Circadian regulation of the transcriptome in a complex polyploid crop.

The circadian clock is a finely balanced timekeeping mechanism that coordinates programmes of gene expression. It is currently unknown how the clock regulates expression of homoeologous genes in polyploids. Here, we generate a high-resolution time-course dataset to investigate the circadian balance between sets of 3 homoeologous genes (triads) from hexaploid bread wheat. We find a large proportion of circadian triads exhibit imbalanced rhythmic expression patterns, with no specific subgenome favoured. In wheat, period lengths of rhythmic transcripts are found to be longer and have a higher level of variance than in other plant species. Expression of transcripts associated with circadian controlled biological processes is largely conserved between wheat and Arabidopsis; however, striking differences are seen in agriculturally critical processes such as starch metabolism. Together, this work highlights the ongoing selection for balance versus diversification in circadian homoeologs and identifies clock-controlled pathways that might provide important targets for future wheat breeding.

Introgressions lead to reference bias in wheat RNA-seq analysis.

BACKGROUND: RNA-seq is a fundamental technique in genomics, yet reference bias, where transcripts derived from non-reference alleles are quantified less accurately, can undermine the accuracy of RNA-seq quantification and thus the conclusions made downstream. Reference bias in RNA-seq analysis has yet to be explored in complex polyploid genomes despite evidence that they are often a complex mosaic of wild relative introgressions, which introduce blocks of highly divergent genes. RESULTS: Here we use hexaploid wheat as a model complex polyploid, using both simulated and experimental data to show that RNA-seq alignment in wheat suffers from widespread reference bias which is largely driven by divergent introgressed genes. This leads to underestimation of gene expression and incorrect assessment of homoeologue expression balance. By incorporating gene models from ten wheat genome assemblies into a pantranscriptome reference, we present a novel method to reduce reference bias, which can be readily scaled to capture more variation as new genome and transcriptome data becomes available. CONCLUSIONS: This study shows that the presence of introgressions can lead to reference bias in wheat RNA-seq analysis. Caution should be exercised by researchers using non-sample reference genomes for RNA-seq alignment and novel methods, such as the one presented here, should be considered.

Selective CO2 Reduction Electrocatalysis Using AgCu Nanoalloys Prepared by a "Host-Guest" Method.

Multimetallic nanoalloy catalysts have attracted considerable interest for enhancing the efficiency and selectivity of many electrochemically driven chemical processes. However, the preparation of homogeneous bimetallic alloy nanoparticles remains a challenge. Here, we present a room-temperature and scalable, host-guest approach for synthesis of dilute Cu in Ag alloy nanoparticles. In this approach, an ionic silver bromide precursor harboring exogenous Cu cations is reduced to yield ∼20 nm diameter AgCu alloy nanoparticles wherein the % Cu loading can be tuned precisely. AgCu nanoparticles with a 5% nominal loading of Cu exhibit peak activity (-0.23 mA/cm2 normalized partial current density) and selectivity (83.2% faradaic efficiency) for CO product formation from electrocatalytic reduction of CO2 at mild overpotentials. These AgCu nanoalloys exhibit a higher mass activity compared to Ag- and Cu-containing nanomaterials used for similar electrocatalytic transformations. Our host-guest synthesis platform holds promise for production of other nanoalloys with relevance in electrocatalysis and optics.

Electrochemical Synthesis of Nanostructured Ordered Intermetallic Materials under Ambient Conditions.

