Discovery of cytosine deaminases enables base-resolution methylome mapping using a single enzyme.

Deaminases have important uses in modification detection and genome editing. However, the range of applications is limited by the small number of characterized enzymes. To expand the toolkit of deaminases, we developed an in vitro approach that bypasses a major hurdle with their toxicity in cells. We assayed 175 putative cytosine deaminases on a variety of substrates and found a broad range of activity on double- and single-stranded DNA in various sequence contexts, including CpG-specific deaminases and enzymes without sequence preference. We also characterized enzyme selectivity across six DNA modifications and reported enzymes that do not deaminate modified cytosines. The detailed analysis of diverse deaminases opens new avenues for biotechnological and medical applications. As a demonstration, we developed SEM-seq, a non-destructive single-enzyme methylation sequencing method using a modification-sensitive double-stranded DNA deaminase. The streamlined protocol enables accurate, base-resolution methylome mapping of scarce biological material, including cell-free DNA and 10 pg input DNA.

Postinduction molecular MRD identifies patients with NPM1 AML who benefit from allogeneic transplant in first remission.

ABSTRACT: Selection of patients with NPM1-mutated acute myeloid leukemia (AML) for allogeneic transplant in first complete remission (CR1-allo) remains controversial because of a lack of robust data. Consequently, some centers consider baseline FLT3-internal tandem duplication (ITD) an indication for transplant, and others rely on measurable residual disease (MRD) status. Using prospective data from the United Kingdom National Cancer Research Institute AML17 and AML19 studies, we examined the impact of CR1-allo according to peripheral blood NPM1 MRD status measured by quantitative reverse transcription polymerase chain reaction after 2 courses of induction chemotherapy. Of 737 patients achieving remission, MRD was positive in 19%. CR1-allo was performed in 46% of MRD+ and 17% of MRD- patients. We observed significant heterogeneity of overall survival (OS) benefit from CR1-allo according to MRD status, with substantial OS advantage for MRD+ patients (3-year OS with CR1-allo vs without: 61% vs 24%; hazard ratio [HR], 0.39; 95% confidence interval [CI], 0.24-0.64; P < .001) but no benefit for MRD- patients (3-year OS with CR1-allo vs without: 79% vs 82%; HR, 0.82; 95% CI, 0.50-1.33; P = .4). Restricting analysis to patients with coexisting FLT3-ITD, again CR1-allo only improved OS for MRD+ patients (3-year OS, 45% vs 18%; compared with 83% vs 76% if MRD-); no interaction with FLT3 allelic ratio was observed. Postinduction molecular MRD reliably identifies those patients who benefit from allogeneic transplant in first remission. The AML17 and AML19 trials were registered at www.isrctn.com as #ISRCTN55675535 and #ISRCTN78449203, respectively.

Molecular, clinical, and therapeutic determinants of outcome in NPM1-mutated AML.

ABSTRACT: Although NPM1-mutated acute myeloid leukemia (AML) carries a generally favorable prognosis, many patients still relapse and die. Previous studies identified several molecular and clinical features associated with poor outcomes; however, only FLT3-internal tandem duplication (ITD) mutation and adverse karyotype are currently used for risk stratification because of inconsistent results and uncertainty about how other factors should influence treatment, particularly given the strong prognostic effect of postinduction measurable residual disease (MRD). Here, we analyzed a large group of patients with NPM1 mutations (NPM1mut) AML enrolled in prospective trials (National Cancer Research Institute [NCRI] AML17 and AML19, n = 1357) to delineate the impact of baseline molecular and clinical features, postinduction MRD status, and treatment intensity on the outcome. FLT3-ITD (hazard ratio [HR], 1.28; 95% confidence interval [CI], 1.01-1.63), DNMT3A (HR, 1.65; 95% CI, 1.32-2.05), WT1 (HR, 1.74; 95% CI, 1.27-2.38), and non-ABD NPM1mut (HR, 1.64; 95% CI, 1.22-2.21) were independently associated with poorer overall survival (OS). These factors were also strongly associated with MRD positivity. For patients who achieved MRD negativity, these mutations (except FLT3-ITD) were associated with an increased cumulative incidence of relapse (CIR) and poorer OS. However, apart from the few patients with adverse cytogenetics, we could not identify any group of MRD-negative patients with a CIR >40% or with benefit from allograft in first remission. Intensified chemotherapy with the FLAG-Ida (fludarabine, cytarabine, granulocyte colony-stimulating factor, and idarubicin) regimen was associated with improved outcomes in all subgroups, with greater benefits observed in the high-risk molecular subgroups.

