Evidence of Differential Prediction of Anxiety and Depression by Diurnal Alpha-Amylase and Cortisol in Development.

Research and theory suggest an important role of neuroendocrine function in emotional development, particularly under conditions of elevated stress. We provide empirical data to clarify associations between alpha-amylase (AA) and cortisol as well as test the differential linkages among AA, cortisol, and symptoms of anxiety, depression, and posttraumatic stress in children. Children recruited from a low-income elevated violence community (n = 100; mean age = 10, SD = 0.64; 79% Latino; 67% received free or reduced lunch) were assessed on diurnal levels of AA and cortisol along with assessments of anxiety, depression, and posttraumatic stress symptoms (PTSS). Elevated anxiety symptoms were associated with steeper linear slopes of AA with higher levels of AA in the morning but lower levels of AA in the evening. Depression was associated with differential cubic trajectories of AA when PTSSs were included in the model. Anxiety also predicted differential cubic diurnal trends in cortisol, such that greater anxiety symptoms were associated with relatively higher levels of cortisol in the evening. Again, depression symptoms when PTSS were included predicted diurnal cubic trends with elevated depression associated with lower awakening and midday cortisol that reversed to higher evening cortisol compared to youth with fewer self-reported depression symptoms.

Program evaluation of a school-based mental health and wellness curriculum featuring yoga and mindfulness.

BACKGROUND: Interest in the effectiveness of mindfulness-based interventions such as yoga in primary schools has grown. Evidence shows promise, as youth who engage in yoga to promote mindfulness show improved coping skills, increased socio-emotional competence and prosocial skills, academic performance, attention span, and ability to deal with stress. OBJECTIVE: This study reports the results of a program evaluation of a universal health and wellness curriculum, Pure Power, designed to teach youth yoga techniques, mindfulness, and emotion regulation. METHODS: A non-randomized comparison design examined outcomes among participants from schools that completed the intervention with highest fidelity of implementation (n = 461) and from students in matched comparison schools (n = 420). Standard measures of coping, emotion regulation and emotion dysregulation, spelling, and math achievement were collected. RESULTS: Analyses suggest the youth in the intervention schools demonstrated relative improvement on measures of emotion regulation, spelling, and math. CONCLUSIONS: Challenges in implementation in real-life settings are vital to identify. The data provide some real-world evidence for the effectiveness of a universal health and wellness curriculum on emotion regulation and positive academic outcomes. Training school staff to deliver the intervention may foster implementation. Future research should test the effectiveness of who delivers the intervention; for example, teacher-delivered groups vs. other wellness personnel.

bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria.

Bacteria have an extensive adaptive ability to live in close association with eukaryotic hosts, exhibiting detrimental, neutral or beneficial effects on host growth and health. However, the genes involved in niche adaptation are mostly unknown and their functions poorly characterized. Here, we present bacLIFE ( https://github.com/Carrion-lab/bacLIFE ) a streamlined computational workflow for genome annotation, large-scale comparative genomics, and prediction of lifestyle-associated genes (LAGs). As a proof of concept, we analyzed 16,846 genomes from the Burkholderia/Paraburkholderia and Pseudomonas genera, which led to the identification of hundreds of genes potentially associated with a plant pathogenic lifestyle. Site-directed mutagenesis of 14 of these predicted LAGs of unknown function, followed by plant bioassays, showed that 6 predicted LAGs are indeed involved in the phytopathogenic lifestyle of Burkholderia plantarii and Pseudomonas syringae pv. phaseolicola. These 6 LAGs encompassed a glycosyltransferase, extracellular binding proteins, homoserine dehydrogenases and hypothetical proteins. Collectively, our results highlight bacLIFE as an effective computational tool for prediction of LAGs and the generation of hypotheses for a better understanding of bacteria-host interactions.

Taxonomic and metabolic diversity of Actinomycetota isolated from faeces of a 28,000-year-old mammoth.

