Control of 3' splice site selection by the yeast splicing factor Fyv6.

Pre-mRNA splicing is catalyzed in two steps: 5' splice site (SS) cleavage and exon ligation. A number of proteins transiently associate with spliceosomes to specifically impact these steps (1st and 2nd step factors). We recently identified Fyv6 (FAM192A in humans) as a 2nd step factor in S. cerevisiae; however, we did not determine how widespread Fyv6's impact is on the transcriptome. To answer this question, we have used RNA-seq to analyze changes in splicing. These results show that loss of Fyv6 results in activation of non-consensus, branch point (BP) proximal 3' SS transcriptome-wide. To identify the molecular basis of these observations, we determined a high-resolution cryo-EM structure of a yeast product complex spliceosome containing Fyv6 at 2.3 Å. The structure reveals that Fyv6 is the only 2nd step factor that contacts the Prp22 ATPase and that Fyv6 binding is mutually exclusive with that of the 1st step factor Yju2. We then use this structure to dissect Fyv6 functional domains and interpret results of a genetic screen for fyv6Δ suppressor mutations. The combined transcriptomic, structural, and genetic studies allow us to propose a model in which Yju2/Fyv6 exchange facilitates exon ligation and Fyv6 promotes usage of consensus, BP distal 3' SS.

Biochemical and genetic evidence supports Fyv6 as a second-step splicing factor in Saccharomyces cerevisiae.

Precursor mRNA (pre-mRNA) splicing is an essential process for gene expression in eukaryotes catalyzed by the spliceosome in two transesterification steps. The spliceosome is a large, highly dynamic complex composed of five small nuclear RNAs and dozens of proteins, some of which are needed throughout the splicing reaction while others only act during specific stages. The human protein FAM192A was recently proposed to be a splicing factor that functions during the second transesterification step, exon ligation, based on analysis of cryo-electron microscopy (cryo-EM) density. It was also proposed that Fyv6 might be the Saccharomyces cerevisiae functional and structural homolog of FAM192A; however, no biochemical or genetic data has been reported to support this hypothesis. Herein, we show that Fyv6 is a splicing factor and acts during exon ligation. Deletion of FYV6 results in genetic interactions with the essential splicing factors Prp8, Prp16, and Prp22 and decreases splicing in vivo of reporter genes harboring intron substitutions that limit the rate of exon ligation. When splicing is assayed in vitro, whole-cell extracts lacking Fyv6 accumulate first-step products and exhibit a defect in exon ligation. Moreover, loss of Fyv6 causes a change in 3' splice site (SS) selection in both a reporter gene and the endogenous SUS1 transcript in vivo. Together, these data suggest that Fyv6 is a component of the yeast spliceosome that influences 3' SS usage and the potential homolog of human FAM192A.

Effects of Wild Blueberries on Fat Oxidation Rates in Aerobically Trained Males.

Wild blueberries (WBs) have been documented to decrease oxidative stress in active and sedentary populations as well as influence lipolytic enzymes and increase the rate of fat oxidation (FAT-ox) during rest. To examine the effect of WBs on the rate of FAT-ox and lipid peroxidation during submaximal exercise, 11 healthy, aerobically trained males (26 ± 7.5 years, 74.9 ± 7.54 kg, 10.5 ± 3.2% BF) completed a 2-week washout avoiding foods high in anthocyanins, then completed a control exercise protocol cycling at 65% of VO2peak for 40 min. Participants then consumed 375 g/d of anthocyanins for two weeks before repeating the exercise protocol. WBs increased FAT-ox when cycling at 65% of VO2peak by 19.7% at 20, 43.2% at 30, and 31.1% at 40 min, and carbohydrate oxidation (CHO-ox) decreased by 10.1% at 20, 19.2% at 30, and 14.8% at 40 min of cycling at 65% of VO2peak. Lactate was lower with WBs at 20 (WB: 2.6 ± 1.0, C: 3.0 ± 1.1), 30 (WB: 2.2 ± 0.9, C: 2.9 ± 1.0), and 40 min (WB: 1.9 ± 0.8, C: 2.5 ± 0.9). Results indicate that WBs may increase the rate of FAT-ox during moderate-intensity activity in healthy, active males.

