Autoantibodies to type I interferons in patients with systemic mastocytosis.

Background: Autoantibodies to type I interferons have been identified in association with a variety of inflammatory and autoimmune diseases. Type I interferons have demonstrated inhibitory effects on mast cell proliferation and degranulation. Systemic mastocytosis (SM) is a disease characterized by increased mast cell burden and mediator release. Whether autoantibodies to type I interferon are present in the sera of patients with SM, and if so, whether they correlate with characteristics of disease, is unknown. Objective: The purpose of this study was to determine whether autoantibodies to type I interferons are observed in the sera of patients with SM, and if so, whether they correlate with biomarkers of disease severity. Methods: We analyzed sera from 89 patients with SM for concentrations of autoantibodies to type I interferon by using a multiplex particle-based assay and signal neutralization capacity by using a STAT1 activity assay and then compared these measurements with those in a database of information on 1284 healthy controls. Results: Our cohort was predominantly female (57.3%), with a median age of 56 years. Of the cohort members, 13 produced autoantibodies to IFN-ß, 3 to IFN-ω, and 0 to IFN-α. None of the 13 sera demonstrated signal neutralization. Neither autoantibody concentration nor signaling inhibition measurements correlated with tryptase concentrations or D816V allele burden. Conclusion: Although a small subpopulation of patients with SM have autoantibodies to type I interferons, there was no correlation between autoantibody production and signaling inhibition. These data are consistent with the conclusion that autoantibodies to type I interferon do not play a significant role in the pathogenesis or severity of SM.

Sacrificial scaffold-assisted direct ink writing of engineered aortic valve prostheses.

Heart valve disease has become a serious global health problem, which calls for numerous implantable prosthetic valves to fulfill the broader needs of patients. Although current three-dimensional (3D) bioprinting approaches can be used to manufacture customized valve prostheses, they still have some complications, such as limited biocompatibility, constrained structural complexity, and difficulty to make heterogeneous constructs, to name a few. To overcome these challenges, a sacrificial scaffold-assisted direct ink writing approach has been explored and proposed in this work, in which a sacrificial scaffold is printed to temporarily support sinus wall and overhanging leaflets of an aortic valve prosthesis that can be removed easily and mildly without causing any potential damages to the valve prosthesis. The bioinks, composed of alginate, gelatin, and nanoclay, used to print heterogenous valve prostheses have been designed in terms of rheological/mechanical properties and filament formability. The sacrificial ink made from Pluronic F127 has been developed by evaluating rheological behavior and gel temperature. After investigating the effects of operating conditions, complex 3D structures and homogenous/heterogenous aortic valve prostheses have been successfully printed. Lastly, numerical simulation and cycling experiments have been performed to validate the function of the printed valve prostheses as one-way valves.

The colonial legacy of herbaria.

Herbarium collections shape our understanding of Earth's flora and are crucial for addressing global change issues. Their formation, however, is not free from sociopolitical issues of immediate relevance. Despite increasing efforts addressing issues of representation and colonialism in natural history collections, herbaria have received comparatively less attention. While it has been noted that the majority of plant specimens are housed in the Global North, the extent and magnitude of this disparity have not been quantified. Here we examine the colonial legacy of botanical collections, analysing 85,621,930 specimen records and assessing survey responses from 92 herbarium collections across 39 countries. We find an inverse relationship between where plant diversity exists in nature and where it is housed in herbaria. Such disparities persist across physical and digital realms despite overt colonialism ending over half a century ago. We emphasize the need for acknowledging the colonial history of herbarium collections and implementing a more equitable global paradigm for their collection, curation and use.

A Metagenomic Survey of Wood Decay Fungi in the Urban Trees of Singapore.

Mature tropical urban trees are susceptible to root and trunk rot caused by pathogenic fungi. A metagenomic survey of such fungi was carried out on 210 soil and tissue samples collected from 134 trees of 14 common species in Singapore. Furthermore, 121 fruiting bodies were collected and barcoded. Out of the 22,067 OTUs (operational taxonomic units) identified, 10,646 OTUs had annotation information, and most were either ascomycetes (63.4%) or basidiomycetes (22.5%). Based on their detection in the diseased tissues and surrounding soils and/or the presence of fruiting bodies, fourteen basidiomycetes (nine Polyporales, four Hymenochaetales, one Boletales) and three ascomycetes (three species of Scytalidium) were strongly associated with the diseased trees. Fulvifomes siamensis affected the largest number of tree species surveyed. The association of three fungi was further supported by in vitro wood decay studies. Genetic heterogeneity was common in the diseased tissues and fruiting bodies (Ganoderma species especially). This survey identified the common pathogenic fungi of tropical urban trees and laid the foundation for early diagnosis and targeted mitigation efforts. It also illustrated the complexity of fungal ecology and pathogenicity.