Structural and functional characterization of the IpaD π-helix reveals critical roles in DOC interaction, T3SS apparatus maturation, and Shigella virulence.

Shigella spp. are highly pathogenic members of the Enterobacteriaceae family, causing ∼269 million cases of bacillary dysentery and >200,000 deaths each year. Like many Gram-negative pathogens, Shigella rely on their type three secretion system (T3SS) to inject effector proteins into eukaryotic host cells, driving both cellular invasion and evasion of host immune responses. Exposure to the bile salt deoxycholate (DOC) significantly enhances Shigella virulence and is proposed to serve as a critical environmental signal present in the small intestine that prepares Shigella's T3SS for efficient infection of the colonic epithelium. Here, we uncover critical mechanistic details of the Shigella-specific DOC signaling process by describing the role of a π-helix secondary structure element within the T3SS tip protein IpaD. Biophysical characterization and high-resolution structures of IpaD mutants lacking the π-helix show that it is not required for global protein structure, but that it defines the native DOC binding site and prevents off target interactions. Additionally, Shigella strains expressing the π-helix deletion mutants illustrate the pathogenic importance of its role in guiding DOC interaction as flow cytometry and gentamycin protection assays show that the IpaD π-helix is essential for DOC-mediated apparatus maturation and enhanced invasion of eukaryotic cells. Together, these findings add to our understanding of the complex Shigella pathogenesis pathway and its evolution to respond to environmental bile salts by identifying the π-helix in IpaD as a critical structural element required for translating DOC exposure to virulence enhancement.

Conserved Residues at the Mtr4 C-Terminus Coordinate Helicase Activity and Exosome Interactions.

Mtr4 is an essential RNA helicase involved in nuclear RNA processing and degradation and is a member of the Ski2-like helicase family. Ski2-like helicases share a common core architecture that includes two RecA-like domains, a winged helix, and a helical bundle (HB) domain. In Mtr4, a short C-terminal tail immediately follows the HB domain and is positioned at the interface of the RecA-like domains. The tail ends with a SLYΦ sequence motif that is highly conserved in a subset of Ski2-like helicases. Here, we show that this sequence is critical for Mtr4 function. Mutations in the C-terminus result in decreased RNA unwinding activity. Mtr4 is a key activator of the RNA exosome complex, and mutations in the SLYΦ motif produce a slow growth phenotype when combined with a partial exosome defect in S. cerevisiae, suggesting an important role of the C-terminus of Mtr4 and the RNA exosome. We further demonstrate that C-terminal mutations impair RNA degradation activity by the major RNA exosome nuclease Rrp44 in vitro. These data demonstrate a role for the Mtr4 C-terminus in regulating helicase activity and coordinating Mtr4-exosome interactions.

Cosyntropin Stimulation Testing is More Selective than Postoperative Day 1 Basal Cortisol for Diagnosing Secondary Adrenal Insufficiency After Unilateral Adrenalectomy.

