Effect of bowel preparation on intestinal permeability and inflammatory response during postoperative ileus in mice.

BACKGROUND: Postoperative ileus entails pathophysiological changes in mucosal permeability and an intestinal inflammatory immune response. We hypothesized that preoperative selective decontamination of the digestive tract combined with preoperative mechanical bowel preparation might be advantageous to prevent or reduce permeability changes and immune response in postoperative ileus. METHODS: Postoperative ileus was induced in mice by standardized small bowel manipulation. Intervention groups received selective decontamination and/or intestinal lavage with normal saline simulating mechanical bowel preparation before postoperative ileus induction. At 1, 3, and 9 hours after surgery, ileum samples were harvested for measurements of fluorescein (332 Da) permeability, quantification of tumor necrosis factor α-mRNA level, and leukocyte infiltration of the intestinal wall. RESULTS: Mucosal fluorescein permeability increased at 1 hour (8.6 ± 1.1 vs 5.9 ± 0.9 10-6 cm/s; P < .01) and 3 hours (8.5 ± 0.6 vs 6.5 ± 0.2 10-6 cm/s; P < .05) after induction of postoperative ileus. This increase was prevented by mechanical bowel preparation and selective decontamination+mechanical bowel preparation interventions at both points in time. Expression of tumor necrosis factor α was more than 2-fold increased (P < .05) in the very early phase after induction of postoperative ileus but did not occur in mechanical bowel preparation-pretreated animals. Myeloperoxidase staining revealed that mechanical bowel preparation inhibited postoperative ileus-associated leukocyte infiltration of the intestinal muscularis at 3 and 9 hours after surgery, but not selective decontamination + mechanical bowel preparation treatment. The number of leukocytes after mechanical bowel preparation-only treatment remained at the level of sham-controls. CONCLUSION: Mechanical bowel preparation prevents permeability and leukocyte infiltration of the intestinal wall in the early phase of postoperative ileus in mice.

Raloxifene inhibits pancreatic adenocarcinoma growth by interfering with ERß and IL-6/gp130/STAT3 signaling.

PURPOSE: Currently, the exact role of estrogen receptor (ER) signaling in pancreatic cancer is unknown. Recently, we showed that expression of phosphorylated ERß correlates with a poor prognosis in patients with pancreatic ductal adenocarcinoma (PDAC). Here, we hypothesized that raloxifene, a FDA-approved selective ER modulator (SERM), may suppress PDAC tumor growth by interfering with ERß signaling. To test this hypothesis, we studied the impact of raloxifene on interleukin-6/glycoprotein-130/signal transducer and activator of transcription-3 (IL-6/gp130/STAT3) signaling. METHODS: Human PDAC cell lines were exposed to raloxifene after which growth inhibition was assessed using a BrdU assay. ER knockdown was performed using siRNAs specific for ERα and ERß. The effects of raloxifene on IL-6 expression and STAT3 phosphorylation in PDAC cells were assessed by ELISA and Western blotting, respectively. In addition, raloxifene was administered to an orthotopic PDAC tumor xenograft mouse model, after which tumor growth was monitored and immunohistochemistry was performed. RESULTS: Raloxifene inhibited the in vitro growth of PDAC cells, and this effect was reversed by siRNA-mediated knockdown of ERß, but not of ERα, indicating ER isotype-specific signaling. We also found that treatment with raloxifene inhibited the release of IL-6 and suppressed the phosphorylation of STAT3Y705 in PDAC cells. In vivo, we found that orthotopic PDAC tumor growth, lymph node and liver metastases as well as Ki-67 expression were reduced in mice treated with raloxifene. CONCLUSIONS: Inhibition of ERß and the IL-6/gp130/STAT3 signaling pathway by raloxifene leads to potent reduction of PDAC growth in vitro and in vivo. Our results suggest that ERß signaling and IL-6/gp130 interaction may serve as promising drug targets for pancreatic cancer and that raloxifene may serve as an attractive therapeutic option for PDAC patients expressing the ERß isotype.

