biochemical analyses provide new insights towards drought stress response in sugar maple (Acer saccharum Marshall) saplings

Sugar maple (Acer saccharum Marshall) is a temperate tree species in the northeastern parts of the United States and is economically important for its hardwood and syrup production. Sugar maple trees are highly vulnerable to changing climatic conditions, especially drought, so understanding the physiological, biochemical, and molecular responses is critical. The sugar maple saplings were subjected to drought stress for 7, 14, and 21 days and physiological data collected at 7, 14, and 21 days after stress (DAS) showed significantly reduced chlorophyll and Normalized Difference Vegetation Index with increasing drought stress time. The drought stress-induced biochemical changes revealed a higher accumulation of malondialdehyde, proline, and peroxidase activity in response to drought stress. Transcriptome analysis identified a total of 14,099 differentially expressed genes (DEGs); 328 were common among all stress periods. Among the DEGs, transcription factors (including NAC, HSF, ZFPs, GRFs, and ERF), chloroplast-related and stress-responsive genes such as peroxidases, membrane transporters, kinases, and protein detoxifiers were predominant. GO enrichment and KEGG pathway analysis revealed significantly enriched processes related to protein phosphorylation, transmembrane transport, nucleic acids, and metabolic, secondary metabolite biosynthesis pathways, circadian rhythm-plant, and carotenoid biosynthesis in response to drought stress. Time-series transcriptomic analysis revealed changes in gene regulation patterns in eight different clusters, and pathway analysis by individual clusters revealed a hub of stress-responsive pathways. In addition, qRT-PCR validation of selected DEGs revealed that the expression patterns were consistent with transcriptome analysis. The results from this study provide insights into the dynamics of physiological, biochemical, and gene responses to progressive drought stress and reveal the important stress-adaptive mechanisms of sugar maple saplings in response to drought stress.

Long-term response of wetland plant communities to management intensity, grazing abandonment, and prescribed fire

Isolated, seasonal wetlands within agricultural landscapes are important ecosystems. However, they are currently experiencing direct and indirect effects of agricultural management surrounding them. Because wetlands provide important ecosystem services, it is crucial to determine how these factors affect ecological communities. Here, we studied the long-term effects of land-use intensification, cattle grazing, prescribed fires, and their interactions on wetland plant diversity, community dynamics, and functional diversity. To do this, we used vegetation and trait data from a 14-year-old experiment on 40 seasonal wetlands located within seminatural and intensively managed pastures in Florida. These wetlands were allocated different grazing and prescribed fire treatments (grazed vs. ungrazed, burned vs. unburned). Our results showed that wetlands within intensively managed pastures have lower native plant diversity, floristic quality, evenness, and higher nonnative species diversity and exhibited the most resource-acquisitive traits. Wetlands embedded in intensively managed pastures were also characterized by lower species turnover over time. We found that 14 years of cattle exclusion reduced species diversity in both pasture management intensities and had no effect on floristic quality. Fenced wetlands exhibited lower functional diversity and experienced a higher rate of community change, both due to an increase in tall, clonal, and palatable grasses. The effects of prescribed fires were often dependent on grazing treatment. For instance, prescribed fires increased functional diversity in fenced wetlands but not in grazed wetlands. Our study suggests that cattle exclusion and prescribed fires are not enough to restore wetlands in intensively managed pastures and further highlights the importance of not converting seminatural pastures to intensively managed pastures. Our study also suggests that grazing levels applied in seminatural pastures maintained high plant diversity and prevented tree and shrub encroachment and that in the absence of grazing, prescribed fire became crucial to maintaining higher species evenness.

Nanoparticle surface coatings produce distinct antibacterial effects that are consistent across diverse bacterial species

Nanoparticles have been proposed as tunable delivery vehicles for targeted treatments and, in some cases, the active therapeutic agents themselves. Despite the promise of such customizable impacts, little evidence exists to support these claims in the realm of antibiotics. Exploration of the silver and copper nanoparticle antibacterial impacts have been reported with inconsistent results. Here, we investigate the physical, chemical, and bacterial properties of silver and copper core particles stabilized with commonly used surface coatings, namely, polyvinylpyrrolidone (PVP, to confer a neutrally charged surface), cetrimonium bromide (CTAB, positively charged surface), citrate (Cit, negatively charged surface for silver nanoparticles), and ascorbic acid (AA, negatively charged surface for copper nanoparticles. The impacts of these potential antibacterial nanoparticles are measured against three bacterial species spanning deep divisions in the bacterial tree of life and include Escherichia coli, Staphylococcus aureus, and Sphingobacterium multivorum. Varying dose, core composition, surface coating, and bacterial species revealed that nanoparticle surfaces accounted for most of the variation in antibacterial activity. In all experiments, dose produced a linear inhibitory effect. Surprisingly, bacterial species reacted similarly regardless of evolutionary relatedness. There is a high degree of consistency, effectiveness, and efficacy among PVP silver and copper nanoparticle. These findings have implications for the intentional use of nanotechnology in environmental systems.

