Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana.

Single-cell genomics permits a new resolution in the examination of molecular and cellular dynamics, allowing global, parallel assessments of cell types and cellular behaviors through development and in response to environmental circumstances, such as interaction with water and the light-dark cycle of the Earth. Here, we leverage the smallest, and possibly most structurally reduced plant, the semi-aquatic Wolffia australiana to understand dynamics of cell expression in these contexts at the whole plant level. We examined single cell resolution RNA sequencing data, and found Wolffia cells divide into four principal clusters representing the above and below water-situated parenchyma and epidermis. While these tissues share transcriptomic similarity with model plants, they display distinct adaptations that Wolffia has made for the aquatic environment. Within this broad classification, discrete subspecializations are evident with select cells showing unique transcriptomic signatures associated with developmental maturation and specialized physiologies. Assessing this simplified biological system temporally at two key time-of-day (TOD) transitions, we identify additional TOD-responsive genes previously overlooked in whole plant transcriptomic approaches and demonstrate that the core circadian clock machinery and its downstream responses can vary in cell-specific manners, even in this simplified system. Distinctions between cell types and their responses to submergence and/or TOD are driven by expression changes of unexpectedly few genes, characterizing Wolffia as a highly streamlined organism with the majority of genes dedicated to fundamental cellular processes. Wolffia provides a unique opportunity to apply reductionist biology to elucidate signaling functions at the organismal level, for which this work provides a powerful resource.

Allopolyploid origin and diversification of the Hawaiian endemic mints.

Island systems provide important contexts for studying processes underlying lineage migration, species diversification, and organismal extinction. The Hawaiian endemic mints (Lamiaceae family) are the second largest plant radiation on the isolated Hawaiian Islands. We generated a chromosome-scale reference genome for one Hawaiian species, Stenogyne calaminthoides, and resequenced 45 relatives, representing 34 species, to uncover the continental origins of this group and their subsequent diversification. We further resequenced 109 individuals of two Stenogyne species, and their purported hybrids, found high on the Mauna Kea volcano on the island of Hawai'i. The three distinct Hawaiian genera, Haplostachys, Phyllostegia, and Stenogyne, are nested inside a fourth genus, Stachys. We uncovered four independent polyploidy events within Stachys, including one allopolyploidy event underlying the Hawaiian mints and their direct western North American ancestors. While the Hawaiian taxa may have principally diversified by parapatry and drift in small and fragmented populations, localized admixture may have played an important role early in lineage diversification. Our genomic analyses provide a view into how organisms may have radiated on isolated island chains, settings that provided one of the principal natural laboratories for Darwin's thinking about the evolutionary process.

The unusual predominance of maintenance DNA methylation in Spirodela polyrhiza.

Duckweeds are among the fastest reproducing plants, able to clonally divide at exponential rates. However, the genetic and epigenetic impact of clonality on plant genomes is poorly understood. 5-methylcytosine (5mC) is a modified base often described as necessary for the proper regulation of certain genes and transposons and for the maintenance of genome integrity in plants. However, the extent of this dogma is limited by the current phylogenetic sampling of land plant species diversity. Here we analyzed DNA methylomes, small RNAs, mRNA-seq, and H3K9me2 histone modification for Spirodela polyrhiza. S. polyrhiza has lost highly conserved genes involved in de novo methylation of DNA at sites often associated with repetitive DNA, and within genes, however, symmetrical DNA methylation and heterochromatin are maintained during cell division at certain transposons and repeats. Consequently, small RNAs that normally guide methylation to silence repetitive DNA like retrotransposons are diminished. Despite the loss of a highly conserved methylation pathway, and the reduction of small RNAs that normally target repetitive DNA, transposons have not proliferated in the genome, perhaps due in part to the rapid, clonal growth lifestyle of duckweeds.

Biosynthesis of Haloterpenoids in Red Algae via Microbial-like Type I Terpene Synthases.

Red algae or seaweeds produce highly distinctive halogenated terpenoid compounds, including the pentabromochlorinated monoterpene halomon that was once heralded as a promising anticancer agent. The first dedicated step in the biosynthesis of these natural product molecules is expected to be catalyzed by terpene synthase (TS) enzymes. Recent work has demonstrated an emerging class of type I TSs in red algal terpene biosynthesis. However, only one such enzyme from a notoriously haloterpenoid-producing red alga (Laurencia pacifica) has been functionally characterized and the product structure is not related to halogenated terpenoids. Herein, we report 10 new type I TSs from the red algae Portieria hornemannii, Plocamium pacificum, L. pacifica, and Laurencia subopposita that produce a diversity of halogenated mono- and sesquiterpenes. We used a combination of genome sequencing, terpenoid metabolomics, in vitro biochemistry, and bioinformatics to establish red algal TSs in all four species, including those associated with the selective production of key halogenated terpene precursors myrcene, trans-ß-ocimene, and germacrene D-4-ol. These results expand on a small but growing number of characterized red algal TSs and offer insight into the biosynthesis of iconic halogenated algal compounds that are not without precedence elsewhere in biology.