ConspectusThe enhanced catalytic properties of alloy nanostructures have made them a focus of extensive research in the field of catalysis. Alloy nanostructures can be classified into two types: disordered alloys (also known as solid solutions) and ordered intermetallics. The latter are of particular interest as they possess long-range atomic scale ordering, which leads to well-defined active sites that can be used to accurately assess structure-property relationships and their impact on (electro)catalytic performance.While many ordered intermetallics (OICs) have been synthesized and evaluated as electrocatalysts, there is still a lack of understanding on how the local structure of atoms controls their catalytic performance. Ordered intermetallics are difficult to synthesize and often require high-temperature annealing for the atoms to equilibrate into ordered structures. High temperature processing results in aggregated structures (usually >30 nm) and/or contamination from the support, which can decrease their performance and preclude these materials from being used as model systems for elucidating insight into structure and electrochemical properties. Therefore, alternative methods are required to enable more efficient atomic ordering while maintaining some level of morphological control.This Account delves into the potential of electrochemical methods as a practical alternative for synthesizing ordered intermetallics at lower temperatures. Specifically, it explores the viability of electrochemical dealloying and electrochemical deposition to synthesize Pd-Bi and Cu-Zn intermetallics at room temperature and atmospheric pressure. These methods have proven useful in synthesizing phases that are typically inaccessible under ambient conditions. The high homologous temperatures at which these materials are synthesized provide the necessary atomic mobility required for equilibration and formation of ordered phases, thus making the direct synthesis of ordered intermetallic materials at room temperature by electrochemical means a reality.Beyond synthesis, the electrocatalytic performance of these intermetallics was assessed for the oxygen reduction reaction (ORR), which is an important process employed in fuel cells. The OICs displayed increased performance with respect to commercial Pd/C and Pt/C benchmarks because of lower coverages of spectator species. Furthermore, these materials exhibited improved methanol tolerance.This Account provides valuable insights into the electrochemical synthesis of ordered intermetallics and their potential use as highly effective catalysts for electrocatalytic reactions. By using electrochemical methods, it is possible to obtain ordered intermetallics with unique atomic arrangements and tailored properties, which can be optimized for specific catalytic applications. With further research, electrochemical synthesis methods may enable the development of new and improved ordered intermetallics with even higher catalytic activity and selectivity, making them ideal candidates for use in a wide range of industrial processes. Furthermore, the ability to access intermetallics under milder conditions may accelerate the ability to use these materials as model systems for revealing fundamental insight into electrocatalyst structure and function.

Cutaneous Disease of Penoscrotal Skin Part I: Benign and Neoplastic Lesions.

Penoscrotal skin diseases encompass an array of pathologies that present with unique clinical features. A patient-tailored approach to management is necessary. This article, part of a continuing medical education series, is dedicated to offering insights for managing penoscrotal dermatoses. The first article will provide an overview of normal variations, benign lesions, and malignant growths. We will then highlight up-to-date diagnostic and treatment protocols. In the second article, we will discuss inflammatory and infectious conditions, reviewing common diseases such as syphilis, human papilloma virus, and psoriasis, as well as rarer, difficult to treat diseases such as lichen sclerosus, lichen planus, and genital dyesthesias. Considering 70% of patients with genital skin diseases report that physicians lack awareness of these conditions,1 this CME series will help practitioners identify penoscrotal diseases, expand differential diagnoses, and discuss appropriate and emerging therapies.

Interpreting machine learning models to investigate circadian regulation and facilitate exploration of clock function.

The circadian clock is an important adaptation to life on Earth. Here, we use machine learning to predict complex, temporal, and circadian gene expression patterns in Arabidopsis Most significantly, we classify circadian genes using DNA sequence features generated de novo from public, genomic resources, facilitating downstream application of our methods with no experimental work or prior knowledge needed. We use local model explanation that is transcript specific to rank DNA sequence features, providing a detailed profile of the potential circadian regulatory mechanisms for each transcript. Furthermore, we can discriminate the temporal phase of transcript expression using the local, explanation-derived, and ranked DNA sequence features, revealing hidden subclasses within the circadian class. Model interpretation/explanation provides the backbone of our methodological advances, giving insight into biological processes and experimental design. Next, we use model interpretation to optimize sampling strategies when we predict circadian transcripts using reduced numbers of transcriptomic timepoints. Finally, we predict the circadian time from a single, transcriptomic timepoint, deriving marker transcripts that are most impactful for accurate prediction; this could facilitate the identification of altered clock function from existing datasets.

Uveitis masquerade syndromes: An approach to diagnosis.

Uveitis masquerade syndromes are a diverse group of clinical entities which mimic conventional immune-mediated uveitis due to the presence of inflammatory signs but are resistant to anti-inflammatory therapy. Misdiagnosis hinders appropriate management in these conditions and may result in poor outcomes. This review discusses commonly encountered neoplastic and non-neoplastic disease processes that masquerade as intraocular inflammation with a focus on relevant clinical features and adjunctive investigations that are helpful in reaching a correct diagnosis.

