Correction: Towards identification of postharvest fruit quality transcriptomic markers in Malus domestica.

[This corrects the article DOI: 10.1371/journal.pone.0297015.].

Towards identification of postharvest fruit quality transcriptomic markers in Malus domestica.

Gene expression is highly impacted by the environment and can be reflective of past events that affected developmental processes. It is therefore expected that gene expression can serve as a signal of a current or future phenotypic traits. In this paper we identify sets of genes, which we call Prognostic Transcriptomic Biomarkers (PTBs), that can predict firmness in Malus domestica (apple) fruits. In apples, all individuals of a cultivar are clones, and differences in fruit quality are due to the environment. The apples transcriptome responds to these differences in environment, which makes PTBs an attractive predictor of future fruit quality. PTBs have the potential to enhance supply chain efficiency, reduce crop loss, and provide higher and more consistent quality for consumers. However, several questions must be addressed. In this paper we answer the question of which of two common modeling approaches, Random Forest or ElasticNet, outperforms the other. We answer if PTBs with few genes are efficient at predicting traits. This is important because we need few genes to perform qPCR, and we answer the question if qPCR is a cost-effective assay as input for PTBs modeled using high-throughput RNA-seq. To do this, we conducted a pilot study using fruit texture in the 'Gala' variety of apples across several postharvest storage regiments. Fruit texture in 'Gala' apples is highly controllable by post-harvest treatments and is therefore a good candidate to explore the use of PTBs. We find that the RandomForest model is more consistent than an ElasticNet model and is predictive of firmness (r2 = 0.78) with as few as 15 genes. We also show that qPCR is reasonably consistent with RNA-seq in a follow up experiment. Results are promising for PTBs, yet more work is needed to ensure that PTBs are robust across various environmental conditions and storage treatments.

Dramatic Response to Anti-IL-6 Receptor Therapy in Children With Life-Threatening Myelin Oligodendrocyte Glycoprotein-Associated Disease.

OBJECTIVES: Myelin oligodendrocyte glycoprotein antibody-associated disease (MOGAD) is an immune-mediated neuroinflammatory disorder leading to demyelination of the CNS. Interleukin (IL)-6 receptor blockade is under study in relapsing MOGAD as a preventative strategy, but little is known about the role of such treatment for acute MOGAD attacks. METHODS: We discuss the cases of a 7-year-old boy and a 15-year-old adolescent boy with severe acute CNS demyelination and malignant cerebral edema with early brain herniation associated with clearly positive serum titers of MOG-IgG, whose symptoms were incompletely responsive to standard acute therapies (high-dose steroids, IV immunoglobulins (IVIGs), and therapeutic plasma exchange). RESULTS: Both boys improved quickly with IL-6 receptor inhibition, administered as tocilizumab. Both patients have experienced remarkable neurologic recovery. DISCUSSION: We propose that IL-6 receptor therapies might also be considered in acute severe life-threatening presentations of MOGAD.

Transcriptomic approach to uncover dynamic events in the development of mid-season sunburn in apple fruit.

Apples grown in high heat, high light, and low humidity environments are at risk for sun injury disorders like sunburn and associated crop losses. Understanding the physiological and molecular mechanisms underlying sunburn will support improvement of mitigation strategies and breeding for more resilient varieties. Numerous studies have highlighted key biochemical processes involved in sun injury, such as the phenylpropanoid and reactive oxygen species (ROS) pathways, demonstrating both enzyme activities and expression of related genes in response to sunburn conditions. Most previous studies have focused on at-harvest activity of a small number of genes in response to heat stress. Thus, it remains unclear how stress events earlier in the season affect physiology and gene expression. Here, we applied heat stress to mid-season apples in the field and collected tissue along a time course-24, 48, and 72 h following a heat stimulus-to investigate dynamic gene expression changes using a transcriptomic lens. We found a relatively small number of differentially expressed genes (DEGs) and enriched functional terms in response to heat treatments. Only a few of these belonged to pathways previously described to be involved in sunburn, such as the AsA-GSH pathway, while most DEGs had not yet been implicated in sunburn or heat stress in pome fruit.

Building a foundation for gene family analysis in Rosaceae genomes with a novel workflow: A case study in Pyrus architecture genes.

