A global phylogenomic analysis of the shiitake genus Lentinula.

Lentinula is a broadly distributed group of fungi that contains the cultivated shiitake mushroom, L. edodes. We sequenced 24 genomes representing eight described species and several unnamed lineages of Lentinula from 15 countries on four continents. Lentinula comprises four major clades that arose in the Oligocene, three in the Americas and one in Asia-Australasia. To expand sampling of shiitake mushrooms, we assembled 60 genomes of L. edodes from China that were previously published as raw Illumina reads and added them to our dataset. Lentinula edodes sensu lato (s. lat.) contains three lineages that may warrant recognition as species, one including a single isolate from Nepal that is the sister group to the rest of L. edodes s. lat., a second with 20 cultivars and 12 wild isolates from China, Japan, Korea, and the Russian Far East, and a third with 28 wild isolates from China, Thailand, and Vietnam. Two additional lineages in China have arisen by hybridization among the second and third groups. Genes encoding cysteine sulfoxide lyase (lecsl) and γ-glutamyl transpeptidase (leggt), which are implicated in biosynthesis of the organosulfur flavor compound lenthionine, have diversified in Lentinula. Paralogs of both genes that are unique to Lentinula (lecsl 3 and leggt 5b) are coordinately up-regulated in fruiting bodies of L. edodes. The pangenome of L. edodes s. lat. contains 20,308 groups of orthologous genes, but only 6,438 orthogroups (32%) are shared among all strains, whereas 3,444 orthogroups (17%) are found only in wild populations, which should be targeted for conservation.

T-cells and CD45-cells discovery in the central nervous system of healthy and nodavirus-infected teleost fish Dicentrarchuslabrax.

To achieve insights in antiviral immune defense of the central nervous system (CNS), we investigated T cells and CD45 cells in the marine fish model Dicentrarchus labrax infected with the CNS-tropic virus betanodavirus. By employing markers for pan-T cells (mAb DLT15) and CD45-cells (mAb DLT22) in immunofluorescence (IIF) of leukocytes from brain, we obtained 3,7 ± 2.3 % of T cells and 7.3 ± 3.2 % of CD45+ cells. Both IIF and immunoelectron microscopy confirmed a leukocyte/glial morphology for the immunoreactive cells. Quantitative immunohistochemistry (qIHC) of brain/eye sections showed 1.9 ± 0.8 % of T+ cells and 2 ± 0.9 % of CD45+ cells in the brain, and 3.6 ± 1.9 % and 4.1 ± 2.2 % in the eye, respectively. After in vivo RGNNV infection the number of T cells/CD45+ leukocytes in the brain increased to 8.3 ± 2.1 % and 11.6 ± 4.4 % (by IIF), and 26.1 ± 3.4 % and 45.6 ± 5.9 % (by qIHC), respectively. In the eye we counted after infection 8.5 ± 4.4 % of T cells and 10.2 ± 5.8 % of CD45 cells. Gene transcription analysis of brain mRNA revealed a strong increase of gene transcripts coding for: antiviral proteins Mx and ISG-12; T-cell related CD3ε/δ, TcRß, CD4, CD8α, CD45; and for immuno-modulatory cytokines TNFα, IL-2, IL-10. A RAG-1 gene product was also present and upregulated, suggesting somatic recombination in the fish brain. Similar transcription data were obtained in the eye, albeit with differences. Our findings provide first evidence for a recruitment and involvement of T cells and CD45+ leukocytes in the fish eye-brain axis during antiviral responses and suggest similarities in the CNS immune defense across evolutionary distant vertebrates.

Translation-complex profiling of fission yeast cells reveals dynamic rearrangements of scanning ribosomal subunits upon nutritional stress.

