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The rapid invasion of the non-native Phragmites australis (Poaceae, subfamily Arundinoideae) is a major threat to native wetland ecosystems in North America and elsewhere. We describe the first reference genome for P. australis and compare invasive (ssp. australis) and native (ssp. americanus) genotypes collected from replicated populations across the Laurentian Great Lakes to deduce genomic bases driving its invasive success. Here, we report novel genomic features including a Phragmites lineage-specific whole genome duplication, followed by gene loss and preferential retention of genes associated with transcription factors and regulatory functions in the remaining duplicates. Comparative transcriptomic analyses revealed that genes associated with biotic stress and defence responses were expressed at a higher basal level in invasive genotypes, but native genotypes showed a stronger induction of defence responses when challenged by a fungal endophyte. The reference genome and transcriptomes, combined with previous ecological and environmental data, add to our understanding of mechanisms leading to invasiveness and support the development of novel, genomics-assisted management approaches for invasive Phragmites.

In the North American Northern Great Plains, Kentucky bluegrass (Poa pratensis L.) and smooth bromegrass (Bromus inermis Leyss. subsp. inermis) pose a serious threat to native grassland integrity and function. This study's objectives were to 1) determine drought resistance of non-native grassland and invaded-native tallgrass prairie during 1 and 2 yr of drought and 2) determine drought resilience of non-native grassland and invaded-native tallgrass prairie after 1 yr of drought and 1 yr of recovery with 100% of average precipitation. Three rainout shelters, 3.6 m x 4 m, were installed on non-native and invaded-native grassland in eastern South Dakota to simulate drought conditions by excluding ambient rainfall. The shelter system was constructed on a track whereby the shelter automatically moved over the experimental plots when it rained and moved away from the plots when it stopped raining. Weekly watering treatments consisted of ambient, 75%, 100%, 125%, and 250% of the 30-yr average in 2013 and 2014 (Experiment I). Also, in 2014 a second set of the 75%, 100%, and 125% watering treatments were watered to 100% of the 30-yr average (Experiment II). Drought reduced biomass production in both non-native and invaded-native grassland sites. When plots were watered to 100% of the 30-yr average, the non-native site had similar amount of biomass compared with the drought year, but the invaded-native site had lower biomass. This response provides more evidence regarding the aggressive nature of these two introduced cool-season grasses and a mechanism to explain their continual dominance and expansion in this region.

Rhabdomyosarcomas (RMS) represent a family of aggressive soft tissue sarcomas that present in both children and adults. Pathologic risk stratification for RMS has been based on histologic subtype, with poor outcomes observed in alveolar rhabdomyosarcoma (ARMS) and the adult-type pleomorphic rhabdomyosarcoma (PRMS) compared to embryonal rhabdomyosarcoma (ERMS). Genomic sequencing studies have expanded the spectrum of RMS, with several new molecularly defined entities, including fusion-driven spindle cell/sclerosing rhabdomyosarcoma (SC/SRMS) and MYOD1-mutant SC/SRMS. Comprehensive genomic analysis has previously defined the mutational and copy number spectrum for the more common ERMS and ARMS and revealed corresponding methylation signatures. Comparatively, less is known about epigenetic correlates for the rare SC/SRMS or PRMS histologic subtypes. Herein, we present exome and RNA sequencing, copy number analysis, and methylation profiling of the largest cohort of molecularly characterized RMS samples to date. In addition to ARMS and ERMS, we identify two novel methylation subtypes, one having SC/SRMS histology and defined by MYOD1 p. L122R mutations and the other matching adult-type PRMS. Selected tumors from adolescent patients grouped with the PRMS methylation class, expanding the age range of these rare tumors. Limited follow-up data suggest that pediatric tumors with MYOD1-mutations are associated with an aggressive clinical course.

The UCSC Genome Browser, https://genome.ucsc.edu, is a graphical viewer for exploring genome annotations. The website provides integrated tools for visualizing, comparing, analyzing, and sharing both publicly available and user-generated genomic datasets. Data highlights this year include a collection of easily accessible public hub assemblies on new organisms, now featuring BLAT alignment and PCR capabilities, and new and updated clinical tracks (gnomAD, DECIPHER, CADD, REVEL). We introduced a new Track Sets feature and enhanced variant displays to aid in the interpretation of clinical data. We also added a tool to rapidly place new SARS-CoV-2 genomes in a global phylogenetic tree enabling researchers to view the context of emerging mutations in our SARS-CoV-2 Genome Browser. Other new software focuses on usability features, including more informative mouseover displays and new fonts.

SummaryMany bacteria can migrate from a free-living, planktonic state to an attached, biofilm existence. One factor regulating this transition in the facultative plant pathogen Agrobacterium tumefaciens is the ExoR-ChvG-ChvI system. Periplasmic ExoR regulates activity of the ChvG-ChvI two-component system in response to environmental stress, most notably low pH. ChvI impacts hundreds of genes, including those required for type VI secretion, virulence, biofilm formation, and flagellar motility. Previous studies revealed that activated ChvG-ChvI represses expression of most of class II and class III flagellar biogenesis genes, but not the master motility regulators visN, visR, and rem. In this study, we characterized the integration of the ExoR-ChvG-ChvI and VisNR-Rem pathways. We isolated motile suppressors of the non-motile ΔexoR mutant and thereby identified the previously unannotated mirA gene encoding a 76 amino acid protein. We report that the MirA protein interacts directly with the Rem DNA-binding domain, sequestering Rem and preventing motility gene activation. The ChvG-ChvI pathway activates mirA expression and elevated mirA is sufficient to block motility. This study reveals how the ExoR-ChvG-ChvI pathway prevents flagellar motility in A. tumefaciens. MirA is also conserved among other members of the Rhizobiales suggesting similar mechanisms of motility regulation.Plain language summaryAgrobacterium tumefaciens is a plant pathogen that responds to low pH, stressful environments via a complex two-component regulatory system. This regulatory system can completely inhibit bacterial locomotion by flagella, and in this study we define the mechanism for this inhibition and identify a novel small protein regulator that blocks flagellar gene expression.

