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Background Current data about long-term use of vedolizumab (VDZ) in ulcerative colitis (UC) versus Crohn’s disease (CD) patients are limited. We aimed to assess whether there are differences in term of long-term efficacy and safety of VDZ in UC vs. CD patients. Methods Clinical activity was scored according to the Mayo score in UC and to the Harvey-Bradshaw Index (HBI) in CD. The primary endpoints were the achievement of clinical remission within 6 month of treatment, maintenance of clinical remission during a long follow-up, and safety. Secondary endpoints were clinical response to treatment, achievement of mucosal healing (MH), steroid discontinuation, and treatment optimization during the follow-up. Results The study group consisted of 729 patients (475 patients with UC and 254 CD patients with CD) with a median follow-up of 18 (interquartile range 6-36) months. Clinical remission at the 6th month of treatment was achieved in 488 (66.9%) patients, higher in CD patients (74.4 vs. 62.9, p Conclusion Overall, no significant differences were found about the long-term use of VDZ in UC vs. CD. However, we identified some parameters the can help the physician to predict the long-term efficacy of this drug.

Background Inflammatory bowel diseases (IBDs), Crohn's disease (CD) and ulcerative colitis (UC), are chronic and immune-mediated diseases with a relapsing-remitting trend. The overall incidence of these diseases is increasing. However, it is estimated that more than one third of patients experienced symptoms for more than one year before diagnosis. Delay in IBD diagnosis has several clinical, therapeutic and economic implications. Early diagnosis and proper treatment are the cornerstones for improving the standard of care for these patients. This study aims to evaluate the diagnostic delay (DD) in patients with IBD and to analyze the clinical burden of the delay in IBD diagnosis in patients treated with biological drugs. Methods An observational and retrospective study was performed in IBD patients, regularly followed in four IBD Units. Data regarding delay in IBD diagnosis were assessed through a questionnaire evaluating the disease course. Moreover, data about biologics dispensation were obtained from the medical records in the period 2020-2022 Results 135 IBD patients were enrolled (UC 72, CD 63, M 80, F 55). Median age at diagnosis was 32 years (IQR 22-45); 7% of patients were ≤ 16 years old at diagnosis. Median age on erollement was 47 ( IQR 4-59) Median DD was 12 months (IQR: 6-24). No significant difference was found in median DD between UC [12 months (IQR: 4.5-12.0)] and CD patients [12 months (IQR: 12-48)]. However, the proportion of patients with a DD >24 months was significantly (p=0.007) higher in CD (21/63 = 33%) than in UC patients (10/72=13%). After a median disease duration of 10 years (IQR: 4-17), overall, 67 patients (49.7%) were exposed to one biologic agent, 43 patients (31.8%) were exposed to two biologic agents, 25 (18.5%) to three or more biologic agents. 23% of patients (31/135) underwent surgery. The statistical analysis showed that DD >24 months was not statistically significant associated with history of ≥ 2 biological drugs (p=0.51). Conversely, there was association with surgical treatment (p=0.004). Conclusion The diagnostic delay in IBD represents a challenge with clinical and, therapeutic impact. It’s crucial to cooperate with general practitioner and gastroenterologists not dedicated to IBD in order to reduce the diagnostic delay and guarantee an effective, appropriate and early treatment that will improve the patients’ quality of life and meanwhile reduce the health care system costs.

In this study, we characterize the response of the free-living oligotrophic alphaproteobacterium Caulobacter crescentus to low temperatures by global transcriptomic analysis. Our results showed that 656 genes were upregulated and 619 were downregulated at least 2-fold after a temperature downshift. The identified differentially expressed genes (DEG) belong to several functional categories, notably inorganic ion transport and metabolism, and a subset of these genes had their expression confirmed by reverse transcription quantitative real-time PCR (RT-qPCR). Several genes belonging to the ferric uptake regulator (Fur) regulon were downregulated, indicating that iron homeostasis is relevant for adaptation to cold. Several upregulated genes encode proteins that interact with nucleic acids, particularly RNA: cspA, cspB, and the DEAD box RNA helicases rhlE, dbpA, and rhlB. Moreover, 31 small regulatory RNAs (sRNAs), including the cell cycle-regulated noncoding RNA (ncRNA) CcnA, were upregulated, indicating that posttranscriptional regulation is important for the cold stress response. Interestingly, several genes related to transport were upregulated under cold stress, including three AcrB-like cation/multidrug efflux pumps, the nitrate/nitrite transport system, and the potassium transport genes kdpFABC. Further characterization showed that kdpA is upregulated in a potassium-limited medium and at a low temperature in a SigT-independent way. kdpA mRNA is less stable in rho and rhlE mutant strains, but while the expression is positively regulated by RhlE, it is negatively regulated by Rho. A kdpA-deleted strain was generated, and its viability in response to osmotic, acidic, or cold stresses was determined. The implications of such variation in the gene expression for cold adaptation are discussed. IMPORTANCE Low-temperature stress is an important factor for nucleic acid stability and must be circumvented in order to maintain the basic cell processes, such as transcription and translation. The oligotrophic lifestyle presents further challenges to ensure the proper nutrient uptake and osmotic balance in an environment of slow nutrient flow. Here, we show that in Caulobacter crescentus, the expression of the genes involved in cation transport and homeostasis is altered in response to cold, which could lead to a decrease in iron uptake and an increase in nitrogen and high-affinity potassium transport by the Kdp system. This previously uncharacterized regulation of the Kdp transporter has revealed a new mechanism for adaptation to low temperatures that may be relevant for oligotrophic bacteria.