Genomic insights into rapid speciation within the world's largest tree genus Syzygium.

Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium, the most species-rich tree genus worldwide. Genomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that while Syzygium shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. Phylogenomics confirms that Syzygium originated in Australia-New Guinea and diversified in multiple migrations, eastward to the Pacific and westward to India and Africa, in bursts of speciation visible as poorly resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting that stepwise geographic speciation, a neutral process, has been important in Syzygium diversification.

Notes on Amanita section Validae in Hainan Island, China.

Hainan is the second largest island in China with the most extensive and well-preserved tropical forests and is also the largest island of the Indo Burma Biodiversity Hotspot. It provides in situ conservation for the unique ecosystem of the island. Recent studies have shown that there are diverse fungal species in Hainan. In this study, about 40 collections of the genus Amanita have been studied based on the morphology and molecular systematics, including 35 Chinese specimens (24 from Hainan, and eleven from other regions) and three specimens from other countries (Singapore and Malaysia). In total, five new species belonging to Amanita section Validae are described: A. cacaina, A. parvigrisea, A. pseudofritillaria, A. pseudosculpta, and A. yangii. Amanita parvifritillaria is recorded for the first time in Hainan. It is also the first report of this fungus occurring, outside Yunnan Province, China. Among the five new species, two are unique in this section because of the appendiculate pileus margin and the absence of an annulus. Based on these new findings, the diagnosis of the section Validae should be slightly modified to include a few species with appendiculate margin and the lack of annulus.

Oceanographic anomalies coinciding with humpback whale super-group occurrences in the Southern Benguela.

Seasonal feeding behaviour of humpback whales (Megaptera novaeangliae) has been observed in the coastal waters of the Southern Benguela where the species has been observed forming super-groups during the austral spring in recent years since 2011. Super-groups are unprecedented densely-packed aggregations of between 20 and 200 individuals in low-latitude waters and their occurrences indicate possible changes in feeding behaviour of the species. We accessed published data on super-groups occurrence in the study area in 2011, 2014 and 2015, and investigated oceanographic drivers that support prey availability in this region. We found that enhanced primary production is a necessary but not sufficient condition for super-groups to occur. Positive chlorophyll anomalies occurring one month prior to the super-group occurrences were identified, but only a concurrent significantly reduced water volume export from the region throughout October were conducive to the aggregations in the specific years. Hydrodynamic model results attributed the anomalous decreased volume export to the strength and orientation of the Goodhope Jet and associated eddy activity. The combination of random enhanced primary production typical of the region and emerging anomalous conditions of reduced water export in October since 2011 resulted in favourable food availability leading to the unique humpback whale aggregations. The novelty of this grouping behaviour is indicative of the lack of such oceanographic conditions in the past. Given the recency of the events, it is difficult to attribute this reduction in ocean transport to climatic regime shifts, and the origin should be likely investigated in the distant water mass interaction with the greater Agulhas system rather than in local intensifications of the upwelling conditions. A positive trend in the humpback whale population abundance points to the need to monitor the exposure of the species to the changing climate conditions.

Spongispora temasekensis, a new boletoid genus and species from Singapore.

Dipterocarp forests are a typical and widespread type of vegetation in tropical lowlands of southeast Asia that harbor a high diversity of ectomycorrhizal fungi, including boletes. Based on molecular and morphological characters, a unique bolete found in Singapore associated with the dipterocarp Hopea odorata was proven to represent a new species in the proposed new genus Spongispora. Phylogenetic analyses of five loci indicate that Spongispora is nested in the subfamily Leccinoideae of the Boletaceae, most closely related to an inclusive clade of Leccinum, Leccinellum, Octaviania, Rossbeevera, and Turmalinea. However, genetic distances between Spongispora and genera in Leccinoideae are mostly higher than that between any two known genera in this subfamily, which supports the proposal of a new genus. Spongispora temasekensis is characterized by a whitish to pale yellow hymenophore that stains brown where injured, coarsely reticulate stipe, interwoven trichodermial pileipellis, and broadly elliptical to ovoid basidiospores with sponge-like ornamentation perforated by irregular clefts, cracks, and warts under scanning electron microscopy. Morphological descriptions, illustrations, and comparisons with allied taxa are made, and a key to the genera of the subfamily Leccinoideae is provided.