Rethinking the TNM Classification Regarding Direct Lymph Node Invasion in Pancreatic Ductal Adenocarcinoma.

Mechanisms of lymph node invasion seem to play a prognostic role in pancreatic ductal adenocarcinoma (PDAC) after resection. However, the 8th edition of the TNM classification of the American Joint Committee on Cancer (AJCC) does not consider this. The aim of this study was to analyse the prognostic role of different mechanisms of lymph node invasion on PDAC. One hundred and twenty-two patients with resected PDAC were examined. We distinguished three groups: direct (per continuitatem, Nc) from the main tumour, metastasis (Nm) without any contact to the main tumour, and a mixed mechanism (Ncm). Afterwards, the prognostic power of the different groups was analysed concerning overall survival (OS). In total, 20 patients displayed direct lymph node invasion (Nc = 16.4%), 44 were classed as Nm (36.1%), and 21 were classed as Ncm (17.2%). The difference in OS was not statistically significant between N0 (no lymph node metastasis, n = 37) and Nc (p = 0.134), while Nm had worse OS than N0 (p < 0.001). Direct invasion alone had no statistically significant effect on OS (p = 0.885). Redefining the N0 stage by including Nc patients showed a more precise OS prediction among N stages (p = 0.001 vs. p = 0.002). Nc was more similar to N0 than to Nm; hence, we suggest a rethinking of TNM classification based on the mechanisms of lymph node metastases in PDAC. Overall, this novel classification is more precise.

Altered thyroid hormone levels affect the capacity for temperature-induced developmental plasticity in larvae of Rana temporaria and Xenopus laevis.

Anuran larvae show phenotypic plasticity in age and size at metamorphosis as a response to temperature variation. The capacity for temperature-induced developmental plasticity is determined by the thermal adaptation of a population. Multiple factors such as physiological responses to changing environmental conditions, however, might influence this capacity as well. In anuran larvae, thyroid hormone (TH) levels control growth and developmental rate and changes in TH status are a well-known stress response to sub-optimal environmental conditions. We investigated how chemically altered TH levels affect the capacity to exhibit temperature-induced developmental plasticity in larvae of the African clawed frog (Xenopus laevis) and the common frog (Rana temporaria). In both species, TH level influenced growth and developmental rate and modified the capacity for temperature-induced developmental plasticity. High TH levels reduced thermal sensitivity of metamorphic traits up to 57% (R. temporaria) and 36% (X. laevis). Rates of growth and development were more plastic in response to temperature in X. laevis (+30%) than in R. temporaria (+6%). Plasticity in rates of growth and development is beneficial to larvae in heterogeneous habitats as it allows a more rapid transition into the juvenile stage where rates of mortality are lower. Therefore, environmental stressors that increase endogenous TH levels and reduce temperature-dependent plasticity may increase risks and the vulnerability of anuran larvae. As TH status also influences metabolism, future studies should investigate whether reductions in physiological plasticity also increases the vulnerability of tadpoles to global change.

Reduction of Postoperative Wound Infections by Antiseptica (RECIPE)?: A Randomized Controlled Trial.