Whole-genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/Ambylopyrum muticum introgression lines.

Wheat is a globally vital crop, but its limited genetic variation creates a challenge for breeders aiming to maintain or accelerate agricultural improvements over time. Introducing novel genes and alleles from wheat's wild relatives into the wheat breeding pool via introgression lines is an important component of overcoming this low variation but is constrained by poor genomic resolution and limited understanding of the genomic impact of introgression breeding programmes. By sequencing 17 hexaploid wheat/Ambylopyrum muticum introgression lines and the parent lines, we have precisely pinpointed the borders of introgressed segments, most of which occur within genes. We report a genome assembly and annotation of Am. muticum that has facilitated the identification of Am. muticum resistance genes commonly introgressed in lines resistant to stripe rust. Our analysis has identified an abundance of structural disruption and homoeologous pairing across the introgression lines, likely caused by the suppressed Ph1 locus. mRNAseq analysis of six of these introgression lines revealed that novel introgressed genes are rarely expressed and those that directly replace a wheat orthologue have a tendency towards downregulation, with no discernible compensation in the expression of homoeologous copies. This study explores the genomic impact of introgression breeding and provides a schematic that can be followed to characterize introgression lines and identify segments and candidate genes underlying the phenotype. This will facilitate more effective utilization of introgression pre-breeding material in wheat breeding programmes.

Long term outcome and prognostic indicators in Posner Schlossman syndrome.

BACKGROUND: Posner Schlossman syndrome is a well-defined uveitis entity that is characterised by relapsing remitting unilateral anterior uveitis with markedly raised intraocular pressure. The aim of this study was to determine the risk factors for progression in patients with Posner Schlossman syndrome. METHODS: Ninety-eight patients were enrolled in a retrospective case series. Progression was defined as a composite endpoint of any of development of permanent glaucoma (in patients with no evidence of glaucomatous loss on presentation), corneal failure, or chronic inflammation. Relapse was defined as a resolving episode of inflammation not meeting the criteria for progression. RESULTS: Seventy seven percent of patients relapsed on average each 2.2 years. Forty percent of patients progressed. On univariate analysis, increased age at enrolment, immunocompromise at enrolment, the presence of glaucomatous optic neuropathy at enrolment, the performance of an anterior chamber tap and a positive anterior chamber tap were all associated with increased risk of progression. On multivariate analysis, age at enrolment, immunocompromise at enrolment, the performance of an anterior chamber tap, and the presence of glaucomatous optic neuropathy at enrolment were independently associated with increased risk of disease progression. CONCLUSIONS: Posner Schlossman syndrome is not a benign uveitis entity and risk of both relapse and progression are high. Older patients, immunocompromised patients, patients with glaucomatous optic neuropathy at enrolment and those with a positive anterior chamber tap are all at increased risk of progression.

Circadian and diel regulation of photosynthesis in the bryophyte Marchantia polymorpha.

Circadian rhythms are 24-h biological cycles that align metabolism, physiology, and development with daily environmental fluctuations. Photosynthetic processes are governed by the circadian clock in both flowering plants and some cyanobacteria, but it is unclear how extensively this is conserved throughout the green lineage. We investigated the contribution of circadian regulation to aspects of photosynthesis in Marchantia polymorpha, a liverwort that diverged from flowering plants early in the evolution of land plants. First, we identified in M. polymorpha the circadian regulation of photosynthetic biochemistry, measured using two approaches (delayed fluorescence, pulse amplitude modulation fluorescence). Second, we identified that light-dark cycles synchronize the phase of 24 h cycles of photosynthesis in M. polymorpha, whereas the phases of different thalli desynchronize under free-running conditions. This might also be due to the masking of the underlying circadian rhythms of photosynthesis by light-dark cycles. Finally, we used a pharmacological approach to identify that chloroplast translation might be necessary for clock control of light-harvesting in M. polymorpha. We infer that the circadian regulation of photosynthesis is well-conserved amongst terrestrial plants.

Phenotypic variation in photosynthetic traits in wheat grown under field versus glasshouse conditions.