Ustekinumab (UST) is an anti-IL12/23 antibody for the treatment of Crohn's Disease (CD). The aim of this study was to compare the efficacy and safety of UST in a large population-based cohort of CD patients who failed previous treatment with other biologics.194 CD patients (108 males and 86 females, mean age 48 years (range 38-58 years) were retrospectively reviewed. 147 patients were already treated with anti-TNFα (75.8%), and 47 (24.2%) patients were already treated with anti-TNFα and vedolizumab. Concomitant treatment with steroids was present in 177 (91.2%) patients.At week 12, clinical remission was achieved in 146 (75.2%) patients. After a mean follow-up of 6 months, clinical remission was maintained in 135 (69.6%) patients; at that time, mucosal healing was assessed in 62 (31.9%) patients, and it was achieved in 33 (53.2) patients. Three (1.5%) patients were submitted to surgery. Steroid-free remission was achieved in 115 (59.3%) patients. Both serum C-Reactive Protein and Fecal Calprotectin (FC) levels were significantly reduced with respect to baseline levels during follow-up. A logistic regression, UST therapy as third-line therapy (after both anti-TNFα and vedolizumab), FC200 µg/g, and HBI ≥8 were significantly associated with lack of remission. Adverse events occurred in 5 (2.6%) patients, and four of them required suspension of treatment.UST seemed to be really effective and safe in CD patients unresponsive to other biologic treatments, especially when used as second-line treatment.

Post-transcriptional processing of messenger RNA is an important regulatory strategy that allows relatively fast responses to changes in environmental conditions. In halophile systems biology, the protein perspective of this problem (i.e., ribonucleases which implement the cleavages) is generally more studied than the RNA perspective (i.e., processing sites). In the present in silico work, we mapped genome-wide transcriptional processing sites (TPS) in two halophilic model organisms, Halobacterium&nbsp, salinarum NRC-1 and Haloferax&nbsp, volcanii DS2. TPS were established by reanalysis of publicly available differential RNA-seq (dRNA-seq) data, searching for non-primary (monophosphorylated RNAs) enrichment. We found 2093 TPS in 43% of H. salinarum genes and 3515 TPS in 49% of H. volcanii chromosomal genes. Of the 244 conserved TPS sites found, the majority were located around start and stop codons of orthologous genes. Specific genes are highlighted when discussing antisense, ribosome and insertion sequence associated TPS. Examples include the cell division gene ftsZ2, whose differential processing signal along growth was detected and correlated with post-transcriptional regulation, and biogenesis of sense overlapping transcripts associated with IS200/IS605. We hereby present the comparative, transcriptomics-based processing site maps with a companion browsing interface.