Genetic Mapping, Identification, and Characterization of a Candidate Susceptibility Gene for Powdery Mildew in Cannabis sativa.

Powdery mildew (PM) in Cannabis sativa is most frequently caused by the biotrophic fungus Golovinomyces ambrosiae. Based on previously characterized variation in susceptibility to PM, biparental populations were developed by crossing the most resistant cultivar evaluated, 'FL 58', with a susceptible cultivar, 'TJ's CBD'. F1 progeny were evaluated and displayed a range of susceptibility, and two were self-pollinated to generate two F2 populations. In 2021, the F2 populations (n = 706) were inoculated with PM and surveyed for disease severity. In both F2 populations, 25% of the progeny were resistant, while the remaining 75% showed a range of susceptibility. The F2 populations, as well as selected F1 progeny and the parents, were genotyped with a single-nucleotide polymorphism array, and a consensus genetic map was produced. A major effect quantitative trait locus on C. sativa chromosome 1 (Chr01) and other smaller-effect quantitative trait loci (QTL) on four other chromosomes were identified. The most associated marker on Chr01 was located near CsMLO1, a candidate susceptibility gene. Genomic DNA and cDNA sequencing of CsMLO1 revealed a 6.8-kb insertion in FL 58, relative to TJ's CBD, of which 846 bp are typically spliced into the mRNA transcript encoding a premature stop codon. Molecular marker assays were developed using CsMLO1 sequences to distinguish PM-resistant and PM-susceptible genotypes. These data support the hypothesis that a mutated MLO susceptibility gene confers resistance to PM in C. sativa and provides new genetic resources to develop resistant cultivars. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Role of artificial intelligence in imaging and endoscopy for the diagnosis, monitoring and prognostication of inflammatory bowel disease: a scoping review protocol.

INTRODUCTION: Inflammatory bowel diseases (IBD) are immune-mediated conditions that are increasing in incidence and prevalence worldwide. Their assessment and monitoring are becoming increasingly important, though complex. The best disease control is achieved through tight monitoring of objective inflammatory parameters (such as serum and stool inflammatory markers), cross-sectional imaging and endoscopic assessment. Considering the complexity of the information obtained throughout a patient's journey, artificial intelligence (AI) provides an ideal adjunct to existing tools to help diagnose, monitor and predict the course of disease of patients with IBD. Therefore, we propose a scoping review assessing AI's role in diagnosis, monitoring and prognostication tools in patients with IBD. We aim to detect gaps in the literature and address them in future research endeavours. METHODS AND ANALYSIS: We will search electronic databases, including Medline, Embase, Cochrane CENTRAL, CINAHL Complete, Web of Science and IEEE Xplore. Two reviewers will independently screen the abstracts and titles first and then perform the full-text review. A third reviewer will resolve any conflict. We will include both observational studies and clinical trials. Study characteristics will be extracted using a data extraction form. The extracted data will be summarised in a tabular format, following the imaging modality theme and the study outcome assessed. The results will have an accompanying narrative review. ETHICS AND DISSEMINATION: Considering the nature of the project, ethical review by an institutional review board is not required. The data will be presented at academic conferences, and the final product will be published in a peer-reviewed journal.

Generating high-quality plant and fish reference genomes from field-collected specimens by optimizing preservation.

Sample preservation often impedes efforts to generate high-quality reference genomes or pangenomes for Earth's more than 2 million plant and animal species due to nucleotide degradation. Here we compare the impacts of storage methods including solution type, temperature, and time on DNA quality and Oxford Nanopore long-read sequencing quality in 9 fish and 4 plant species. We show 95% ethanol largely protects against degradation for fish blood (22 °C, ≤6 weeks) and plant tissue (4 °C, ≤3 weeks). From this furthest storage timepoint, we assemble high-quality reference genomes of 3 fish and 2 plant species with contiguity (contig N50) and completeness (BUSCO) that achieve the Vertebrate Genome Project benchmarking standards. For epigenetic applications, we also report methylation frequency compared to liquid nitrogen control. The results presented here remove the necessity for cryogenic storage in many long read applications and provide a framework for future studies focused on sampling in remote locations, which may represent a large portion of the future sequencing of novel organisms.