BACKGROUND: Secondary adrenal insufficiency (SAI) may occur in patients after unilateral adrenalectomy for adrenal-dependent hypercortisolism (HC) or primary aldosteronism (PA). This study aimed to assess whether postoperative day (POD) 1 basal cortisol was predictive of an abnormal cosyntropin stimulation test (CST) result and the need for glucocorticoid replacement (GR). METHODS: A retrospective review of consecutive patients who underwent unilateral adrenalectomy for HC, PA, or both between September 2014 and September 2022 was performed. On POD1, CST was performed for all the patients with HC, and before 2021 for all the patients with PA. The patients with an abnormal CST result were deemed at risk of SAI and discharged with GR. Receiver operating characteristic (ROC) curves were generated to evaluate the sensitivity (SN) and specificity (SP) of basal cortisol thresholds to predict an abnormal CST result. RESULTS: The patients underwent unilateral adrenalectomy for overt hypercortisolism (OH; n = 42), mild autonomous cortisol excess (MACE; n = 70), mixed PA/HC (n = 22), or PA (n = 73). On POD1, CST was performed for 152 patients (93% OH, 96% MACE,73% PA/HC, 41% PA), and 80 patients (53%) had SAI (67% OH, 55% MACE, 44% PA/HC, 33% PA). The SN and SP of a basal cortisol level of 10 µg/dL or lower to predict an abnormal CST were respectively 92% and 77% for OH, 94% and 73% for MACE, 100% and 85% for PA, and 100% and 67% for PA/HC. The optimal basal cortisol level for predicting an abnormal CST for patients with PA or PA/HC was 5 µg/dL or lower (SN/SP, 100%). CONCLUSIONS: After unilateral adrenalectomy for HC, PA, or mixed PA/HC, POD1 CST improved identification of patients at risk for SAI compared with basal cortisol levels alone. The authors recommend that POD1 CST be performed to determine the risk for SAI and the need for postoperative GR after unilateral adrenalectomy for patients with HC.

Patterning optimization for device realization of patterned GaAsSbN nanowire photodetectors.

Vertically grown nanowires (NWs) are a research interest in optoelectronics and photovoltaic applications due to their high surface to volume ratio and good light trapping capabilities. This study presents the effects of process and design parameters on self-catalyzed GaAsSbN NWs grown by plasma-assisted molecular beam epitaxy on patterned silicon substrates using electron beam lithography. Vertical alignment of the patterned NWs examined via scanning electron microscopy show the sensitivity of patterned NW growth to the parameters of NW diameter, pitch, dose time, etching techniques and growth plan. Diameters range from 90 nm to 250 nm. Pitch lengths of 200 nm, 400 nm, 600 nm, 800 nm, 1000 nm, and 1200 nm were examined. Dry etching of the oxide layer of the silicon substrate and PMMA coating is performed using reactive ion etching (RIE) for 20 s and 120 s respectively. Comparisons of different HF etch durations performed pre and post PMMA removal are presented. Additionally, the report of an observed surfactant effect in dilute nitride GaAsSbN NWs in comparison to non-nitride GaAsSb is presented. Optimizations to patterning, RIE, and HF etching are presented to obtain higher vertical yield of patterned GaAsSbN NWs, achieving ∼80% of the expected NWµm2. Room temperature and 4 K photoluminescence results show the effect of nitride incorporation for further bandgap tuning, and patterned pitch on the optical characteristics of the NWs which gives insights to the compositional homogeneity for NWs grown at each pitch length.

Hydrogen-deuterium exchange mass spectrometry of Mtr4 with diverse RNAs reveals substrate-dependent dynamics and interfaces in the arch.

Mtr4 is a eukaryotic RNA helicase required for RNA decay by the nuclear exosome. Previous studies have shown how RNA en route to the exosome threads through the highly conserved helicase core of Mtr4. Mtr4 also contains an arch domain, although details of potential interactions between the arch and RNA have been elusive. To understand the interaction of Saccharomyces cerevisiae Mtr4 with various RNAs, we have characterized RNA binding in solution using hydrogen-deuterium exchange mass spectrometry, and affinity and unwinding assays. We have identified RNA interactions within the helicase core that are consistent with existing structures and do not vary between tRNA, single-stranded RNA and double-stranded RNA constructs. We have also identified novel RNA interactions with a region of the arch known as the fist or KOW. These interactions are important for RNA unwinding and vary in strength depending on RNA structure and length. They account for Mtr4 discrimination between different RNAs. These interactions further drive Mtr4 to adopt a closed conformation characterized by reduced dynamics of the arch arm and intra-domain contacts between the fist and helicase core.

Protease-Activated Receptor 2 Controls Vascular Smooth Muscle Cell Proliferation in Cyclic AMP-Dependent Protein Kinase/Mitogen-Activated Protein Kinase Kinase 1/2-Dependent Manner.