Bacterial two-component regulatory systems (TCSs) mediate signal transduction by transferring phosphoryl groups between sensor kinase and response regulator proteins, sometimes using intermediary histidine-phosphotransferase (Hpt) domains to form multistep phosphorelays. Because (i) almost all known fungal sensor kinases exhibit a domain architecture characteristic of bacterial TCS phosphorelays, (ii) all known fungal Hpts are stand-alone proteins suited to shuttle between cytoplasm and nucleus, and (iii) the best-characterized fungal TCS is a canonical phosphorelay, it is widely assumed that most or all fungal TCSs function via phosphorelays. However, fungi generally encode more sensor kinases than Hpts or response regulators, leading to a disparity between putative phosphorelay inputs and outputs. The simplest resolution of this paradox is to hypothesize that most fungal sensor kinases do not participate in phosphorelays. Reimagining how fungal TCSs might function leads to multiple testable predictions.

Low dietary energy and decreased intake of herbage have been attributed to the reduced performance of grazing dairy cattle. We hypothesized that grasses with inherently greater energy would interact in a complementary way with condensed tannins (CT) in birdsfoot trefoil to increase herbage intake by grazing dairy heifers. Eight pasture treatments comprising high-sugar perennial ryegrass (Lolium perenne L.), orchardgrass (Dactylis glomerata L.), meadow bromegrass (Bromus riparius Rehmann), and tall fescue [Schendonorus arundinaceus (Schreb.) Dumort] were established in Lewiston, Utah as monocultures and binary mixtures with birdsfoot trefoil (Lotus corniculatus L.; BFT). Pasture treatments were rotationally stocked by Jersey heifers for 105 d in 2017 and 2018, and herbage samples were collected pre- and postgrazing for each 7-d grazing period and analyzed for herbage mass, nutritive value, and apparent herbage intake. We observed differences among pasture treatments in herbage quantity and nutritive value, as well as differences in herbage intake by grazing Jersey heifers. On average, grass-BFT mixtures had greater herbage intake than grass monocultures, and every grass-BFT treatment individually had greater herbage intake than their respective grass monocultures. Using multivariate analyses, we determined that approximately 50% of the variation in herbage intake was due to nutritive and physical herbage characteristics, with the most explanatory being characteristics related to fiber and energy, followed by those related to the percent of BFT in the herbage. Grass monocultures exhibited a range of inherent dietary energy, but there was indication that an imbalance of energy to crude protein (e.g., protein deficient) reduced intake of grass monocultures. Moreover, there was some evidence of a complementary effect between increased dietary energy and CT; however, low CT levels made it impossible to determine the effect of CT on herbage intake per se. This study confirmed that chemical and physical characteristics inherent to different pasture species have a large effect on herbage intake by grazing cattle. Pastures planted to binary mixtures of nutritious grasses and birdsfoot trefoil increase herbage intake of temperate pastures by grazing Jersey heifers.

Dairy heifers developed in certified organic programs, especially those utilizing pasture-based management schemes, have lower rates of gain than heifers raised in nonorganic confinement production systems in temperate climates, such as in the Intermountain West region of the United States. This study investigates the effects that different forages in a rotational grazing system have on development of organically raised Jersey heifers. Over 3 years, 210 yearling Jersey heifers were randomly assigned to one of 9 treatments, including a conventional confinement control where animals were fed a total mixed ration or one of 8 pasture treatments: Cache Meadow bromegrass (Bromus riparius Rehmann), QuickDraw orchard grass (Dactylis glomerata L.), Amazon perennial ryegrass (Lolium perenne L.), or Fawn tall fescue (Schendonorus arundinaceus [Schreb.] Dumort) and each individual grass interseeded with birdsfoot trefoil (Lotus corniculatus L., BFT). Each treatment had 3 blocks/yr over the 3-yr period, with each block having a 0.4 ha pasture of each treatment. Every 35 d, over a 105-d period, heifers were weighed and measured for hip height, and blood samples were collected to determine serum insulin-like growth factor-1 and blood urea nitrogen concentrations. Fecal egg counts were also assessed. Heifer body weight (BW), blood urea nitrogen, and insulin-like growth factor-1 concentrations were affected by treatment when analyzed over time. Heifers on grass-BFT pastures had increased BW compared with heifers on monoculture grass pastures. Heifers receiving a total mixed ration or perennial ryegrass+BFT had increased BW gain over the 105-d period compared with heifers grazing tall fescue+BFT, orchard grass, perennial ryegrass, meadow bromegrass, or tall fescue. Individually for all grass species, heifers grazing +BFT pastures had greater ending BW and weight gain than heifers grazing the respective grass monocultures. Furthermore, weight gain for heifers on perennial ryegrass+BFT, meadow bromegrass+BFT, and orchard grass+BFT were not different from those on a total mixed ration. Heifers grazing grass-BFT pastures had increased blood urea nitrogen compared with heifers grazing monoculture grass pastures. Heifer hip height and fecal egg counts were not affected by treatment. These results show that the addition of BFT to organic pasture improves growth of grazing replacement heifers. Economic analyses also demonstrate that interseeding grass pastures with BFT results in an increased economic return compared with grazing monoculture grass pastures. Grass pastures interseeded with BFT may be a sustainable option to achieve adequate growth of Jersey heifers raised in an organic pasture scenario in a temperate climate.