Ancient environmental samples, including permafrost soils and frozen animal remains, represent an archive with microbial communities that have barely been explored. This yet unexplored microbial world is a genetic resource that may provide us with new evolutionary insights into recent genomic changes, as well as novel metabolic pathways and chemistry. Here, we describe Actinomycetota Micromonospora, Oerskovia, Saccharopolyspora, Sanguibacter and Streptomyces species were successfully revived and their genome sequences resolved. Surprisingly, the genomes of these bacteria from an ancient source show a large phylogenetic distance to known strains and harbour many novel biosynthetic gene clusters that may well represent uncharacterised biosynthetic potential. Metabolic profiles of the strains display the production of known molecules like antimycin, conglobatin and macrotetrolides, but the majority of the mass features could not be dereplicated. Our work provides insights into Actinomycetota isolated from an ancient source, yielding unexplored genomic information that is not yet present in current databases.

Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness.

BACKGROUND: Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere microbiome. Here, we studied this remarkable phenomenon for Bipolaris sorokiniana in two wheat cultivars differing in resistance to this fungal root pathogen. RESULTS: The results showed that repeated exposure of the susceptible wheat cultivar to the pathogen led to a significant reduction in disease severity after five successive growth cycles. Surprisingly, the resistant wheat cultivar, initially included as a control, showed the opposite pattern with an increase in disease severity after repeated pathogen exposure. Amplicon analyses revealed that the bacterial families Chitinophagaceae, Anaerolineaceae and Nitrosomonadaceae were associated with disease suppressiveness in the susceptible wheat cultivar; disease suppressiveness in the resistant wheat cultivar was also associated with Chitinophagaceae and a higher abundance of Comamonadaceae. Metagenome analysis led to the selection of 604 Biosynthetic Gene Clusters (BGCs), out of a total of 2,571 identified by AntiSMASH analysis, that were overrepresented when the soil entered the disease suppressive state. These BGCs are involved in the biosynthesis of terpenes, non-ribosomal peptides, polyketides, aryl polyenes and post-translationally modified peptides. CONCLUSION: Combining taxonomic and functional profiling we identified key changes in the rhizosphere microbiome during disease suppression. This illustrates how the host plant relies on the rhizosphere microbiome as the first line of defense to fight soil-borne pathogens. Microbial taxa and functions identified here can be used in novel strategies to control soil-borne fungal pathogens.

Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease.

It is widely known that some soils have strong levels of disease suppression and prevent the establishment of pathogens in the rhizosphere of plants. However, what soils are better suppressing disease, and how management can help us to boost disease suppression remain unclear. Here, we used field, greenhouse and laboratory experiments to investigate the effect of management (monocropping and rotation) on the capacity of rhizosphere microbiomes in suppressing peanut root rot disease. Compared with crop rotations, monocropping resulted in microbial assemblies that were less effective in suppressing root rot diseases. Further, the depletion of key rhizosphere taxa in monocropping, which were at a disadvantage in the competition for limited exudates resources, reduced capacity to protect plants against pathogen invasion. However, the supplementation of depleted strains restored rhizosphere resistance to pathogen. Taken together, our findings highlight the role of native soil microbes in fighting disease and supporting plant health, and indicate the potential of using microbial inocula to regenerate the natural capacity of soil to fight disease.

Microbiome engineering optimized by Antarctic microbiota to support a plant host under water deficit.

Climate change challenges modern agriculture to develop alternative and eco-friendly solutions to alleviate abiotic and/or biotic stresses. The use of soil microbiomes from extreme environments opens new avenues to discover novel microorganisms and microbial functions to protect plants. In this study we confirm the ability of a bioinoculant, generated by natural engineering, to promote host development under water stress. Microbiome engineering was mediated through three factors i) Antarctic soil donation, ii) water deficit and iii) multigenerational tomato host selection. We revealed that tomato plants growing in soils supplemented with Antarctic microbiota were tolerant to water deficit stress after 10 generations. A clear increase in tomato seedling tolerance against water deficit stress was observed in all soils over generations of Host Mediated Microbiome Engineering, being Fildes mixture the most representatives, which was evidenced by an increased survival time, plant stress index, biomass accumulation, and decreased leaf proline content. Microbial community analysis using 16s rRNA gene amplicon sequencing data suggested a microbiome restructuring that could be associated with increased tolerance of water deficit. Additionally, the results showed a significant increase in the relative abundance of Candidatus Nitrosocosmicus and Bacillus spp. which could be key taxa associated with the observed tolerance improvement. We proposed that in situ microbiota engineering through the evolution of three factors (long-standing extreme climate adaption and host and stress selection) could represent a promising strategy for novel generation of microbial inoculants.

