Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes.

East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs. The expanded piwil1 copies have signatures of positive selection and retain amino acid residues essential for catalytic activity. Furthermore, the gonads of African cichlids express a Piwi-interacting RNA (piRNA) pathway that target TEs. We define the genomic sites of piRNA production in African cichlids and find divergence in closely related species, in line with fast evolution of piRNA-producing loci. Our findings suggest dynamic co-evolution of TEs and host silencing pathways in the African cichlid radiations. We propose that this co-evolution has contributed to cichlid genomic diversity.

rnaCrosslinkOO: an object-oriented R package for the analysis of RNA structural data generated by RNA crosslinking experiments.

SUMMARY: RNA (ribonucleic acid) molecules have secondary and tertiary structures in vivo which play a crucial role in cellular processes such as the regulation of gene expression, RNA processing and localization. The ability to investigate these structures will enhance our understanding of their function and contribute to the diagnosis and treatment of diseases caused by RNA dysregulation. However, there are no mature pipelines or packages for processing and analyzing complex in vivo RNA structural data. Here, we present rnaCrosslinkOO (RNA Crosslink Object-Oriented), a novel software package for the comprehensive analysis of data derived from the COMRADES (Crosslinking of Matched RNA and Deep Sequencing) method. rnaCrosslinkOO offers a comprehensive pipeline from raw sequencing reads to the identification and comparison of RNA structural features. It includes read processing and alignment, clustering of duplexes, data exploration, folding and comparisons of RNA structures. rnaCrosslinkOO also enables comparisons between conditions, the identification of inter-RNA interactions, and the incorporation of reactivity data to improve structure prediction. AVAILABILITY AND IMPLEMENTATION: rnaCrosslinkOO is freely available to noncommercial users and implemented in R, with the source code and documentation accessible at https://CRAN.R-project.org/package=rnaCrosslinkOO. The software is supported on Linux, macOS, and Windows platforms.

The histone chaperone SPT2 regulates chromatin structure and function in Metazoa.

Histone chaperones control nucleosome density and chromatin structure. In yeast, the H3-H4 chaperone Spt2 controls histone deposition at active genes but its roles in metazoan chromatin structure and organismal physiology are not known. Here we identify the Caenorhabditis elegans ortholog of SPT2 (CeSPT-2) and show that its ability to bind histones H3-H4 is important for germline development and transgenerational epigenetic gene silencing, and that spt-2 null mutants display signatures of a global stress response. Genome-wide profiling showed that CeSPT-2 binds to a range of highly expressed genes, and we find that spt-2 mutants have increased chromatin accessibility at a subset of these loci. We also show that SPT2 influences chromatin structure and controls the levels of soluble and chromatin-bound H3.3 in human cells. Our work reveals roles for SPT2 in controlling chromatin structure and function in Metazoa.

Solute depletion and reduced hydrological connectivity in subarctic patterned peatlands disturbed by mine dewatering.

Patterned bog and fen peatlands of the Hudson Bay Lowlands, which form one of the largest continuous peatland complexes in the world, are globally significant stores of carbon and important water conveyance and storage features on the landscape. However, expansion of resource exploration and extraction combined with warmer temperatures associated with climate change may result in reduced water availability to these peatland complexes, potentially disrupting peatland hydrological connectivity and hydrogeochemical cycling. A case study on the effects of reduced water availability on peatland hydrological and geochemical function was conducted near the De Beers Victor Diamond Mine, located 90 km west of Attawapiskat. Active dewatering occurred here over a 12-year period (2007-2019) during which a 1.5 km transect was monitored within the mine impacted radius. Hydrological (streamflow and groundwater levels) and chemical (porewater and surface water samples) parameters were collected at the impacted transect and two nearby unimpacted reference sites. Results demonstrated that impacted peatlands had depleted water storage and spent an average of 50 % less time hydrologically connected than unimpacted peatlands. By the end of the study period, increasingly depleted water storage within the dewatering radius resulted in disproportionately lower flowrates in two tributaries downgradient of the mine-impacted peatlands when compared with the reference sites. Moreover, diminished water storage allowed solute-depleted precipitation to reach greater depths within the peat profile, while stronger downwards gradients suppressed upwards flow into fens, limiting the amount of solute-enriched water reaching the surface. The recovery of fen solute concentrations will be a prolonged process (i.e., decades to centuries) due to the slow rate of upwards diffusion, which may result in the transition of these systems towards ombrotrophic bogs. Further studies should focus on the susceptibility of these impacted systems to further reductions in water availability due to climate change.