Efforts to remove invasive species may benefit native species, but the effects can be complex and unpredictable. Thus, studies of invasive-species removal provide important information for guiding management and providing insight about variation in post-removal impacts within the community. Using southern pine-grassland ecosystems as a model system, we hypothesized that removal of the long-established red-imported fire ant (Solenopsis invicta, hereafter RIFA) would positively influence altricial Peromyscus species, due to increased survival of young in the nest and thus increased recruitment to the population, but would not impact semi-precocial hispid cotton rats (Sigmodon hispidus), which are mobile more quickly after birth and thus at less risk of depredation by RIFA. We compared small mammal populations on sites treated with a granular insecticide (Extinguish Plus) to remove RIFA in southwestern Georgia, United States, from April 2018 to December 2019. As expected, we detected no difference in cotton rat recruitment. However, contrary to our prediction, the same was true for cotton mice (Peromyscus gossypinus) and oldfield mice (Peromyscus polionotus). We found RIFA removal increased survival both of cotton rats and cotton mice, increasing average population rate of change (λ) on treated sites during the study period. In contrast, we observed lower survival of oldfield mice, with similar λ estimates on treated and untreated sites, but low sample sizes were problematic for this species. Our results show that removal of invasive species can have positive impacts for native species, but both the magnitude of RIFA effects on small mammals and mechanisms by which impacts occur are complex.

Bempedoic acid is an inhibitor of adenosine triphosphate–citrate lyase approved for use in adults with hypercholesterolemia. Nonclinical studies assessed binding to the human ether‐a‐go‐go–related gene (hERG) potassium channel in vitro and the effect of bempedoic acid on QT/QTc in cynomolgus monkeys. A randomized, double‐blind, parallel‐design clinical study assessed the effects of steady‐state bempedoic acid at a supratherapeutic dose (240 mg/day, 33.3% higher the180 mg/day therapeutic dose), placebo, and moxifloxacin (400 mg) in healthy subjects. In vitro binding potency for bempedoic acid to the hERG potassium channel was weak, with half‐maximal inhibition (IC50) estimated at greater than 1000 μM (>1670‐fold the bempedoic acid 180 mg/day steady‐state unbound maximum concentration). In monkeys, individual rate‐corrected QT intervals showed no time‐ or dose‐dependent changes up to 100 mg/kg of bempedoic acid. In human subjects, the upper 90% confidence interval (CI) for the difference in QTc interval, corrected using Fridericia’s formula (QTcF), between bempedoic acid and placebo was less than 5 msec at all time points. Concentration‐QTcF analysis showed that maximum bempedoic acid concentration at steady‐state was attained at a median 2.1 h postdose, and the predicted mean change (90% CI) in QTcF at the observed mean bempedoic acid concentration 2 h postdose was −0.5 (−5.0, 4.0) msec. The lower bound of the moxifloxacin 90% CI exceeded 5 msec at prespecified time points, establishing study sensitivity. Steady‐state bempedoic acid at a supratherapeutic dose of 240 mg was generally well‐tolerated and not associated with QTc prolongation in healthy subjects.

International audience; Understanding how predators affect prey species is a central endeavor in applied ecology. Game birds are a culturally and economically important group of birds throughout the world. Specifically, northern bobwhite (Colinus virginianus) is an imperiled game bird native to North America that has declined precipitously over the past 65 years. Concurrently, raptor populations increased substantially as a result of pesticide bans and legal protections. However, relationships between raptors and bobwhites are not well-understood because of limited long-term data. We analyzed long-term raptor survey and bobwhite survival datasets from 2008 to 2018 to determine if oscillations in raptor abundance affected bobwhite survival. We used a novel open multi-species dynamics hierarchical distance sampling model to estimate the abundance of raptors. We used a known-fate survival model to determine if variation in raptor abundance affected bobwhite survival. We had multiple working hypotheses regarding biological relationships between raptor abundance and bobwhite survival. Raptors affected bobwhites in every biological season but were more influential in the breeding season and late winter supporting the notion of bobwhite behavior and raptor migration were driving observed patterns. Our results suggest that even in areas with abundant habitat, predators exert top-down influences on vital rates suggesting similar or greater influences on populations under poor habitat conditions.

The association between dry period length (DPL) and time to culling and pregnancy in the subsequent lactation may be important for the economically optimal length of the dry period. Therefore, this study aimed to (1) quantify the association between DPL and hazard of culling and pregnancy in the subsequent lactation; (2) develop continuous functions of DPL for the hazard ratios of culling and pregnancy; and (3) investigate the effect of a cause-specific hazards model and a subdistribution model to analyze competing events. The data used in this observational cohort study were from dairy herd improvement milk test lactation records from 40 states in the United States. After edits, there remained 1,108,515 records from 6,730 herds with the last days dry in 2014 or 2015. The records from 2 adjacent lactations (current, subsequent) were concatenated with the DPL of interest, 21 to 100 d, in between both lactations. We defined 8 DPL categories of 10 d each. Kaplan-Meier survival curves were used to show associations between DPL and time to culling or pregnancy for 3 lactation groups: lactation 1 and 2, lactation 2 and 3, and lactation 3 and greater. To control for confounding factors in Cox proportional models, we included 6 current lactation covariates and 3 time-dependent variables in the survival models. Hazard ratios of culling were estimated for 4 days in milk (DIM) categories from 1 to 450 DIM. Hazard ratios of pregnancy were estimated for 3 DIM categories from 61 to 300 DIM. Competing risk analysis of 8 disposal codes (i.e., farmer reported reasons) for culling and the culling event for pregnancy were conducted by a cause-specific hazards model and a subdistribution model. Hazard ratios were also estimated as quadratic polynomials of DPL. Compared with the reference DPL category of 51 to 60 d, hazard ratios of culling and pregnancy of the other 7 DPL categories ranged between 0.70 and 1.49, and 0.93 and 1.15, respectively. Short DPL were associated with lower risk of culling in the early lactation but not over the entire lactation. Short DPL were associated with greater hazard of pregnancy. Trends in hazard ratios over the ranges of the 8 DPL categories were not always consistent. Competing risk analysis with both models provided little differences in hazard ratios of culling and pregnancy. In conclusion, variations in DPL were associated with meaningful differences in the hazard ratios for culling and pregnancy and minor differences in the relative frequency of disposal codes. Subdistribution hazards models produced hazard ratios similar to cause-specific hazard models. The quadratic polynomials may be useful for decision support on customization of DPL for individual cows.

