Profiling dynamic RNA-protein interactions using small-molecule-induced RNA editing.

RNA-binding proteins (RBPs) play an important role in biology, and characterizing dynamic RNA-protein interactions is essential for understanding RBP function. In this study, we developed targets of RBPs identified by editing induced through dimerization (TRIBE-ID), a facile strategy for quantifying state-specific RNA-protein interactions upon rapamycin-mediated chemically induced dimerization and RNA editing. We performed TRIBE-ID with G3BP1 and YBX1 to study RNA-protein interactions during normal conditions and upon oxidative stress-induced biomolecular condensate formation. We quantified editing kinetics to infer interaction persistence and show that stress granule formation strengthens pre-existing RNA-protein interactions and induces new RNA-protein binding events. Furthermore, we demonstrate that G3BP1 stabilizes its targets under normal and oxidative stress conditions independent of stress granule formation. Finally, we apply our method to characterize small-molecule modulators of G3BP1-RNA binding. Taken together, our work provides a general approach to profile dynamic RNA-protein interactions in cellular contexts with temporal control.

Targeting DNA polymerase to DNA double-strand breaks reduces DNA deletion size and increases templated insertions generated by CRISPR/Cas9.

Most insertions or deletions generated by CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) endonucleases are short (<25 bp), but unpredictable on-target long DNA deletions (>500 bp) can be observed. The possibility of generating long on-target DNA deletions poses safety risks to somatic genome editing and makes the outcomes of genome editing less predictable. Methods for generating refined mutations are desirable but currently unavailable. Here, we show that fusing Escherichia coli DNA polymerase I or the Klenow fragment to Cas9 greatly increases the frequencies of 1-bp deletions and decreases >1-bp deletions or insertions. Importantly, doing so also greatly decreases the generation of long deletions, including those >2 kb. In addition, templated insertions (the insertion of the nucleotide 4 nt upstream of the protospacer adjacent motif) were increased relative to other insertions. Counteracting DNA resection was one of the mechanisms perturbing deletion sizes. Targeting DNA polymerase to double-strand breaks did not increase off-targets or base substitution rates around the cleavage sites, yet increased editing efficiency in primary cells. Our strategy makes it possible to generate refined DNA mutations for improved safety without sacrificing efficiency of genome editing.

Global Discovery of Covalent Modulators of Ribonucleoprotein Granules.

Stress granules (SGs) and processing-bodies (PBs, P-bodies) are ubiquitous and widely studied ribonucleoprotein (RNP) granules involved in cellular stress response, viral infection, and the tumor microenvironment. While proteomic and transcriptomic investigations of SGs and PBs have provided insights into molecular composition, chemical tools to probe and modulate RNP granules remain lacking. Herein, we combine an immunofluorescence (IF)-based phenotypic screen with chemoproteomics to identify sulfonyl-triazoles (SuTEx) capable of preventing or inducing SG and PB formation through liganding of tyrosine (Tyr) and lysine (Lys) sites in stressed cells. Liganded sites were enriched for RNA-binding and protein-protein interaction (PPI) domains, including several sites found in RNP granule-forming proteins. Among these, we functionally validate G3BP1 Y40, located in the NTF2 dimerization domain, as a ligandable site that can disrupt arsenite-induced SG formation in cells. In summary, we present a chemical strategy for the systematic discovery of condensate-modulating covalent small molecules.

Aerial warfare: An inducible production of volatile bioactive metabolites in a novel species of Scytinostroma sp.