INTRODUCTION: Cardiovascular disorders are characterized by vascular smooth muscle (VSM) transition from a contractile to proliferative state. Protease-activated receptor 2 (PAR2) involvement in this phenotypic conversion remains unclear. We hypothesized that PAR2 controls VSM cell proliferation in phenotype-dependent manner and through specific protein kinases. METHODS: Rat clonal low (PLo; P3-P6) and high passage (PHi; P10-P15) VSM cells were established as respective models of quiescent and proliferative cells, based on reduced PKG-1 and VASP. Western blotting determined expression of cytoskeletal/contractile proteins, PAR2, and select protein kinases. DNA synthesis and cell proliferation were measured 24-72 h following PAR2 agonism (SLIGRL; 100 nM-10 µm) with/without PKA (PKI; 10 µm), MEK1/2 (PD98059; 10 µm), and PI3K (LY294002; 1 µm) blockade. RESULTS: PKG-1, VASP, SM22α, calponin, cofilin, and PAR2 were reduced in PHi versus PLo cells. Following PAR2 agonism, DNA synthesis and cell proliferation increased in PLo cells but decreased in PHi cells. Western analyses showed reduced PKA, MEK1/2, and PI3K in PHi versus PLo cells, and kinase blockade revealed PAR2 controls VSM cell proliferation through PKA/MEK1/2. DISCUSSION: Findings highlight PAR2 and PAR2-driven PKA/MEK1/2 in control of VSM cell growth and provide evidence for continued investigation of PAR2 in VSM pathology.

Comparing the Accuracy of Mini-BAL to Bronchoscopic BAL in the Diagnosis of Pneumonia Among Ventilated Patients: A Systematic Literature Review.

Background: Despite its widespread use, there are no direct studies comparing mini-bronchoalveolar lavage (mini-BAL) to bronchoscopic bronchoalveolar lavage (BAL) for diagnosing pneumonia in ventilated patients. The aim of this study was to perform a systematic review of studies comparing ventilated patients undergoing both bronchoscopic BAL and mini-BAL, to determine the mini-BAL's diagnostic accuracy. Methods: We conducted a systematic review searching the databases PubMed (MEDLINE), EMBASE, Cochrane Library, Scopus, and clinicaltrials.gov from inception until January 2022, in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Search terms included variations on "pneumonia," "critical illness," and "mini-bronchoalveolar lavage." Article screening and data extraction were performed independently by 2 reviewers. Results: Our search yielded 4296 abstracts. This was narrowed to 6 studies in which each patient underwent both mini-BAL and bronchoscopic BAL in succession. Included patients had a mean APACHE II score of 20.02 ± 3.81 and 15.95 ± 11.46 ventilator days. The sensitivity of the mini-BAL for diagnosis of pneumonia was 0.90 (95% confidence interval [CI]: 0.778-1.000) and the specificity was 0.827 (95% CI: 0.716-0.938). Limitations included inconsistency in volume of saline instilled and heterogeneity in included patients Conclusion: This study is the first to compile data from multiple publications directly comparing the mini-BAL to bronchoscopic BAL for diagnosing pneumonia in ventilated patients. Our data demonstrate a high degree of both sensitivity and specificity of mini-BAL for the diagnosis of pneumonia in ventilated patients and indicate that mini-BAL could be considered as an acceptable alternative diagnostic study.

A novel algorithmic approach to generate consensus treatment guidelines in adult acute myeloid leukaemia.

Induction therapy for acute myeloid leukaemia (AML) has changed with the approval of a number of new agents. Clinical guidelines can struggle to keep pace with an evolving treatment and evidence landscape and therefore identifying the most appropriate front-line treatment is challenging for clinicians. Here, we combined drug eligibility criteria and genetic risk stratification into a digital format, allowing the full range of possible treatment eligibility scenarios to be defined. Using exemplar cases representing each of the 22 identified scenarios, we sought to generate consensus on treatment choice from a panel of nine aUK AML experts. We then analysed >2500 real-world cases using the same algorithm, confirming the existence of 21/22 of these scenarios and demonstrating that our novel approach could generate a consensus AML induction treatment in 98% of cases. Our approach, driven by the use of decision trees, is an efficient way to develop consensus guidance rapidly and could be applied to other disease areas. It has the potential to be updated frequently to capture changes in eligibility criteria, novel therapies and emerging trial data. An interactive digital version of the consensus guideline is available.

A Comparison Between Ecological Momentary Assessment and the Adapted-Quick Drinking Screen: Alcohol Mixed With Energy Drinks.