Control of mRNA translation is key for stress responses. Translation initiation is usually rate-limiting and, in eukaryotes, involves mRNA scanning by the small ribosomal subunit. Despite its importance, many aspects of translation in vivo have not been explored fully, especially at the transcriptome-wide level. A recent method termed translation-complex profiling (TCP-seq) allows transcriptome-wide views of scanning ribosomal subunits. We applied TCP-seq to nutritional stress in the fission yeast Schizosaccharomyces pombe. At initiation sites, we observed multiple complexes resembling those of mammals, and consistent with queuing of scanning subunits. In 5' UTRs, small subunit accumulations were common and may reflect impediments to scanning. A key mediator of stress responses in S. pombe is the Fil1 transcription factor, which is regulated translationally by a poorly-understood mechanism involving upstream Open Reading Frames (uORFs). TCP-seq data of fil1 shows that stress allows scanning subunits to by-pass specific uORFs and reach the fil1 coding sequence. The integration of these observations with reporter assays revealed that fil1 translational control is mediated by a combination of scanning reinitiation-repressive and permissive uORFs, and establishes fil1 as a model for uORF-mediated translational control. Altogether, our transcriptome-wide study reveals general and gene-specific features of translation in a model eukaryote.

Ribosome profiling reveals ribosome stalling on tryptophan codons and ribosome queuing upon oxidative stress in fission yeast.

Translational control is essential in response to stress. We investigated the translational programmes launched by the fission yeast Schizosaccharomyces pombe upon five environmental stresses. We also explored the contribution of defence pathways to these programmes: The Integrated Stress Response (ISR), which regulates translation initiation, and the stress-response MAPK pathway. We performed ribosome profiling of cells subjected to each stress, in wild type cells and in cells with the defence pathways inactivated. The transcription factor Fil1, a functional homologue of the yeast Gcn4 and the mammalian Atf4 proteins, was translationally upregulated and required for the response to most stresses. Moreover, many mRNAs encoding proteins required for ribosome biogenesis were translationally downregulated. Thus, several stresses trigger a universal translational response, including reduced ribosome production and a Fil1-mediated transcriptional programme. Surprisingly, ribosomes stalled on tryptophan codons upon oxidative stress, likely due to a decrease in charged tRNA-Tryptophan. Stalling caused ribosome accumulation upstream of tryptophan codons (ribosome queuing/collisions), demonstrating that stalled ribosomes affect translation elongation by other ribosomes. Consistently, tryptophan codon stalling led to reduced translation elongation and contributed to the ISR-mediated inhibition of initiation. We show that different stresses elicit common and specific translational responses, revealing a novel role in Tryptophan-tRNA availability.

Global phylogeny of the Shiitake mushroom and related Lentinula species uncovers novel diversity and suggests an origin in the Neotropics.

Lentinula (Basidiomycota, Agaricales) includes the most widely cultivated mushroom in the world, Lentinula edodes, also known as shiitake (Japanese) or xiang-gu (Chinese). At present, nine species are recognized in the genus, based on morphology, mating criteria, and geographic distribution. However, analyses of internal transcribed spacers (ITS) of ribosomal RNA genes have suggested that there are cryptic lineages. We analyzed a global-scale phylogenetic dataset from 325 Lentinula individuals from 24 countries in Asia-Australasia and the Americas plus Madagascar, with 325 sequences of ITS, 80 LSU sequences, and 111 sequences of translation elongation factor (tef1-α) genes. We recovered 15 independent lineages (Groups 1-15) that may correspond to species. Lineages in Asia-Australasia (Groups 1-5) and the Americas plus Madagascar (Groups 6-15) formed sister clades. Four lineages are represented only by sequences from single individuals and require further molecular sampling, including L. aff. raphanica (Group 7), L. ixodes (Group 8), L. boryana (Group 12), and L. aff. aciculospora (Group 14). Groups 1 and 5 are here referred to L. edodes and L. aff. edodes, respectively. However, these groups most likely represent the same species and are only recognized as (unsupported) monophyletic lineages by maximum likelihood analyses of ITS alone. Other putative species resolved here include L. lateritia (Group 2), L. novae-zelandieae (Group 3), L. aff. lateritia (Group 4), L. raphanica (Group 6), L. aff. detonsa (Group 9), L. detonsa (Group 10), L. guzmanii sp. nov. (Group 11), L. aciculospora (Group 13), and L. madagasikarensis (Group 15). Groups 9-12 represent the "L. boryana complex". Molecular clock and historical biogeographic analyses suggest that the most recent common ancestor (MRCA) of Lentinula can be placed in the middle Oligocene, ca. 30 million years ago (Ma), and had a likely presence in neotropical America. The MRCA of Lentinula in the Americas and Madagascar lived ca. 22 Ma in the Neotropics and the MRCA of Lentinula in Asia-Australasia lived ca. 6 Ma in Oceania. Given the current knowledge about plate tectonics and paleoclimatic models of the last 30 Myr, our phylogenetic hypothesis suggests that the extant distribution of Lentinula is likely to have arisen, in large part, due to long-distance dispersal. Lentinula collections include at least four dubious taxa that need further taxonomic studies: L. reticeps from the USA (Ohio); L. guarapiensis from Paraguay; Lentinus puiggarii from Brazil (São Paulo); and "L. platinedodes" from Vietnam. Approximately ten of the fifteen Groups are reported on Fagaceae, which appears to be the ancestral substrate of Lentinula.