OBJECTIVE: To evaluate whether intraoperative subcutaneous wound irrigation with 0.04% polyhexanide can reduce surgical site infection (SSI) in elective laparotomies compared to saline. BACKGROUND: SSI is a common complication after gastrointestinal surgery. To date, there is a lack of evidence whether subcutaneous wound irrigation is beneficial in terms of reduction of SSI. METHODS: The RECIPE trial was an investigator initiated single-center, single-blind prospective, randomized controlled trial with 2 parallel treatment groups, comparing wound irrigation with 0.9% saline to antiseptic 0.04% polyhexanide solution in elective laparotomies. Primary endpoint was the rate of SSI within 30 days postoperatively according to Centers for Disease Control and Prevention criteria. RESULTS: Between February 02, 2015, and May 23, 2018, 456 patients were randomly assigned to saline (n = 228) or polyhexanide (n = 228). Final cohort for analysis comprised 393 patients (202 in the saline and 191 in the polyhexanide group). Overall rate of SSI was 28.2%, n = 111. Simple analysis with cross tabulation revealed that significantly fewer SSIs occurred in the polyhexanide group: n = 70 (34.7%) versus n = 41 (21.5%); P = 0.004. In a multiple logistic regression model the factor wound irrigation with polyhexanide [odds ratio (OR) 0.44; 95% confidence interval (CI) 0.27-0.72; P = 0.001) was associated with risk reduction of SSI. Preoperative anemia (OR 2.08; 95% CI 1.27-3.40; P = 0.004) and more than 5 prior abdominal operations compared to none (OR 8.51; 95% CI 2.57-28.21; P < 0.001) were associated with SSI. CONCLUSIONS: Intraoperative subcutaneous wound irrigation with antiseptic 0.04% polyhexanide solution is effective in reducing SSI after elective laparotomies.

Time-Dependent Alterations of Gut Wall Integrity in Small Bowel Obstruction in Mice.

BACKGROUND: Small bowel obstruction (SBO) is one of the most common disorders in surgical emergency departments. Without resolution of the obstructed bowel segments, patients may develop multiorgan failure. The aim of this study was to investigate whether morphological damage of the intestinal wall during SBO may lead to molecular translocation and how this may impair intestinal motility. METHODS: C57Bl6 mice were laparotomized, and the small intestine was ligated 5 cm oral to the coecum for SBO. Controls received minilaparotomy only. Animals were sacrificed 3 h, 9 h, and 24 h after SBO. Morphological changes were evaluated on hematoxylin and eosin histology by a standardized score. Intestinal motility was determined by recording intraluminal pressure of the small intestine in vitro. Permeability was measured by fluorospectroscopy and ELISA of blood samples after oral gavage with fluorescein isothiocyanate (FITC)-dextrane and horse radish peroxidase. Data are mean ± SD. RESULTS: Three hours after SBO, FITC-dextrane uptake was increased to 187.6 ± 15.2 ng/mL compared to controls (P = 0.011). At 9 h, uptake of horse radish peroxidase (23.0 ± 8.6 ng/mL, 9.0 ± 6.3 ng/mL, P = 0.039) and FITC-dextrane (86.8 ± 17.8 ng/mL, 62.0 ± 1.6 ng/mL, P = 0.029) was higher compared to controls. Motility was increased to 162.2 ± 20.2 area under the curve (AUC) compared to 121.3 ± 20.3 AUC in controls, P = 0.009 and an increased histology score was observed at 9 h (3.2 ± 1.8 versus 0.6 ± 0.7, P = 0.003). Twenty-four hours after SBO, histology score was 3.8 ± 1.7, which was higher than 0.9 ± 0.7 in controls (P = 0.001). Intestinal motility was decreased 24 h after SBO compared to sham controls (146.0 ± 21.4 AUC versus 198.9 ± 21.2 AUC, P = 0.003). CONCLUSIONS: SBO entails a time dependent epithelial damage to the mucosa. In parallel, molecular changes in the gut mucosal barrier occur as early as 3 h after the onset of SBO with a subsequent increase in permeability. Initial intestinal hypermotility is followed by a decrease in motility.

Thyroid hormone levels and temperature during development alter thermal tolerance and energetics of Xenopus laevis larvae.