Cued fear memory generalization increases over time.

Fear memory is a highly stable and durable form of memory, even over vast (remote) time frames. Nevertheless, some elements of fear memory can be forgotten, resulting in generalization. The purpose of this study is to determine how cued fear memory generalizes over time and measure underlying patterns of cortico-amygdala synaptic plasticity. We established generalization gradients at recent (1-d) and remote (30-d) retention intervals following auditory cued fear conditioning in adult male C57BL/6 mice. Results revealed a flattening of the generalization gradient (increased generalization) that was dissociated from contextual fear generalization, indicating a specific influence of time on cued fear memory performance. This effect reversed after a brief exposure to the novel stimulus soon after learning. Measurements from cortico-amygdala imaging of the activity-regulated cytoskeletal Arc/arg 3.1 (Arc) protein using immunohistochemistry after cued fear memory retrieval revealed a stable pattern of Arc expression in the dorsolateral amygdala, but temporally dynamic expression in the cortex. Over time, increased fear memory generalization was associated with a reduction in Arc expression in the agranular insular and infralimbic cortices while discrimination learning was associated with increased Arc expression in the prelimbic cortex. These data identify the dorsolateral amygdala, medial prefrontal, and insular cortices as loci for synaptic plasticity underlying cued fear memory generalization over time.

Rhabdomyosarcoma of the head and neck: impact of demographic and clinicopathologic factors on survival.

OBJECTIVE: To determine the survival factors for patients diagnosed with rhabdomyosarcoma of the head and neck. STUDY DESIGN: Data on patients diagnosed with rhabdomyosarcoma of the head and neck between 1973 and 2012 were extracted from the Surveillance, Epidemiology, and End Results database. Kaplan-Meier and Cox proportional hazard regression models were used to determine the demographic characteristics, prognostic factors, and treatment modalities that determine overall survival (OS) and disease-specific survival (DSS). RESULTS: Data on 503 patients diagnosed with rhabdomyosarcoma of the head and neck were analyzed; 51.3% were male and 48.7% were female, with a median OS of 4.9 years. Kaplan-Meier analysis determined 5-year survival rates of 30% for OS and 50% for DSS. Multivariate analysis found that age at diagnosis, tumor extent of disease, surgical resection, and radiation therapy were independent predictors of OS and DSS. CONCLUSIONS: To our knowledge, this is the largest year-span study to date to determine the factors of survival for rhabdomyosarcoma of the head and neck. Older age at diagnosis, histologic subtype of alveolar rhabdomyosarcoma, and further extent of disease were associated with decreased survival. Surgical resection improves survival in patients with localized or regional disease, and radiation therapy confers survival benefits in patients with distant extent.

Importance of tumor extent in adenosquamous carcinoma of the head and neck: a retrospective cohort study.

OBJECTIVE: The aim of this study was to determine the correlates of survival for patients diagnosed with adenosquamous carcinoma (ASC) of the head and neck. STUDY DESIGN: Patients diagnosed with ASC of the head and neck between 1973 and 2012 were identified from the Surveillance, Epidemiology, and End Results (SEER) database. Kaplan-Meier and Cox proportional hazard regression analyses were conducted to investigate the prognostic factors and treatment modalities that determine overall survival (OS) and disease-specific survival (DSS). RESULTS: In the analysis, of the 235 patients diagnosed with adenosquamous of the head and neck, 66.8% were male and 33.2% were female with a median age at diagnosis of 64 years. Kaplan-Meier analysis determined 5-year survival rates of 30% for OS and 50% for DSS. Univariate and multivariate analyses found that age at diagnosis, tumor size, tumor extent of disease, surgical resection, and radiation therapy were independent predictors of OS and DSS. CONCLUSIONS: This study, to our knowledge, is the largest study, to date, determining the correlates of survival for ASC of the head and neck. Older age at diagnosis, larger tumor size, and further extent of disease were correlated with decreased survival. Surgical resection improves survival in patients with localized or regional disease, whereas radiation therapy confers survival benefit in patients with distant extent.