BackgroundRespiratory tract infections (RTIs) are the most common infections in patients with rheumatic diseases under immunosuppressive treatment. RTIs may cause significant morbidity with reduced quality of life (QOL), increased healthcare costs and may lead to interruption of DMARD therapy. However, to date only limited data on infection risk in spondyloarthritis (SpA) patients are available.ObjectivesTo assess the occurrence of respiratory tract infections in a real-world SpA cohort and determine associated factors.MethodsQuestionnaire-based screening and retrospective medical chart analysis of a monocentric cohort of 314 SpA patients comprising 168 psoriatic arthritis (PsA) and 146 axial spondyloarthritis (axSpA) patients.ResultsOut of 314 SpA patients, 89% had a history of upper respiratory tract infections (URTI) and 31.1% of lower respiratory tract infections (LRTI) within the last two years (Table 1). In a linear regression model LRTIs were associated with glucocorticoid (GC) therapy (p=0.015), CRP level (p=0.018), previous history of severe respiratory infections (p=0.007) as well as absence of HLA B27 (p=0.024). In general, patients with LRTIs were significantly older (p=0.007), had increased functional impairment (pTable 1.Patient characteristics and infectionsaxSpA (n=146)PsA (n=168)Total (n=314)Age, years, mean (SD)49.6 (14.2)57.4 (12.4)53.8 (13.9)Male / Female, %56.8 / 43.253.0 / 47.054.8 / 45.2BMI, kg/m2, mean (SD)27.1 (7.2)27.4 (5.4)27.3 (6.2)Smokers, n (%)41 (31.8)27 (16.3)68 (23.1)HLA B27, n (%) (n=230)97 (71.9)23 (24)120 (52.2)Therapy:n (%) csDMARD29 (19.6)84 (50.6)113 (36.2) bDMARD109 (75.2)102 (60.7)211 (67.4) Glucocorticoids14 (9.9)15 (8.9)29 (9.4)Hypogammaglobulinemia (IgG5 (3.5)6 (3.6)11 (3.6)Polyclonal IgA (>4g/l) elevation, n (%)15 (10.9)29 (17.8)44 (14.7)URTI: n (%)114 (88.4)148 (90.2)262 (89.4)Rhinitis, %87.187.587.3Laryngitis/pharyngitis, %3736.936.9Sinusitis, %40.530.234.7Otitis media, %14.36.810.1LRTI: n (%)39 (30.5)52 (32.1)91 (31.1)Bronchitis, %28.030.629.6Pneumonia, %3.93.13.4Pleuritis, %2.41.21.7There were no significant differences between PsA and axSpA regarding frequency of URTI or LRTI, though PsA patients had tendentially more overall RTIs. Biological therapy did not lead to a significantly increased occurrence of infections, but was associated with increased antibiotic therapy (p=0.039). Patients with a history of pneumonia had received anti-IL17 therapy more frequently (p=0.002), while there was no significant association with anti-TNF therapy (p=0.156). Patients on GC had a relative risk for LRTIs of 2.04.Hypogammaglobulinemia was rare in SpA patients (3.6%) despite continuous immunosuppressive treatment, occurred with equal frequency in axSpa and PsA patients and was associated with pneumonia (p=0.007) and increased antibiotic use (p=0.016). Polyclonal IgA elevation was observed in 14.7% of patients (mean 4.98g/l) and was associated with fewer episodes of rhinitis (p=0.027), whereas LRTIs and antibiotic use did not differ significantly.ConclusionThis study quantifies the incidence and effects of RTIs in a real-world SpA cohort. While infections constitute significant adverse events of biologicals, and URTI were common, severe respiratory tract infections were rare. Differences in infection risk between SpA and PsA need to be studied more closely.Disclosure of InterestsNatalie Frede Grant/research support from: Novartis study grant, Eva Rieger: None declared, Raquel Lorenzetti Grant/research support from: Novartis study grant, Ana Venhoff: None declared, Anna-Maria Kanne: None declared, Marcus von Deimling: None declared, Nora Bartholomä: None declared, Jens Thiel Speakers bureau: Novartis, AbbVie, Pfizer, BMS, UCB, Consultant of: Novartis, AbbVie, Pfizer, BMS, UCB, Grant/research support from: BMS, Novartis study grants, Reinhard Voll Speakers bureau: Novartis, AbbVie, Pfizer, BMS, UCB, Consultant of: Novartis, AbbVie, Pfizer, BMS, UCB, Lilly, Grant/research support from: Novartis study grant, Nils Venhoff Speakers bureau: Novartis, AbbVie, Pfizer, BMS, UCB, Consultant of: Novartis, AbbVie, Grant/research support from: Novartis study grant

BackgroundB differentiation in the bone marrow (BM) is impaired in patients carrying mutation in the IKFZ1 gene, coding for Ikaros a zinc-finger transcription factor. High Ikaros expression is on the contrary associated with systemic lupus erythematosus[1] and multiple myeloma[2]. Targeted treatment with iberdomide, a cereblon modulator which enhances degradation of Ikaros and Aiolos, is under clinical investigation in multiple myeloma patients and systemic lupus erythematosus. However, consequences of the treatment on human early B cell development remain elusive. Immature B cells develop in the BM from hematopoietic stem cells. An intricate network of transcription factors regulates the maturation process. Ikaros and Aiolos regulate gene expression during B cell development. As reported in mice, Ikaros is essential for the commitment to the lymphoid lineage and later, together with Aiolos, ensures the transition from pre-BII large to pre-BII small cells.ObjectivesInvestigate the effect of iberdomide (CC-220) on human early B cell development simulated in vitro.MethodsWe tested the impact of iberdomide on short term culture of BM-derived lymphocytes and in a unique in vitro modeling of early B cell development starting from cord blood (CB)- CD34+ progenitors [3, 4]. We used multi-dimensional spectra flow cytometry (17-color pan-el) to dissect early B cell subpopulations.ResultsIberdomide treatment led to enhanced degradation of Ikaros and Aiolos in both BM- and CB-derived cultures. Addition of iberdomide early (day 7) to the CB-derived culture impaired the specification to the lymphoid lineage and later also the commitment to the B cell lineage. These observations were confirmed by reduced E2A and PAX5 gene expression, respectively. Treatment with iberdomide on B cell precursors (pro- and pre-B cells, day 28 of culture) on one side it enhanced the proliferation of early progenitors resulting in increased amount of CD10+CD38+ lymphoid-committed cells. On the other side, it resulted in a accumulation of pre-B cells and inefficient development of immature B cells.ConclusionIberdomide impairs the commitment to the lymphoid lineage by enhancing Ikaros’ degrada-tion. When targeting already committed B cells, iberdomide treatment undermines the transition of pre-BII large to pre-BII small cells due to increased Aiolos’ degradation, conse-quently impairing the development of immature B cells. Our data can instruct immunologi-cal monitoring of patients treated with iberdomide, and provide insights in the mechanisms of therapeutic efficacy.References[1]Rivellese, F., et al., Effects of targeting the transcription factors Ikaros and Aiolos on B cell activation and differentiation in systemic lupus erythematosus. Lupus Sci Med, 2021. 8(1).[2]Thakurta, A., et al., Developing next generation immunomodulatory drugs and their combinations in multiple myeloma. Oncotarget, 2021. 12(15): p. 1555-1563.[3]Kraus, H., et al., A Feeder-Free Differentiation System Identifies Autonomously Proliferating B Cell Precursors in Human Bone Marrow. The Journal of Immunology, 2014. 192(3): p. 1044-1054.[4]Troilo, A., et al., Nonpermissive bone marrow environment impairs early B-cell development in common variable immunodeficiency. Blood, 2020. 135(17): p. 1452-1457.Disclosure of InterestsIga Janowska: None declared, Jakov Korzhenevich: None declared, Julian Staniek: None declared, Raquel Lorenzetti: None declared, Lukas Konstantinidis: None declared, Miriam Erlacher: None declared, Peter Schafer Employee of: BMS, Reinhard Voll: None declared, Jens Thiel Grant/research support from: BMS (former Cellgene), Nils Venhoff: None declared, Marta Rizzi Grant/research support from: BMS (former Cellgene)