Environmental variation induced by natural and anthropogenic processes including climate change may threaten species by causing environmental stress. Anuran larvae experiencing environmental stress may display altered thyroid hormone (TH) status with potential implications for physiological traits. Therefore, any capacity to adapt to environmental changes through plastic responses provides a key to determining species vulnerability to environmental variation. We investigated whether developmental temperature (T dev), altered TH levels and whether the interactive effect of both affect standard metabolic rate (SMR), body condition (BC), survival and thermal tolerance in larvae of the African clawed frog (Xenopus laevis) reared at five temperatures with experimentally altered TH levels. At metamorphosis, SMR, BC and survival were significantly affected by T dev, TH status and their interaction with the latter often intensified impacts. Larvae developing at warmer temperatures exhibited significantly higher SMRs and BC was reduced at warm T dev and high TH levels suggesting decreased ability to acclimate to variation in temperature. Accordingly, tadpoles that developed at warm temperatures had higher maximum thermal limits but more narrow thermal tolerance windows. High and low TH levels decreased and increased upper thermal limits, respectively. Thus, when experiencing both warmer temperatures and environmental stress, larvae may be less able to compensate for changes in T dev. Our results demonstrate that physiological traits in larvae of X. laevis are strongly affected by increased TH levels and warmer temperatures. Altered TH levels and increasing T dev due to global change may result in a reduced capacity for physiological plasticity. This has far reaching consequences since the energetic requirement at the onset of metamorphosis is known to determine metamorphic success and thus, is indirectly linked to individual fitness in later life stages.

Altered thyroid hormone levels affect body condition at metamorphosis in larvae of Xenopus laevis.

Chemical, physical and biological environmental stressors may affect the endocrine system, such as the thyroid hormone (TH) axis in larval amphibians with consequences for energy partitioning among development, growth and metabolism. We studied the effects of two TH level affecting compounds, exogenous l-thyroxine (T4 ) and sodium perchlorate (SP), on various measures of development and body condition in larvae of the African clawed frog (Xenopus laevis). We calculated the scaled mass index, hepatosomatic index and relative tail muscle mass as body condition indices to estimate fitness. Altered TH levels significantly altered the growth, development, survival and body condition in metamorphic larvae in different directions. While exogeno us T4 reduced growth and accelerated development, SP treatment increased growth but slowed down development. Altered TH levels improved body conditions in both treatments and particularly in larvae of the SP treatment but to the detriment of lower survival rates in both TH level altering treatments. The hepatosomatic index was negatively affected by exogenous T4 , but not by SP treatment indicating a lower lipid reserve in the liver in larvae of T4 treatment. These altered TH levels as caused by several environmental stressors may have an influence on individual fitness across life, as body condition at the onset of metamorphosis determines metamorphic and juvenile survival. Further research is needed to determine synergetic effects of environmental stressors on TH levels and its effects on physiological traits such as metabolic rate.

Subcellular Compartmentation of Alternatively Spliced Transcripts Defines SERINE/ARGININE-RICH PROTEIN30 Expression.

Alternative splicing (AS) is prevalent in higher eukaryotes, and generation of different AS variants is tightly regulated. Widespread AS occurs in response to altered light conditions and plays a critical role in seedling photomorphogenesis, but despite its frequency and effect on plant development, the functional role of AS remains unknown for most splicing variants. Here, we characterized the light-dependent AS variants of the gene encoding the splicing regulator Ser/Arg-rich protein SR30 in Arabidopsis (Arabidopsis thaliana). We demonstrated that the splicing variant SR30.2, which is predominantly produced in darkness, is enriched within the nucleus and strongly depleted from ribosomes. Light-induced AS from a downstream 3' splice site gives rise to SR30.1, which is exported to the cytosol and translated, coinciding with SR30 protein accumulation upon seedling illumination. Constitutive expression of SR30.1 and SR30.2 fused to fluorescent proteins revealed their identical subcellular localization in the nucleoplasm and nuclear speckles. Furthermore, expression of either variant shifted splicing of a genomic SR30 reporter toward SR30.2, suggesting that an autoregulatory feedback loop affects SR30 splicing. We provide evidence that SR30.2 can be further spliced and, unlike SR30.2, the resulting cassette exon variant SR30.3 is sensitive to nonsense-mediated decay. Our work delivers insight into the complex and compartmentalized RNA processing mechanisms that control the expression of the splicing regulator SR30 in a light-dependent manner.