AIMS: To compare alcohol consumption and risk-taking behaviours on alcohol mixed with energy drink (AMED) and alcohol-only (AO) drinking occasions collected via ecological momentary assessment (EMA) versus retrospective survey methods (adapted-Quick Drinking Screen: a-QDS). METHODS: Completing participants were 52 university students who reported AMED consumption during the 30-day data collection period. Alcohol consumption and risk-taking behaviours were captured for recreational AMED and AO consumption occasions using a smartphone-based app across 30 days. Data were aggregated for comparison with the a-QDS conducted at the end of data collection. RESULTS: Irrespective of data collection method, alcohol was consumed more frequently and at higher quantities on the heaviest drinking occasions when consumed alone compared with when it was mixed with energy drinks. Consistent with this finding, more risk-taking behaviours were experienced on AO occasions compared with AMED occasions. Compared with the a-QDS, the quantity of alcohol consumed on the average and heaviest drinking occasion was significantly higher when reported via EMA. This was consistent across both AO and AMED drinking occasions. CONCLUSION: EMA provides a more valid measure of consumption quantity compared with retrospective recall, which was susceptible to under-reporting, although this was not differentially affected across consumption occasions. In line with previous research, this study demonstrated that mixing alcohol with energy drinks does not increase alcohol consumption or risk-taking behaviours.

Significant Loop Motions in the SsoPTP Protein Tyrosine Phosphatase Allow for Dual General Acid Functionality.

Conformational dynamics are important factors in the function of enzymes, including protein tyrosine phosphatases (PTPs). Crystal structures of PTPs first revealed the motion of a protein loop bearing a conserved catalytic aspartic acid, and subsequent nuclear magnetic resonance and computational analyses have shown the presence of motions, involved in catalysis and allostery, within and beyond the active site. The tyrosine phosphatase from the thermophilic and acidophilic Sulfolobus solfataricus (SsoPTP) displays motions of its acid loop together with dynamics of its phosphoryl-binding P-loop and the Q-loop, the first instance of such motions in a PTP. All three loops share the same exchange rate, implying their motions are coupled. Further evidence of conformational flexibility comes from mutagenesis, kinetics, and isotope effect data showing that E40 can function as an alternate general acid to protonate the leaving group when the conserved acid, D69, is mutated to asparagine. SsoPTP is not the first PTP to exhibit an alternate general acid (after VHZ and TkPTP), but E40 does not correspond to the sequence or structural location of the alternate general acids in those precedents. A high-resolution X-ray structure with the transition state analogue vanadate clarifies the role of the active site arginine R102, which varied in structures of substrates bound to a catalytically inactive mutant. The coordinated motions of all three functional loops in SsoPTP, together with the function of an alternate general acid, suggest that catalytically competent conformations are present in solution that have not yet been observed in crystal structures.

The biosynthesis of the anti-microbial diterpenoid leubethanol in Leucophyllum frutescens proceeds via an all-cis prenyl intermediate.

Serrulatane diterpenoids are natural products found in plants from a subset of genera within the figwort family (Scrophulariaceae). Many of these compounds have been characterized as having anti-microbial properties and share a common diterpene backbone. One example, leubethanol from Texas sage (Leucophyllum frutescens) has demonstrated activity against multi-drug-resistant tuberculosis. Leubethanol is the only serrulatane diterpenoid identified from this genus; however, a range of such compounds have been found throughout the closely related Eremophila genus. Despite their potential therapeutic relevance, the biosynthesis of serrulatane diterpenoids has not been previously reported. Here we leverage the simple product profile and high accumulation of leubethanol in the roots of L. frutescens and compare tissue-specific transcriptomes with existing data from Eremophila serrulata to decipher the biosynthesis of leubethanol. A short-chain cis-prenyl transferase (LfCPT1) first produces the rare diterpene precursor nerylneryl diphosphate, which is cyclized by an unusual plastidial terpene synthase (LfTPS1) into the characteristic serrulatane diterpene backbone. Final conversion to leubethanol is catalyzed by a cytochrome P450 (CYP71D616) of the CYP71 clan. This pathway documents the presence of a short-chain cis-prenyl diphosphate synthase, previously only found in Solanaceae, which is likely involved in the biosynthesis of other known diterpene backbones in Eremophila. LfTPS1 represents neofunctionalization of a compartment-switching terpene synthase accepting a novel substrate in the plastid. Biosynthetic access to leubethanol will enable pathway discovery to more complex serrulatane diterpenoids which share this common starting structure and provide a platform for the production and diversification of this class of promising anti-microbial therapeutics in heterologous systems.