Developmental care pathway for hospitalised infants with CHD: on behalf of the Cardiac Newborn Neuroprotective Network, a Special Interest Group of the Cardiac Neurodevelopmental Outcome Collaborative.

Infants and children born with CHD are at significant risk for neurodevelopmental delays and abnormalities. Individualised developmental care is widely recognised as best practice to support early neurodevelopment for medically fragile infants born premature or requiring surgical intervention after birth. However, wide variability in clinical practice is consistently demonstrated in units caring for infants with CHD. The Cardiac Newborn Neuroprotective Network, a Special Interest Group of the Cardiac Neurodevelopmental Outcome Collaborative, formed a working group of experts to create an evidence-based developmental care pathway to guide clinical practice in hospital settings caring for infants with CHD. The clinical pathway, "Developmental Care Pathway for Hospitalized Infants with Congenital Heart Disease," includes recommendations for standardised developmental assessment, parent mental health screening, and the implementation of a daily developmental care bundle, which incorporates individualised assessments and interventions tailored to meet the needs of this unique infant population and their families. Hospitals caring for infants with CHD are encouraged to adopt this developmental care pathway and track metrics and outcomes using a quality improvement framework.

Biochemical and Genetic Evidence Supports Fyv6 as a Second-Step Splicing Factor in Saccharomyces cerevisiae.

Precursor mRNA (pre-mRNA) splicing is an essential process for gene expression in eukaryotes catalyzed by the spliceosome in two transesterification steps. The spliceosome is a large, highly dynamic complex composed of 5 small nuclear RNAs and dozens of proteins, some of which are needed throughout the splicing reaction while others only act during specific stages. The human protein FAM192A was recently proposed to be a splicing factor that functions during the second transesterification step, exon ligation, based on analysis of cryo-electron microscopy (cryo-EM) density. It was also proposed that Fyv6 might be the functional S. cerevisiae homolog of FAM192A; however, no biochemical or genetic data has been reported to support this hypothesis. Herein, we show that Fyv6 is a splicing factor and acts during exon ligation. Deletion of FYV6 results in genetic interactions with the essential splicing factors Prp8, Prp16, and Prp22; decreases splicing in vivo of reporter genes harboring intron substitutions that limit the rate of exon ligation; and changes 3’ splice site (SS) selection. Together, these data suggest that Fyv6 is a component of the spliceosome and the potential functional and structural homolog of human FAM192A.

Foraging strategy influences the quantity of ingested micro- and nanoplastics in shorebirds.

Coastlines, including estuaries, mudflats, and beaches, are particularly susceptible to plastic pollution, which can accumulate from both marine and terrestrial sources. While numerous studies have confirmed the presence of microplastics (1-5 mm) along coastlines, few have focused on very small particles (<1 µm) or quantified exposure within the organisms that inhabit these areas, such as shorebirds. Here, we quantified small plastics (200 nm-70 µm) in two resident shorebird species in Tasmania, and compared this to quantities found in the surrounding sediments in order to investigate the potential exposure and transfer of particles within these ecosystems. Analysis was performed using a combination of flow cytometry for quantification of micro- and nanoplastics (200 nm-70 µm), and µm-FT-IR for validation and polymer identification of particles >5.5 × 5.5 µm. Micro- and nano-plastics were detected in 100% of guano samples from surface-feeding Eastern Hooded Plovers (Thinornis cucullatus) and 90% of Australian Pied Oystercatcher (Haematopus longirostris) guano, a species that forages for coastal invertebrates at 60-90 mm depth, and 100% of beach sediments. Hooded Plover guano contained 32 × more plastics, on average, than Pied Oystercatcher guano. Interestingly, the abundance of plastic particles within sediments collected from shorebird foraging sites did not appear to have a significant effect on the number of plastics the birds had ingested, suggesting the difference between species is likely a result of other variables, such as prey selection. The results of this study highlight the importance of including techniques that provide quantitative data on the abundance and size of the smallest possible particle sizes, and demonstrate the significant proportion of small plastics that are 'missed' using standard analysis tools.