DNA double-strand breaks in blood lymphocytes induced by two-day 99mTc-MIBI myocardial perfusion scintigraphy.

OBJECTIVES: To investigate DNA double-strand breaks (DSBs) in blood lymphocytes induced by two-day 99mTc-MIBI myocardial perfusion scintigraphy (MPS) using y-H2AX immunofluorescence microscopy and to correlate the results with 99mTc activity in blood samples. METHODS: Eleven patients who underwent two-day MPS were included. DSB blood sampling was performed before and 5min, 1h and 24h after the first and second radiotracer injections. 99mTc activity was measured in each blood sample. For immunofluorescence microscopy, distinct foci representing DSBs were quantified in lymphocytes after staining for the phosphorylated histone variant y-H2AX. RESULTS: The 99mTc-MIBI activity measured on days one and two was similar (254±25 and 258±27 MBq; p=0.594). Compared with baseline DSB foci (0.09±0.05/cell), a significant increase was found at 5min (0.19±0.04/cell) and 1h (0.18±0.04/cell) after the first injection and at 5min and 1h after the second injection (0.21±0.03 and 0.19±0.04/cell, respectively; p=0.003 for both). At 24h after the first and second injections, the number of DSB foci had returned to baseline (0.06±0.02 and 0.12±0.05/cell, respectively). 99mTc activity levels in peripheral blood samples correlated well with DSB counts (r=0.451). CONCLUSIONS: DSB counts reflect 99mTc-MIBI activity after injection for two-day MPS, and might allow individual monitoring of biological effects of cardiac nuclear imaging. KEY POINTS: • Myocardial perfusion scintigraphy using 99mTc induces time-dependent double-strand breaks (DSBs) • γ-H2AX immunofluorescence microscopy shows DSB as an early response to radiotracer injection • Activity measurements of 99mTc correlate well with detected DSB • DSB foci induced by 99mTc return to baseline 24h after radiotracer injection.

Severe Aortic Valve Stenosis in Adults is Associated with Increased Levels of Circulating Intermediate Monocytes.

Individual monocyte subsets have been associated with atherosclerotic disease, but their distribution has not been evaluated in aortic valve stenosis (AS) so far. In the present study, we have asked whether levels of the circulating intermediate monocyte subset are increased in AS. Classical (CD14++CD16-), intermediate (CD14++CD16+), and non-classical (CD14+CD16++) CD86-positive monocytes and monocyte activation (intensity of CD11b expression) were determined by flow cytometry in peripheral blood of patients with severe AS (n = 100) and matched AS-free controls (n = 75). AS patients exhibited significantly higher levels of circulating intermediate monocytes, while levels of circulating classical and non-classical monocytes or monocyte activation did not differ compared to controls. The difference in levels of intermediate monocytes between groups was independent of age, gender, BMI, LDL-C, NT-proBNP, NYHA functional class, or creatinine levels. The present pilot study provides evidence of an association of severe AS with increased levels of circulating intermediate monocytes. Further studies need to clarify whether this finding is related to the inflammatory status and hemodynamic disturbances associated with severe AS.

Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis.

Plants use light as source of energy and information to detect diurnal rhythms and seasonal changes. Sensing changing light conditions is critical to adjust plant metabolism and to initiate developmental transitions. Here, we analyzed transcriptome-wide alterations in gene expression and alternative splicing (AS) of etiolated seedlings undergoing photomorphogenesis upon exposure to blue, red, or white light. Our analysis revealed massive transcriptome reprogramming as reflected by differential expression of ∼20% of all genes and changes in several hundred AS events. For more than 60% of all regulated AS events, light promoted the production of a presumably protein-coding variant at the expense of an mRNA with nonsense-mediated decay-triggering features. Accordingly, AS of the putative splicing factor REDUCED RED-LIGHT RESPONSES IN CRY1CRY2 BACKGROUND1, previously identified as a red light signaling component, was shifted to the functional variant under light. Downstream analyses of candidate AS events pointed at a role of photoreceptor signaling only in monochromatic but not in white light. Furthermore, we demonstrated similar AS changes upon light exposure and exogenous sugar supply, with a critical involvement of kinase signaling. We propose that AS is an integration point of signaling pathways that sense and transmit information regarding the energy availability in plants.