The first Paraguayan records of the Broad-winged Hawk Buteo platypterus are reported from Itapúa and Central departments.

Bark beetles and root weevils can impact forests through tree death on landscape scales. Recently, subterranean termites have been linked to these beetles via the presence of bluestain fungi (Ascomycota: Ophiostomataceae), which are vectored to trees by beetles. However, only a small subset of bluestain species have been examined. Here, we tested whether termite-bluestain association patterns in the field reflect termite feeding preference in laboratory choice trials. We documented the presence of four bluestain fungi (Leptographium procerum (W.B. Kendr.), L. terebrantis (Barras & Perry), Grosmannia huntii (Rob.-Jeffr.), and G. alacris (T.A. Duong, Z.W. de Beer & M.J. Wingf.) in the roots of 2,350 loblolly pine trees in the southeastern United States and whether termites were present or absent on these roots and paired this with laboratory choice feeding trials. Termites were found 2.5-fold on tree roots with at least one bluestain fungus present than tree roots without bluestain fungi. Although termites in this study and others were associated with L. procerum, L. terebrantis, and marginally G. huntii, termites only showed preferential feeding on wood inoculated with G. huntii in laboratory trials. This suggests that increased termite presence on wood with bluestain fungi may be driven by factors other than increased wood palatability. Termites could thus disproportionately affect wood turnover rates for specific pools (e.g., bark beetle and root weevil attacked trees) and in some cases (e.g., G. huntii) accelerate wood decomposition. This study supports the growing evidence that the association between subterranean termites and bluestain fungi is spatially and taxonomically widespread.

Bighead Carp Hypothalmichthys nobilis and Silver Carp Hypothalmichthys moltrix (hereafter collectively referred to as Bigheaded Carp) have spread throughout the majority of the Mississippi River since the 1970s. The current northern invasion edge of Bigheaded Carp in the Upper Mississippi River (UMR) spans between Pools 14 and 20 because of limited passage at Lock and Dam (LD) 19. Mechanisms limiting adult Bigheaded Carp abundance above LD19 are unknown but may be due in part to lack of reproductive success influenced by adult abundance and environmental factors. Our objective was to investigate how relative adult biomass and river temperature and discharge affect maximum annual Bigheaded Carp larval production in the UMR using a Ricker stock-recruitment model. Adult Bigheaded Carp relative biomass (kg/h) was estimated annually with boat electrofishing and larvae were collected every 10 d between May and August 2014–2017 in Pools 14–20 in the UMR. Adult relative biomass ranged from 0.0 to 880.9 kg/h, whereas maximum annual larval densities ranged from 0.0 to 2,869.4 larvae/m3. After accounting for variability among pools and years, the most supported linear Ricker stock-recruitment model indicated the number of recruits per spawner decreased with increasing adult relative biomass and increased with mean discharge. Our results highlight the importance of adult biomass and river discharge conditions for reproduction of Bigheaded Carp along leading edges of invasion. Management strategies that aim to maintain low adult abundance where reproduction is not yet occurring could help limit population increases via reproduction, whereas reducing high adult biomass (e.g., commercial harvest, barriers) may result in greater Bigheaded Carp reproductive output in the UMR.

Junglerice is becoming more prevalent in Tennessee, Arkansas, and Mississippi row crop fields. The evolution of glyphosate-resistant (GR) junglerice populations is one reason for the increase. Another possible explanation is that glyphosate and clethodim grass activity is being antagonized by dicamba. This question has led to research to examine whether sequential applications alleviate antagonism observed with dicamba plus glyphosate and/or clethodim mixtures and determine whether sequential treatments with those herbicides at 24 h, 72 h, or 168 h can improve junglerice control. Glyphosate + clethodim applications provided >90% junglerice control. The observed levels of antagonism varied by whether the location of the test was in the greenhouse or the field, and the timing of applications. In the greenhouse, clethodim + dicamba provided excellent control, whereas in the field, the same treatment showed a greater than 30% reduction in junglerice control compared with clethodim alone. However, control was restored by using a mixture of glyphosate + clethodim without dicamba. The environment at the time of application and relative GR level of the junglerice influenced the overall control of these sequential applications. When clethodim applied first followed by dicamba at 72 h or 168 h, better control was observed compared with applying dicamba followed by clethodim. Overall, mixing glyphosate + clethodim provided the most complete junglerice control regardless of timing. These data confirm that leaving dicamba out of the spray tank will mitigate herbicide antagonism on junglerice control. These data would also indicate that avoiding dicamba and glyphosate mixtures will also improve the consistency of control with glyphosate-susceptible junglerice.