BackgroundAxial spondyloarthritis (axSpA) and psoriatic arthritis (PsA) may have a profound impact on health-related quality of life (HRQoL) and sleep despite effective treatment.ObjectivesTo assess sleep and HRQoL in SpA and determine associated factors.MethodsMonocentric questionnaire-based assessment of HRQoL, function, sleep and depression in 314 SpA patients (n=168 PsA, n=146 axSpA).ResultsUnder effective treatment 138 SpA patients (46.5%) demonstrated abnormal sleep behaviour. 49.3% reported not being able to sleep through the night, with 6.1 % needing sleeping pills. 11.9% indicated feeling unrefreshed most mornings. Abnormal sleep behaviour was associated with female sex (p=0.005), HLAB27 (p=0.034), functional impairment (p=0.001) and depression (pConclusionDespite treatment many SpA patients have a reduced HRQoL and impaired sleep quality with significant differences between male and female patients. Impact of COVID19 pandemic was low.Table 1.Patient characteristicsTotal (n=314)Women n=142 (45.2%)Men n=172 (54.8%)p-valueAge, years, mean (SD)53.8 (13.9)53.7 (14.5)53.8 (13.4)0.983BMI, kg/m2, mean (SD)27.3 (6.3)27.1 (6.5)27.4 (6.1)0.706Smokers, n (%)68 (23.1)34 (24.6)34 (21.7)0.544HLA B27, n (%) (n=230)120 (52.2)46 (45.1)54 (54.9)0.055CRP, mg/l, mean (SD)6.14 (11.9)5.88 (6.0)6.37 (15.2)0.721Significant functional impairment, n (%)54 (17.5)29 (20.6)25 (15.0)0.198Therapy, n (%) csDMARD113 (36.2)56 (39.7)57 (33.3)0.243 bDMARD211 (67.4)91 (64.1)120 (70.2)0.252Depressive symptoms, n (%) Mild109 (37.5)53 (39.3)56 (35.9)0.040 Moderate/severe48 (16.5)27 (20.0)21 (13.5)WHO-QOL mean (SD) Physical60.2 (19.4)57.4 (19.7)62.6 (19.0)0.019 Mental67.7 (17.2)64.5 (17.8)70.3 (16.2)0.003 Social67.8 (20.0)67.4 (19.6)68.2 (20.3)0.703 Environmental77.3 (13.3)76.6 (13.6)78.0 (13.1)0.363Sleep, n (%) Abnormal sleep behaviour138 (46.5)76 (55.1)62 (39.0)0.006 Inability to sleep through the night145 (49.4)76 (55.1)69 (44.2)0.024 Waking too early89 (30.4)43 (31.4)46 (29.5)0.459 Need for sleeping pills18 (6.1)11 (8.0)7 (4.4)0.133 Unrefreshing sleep most or all nights35 (11.9)24 (17.5)11 (7.0)Figure 1.Female SpA patients have increased depressive symptoms and a reduced HRQoL.Disclosure of InterestsNatalie Frede Grant/research support from: Novartis study grant, Eva Rieger: None declared, Raquel Lorenzetti Grant/research support from: Novartis study grant, Ana Venhoff: None declared, Carolin Hentze: None declared, Ilona Jandova: None declared, Cornelia Glaser: None declared, Jens Thiel Speakers bureau: Novartis, AbbVie, Pfizer, BMS, UCB, Consultant of: Novartis, AbbVie, Pfizer, BMS, UCB, Grant/research support from: BMS, Novartis study grants, Reinhard Voll Speakers bureau: Novartis, AbbVie, Pfizer, BMS, UCB, Consultant of: Novartis, AbbVie, Pfizer, BMS, UCB, Lilly, Grant/research support from: Novartis study grant, Nils Venhoff Speakers bureau: Novartis, AbbVie, Pfizer, BMS, UCB, Consultant of: Novartis, AbbVie, Grant/research support from: Novartis study grant