Antimicrobial volatile organic compounds (VOCs) may provide fungi an advantage over other competing microorganisms. As these defensive metabolites are often produced in response to microbial competitors, they are easily overlooked in axenic cultures. We used media supplemented with spent medium from Candida albicans to induce the expression of a broad-spectrum antimicrobial response in a previously uncharacterised white-rot fungus, Scytinostroma sp. Crude extractions of Scytinostroma sp. metabolites were found to be cytotoxic to fibroblast cells and antimicrobial to filamentous fungi, yeasts and Gram-positive bacteria. Volatile antimicrobial activity was observed for Scytinostroma sp. cultures and metabolite extracts using antimicrobial assays in bi-compartmentalised plates. Culture headspace analysis using solid-phase microextraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS) revealed a pronounced shift in Scytinostroma sp. VOCs when cultured on media supplemented with C. albicans spent medium. We observed a significant increase in the levels of 45 identified VOCs, including 7 metabolites with reported antimicrobial activity. Using preparative HPLC combined with GC-MS, we determined that isovelleral is likely to be the main broad-spectrum antimicrobial metabolite produced by Scytinostroma sp. Isovelleral is a sesquiterpene dialdehyde with both antibiotic and antifeedant properties, previously detected in fruit bodies of other Basidiomycetes.

Mechanisms of epitranscriptomic gene regulation.

Chemical modifications on RNA can regulate fundamental biological processes. Recent efforts have illuminated the chemical diversity of posttranscriptional ("epitranscriptomic") modifications on eukaryotic messenger RNA and have begun to elucidate their biological roles. In this review, we discuss our current molecular understanding of epitranscriptomic RNA modifications and their effects on gene expression. In particular, we highlight the role of modifications in mediating RNA-protein interactions, RNA structure, and RNA-RNA base pairing, and how these macromolecular interactions control biological processes in the cell.

FGF-Dependent, Context-Driven Role for FRS Adapters in the Early Telencephalon.

FGF signaling, an important component of intercellular communication, is required in many tissues throughout development to promote diverse cellular processes. Whether FGF receptors (FGFRs) accomplish such varied tasks in part by activating different intracellular transducers in different contexts remains unclear. Here, we used the developing mouse telencephalon as an example to study the role of the FRS adapters FRS2 and FRS3 in mediating the functions of FGFRs. Using tissue-specific and germline mutants, we examined the requirement of Frs genes in two FGFR-dependent processes. We found that Frs2 and Frs3 are together required for the differentiation of a subset of medial ganglionic eminence (MGE)-derived neurons, but are dispensable for the survival of early telencephalic precursor cells, in which any one of three FGFRs (FGFR1, FGFR2, or FGFR3) is sufficient for survival. Although FRS adapters are dispensable for ERK-1/2 activation, they are required for AKT activation within the subventricular zone of the developing MGE. Using an FRS2,3-binding site mutant of Fgfr1, we established that FRS adapters are necessary for mediating most or all FGFR1 signaling, not only in MGE differentiation, but also in cell survival, implying that other adapters mediate at least in part the signaling from FGFR2 and FGFR3. Our study provides an example of a contextual role for an intracellular transducer and contributes to our understanding of how FGF signaling plays diverse developmental roles.SIGNIFICANCE STATEMENT FGFs promote a range of developmental processes in many developing tissues and at multiple developmental stages. The mechanisms underlying this multifunctionality remain poorly defined in vivo Using telencephalon development as an example, we show here that FRS adapters exhibit some selectivity in their requirement for mediating FGF receptor (FGFR) signaling and activating downstream mediators that depend on the developmental process, with a requirement in neuronal differentiation but not cell survival. Differential engagement of FRS and non-FRS intracellular adapters downstream of FGFRs could therefore in principle explain how FGFs play several distinct roles in other developing tissues and developmental stages.

Enhanced superconductivity in surface-electron-doped iron pnictide Ba(Fe1.94Co0.06)2As2.

The superconducting transition temperature (TC) in a FeSe monolayer on SrTiO3 is enhanced up to 100 K (refs ,,,). High TC is also found in bulk iron chalcogenides with similar electronic structure to that of monolayer FeSe, which suggests that higher TC may be achieved through electron doping, pushing the Fermi surface (FS) topology towards leaving only electron pockets. Such an observation, however, has been limited to chalcogenides, and is in contrast to the iron pnictides, for which the maximum TC is achieved with both hole and electron pockets forming considerable FS nesting instability. Here, we report angle-resolved photoemission characterization revealing a monotonic increase of TC from 24 to 41.5 K upon surface doping on optimally doped Ba(Fe1-xCox)2As2. The doping changes the overall FS topology towards that of chalcogenides through a rigid downward band shift. Our findings suggest that higher electron doping and concomitant changes in FS topology are favourable conditions for the superconductivity, not only for iron chalcogenides, but also for iron pnictides.