Targeting the VCP-binding motif of ataxin-3 improves phenotypes in Drosophila models of Spinocerebellar Ataxia Type 3.

Of the family of polyglutamine (polyQ) neurodegenerative diseases, Spinocerebellar Ataxia Type 3 (SCA3) is the most common. Like other polyQ diseases, SCA3 stems from abnormal expansions in the CAG triplet repeat of its disease gene resulting in elongated polyQ repeats within its protein, ataxin-3. Various ataxin-3 protein domains contribute to its toxicity, including the valosin-containing protein (VCP)-binding motif (VBM). We previously reported that VCP, a homo-hexameric protein, enhances pathogenic ataxin-3 aggregation and exacerbates its toxicity. These findings led us to explore the impact of targeting the SCA3 protein by utilizing a decoy protein comprising the N-terminus of VCP (N-VCP) that binds ataxin-3's VBM. The notion was that N-VCP would reduce binding of ataxin-3 to VCP, decreasing its aggregation and toxicity. We found that expression of N-VCP in Drosophila melanogaster models of SCA3 ameliorated various phenotypes, coincident with reduced ataxin-3 aggregation. This protective effect was specific to pathogenic ataxin-3 and depended on its VBM. Increasing the amount of N-VCP resulted in further phenotype improvement. Our work highlights the protective potential of targeting the VCP-ataxin-3 interaction in SCA3, a key finding in the search for therapeutic opportunities for this incurable disorder.

Mtr4 RNA helicase structures and interactions.

Mtr4 is a Ski2-like RNA helicase that plays a central role in RNA surveillance and degradation pathways as an activator of the RNA exosome. Multiple crystallographic and cryo-EM studies over the past 10 years have revealed important insight into the Mtr4 structure and interactions with protein and nucleic acid binding partners. These structures place Mtr4 at the center of a dynamic process that recruits RNA substrates and presents them to the exosome. In this review, we summarize the available Mtr4 structures and highlight gaps in our current understanding.

Application of a convolutional neural network for seismic phase picking of mining-induced seismicity.

Monitoring mining-induced seismicity (MIS) can help engineers understand the rock mass response to resource extraction. With a thorough understanding of ongoing geomechanical processes, engineers can operate mines, especially those mines with the propensity for rock-bursting, more safely and efficiently. Unfortunately, processing MIS data usually requires significant effort from human analysts, which can result in substantial costs and time commitments. The problem is exacerbated for operations that produce copious amounts of MIS, such as mines with high-stress and/or extraction ratios. Recently, deep learning methods have shown the ability to significantly improve the quality of automated arrival-time picking on earthquake data recorded by regional seismic networks. However, relatively little has been published on applying these techniques to MIS. In this study, we compare the performance of a convolutional neural network (CNN) originally trained to pick arrival times on the Southern California Seismic Network (SCSN) to that of human analysts on coal-mine-related MIS. We perform comparisons on several coal-related MIS data sets recorded at various network scales, sampling rates and mines. We find that the Southern-California-trained CNN does not perform well on any of our data sets without retraining. However, applying the concept of transfer learning, we retrain the SCSN model with relatively little MIS data after which the CNN performs nearly as well as a human analyst. When retrained with data from a single analyst, the analyst-CNN pick time residual variance is lower than the variance observed between human analysts. We also compare the retrained CNN to a simpler, optimized picking algorithm, which falls short of the CNN's performance. We conclude that CNNs can achieve a significant improvement in automated phase picking although some data set-specific training will usually be required. Moreover, initializing training with weights found from other, even very different, data sets can greatly reduce the amount of training data required to achieve a given performance threshold.

A Randomized Comparison of Positional Stability: The EZ-Blocker Versus Left-Sided Double-Lumen Endobronchial Tubes in Adult Patients Undergoing Thoracic Surgery.