Made available in DSpace on 2019-10-04T12:33:56Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-01-01 Brazilian Coffee Research Consortium Fundacao Araucaria Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Coffea arabica L. is an important agricultural commodity, accounting for 60% of traded coffee worldwide. Nitrogen (N) is a macronutrient that is usually limiting to plant yield; however, molecular mechanisms of plant acclimation to N limitation remain largely unknown in tropical woody crops. In this study, we investigated the transcriptome of coffee roots under N starvation, analyzing poly-A+ libraries and small RNAs. We also evaluated the concentration of selected amino acids and N-source preferences in roots. Ammonium was preferentially taken up over nitrate, and asparagine and glutamate were the most abundant amino acids observed in coffee roots. We obtained 34,654 assembled contigs by mRNA sequencing, and validated the transcriptional profile of 12 genes by RT-qPCR. Illumina small RNA sequencing yielded 8,524,332 non-redundant reads, resulting in the identification of 86 microRNA families targeting 253 genes. The transcriptional pattern of eight miRNA families was also validated. To our knowledge, this is the first catalog of differentially regulated amino acids, N sources, mRNAs, and sRNAs in Arabica coffee roots. Inst Agron Parana, Lab Biotecnol Vegetal, BR-86047902 Londrina, Brazil Univ Oeste Paulista, Rodovia Raposo Tavares Km 572, BR-19067175 Presidente Prudente, Brazil Univ Sao Paulo, Ctr Energia Nucl Agr, BR-13400970 Piracicaba, Brazil Univ Fed Minas Gerais, Inst Ciencias Biol, Dept Bot, BR-31270901 Belo Horizonte, MG, Brazil Univ Tecnol Fed Parana, Programa Posgrad Bioinformat, BR-86300000 Cornelio Procopio, Brazil Univ Estadual Paulista, Inst Biociencias Rio Claro, Dept Bot, BR-13506900 Rio Claro, Brazil Univ Paranaense, Lab Biol Mol, BR-87502210 Umuarama, Brazil Univ Estadual Londrina, Programa Posgrad Genet & Biol Mol, BR-86057970 Londrina, Brazil Inst Butantan, Lab Especial Toxinol Aplicada, BR-05503900 Sao Paulo, Brazil Univ Estadual Campinas, Inst Biol, Dept Biol Vegetal, BR-13083970 Campinas, SP, Brazil COFFEEADAPT, UMR IPME, IRD, BP 64501, F-34394 Montpellier 5, France Univ Estadual Campinas, Life Sci Core Facil LaCTAD, BR-13083886 Campinas, SP, Brazil Embrapa Cafe, BR-70770901 Brasilia, DF, Brazil Univ Estadual Paulista, Inst Biociencias Rio Claro, Dept Bot, BR-13506900 Rio Claro, Brazil CAPES: PVE 084/2013

Our findings demonstrate conclusively that low abundance and upregulated transcripts are preferentially translated, potentially by environment-specific translation systems with distinct ribosomal protein composition. We show that a complex interplay of transcriptional and posttranscriptional regulation underlies the conditional and modular regulatory programs that generate ribosomes of distinct protein composition. The modular regulation of ribosomal proteins with other transcription, translation, and metabolic genes is generalizable to bacterial and eukaryotic microbes. These findings are relevant to how microorganisms adapt to unfavorable environments when they transition from active growth to quiescence by generating proteins from upregulated transcripts that are in considerably lower abundance relative to transcripts associated with the previous physiological state. Selective translation of transcripts by distinct ribosomes could form the basis for adaptive evolution to new environments through a modular regulation of the translational systems., When organisms encounter an unfavorable environment, they transition to a physiologically distinct, quiescent state wherein abundant transcripts from the previous active growth state continue to persist, albeit their active transcription is downregulated. In order to generate proteins for the new quiescent physiological state, we hypothesized that the translation machinery must selectively translate upregulated transcripts in an intracellular milieu crowded with considerably higher abundance transcripts from the previous active growth state. Here, we have analyzed genome-wide changes in the transcriptome (RNA sequencing [RNA-seq]), changes in translational regulation and efficiency by ribosome profiling across all transcripts (ribosome profiling [Ribo-seq]), and protein level changes in assembled ribosomal proteins (sequential window acquisition of all theoretical mass spectra [SWATH-MS]) to investigate the interplay of transcriptional and translational regulation in Halobacterium salinarum as it transitions from active growth to quiescence. We have discovered that interplay of regulatory processes at different levels of information processing generates condition-specific ribosomal complexes to translate preferentially pools of low abundance and upregulated transcripts. Through analysis of the gene regulatory network architecture of H. salinarum, Escherichia coli, and Saccharomyces cerevisiae, we demonstrate that this conditional, modular organization of regulatory programs governing translational systems is a generalized feature across all domains of life. IMPORTANCE Our findings demonstrate conclusively that low abundance and upregulated transcripts are preferentially translated, potentially by environment-specific translation systems with distinct ribosomal protein composition. We show that a complex interplay of transcriptional and posttranscriptional regulation underlies the conditional and modular regulatory programs that generate ribosomes of distinct protein composition. The modular regulation of ribosomal proteins with other transcription, translation, and metabolic genes is generalizable to bacterial and eukaryotic microbes. These findings are relevant to how microorganisms adapt to unfavorable environments when they transition from active growth to quiescence by generating proteins from upregulated transcripts that are in considerably lower abundance relative to transcripts associated with the previous physiological state. Selective translation of transcripts by distinct ribosomes could form the basis for adaptive evolution to new environments through a modular regulation of the translational systems.