Impact of the fungal pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root microbiome.

BACKGROUND: Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective success. If and how invading fungal root pathogens can disrupt microbiome assembly and gene expression is still largely unknown. Here, we investigated the impact of the fungal pathogen Fusarium oxysporum (fox) on the assembly of rhizosphere and endosphere microbiomes of a fox-susceptible and fox-resistant common bean cultivar. RESULTS: Integration of 16S-amplicon, shotgun metagenome as well as metatranscriptome sequencing with community ecology analysis showed that fox infections significantly changed the composition and gene expression of the root microbiome in a cultivar-dependent manner. More specifically, fox infection led to increased microbial diversity, network complexity, and a higher proportion of the genera Flavobacterium, Bacillus, and Dyadobacter in the rhizosphere of the fox-resistant cultivar compared to the fox-susceptible cultivar. In the endosphere, root infection also led to changes in community assembly, with a higher abundance of the genera Sinorhizobium and Ensifer in the fox-resistant cultivar. Metagenome and metatranscriptome analyses further revealed the enrichment of terpene biosynthesis genes with a potential role in pathogen suppression in the fox-resistant cultivar upon fungal pathogen invasion. CONCLUSION: Collectively, these results revealed a cultivar-dependent enrichment of specific bacterial genera and the activation of putative disease-suppressive functions in the rhizosphere and endosphere microbiome of common bean under siege.

Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections.

Soil-borne pathogens pose a major threat to food production worldwide, particularly under global change and with growing populations. Yet, we still know very little about how the soil microbiome regulates the abundance of soil pathogens and their impact on plant health. Here we combined field surveys with experiments to investigate the relationships of soil properties and the structure and function of the soil microbiome with contrasting plant health outcomes. We find that soil acidification largely impacts bacterial communities and reduces the capacity of soils to combat fungal pathogens. In vitro assays with microbiomes from acidified soils further highlight a declined ability to suppress Fusarium, a globally important plant pathogen. Similarly, when we inoculate healthy plants with an acidified soil microbiome, we show a greatly reduced capacity to prevent pathogen invasion. Finally, metagenome sequencing of the soil microbiome and untargeted metabolomics reveals a down regulation of genes associated with the synthesis of sulfur compounds and reduction of key traits related to sulfur metabolism in acidic soils. Our findings suggest that changes in the soil microbiome and disruption of specific microbial processes induced by soil acidification can play a critical role for plant health.

Resilience by design: How nature, nurture, environment, and microbiome mitigate stress and allostatic load.

Resilience to psychological stress is defined as adaption to challenging life experiences and not the absence of adverse life events. Determinants of resilience include personality traits, genetic/epigenetic modifications of genes involved in the stress response, cognitive and behavioral flexibility, secure attachment with a caregiver, social and community support systems, nutrition and exercise, and alignment of circadian rhythm to the natural light/dark cycle. Therefore, resilience is a dynamic and flexible process that continually evolves by the intersection of different domains in human's life; biological, social, and psychological. The objective of this minireview is to summarize the existing knowledge about the multitude factors and molecular alterations that result from resilience to stress response. Given the multiple contributing factors in building resilience, we set out a goal to identify which factors were most supportive of a causal role by the current literature. We focused on resilience-related molecular alterations resulting from mind-body homeostasis in connection with psychosocial and environmental factors. We conclude that there is no one causal factor that differentiates a resilient person from a vulnerable one. Instead, building resilience requires an intricate network of positive experiences and a healthy lifestyle that contribute to a balanced mind-body connection. Therefore, a holistic approach must be adopted in future research on stress response to address the multiple elements that promote resilience and prevent illnesses and psychopathology related to stress allostatic load.

