Integration of Phenotypes in Microbiome Networks for Designing Synthetic Communities: a Study of Mycobiomes in the Grafted Tomato System.

Understanding factors influencing microbial interactions, and designing methods to identify key taxa that are candidates for synthetic communities, or SynComs, are complex challenges for achieving microbiome-based agriculture. Here, we study how grafting and the choice of rootstock influences root-associated fungal communities in a grafted tomato system. We studied three tomato rootstocks (BHN589, RST-04-106, and Maxifort) grafted to a BHN589 scion and profiled the fungal communities in the endosphere and rhizosphere by sequencing the internal transcribed spacer (ITS2). The data provided evidence for a rootstock effect (explaining ~2% of the total captured variation, P < 0.01) on the fungal community. Moreover, the most productive rootstock, Maxifort, supported greater fungal species richness than the other rootstocks or controls. We then constructed a phenotype-operational taxonomic unit (OTU) network analysis (PhONA) using an integrated machine learning and network analysis approach based on fungal OTUs and associated tomato yield as the phenotype. PhONA provides a graphical framework to select a testable and manageable number of OTUs to support microbiome-enhanced agriculture. We identified differentially abundant OTUs specific to each rootstock in both endosphere and rhizosphere compartments. Subsequent analyses using PhONA identified OTUs that were directly associated with tomato fruit yield and others that were indirectly linked to yield through their links to these OTUs. Fungal OTUs that are directly or indirectly linked with tomato yield may represent candidates for synthetic communities to be explored in agricultural systems. IMPORTANCE The realized benefits of microbiome analyses for plant health and disease management are often limited by the lack of methods to select manageable and testable synthetic microbiomes. We evaluated the composition and diversity of root-associated fungal communities from grafted tomatoes. We then constructed a phenotype-OTU network analysis (PhONA) using these linear and network models. By incorporating yield data in the network, PhONA identified OTUs that were directly predictive of tomato yield and others that were indirectly linked to yield through their links to these OTUs. Follow-up functional studies of taxa associated with effective rootstocks, identified using approaches such as PhONA, could support the design of synthetic fungal communities for microbiome-based crop production and disease management. The PhONA framework is flexible for incorporation of other phenotypic data, and the underlying models can readily be generalized to accommodate other microbiome or 'omics data.

Biopsychosocial Factors Associated With Attention Problems in Children After Traumatic Brain Injury: A Systematic Review.

OBJECTIVE: The aim of this review was to examine biopsychosocial factors associated with an increased risk of attention problems after a traumatic brain injury in children. DESIGN: A systematic review of the literature was conducted using data sources of MEDLINE, PsycINFO, and CINAHL up to August 30, 2020. Literature primarily examined pediatric patients with traumatic brain injury and attention problems. Risk factors for attention problems posttraumatic brain injury examined in all articles were identified and grouped into broad categories of biological, psychological, and social factors. Methodological quality of each study was assessed using the modified Downs and Black checklist. Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines from 2009 were used in completing this review. RESULTS: Forty articles met inclusion criteria for this study. Overall findings were mixed but suggested that younger age at injury, presence of preinjury attention-deficit/hyperactivity disorder, poorer preinjury adaptive functioning, lower socioeconomic status, and poorer family functioning were associated with increased risk of developing attention problems posttraumatic brain injury. CONCLUSIONS: Development of attention problems after pediatric traumatic brain injury is complex and influenced by an array of biologic, environmental/social, injury-related, and host factors. Evidence is mixed, and further study is needed to better understand the relationships between these factors and how they influence attention after traumatic brain injury. Nonetheless, screening for attention problems in children with risk factors may allow for earlier identification and intervention, minimizing negative impacts of attention problems after traumatic brain injury in children. Limitations of this study included heterogeneity of studies and overall low to moderate methodological quality of studies included as measured by the modified Downs and Black checklist. TO CLAIM CME CREDITS: Complete the self-assessment activity and evaluation online at http://www.physiatry.org/JournalCME. CME OBJECTIVES: Upon completion of this article, the reader should be able to: (1) Describe the importance of recognizing and identifying attention problems after traumatic brain injury in children; (2) Identify risk factors for development of attention problems after pediatric traumatic brain injury; and (3) Recognize gaps in existing literature regarding predictors of attention problems after pediatric traumatic brain injury. LEVEL: Advanced. ACCREDITATION: The Association of Academic Physiatrists is accredited by the Accreditation Council for Continuing Medical Education to provide continuing medical education for physicians.The Association of Academic Physiatrists designates this journal-based CME activity for a maximum of 1.0 AMA PRA Category 1 Credit(s)™. Physicians should only claim credit commensurate with the extent of their participation in the activity.