General amino acid control in fission yeast is regulated by a nonconserved transcription factor, with functions analogous to Gcn4/Atf4.

Eukaryotes respond to amino acid starvation by enhancing the translation of mRNAs encoding b-ZIP family transcription factors (GCN4 in Saccharomyces cerevisiae and ATF4 in mammals), which launch transcriptional programs to counter this stress. This pathway involves phosphorylation of the eIF2 translation factor by Gcn2-protein kinases and is regulated by upstream ORFs (uORFs) in the GCN4/ATF4 5' leaders. Here, we present evidence that the transcription factors that mediate this response are not evolutionarily conserved. Although cells of the fission yeast Schizosaccharomyces pombe respond transcriptionally to amino acid starvation, they lack clear Gcn4 and Atf4 orthologs. We used ribosome profiling to identify mediators of this response in S. pombe, looking for transcription factors that behave like GCN4 We discovered a transcription factor (Fil1) translationally induced by amino acid starvation in a 5' leader and Gcn2-dependent manner. Like Gcn4, Fil1 is required for the transcriptional response to amino acid starvation, and Gcn4 and Fil1 regulate similar genes. Despite their similarities in regulation, function, and targets, Fil1 and Gcn4 belong to different transcription factor families (GATA and b-ZIP, respectively). Thus, the same functions are performed by nonorthologous proteins under similar regulation. These results highlight the plasticity of transcriptional networks, which maintain conserved principles with nonconserved regulators.

Long noncoding RNA repertoire and targeting by nuclear exosome, cytoplasmic exonuclease, and RNAi in fission yeast.

Long noncoding RNAs (lncRNAs), which are longer than 200 nucleotides but often unstable, contribute a substantial and diverse portion to pervasive noncoding transcriptomes. Most lncRNAs are poorly annotated and understood, although several play important roles in gene regulation and diseases. Here we systematically uncover and analyze lncRNAs in Schizosaccharomyces pombe. Based on RNA-seq data from twelve RNA-processing mutants and nine physiological conditions, we identify 5775 novel lncRNAs, nearly 4× the previously annotated lncRNAs. The expression of most lncRNAs becomes strongly induced under the genetic and physiological perturbations, most notably during late meiosis. Most lncRNAs are cryptic and suppressed by three RNA-processing pathways: the nuclear exosome, cytoplasmic exonuclease, and RNAi. Double-mutant analyses reveal substantial coordination and redundancy among these pathways. We classify lncRNAs by their dominant pathway into cryptic unstable transcripts (CUTs), Xrn1-sensitive unstable transcripts (XUTs), and Dicer-sensitive unstable transcripts (DUTs). XUTs and DUTs are enriched for antisense lncRNAs, while CUTs are often bidirectional and actively translated. The cytoplasmic exonuclease, along with RNAi, dampens the expression of thousands of lncRNAs and mRNAs that become induced during meiosis. Antisense lncRNA expression mostly negatively correlates with sense mRNA expression in the physiological, but not the genetic conditions. Intergenic and bidirectional lncRNAs emerge from nucleosome-depleted regions, upstream of positioned nucleosomes. Our results highlight both similarities and differences to lncRNA regulation in budding yeast. This broad survey of the lncRNA repertoire and characteristics in S. pombe, and the interwoven regulatory pathways that target lncRNAs, provides a rich framework for their further functional analyses.

Differential immunogene expression profile of European sea bass (Dicentrarchus labrax, L.) in response to highly and low virulent NNV.