The rapid development of sequencing technologies has led to a deeper understanding of plant genomes. However, direct experimental evidence connecting genes to important agronomic traits is still lacking in most non-model plants. For instance, the genetic mechanisms underlying plant architecture are poorly understood in pome fruit trees, creating a major hurdle in developing new cultivars with desirable architecture, such as dwarfing rootstocks in European pear (Pyrus communis). An efficient way to identify genetic factors for important traits in non-model organisms can be to transfer knowledge across genomes. However, major obstacles exist, including complex evolutionary histories and variable quality and content of publicly available plant genomes. As researchers aim to link genes to traits of interest, these challenges can impede the transfer of experimental evidence across plant species, namely in the curation of high-quality, high-confidence gene models in an evolutionary context. Here we present a workflow using a collection of bioinformatic tools for the curation of deeply conserved gene families of interest across plant genomes. To study gene families involved in tree architecture in European pear and other rosaceous species, we used our workflow, plus a draft genome assembly and high-quality annotation of a second P. communis cultivar, 'd'Anjou.' Our comparative gene family approach revealed significant issues with the most recent 'Bartlett' genome - primarily thousands of missing genes due to methodological bias. After correcting assembly errors on a global scale in the 'Bartlett' genome, we used our workflow for targeted improvement of our genes of interest in both P. communis genomes, thus laying the groundwork for future functional studies in pear tree architecture. Further, our global gene family classification of 15 genomes across 6 genera provides a valuable and previously unavailable resource for the Rosaceae research community. With it, orthologs and other gene family members can be easily identified across any of the classified genomes. Importantly, our workflow can be easily adopted for any other plant genomes and gene families of interest.

Radon-222 Charcoal Canister Steady State Model Calibrations Performed in a Highly Controlled Environmental Chamber and a Natural Indoor Environment.

ABSTRACT: Charcoal canisters are a common method of 222 Rn screening. The calibrations of different batches of activated charcoal used in different canister designs are typically performed in large volume controlled environmental chambers with known and controlled radon concentration, temperature, and humidity. Radon screening could be facilitated in locations without ready access to environmental chambers if canisters could be accurately calibrated and undergo quality control in less controlled environments. This study compares charcoal canister calibrations from a highly controlled radon chamber with calibrations from a basement storage area experiencing temporally varying radon. In addition, the impacts of exposure time and spectral region of interest selection on calibration accuracy are investigated by comparing calibrations calculated using three different choices. Approximately 30 mo after calibrations were completed, groups of canisters were exposed for different durations of time to investigate measurement accuracy and calibration validity over an extended time. A digital simulation of charcoal canister kinetics was also performed to establish limits on how stable radon must be in a space for equilibrium-based calibration to be performed there. Overall, the accuracy of measurements using calibrations from each space differed by less than 10% after 2 d exposure time, showing that carefully controlled conditions are not necessary for the accurate calibration of charcoal canisters. Measurement accuracy differed by less than 2% for different spectral region selections. Accuracy improved slightly with canister exposure duration. Simulations suggest that radon instability is most tolerable near the beginning of canister calibration exposures, but this merits further experimental study.

PlantTribes2: Tools for comparative gene family analysis in plant genomics.

Plant genome-scale resources are being generated at an increasing rate as sequencing technologies continue to improve and raw data costs continue to fall; however, the cost of downstream analyses remains large. This has resulted in a considerable range of genome assembly and annotation qualities across plant genomes due to their varying sizes, complexity, and the technology used for the assembly and annotation. To effectively work across genomes, researchers increasingly rely on comparative genomic approaches that integrate across plant community resources and data types. Such efforts have aided the genome annotation process and yielded novel insights into the evolutionary history of genomes and gene families, including complex non-model organisms. The essential tools to achieve these insights rely on gene family analysis at a genome-scale, but they are not well integrated for rapid analysis of new data, and the learning curve can be steep. Here we present PlantTribes2, a scalable, easily accessible, highly customizable, and broadly applicable gene family analysis framework with multiple entry points including user provided data. It uses objective classifications of annotated protein sequences from existing, high-quality plant genomes for comparative and evolutionary studies. PlantTribes2 can improve transcript models and then sort them, either genome-scale annotations or individual gene coding sequences, into pre-computed orthologous gene family clusters with rich functional annotation information. Then, for gene families of interest, PlantTribes2 performs downstream analyses and customizable visualizations including, (1) multiple sequence alignment, (2) gene family phylogeny, (3) estimation of synonymous and non-synonymous substitution rates among homologous sequences, and (4) inference of large-scale duplication events. We give examples of PlantTribes2 applications in functional genomic studies of economically important plant families, namely transcriptomics in the weedy Orobanchaceae and a core orthogroup analysis (CROG) in Rosaceae. PlantTribes2 is freely available for use within the main public Galaxy instance and can be downloaded from GitHub or Bioconda. Importantly, PlantTribes2 can be readily adapted for use with genomic and transcriptomic data from any kind of organism.