Rootstocks Shape the Rhizobiome: Rhizosphere and Endosphere Bacterial Communities in the Grafted Tomato System.

Root-associated microbes are critical to plant health and performance, although understanding of the factors that structure these microbial communities and the theory to predict microbial assemblages are still limited. Here, we use a grafted tomato system to study the effects of rootstock genotypes and grafting in endosphere and rhizosphere microbiomes that were evaluated by sequencing 16S rRNA. We compared the microbiomes of nongrafted tomato cultivar BHN589, self-grafted BHN589, and BHN589 grafted to Maxifort or RST-04-106 hybrid rootstocks. Operational taxonomic unit (OTU)-based bacterial diversity was greater in Maxifort compared to the nongrafted control, whereas bacterial diversity in the controls (self-grafted and nongrafted) and the other rootstock (RST-04-106) was similar. Grafting itself did not affect bacterial diversity; diversity in the self-graft was similar to that of the nongraft. Bacterial diversity was higher in the rhizosphere than in the endosphere for all treatments. However, despite the lower overall diversity, there was a greater number of differentially abundant OTUs (DAOTUs) in the endosphere, with the greatest number of DAOTUs associated with Maxifort. In a permutational multivariate analysis of variance (PERMANOVA), there was evidence for an effect of rootstock genotype on bacterial communities. The endosphere-rhizosphere compartment and study site explained a high percentage of the differences among bacterial communities. Further analyses identified OTUs responsive to rootstock genotypes in both the endosphere and rhizosphere. Our findings highlight the effects of rootstocks on bacterial diversity and composition. The influence of rootstock and plant compartment on microbial communities indicates opportunities for the development of designer communities and microbiome-based breeding to improve future crop production.IMPORTANCE Understanding factors that control microbial communities is essential for designing and supporting microbiome-based agriculture. In this study, we used a grafted tomato system to study the effect of rootstock genotypes and grafting on bacterial communities colonizing the endosphere and rhizosphere. To compare the bacterial communities in control treatments (nongrafted and self-grafted plants) with the hybrid rootstocks used by farmers, we evaluated the effect of rootstocks on overall bacterial diversity and composition. These findings indicate the potential for using plant genotype to indirectly select bacterial taxa. In addition, we identify taxa responsive to each rootstock treatment, which may represent candidate taxa useful for biocontrol and in biofertilizers.

Secondary Attention-Deficit/Hyperactivity Disorder in Children and Adolescents 5 to 10 Years After Traumatic Brain Injury.

Importance: After traumatic brain injury (TBI), children often experience impairment when faced with tasks and situations of increasing complexity. Studies have failed to consider the potential for attention problems to develop many years after TBI or factors that may predict the development of secondary attention-deficit/hyperactivity disorder (SADHD). Understanding these patterns will aid in timely identification of clinically significant problems and appropriate initiation of treatment with the hope of limiting additional functional impairment. Objective: To examine the development of SADHD during the 5 to 10 years after TBI and individual (sex, age at injury, and injury characteristics) and environmental (socioeconomic status and family functioning) factors that may be associated with SADHD. Design, Setting, and Participants: Concurrent cohort/prospective study of children aged 3 to 7 years hospitalized overnight for TBI or orthopedic injury (OI; used as control group) who were screened at 3 tertiary care children's hospitals and 1 general hospital in Ohio from January 2003 to June 2008. Parents completed assessments at baseline (0-3 months), 6 months, 12 months, 18 months, 3.4 years, and 6.8 years after injury. A total of 187 children and adolescents were included in the analyses: 81 in the TBI group and 106 in the OI group. Main Outcomes and Measures: Diagnosis of SADHD was the primary outcome. Assessments were all completed by parents. Secondary ADHD was defined as an elevated T score on the DSM-Oriented Attention-Deficit/Hyperactivity Problems Scale of the parent-reported Child Behavior Checklist, report of an ADHD diagnosis, and/or current treatment with stimulant medication not present at the baseline assessment. The Family Assessment Device-Global Functioning measurement was used to assess family functioning; scores ranged from 1 to 4, with greater scores indicating poorer family functioning. Results: The analyzed sample included 187 children with no preinjury ADHD. Mean (SD) age was 5.1 (1.1) years; 108 (57.8%) were male, and 50 (26.7%) were of nonwhite race/ethnicity. Of the 187 children, 48 (25.7%) met our definition of SADHD. Severe TBI (hazard ratio [HR], 3.62; 95% CI, 1.59-8.26) was associated with SADHD compared with the OI group. Higher levels of maternal education (HR, 0.33; 95% CI, 0.17-0.62) were associated with a lower risk of SADHD. Family dysfunction was associated with increased risk of SADHD within the TBI group (HR, 4.24; 95% CI, 1.91-9.43), with minimal association within the OI group (HR, 1.32; 95% CI, 0.36-4.91). Conclusions and Relevance: Early childhood TBI was associated with increased risk for SADHD. This finding supports the need for postinjury monitoring for attention problems. Consideration of factors that may interact with injury characteristics, such as family functioning, will be important in planning clinical follow-up of children with TBI.