Modeling-informed Engineered Genetic Incompatibility strategies to overcome resistance in the invasive Drosophila suzukii

Engineered Genetic Incompatibility (EGI) is an engineered extreme underdominance genetic system wherein hybrid animals are not viable, functioning as a synthetic speciation event. There are several strategies in which EGI could be leveraged for genetic biocontrol of pest populations. We used an agent-based model of Drosophila suzukii (Spotted Wing Drosophila) to determine how EGI would fare with high rates of endemic genetic resistance alleles. We discovered a surprising failure mode wherein field-generated females convert an incompatible male release program into a population replacement gene drive. Local suppression could still be attained in two seasons by tailoring the release strategy to take advantage of this effect, or alternatively in one season by altering the genetic design of release agents. We show in this work that data from modeling can be utilized to recognize unexpected emergent phenomena and a priori inform genetic biocontrol treatment design to increase efficacy.

A multi-omics framework reveals strawberry flavor genes and their regulatory elements

Flavor is essential to consumer preference of foods and is an increasing focus of plant breeding programs. In fruit crops, identifying genes underlying volatile organic compounds has great promise to accelerate flavor improvement, but polyploidy and heterozygosity in many species have slowed progress. Here we use octoploid cultivated strawberry to demonstrate how genomic heterozygosity, transcriptomic intricacy and fruit metabolomic diversity can be treated as strengths and leveraged to uncover fruit flavor genes and their regulatory elements. Multi-omics datasets were generated including an expression quantitative trait loci map with 196 diverse breeding lines, haplotype-phased genomes of a highly-flavored breeding selection, a genome-wide structural variant map using five haplotypes, and volatile genome-wide association study (GWAS) with &gt; 300 individuals. Overlaying regulatory elements, structural variants and GWAS-linked allele-specific expression of numerous genes to variation in volatile compounds important to flavor. In one example, the functional role of anthranilate synthase alpha subunit 1 in methyl anthranilate biosynthesis was supported via fruit transient gene expression assays. These results demonstrate a framework for flavor gene discovery in fruit crops and a pathway to molecular breeding of cultivars with complex and desirable flavor.

Evaluation of macadamia felted coccid (Hemiptera: Eriococcidae) damage and cultivar susceptibility using imagery from a small unmanned aerial vehicle (sUAV), combined with ground truthing

BACKGROUND

Macadamia felted coccid, Acanthococcus ioronsidei (Williams) (Hemiptera: Eriococcidae), is a significant pest of macadamia nut, Macadamia integrifolia Maiden & Betche (Protaceae), in Hawaii, and heavy infestations can kill branches, resulting in characteristic dead, copper-colored leaves. Small Unmanned Aerial Vehicles (sUAV) or 'drones,' combined with spatial data analysis, can provide growers with accurate and high-resolution detection of plant stress due to pest infestations. We investigated the feasibility of using RGB (red-green-blue) color images from sUAV to detect dieback caused by macadamia felted coccid infestation and compared sUAV estimates with ground-based damage estimates (ground truthing).

RESULTS

Spatial analysis showed clustering of foliar damage that reflected cultivar susceptibility to macadamia felted coccid infestation, with cultivars 344 and 856 being susceptible, and cultivars 800 and 333 being tolerant. sUAV and ground-based estimates of foliar damage were similar for the cultivar 344, but ground-based assessments were higher than sUAV for cultivar 856, possibly due to the differences in canopy architecture and significant early dieback in the lower canopy. At foliar damage levels <10%, sUAV and ground truthing data were significantly positively correlated, suggesting sUAV may be useful in detecting early stages of macadamia felted coccid infestation.

CONCLUSIONS

Cultivars showed varying susceptibility to macadamia felted coccid infestation and the foliage damage appeared in clusters. sUAV was able to detect the foliage damage under high and low infestation scenarios suggesting that it can be effectively used for the early detection of infestations. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Evaluation of chemical and microbial control options for Pangaeus bilineatus (Say) (Hemiptera: Cydnidae) infesting peanut crop

BACKGROUND

The peanut burrower bug, Pangaeus bilineatus is a major crop pest of peanuts in the southern United States. Peanuts infested by P. bilineatus exhibit weight and quality losses and could be discounted by ≤50% of the prevailing market price. Control of this pest is difficult because it attacks peanut pods underground, thus rendering foliar pesticide applications ineffective. Integration of entomopathogenic fungi and nematodes (EPF/EPNs) with chemical insecticides in the management of P. bilineatus was investigated as a potential integrated pest management containment tool.

RESULTS

The nymphs were less susceptible than adults of P. bilineatus to EPNs. Comparison of six strains of both Heterorhabditis spp. and Steinernema spp. demonstrated that Steinernema carpocapsae (All) was the most virulent EPN, causing 75.54% mortality of P. bilineatus adults after 7 days postinoculation (dpi), whereas the mortality generated by the application of the rest of the nematodes ranged between 17.03% (H. bacteriophora - Lewis) and 50% (H. bacteriophora VS). Application of imidacloprid by itself at ½FR (field rate) did not result in any significant mortality of P. bilineatus adults but application of chlorpyrifos at 1/8FR caused significant mortality (27.41-61.35%) at 7-14 dpi. However, combined applications of S. carpocapsae and imidacloprid resulted in significant mortality starting at 3 dpi. The interactions between S. carpocapsae and imidacloprid were synergistic at 3-5 dpi, but became additive at 7-14 dpi. Both chlorpyrifos and imidacloprid did not negatively impact the reproduction of S. carpocapsae.

CONCLUSION

The compatibility between S. carpocapsae and imidacloprid makes a case for the combination to be used for the management of P. bilineatus. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.