Impact of intraoperatively salvaged and washed blood on stimulated cytokine release in vitro.

BACKGROUND: Intraoperative blood salvage and processing it with commercially available devices is a widespread standard procedure to reduce allogeneic blood transfusion in patients undergoing major orthopedic surgery. The aim of this study was to investigate the impact of such processed blood on the immune system by measuring pro- and anti-inflammatory cytokines. STUDY DESIGN AND METHODS: Salvaged blood from 20 patients undergoing hip arthroplasty was processed with a continuous autotransfusion system. One part of the processed blood was left without further treatment, one part was additionally leukoreduced, one part was irradiated, and one part was separated into its cellular and soluble fraction by centrifugation. Specimens from each part were mixed in vitro with venous blood from the patient in ratios of 3:1, 1:1, and 1:3 and incubated with endotoxin for 24 hours. Tumor necrosis factor (TNF)-α and interleukin (IL)-10 were measured in cell culture supernatants by enzyme-linked immunosorbent assay. RESULTS: All parts of the salvaged blood were without a significant influence on TNF-α release. In contrast, IL-10 was significantly increased, independently of the admixtured salvaged blood being plain, additionally irradiated, or additionally leukoreduced. This IL-10 increase was also found with the cellular fraction of the plain salvaged blood, whereas the soluble fraction had no influence on IL-10 release. CONCLUSION: Intraoperative salvaged blood is not immunologically inert. We observed a significant increase in the anti-inflammatory IL-10 response without affecting the proinflammatory TNF-α release. Neither leukofiltration nor gamma irradiation eliminated this effect that was limited only to the cellular fraction of the salvaged blood, suggesting red blood cells to be responsible for the observed immunomodulation.

NMD: nonsense-mediated defense.

Initially described as an RNA surveillance pathway, nonsense-mediated decay (NMD) is also recognized to function in the regulation of host gene expression. In this issue of Cell Host & Microbe, three studies describe NMD-mediated defense strategies of plants and mammalian cells in response to pathogen infection.

Computer-aided CT coronary artery stenosis detection: comparison with human reading and quantitative coronary angiography.

To evaluate computer-aided stenosis detection for computed tomography coronary angiography (CTA) in comparison with human reading and conventional coronary angiography (CCA) as the reference standard. 50 patients underwent CTA and CCA and out of these 44 were evaluable for computer-aided stenosis detection. The diagnostic performance of the software and of human reading were compared and quantitative coronary angiography (QCA) served as the reference standard for the detection of significant stenosis (>50 %). Overall, three readers with high (reader 1), intermediate (reader 2) and low (reader 3) experience in cardiac CT imaging performed the manual CTA evaluation on a commercially available workstation, whereas the automated software processed the datasets without any human interaction. The prevalence of coronary artery disease was 41 % (18/44) and QCA indicated significant stenosis (>50 %) in 33 coronary vessels. The automated software accurately diagnosed 18 individuals with significant coronary artery disease (CAD), and correctly ruled out CAD in 10 patients. In summary the sensitivity of computer-aided detection was 100 %/94 % (per-patient/per-vessel) and the specificity was 38 %/70 %, the positive predictive value (PPV) was 53 %/42 % and the negative predictive value (NPV) was 100 %/98 %. In comparison, reader 1-3 showed per-patient sensitivities of 100/94/89 %, specificities of 73/69/50 %, PPVs of 72/68/55 % and NPVs of 100/95/87 %. Computer-aided detection yields a high NPV that is comparable to more experienced human readers. However, PPV is rather low and in the range of an unexperienced reader.