Prokaryotic genomes show a high level of information compaction often with different molecules transcribed from the same locus. Although antisense RNAs have been relatively well studied, RNAs in the same strand, internal RNAs (intraRNAs), are still poorly understood. The question of how common is the translation of overlapping reading frames remains open. We address this question in the model archaeon Halobacterium salinarum. In the present work we used differential RNA-seq (dRNA-seq) in H. salinarum NRC-1 to locate intraRNA signals in subsets of internal transcription start sites (iTSS) and establish the open reading frames associated to them (intraORFs). Using C-terminally flagged proteins, we experimentally observed isoforms accurately predicted by intraRNA translation for kef1, acs3 and orc4 genes. We also recovered from the literature and mass spectrometry databases several instances of protein isoforms consistent with intraRNA translation such as the gas vesicle protein gene gvpC1. We found evidence for intraRNAs in horizontally transferred genes such as the chaperone dnaK and the aerobic respiration related cydA in both H. salinarum and Escherichia coli. Also, intraRNA translation evidence in H. salinarum, E. coli and yeast of a universal elongation factor (aEF-2, fusA and eEF-2) suggests that this is an ancient phenomenon present in all domains of life.

Rickettsia helvetica is an emerging human pathogen, belonging to the spotted fever group (SFG) rickettsiae, associated with generally aneruptive fever, meningitis, and sudden death in chronic perimyocarditis. In this study, we describe the detection of R. helvetica in human-parasitizing and free-living Ixodes ricinus from the Metropolitan City of Rome. The pathogen was found in a tick acquired by a woman in an urban park. The circulation of R. helvetica was further confirmed by its detection in free-living ticks from a wild green area. These findings demonstrate that urban as well as wild green areas can represent a risk of infection to humans by R. helvetica, with potentially severe sequelae. To the best of our knowledge, this is the first report of R. helvetica in the Lazio region. Large-scale studies are needed to evaluate and quantify the presence of R. helvetica and other SFG rickettsiae in the urban and periurban context and to assess the risk to humans and animals related to their frequentation.

Antisense RNAs (asRNAs) are present in diverse organisms and play important roles in gene regulation. In this work, we mapped the primary antisense transcriptome in the halophilic archaeon Halobacterium salinarum NRC-1. By reanalyzing publicly available data, we mapped antisense transcription start sites (aTSSs) and inferred the probable 3′ ends of these transcripts. We analyzed the resulting asRNAs according to the size, location, function of genes on the opposite strand, expression levels and conservation. We show that at least 21% of the genes contain asRNAs in H. salinarum. Most of these asRNAs are expressed at low levels. They are located antisense to genes related to distinctive characteristics of H. salinarum, such as bacteriorhodopsin, gas vesicles, transposases and other important biological processes such as translation. We provide evidence to support asRNAs in type II toxin–antitoxin systems in archaea. We also analyzed public Ribosome profiling (Ribo-seq) data and found that ~10% of the asRNAs are ribosome-associated non-coding RNAs (rancRNAs), with asRNAs from transposases overrepresented. Using a comparative transcriptomics approach, we found that ~19% of the asRNAs annotated in H. salinarum belong to genes with an ortholog in Haloferax volcanii, in which an aTSS could be identified with positional equivalence. This shows that most asRNAs are not conserved between these halophilic archaea.