Demonstration of an Integrated Pest Management Program for Wheat in Tajikistan.

Wheat is an important food security crop in central Asia but frequently suffers severe damage and yield losses from insect pests, pathogens, and weeds. With funding from the United States Agency for International Development, a team of scientists from three U.S. land-grant universities in collaboration with the International Center for Agricultural Research in Dry Areas and local institutions implemented an integrated pest management (IPM) demonstration program in three regions of Tajikistan from 2011 to 2014. An IPM package was developed and demonstrated in farmer fields using a combination of crop and pest management techniques including cultural practices, host plant resistance, biological control, and chemical approaches. The results from four years of demonstration/research indicated that the IPM package plots almost universally had lower pest abundance and damage and higher yields and were more profitable than the farmer practice plots. Wheat stripe rust infestation ranged from 30% to over 80% in farmer practice plots, while generally remaining below 10% in the IPM package plots. Overall yield varied among sites and years but was always at least 30% to as much as 69% greater in IPM package plots. More than 1,500 local farmers-40% women-were trained through farmer field schools and field days held at the IPM demonstration sites. In addition, students from local agricultural universities participated in on-site data collection. The IPM information generated by the project was widely disseminated to stakeholders through peer-reviewed scientific publications, bulletins and pamphlets in local languages, and via Tajik national television.

Design and synthesis of a crosslinker for studying intracellular steroid trafficking pathways.

A crosslinker was designed and synthesized as a molecular tool for potential use in probing the intracellular trafficking pathways of steroids. The design was guided by computational modeling based upon a model for the transfer of cholesterol between two proteins, NPC1 and NPC2. These proteins play critical roles in the transport of low-density lipoprotein-derived cholesterol from the lumen of lysosomes to other subcellular compartments. Two modified cholesterol residues were covalently joined by a tether based on molecular modeling of the transient interaction of NPC1 and NPC2 during the transfer of cholesterol from the binding site of one of these proteins to the other. With two cholesterol molecules appropriately connected, we hypothesize that the cholesterol binding sites of both proteins will be simultaneously occupied in a manner that will stabilize the protein-protein interaction to permit detailed structural analysis of the resulting complex. A photoaffinity label has also been introduced into one of the cholesterol cores to permit covalent attachment of one of the units into its respective protein-binding pocket. The basic design of these crosslinkers should render them useful for examining interactions of the NPC1/NPC2 pair as well as other sterol transport proteins.

Effect of Cultivation and Timing of Nitrogen Fertilization on Large Patch Disease of Zoysiagrass.