European sea bass is highly susceptible to the nervous necrosis virus, RGNNV genotype, whereas natural outbreaks caused by the SJNNV genotype have not been recorded. The onset and severity of an infectious disease depend on pathogen virulence factors and the host immune response. The importance of RGNNV capsid protein amino acids 247 and 270 as virulence factors has been previously demonstrated in European sea bass; however, sea bass immune response against nodaviruses with different levels of virulence has been poorly characterized. Knowing the differences between the immune response against both kinds of isolates may be key to get more insight into the host mechanisms responsible for NNV virulence. For this reason, this study analyses the transcription of immunogenes differentially expressed in European sea bass inoculated with nodaviruses with different virulence: a RGNNV virus obtained by reverse genetics (rDl956), highly virulent to sea bass, and a mutated virus (Mut247+270Dl956, RGNNV virus displaying SJNNV-type amino acids at positions 247 and 270 of the capsid protein), presenting lower virulence. This study has been performed in brain and head kidney, and the main differences between the immunogene responses triggered by both viruses have been observed in brain. The immunogene response in this organ is stronger after inoculation with the most virulent virus, and the main differences involved genes related with IFN I system, inflammatory response, cell-mediated response, and apoptosis. The lower virulence of Mut247+270Dl956 to European sea bass can be associated with a delayed IFN I response, as well as an early and transitory inflammation and cell-mediated responses, suggesting that those can be pivotal elements in controlling the viral infection, and therefore, their functional activity could be analysed in future studies. In addition, this study supports the role of capsid amino acids at positions 247 and 270 as important determinants of RGNNV virulence to European sea bass.

Is there a gender bias in the advancement to SAGES leadership?

BACKGROUND: The proportion of women in surgery has risen significantly yet there remains gender discrepancies in upper leadership positions in academia. Specialty societies play an important role in academic advancement but the progression of women in surgical societies has not been studied. The purpose of this study was to determine if there are gender differences in advancement within the Society of American Gastrointestinal and Endoscopic Surgeons (SAGES) leadership. METHODS: A retrospective audit of all SAGES committee members (CM) from 1992 to 2018 was performed. The overall membership gender distribution was available from 2010 to 2018. Leadership positions included Committee Chair/Co-chair, Board of Governors, and Executive Committee. Three phenomena were investigated: "pipeline," by determining the change in women CMs compared to overall membership over time; "sticky floors," by comparing advancement beyond CM by gender; "glass-ceiling," by analyzing the promotion trajectory and time to leadership positions between genders. Statistical analysis comparing trends over time was performed using Kendall-tau. RESULTS: There were 1546 surgeons who served on at least one committee during the study period. Women represented 21% of CMs, 18% of chairs/co-chairs, 16% of board members and 14% of executives, with one woman President. The proportion of women CMs has significantly increased over time from 3% in 1992 to 27% in 2018 (p-trend < 0.001). A similar proportion of women and men advanced beyond CM (17% vs. 14%, p = 0.194), with no difference in time to advancement. From 2010 to 2018, the increase in the proportion of women CMs and board members outpaced that of overall women members (p < 0.05). Women executives surpassed overall women members in 2018 (29% vs. 19%). A similar proportion of men and women "skipped ranks" to reach the Board/Executive (37% vs. 25%, p = 0.307). CONCLUSION: The proportion of women in leadership positions within SAGES is higher than in the overall membership. There were no gender differences in the advancement of CMs to leadership positions. While these data are encouraging, SAGES should continue to foster the advancement of women surgeons.

A mobile device application (app) to improve adherence to an enhanced recovery program for colorectal surgery: a randomized controlled trial.

BACKGROUND: Increased adherence with enhanced recovery pathways (ERP) is associated with improved outcomes. However, adherence to postoperative elements that rely on patient participation remains suboptimal. Mobile device apps may improve delivery of health education material and have the potential to foster behavior change and improve patient compliance. The objective of this study was to estimate the extent to which a novel mobile device app affects adherence to an ERP for colorectal surgery in comparison to standard written education. METHODS: This was a superiority, parallel-group, assessor-blind, sham-controlled randomized trial involving 97 patients undergoing colorectal resection. Participants were randomly assigned with a 1:1 ratio into one of two groups: (1) iPad including a novel mobile device app for postoperative education and self-assessment of recovery, or (2) iPad without the app. The primary outcome measure was mean adherence (%) to a bundle of five postoperative ERP elements requiring patient participation: mobilization, gastrointestinal motility stimulation, breathing exercises, and consumption of oral liquids and nutritional drinks. RESULTS: In the intervention group, app usage was high (94% completed surveys on POD0, 82% on POD1, 72% on POD2). Mean overall adherence to the bundle on the two first postoperative days was similar between groups: 59% (95% CI 52-66%) in the intervention group and 62% (95% CI 56-68%) in the control group [Adjusted mean difference 2.4% (95% CI - 5 to 10%) p = 0.53]. CONCLUSIONS: In this randomized trial, access to a mobile health application did not improve adherence to a well-established enhanced recovery pathway in colorectal surgery patients, when compared to standard written patient education. Future research should evaluate the impact of applications integrating novel behavioral change techniques, particularly in contexts where adherence is low.