Post-COVID-19 Acute Disseminated Encephalomyelitis in a 17-Month-Old.

Neurologic manifestations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in pediatric patients have been reported in the acute and postinfectious stages of coronavirus disease 2019. Acute disseminated encephalomyelitis (ADEM) typically presents in children after a viral illness at a mean age of 3 to 7 years. A total of 60% to 90% of literature-reported pediatric patients with ADEM have minimal to no neurologic deficits at long-term follow-up. We present a 17-month-old developmentally typical girl with parental complaints of irritability, upper extremity weakness, and gait disturbance. She presented to the hospital afebrile and irritable with right-sided nasolabial fold flattening, neck stiffness, left upper extremity rigidity, right upper extremity paresis, bilateral lower extremity hyperreflexia, and truncal ataxia. During her hospital course, she became somnolent with autonomic instability and was transferred to intensive care. Contrasted brain MRI revealed diffuse patchy T2 hyperintensities without contrast enhancement. Nasopharyngeal SARS-CoV-2 polymerase chain reaction and serum antibody testing results were positive. Cerebral spinal fluid analysis was unremarkable. Respiratory viral panel and autoimmune encephalitis and demyelinating disorders panel results were negative. She was started on high-dose methylprednisolone and intravenous immunoglobulin, with improvement in mental status, focal deficits, and ambulation. After hospital discharge, she received inpatient rehabilitation for 2 weeks and at 2 month follow-up had a full neurologic recovery. We report the youngest case of postinfectious ADEM due to SARS-CoV-2 in a toddler. Early recognition of autoimmune and inflammatory complications of SARS-CoV-2 is vital for early aggressive immunomodulatory treatment and, consequently, improved morbidity in these patients.

Prenatal exposure to bisphenols affects pregnancy outcomes and offspring development in rats.

The objective of this study was to evaluate the effects of gestational exposure to low doses of bisphenol A (BPA), bisphenol S (BPS), and bisphenol F (BPF) on pregnancy outcomes and offspring development. Pregnant Sprague-Dawley rats were orally dosed with vehicle, 5 µg/kg body weight (BW)/day of BPA, BPS and BPF, or 1 µg/kg BW/day of BPF on gestational days 6-21. Pregnancy and gestational outcomes, including number of abortions and stillbirths, were monitored. Male and female offspring were subjected to morphometry at birth, followed by pre- and post-weaning body weights, post-weaning food and water intakes, and adult organ weights. Ovarian follicular counts were also obtained from adult female offspring. We observed spontaneous abortions in over 80% of dams exposed to 5 µg/kg of BPF. BPA exposure increased Graafian follicles in female offspring, while BPS and BPF exposure decreased the number of corpora lutea, suggesting reduced ovulation rates. Moreover, BPA exposure increased male kidney and prostate gland weights, BPF decreased epididymal adipose tissue weights, and BPS had modest effects on male abdominal adipose tissue weights. Prenatal BPS exposure reduced anogenital distance (AGD) in male offspring, suggesting possible feminization, whereas both BPS and BPA induced oxidative stress in the testes. These results indicate that prenatal exposure to BPF affects pregnancy outcomes, BPS alters male AGD, and all three bisphenols alter certain organ weights in male offspring and ovarian function in female offspring. Altogether, it appears that prenatal exposure to BPA or its analogues can induce reproductive toxicity even at low doses.

Executive functions in agenesis of the corpus callosum: Working memory and sustained attention in the BTBR inbred mouse strain.