Structural equation modeling of treatment-related changes in neural connectivity for youth with PTSD.

BACKGROUND: Previous studies suggest that improvement in symptoms of posttraumatic stress disorder (PTSD) is accompanied by changes in neural connectivity, however, few studies have investigated directional (effective) connectivity. The current study assesses treatment-related changes in effective connectivity in youth with PTSD undergoing Trauma-Focused Cognitive Behavioral Therapy (TF-CBT). METHODS: Functional MRI scans before and after 16 weeks of TF-CBT for 20 youth with PTSD, or the same time interval for 20 healthy controls (HC) were included in the analysis. Structural equation modeling was used to model group differences in directional connectivity at baseline, and changes in connectivity from pre- to post-treatment. RESULTS: At baseline, the PTSD group, relative to the HC group, had significantly greater connectivity in the path from dorsal cingulate to anterior cingulate and from dorsal cingulate to posterior cingulate corticies. From pre- to post-treatment, connectivity in these paths decreased significantly in the PTSD group, as did connectivity from right hippocampus to left superior temporal gyrus. Connectivity from the left amygdala to the lateral orbital frontal cortex was significantly lower in PTSD vs HC at baseline, but did not change from pre- to post-treatment. CONCLUSION: Although based on a small sample, these results converge with previous studies in suggesting a central role for the dorsal cingulate cortex in PTSD symptoms. The direction of this connectivity suggests that the dorsal cingulate is the source of modulation of anterior and posterior cingulate cortex during trauma-focused cognitive behavioral therapy.

Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning.

Bacteroidetes are prevalent in soil ecosystems and are associated with various eukaryotic hosts, including plants, animals, and humans. The ubiquity and diversity of Bacteroidetes exemplify their impressive versatility in niche adaptation and genomic plasticity. Over the past decade, a wealth of knowledge has been obtained on the metabolic functions of clinically relevant Bacteroidetes, but much less attention has been given to Bacteroidetes living in close association with plants. To improve our understanding of the functional roles of Bacteroidetes for plants and other hosts, we review the current knowledge of their taxonomy and ecology, in particular their roles in nutrient cycling and host fitness. We highlight their environmental distribution, stress resilience, genomic diversity, and functional importance in diverse ecosystems, including, but not limited to, plant-associated microbiomes.

baseLess: lightweight detection of sequences in raw MinION data.

Summary: With its candybar form factor and low initial investment cost, the MinION brought affordable portable nucleic acid analysis within reach. However, translating the electrical signal it outputs into a sequence of bases still requires mid-tier computer hardware, which remains a caveat when aiming for deployment of many devices at once or usage in remote areas. For applications focusing on detection of a target sequence, such as infectious disease monitoring or species identification, the computational cost of analysis may be reduced by directly detecting the target sequence in the electrical signal instead. Here, we present baseLess, a computational tool that enables such target-detection-only analysis. BaseLess makes use of an array of small neural networks, each of which efficiently detects a fixed-size subsequence of the target sequence directly from the electrical signal. We show that baseLess can accurately determine the identity of reads between three closely related fish species and can classify sequences in mixtures of 20 bacterial species, on an inexpensive single-board computer. Availability and implementation: baseLess and all code used in data preparation and validation are available on Github at https://github.com/cvdelannoy/baseLess, under an MIT license. Used validation data and scripts can be found at https://doi.org/10.4121/20261392, under an MIT license. Supplementary information: Supplementary data are available at Bioinformatics Advances online.

Cortical activation predicts posttraumatic improvement in youth treated with TF-CBT or CCT.