Preoperative Exercise Rehabilitation in Cardiac and Vascular Interventions.

BACKGROUND: Exercise-based interventions have become part of the standard of care in rehabilitation programs for cardiovascular risk reduction and the promotion of a healthy lifestyle. The systematic review describes the current state of knowledge of the effects of preoperative exercise training (prehabilitation) on perioperative clinical outcomes in patients undergoing cardiac and vascular interventions. METHODS: Studies were systematically searched within 14 databases from inception to October 2016. Only studies that assessed a preoperative exercise program in adult patients undergoing cardiac or vascular interventions with clinical or patient-centered endpoints were included in the review. Two independent reviewers selected studies for inclusion, extracted data, and assessed quality using Cochrane Collaboration's tool for RCTs11111111111111111 and ROBINS-I tool for nonrandomized studies. RESULTS: Nine studies met our inclusion criteria and were stratified for qualitative analyses by cardiac (n = 7) and vascular (n = 2) procedures. Prehabilitation was associated with decreased length of stay, reduced postoperative complications, improved objective physical functioning, and improved subjective quality of life (SF-36 physical and mental health domains) measures in patients undergoing cardiac and vascular procedures. Given the amount of heterogeneity that was present in the designs, populations, and comparators among the included studies, we were unable to statistically pool data across trials. CONCLUSIONS: Our qualitative findings suggest that prehabilitation may improve clinical outcomes, physical performance, and health-related quality-of-life measures in patients undergoing cardiac and vascular surgery procedures.

Incidence and predictors of prolonged postoperative ileus after colorectal surgery in the context of an enhanced recovery pathway.

BACKGROUND: Prolonged postoperative ileus (PPOI) is common after colorectal surgery but has not been widely studied in the context of enhanced recovery pathways (ERPs) that include interventions aimed to accelerate gastrointestinal recovery. The aim of this study is to estimate the incidence and predictors of PPOI in the context of an ERP for colorectal surgery. METHODS: We analyzed data from an institutional colorectal surgery ERP registry. Incidence of PPOI was estimated according to a definition adapted from Vather (intolerance of solid food and absence of flatus or bowel movement for ≥ 4 days) and compared to other definitions in the literature. Potential risk factors for PPOI were identified from previous studies, and their predictive ability was evaluated using Bayesian model averaging (BMA). Results are presented as posterior effect probability (PEP). Evidence of association was categorized as: no evidence (PEP < 50%), weak evidence (50-75%), positive evidence (75-95%), strong evidence (95-99%), and very strong evidence (> 99%). RESULTS: There were 323 patients analyzed (mean age 63.5 years, 51% males, 74% laparoscopic, 33% rectal resection). The incidence of PPOI was 19% according to the primary definition, but varied between 11 and 59% when using other definitions. On BMA analysis, intraoperative blood loss (PEP 99%; very strong evidence), administration of any intravenous opioids in the first 48 h (PEP 94%; strong evidence), postoperative epidural analgesia (PEP 56%; weak evidence), and non-compliance with intra-operative fluid management protocols (3 ml/kg/h for laparoscopic and 5 ml/kg/h for open; PEP 55%, weak evidence) were predictors of PPOI. CONCLUSIONS: The incidence of PPOI after colorectal surgery is high even within an established ERP and varied considerably by diagnostic criteria, highlighting the need for a consensus definition. The use of intravenous opioids is a modifiable strong predictor of PPOI within an ERP, while the role of epidural analgesia and intraoperative fluid management should be further evaluated.

Incisional Hernia After Midline Versus Transverse Specimen Extraction Incision: A Randomized Trial in Patients Undergoing Laparoscopic Colectomy.