OBJECTIVE: To assess if there is a difference in the repositioning rate of the EZ-Blocker versus a left-sided double-lumen endobronchial tube (DLT) in patients undergoing thoracic surgery and one-lung ventilation. DESIGN: Prospective, randomized. SETTING: Single center, university hospital. PARTICIPANTS: One hundred sixty-three thoracic surgery patients. INTERVENTIONS: Patients were randomized to either EZ-Blocker or a DLT. MEASUREMENTS AND MAIN RESULTS: The primary outcome was positional stability of either the EZ-Blocker or a left-sided double-lumen endobronchial tube, defined as the number of repositionings per hour of surgery and one-lung ventilation. Secondary outcomes included an ordinal isolation score from 1 to 3, in which 1 was poor, up to 3, which represented excellent isolation, and a visual analog postoperative sore throat score (0-100) on postoperative days (POD) one and two. Rate of repositionings per hour during one-lung ventilation and surgical manipulation in left-sided cases was similar between the two devices: 0.08 ± 0.15 v 0.11 ± 0.3 (p = 0.72). In right-sided cases, the rate of repositioning was higher in the EZ-Blocker group compared with DLT: 0.38 ± 0.65 v 0.09 ± 0.21 (p = 0.03). Overall, mean isolation scores for the EZ-Blocker versus the DLT were 2.76 v 2.92 (p = 0.04) in left-sided cases and 2.70 v 2.83 (p = 0.22) in right-sided cases. Median sore throat scores for left sided cases were 0 v 5 (p = 0.13) POD one and 0 v 5 (p = 0.006) POD two for the EZ-Blocker and left-sided DLT, respectively. CONCLUSION: For right-sided procedures, the positional stability of the EZ-Blocker is inferior to a DLT. In left-sided cases, the rate of repositioning for the EZ-Blocker and DLT are not statistically different.

A database-driven approach identifies additional diterpene synthase activities in the mint family (Lamiaceae).

Members of the mint family (Lamiaceae) accumulate a wide variety of industrially and medicinally relevant diterpenes. We recently sequenced leaf transcriptomes from 48 phylogenetically diverse Lamiaceae species. Here, we summarize the available chemotaxonomic and enzyme activity data for diterpene synthases (diTPSs) in the Lamiaceae and leverage the new transcriptomes to explore the diTPS sequence and functional space. Candidate genes were selected with an intent to evenly sample the sequence homology space and to focus on species in which diTPS transcripts were found, yet from which no diterpene structures have been previously reported. We functionally characterized nine class II diTPSs and 10 class I diTPSs from 11 distinct plant species and found five class II activities, including two novel activities, as well as a spectrum of class I activities. Among the class II diTPSs, we identified a neo-cleroda-4(18),13E-dienyl diphosphate synthase from Ajuga reptans, catalyzing the likely first step in the biosynthesis of a variety of insect-antifeedant compounds. Among the class I diTPSs was a palustradiene synthase from Origanum majorana, leading to the discovery of specialized diterpenes in that species. Our results provide insights into the diversification of diterpene biosynthesis in the mint family and establish a comprehensive foundation for continued investigation of diterpene biosynthesis in the Lamiaceae.

Degron capability of the hydrophobic C-terminus of the polyglutamine disease protein, ataxin-3.

Ataxin-3 is a deubiquitinase and polyglutamine disease protein whose cellular properties and functions are not entirely understood. Mutations in ataxin-3 cause spinocerebellar ataxia type 3 (SCA3), a neurodegenerative disorder that is a member of the polyglutamine family of diseases. Two major isoforms arise from alternative splicing of ATXN3 and are differently toxic in vivo as a result of faster proteasomal degradation of one isoform compared to the other. The isoforms vary only at their C-termini, suggesting that the hydrophobic C-terminus of the more quickly degraded form of ataxin-3 (here referred to as isoform 2) functions as a degron-that is, a peptide sequence that expedites the degradation of its host protein. We explored this notion in this study and present evidence that: (a) the C-terminus of ataxin-3 isoform 2 signals its degradation in a proteasome-dependent manner, (b) this effect from the C-terminus of isoform 2 does not require the ubiquitination of ataxin-3, and (c) the isolated C-terminus of isoform 2 can enhance the degradation of an unrelated protein. According to our data, the C-terminus of ataxin-3 isoform 2 is a degron, increasing overall understanding of the cellular properties of the SCA3 protein.