INTRODUCTION: Agenesis of the corpus callosum (AgCC) is characterized by the congenital partial or complete absence of the corpus callosum. Several strains of mice have been reported to carry AgCC, with the BTBR T+ Itpr3tf /J (BTBR) inbred mouse strain consistently showing a complete absence of the corpus callosum, as well as a variable reduction in the size of the hippocampal commissure. While much research has focused on the social deficits of the BTBR strain, little research on its cognitive behavior has been conducted. The goal of our study was to compare two facets of executive functioning, spatial working memory, and sustained attention between the BTBR and C57BL/6J (B6) strains. METHODS: Spatial working memory was measured utilizing a delayed matching-to-position (DMTP) task and sustained attention was measured utilizing an operant task in which mice were trained to distinguish signal and nonsignal events. RESULTS: Both the BTBR and B6 mice demonstrated a predictable decline in performance on the DMTP task as the delay interval increased and predictable increase in performance on the sustained attention task as the duration of the signal event increased. Although no significant differences were found between strains on the performance of these tasks, there was a significant difference in learning the association between lever pressing and food reward. Histological investigation confirmed the complete absence of commissural fibers from the corpus callosum, but also the hippocampal commissure, counter to a previous study. CONCLUSION: The results suggest spatial working memory and sustained attention are unaffected by the absence of these commissural fibers alone.

Radon kinetics in a natural indoor radon chamber.

An unusual 180 m3 storage room in the basement of a two-story laboratory building is unventilated, and separated from occupiable rooms by double steel doors. The space completely borders on soil through the concrete floor and two of its concrete walls. The room also contains a separate inner chamber with 1 m thick concrete walls designed to damp vibrations in the room above it. The space boasts a relatively high radon level, 1083 Bq m-3, which varies with local outdoor environmental conditions. Measurements were made of radon concentrations at various locations and heights within the facility. More than a year of continuous radon concentration data corresponding to a single location are also available, along with measurements of indoor and outdoor pressure, temperature, and humidity. Data were also collected with as many as five fans placed in different locations and cycled on for variable time periods. First order linear kinetic models were created to explain the observed approaches to steady state due to changing conditions and wash-out resulting from intentional ventilation. Results demonstrate a good fit between changes in the radon concentration level and the developed compartmental models. However, no significant differences were observed between radon concentration at different locations or heights in the chamber.

Metagenome Sequences from Tidal Marsh and Marine Sediment from the Great Bay Estuary of New Hampshire.

Tidal marsh and estuarine marine microbial sediment metagenomes from the Great Bay Estuary of New Hampshire were sequenced and found to be dominated by Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Both types of sediment contained many unclassified bacterial sequences, including the mollusk pathogen Perkinsus marinus, and detectable xenobiotic degradation and nitrogen transformation genes.

Soil hydrology drives ecological niche differentiation in a native prairie microbiome.

While the impacts of soil moisture on soil microbiome diversity and composition are well characterized, the influence of hydrological regime has been overlooked. As precipitation patterns are altered by climate change, understanding the impact of soil hydrology on community structure and function is critical. In this work, water level was continuously monitored for over a year in a Midwestern prairie-wetland at 10 cm depth increments up to a depth of 120 cm in 10 locations. We analyzed microbiome composition and edaphic factors in soil cores collected from this unique spatially distributed, longitudinal data set. We demonstrate that the fraction of time that each sample was inundated explains more variability in diversity and composition across this site than other commonly assessed edaphic factors, such as soil pH or depth. Finally, we show that these compositional changes influence abundance of ammonia oxidizers. The observed patterns in community composition and diversity are fundamentally regulated by the interaction of water with a structured landscape, particularly an elevated sand ridge characterized by drier conditions and a lower-lying wetland with more clayey soils. Similar processes are generally expected to influence the biogeography of many terrestrial environments, as morphology, hydrology and soil properties generally co-vary.

Risk versus reward: host dependent parasite mortality rates and phenotypes in the facultative generalist Triphysaria versicolor.