Antisense RNAs (asRNAs) are present in diverse organisms and play important roles in gene regulation. In this work, we mapped the primary antisense transcriptome in the halophilic archaeon Halobacterium salinarum NRC-1. By reanalyzing publicly available data, we mapped antisense transcription start sites (aTSSs) and inferred the probable 3&prime, ends of these transcripts. We analyzed the resulting asRNAs according to the size, location, function of genes on the opposite strand, expression levels and conservation. We show that at least 21% of the genes contain asRNAs in H. salinarum. Most of these asRNAs are expressed at low levels. They are located antisense to genes related to distinctive characteristics of H. salinarum, such as bacteriorhodopsin, gas vesicles, transposases and other important biological processes such as translation. We provide evidence to support asRNAs in type II toxin&ndash, antitoxin systems in archaea. We also analyzed public Ribosome profiling (Ribo-seq) data and found that ~10% of the asRNAs are ribosome-associated non-coding RNAs (rancRNAs), with asRNAs from transposases overrepresented. Using a comparative transcriptomics approach, we found that ~19% of the asRNAs annotated in H. salinarum belong to genes with an ortholog in Haloferax volcanii, in which an aTSS could be identified with positional equivalence. This shows that most asRNAs are not conserved between these halophilic archaea.

Made available in DSpace on 2018-12-11T16:42:09Z (GMT). No. of bitstreams: 0 Previous issue date: 2016-05-01 Transposable elements (TEs) comprise a major fraction of many plant genomes and are known to drive their organization and evolution. Several studies show that these repetitive elements have a prominent role in shaping noncoding regions of the genome such as microRNA (miRNA) loci, which are components of post-transcriptional regulation mechanisms. Although some studies have reported initial formation of miRNA loci from TE sequences, especially in model plants, the approaches that were used did not employ systems that would allow results to be delivered by a user-friendly database. In this study, we identified 152 precursor miRNAs overlapping TEs in 10 plant species. PlanTE-MIR DB was designed to assemble this data and deliver it to the scientific community interested in miRNA origin, evolution, and regulation pathways. Users can browse the database through a web interface and search for entries using various parameters. This resource is cross-referenced with repetitive element (Repbase Update) and miRNA (miRBase) repositories, where sequences can be checked for further analysis. All data in PlanTE-MIR DB are publicly available for download in several file formats to facilitate their understanding and use. The database is hosted at http://bioinfo-tool.cp.utfpr.edu.br/plantemirdb/. Graduation Program in Genetics and Molecular Biology Universidade Estadual de Londrina Bioinformatics Laboratory Universidade Tecnológica Federal do Paraná UTFPR Department of Botany Instituto de Biociências Universidade Estadual Paulista UNESP Department of Botany Instituto de Biociências Universidade Estadual Paulista UNESP

Background:ALPS patients show impaired generation of humoral memory for T independent antigens whereas they generate memory for self-antigens due to impaired FAS-dependent removal of autoreactive germinal center B cells. It is known that FAS signaling via caspase activation results in cell apoptosis. However, FAS ligation may also initiate or modulate non-apoptotic signaling as shown for example by its ability to activate NF-κB. Recent data implicate a regulatory role of FAS in the modulation of mTOR signaling in ALPS double-negative T cells. Moreover, a recently described C194V FAS mutation disturbs its post-translational modification leading to impaired apoptosis induction while non-apoptotic signalling is still intact. Consequently, C194V FAS protects from the autoimmune phenotype in the murine ALPS system. This supports the view that FAS may prevent autoimmunity with other mechanisms than inducing apoptosis.Objectives:We hypothesize that FAS mutations impair this modulatory signaling, leading to hyper-activation of B cells. Therefore we aim to investigate non apoptotic FAS signaling in B cells derived from healthy individuals and ALPS patients.Methods:We studied resting and activated B cells in ALPS patients in presence or absence of FAS ligand by flow cytometry analysing relevant molecules to the CD40 signaling pathway. We used mass cytometry to perform functional phenotyping of B cells isolated from secondary lymphoid organs. Proteomic studies were performed to identify potential signaling circuits and RNA sequencing to study the consequences of FAS signaling on B cell fate.Results:In CD40L activated B cells, FAS signaling results in specific modulation of the mTOR signaling pathway. This modulation is absent in ALPS derived B cells. In line with these data germinal center B cells and plasmablast from secondary lymphoid organs of ALPS patients show hyperactive mTOR signaling pathway. Proteomic studies identify a circuit that links FAS to the phosphatase PTEN via DAXX and the deubiquitinase USP7.Conclusion:We describe a new role of FAS in the regulation of B cell activation. Defects in FAS signaling in ALPS contribute to dysregulation of the mTOR signaling pathway and disturbed B cell development.Disclosure of Interests:None declared