Determining the epidemiologic, outcome, and prognostic factors of oral malignant melanoma by using the Surveillance, Epidemiology, and End Results database.

BACKGROUND: The authors conducted a retrospective analysis to determine the epidemiologic, outcome, and prognostic factors in patients with oral malignant melanoma (OMM). METHODS: The authors used the US National Cancer Institute's Surveillance, Epidemiology, and End Results database to analyze patients with OMM from 1973 to 2012. Study variables included age, sex, race, decade of diagnosis, extent of disease, tumor size, treatment modality, and socioeconomic status (SES). RESULTS: The search identified 232 patients with OMM. Overall survival (OS) and disease-specific survival (DSS) were 25% and 40%, respectively, at 5 years. Age (OS, P = .004; DSS, P = .294), surgical resection (OS, P = .046; DSS, P = .005), and extent of disease (OS, P < .001; DSS, P < .001) were independent survival determinants; tumor size was an independent predictor of OS (P = .085). For confined and locally invasive disease, surgery (OS, P = .001; DSS, P = .004) and size (OS, P = .154; DSS, P = .007) were independent determinants of OS and DSS. For metastatic disease, surgery (OS, P = .675; DSS, P = .518) was a survival determinant for both OS and DSS, whereas radiotherapy predicted improved OS (hazard ratio, 0.18; 95% confidence interval, 0.03 to 0.99; P = .049). CONCLUSIONS: Age at diagnosis, decade of diagnosis, extent of disease, tumor size, and SES are prognostic factors related to OMM survival. Surgical resection and radiation therapy both improve OMM survival. PRACTICAL IMPLICATIONS: Early and detailed examinations for OMM are critical to improving the survival rate in patients with OMM, especially in older patients and patients of lower SES.

Stage-Specific Demethylation in Primordial Germ Cells Safeguards against Precocious Differentiation.

Remodeling DNA methylation in mammalian genomes can be global, as seen in preimplantation embryos and primordial germ cells (PGCs), or locus specific, which can regulate neighboring gene expression. In PGCs, global and locus-specific DNA demethylation occur in sequential stages, with an initial global decrease in methylated cytosines (stage I) followed by a Tet methylcytosine dioxygenase (Tet)-dependent decrease in methylated cytosines that act at imprinting control regions (ICRs) and meiotic genes (stage II). The purpose of the two-stage mechanism is unclear. Here we show that Dnmt1 preserves DNA methylation through stage I at ICRs and meiotic gene promoters and is required for the pericentromeric enrichment of 5hmC. We discovered that the functional consequence of abrogating two-stage DNA demethylation in PGCs was precocious germline differentiation leading to hypogonadism and infertility. Therefore, bypassing stage-specific DNA demethylation has significant consequences for progenitor germ cell differentiation and the ability to transmit DNA from parent to offspring.

PGC Reversion to Pluripotency Involves Erasure of DNA Methylation from Imprinting Control Centers followed by Locus-Specific Re-methylation.

Primordial germ cells (PGCs) are fate restricted to differentiate into gametes in vivo. However, when removed from their embryonic niche, PGCs undergo reversion to pluripotent embryonic germ cells (EGCs) in vitro. One of the major differences between EGCs and embryonic stem cells (ESCs) is variable methylation at imprinting control centers (ICCs), a phenomenon that is poorly understood. Here we show that reverting PGCs to EGCs involved stable ICC methylation erasure at Snrpn, Igf2r, and Kcnqot1. In contrast, the H19/Igf2 ICC undergoes erasure followed by de novo re-methylation. PGCs differentiated in vitro from ESCs completed Snrpn ICC erasure. However, the hypomethylated state is highly unstable. We also discovered that when the H19/Igf2 ICC was abnormally hypermethylated in ESCs, this is not erased in PGCs differentiated from ESCs. Therefore, launching PGC differentiation from ESC lines with appropriately methylated ICCs is critical to the generation of germline cells that recapitulate endogenous ICC erasure.

MORC1 represses transposable elements in the mouse male germline.

The Microrchidia (Morc) family of GHKL ATPases are present in a wide variety of prokaryotic and eukaryotic organisms but are of largely unknown function. Genetic screens in Arabidopsis thaliana have identified Morc genes as important repressors of transposons and other DNA-methylated and silent genes. MORC1-deficient mice were previously found to display male-specific germ cell loss and infertility. Here we show that MORC1 is responsible for transposon repression in the male germline in a pattern that is similar to that observed for germ cells deficient for the DNA methyltransferase homologue DNMT3L. Morc1 mutants show highly localized defects in the establishment of DNA methylation at specific classes of transposons, and this is associated with failed transposon silencing at these sites. Our results identify MORC1 as an important new regulator of the epigenetic landscape of male germ cells during the period of global de novo methylation.