Large patch of zoysiagrass (Zoysia spp.) is caused by Rhizoctonia solani anastomosis group 2-2 LP. The effects of summer cultivation (core-aerification, verticutting, and sand topdressing) and spring and fall versus summer nitrogen (N) fertilization on large patch in fairway height 'Meyer' zoysiagrass were investigated from 2008 to 2011 in Manhattan, Haysville, and Olathe, KS. Disease was assessed by measuring patch diameters or analyzing digital images of affected plot areas to determine the percentage of non-green turfgrass within patches. Cultivation did not affect thatch temperature, soil temperature, soil water content, or turf recovery from large patch in early summer. Furthermore, cultivation did not result in overall significant reductions in patch diameters or average weekly rate of patch diameter increase among plots at the three experimental locations. In some site-year combinations, spring and fall N fertility was associated with lower percentages of non-green turf within affected plot areas in Manhattan and Haysville. In some cases, applications of N during spring and fall may alleviate large patch symptoms.

Pseudomonas syringae two-component response regulator RhpR regulates promoters carrying an inverted repeat element.

The two-component system RhpRS was identified in Pseudomonas syringae as a regulator of the genes encoding the type III secretion system and type III effector proteins (together called the T3 genes). In the absence of the sensor kinase RhpS, the response regulator RhpR represses the induction of the T3 gene regulatory cascade consisting of hrpRS, hrpL, and the T3 genes in a phosphorylation-dependent manner. The repressor activity of RhpR is inhibited by RhpS, which presumably acts as a phosphatase under the T3 gene inducing conditions. Here, we show that RhpR binds and induces its own promoter in a phosphorylation-dependent manner. Deletion and mutagenesis analyses revealed an inverted repeat (IR) element, GTATC-N(6)-GATAC, in the rhpR promoter that confers the RhpR-dependent induction. Computational search of the P. syringae genomes for the putative IR elements and Northern blot analysis of the genes with a putative IR element in the promoter region uncovered five genes that were upregulated and two genes that were downregulated in an RhpR-dependent manner. Two genes that were strongly induced by RhpR were assayed for the IR element activity in gene regulation and, in both cases, the IR element mediated the RhpR-dependent gene induction. Chromatin immunoprecipitation assays indicated that RhpR binds the promoters containing a putative IR element but not the hrpR and hrpL promoters that do not have an IR element, suggesting that RhpR indirectly regulates the transcriptional cascade of hrpRS, hrpL, and the T3 genes.

Evidence that prohexadione-calcium induces structural resistance to fire blight infection.

Mechanisms of fire blight control by the shoot-growth regulator prohexadione-calcium (ProCa) were investigated by comparing disease development in ProCa-treated potted apple trees (cv. Gala) to paclobutrazol (another shoot-growth regulator)-treated and nontreated trees and in ProCa-treated cv. McIntosh trees in the field. Twenty-eight days after inoculation with Erwinia amylovora Ea110, disease incidence on ProCa- and paclobutrazol-treated shoots was significantly reduced compared with that on nontreated shoots. Disease severity (percent shoot length infected) was also significantly lower on both ProCa- and paclobutrazol-treated shoots than on nontreated shoots. However, bacterial populations within inoculated shoots were high and bacterial growth occurred in all treatments. In addition, the mean cell wall width of the cortical parenchyma midvein tissue of the first and second youngest unfolded leaves of ProCa- and paclobutrazol-treated shoots was significantly wider both 0.5 and 2 cm from the leaf tips compared with the cell walls of the nontreated tissue. Taken together, these results suggest that reduction of fire blight symptoms by ProCa and paclobutrazol is not the result of reduced populations of E. amylovora in shoots. Moreover, because paclobutrazol also reduced disease severity and incidence, changes in flavonoid metabolism induced by ProCa but not paclobutrazol does not appear to be responsible for disease control as suggested in recent literature. Finally, although this study did not directly link disease control to the observed cell wall changes, the possibility that an increase in cell wall width impedes the spread of E. amylovora should be investigated in more depth.

Primary Infection, Lesion Productivity, and Survival of Sporangia in the Grapevine Downy Mildew Pathogen Plasmopara viticola.