Recognition of the untapped potential of photosynthesis to improve crop yields has spurred research to identify targets for breeding. The CO2-fixing enzyme Rubisco is characterized by a number of inefficiencies, and frequently limits carbon assimilation at the top of the canopy, representing a clear target for wheat improvement. Two bread wheat lines with similar genetic backgrounds and contrasting in vivo maximum carboxylation activity of Rubisco per unit leaf nitrogen (Vc,max,25/Narea) determined using high-throughput phenotyping methods were selected for detailed study from a panel of 80 spring wheat lines. Detailed phenotyping of photosynthetic traits in the two lines using glasshouse-grown plants showed no difference in Vc,max,25/Narea determined directly via in vivo and in vitro methods. Detailed phenotyping of glasshouse-grown plants of the 80 wheat lines also showed no correlation between photosynthetic traits measured via high-throughput phenotyping of field-grown plants. Our findings suggest that the complex interplay between traits determining crop productivity and the dynamic environments experienced by field-grown plants needs to be considered in designing strategies for effective wheat crop yield improvement when breeding for particular environments.

Coordinated circadian timing through the integration of local inputs in Arabidopsis thaliana.

Individual plant cells have a genetic circuit, the circadian clock, that times key processes to the day-night cycle. These clocks are aligned to the day-night cycle by multiple environmental signals that vary across the plant. How does the plant integrate clock rhythms, both within and between organs, to ensure coordinated timing? To address this question, we examined the clock at the sub-tissue level across Arabidopsis thaliana seedlings under multiple environmental conditions and genetic backgrounds. Our results show that the clock runs at different speeds (periods) in each organ, which causes the clock to peak at different times across the plant in both constant environmental conditions and light-dark (LD) cycles. Closer examination reveals that spatial waves of clock gene expression propagate both within and between organs. Using a combination of modeling and experiment, we reveal that these spatial waves are the result of the period differences between organs and local coupling, rather than long-distance signaling. With further experiments we show that the endogenous period differences, and thus the spatial waves, can be generated by the organ specificity of inputs into the clock. We demonstrate this by modulating periods using light and metabolic signals, as well as with genetic perturbations. Our results reveal that plant clocks can be set locally by organ-specific inputs but coordinated globally via spatial waves of clock gene expression.

Medical and surgical treatment of thyroid eye disease.

Thyroid eye disease is an autoimmune inflammatory disease strongly associated with thyroid disease, principally Graves disease. It can range from mild disease requiring observation or symptomatic treatments only, through to sight-threatening disease requiring major drug therapy and orbital surgery. Severity is graded by the NOSPECS system and activity by the clinical activity score (CAS) to assist in treatment selection. Non-surgical management can extend from observation alone to minor therapy such as oral selenium, then glucocorticoid therapy, cyclosporin, mycophenolate, rituximab, immunoglobulin, teprotumumab, and orbital radiotherapy. High-dose intravenous methylprednisolone therapy is used in active vision-threatening disease with early use of tarsorrhaphy and orbital decompression. Inactive but moderate to severe disease may be treated by orbital decompression, strabismus and eyelid surgery. Systematic assessment and management by both an endocrinologist and ophthalmologist to achieve and maintain euthyroidism and select and sequence treatments according to activity and severity of thyroid eye disease gives the best results for quality of life and vision.

Patient-specific Implants for Orbital Fractures: A Systematic Review.

PURPOSE: Orbital fractures are common facial fractures that can be challenging to repair and require careful attention to avoid unacceptable ophthalmic complications. Customized implants that are unique to an individual patient, or patient-specific implants (PSIs), have been increasingly used to repair orbital wall fractures. This systematic review summarizes the current evidence regarding custom-made orbital wall implants. METHODS: A keyword search of published literature from January 2010 to September 2021 was performed using Ovid MEDLINE, PubMed, and the Cochrane Library databases. Original articles that included more than 3 human subjects with an orbital fracture repaired with a PSI were included. The search results were reviewed, duplicates were removed and relevant articles were included for analysis. RESULTS: Fifteen articles meeting the inclusion criteria. The articles were categorized into 3 separate groups based on the method of PSI fabrication: manual molding of a PSI on a 3D-printed orbital model (53%), directly from a 3D printer (27%), or via a template fabricated from a 3D printer (20%). Three primary postoperative outcomes were assessed: rates of diplopia, enophthalmos, and orbital volume. Postoperative rates of diplopia and enophthalmos improved regardless of the PSI technique, and postoperative orbital volumes were reduced compared with their preoperative state. When PSIs were compared to conventional implants, patient outcomes were comparable. CONCLUSIONS: This review of existing PSI orbital implant literature highlights that while PSI can accurately and safely repair orbital fractures, patient outcomes are largely comparable to orbital fractures repaired by conventional methods, and PSI do not offer a definitive benefit over conventional implants.