BACKGROUND: Identifying neural activation patterns that predict youths' treatment response may aid in the development of imaging-based assessment of emotion dysregulation following trauma and foster tailored intervention. Changes in cortical hemodynamic activity measured with functional near-infrared spectroscopy (fNIRS) may provide a time and cost-effective option for such work. We examined youths' PTSD symptom change following treatment and tested if previously identified activation patterns would predict treatment response. METHODS: Youth (N = 73, mean age = 12.97, SD = 3.09 years) were randomly assigned to trauma-focused cognitive behavioral therapy (TF-CBT), cue-centered therapy (CCT), or treatment as usual (TAU). Parents and youth reported on youth's PTSD symptoms at pre-intervention, post-intervention, and follow-up. Neuroimaging data (N = 31) assessed at pre-intervention were obtained while youth engaged in an emotion expression task. Treatment response slopes were calculated for youth's PTSD symptoms. RESULTS: Overall, PTSD symptoms decreased from pre-intervention through follow-up across conditions, with some evidence of relative benefit of TF-CBT and CCT over TAU but significant individual variation in treatment response. Cortical activation patterns were correlated with PTSD symptom improvement slopes (r = 0.53). In particular, cortical responses to fearful and neutral facial stimuli in six fNIRS channels in the bilateral dlPFC were important predictors of PTSD symptom improvement. CONCLUSIONS: The use of fNIRS provides a method of monitoring and assessing cortical activation patterns in a relatively inexpensive and portable manner. Associations between functional activation and youths' PTSD symptoms improvement may be a promising avenue for understanding emotion dysregulation in clinical populations.

Impact of anxiety and depression on academic achievement among underserved school children: evidence of suppressor effects.

Anxiety and depression symptoms may leave children at risk for lower academic scores, though this unique linkage to academic achievement in underserved youth is less well established. This study aimed to examine how anxiety and depression are uniquely related to spelling and math achievement beyond attention and hyperactivity deficits in children in underserved schools. Children aged 8 to 11 (n = 1085, 47.3% female) from historically underserved groups (Hispanic 75.3%, American Indian 6.4%, Black 4.9%, and White 1.5%) from 13 schools across two public school districts in California participated in the assessment of emotional and behavioral health symptoms that included a spelling and math assessment. While there was no relationship between anxiety or hyperactivity on spelling and math scores, depression and attention problems were significantly negatively related to spelling and math scores. However, when entered simultaneously, evidence of suppressor effects emerged. Anxiety and hyperactivity both became positively predictive of math. Similarly, anxiety became positively predictive of spelling. Subsample analyses showed that these suppressor effects were only in females. The associations among anxiety, depression, attention, and hyperactivity with spelling and math achievement are complex, and when controlling for depression and attention, anxiety levels and hyperactivity may be motivating some level of achievement in these areas.

Disentangling the genetic basis of rhizosphere microbiome assembly in tomato.

Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, we map the molecular features of the rhizosphere microbiome as quantitative traits of a diverse hybrid population of wild and domesticated tomato. Gene content analysis of prioritized tomato quantitative trait loci suggests a genetic basis for differential recruitment of various rhizobacterial lineages, including a Streptomyces-associated 6.31 Mbp region harboring tomato domestication sweeps and encoding, among others, the iron regulator FIT and the water channel aquaporin SlTIP2.3. Within metagenome-assembled genomes of root-associated Streptomyces and Cellvibrio, we identify bacterial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associates with specific tomato QTLs. By integrating 'microbiomics' and quantitative plant genetics, we pinpoint putative plant and reciprocal rhizobacterial traits underlying microbiome assembly, thereby providing a first step towards plant-microbiome breeding programs.

System-Wide Analysis of the GATC-Binding Nucleoid-Associated Protein Gbn and Its Impact on Streptomyces Development.