New Methods for the Quantification of Ingested Nano- and Ultrafine Plastics in Seabirds.

Plastic ingestion has been documented in a plethora of taxa. However, there is a significant gap in the detection of nano- and ultrafine particles due to size limitations of commonly used techniques. Using two Australian seabird species as case studies, the flesh-footed shearwater (FFSH) Ardenna carneipes and short-tailed shearwater (STSH) A. tenuirostris, we tested a novel approach of flow cytometry to quantify ingested particles <70 µm in the fecal precursor (guano; colon and cloacal contents) of both species. This method provided the first baseline data set for these species for plastics in the 200 nm-70 µm particle size ranges and detected a mean of 553.50 ± 91.21 and 350.70 ± 52.08 plastics (count/mg fecal precursor, wet mass) in STSH and FFSH, respectively, whereas Fourier transform infrared spectroscopy (FT-IR) provided accurate measurements of polymer compositions and quantities in the size range above 5.5 × 5.5 µm2. The abundance of nano- and ultrafine particles in the guano (count/mg) was not significantly different between species (p-value = 0.051), suggesting that foraging distribution or prey items, but not species, may contribute to the consumption of small plastics. In addition, there was no correlation between macroplastics in the stomach compared to the fecal precursor, indicating that small particles are likely bioaccumulating (e.g., through shedding and digestive fragmentation) and/or being directly ingested. Combining flow cytometry with FT-IR provides a powerful quantitative and qualitative analysis tool for detecting particles orders of magnitude smaller than that are currently explored with wider applications across taxa and marine environments.

Assessment and management of feeding difficulties for infants with complex CHD.

Early surgical intervention in infants with complex CHD results in significant disruptions to their respiratory, gastrointestinal, and nervous systems, which are all instrumental to the development of safe and efficient oral feeding skills. Standardised assessments or treatment protocols are not currently available for this unique population, requiring the clinician to rely on knowledge based on neonatal literature. Clinicians need to be skilled at evaluating and analysing these systems to develop an appropriate treatment plan to improve oral feeding skill and safety, while considering post-operative recovery in the infant with complex CHD. Supporting the family to re-establish their parental role during the hospitalisation and upon discharge is critical to reducing parental stress and oral feeding success.

Yeast U6 snRNA made by RNA polymerase II is less stable but functional.

U6 small nuclear (sn)RNA is the shortest and most conserved snRNA in the spliceosome and forms a substantial portion of its active site. Unlike the other four spliceosomal snRNAs, which are synthesized by RNA polymerase (RNAP) II, U6 is made by RNAP III. To determine if some aspect of U6 function is incompatible with synthesis by RNAP II, we created a U6 snRNA gene with RNAP II promoter and terminator sequences. This "U6-II" gene is functional as the sole source of U6 snRNA in yeast, but its transcript is much less stable than U6 snRNA made by RNAP III. Addition of the U4 snRNA Sm protein binding site to U6-II increased its stability and led to formation of U6-II•Sm complexes. We conclude that synthesis of U6 snRNA by RNAP III is not required for its function and that U6 snRNPs containing the Sm complex can form in vivo. The ability to synthesize U6 snRNA with RNAP II relaxes sequence restraints imposed by intragenic RNAP III promoter and terminator elements and allows facile control of U6 levels via regulators of RNAP II transcription.

3D Bioprinted Multicellular Vascular Models.