OBJECTIVE: To compare the incidence of incisional hernia (IH) between midline and transverse specimen extraction site in patients undergoing laparoscopic colectomy. BACKGROUND: Midline specimen extraction incision is most commonly used in laparoscopic colectomy, but has high IH risk. IH may be lower for transverse incision. METHODS: A single-center superiority trial was conducted. Eligible patients undergoing laparoscopic colectomy were randomly assigned to midline or transverse specimen extraction. Primary outcome was IH incidence at 1 year. Power calculation required 76 patients per group to detect a reduction in IH from 20% to 5%. Secondary outcomes included perioperative outcomes, pain scores, health-related quality of life (SF-36), and cosmesis (Body Image Questionnaire). RESULTS: A total of 165 patients were randomly assigned to transverse (n = 79) or midline (n = 86) specimen extraction site, of which 141 completed 1-year follow-up (68 transverse, 73 midline). Patient, tumor, surgical data, and perioperative morbidity were similar. Pain scores were similar on each postoperative day. On intention-to-treat analysis, there was no difference in the incidence of IH at 1 year (transverse 2% vs midline 8%, P = 0.065) or after mean 30.3 month (standard deviation 9.4) follow-up (6% vs 14%, P = 0.121). On per-protocol analysis there were more IH after midline incision with longer follow-up (15% vs 2%, P = 0.013). On intention-to-treat analysis, SF-36 domains body pain and social functioning were improved after transverse incision. Cosmesis was higher after midline incision on per-protocol analysis, but without affecting body image. CONCLUSIONS: Per-protocol analysis of this trial demonstrates that a transverse specimen extraction site has a lower incidence of IH compared to midline with longer follow-up but has worse cosmesis.

Widespread exon skipping triggers degradation by nuclear RNA surveillance in fission yeast.

Exon skipping is considered a principal mechanism by which eukaryotic cells expand their transcriptome and proteome repertoires, creating different splice variants with distinct cellular functions. Here we analyze RNA-seq data from 116 transcriptomes in fission yeast (Schizosaccharomyces pombe), covering multiple physiological conditions as well as transcriptional and RNA processing mutants. We applied brute-force algorithms to detect all possible exon-skipping events, which were widespread but rare compared to normal splicing events. Exon-skipping events increased in cells deficient for the nuclear exosome or the 5'-3' exonuclease Dhp1, and also at late stages of meiotic differentiation when nuclear-exosome transcripts decreased. The pervasive exon-skipping transcripts were stochastic, did not increase in specific physiological conditions, and were mostly present at less than one copy per cell, even in the absence of nuclear RNA surveillance and during late meiosis. These exon-skipping transcripts are therefore unlikely to be functional and may reflect splicing errors that are actively removed by nuclear RNA surveillance. The average splicing rate by exon skipping was ∼ 0.24% in wild type and ∼ 1.75% in nuclear exonuclease mutants. We also detected approximately 250 circular RNAs derived from single or multiple exons. These circular RNAs were rare and stochastic, although a few became stabilized during quiescence and in splicing mutants. Using an exhaustive search algorithm, we also uncovered thousands of previously unknown splice sites, indicating pervasive splicing; yet most of these splicing variants were cryptic and increased in nuclear degradation mutants. This study highlights widespread but low frequency alternative or aberrant splicing events that are targeted by nuclear RNA surveillance.

Predictors of adherence to enhanced recovery pathway elements after laparoscopic colorectal surgery.

INTRODUCTION: Enhanced recovery pathways (ERP) include a bundle of evidence-based preoperative, intraoperative, and postoperative interventions that together reduce morbidity and length of stay after colorectal surgery. Increased adherence with the bundle is associated with better postoperative outcomes, but adherence is lowest in the postoperative period. Identifying risk factors for lower adherence may help design quality improvement strategies. The aim of this study was to estimate the extent to which patient, procedural, and organizational factors predict adherence to postoperative ERP elements in laparoscopic colorectal surgery. METHODS: Patients in an institutional ERP registry undergoing elective laparoscopic colorectal surgery between 2012 and 2014 were analyzed. The ERP included 10 postoperative ERP elements classified into 2 groups: those requiring patient participation (PP, 5 elements, including nutritional intake and mobilization) and those provided by the clinical team (CT, 5 elements, including removal of catheters and type of analgesia). The impact of baseline and intraoperative factors on adherence was estimated using stepwise linear regression. RESULTS: A total of 223 patients were included (mean age 60, 48% male). Mean adherence was 79% to the PP bundle (range 65-93% for individual elements), and 82% for the CT bundle (range 68-98% for individual elements). The occurrence of nausea/vomiting in the first 24 h was associated with lower adherence to both bundles. In the PP bundle, patients who arrived at the ward after 6 p.m. had lower adherence. In the CT bundle, patients who had rectal resection had lower adherence while thoracic epidural was associated with higher adherence. CONCLUSIONS: With the exception of postoperative nausea and vomiting, predictors of adherence to ERP elements after colorectal surgery differed for elements requiring patient participation and those provided by the clinical team. Strategies to improve ERP adherence should target staff education and engagement of patients at risk for lower adherence.