BACKGROUND: Parasitic plants engage in a complex molecular dialog with potential host plants to identify a host and overcome host defenses to initiate development of the parasitic feeding organ, the haustorium, invade host tissues, and withdraw water and nutrients. While one of two critical signaling events in the parasitic plant life cycle (germination via stimulant chemicals) has been relatively well-studied, the signaling event that triggers haustorium formation remains elusive. Elucidation of this poorly understood molecular dialogue will shed light on plant-plant communication, parasitic plant physiology, and the evolution of parasitism in plants. RESULTS: Here we present an experimental framework that develops easily quantifiable contrasts for the facultative generalist parasitic plant, Triphysaria, as it feeds across a broad range of diverse flowering plants. The contrasts, including variable parasite growth form and mortality when grown with different hosts, suggest a dynamic and host-dependent molecular dialogue between the parasite and host. Finally, by comparing transcriptome datasets from attached versus unattached parasites we gain insight into some of the physiological processes that are altered during parasitic behavior including shifts in photosynthesis-related and stress response genes. CONCLUSIONS: This work sheds light on Triphysaria's parasitic life habit and is an important step towards understanding the mechanisms of haustorium initiation factor perception, a unique form of plant-plant communication.

An assessment of the microbial community in an urban fringing tidal marsh with an emphasis on petroleum hydrocarbon degradative genes.

Small fringing marshes are ecologically important habitats often impacted by petroleum. We characterized the phylogenetic structure (16S rRNA) and petroleum hydrocarbon degrading alkane hydroxylase genes (alkB and CYP 153A1) in a sediment microbial community from a New Hampshire fringing marsh, using alkane-exposed dilution cultures to enrich for petroleum degrading bacteria. 16S rRNA and alkB analysis demonstrated that the initial sediment community was dominated by Betaproteobacteria (mainly Comamonadaceae) and Gammaproteobacteria (mainly Pseudomonas), while CYP 153A1 sequences predominantly matched Rhizobiales. 24 h of exposure to n-hexane, gasoline, dodecane, or dilution culture alone reduced functional and phylogenetic diversity, enriching for Gammaproteobacteria, especially Pseudomonas. Gammaproteobacteria continued to dominate for 10 days in the n-hexane and no alkane exposed samples, while dodecane and gasoline exposure selected for gram-positive bacteria. The data demonstrate that small fringing marshes in New England harbor petroleum-degrading bacteria, suggesting that petroleum degradation may be an important fringing marsh ecosystem function.

Consistent hypersocial behavior in mice carrying a deletion of Gtf2i but no evidence of hyposocial behavior with Gtf2i duplication: Implications for Williams-Beuren syndrome and autism spectrum disorder.

Introduction: Williams-Beuren syndrome (WBS) is a developmental disorder caused by hemizygous deletion of human chromosome 7q11.23. Hypersocial behavior is one symptom of WBS and contrasts with hyposociality observed in autism spectrum disorder (ASD). Interestingly, duplications of 7q11.23 have been associated with ASD. The social phenotype of WBS has been linked to GTF2I or general transcription factor IIi (TFII-I). Duplication of GTF2I has also been associated with ASD. Methods: We compared mice having either a deletion (Gtf2i+/- ) or duplication (Gtf2i+/dup ) of Gtf2i to wild-type (Gtf2i+/+ ) littermate controls in a series of behavioral tasks including open-field activity monitoring, olfactory probes, a social choice task, social transmission of food preference, habituation-dishabituation, and operant social motivation paradigms. Results: In open-field observations, Gtf2i+/- and Gtf2i+/dup mice demonstrated normal activity and thigmotaxis, and surprisingly, each strain showed a significant preference for a stimulus mouse that was not observed in Gtf2i+/+ siblings. Both Gtf2i+/- and Gtf2i+/dup mice demonstrated normal olfaction in buried food probes, but the Gtf2i+/- mice spent significantly more time investigating urine scent versus water, which was not observed in the other strains. Gtf2i+/- mice also spent significantly more time in nose-to-nose contact compared to Gtf2i+/+ siblings during the open-field encounter of the social transmission of food preference task. In operant tasks of social motivation, Gtf2i+/- mice made significantly more presses for social rewards than Gtf2i+/+ siblings, while there was no difference in presses for the Gtf2i+/dup mice. Discussion: Results were remarkably consistent across testing paradigms supporting a role for GTF2i in the hypersocial phenotype of WBS and more broadly in the regulation of social behavior. Support was not observed for the role of GTF2i in ASD.