Accurate detection of differential RNA processing.

Deep transcriptome sequencing (RNA-Seq) has become a vital tool for studying the state of cells in the context of varying environments, genotypes and other factors. RNA-Seq profiling data enable identification of novel isoforms, quantification of known isoforms and detection of changes in transcriptional or RNA-processing activity. Existing approaches to detect differential isoform abundance between samples either require a complete isoform annotation or fall short in providing statistically robust and calibrated significance estimates. Here, we propose a suite of statistical tests to address these open needs: a parametric test that uses known isoform annotations to detect changes in relative isoform abundance and a non-parametric test that detects differential read coverages and can be applied when isoform annotations are not available. Both methods account for the discrete nature of read counts and the inherent biological variability. We demonstrate that these tests compare favorably to previous methods, both in terms of accuracy and statistical calibrations. We use these techniques to analyze RNA-Seq libraries from Arabidopsis thaliana and Drosophila melanogaster. The identified differential RNA processing events were consistent with RT-qPCR measurements and previous studies. The proposed toolkit is available from http://bioweb.me/rdiff and enables in-depth analyses of transcriptomes, with or without available isoform annotation.

Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes.

Deep sequencing of transcriptomes allows quantitative and qualitative analysis of many RNA species in a sample, with parallel comparison of expression levels, splicing variants, natural antisense transcripts, RNA editing and transcriptional start and stop sites the ideal goal. By computational modeling, we show how libraries of multiple insert sizes combined with strand-specific, paired-end (SS-PE) sequencing can increase the information gained on alternative splicing, especially in higher eukaryotes. Despite the benefits of gaining SS-PE data with paired ends of varying distance, the standard Illumina protocol allows only non-strand-specific, paired-end sequencing with a single insert size. Here, we modify the Illumina RNA ligation protocol to allow SS-PE sequencing by using a custom pre-adenylated 3' adaptor. We generate parallel libraries with differing insert sizes to aid deconvolution of alternative splicing events and to characterize the extent and distribution of natural antisense transcription in C. elegans. Despite stringent requirements for detection of alternative splicing, our data increases the number of intron retention and exon skipping events annotated in the Wormbase genome annotations by 127% and 121%, respectively. We show that parallel libraries with a range of insert sizes increase transcriptomic information gained by sequencing and that by current established benchmarks our protocol gives competitive results with respect to library quality.

mGene: accurate SVM-based gene finding with an application to nematode genomes.

We present a highly accurate gene-prediction system for eukaryotic genomes, called mGene. It combines in an unprecedented manner the flexibility of generalized hidden Markov models (gHMMs) with the predictive power of modern machine learning methods, such as Support Vector Machines (SVMs). Its excellent performance was proved in an objective competition based on the genome of the nematode Caenorhabditis elegans. Considering the average of sensitivity and specificity, the developmental version of mGene exhibited the best prediction performance on nucleotide, exon, and transcript level for ab initio and multiple-genome gene-prediction tasks. The fully developed version shows superior performance in 10 out of 12 evaluation criteria compared with the other participating gene finders, including Fgenesh++ and Augustus. An in-depth analysis of mGene's genome-wide predictions revealed that approximately 2200 predicted genes were not contained in the current genome annotation. Testing a subset of 57 of these genes by RT-PCR and sequencing, we confirmed expression for 24 (42%) of them. mGene missed 300 annotated genes, out of which 205 were unconfirmed. RT-PCR testing of 24 of these genes resulted in a success rate of merely 8%. These findings suggest that even the gene catalog of a well-studied organism such as C. elegans can be substantially improved by mGene's predictions. We also provide gene predictions for the four nematodes C. briggsae, C. brenneri, C. japonica, and C. remanei. Comparing the resulting proteomes among these organisms and to the known protein universe, we identified many species-specific gene inventions. In a quality assessment of several available annotations for these genomes, we find that mGene's predictions are most accurate.