Systematic analysis of the role of RNA-binding proteins in the regulation of RNA stability.

mRNA half-lives are transcript-specific and vary over a range of more than 100-fold in eukaryotic cells. mRNA stabilities can be regulated by sequence-specific RNA-binding proteins (RBPs), which bind to regulatory sequence elements and modulate the interaction of the mRNA with the cellular RNA degradation machinery. However, it is unclear if this kind of regulation is sufficient to explain the large range of mRNA stabilities. To address this question, we examined the transcriptome of 74 Schizosaccharomyces pombe strains carrying deletions in non-essential genes encoding predicted RBPs (86% of all such genes). We identified 25 strains that displayed changes in the levels of between 4 and 104 mRNAs. The putative targets of these RBPs formed biologically coherent groups, defining regulons involved in cell separation, ribosome biogenesis, meiotic progression, stress responses and mitochondrial function. Moreover, mRNAs in these groups were enriched in specific sequence motifs in their coding sequences and untranslated regions, suggesting that they are coregulated at the posttranscriptional level. We performed genome-wide RNA stability measurements for several RBP mutants, and confirmed that the altered mRNA levels were caused by changes in their stabilities. Although RBPs regulate the decay rates of multiple regulons, only 16% of all S. pombe mRNAs were affected in any of the 74 deletion strains. This suggests that other players or mechanisms are required to generate the observed range of RNA half-lives of a eukaryotic transcriptome.

Cost-effectiveness of Enhanced Recovery Versus Conventional Perioperative Management for Colorectal Surgery.

OBJECTIVE: To determine the cost-effectiveness of enhanced recovery pathways (ERPs) versus conventional care for patients undergoing elective colorectal surgery. BACKGROUND: ERPs for colorectal surgery are clinically effective, but their cost-effectiveness is unknown. METHODS: A multi-institutional prospective cohort cost-effectiveness analysis was performed. Adult patients undergoing elective colorectal resection at 2 university-affiliated institutions from October 2012 to October 2013 were enrolled. One center used an ERP, whereas the other did not. Postoperative outcomes were recorded up to 60 days. Total costs were reported in 2013 Canadian dollars. Effectiveness was measured using the SF-6D, a health utility measure validated for postoperative recovery. Uncertainty was expressed using bootstrapped estimates (10,000 repetitions). RESULTS: A total of 180 patients were included (conventional care: n = 95; ERP: n = 95). There were no differences in patient characteristics except for a higher proportion of laparoscopy in the ERP group. Mean length of stay was shorter in the ERP group (6.5 vs 9.8 days; P = 0.017), but there were no differences in complications or readmissions. Patients in the ERP group returned to work quicker and had less caregiver burden. There was no difference in quality of life between the 2 groups. The cost of the ERP program was $153 per patient. Overall societal costs were lower in the ERP group (mean difference = -2985; 95% confidence interval, -5753 to -373). The ERP had a greater than 99% probability of cost-effectiveness. The results were insensitive to a range of assumptions and subgroups. CONCLUSIONS: Enhanced recovery is cost-effective compared with conventional perioperative management for elective colorectal resection.

Validity of the EuroQol-5 dimensions as a measure of recovery after pulmonary resection.