Very long-lasting spinal anesthesia with dexmedetomidine: A report of two cases.

Spinal anesthesia usually lasts up to two hours, but an infusion of IV dexmedetomidine can prolong it to three to four hours. We report two cases where single spinal anesthesia with IV dexmedetomidine was maintained for more than six hours during tibia fracture surgery. The spinal anesthesia was maintained for 350 and 390 minutes without another medication, and the sensory level confirmed after the surgery was T10 and L1. Dexmedetomidine can very-prolong the duration of spinal anesthesia beyond what has been reported. However, longer infusion times can also result in longer recovery times.

RTK-Dependent Inducible Degradation of Mutant PI3Kα Drives GDC-0077 (Inavolisib) Efficacy.

PIK3CA is one of the most frequently mutated oncogenes; the p110a protein it encodes plays a central role in tumor cell proliferation. Small-molecule inhibitors targeting the PI3K p110a catalytic subunit have entered clinical trials, with early-phase GDC-0077 studies showing antitumor activity and a manageable safety profile in patients with PIK3CA-mutant breast cancer. However, preclinical studies have shown that PI3K pathway inhibition releases negative feedback and activates receptor tyrosine kinase signaling, reengaging the pathway and attenuating drug activity. Here we discover that GDC-0077 and taselisib more potently inhibit mutant PI3K pathway signaling and cell viability through unique HER2-dependent mutant p110a degradation. Both are more effective than other PI3K inhibitors at maintaining prolonged pathway suppression. This study establishes a new strategy for identifying inhibitors that specifically target mutant tumors by selective degradation of the mutant oncoprotein and provide a strong rationale for pursuing PI3Kα degraders in patients with HER2-positive breast cancer. SIGNIFICANCE: The PI3K inhibitors GDC-0077 and taselisib have a unique mechanism of action; both inhibitors lead to degradation of mutant p110a protein. The inhibitors that have the ability to trigger specific degradation of mutant p110a without significant change in wild-type p110a protein may result in improved therapeutic index in PIK3CA-mutant tumors.See related commentary by Vanhaesebroeck et al., p. 20.This article is highlighted in the In This Issue feature, p. 1.

Prevalence of chronic obstructive pulmonary disease in Korea: the fourth Korean National Health and Nutrition Examination Survey, 2008.

BACKGROUND AND OBJECTIVE: Because the mortality and social burden associated with COPD is increasing, repeated surveys of the prevalence of COPD have been used to assess risk factors, detect potential patients, and establish early diagnoses and management protocols. We report the prevalence of spirometrically detected COPD in Korea in 2008, using data from the fourth Korean National Health and Nutrition Survey. METHODS: Using nationwide stratified random sampling, based on the Korean Statistical Office census, 6840 subjects aged ≥19years underwent spirometry, which was performed by four trained technicians, during 2008. The place of residence, levels of education and income and smoking status, as well as other results from a COPD survey questionnaire were also assessed. RESULTS: Airflow obstruction (FEV(1) /FVC<0.7) was detected in 8.8% of subjects aged ≥19years (11.6% of men and 5.9% of women) and COPD was detected in 13.4% of subjects aged ≥40years (19.4% of men and 7.9% of women). Of the 6840 subjects, 27.3% were current smokers and 17.2% were former smokers, and the prevalence of COPD was higher in current and former smokers than in never smokers. Approximately 94% of patients with COPD had mild-to-moderate disease, without apparent symptoms; only 2.4% had been diagnosed by a physician and only 2.1% of patients had been treated. The independent risk factors for COPD were smoking, advanced age and male gender. CONCLUSIONS: Although the prevalence of COPD in Korea is high, the disease is underdiagnosed and most COPD patients are under-treated.