Bacterial chromosome structure is, to a great extent, organized by a diverse group of proteins collectively referred to as nucleoid-associated proteins (NAPs). Many NAPs have been well studied in Streptomyces, including Lsr2, HupA, HupS, and sIHF. Here, we show that SCO1839 represents a novel family of Actinobacteria NAPs and recognizes a consensus sequence consisting of GATC followed by (A/T)T. The protein, which is expressed in particular during sporulation, was designated Gbn for GATC-binding NAP. Deletion of gbn led to alterations in development and antibiotic production in Streptomyces coelicolor. Chromatin immunoprecipitation sequencing (ChIP-Seq) detected more than 2,800 binding regions, encompassing around 3,600 GATCWT motifs. This amounts to 55% of all such sequences in the S. coelicolor genome. DNA binding of Gbn in vitro minimally changes DNA conformation, suggesting a modest role in chromosome organization only, in addition to a gene regulatory role. Transcriptomics analysis showed that Gbn binding generally leads to reduced gene expression. The DNA binding profiles were nearly identical between vegetative and aerial growth. Exceptions are SCO1311 and SCOt32, for a tRNA editing enzyme and a tRNA that recognizes the rare leucine codon CUA, respectively, which nearly exclusively bound during vegetative growth. Taken together, our data show that Gbn is a highly pleiotropic NAP that impacts growth and development in streptomycetes. IMPORTANCE A large part of the chemical space of bioactive natural products is derived from Actinobacteria. Many of the biosynthetic gene clusters for these compounds are cryptic; in others words, they are expressed in nature but not in the laboratory. Understanding the global regulatory networks that control gene expression is key to the development of approaches to activate this biosynthetic potential. Chromosome structure has a major impact on the control of gene expression in eukaryotes. In bacteria, the organization of chromosome structure is mediated by multiple factors, including macromolecular biophysics processes, biological processes, and, more importantly, a diverse group of proteins referred to collectively as nucleoid-associated proteins (NAPs). We here present the discovery of a novel and extremely pleiotropic NAP, which we refer to as Gbn. Gbn is an Actinobacteria-specific protein that binds to GATC sequences, with a subtle but broad effect on global gene expression, especially during the late developmental stage. The discovery of Gbn is a new step toward better understanding of how gene expression and chromosome structure are governed in antibiotic-producing streptomycetes.

A school-based health and mindfulness curriculum improves children's objectively measured sleep: a prospective observational cohort study.

STUDY OBJECTIVES: Poor sleep impedes children's cognitive, emotional, and psychosocial development. Pediatric sleep dysregulation is common, and children who live in communities of low socioeconomic status experience additional risk factors for short sleep duration and poor sleep quality. School-based training in mindfulness and yoga-informed practices can improve children's behavior and well-being, but effects on objectively measured sleep are unknown. METHODS: Effects of a school-based health and mindfulness curriculum, which taught practices such as paced breathing, on sleep and stress were examined in 115 children (49 girls, ages 8 to 11 at baseline). Fifty-eight children in a community of low socioeconomic status received the curriculum twice weekly for 2 years. Fifty-seven children in a socioeconomic status-matched community engaged in their usual physical education class instead. In-home ambulatory polysomnography and perceived social stress were measured in all children at 3 time points: at baseline (ie, prior to curriculum exposure) and at 2 yearly follow-ups. RESULTS: Children receiving the curriculum gained an average of 74 minutes of total sleep time, and 24 minutes of rapid eye movement sleep, per night over the 2-year study period. Children not receiving the curriculum experienced a decrease in total sleep time averaging 64 minutes per night, with no changes in rapid eye movement sleep. Sleep improved within the first 3 months of curriculum exposure, in a dose-dependent fashion. Higher curriculum engagement (eg, using the breathing exercises outside of class) was associated with larger gains in total and rapid eye movement sleep duration. Aggregate within-group changes in social stress were not significant. However, among children receiving the curriculum, those who experienced larger gains in total and rapid eye movement sleep duration also experienced larger increases in perceived social stress. CONCLUSIONS: A school-based health and mindfulness curriculum improved children's objectively measured sleep over 2 years. Social stress did not mediate these effects; instead, mindfulness training may have increased awareness of environmental stressors, while developing tools to reduce stress vulnerability. CITATION: Chick CF, Singh A, Anker LA, et al. A school-based health and mindfulness curriculum improves children's objectively measured sleep: a prospective observational cohort study. J Clin Sleep Med. 2022;18(9):2261-2271.