PRMT5 is required for human embryonic stem cell proliferation but not pluripotency.

Human pluripotent stem cells (PSCs) are critical in vitro tools for understanding mechanisms that regulate lineage differentiation in the human embryo as well as a potentially unlimited supply of stem cells for regenerative medicine. Pluripotent human and mouse embryonic stem cells (ESCs) derived from the inner cell mass of blastocysts share a similar transcription factor network to maintain pluripotency and self-renewal, yet there are considerable molecular differences reflecting the diverse environments in which mouse and human ESCs are derived. In the current study we evaluated the role of Protein arginine methyltransferase 5 (PRMT5) in human ESC (hESC) self-renewal and pluripotency given its critical role in safeguarding mouse ESC pluripotency. Unlike the mouse, we discovered that PRMT5 has no role in hESC pluripotency. Using microarray analysis we discovered that a significant depletion in PRMT5 RNA and protein from hESCs changed the expression of only 78 genes, with the majority being repressed. Functionally, we discovered that depletion of PRMT5 had no effect on expression of OCT4, NANOG or SOX2, and did not prevent teratoma formation. Instead, we show that PRMT5 functions in hESCs to regulate proliferation in the self-renewing state by regulating the fraction of cells in Gap 1 (G1) of the cell cycle and increasing expression of the G1 cell cycle inhibitor P57. Taken together our data unveils a distinct role for PRMT5 in hESCs and identifies P57 as new target.

Stage-specific roles for tet1 and tet2 in DNA demethylation in primordial germ cells.

Primordial germ cells (PGCs) undergo dramatic rearrangements to their methylome during embryogenesis, including initial genome-wide DNA demethylation that establishes the germline epigenetic ground state. The role of the 5-methylcytosine (5mC) dioxygenases Tet1 and Tet2 in the initial genome-wide DNA demethylation process has not been examined directly. Using PGCs differentiated from either control or Tet2(-/-); Tet1 knockdown embryonic stem cells (ESCs), we show that in vitro PGC (iPGC) formation and genome-wide DNA demethylation are unaffected by the absence of Tet1 and Tet2, and thus 5-hydroxymethylcytosine (5hmC). However, numerous promoters and gene bodies were hypermethylated in mutant iPGCs, which is consistent with a role for 5hmC as an intermediate in locus-specific demethylation. Altogether, our results support a revised model of PGC DNA demethylation in which the first phase of comprehensive 5mC loss does not involve 5hmC. Instead, Tet1 and Tet2 have a locus-specific role in shaping the PGC epigenome during subsequent development.

Hydrodynamic stretching of single cells for large population mechanical phenotyping.

Cell state is often assayed through measurement of biochemical and biophysical markers. Although biochemical markers have been widely used, intrinsic biophysical markers, such as the ability to mechanically deform under a load, are advantageous in that they do not require costly labeling or sample preparation. However, current techniques that assay cell mechanical properties have had limited adoption in clinical and cell biology research applications. Here, we demonstrate an automated microfluidic technology capable of probing single-cell deformability at approximately 2,000 cells/s. The method uses inertial focusing to uniformly deliver cells to a stretching extensional flow where cells are deformed at high strain rates, imaged with a high-speed camera, and computationally analyzed to extract quantitative parameters. This approach allows us to analyze cells at throughputs orders of magnitude faster than previously reported biophysical flow cytometers and single-cell mechanics tools, while creating easily observable larger strains and limiting user time commitment and bias through automation. Using this approach we rapidly assay the deformability of native populations of leukocytes and malignant cells in pleural effusions and accurately predict disease state in patients with cancer and immune activation with a sensitivity of 91% and a specificity of 86%. As a tool for biological research, we show the deformability we measure is an early biomarker for pluripotent stem cell differentiation and is likely linked to nuclear structural changes. Microfluidic deformability cytometry brings the statistical accuracy of traditional flow cytometric techniques to label-free biophysical biomarkers, enabling applications in clinical diagnostics, stem cell characterization, and single-cell biophysics.