3D bioprinting is an emerging additive manufacturing technique to fabricate constructs for human disease modeling. However, current cell-laden bioinks lack sufficient biocompatibility, printability, and structural stability needed to translate this technology to preclinical and clinical trials. Here, a new class of nanoengineered hydrogel-based cell-laden bioinks is introduced, that can be printed into 3D, anatomically accurate, multicellular blood vessels to recapitulate both the physical and chemical microenvironments of native human vasculature. A remarkably unique characteristic of this bioink is that regardless of cell density, it demonstrates a high printability and ability to protect encapsulated cells against high shear forces in the bioprinting process. 3D bioprinted cells maintain a healthy phenotype and remain viable for nearly one-month post-fabrication. Leveraging these properties, the nanoengineered bioink is printed into 3D cylindrical blood vessels, consisting of living co-culture of endothelial cells and vascular smooth muscle cells, providing the opportunity to model vascular function and pathophysiology. Upon cytokine stimulation and blood perfusion, this 3D bioprinted vessel is able to recapitulate thromboinflammatory responses observed only in advanced in vitro preclinical models or in vivo. Therefore, this 3D bioprinted vessel provides a potential tool to understand vascular disease pathophysiology and assess therapeutics, toxins, or other chemicals.

Mechanotransduction-on-chip: vessel-chip model of endothelial YAP mechanobiology reveals matrix stiffness impedes shear response.

Endothelial mechanobiology is a key consideration in the progression of vascular dysfunction, including atherosclerosis. However mechanistic connections between the clinically associated physical stimuli, vessel stiffness and shear stress, and how they interact to modulate plaque progression remain incompletely characterized. Vessel-chip systems are excellent candidates for modeling vascular mechanobiology as they may be engineered from the ground up, guided by the mechanical parameters present in human arteries and veins, to recapitulate key features of the vasculature. Here, we report extensive validation of a vessel-chip model of endothelial yes-associated protein (YAP) mechanobiology, a protein sensitive to both matrix stiffness and shearing forces and, importantly, implicated in atherosclerotic progression. Our model captures the established endothelial mechanoresponse, with endothelial alignment, elongation, reduction of adhesion molecules, and YAP cytoplasmic retention under high laminar shear. Conversely, we observed disturbed morphology, inflammation, and nuclear partitioning under low, high, and high oscillatory shear. Examining targets of YAP transcriptional co-activation, connective tissue growth factor (CTGF) is strongly downregulated by high laminar shear, whereas it is strongly upregulated by low shear or oscillatory flow. Ankyrin repeat domain 1 (ANKRD1) is only upregulated by high oscillatory shear. Verteporfin inhibition of YAP reduced the expression of CTGF but did not affect ANKRD1. Lastly, substrate stiffness modulated the endothelial shear mechanoresponse. Under high shear, softer substrates showed the lowest nuclear localization of YAP whereas stiffer substrates increased nuclear localization. Low shear strongly increased nuclear localization of YAP across stiffnesses. Together, we have validated a model of endothelial mechanobiology and describe a clinically relevant biological connection between matrix stiffness, shear stress, and endothelial activation via YAP mechanobiology.

Disruptions in the development of feeding for infants with congenital heart disease.

Congenital heart disease (CHD) is the most common birth defect for infants born in the United States, with approximately 36,000 affected infants born annually. While mortality rates for children with CHD have significantly declined, there is a growing population of individuals with CHD living into adulthood prompting the need to optimise long-term development and quality of life. For infants with CHD, pre- and post-surgery, there is an increased risk of developmental challenges and feeding difficulties. Feeding challenges carry profound implications for the quality of life for individuals with CHD and their families as they impact short- and long-term neurodevelopment related to growth and nutrition, sensory regulation, and social-emotional bonding with parents and other caregivers. Oral feeding challenges in children with CHD are often the result of medical complications, delayed transition to oral feeding, reduced stamina, oral feeding refusal, developmental delay, and consequences of the overwhelming intensive care unit (ICU) environment. This article aims to characterise the disruptions in feeding development for infants with CHD and describe neurodevelopmental factors that may contribute to short- and long-term oral feeding difficulties.