ABSTRACT Several aspects of grapevine downy mildew epidemiology that are fundamental to model predictions were investigated. Simple rainfall-, temperature-, and phenology-based thresholds (rain > 2.5 mm; temperature > 11 degrees C; and phenology > Eichorn and Lorenz [E&L] growth stage 12) were evaluated to forecast primary (oosporic) infection by Plasmopara viticola. The threshold was consistent across 15 years of historical data on the highly susceptible cv. Chancellor at one site, and successfully predicted the initial outbreak of downy mildew for 2 of 3 years at three additional sites. Field inoculations demonstrated that shoot tissue was susceptible to infection as early as E&L stage 5, suggesting that initial germination of oospores, rather than acquisition of host susceptibility, was probably the limiting factor in the initiation of disease outbreaks. We also found that oospores may continue to germinate and cause infections throughout the growing season, in contrast to the widely-held assumption that the supply of oospores is depleted shortly after bloom. Lesion productivity (sporangia/lesion) did not decline with age of a lesion in the absence of suitable weather to induce sporulation. However, the productivity of all lesions declined rapidly through repeated cycles of sporulation. Extremely high temperatures (i.e., one day reaching 42.8 degrees C) had an eradicative effect under vineyard conditions, and permanently reduced sporulation from existing (but not incubating) lesions to trace levels, despite a later return to weather conducive to sporulation. In fair weather, most sporangia died sometime during the daylight period immediately following their production. However, over 50% of sporangia still released zoospores after 12 to 24 h of exposure to overcast conditions.

Vapor Activity and Systemic Movement of Mefenoxam Control Grapevine Downy Mildew.

Metalaxyl is translocated from roots to leaves to control a number of oomycete pathogens, but systemic movement from vegetative organs into fruit and vapor activity against Plasmopara viticola, the causal agent of grapevine downy mildew, has not been examined experimentally. We inoculated fruit clusters of grapevines with P. viticola at prebloom, bloom, or 1 week postbloom. We then selectively applied mefenoxam (288 mg/liter), the active enantiomer of metalaxyl, to the leaves or stem tissue 12 to 48 h after inoculation. Little to no downy mildew developed on fruit when mefenoxam was applied to leaf tissue, stem tissue, or both. In contrast, downy mildew symptoms were severe on inoculated clusters on untreated shoots. When potential vapor activity was blocked, we observed fungicidal activity on seedling foliage in response to apparent systemic movement from treated stems and soil, but not from leaves. However, when vapor activity was permitted, mefenoxam residues on treated leaves controlled disease on other, untreated leaves. In subsequent vineyard experiments, vapor and systemic activity provided equivalent and near-complete suppression of downy mildew on clusters 48 h post inoculation. Furthermore, inoculated grape seedlings that were placed near mefenoxam-treated seedlings in open and closed systems developed nil to trace levels of downy mildew compared with controls, further indicating that the material has strong vapor activity.

Seasonal development of ontogenic resistance to downy mildew in grape berries and rachises.

ABSTRACT Clusters of Vitis vinifera and V. labrusca are reported to become resistant to Plasmopara viticola at stages of development ranging from 1 to 6 weeks postbloom. It has been suggested that resistance is associated with loss of the infection court as stomata are converted to lenticels, but the time of onset, cultivar variation, and seasonal variation in ontogenic resistance has remained uncertain, as has the comparative susceptibility of stem tissue within the fruit cluster. In New York, we inoculated clusters of V. vinifera cvs. Chardonnay and Riesling and V. labrusca cvs. Concord and Niagara at stages from prebloom until 5 to 6 weeks postbloom. Berries were infected and supported profuse sporulation until 2 weeks postbloom, and pedicel tissue remained susceptible until 4 weeks postbloom. Although berries on later-inoculated clusters failed to support sporulation, discoloration and necrosis of berry tissues was often noted, and necrosis of the pedicel within such clusters often led to further discoloration, shriveling, reduced size, or loss of berries. When the epidermis of discolored berries that initially failed to support sporulation was cut, the pathogen emerged and sporulated through incisions, indicating that lack of sporulation on older symptomatic berries was due to infection at an early stage of berry development followed by conversion of functional stomata to lenticels during latency. We repeated the study on Chardonnay and Riesling vines in South Australia and found that the period of berry and rachis susceptibility was greatly increased. The protracted susceptibility of the host was related to the increased duration and phenological heterogeneity of bloom and berry development in the warmer climate of South Australia. The time of onset and subsequent expression of ontogenic resistance to P. viticola may thus be modified by climate and should be weighed in transposing results from one climatic area to another. Our results can be used to refine forecast models for grapevine downy mildew to account for changes in berry and rachis susceptibility, and to focus fungicide application schedules upon the most critical periods for protection of fruit.