Pasteurella Cerebral Mycotic Aneurysm: A Case Report and Review of the Literature.

Pasteurella species (spp.) are pleomorphic, Gram-negative, facultatively anaerobic bacilli commonly found in the upper respiratory tract and oral cavities of wild and domesticated animals such as dogs and cats. Pasteurella spp. infections in humans are typically caused by animal bites or scratches, or other inadvertent exposure of an open skin lesion to oral secretions of the animal. While skin and soft tissue infections are relatively common, respiratory infections, endocarditis, osteomyelitis, meningitis, and mycotic aneurysms have also been documented. To date, nine cases of mycotic aneurysms caused by Pasteurella spp. have been reported. However, only one of those cases has involved a cerebral mycotic aneurysm, and it had a fatal outcome. This report describes a successfully managed Pasteurella cerebral mycotic aneurysm that had occurred as a complication of underlying mitral valve endocarditis.

Unveiling unconventional magnetism at the surface of Sr2RuO4.

Materials with strongly correlated electrons often exhibit interesting physical properties. An example of these materials is the layered oxide perovskite Sr2RuO4, which has been intensively investigated due to its unusual properties. Whilst the debate on the symmetry of the superconducting state in Sr2RuO4 is still ongoing, a deeper understanding of the Sr2RuO4 normal state appears crucial as this is the background in which electron pairing occurs. Here, by using low-energy muon spin spectroscopy we discover the existence of surface magnetism in Sr2RuO4 in its normal state. We detect static weak dipolar fields yet manifesting at an onset temperature higher than 50 K. We ascribe this unconventional magnetism to orbital loop currents forming at the reconstructed Sr2RuO4 surface. Our observations set a reference for the discovery of the same magnetic phase in other materials and unveil an electronic ordering mechanism that can influence electron pairing with broken time reversal symmetry.

YTHDF2 Recognition of N1-Methyladenosine (m1A)-Modified RNA Is Associated with Transcript Destabilization.

Epitranscriptomic modifications play an important role in RNA function and can impact gene expression. Here, we apply a chemical proteomics approach to investigate readers of N1-methyladenosine (m1A), a poorly characterized modification on mammalian mRNA. We find that YTHDF proteins, known m6A readers, recognize m1A-modified sequences in a methylation-specific manner. We characterize binding of recombinant YTHDF1/2 proteins to m1A-modified oligonucleotides to demonstrate that these interactions can exhibit comparable affinity to m6A-recognition events and occur in diverse sequence contexts. Further, we demonstrate YTHDF2 interacts specifically with endogenously modified m1A transcripts. Finally, we deplete cellular YTHDF2 to show that the abundance of m1A-modified transcripts is increased in its absence. Similarly, increasing m1A levels through depletion of ALKBH3, an m1A eraser protein, destabilizes known m1A-containing RNAs. Our results shed light on the function of m1A on mRNA and provide a mechanistic framework to further evaluate the role of m1A in biological processes.

A tissue-engineered uterus supports live births in rabbits.

Bioengineered uterine tissue could provide a treatment option for women with uterine factor infertility. In large animal models, reconstruction of the uterus has been demonstrated only with xenogeneic tissue grafts. Here we use biodegradable polymer scaffolds seeded with autologous cells to restore uterine structure and function in rabbits. Rabbits underwent a subtotal uterine excision and were reconstructed with autologous cell-seeded constructs, with nonseeded scaffolds or by suturing. At 6 months postimplantation, only the cell-seeded engineered uteri developed native tissue-like structures, including organized luminal/glandular epithelium, stroma, vascularized mucosa and two-layered myometrium. Only rabbits with cell-seeded constructs had normal pregnancies (four in ten) in the reconstructed segment of the uterus and supported fetal development to term and live birth. With further development, this approach may provide a regenerative medicine solution to uterine factor infertility.

Momentum dependent [Formula: see text] band splitting in LaFeAsO.