Early Intestinal Ultrasound Response to Biologic Therapy Predicts Endoscopic Remission in Children with Ileal Crohn's Disease: Results from the Prospective Super Sonic Study.

BACKGROUND AND AIMS: STRIDE-II recommends early biomarker targets for treatment optimization to achieve treat-to-target (T2T) endoscopic remission (ER) in Crohn's disease (CD). Predictive capabilities of intestinal ultrasound (IUS) for T2T ER remains unknown. We aimed to evaluate IUS response to predict ER in children with CD. METHODS: Prospective longitudinal cohort study of children with ileal (TI) CD initiating biologic therapy undergoing IUS, clinical disease activity, and C-reactive protein (CRP) assessments at baseline, week 8, 6 months, and T2T within 1 year. Primary outcome was the accuracy of optimal cut-points to predict TI ER (SES-CD < 2) for change in bowel wall thickness (BWT) on IUS from baseline to week 8, and BWT at week 8. Area under the receiver operating curve analysis was performed and univariate analysis tested associations. RESULTS: 44 children (median age 13 [IQR 12-17] years, 29 (66%) biologic naïve) were included, 29 (66%) achieved ER. A > 18% decrease in TI BWT at week 8 predicted ER with an AUROC of 0.99 [95% CI 0.98-1.00], 100% sensitivity, 93% specificity, 97% PPV, and 100% NPV, superior to a > 46% decrease in PCDAI (AUROC 0.67 [95% CI 0.49-0.84]) and > 84% decrease in CRP (AUROC 0.49 [95% CI 0.31-0.67]) at week 8. CONCLUSIONS: Early change in TI BWT on IUS is highly predictive of ER in children with CD and superior to symptoms and CRP. Our findings suggest that IUS could be used for treatment optimization and tight control to guide T2T strategy.

Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis.

Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here we generated a chromosome-scale genome assembly of the Asian pitcher plant Nepenthes gracilis to analyse how its novel traits (dioecy and carnivorous pitcher leaves) are linked to genomic evolution. We found a decaploid karyotype and a clear indication of subgenome dominance. A male-linked and pericentromerically located region on the putative sex chromosome was identified in a recessive subgenome and was found to harbour three transcription factors involved in flower and pollen development, including a likely neofunctionalized LEAFY duplicate. Transcriptomic and syntenic analyses of carnivory-related genes suggested that the paleopolyploidization events seeded genes that subsequently formed tandem clusters in recessive subgenomes with specific expression in the digestive zone of the pitcher, where specialized cells digest prey and absorb derived nutrients. A genome-scale analysis suggested that subgenome dominance likely contributed to evolutionary innovation by permitting recessive subgenomes to diversify functions of novel tissue-specific duplicates. Our results provide insight into how polyploidy can give rise to novel traits in divergent and successful high-ploidy lineages.

PanKmer: k-mer-based and reference-free pangenome analysis.

SUMMARY: Pangenomes are replacing single reference genomes as the definitive representation of DNA sequence within a species or clade. Pangenome analysis predominantly leverages graph-based methods that require computationally intensive multiple genome alignments, do not scale to highly complex eukaryotic genomes, limit their scope to identifying structural variants (SVs), or incur bias by relying on a reference genome. Here, we present PanKmer, a toolkit designed for reference-free analysis of pangenome datasets consisting of dozens to thousands of individual genomes. PanKmer decomposes a set of input genomes into a table of observed k-mers and their presence-absence values in each genome. These are stored in an efficient k-mer index data format that encodes SNPs, INDELs, and SVs. It also includes functions for downstream analysis of the k-mer index, such as calculating sequence similarity statistics between individuals at whole-genome or local scales. For example, k-mers can be "anchored" in any individual genome to quantify sequence variability or conservation at a specific locus. This facilitates workflows with various biological applications, e.g. identifying cases of hybridization between plant species. PanKmer provides researchers with a valuable and convenient means to explore the full scope of genetic variation in a population, without reference bias. AVAILABILITY AND IMPLEMENTATION: PanKmer is implemented as a Python package with components written in Rust, released under a BSD license. The source code is available from the Python Package Index (PyPI) at https://pypi.org/project/pankmer/ as well as Gitlab at https://gitlab.com/salk-tm/pankmer. Full documentation is available at https://salk-tm.gitlab.io/pankmer/.

The Role of Time Perspective and Mindfulness on Life Satisfaction in the United States of America, Spain, Poland and Japan: A Cross-Cultural Study.