BACKGROUND: Surgical innovations advocated to improve patient recovery are often costly. Economic evaluation requires preference-based measures that reflect the construct of patient recovery. We investigated the responsiveness and construct validity of the EuroQol-5 dimensions (EQ-5D) as a measure of postoperative recovery after planned pulmonary resection for suspected malignant tumors. METHODS: Patients undergoing pulmonary resection completed the EQ-5D questionnaire and visual analog scales (VAS) for pain and fatigue at baseline (preoperatively) and at 1 and 3 mo postoperatively. Responsiveness and construct validity (discriminant and convergent) were investigated by testing a priori hypotheses. RESULTS: Fifty-five patients were analyzed (45% male, 62 ± 12 y, 29% video-assisted). There was no significant difference between median EQ-5D scores obtained at baseline (0.83 [interquartile range {IQR 0.80-1}]) compared to scores at 1 mo (0.83 [0.80-1], P = 0.86) and 3 mo after surgery (1 [0.83-1]; P = 0.09). At 1 mo after surgery, EQ-5D scores were significantly lower in patients undergoing thoracotomy versus video-assisted surgery (0.82 [IQR 0.77-0.89] versus 1 [0.83-1], P = 0.003), but there were no significant differences between patients ≥ 70-y old versus younger (0.95 [IQR 0.82-1] versus 0.83 [0.77-1], P = 0.09) or between patients with versus without complications (0.82 [IQR 0.79-0.95] versus 0.83 [0.80-1], P = 0.10). There was a low but significant correlation between EQ-5D and VAS scores of pain and fatigue (Rho -0.30 to -0.47, P ≤ 0.01). CONCLUSIONS: Despite evidence of convergent validity, the EQ-5D was not sensitive to the hypothesized trajectory of postoperative recovery and showed limited discriminant validity. This study suggests that the EQ-5D may not be appropriate to value recovery after lung resection.

Cotranslational protein-RNA associations predict protein-protein interactions.

BACKGROUND: Most cellular proteins function as part of stable protein complexes. We recently showed that around 38% of proteins associate with mRNAs that encode interacting proteins, reflecting the cotranslational formation of the complex between the bait protein and the nascent peptides encoded by the interacting mRNAs. Here we hypothesise that these cotranslational protein-mRNA associations can be used to predict protein-protein interactions. RESULTS: We found that the fission yeast Exo2 protein, which encodes an exonuclease of the XRN1 family, coimmunoprecipitates with the eti1 mRNA, which codes for a protein of unknown function and uninformative sequence. Based on this protein-mRNA association, we predicted that the Exo2 and Eti1 protein are part of the same complex, and confirmed this hypothesis by coimmunoprecipitation and colocalization of the proteins. Similarly, we show that the cotranslational interaction between the Sty1 MAP kinase and the cip2 mRNA, which encodes an RNA-binding protein, predicts a complex between Sty1 and Cip2. CONCLUSIONS: Our results demonstrate that cotranslational protein-mRNA associations can be used to identify new components of protein complexes.

A comparison of the validity of two indirect utility instruments as measures of postoperative recovery.

BACKGROUND: Cost-effectiveness analyses of surgical interventions require valid measures of postoperative recovery. The objective of this study was to compare the validity of two indirect utility instruments, the Short Form 6D (SF-6D) and EuroQol 5D (EQ-5D), as measures of postoperative recovery. MATERIALS AND METHODS: A prospective cohort of patients undergoing elective colorectal resection at two university-affiliated institutions from October 2012-October 2013 completed the SF-6D and EQ-5D (including the EQ-visual analog scale [EQ-VAS]) at baseline (before surgery), and at 4 and 8 wk after surgery. Responsiveness and construct validity were assessed through a priori hypotheses. RESULTS: A total of 165 patients were included. The SF-6D was the most responsive to the expected postoperative changes at 4 and 8 wk compared with the EQ-5D and the EQ-VAS. The 4-wk SF-6D, EQ-5D, and EQ-VAS discriminated between patients with and without complications after controlling for confounders with adjusted mean differences of -0.070 (95% confidence interval [CI] -0.126 to -0.015), -0.133 (95% CI -0.231, -0.030), and -7.91 (95% CI -14.77, -1.04), respectively. Mean SF-6D and EQ-5D values were significantly different from the US population norms at all time points, but the magnitude of change was highest for the SF-6D. The strength of correlation between all three instruments was moderate at all time points (r=0.550-0.684, all P<0.05). CONCLUSIONS: The SF-6D preference-based health index appears to be a more valid measure of postoperative recovery than the EQ-5D and EQ-VAS in surgical cost-effectiveness analyses.