The loops of modular polyketide synthases (PKSs) serve diverse functions but are largely uncharacterized. They frequently contain amino acid repeats resulting from genetic events such as slipped-strand mispairing. Determining the tolerance of loops to amino acid changes would aid in understanding and engineering these multidomain molecule factories. Here, tandem repeats in the DNA encoding 949 modules within 129 cis-acyltransferase PKSs were catalogued, and the locations of the corresponding amino acids within the module were identified. The most frequently inserted interdomain loop corresponds with the updated module boundary immediately downstream of the ketosynthase (KS), while the loops bordering the dehydratase (DH) are nearly intolerant to such insertions. From the 949 modules, no repetitive sequence loop insertions are located within ACP, and only 2 reside within KS, indicating the sensitivity of these domains to alteration.

Puberty in female pigs is defined as age at first estrus and gilts that have an earlier age at puberty are more likely to have greater lifetime productivity. Because age at puberty is predictive for sow longevity and lifetime productivity, but not routinely measured in commercial herds, it would be beneficial to use genomic or marker-assisted selection to improve these traits. A GWAS at the US Meat Animal Research Center (USMARC) identified several loci associated with age at puberty in pigs. Candidate genes in these regions were scanned for potential functional variants using sequence information from the USMARC swine population founder animals and public databases. In total, 135 variants (SNP and insertion/deletions) in 39 genes were genotyped in 1284 phenotyped animals from a validation population sired by Landrace and Yorkshire industry semen using the Agena MassArray system. Twelve variants in eight genes were associated with age at puberty (P < 0.005) with estimated additive SNP effects ranging from 1.6 to 5.3 days. Nine of these variants were non-synonymous coding changes in AHR, CYP1A2, OR2M4, SDCCAG8, TBC1D1 and ZNF608, two variants were deletions of one and four codons in aryl hydrocarbon receptor, AHR, and the most significant SNP was near an acceptor splice site in the acetyl-CoA carboxylase alpha, ACACA. Several of the loci identified have a physiological and a genetic role in sexual maturation in humans and other animals and are involved in AHR-mediated pathways. Further functional validation of these variants could identify causative mutations that influence age at puberty in gilts and possibly sow lifetime productivity.

The TP53-R337H founder mutation exists at a high frequency throughout southern Brazil and represents one of the most common germline TP53 mutations reported to date. It was identified in pediatric adrenocortical tumors in families with a low incidence of cancer. The R337H mutation has since been found in association with early-onset breast cancers and Li–Fraumeni syndrome (LFS). To study this variability in tumor susceptibility, we generated a knockin mutant p53 mouse model (R334H). Endogenous murine p53-R334H protein was naturally expressed at high levels in multiple tissues and was functionally compromised in a tissue- and stress-specific manner. Mutant p53-R334H mice developed tumors with long latency and incomplete penetrance, consistent with many human carriers being at a low but elevated risk for cancer. These findings suggest the involvement of additional cooperating genetic alterations when TP53-R337H occurs in the context of LFS, which has important implications for genetic counseling and long-term clinical follow-up. Significance: A p53-R334H knockin mouse serves as an important model for studying the most common inherited germline TP53 mutation (R337H) that is associated with variable tumor susceptibility.

Research into the patterns and drivers of juvenile migration is important for understanding the development of individual migration strategies. Although several recent studies have tracked adult large gulls throughout the annual cycle, the movements of juveniles remain poorly understood. We fitted Global Positioning System (GPS) devices that transmit locations through the Global System for Mobile Communications (GSM) to ten juvenile Lesser Black‐backed Gulls Larus fuscus prior to fledging on the island of Spiekeroog, Germany, to study their first autumn migration and wintering behaviour. The tracked birds initially departed on similar compass bearings south to southwest, after which migration routes diverged. Individuals took 38–107 days to reach their wintering sites in Algeria, Morocco or Spain. Birds visited 6.7 ± 3.7 (mean ± sd) stopover sites en route and spent substantial time in northern Europe, with some individuals converging at the same sites over small spatial scales (< 1km), but not over the same time periods. Birds increased travel speeds in the second half of their migration. They showed relatively high site-fidelity after arrival at wintering sites, and there was no evidence that the size of foraging areas increased over time, suggesting limited exploratory behaviour. Individuals used the same predominant habitats – cropland, open water and built-up areas – to varying degrees, but showed limited variation in habitat use over time. Overall, the migration routes and timings of juveniles broadly resembled those of previously tracked adults. Given their similar initial bearings and abundance of large gulls on the flyway, we suggest that social learning is likely to be an important process shaping the individual migration and wintering strategies of juvenile gulls.

Osteoarticular infection with Mycobacterium bovis (M. bovis) is a rare complication of bladder cancer treatment with intravesical Bacillus Calmette–Guèrin (BCG). We describe a case of disseminated Mycobacterium bovis BCG infection masquerading as a chronic prosthetic joint infection in a patient with several risk factors for progressive mycobacterial infection.