Suppressor of IKKepsilon forms direct interactions with cytoskeletal proteins, tubulin and α-actinin, linking innate immunity to the cytoskeleton.

Suppressor of IKKepsilon (SIKE) is associated with the type I interferon response of the innate immune system through TANK-binding kinase 1 (TBK1). Originally characterized as an endogenous inhibitor of TBK1 when overexpressed in viral infection and pathological cardiac hypertrophic models, a mechanistic study revealed that SIKE acts as a high-affinity substrate of TBK1, but its function remains unknown. In this work, we report that scratch assay analysis of parental and SIKE CRISPR/Cas9 knockout HAP1 cells showed an ~ 20% decrease in cell migration. Investigation of the SIKE interaction network through affinity purification/mass spectrometry showed that SIKE formed interactions with cytoskeletal proteins. In immunofluorescence assays, endogenous SIKE localized to cytosolic puncta in both epithelial and myeloid cells and to nuclear puncta in myeloid cells, while in epithelial cells additional staining occurred in stress fiber-like structures and adjacent to the plasma membrane. Using cellular markers, co-occurrence of SIKE fluorescence with actin, α-actinin, and ezrin was detected. Reciprocal immunoprecipitation revealed a SIKE:tubulin interaction sensitive to the phosphorylation state of SIKE, but a SIKE:α-actinin interaction was unchanged by SIKE phosphorylation. In vitro precipitation assays confirmed a direct SIKE interaction with tubulin and α-actinin. These results indicate that SIKE may promote cell migration by directly associating with the cytoskeleton. In this role, SIKE may mediate cytoskeletal rearrangement necessary in innate immunity, but also link a key catalytic hub, TBK1, to the cytoskeleton. DATABASE: The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD007262.

Hemostatic and Absorbent PolyHIPE-Kaolin Composites for 3D Printable Wound Dressing Materials.

A novel hemostatic and absorbent wound dressing material compatible with 3D printing is developed to address deficiencies in current wound dressing protocol. The design involves an open celled, microporous hydrogel foam via a high internal phase emulsion (HIPE) template with biocompatible components and tunable hemostatic character by kaolin loading, the viscosity and cure kinetics of which are tailored for 3D printing applications. The use of nontoxic mineral oil organic phase results in cytocompatability with human dermal fibroblasts. Kaolin distribution is shown by X-ray diffraction and elemental dispersive spectroscopy to be exfoliated and dispersed in the hydrogel dressing. In addition to demonstrating high fluid absorption and noncytotoxicity of relevant cell lines, the high internal phase emulsion polymers (polyHIPEs) also match the hemostatic performance of commercial wound dressing materials. Furthermore, the polyHIPEs display the requisite rheological properties for 3D printing that result in the fabrication of a prototype dressing with hierarchical porosity and a large number of controllable form factors.

Nanoengineered Colloidal Inks for 3D Bioprinting.

Nanoengineered hydrogels offer the potential to design shear-thinning bioinks for three-dimensional (3D) bioprinting. Here, we have synthesized colloidal bioinks composed of disk-shaped two-dimensional (2D) nanosilicates (Laponite) and poly(ethylene glycol) (PEG). The addition of Laponite reinforces the PEG network and increases viscosity, storage modulus, and network stability. PEG-Laponite hydrogels display shear-thinning and self-recovery characteristics due to rapid internal phase rearrangement. As a result, a range of complex patterns can be printed using PEG-Laponite bioinks. The 3D bioprinted structure has similar mechanical properties compared to the as-casted structure. In addition, encapsulated cells within the PEG-Laponite bioink show high viability after bioprinting. Overall, this study introduces a new class of PEG-Laponite colloidal inks for bioprinting and cell delivery.

A different placement of the stone; rhinolithiasis.