Diurnal temperature range as a key predictor of plants' elevation ranges globally.

A prominent hypothesis in ecology is that larger species ranges are found in more variable climates because species develop broader environmental tolerances, predicting a positive range size-temperature variability relationship. However, this overlooks the extreme temperatures that variable climates impose on species, with upper or lower thermal limits more likely to be exceeded. Accordingly, we propose the 'temperature range squeeze' hypothesis, predicting a negative range size-temperature variability relationship. We test these contrasting predictions by relating 88,000 elevation range sizes of vascular plants in 44 mountains to short- and long-term temperature variation. Consistent with our hypothesis, we find that species' range size is negatively correlated with diurnal temperature range. Accurate predictions of short-term temperature variation will become increasingly important for extinction risk assessment in the future.

Principles of Child Health Care Financing.

The American Academy of Pediatrics believes that the United States can and should ensure that all children, adolescents, and young adults from birth through the age of 26 years who reside within its borders have affordable access to high-quality comprehensive health care. Comprehensive, high-quality care addresses issues, challenges, and opportunities unique to children and young adults and addresses the effects of historic and present inequities. All families should have equitable access to professionals and facilities with expertise in the care of children within a reasonable distance of their residence. Payment methodologies should be structured to guarantee the economic viability of the pediatric medical home and of pediatric specialty and subspecialty practices. The recent increase in child uninsurance over the last several years is a threat to the well-being of children and families in the short- and long-term. Deficiencies in plans currently covering insured children pose similar threats. The AAP believes that the United States must not sacrifice recent hard-won gains for our children and that child health care financing should be based on the following guiding principles: (1) coverage with quality, affordable health insurance should be universal; (2) comprehensive pediatric services should be covered; (3) cost sharing should be affordable and should not negatively affect care; (4) payment should be adequate to strengthen family- and patient-centered medical homes; (5) child health financing policy should promote equity and address longstanding health and health care disparities; and (6) the unique characteristics and needs of children should be reflected.

Assembly of functional diversity in an oceanic island flora.

Oceanic island floras are well known for their morphological peculiarities and exhibit striking examples of trait evolution1-3. These morphological shifts are commonly attributed to insularity and are thought to be shaped by the biogeographical processes and evolutionary histories of oceanic islands2,4. However, the mechanisms through which biogeography and evolution have shaped the distribution and diversity of plant functional traits remain unclear5. Here we describe the functional trait space of the native flora of an oceanic island (Tenerife, Canary Islands, Spain) using extensive field and laboratory measurements, and relate it to global trade-offs in ecological strategies. We find that the island trait space exhibits a remarkable functional richness but that most plants are concentrated around a functional hotspot dominated by shrubs with a conservative life-history strategy. By dividing the island flora into species groups associated with distinct biogeographical distributions and diversification histories, our results also suggest that colonization via long-distance dispersal and the interplay between inter-island dispersal and archipelago-level speciation processes drive functional divergence and trait space expansion. Contrary to our expectations, speciation via cladogenesis has led to functional convergence, and therefore only contributes marginally to functional diversity by densely packing trait space around shrubs. By combining biogeography, ecology and evolution, our approach opens new avenues for trait-based insights into how dispersal, speciation and persistence shape the assembly of entire native island floras.

Association between 6-thioguanine nucleotide levels and preventing production of antibodies to infliximab in patients with inflammatory bowel disease.