We assessed the cross-cultural role of Time Perspective (TP) tendencies [Past Positive (PP), Past Negative (PN), Present Hedonistic (PH), Present Fatalistic (PF), and Future (F)], the Deviation from a Balanced Time Perspective (DBTP) profile, the Deviation from a Negative Time Perspective (DNTP) profile, and mindfulness on life satisfaction (LS). The sample consisted of psychology undergraduate students (N= 867, MAGE= 20.19, SD= 3.417) in four countries: USA, Spain, Poland and Japan. We used a 17-item short version of the Zimbardo Time Perspective Inventory (ZTPI), the Mindful Attention Awareness Scale (MAAS), and the Satisfaction with Life Scale (SWLS) in all countries. For ensuring measurement invariance, we conducted pairwise CFAs for the ZTPI-17, MAAS and SWLS. Regression analyses showed that PN predicted decreased LS in Poland and Japan. PP predicted increased LS in Spain. F predicted increased LS in Poland. DNTP predicted decreased LS in Poland. Mindfulness predicted decreased LS in Japan and increased LS in USA, Spain and Poland. Moreover, mediation analyses revealed that the DBTP partially mediated the relationship between mindfulness and LS in Spain and USA. The DNTP partially mediated the relationship between mindfulness and LS in Spain, Poland and Japan (opposite direction). The findings suggest that the association of TP, mindfulness and LS differs across the investigated countries as a function of culture.

The Role of Noninvasive Surrogates of Inflammation in Monitoring Pediatric Inflammatory Bowel Diseases: The Old and the New.

Effectiveness of limited available therapies for pediatric inflammatory bowel disease has reached stagnation. Previous non-invasive monitoring strategies have relied upon cumbersome tools to evaluate clinical symptoms and biochemical markers that do not reflect endoscopic activity or respond quickly to treatments. Novel, patient-centric, and highly accurate, monitoring strategies with a focus on intestinal ultrasound for a direct, precise monitoring of activity to achieve disease modification are now possible. Ultimately, research on the optimal tight control monitoring strategies, individualized to each pediatric inflammatory bowel disease patient, are in development and offer a hope to potential therapeutic ceiling breakthrough on the horizon.

Point-of-Care Intestinal Ultrasound in Pediatric Inflammatory Bowel Disease.

PURPOSE OF REVIEW: Intestinal ultrasound (IUS) is an emerging non-invasive point-of-care tool utilized by pediatric gastroenterologists for accurately detecting and monitoring inflammatory bowel disease (IBD) activity. In this article, we reviewed the evidence supporting and technique to perform IUS for children with IBD. RECENT FINDINGS: IUS technique can visualize the colon from the distal sigmoid until the cecum and the terminal ileum without the need for bowel preparation, fasting, or sedation in children with IBD. IUS has been shown to be accurate to endoscopy in children with ulcerative colitis and Crohn's disease. IUS may be the most accurate biomarker to follow as a marker of treatment response that is predictive of endoscopic outcomes in children with IBD. Multiple studies have demonstrated that IUS can be performed at the point-of-care for IBD activity assessment in children. Recent studies have demonstrated the accuracy of IUS to endoscopy and magnetic resonance enterography with an ability to be repeated as a monitor of treatment response for tight control monitoring.

Improved Outcomes After Reinforced Radial Meniscus Repair Augmented With Bone Marrow Aspirate Concentrate.

Purpose: To assess clinical outcomes of patients who have undergone surgical repair of radial meniscal tears with reinforced suture bar (rebar) technique augmented with bone marrow aspirate concentrate. Methods: This is a retrospective study of a single fellowship-trained sports medicine surgeon's experience on all patients who underwent a reinforced repair (rebar) of a radial meniscus tear from November 2016 to 2018, with a minimum of 12-month follow-up. Lysholm scores, IKDC (International Knee Documentation Committee) Subjective Knee Form scores, and Tegner scale were collected postoperatively at periods for at least 1 year and retrospectively studied. Results: Patients were followed for an average of 36.3 ± 25.0 months [range: 12.0-69.0 months]. Pain scores improved from 6.1 ± 2.1 to 0.4 ± 1.4 at 1 year (P < .001). IKDC Subjective Knee Form scores improved from 63 ± 26 to 90 ± 13 (P = .021). Lysholm scores improved from 64 ± 28 to 94 ± 9 (P = .025). Based on a calculated minimal clinical important difference (MCID) of 1.5, 100% of patients had improvement above the MCID. In addition, 88% of patients had a 1-year IKDC Subjective Knee Form score above the patient acceptable symptomatic state. Preoperative Tegner activity scale improved from 3 ± 1.5 to 8 ± 2.6 (P = .007). Patients returned to their preinjury activity with little difference in the Tegner activity scale when we compared preinjury and 1-year postoperative (8.1 ± 1.3 vs 8.0 ± 2.6 respectively, P = .317). Conclusions: The rebar repair technique for radial meniscus tears, with bone marrow aspirate concentrate augmentation, showed improved outcomes in both pain and function at minimum follow-up of 12 months. Patients were able to return to a high preinjury activity level by 1 year, and 100% of patients had improvement above the MCID and 88% met patient acceptable symptomatic state. Level of Evidence: Level IV, therapeutic case series.