The nematic phase in iron based superconductors (IBSs) has attracted attention with a notion that it may provide important clue to the superconductivity. A series of angle-resolved photoemission spectroscopy (ARPES) studies were performed to understand the origin of the nematic phase. However, there is lack of ARPES study on LaFeAsO nematic phase. Here, we report the results of ARPES studies of the nematic phase in LaFeAsO. Degeneracy breaking between the [Formula: see text] and [Formula: see text] hole bands near the [Formula: see text] and M point is observed in the nematic phase. Different temperature dependent band splitting behaviors are observed at the [Formula: see text] and M points. The energy of the band splitting near the M point decreases as the temperature decreases while it has little temperature dependence near the [Formula: see text] point. The nematic nature of the band shift near the M point is confirmed through a detwin experiment using a piezo device. Since a momentum dependent splitting behavior has been observed in other iron based superconductors, our observation confirms that the behavior is a universal one among iron based superconductors.

Can efficient supply management in the operating room save millions?

PURPOSE OF REVIEW: Supply expenses occupy an ever-increasing portion of the expense budget in today's increasingly technologically complex operating rooms. Yet, little has been studied and published in the anesthesia literature. This review attempts to bring the topic of supply management to anesthesiologists, who play a significant role in operating room management. RECENT FINDINGS: Little investigative work has been performed on supply management. Anecdotal reports suggest the benefits of a perpetual inventory system over a periodic inventory system. A perpetual inventory system uses utilization data to update inventory on hand continually and this information is linked to purchasing and restocking, whereas a periodic inventory system counts inventory at some regular intervals (such as annually) and uses average utilization to set par levels. SUMMARY: On the basis of application of operational management concepts, ways of taking advantage of a perpetual inventory system to achieve savings in supply expenses are outlined. These include linking the operating room scheduling and supply order system, distributor-driven just-in-time delivery of case carts, continual updating of preference lists based on utilization patterns, increasing inventory turnovers, standardizing surgical practices, and vendor consignment of high unit-cost items such as implants. In addition, Lean principles of visual management and elimination of eight wastes may be applicable to supply management.

Strong One-Dimensional Characteristics of Hole-Carriers in ReS2 and ReSe2.

Each plane of layered ReS2 and ReSe2 materials has 1D chain structure, from which intriguing properties such as 1D character of the exciton states and linearly polarized photoluminescence originate. However, systematic studies on the 1D character of charge carriers have not been done yet. Here, we report on systematic and comparative studies on the energy-momentum dispersion relationships of layered transition metal dichalcogenides ReS2 and ReSe2 by angle resolved photoemission. We found that the valence band maximum or the minimum energy for holes is located at the high symmetric Z-point for both materials. However, the out-of-plane ([Formula: see text]) dispersion for ReSe2 (20 meV) is found to be much smaller than that of ReS2 (150 meV). We observe that the effective mass of the hole carriers along the direction perpendicular to the chain is about 4 times larger than that along the chain direction for both ReS2 and ReSe2. Remarkably, the experimentally measured hole effective mass is about twice heavier than that from first principles calculation for ReS2 although the in-plane anisotropy values from the experiment and calculations are comparable. These observation indicate that bulk ReS2 and ReSe2 are unique semiconducting transition metal dichalcogenides having strong one-dimensional characters.

Pamapimod, a novel p38 mitogen-activated protein kinase inhibitor: preclinical analysis of efficacy and selectivity.