Hidden variation in polyploid wheat drives local adaptation.

Wheat has been domesticated into a large number of agricultural environments and has the ability to adapt to diverse environments. To understand this process, we survey genotype, repeat content, and DNA methylation across a bread wheat landrace collection representing global genetic diversity. We identify independent variation in methylation, genotype, and transposon copy number. We show that these, so far unexploited, sources of variation have had a significant impact on the wheat genome and that ancestral methylation states become preferentially "hard coded" as single nucleotide polymorphisms (SNPs) via 5-methylcytosine deamination. These mechanisms also drive local adaption, impacting important traits such as heading date and salt tolerance. Methylation and transposon diversity could therefore be used alongside SNP-based markers for breeding.

Uncovering candidate genes involved in photosynthetic capacity using unexplored genetic variation in Spring Wheat.

To feed an ever-increasing population we must leverage advances in genomics and phenotyping to harness the variation in wheat breeding populations for traits like photosynthetic capacity which remains unoptimized. Here we survey a diverse set of wheat germplasm containing elite, introgression and synthetic derivative lines uncovering previously uncharacterized variation. We demonstrate how strategic integration of exotic material alleviates the D genome genetic bottleneck in wheat, increasing SNP rate by 62% largely due to Ae. tauschii synthetic wheat donors. Across the panel, 67% of the Ae. tauschii donor genome is represented as introgressions in elite backgrounds. We show how observed genetic variation together with hyperspectral reflectance data can be used to identify candidate genes for traits relating to photosynthetic capacity using association analysis. This demonstrates the value of genomic methods in uncovering hidden variation in wheat and how that variation can assist breeding efforts and increase our understanding of complex traits.

Naturally occurring circadian rhythm variation associated with clock gene loci in Swedish Arabidopsis accessions.

Circadian clocks have evolved to resonate with external day and night cycles. However, these entrainment signals are not consistent everywhere and vary with latitude, climate and seasonality. This leads to divergent selection for clocks which are locally adapted. To investigate the genetic basis for this circadian variation, we used a delayed fluorescence imaging assay to screen 191 naturally occurring Swedish Arabidopsis accessions for their circadian phenotypes. We demonstrate that the period length co-varies with both geography and population sub-structure. Several candidate loci linked to period, phase and relative amplitude error (RAE) were revealed by genome-wide association mapping and candidate genes were investigated using TDNA mutants. We show that natural variation in a single non-synonymous substitution within COR28 is associated with a long-period and late-flowering phenotype similar to that seen in TDNA knock-out mutants. COR28 is a known coordinator of flowering time, freezing tolerance and the circadian clock; all of which may form selective pressure gradients across Sweden. We demonstrate the effect of the COR28-58S SNP in increasing period length through a co-segregation analysis. Finally, we show that period phenotypic tails remain diverged under lower temperatures and follow a distinctive "arrow-shaped" trend indicative of selection for a cold-biased temperature compensation response.

Case Studies Discussing the Pathology, Immunogenicity, and Proposed Mechanism of Toxicity of an Inhaled Anti-TGFß Humanized Fab Antibody in Non-Human Primates and Mice.