Abrasive weeding is a nonchemical weed control tactic that uses small, gritty materials propelled with compressed air to destroy weed seedlings. Organic fertilizers have been used successfully as abrasive grits to control weeds, but the goal for this study was to explore the effects of fertilizer grit, application rates, and background soil fertility on weeds, plant available nitrogen (N) uptake, and crop yield. Field trials were conducted in organic ‘Carmen’ sweet red pepper (Capsicum annuum) and organic ‘Gypsy’ broccoli (Brassica oleracea var. italica) and treatments included organic fertilizer grit (8N–0.9P–3.3K vs. 3N–3.1P–3.3K), grit application rates (low vs. high), compost amendments (with and without), and weedy and weed-free controls. Weed biomass was harvested at 84 days and 65 days after transplanting for pepper and broccoli, respectively. Simulated total plant available N (nitrate + ammonium) uptake was measured with ion exchange resin stakes between 7 and 49 days after the first of two grit applications. Produce was harvested at maturity, graded for marketability, and weighed. The higher grit application rate, regardless of fertilizer type, reduced the weed biomass by 75% to 89% for pepper and by 86% to 99% for broccoli. By 5 weeks after the first grit application, simulated plant N uptake was greatest following grit application with the 8% N fertilizer, followed by the 3% N fertilizer, and lowest in the weedy control. The high grit application rate of 8% N fertilizer increased pepper yield by 112% compared with the weedy control, but it was similar to that of the weed-free control. Broccoli was less responsive to abrasive grits, with yield changes ranging from no difference to up to a 36% increase (relative to the weedy control) depending on the application rate and compost amendment. This is the first evidence indicating that the nutrient composition of organic fertilizer abrasive grits can influence in-season soil N dynamics, weed competition, and crop yield. The results suggest that abrasive weeding technology could be leveraged to improve the precision of in-season fertilizer management of organic crops.

Nectar is a primary reward mediating plant–animal mutualisms to improve plant fitness and reproductive success. Four distinct trichomatic nectaries develop in cotton (Gossypium hirsutum), one floral and three extrafloral, and the nectars they secrete serve different purposes. Floral nectar attracts bees for promoting pollination, while extrafloral nectar attracts predatory insects as a means of indirect protection from herbivores. Cotton therefore provides an ideal system for contrasting mechanisms of nectar production and nectar composition between different nectary types. Here, we report the transcriptome and ultrastructure of the four cotton nectary types throughout development and compare these with the metabolomes of secreted nectars. Integration of these datasets supports specialization among nectary types to fulfill their ecological niche, while conserving parallel coordination of the merocrine-based and eccrine-based models of nectar biosynthesis. Nectary ultrastructures indicate an abundance of rough endoplasmic reticulum positioned parallel to the cell walls and a profusion of vesicles fusing to the plasma membranes, supporting the merocrine model of nectar biosynthesis. The eccrine-based model of nectar biosynthesis is supported by global transcriptomics data, which indicate a progression from starch biosynthesis to starch degradation and sucrose biosynthesis and secretion. Moreover, our nectary global transcriptomics data provide evidence for novel metabolic processes supporting de novo biosynthesis of amino acids secreted in trace quantities in nectars. Collectively, these data demonstrate the conservation of nectar-producing models among trichomatic and extrafloral nectaries.

Junglerice has become a major weed in the mid-south and other areas of the United States. Glyphosate resistance has been documented in junglerice populations and is part of the reason for the increase in its prevalence. However, reduced junglerice control with glyphosate + dicamba and clethodim + dicamba mixtures has been observed in many production fields where glyphosate resistance has not yet evolved. Therefore, research was conducted to assess reduced junglerice control with glyphosate and clethodim when applied with dicamba. Adding dicamba to the spray tank with glyphosate reduced junglerice control by 27%. Adding dicamba to the spray tank with clethodim reduced junglerice control by 11%. The use of Turbo Teejet Induction (TTI) nozzles reduced junglerice control an additional 8% compared to applications with an air induction extended range (AIXR) nozzle. When a drift reduction agent (DRA) was added to dicamba mixtures with glyphosate or clethodim, junglerice control was reduced 36%. Junglerice control was similar with the glyphosate + dicamba treatment compared to the glyphosate + 2,4-D mixture. There was no interaction between nozzles and herbicide treatment. Regardless of herbicide treatment junglerice control was always lower when applied with the ultracourse TTI nozzle. Many applicators in Tennessee prefer to make one application of glyphosate + dicamba in a mixture to save time (authors' personal experience). These results show that the addition of dicamba to glyphosate or clethodim applied with labeled nozzles and a DRA results in reduced junglerice control and should be avoided. Nomenclature: junglerice; Echinochloa colona (L.) Link

Beaches are under increasing pressure from a wide range of anthropogenic threats, including human trampling, vehicular crushing, and horse riding/training. The impacts of horses on beaches are unknown. We index the relative abundance, diversity and assemblage composition of beach invertebrates at paired sites with and without horses at nine beaches (locations) across Victoria, Australia. Horses were more common at sites where they were allowed and sites (horse versus no horse) within beaches were well matched, having similar slope, seaweed coverage, human and dog activity—attributes which varied among locations. At sites with horse activity, there was less sand compaction in the upper beach (above the previous high tide) suggesting horses disrupt (i.e. mobilise) the sand matrix there. While invertebrates sampled by pitfall traps did not differ in richness or abundance between horse and no horse sites, the assemblage composition differed between horse/no horse sites, at seven of nine locations. Core samples revealed no differences in assemblages, but a greater richness of invertebrates at sites without horses, and a general but not universal pattern for a greater abundance of invertebrates at sites without horses. This study shows that horses disrupt the sand matrix on beaches and might alter assemblage structures of surface invertebrates, and richness and abundance of burrowing invertebrates, at many beaches. The extent to which this alteration compromises the function of sandy shore food webs should be the subject of further, experimental study.