OBJECTIVE: Combination therapy with infliximab and a thiopurine has been shown to be more effective than monotherapy in patients with inflammatory bowel disease (IBD). The therapeutic efficacy of thiopurines is correlated with 6-thioguanine (6-TGN) levels between 235 and 450 pmol/8×108 erythrocytes. The primary aim of the study was to investigate the association between 6-TGN levels and inhibition prevention of the production of antibodies to infliximab (ATI). DESIGN: We performed a retrospective review of the medical records of patients being treated with infliximab for IBD at University Hospitals Bristol NHS Foundation Trust. Demographic and biochemical data were extracted, alongside thiopurine metabolite levels, trough levels of infliximab and the presence of ATI. χ2 tests were used to investigate the association between 6-TGN levels and prevention of ATI. Logistic regression was used to compare the odds of prevented ATI between those with a 6-TGN level between 235 and 450 pmol/8×108 erythrocytes, those with a 6-TGN level outside of this range, and the baseline group who were on infliximab monotherapy. RESULTS: Data were extracted for 100 patients. Six of 32 patients with a 6-TGN level between 235 and 450 pmol/8×108 erythrocytes developed ATI (18.8%) compared with 14 out of 22 (63.6%) patients with a 6-TGN outside of this range and 32 out of 46 (69.6%) patients on monotherapy (p=0.001). The OR (95% CI) for prevented ATI in those with a 6-TGN between 235 and 450 pmol/8×108 erythrocytes compared with a 6-TGN outside of this range was 7.6 (2.2, 26.3) (p=0.001) and compared with monotherapy was 9.9 (3.3, 29.4) (p=0.001). CONCLUSION: 6-TGN levels between 235 and 450 pmol/8×108 erythrocytes prevented production of ATI. This supports therapeutic drug monitoring to help guide treatment and maximise the beneficial effects of combination therapy for patients with IBD.

Multiphase flow behavior of diesel in bog, fen, and swamp peats.

Hydrocarbon fate and transport in various categories of peatlands is complicated by the botanical origin, and thus variations in the hydraulic structures and surface chemistry of its peat soils. There has been no systematic evaluation of the role of different peat types on hydrocarbon migration. Thus, two-phase, and three-phase flow experiments were performed for living and partially decomposed peat cores from bog, fen, and swamp peatlands. Numerical simulations of water drainage were performed using HYDRUS-1D, diesel-water and diesel-water-air flow using MATLAB Reservoir Simulation Toolbox (MRST). Five water table (WT) fluctuations were imposed to explore its potential to reduce residual diesel saturation in peat columns. Our results demonstrate a good match of the relative water permeability (krw) - saturation (S) relations estimated using the unsaturated hydraulic conductivity-S relation derived from HYDRUS-1D modeling of two-phase flow, and krw - S from MRST for three-phase flow, for all tested peat columns. Thus, we recommended using two-phase system based krw - S predictions if multiphase data are unavailable for peatland sites' spill management plans. We found the discharge of water and diesel both increase with increasing hydraulic conductivity, while residual water and diesel were within the range of 0.42-0.52 and of 0.04-0.11, respectively. High diesel discharge rates suggest that quick spill-response is required to manage its spread in peatlands. Up to 29% of residual diesel saturation was yielded by the five WT fluctuations, and thus we strongly recommend WT manipulation as a first step towards diesel decontamination progression in peatlands.

Evolutionary genomics of oceanic island radiations.

A recurring feature of oceanic archipelagos is the presence of adaptive radiations that generate endemic, species-rich clades that can offer outstanding insight into the links between ecology and evolution. Recent developments in evolutionary genomics have contributed towards solving long-standing questions at this interface. Using a comprehensive literature search, we identify studies spanning 19 oceanic archipelagos and 110 putative adaptive radiations, but find that most of these radiations have not yet been investigated from an evolutionary genomics perspective. Our review reveals different gaps in knowledge related to the lack of implementation of genomic approaches, as well as undersampled taxonomic and geographic areas. Filling those gaps with the required data will help to deepen our understanding of adaptation, speciation, and other evolutionary processes.

The Unique Value Proposition of Pediatric Health Care.

This document provides a framework for the value proposition of pediatric health care. It is intended to provide a succinct set of principles for establishing this proposition that demonstrates the short- and long-term value to the child and family, the health care system, and society as a whole.

Loss of the E3 ubiquitin ligases UBR-5 or HECD-1 restores Caenorhabditis elegans development in the absence of SWI/SNF function.