P38alpha is a protein kinase that regulates the expression of inflammatory cytokines, suggesting a role in the pathogenesis of diseases such as rheumatoid arthritis (RA) or systemic lupus erythematosus. Here, we describe the preclinical pharmacology of pamapimod, a novel p38 mitogen-activated protein kinase inhibitor. Pamapimod inhibited p38alpha and p38beta enzymatic activity, with IC(50) values of 0.014 +/- 0.002 and 0.48 +/- 0.04 microM, respectively. There was no activity against p38delta or p38gamma isoforms. When profiled across 350 kinases, pamapimod bound only to four kinases in addition to p38. Cellular potency was assessed using phosphorylation of heat shock protein-27 and c-Jun as selective readouts for p38 and c-Jun NH(2)-terminal kinase (JNK), respectively. Pamapimod inhibited p38 (IC(50), 0.06 microM), but inhibition of JNK was not detected. Pamapimod also inhibited lipopolysaccharide (LPS)-stimulated tumor necrosis factor (TNF) alpha production by monocytes, interleukin (IL)-1beta production in human whole blood, and spontaneous TNFalpha production by synovial explants from RA patients. LPS- and TNFalpha-stimulated production of TNFalpha and IL-6 in rodents also was inhibited by pamapimod. In murine collagen-induced arthritis, pamapimod reduced clinical signs of inflammation and bone loss at 50 mg/kg or greater. In a rat model of hyperalgesia, pamapimod increased tolerance to pressure in a dose-dependent manner, suggesting an important role of p38 in pain associated with inflammation. Finally, an analog of pamapimod that has equivalent potency and selectivity inhibited renal disease in lupus-prone MRL/lpr mice. Our study demonstrates that pamapimod is a potent, selective inhibitor of p38alpha with the ability to inhibit the signs and symptoms of RA and other autoimmune diseases.

Relationship between adipokines and manifestations of childhood asthma.

Although the prevalences of asthma and obesity are increasing substantially in recent decades, very little is known about the possible association between them. We evaluated the roles of leptin, adiponectin, and resistin, which are adipokines produced by adipose tissue, on childhood asthma, and their association with pulmonary function and bronchial hyperresponsiveness. We studied 149 atopic asthmatic children, 37 non-atopic asthmatic children, and 54 healthy children. Body mass index was calculated using height and weight, which were measured on the same day that pulmonary function tests and methacholine challenge tests were performed. Skin prick tests were performed, and total eosinophil count, total serum immunoglobulin E (IgE), serum eosinophil cationic protein, leptin, adiponectin, and resistin were measured in all subjects. Atopic asthmatics had lower resistin levels compared with non-atopic asthma and control groups, but leptin and adiponectin did not show any difference among these three groups. Resistin demonstrated positive correlation with methacholine PC(20) and negative correlations with eosinophil count and serum total IgE. Leptin and adiponectin showed associations with forced expiratory volume in 1 s or forced expiratory flow between 25-75%. Multiple regression analysis revealed that resistin was a significant predictive factor for asthma. There was no direct association between asthma and leptin or adiponectin. Our findings suggest that resistin may play a negative predictive role in asthma. Adiponectin and leptin showed close associations with pulmonary function and may have disease-modifying effects in children with asthma.

The safety and efficacy in humans of endoscopic mucosal resection with hydroxypropyl methylcellulose as compared with normal saline.

BACKGROUND AND STUDY AIMS: Endoscopic mucosal resection (EMR) is a therapeutic modality that utilizes fluid to form a submucosal fluid cushion (SFC) for the treatment of early gastrointestinal neoplasia. The goal of this study was to determine the safety and efficacy in humans of EMR with hydroxypropyl methylcellulose (HPMC) as compared with historical controls of EMR performed with normal saline. PATIENTS AND METHODS: A retrospective cohort study presented data on EMR performed in 89 lesions in 88 patients was compared with 22 control EMRs performed with normal saline. Indications for EMR included known or suspected cancerous or precancerous lesions of the gastrointestinal tract. Efficacy of EMR was based on rates of complete excision and tumor recurrence. RESULTS: EMR was performed in 89 lesions with HPMC-EMR used in 67 lesions and compared with 22 historical control lesions treated with saline EMR by the same five endoscopists. Lesion size and location were similar in both HPMC and saline groups. Complications were observed in six patients [5/67 (8%) HPMC and 1/22 (5%) saline, p > 0.2]. Long-term follow-up with repeat endoscopy was available on 43 lesions and identified 35/43 to be completely excised [20/25 (80%) HPMC-EMR and 15/18 (83%) saline EMR, p > 0.2]. Size of the lesion was not associated with success. CONCLUSION: Both HPMC and normal saline are effective agents for creating a submucosal cushion for EMR. Larger randomized studies are needed to determine statistically significant differences in efficacy.