Two antibodies against flaviviruses Flaviviruses are a group of RNA viruses that include the human pathogens dengue virus, Zika virus, and West Nile virus. The envelope protein (E) on the virus surface has been the target of vaccine development, but problems have arisen with antibodies against E, leading to enhanced infection. Now, Modhiran et al. and Biering et al. describe two different antibodies that bind to the flavivirus NS1 protein and prevent it from disrupting epithelial cells, which is associated with severe disease. Both antibodies cross-react with multiple flavivirus NS1 proteins. The antibodies reduce viremia and increase survival in mouse models of flavivirus disease. Both papers include structures of NS1 bound to an antibody, which give insight into the protective mechanism. Science , this issue p. 190 , p. 194

The Topeka shiner (Notropis topeka), a federally endangered species of minnow endemic to the Great Plains region of the central United States, has experienced widespread population declines resulting from loss of habitat. N. topeka habitat in Iowa, most notably oxbow wetlands, was mostly eliminated from the landscape during European settlement and agriculturalization of the region. Over the last two decades, restoration of oxbow habitats in Iowa has been increasing. Restorations provide critical habitat for N. topeka and regenerate a variety of ecosystem services that benefit many species of flora and fauna. There are signs that restoration of oxbow ecosystems is generating positive impacts on N. topeka recovery. Recent studies revealed that N. topeka populations are recovering within a few Iowa watersheds. In the investigation described here, we report the 2020 discovery of two N. topeka specimens in different restored oxbows within the White Fox Creek HUC10 of north central Iowa. Prior to these collections, the species had been undetected within this basin for 36 years. (It is possible that N. topeka persisted within the basin but remained undetected during sampling efforts.) Multiple oxbows have been restored within the White Fox Creek basin in recent years, and significant source populations of N. topeka can be found in nearby watersheds. These collections suggest that as oxbow restorations continue and land stewardship practices improve, N. topeka populations might recover and become reestablished within the historical range.

Assembly of transcriptomes encoding unique neuronal identities requires selective accessibility of transcription factors to cis-regulatory sequences in nucleosome-embedded postmitotic chromatin. Yet, the mechanisms controlling postmitotic neuronal chromatin accessibility are poorly understood. Here, we show that unique distal enhancers define the Pet1 neuron lineage that generates serotonin (5-HT) neurons in mice. Heterogeneous single-cell chromatin landscapes are established early in postmitotic Pet1 neurons and reveal the putative regulatory programs driving Pet1 neuron subtype identities. Distal enhancer accessibility is highly dynamic as Pet1 neurons mature, suggesting the existence of regulatory factors that reorganize postmitotic neuronal chromatin. We find that Pet1 and Lmx1b control chromatin accessibility to select Pet1-lineage-specific enhancers for 5-HT neurotransmission. Additionally, these factors are required to maintain chromatin accessibility during early maturation suggesting that postmitotic neuronal open chromatin is unstable and requires continuous regulatory input. Together, our findings reveal postmitotic transcription factors that reorganize accessible chromatin for neuron specialization.

The success of dicamba-tolerant soybean [Glycine max(L.) Merr.] has revived concerns about plant growth regulator (PGR) herbicide exposure to conventional soybean. In laboratory studies, soybean root nodulation is inhibited by excess auxin, which is the mechanism of action of PGR herbicides. Soybean exposed to PGRs in a field environment may have a similar response, and if nodulation is compromised, nitrogen (N) fixation may be reduced, with subsequent seed yield or protein content decreases. Many soybean–N studies report minimal impact to soybean yield. However, if soybeans show foliar PGR injury symptoms, could N application compensate for a potential nodulation inhibition response? This study examined the response of non–PGR tolerant soybean to N after exposure to low doses of 2,4-D and dicamba applied once (at soybean growth stages V1, V3, and early reproduction [R1 or R2]) or twice (V1 + V3 or V3 + R). N was either foliar or soil applied at early (∼5 d after PGR application) or late (10 d after PGR application) timings. Nodulation and plant growth were evaluated at R3, and grain yield and seed protein and oil content were quantified at maturity. Plant biomass and nodulation were reduced by 10% with some PGR treatments, and early foliar N application after PGR injury resulted in reduction up to 25%. N applications to non–PGR treated soybean did not increase yield. Soybean treated with PGR at V1 or V3, with or without N, had yields similar to control treatments. However, yield reductions of up to 20% were observed when PGRs were applied at V5 or R stages or when double PGR applications were followed by early foliar N application. Seed protein and oil content were not affected by PGR or N treatment.

Fungal natural products (NPs) comprise a vast number of bioactive molecules with diverse activities, and among them are many important drugs. However, the yields of fungal NPs from native producers are usually low, and total synthesis of structurally complex NPs is challenging. As such, downstream derivatization and optimization of lead fungal NPs can be impeded by the high cost of obtaining sufficient starting material. In recent years, reconstitution of NP biosynthetic pathways in heterologous hosts has become an attractive alternative approach to produce complex NPs. Here, we present an efficient, cloning-free strategy for the cluster refactoring and total biosynthesis of fungal NPs in Aspergillus nidulans. Our platform places our genes of interest (GOIs) under the regulation of the robust asperfuranone afo biosynthesis gene machinery, allowing for their concerted activation upon induction. We demonstrated the utility of our system by creating strains that can synthesize high-value NPs, citreoviridin (1), mutilin (2), and pleuromutilin (3), with good to high yield and purity. This platform can be used not only for producing NPs of interests (i.e., total biosynthesis) but also for elucidating cryptic biosynthesis pathways.

The Typhonomachy (Theogony 821 – 880) has long been deemed an anomalous and inorganic intrusion into the Hesiodic text. The main reason for such a judgment is that the Typhoeus episode is an unnecessary and redundant doublet of the Titanomachy that precedes. In addition, Gaia’s role in giving birth to the monster seems to contradict her benign role both before (624 – 628) and after the Typhoeus episode (883 – 885). Looking afresh at the passage through the wider lens of the cosmogonic program of the Theogony allows us to grasp its function within the overall economy of the poem. Typhoeus, offspring of Gaia and Tartarus, takes us back to the very origins of cosmogony. The Typhonomachy brings us to a critical temporal crossroad where a recrudescence of the primeval irrupts into and threatens the evolved universe. If at issue in the Titanomachy was the kingship in Heaven, at stake in the Typhonomachy is the very existence of the cosmos itself.