Genomics of turions from the Greater Duckweed reveal its pathways for dormancy and re-emergence strategy.

Over 15 families of aquatic plants are known to use a strategy of developmental switching upon environmental stress to produce dormant propagules called turions. However, few molecular details for turion biology have been elucidated due to the difficulties in isolating high-quality nucleic acids from this tissue. We successfully developed a new protocol to isolate high-quality transcripts and carried out RNA-seq analysis of mature turions from the Greater Duckweed Spirodela polyrhiza. Comparison of turion transcriptomes to that of fronds, the actively growing leaf-like tissue, were carried out. Bioinformatic analysis of high confidence, differentially expressed transcripts between frond and mature turion tissues revealed major pathways related to stress tolerance, starch and lipid metabolism, and dormancy that are mobilized to reprogram frond meristems for turion differentiation. We identified the key genes that are likely to drive starch and lipid accumulation during turion formation, as well as those in pathways for starch and lipid utilization upon turion germination. Comparison of genome-wide cytosine methylation levels also revealed evidence for epigenetic changes in the formation of turion tissues. Similarities between turions and seeds provide evidence that key regulators for seed maturation and germination were retooled for their function in turion biology.

Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria.

The bacterial colonization dynamics of plants can differ between phylogenetically similar bacterial strains and in the context of complex bacterial communities. Quantitative methods that can resolve closely related bacteria within complex communities can lead to a better understanding of plant-microbe interactions. However, current methods often lack the specificity to differentiate phylogenetically similar bacterial strains. In this study, we describe molecular strategies to study duckweed-associated bacteria. We first systematically optimized a bead-beating protocol to co-isolate nucleic acids simultaneously from duckweed and bacteria. We then developed a generic fingerprinting assay to detect bacteria present in duckweed samples. To detect specific duckweed-bacterium associations, we developed a genomics-based computational pipeline to generate bacterial strain-specific primers. These strain-specific primers differentiated bacterial strains from the same genus and enabled the detection of specific duckweed-bacterium associations present in a community context. Moreover, we used these strain-specific primers to quantify the bacterial colonization of duckweed by normalization to a plant reference gene and revealed differences in colonization levels between strains from the same genus. Lastly, confocal microscopy of inoculated duckweed further supported our PCR results and showed bacterial colonization of the duckweed root-frond interface and root interior. The molecular methods introduced in this work should enable the tracking and quantification of specific plant-microbe associations within plant-microbial communities.

The phylogenomics and evolutionary dynamics of the organellar genomes in carnivorous Utricularia and Genlisea species (Lentibulariaceae).

Utricularia and Genlisea are highly specialized carnivorous plants whose phylogenetic history has been poorly explored using phylogenomic methods. Additional sampling and genomic data are needed to advance our phylogenetic and taxonomic knowledge of this group of plants. Within a comparative framework, we present a characterization of plastome (PT) and mitochondrial (MT) genes of 26 Utricularia and six Genlisea species, with representatives of all subgenera and growth habits. All PT genomes maintain similar gene content, showing minor variation across the genes located between the PT junctions. One exception is a major variation related to different patterns in the presence and absence of ndh genes in the small single copy region, which appears to follow the phylogenetic history of the species rather than their lifestyle. All MT genomes exhibit similar gene content, with most differences related to a lineage-specific pseudogenes. We find evidence for episodic positive diversifying selection in PT and for most of the Utricularia MT genes that may be related to the current hypothesis that bladderworts' nuclear DNA is under constant ROS oxidative DNA damage and unusual DNA repair mechanisms, or even low fidelity polymerase that bypass lesions which could also be affecting the organellar genomes. Finally, both PT and MT phylogenetic trees were well resolved and highly supported, providing a congruent phylogenomic hypothesis for Utricularia and Genlisea clade given the study sampling.