SWItch/sucrose non-fermenting (SWI/SNF) complexes are a family of chromatin remodelers that are conserved across eukaryotes. Mutations in subunits of SWI/SNF cause a multitude of different developmental disorders in humans, most of which have no current treatment options. Here, we identify an alanine-to-valine-causing mutation in the SWI/SNF subunit snfc-5 (SMARCB1 in humans) that prevents embryonic lethality in Caenorhabditis elegans nematodes harboring a loss-of-function mutation in the SWI/SNF subunit swsn-1 (SMARCC1/2 in humans). Furthermore, we found that the combination of this specific mutation in snfc-5 and a loss-of-function mutation in either of the E3 ubiquitin ligases ubr-5 (UBR5 in humans) or hecd-1 (HECTD1 in humans) can restore development to adulthood in swsn-1 loss-of-function mutants that otherwise die as embryos. Using these mutant models, we established a set of 335 genes that are dysregulated in SWI/SNF mutants that arrest their development embryonically but exhibit near wild-type levels of expression in the presence of suppressor mutations that prevent embryonic lethality, suggesting that SWI/SNF promotes development by regulating some subset of these 335 genes. In addition, we show that SWI/SNF protein levels are reduced in swsn-1; snfc-5 double mutants and partly restored to wild-type levels in swsn-1; snfc-5; ubr-5 triple mutants, consistent with a model in which UBR-5 regulates SWI/SNF levels by tagging the complex for proteasomal degradation. Our findings establish a link between two E3 ubiquitin ligases and SWI/SNF function and suggest that UBR5 and HECTD1 could be potential therapeutic targets for the many developmental disorders caused by missense mutations in SWI/SNF subunits.

Aquifer depressurization and water table lowering induces landscape scale subsidence and hydrophysical change in peatlands of the Hudson Bay Lowlands.

The depositional history of the Hudson Bay Lowlands (HBL) in Ontario, Canada has created a low relief, poorly drained landscape, favouring the formation of one of the largest peatland complexes in the world. High volume dewatering associated with resource extraction in this area, such as the De Beers Victor Diamond Mine, tests the ability of the underlying confining layer to limit water losses in the peatlands above. This research quantifies the deepening of water tables and increase in effective stress related to mine dewatering and the resulting changes to bog and fen peatland hydrophysical structure and function. Long-term implications of these impacts are discussed. One impacted and two unimpacted transects were instrumented for meteorological (precipitation and evapotranspiration) and hydrophysical (hydraulic head, hydraulic conductivity (Ksat), and surface elevation) monitoring over a 12-year period in the vicinity of the Victor Mine. Over this study period, the unimpacted peatlands operated within relative hydrological equilibrium, demonstrated through shallow water tables, negligible subsidence, and stable Ksat. Contrastingly, all impacted peatlands experienced deeper watertables, larger downwards gradients, and measurable long-term subsidence (4-15 cm). Hydrological impacts were highest in bogs with a thin underlying confining layer even if they were farther from the point of dewatering, highlighting the need for environmental monitoring programs which incorporate an assessment of aquitard thickness. Where subsidence occurred, associated decreases in Ksat deflected bog-fen-tributary flow-paths deeper, reducing the upwards transport of solute rich water to downgradient fens. The long-term effects of these landscape scale changes should be studied further, particularly since climate change in this region will potentially increase water deficits and further alter peatland connectivity. Peatland studies should be conducted in different landscapes experiencing water table lowering due to drought or depressurization in order to better understand the associated subsidence patterns and hydrophysical changes in varying geological and morphological regimes.

(The shift to) online delivery of a rural faculty development program in research skills: lessons learned.