Phylogenetic distance among host species represents a proxy for host traits that act as biotic filters to shape host‐associated microbiome community structure. However, teasing apart potential biotic assembly mechanisms, such as host specificity or local species interactions, from abiotic factors, such as environmental specificity or dispersal barriers, in hyperdiverse, horizontally transmitted microbiomes remains a challenge. In this study, we tested whether host phylogenetic relatedness among 18 native Asteraceae plant species and spatial distance between replicated plots in a common garden affects foliar fungal endophyte (FFE) community structure. We found that FFE community structure varied significantly among host species, as well as host tribes, but not among host subfamilies. However, FFE community dissimilarity between host individuals was not significantly correlated with phylogenetic distance between host species. There was a significant effect of spatial distance among host individuals on FFE community dissimilarity within the common garden. The significant differences in FFE community structure among host species, but lack of a significant host phylogenetic effect, suggest functional differences among host species not accounted for by host phylogenetic distance, such as metabolic traits or phenology, may drive FFE community dissimilarity. Overall, our results indicate that host species identity and the spatial distance between plants can determine the similarity of their microbiomes, even across a single experimental field, but that host phylogeny is not closely tied to FFE community divergence in native Asteraceae., We tested whether foliar fungal endophyte communities are structured by host phylogenetic relatedness using a common garden experimental design and an explicit selection of host species from a defined phylogenetic range. We found that host species identity was a significant driver of foliar fungal endophyte community structure. However, we did not find that pairwise phylogenetic distance between host species was significantly correlated with foliar fungal endophyte community dissimilarity between host individuals.

Floral nectar is a sugary solution produced by nectaries to attract and reward pollinators. Nectar metabolites, such as sugars, are synthesized within the nectary during secretion from both pre-stored and direct phloem-derived precursors. In addition to sugars, nectars contain nitrogenous compounds such as amino acids; however, little is known about the role(s) of nitrogen (N) compounds in nectary function. In this study, we investigated N metabolism in Cucurbita pepo (squash) floral nectaries in order to understand how various N-containing compounds are produced and determine the role of N metabolism in nectar secretion. The expression and activity of key enzymes involved in primary N assimilation, including nitrate reductase (NR) and alanine aminotransferase (AlaAT), were induced during secretion in C. pepo nectaries. Alanine (Ala) accumulated to about 35% of total amino acids in nectaries and nectar during peak secretion; however, alteration of vascular nitrate supply had no impact on Ala accumulation during secretion, suggesting that nectar(y) amino acids are produced by precursors other than nitrate. In addition, nitric oxide (NO) is produced from nitrate and nitrite, at least partially by NR, in nectaries and nectar. Hypoxia-related processes are induced in nectaries during secretion, including lactic acid and ethanolic fermentation. Finally, treatments that alter nitrate supply affect levels of hypoxic metabolites, nectar volume and nectar sugar composition. The induction of N metabolism in C. pepo nectaries thus plays an important role in the synthesis and secretion of nectar sugar.

Junglerice has become a major weed in Tennessee cotton and soybean fields. Glyphosate has been relied on to control these accessions over the past two decades, but in recent years cotton and soybean producers have reported junglerice escapes after glyphosate + dicamba and/or clethodim applications. In the growing seasons of 2018 and 2019, a survey was conducted of weed escapes in dicamba-resistant (DR) crops. Junglerice was the most prevalent weed escape in these DR (Roundup Ready Xtend®) cotton and soybean fields in both years of the study. In 2018 and 2019, junglerice was found 76% and 64% of the time in DR cotton and soybean fields, respectively. Progeny from junglerice seeds collected during this survey was screened for glyphosate and clethodim resistance. Seventy percent of the junglerice accessions tested had an effective relative resistance factor to glyphosate of 3.1 to 8.5. In all, 13% of the junglerice accessions could no longer be effectively controlled with glyphosate. This research also showed that all sampled accessions could still be controlled with clethodim in a greenhouse environment, but less control was observed in the field. These data also suggest that another cause for the poor junglerice control is dicamba antagonism of glyphosate and clethodim activity. Nomenclature: Clethodim; dicamba; glyphosate; junglerice [Echinochloa colona (L.) Link]; cotton (Gossypium hirsutum L.); soybean [Glycine max (L.) Merr.]

FoxP3+ regulatory T cells (Tregs) control inflammation and maintain mucosal homeostasis, but their functions during infection are poorly understood. Th1, Th2 and Th17 cells can be identified by master transcription factors (TFs) T-bet, GATA3 and RORγT; Tregs also express these TFs. While T-bet+ Tregs can selectively suppress Th1 cells, it is unclear whether distinct Treg populations can alter Th bias. To address this, we used Salmonella enterica serotype Typhimurium to induce non-lethal colitis. Following infection, we observed an early colonic Th17 response within total CD4 T cells, followed by a Th1 bias. The early Th17 response, which contains both Salmonella-specific and non-Salmonella-specific cells, parallels an increase in T-bet+ Tregs. Later, Th1 cells and RORγT+ Tregs dominate. This reciprocal dynamic may indicate that Tregs selectively suppress Th cells, shaping the immune response. Treg depletion 1-2 days post-infection shifted the early Th17 response to a Th1 bias; however, depletion 6-7 days post-infection abrogated the Th1 bias. Thus, Tregs are necessary for the early Th17 response, and for a maximal Th1 response later. These data show that Tregs shape the overall tissue CD4 T cell response and highlight the potential for subpopulations of Tregs to be used in targeted therapeutic approaches.