Treatment of nonhuman primates and mice with a humanized antigen-binding fragment (Fab) antibody (UCBFab) inhibiting transforming growth factor ß via daily inhalation for up to 13 weeks resulted in low systemic exposure but high local exposure in the lung. Target engagement was demonstrated by reduced levels of signal transducers, phosphoSMAD and plasminogen activator inhibitor-1 in the bronchoalveolar lavage fluid (BALF). Treatment was associated with a high frequency and titer of antidrug antibodies, indicating high local immunogenicity, and local pathology within the lung and draining lymph nodes. Microscopic changes were characterized by perivascular (PV) and peribronchiolar (PB) mononuclear inflammatory cell (MIC) infiltrates that were principally lymphocytic in nature and mixed inflammatory cell infiltrates and/or inflammation within the alveoli. Immunohistochemical investigation revealed a predominantly CD68-positive macrophage and CD3- and CD8>CD4-positive T-cell response in the alveoli, whereas within the airways, there was a variable mixture of CD3-positive T cells, CD20-positive B cells, and CD68-positive macrophages. Increased cellularity of the draining lymph nodes was also noted, indicating the presence of an immune response to the inhaled test article. Morphologic changes did not progress over time, and all changes partially recovered. Increased leukocytes (principally macrophages) in BALF cytology correlated with the changes seen by histopathology.

Recommendations for the management of childhood juvenile idiopathic arthritis-type chronic anterior uveitis.

IMPORTANCE: Australian- and New Zealand-based, uveitis-specialized ophthalmologists have produced recommendations for the management of juvenile idiopathic arthritis (JIA)-type chronic anterior uveitis. BACKGROUND: Historically, the visual prognosis of JIA-type chronic anterior uveitis has been poor. New medical advances are likely to improve outcomes, but recently published guidelines are tailored for ophthalmic care in Europe and the United States. DESIGN: This work involved a consensus survey and a panel meeting. PARTICIPANTS: The Australian and New Zealand JIA-Uveitis Working Group (29 ophthalmologists) participated in the work. METHODS: The Delphi technique was used to achieve consensus. MAIN OUTCOME MEASURES: This work yielded consensus statements. RESULTS: The Working Group achieved consensus around 18 statements related to clinical evaluation, use of topical and regional corticosteroids, use of systemic corticosteroid and non-corticosteroid immunomodulatory drugs, and management of secondary cataract and glaucoma in childhood JIA-type uveitis. CONCLUSIONS AND RELEVANCE: Recommendations of the Australian and New Zealand JIA-Uveitis Working Group provide current and regionally applicable advice for managing chronic anterior uveitis in children with JIA.

Patterns of Vitamin D Levels and Exposures in Active and Inactive Noninfectious Uveitis Patients.

PURPOSE: To compare serum vitamin D levels and patterns of ultraviolet light and dietary exposure among patients with active and inactive noninfectious uveitis and population controls. DESIGN: Prospective case-control study. All participants (n = 151) underwent serum 25-hydroxy vitamin D measurement and completed a questionnaire on vitamin D intake and ultraviolet light exposure. Serum 25-hydroxy vitamin D levels were compared between active and inactive uveitis groups and with local population estimates. PARTICIPANTS: Adult patients with active and inactive noninfectious uveitis were recruited from 2 Victorian tertiary hospitals and 1 private ophthalmic practice. METHODS: Serum 25-hydroxy vitamin D levels were compared between patients with active and inactive uveitis and population-based estimates of serum 25-hydroxy vitamin D levels, stratified by geographic region and season. Vitamin D intakes and exposures based on questionnaire results, including vitamin D supplementation and sunlight exposures on weekdays and weekends, were compared between active and inactive uveitis groups. MAIN OUTCOME MEASURES: Serum vitamin D levels, intake of vitamin D, and exposure to sources of vitamin D. RESULTS: The median level of serum vitamin D in those with active uveitis (n = 74) was 46 nmol/l (interquartile range [IQR], 29-70 nmol/l), significantly lower than in the inactive control group (n = 77) at 64 nmol/l (IQR, 52-79 nmol/l; P < 0.001). The active uveitis group also showed lower median serum vitamin D levels than the local population median of 62 nmol/l (IQR, 46-77 nmol/l). Vitamin D supplementation also was associated significantly with uveitis inactivity (P = 0.026, Kendall's τ test). In a subanalysis of vitamin D-deficient participants, sun exposure was associated significantly with uveitis inactivity (P = 0.014 for weekday and weekend analyses). CONCLUSIONS: Participants with active uveitis showed significantly lower serum 25-hydroxy vitamin D levels than inactive uveitis patients and local population-based estimates. Vitamin D supplementation was found to be associated with decreased uveitis activity, as was sun exposure in those with vitamin D deficiency. These results suggest that vitamin D supplementation should be studied as an option for the prevention of uveitis relapse in at-risk patients.