BACKGROUND: While rural physicians are the ideal candidates to investigate health and healthcare issues in rural communities, they often lack the required skills, competencies, and resources. As a result, research skills development programs are crucial to help ensure communities receive the quality of care they deserve. Memorial University of Newfoundland created a research skills development program called 6for6 to empower and enable rural physicians to research solutions to community-specific health needs. 6for6 program delivery was exclusively in-person until 2019. However, with limitations introduced due to the COVID-19 pandemic, organizations around the globe needed to respond quickly. As we work to return to a post-pandemic environment, program administrators and educators worldwide are unsure whether to retain or remove the changes made to programs to adapt to the pandemic restrictions. Therefore, this work addresses the impact of the online delivery model in two areas: 1) attainment of competencies (specifically research skills, knowledge, and attitudes); and 2) participant experiences, defined as the ease of attendance, the capacity to interact with team members and peers, and challenges or barriers associated with navigating program resources. METHODS: We compared the effect of an online delivery model pivoted to adapt pandemic restrictions with the original model (primarily face-to-face) on the acquisition of learning competencies and participant experience using a mixed-methods study. Various data collection methods, such as a pre-post program survey, post-program focus group, and structured observation, were utilized. RESULTS: From 2014 to 2021, 35 physicians attended the program (30 face-to-face and five online). The Wilcoxon-sign-rank test did not show any significant differences in the participants' median change of research competency scores who attended face-to-face and online learning, respectively: knowledge (32.6, 26.8), attitudes (3.8, 3.5), and skills (32.4, 20.0). Flexibility and accessibility were key aspects of participants' experiences during the online model. Comparison with previous years demonstrated no significant challenges with the virtual delivery model, yet participants struggled with mentorship challenges and learning-life balance. CONCLUSIONS: Although presenting some unique challenges, the online model did not negatively affect learner competencies. Likewise, it provided opportunities for rural physicians to attend learning sessions and interact with experts and peers while remaining in their communities.

Predictable and stable epimutations induced during clonal plant propagation with embryonic transcription factor.

Clonal propagation is frequently used in commercial plant breeding and biotechnology programs because it minimizes genetic variation, yet it is not uncommon to observe clonal plants with stable phenotypic changes, a phenomenon known as somaclonal variation. Several studies have linked epigenetic modifications induced during regeneration with this newly acquired phenotypic variation. However, the factors that determine the extent of somaclonal variation and the molecular changes underpinning this process remain poorly understood. To address this gap in our knowledge, we compared clonally propagated Arabidopsis thaliana plants derived from somatic embryogenesis using two different embryonic transcription factors- RWP-RK DOMAIN-CONTAINING 4 (RKD4) or LEAFY COTYLEDON2 (LEC2) and from two epigenetically distinct founder tissues. We found that both the epi(genetic) status of the explant and the regeneration protocol employed play critical roles in shaping the molecular and phenotypic landscape of clonal plants. Phenotypic variation in regenerated plants can be largely explained by the inheritance of tissue-specific DNA methylation imprints, which are associated with specific transcriptional and metabolic changes in sexual progeny of clonal plants. For instance, regenerants were particularly affected by the inheritance of root-specific epigenetic imprints, which were associated with an increased accumulation of salicylic acid in leaves and accelerated plant senescence. Collectively, our data reveal specific pathways underpinning the phenotypic and molecular variation that arise and accumulate in clonal plant populations.

Guiding Principles for Managed Care Arrangements for the Health of Newborns, Infants, Children, Adolescents and Young Adults.

Managed care arrangements are an approach to health care delivery in which the payer or other health care entity has policies that affect where care is delivered, what services are covered, and how payment is determined. When policies are intentionally designed, transparently administered, and continuously monitored, they are more likely to improve the population's utilization of services, access to quality primary and specialty care, and access to appropriate medications. When managed care arrangements are designed well, particularly within evolving payment models, health care can be delivered in a manner that supports the goals of the Quadruple Aim: to reduce per capita costs of health care, to improve the health of populations, to improve the experience of patients receiving care, and to improve the experience of those who are providing care. The American Academy of Pediatrics (AAP) urges payers and health care entities to use the key principles outlined in this statement when designing and implementing managed care arrangements and policies that cover newborn infants, infants, children, adolescents, and young adults to support the goal of improving the effectiveness of the health care delivery system for the pediatric population. The principles described in this statement are intended to complement those previously published in other AAP policies including "Principles of Child Health Care Financing," "Scope of Health Care Benefits for Children From Birth Through Age 26," "Patient- and Family-Centered Care and the Pediatrician's Role," and the "AAP Access Principles."

Projecting the hydrochemical trajectory of a constructed fen watershed: Implications for long-term wetland function.