INTRODUCTION: Rhinolithiasis is a rare disease and formed by mineralization in the nasal cavity. Precipitated calcareous material on intranasal foreign substances forms the rhinoliths. It is start time could have since childhood. MATERIALS AND METHODS: In this article, we present eight cases of rhinolithiasis who admitted to our Clinic between January 2001 and December 2010 with unilateral chronic nasal discharge, nasal obstruction and oral malodor. CONCLUSIONS: Rhinolithiasis mostly manifests itself with unilateral purulent rhinorrhea, nasal obstruction and facial pain symptoms. We aimed to discuss these entity with similar cases in the literature.

Common strategies to prevent and modulate experimental cerebral malaria in mouse strains with different susceptibilities.

Cerebral malaria (CM) is a severe complication of Plasmodium falciparum infection, predominantly experienced by children and nonimmune adults, which results in significant mortality and long-term sequelae. Previous studies have reported distinct susceptibility gene loci in CBA/CaH (CBA) and C57BL/6 (B6) mice with experimental CM (ECM) caused by infection with Plasmodium berghei ANKA. Here we present an analysis of genome-wide expression profiles in brain tissue taken from B6 and CBA mice with ECM and report significant heterogeneity between the two mouse strains. Upon comparison of the leukocyte composition of ECM brain tissue, microglia were expanded in B6 mice but not CBA mice. Furthermore, circulating levels of gamma interferon, interleukin-10, and interleukin-6 were significantly higher in the serum of B6 mice than in that of CBA mice with ECM. Two therapeutic strategies were applied to B6 and CBA mice, i.e., (i) depletion of regulatory T (Treg) cells prior to infection and (ii) depletion of CD8(+) T cells after the establishment of ECM. Despite the described differences between susceptible mouse strains, depletion of Treg cells before infection attenuated ECM in both B6 and CBA mice. In addition, the depletion of CD8(+) T cells when ECM symptoms are apparent leads to abrogation of ECM in B6 mice and a lack of progression of ECM in CBA mice. These results may have important implications for the development of effective treatments for human CM.

Cutting edge: conventional dendritic cells are the critical APC required for the induction of experimental cerebral malaria.

Cerebral malaria (CM) is a serious complication of Plasmodium falciparum infection, causing significant morbidity and mortality among young children and nonimmune adults in the developing world. Although previous work on experimental CM has identified T cells as key mediators of pathology, the APCs and subsets therein required to initiate immunopathology remain unknown. In this study, we show that conventional dendritic cells but not plasmacytoid dendritic cells are required for the induction of malaria parasite-specific CD4+ T cell responses and subsequent experimental CM. These data have important implications for the development of malaria vaccines and the therapeutic management of CM.

Incidence of respiratory cancer among workers exposed to chloromethyl-ethers.

A factory in France had used technical-grade chloromethyl-methyl-ether in the manufacture of anion exchange resins since 1958. Technical-grade chloromethyl-methyl-ether contains a human lung carcinogen, bis-chloromethyl-ether. The purpose of this cohort study was to determine if workers at the factory whose jobs had involved potential exposure to technical chloromethyl-methyl-ether had a higher incidence of lung cancer than coworkers, or others without potential exposure. Lung cancer occurred at a higher rate among potentially exposed workers than among nonexposed workers at the same plant (rate ratio (RR) = 5.0, 95% confidence interval (CI) 2.0-12.3), or among an external reference population (RR = 7.6, 95% CI 4.3-13.5). The average age at diagnosis for exposed cases was 10.5 years lower than for nonexposed cases. The predominantly small-cell cancers of the exposed were mostly oat-cell. There was a positive dose-response relation. The mean time from first exposure to diagnosis was 13 years (95% CI 8-18). Cumulative dose and induction time were not associated. The rate for the exposed workers peaked between 7 and 13 years after the start-up of the chloromethylation process, and was still above background in 1986, the end of the study period.