Surface mining operations for bitumen have fundamentally altered large areas of boreal forest and fen peatland in the Athabasca Oil Sands Region (AOSR) of Alberta, Canada. Pilot projects intended to assess the feasibility of fen construction as a reclamation option have been designed, built, and are currently undergoing monitoring. Initial assessments of ecohydrologic function have been conducted for these systems but offer limited insight into their evolution and likely successional pathway. Thus, this study projects the hydrologic and geochemical behaviour of a constructed fen watershed to understand whether the system will be capable of supporting peatland processes into the future. A numerical groundwater flow and sodium transport model was calibrated and validated with 7 years of hydraulic head, water flux, and water chemistry data. Based on Monte Carlo simulations, the projected fen water table would be stable and remain close to the surface (<15 cm), indicating that the design of the system can generate sufficient water quantity to meet evaporative demand and maintain surface water discharge. However, water quality was more sensitive to climatic variability, which induced a large range in potential sodium concentrations at the fen surface (450-850 mg L-1). Evapoconcentration of salts across the surface of the fen will likely limit moss establishment for decades following construction. Yet stress-thresholds of salt-tolerant vegetation like sedges will not be exceeded. Ultimately, these projections support the original design principles and philosophy that guided the creation of the watershed. Nonetheless, this work indicates that increasing the area of the fen relative to the upland would not have a detrimental impact on the ability of the system to maintain a high water table. This could allow for the proportion of peatlands on the reclamation landscape to reflect the pre-disturbance environment more faithfully.

Characterizing the hydraulic and transport properties of a constructed coarse tailings sand aquifer.

Millions of tonnes of coarse tailings sand are produced every year as a byproduct of the bitumen extraction process in the Athabasca Oil Sands Region. These tailings materials contain residual quantities of mobile solutes, which can be transported through groundwater to downgradient terrestrial and aquatic ecosystems. The anticipated ubiquity of coarse tailings sand on the post-mined landscape necessitates the characterization of its hydraulic and transport properties. Hydraulic conductivity and dispersivity was evaluated at multiple scales, and included the first field-scale tracer test conducted in a tailings sand aquifer. Average hydraulic conductivity derived using laboratory cores, single-well response tests, and the tracer test were 3.2 m d-1, 2.9 m d-1, and 3.4 m d-1, respectively. These measurements demonstrated close agreement and were consistent with expectations of a material that experiences some grain-size segregation and homogenization due to the oil sands process and the nature of deposition. The field-scale tracer test appeared to obtain the asymptotic dispersivity of the coarse tailings sand aquifer, reaching a maximum value of 0.5 m after 18 m of displacement. Coarse tailings in the oil sands that experience similar processes of segregation, settling, and deposition on the reclamation landscape could be expected to have similar hydraulic properties.

RNA uridyl transferases TUT4/7 differentially regulate miRNA variants depending on the cancer cell type.

The human terminal uridyl transferases TUT4 and TUT7 (TUT4/7) catalyze the additions of uridines at the 3' end of RNAs, including the precursors of the tumor suppressor miRNA let-7 upon recruitment by the oncoprotein LIN28A. As a consequence, let-7 family miRNAs are down-regulated. Disruption of this TUT4/7 activity inhibits tumorigenesis. Hence, targeting TUT4/7 could be a potential anticancer therapy. In this study, we investigate TUT4/7-mediated RNA regulation in two cancer cell lines by establishing catalytic knockout models. Upon TUT4/7 mutation, we observe a significant reduction in miRNA uridylation, which results in defects in cancer cell properties such as cell proliferation and migration. With the loss of TUT4/7-mediated miRNA uridylation, the uridylated miRNA variants are replaced by adenylated isomiRs. Changes in miRNA modification profiles are accompanied by deregulation of expression levels in specific cases. Unlike let-7s, most miRNAs do not depend on LIN28A for TUT4/7-mediated regulation. Additionally, we identify TUT4/7-regulated cell-type-specific miRNA clusters and deregulation in their corresponding mRNA targets. Expression levels of miR-200c-3p and miR-141-3p are regulated by TUT4/7 in a cancer cell-type-specific manner. Subsequently, BCL2, which is a well-established target of miR-200c is up-regulated. Therefore, TUT4/7 loss causes deregulation of miRNA-mRNA networks in a cell-type-specific manner. Understanding of the underlying biology of such cell-type-specific deregulation will be an important aspect of targeting TUT4/7 for potential cancer therapies.