Background:Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare form of systemic vasculitis, which is characterized by bronchial asthma, hypereosinophilia, and systemic vasculitis. B-lymphocytes play a key role in EGPA as producers of IgE and anti-neutrophil cytoplasmic antibodies (ANCAs). Indeed, the neutrophils that are targeted by these antibodies are widely described as the mechanism of endothelial damage in this disease. On the other side, the therapeutic response to rituximab in EGPA patients provides evidence for a role of B-cells in the pathogenesis of EGPA. Therefore characterizing B cell subpopulations may help in understanding the disease and the treatment.Objectives:To characterize the peripheral B cell compartment in patients with EGPA and to analyze the in vivo potential of B lymphocytes to class-switch to IgE and to assess in vitro the differentiation potential of naïve B cells of EGPA patients into IgE-secreting plasmablasts.Methods:Clinical characteristics of the patients, including organ involvement and treatment regimen were evaluated. Laboratory work-up included ANCA-status, eosinophils, IgE, IgG, IgA, IgM, and peripheral CD19+B-cell count. For immunophenotyping isolated PBMCs were stained with monoclonal or polyclonal antibodies and B cells were classified into: naïve, marginal zone, class-switched memory B cells, unconventional memory B cells, transitional and plasmablasts. Furthermore, the expression of IgG+ and subclasses IgG1-4, IgA+, IgE+B cells, BAFFR and TACI was quantified. For in vitro differentiation assays magnetically isolated B lymphocytes from EGPA patients and age-matched healthy controls were stimulated with CD40L, IL-21 and IL-4. Starting the culture with equal number of B cells, the absolute number of plasmablasts, and IgE class switched cells after 9 days was determined by counting the events in the CD27highCD38high gate or the IgG/A/D-IgE+gate by flow cytometry. IgE secretion in the supernatant was measured by ELISA. JAK-STAT signalling pathway was analyzed in response to IL-4 and IL-21 stimulation and phosphorylation of STAT5 and 6 measured by flow cytometry.Results:34 patients with EGPA diagnosed according to ACR and CHC-criteria were included into the study. Ten of these patients were analysed separately because they received rituximab therapy. Peripheral B cell numbers in EGPA patients were markedly diminished. B cell subpopulation phenotyping showed in average 57.9% naïve B cells, 12.5 % marginal zone like B cells and 19.2% switched memory B cells. Plasmablasts constituted in average 1.15% of the peripheral B cell compartment, transitional B cells 2.0%. Interestingly, the expression of BAFF receptor and TACI in the memory B cell subset was significantly decreased in EGPA patients when compared with healthy donors. In vitro assays of isolated B cells from EGPA patients demonstrated an increased proportion of IgE-class-switched B cells after 9 days of culture under IL4 stimulation compared with controls. However, no differences were observed in the phosphorylation of STAT5 and STAT6 after stimulation with IL-4 or IL-21.Conclusion:In the EGPA-patients we observed markedly diminished B-cells despite of normal lymphocyte counts. B cells showed a reduced expression of BAFF-R and TACI. Class switch to IgE is enhanced in EGPA patients.Disclosure of Interests:None declared

Oxidative stress generated by hydrogen peroxide is faced by bacteria when encountering hostile environments. In order to define the physiological and regulatory networks controlling the oxidative stress response in the free-living bacterium Caulobacter crescentus, a whole transcriptome analysis of wild type and ΔoxyR strains in the presence of hydrogen peroxide for two different exposure times was carried out. The C. crescentus response to H2O2 includes a decrease of the assimilative sulfate reduction and a shift in the amino acid synthesis pathways into favoring the synthesis of histidine. Moreover, the expression of genes encoding enzymes for the depolymerization of polyhydroxybutyrate was increased, and the RpoH-dependent genes were severely repressed. Based on the expression pattern and sequence analysis, we postulate that OxyR is probably directly required for the induction of three genes (katG, ahpCF). The putative binding of OxyR to the ahpC regulatory region could be responsible for the use of one of two alternative promoters in response to oxidative stress. Nevertheless, OxyR is required for the expression of 103 genes in response to H2O2. Fur and part of its regulon were differentially expressed in response to hydrogen peroxide independently of OxyR. The non-coding RNA OsrA was upregulated in both strains, and an in silico analysis indicated that it may have a regulatory role. This work characterizes the physiological response to H2O2 in C. crescentus, the regulatory networks and differentially regulated genes in oxidative stress and the participation of OxyR in this process. It is proposed that besides OxyR, a second layer of regulation may be achieved by a small regulatory RNA and other transcriptional regulators.

Made available in DSpace on 2018-11-26T17:55:27Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-09-13 Universidade Tecnologica Federal do Parana Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Pro-Reitoria de Pesquisa e Pos-Graduacao (PROPPG-UTFPR) Transposable elements (TEs) play an essential role in the genetic variability of eukaryotic species. In plants, they may comprise up to 90% of the total genome. Non-coding RNAs (ncRNAs) are known to control gene expression and regulation. Although the relationship between ncRNAs and TEs is known, obtaining the organized data for sequenced genomes is not straightforward. In this study, we describe the PlaNC-TE :(http//planc-te.cp.utfpr.edu.br), a user-friendly portal harboring a knowledgebase created by integrating and analysing plant ncRNA-TE data. We identified a total of 14 350 overlaps between ncRNAs and TEs in 40 plant genomes. The database allows users to browse, search and download all ncRNA and TE data analysed. Overall, PlaNC-TE not only organizes data and provides insights about the relationship between ncRNA and TEs in plants but also helps improve genome annotation strategies. Moreover, this is the first database to provide resources to broadly investigate functions and mechanisms involving TEs and ncRNAs in plants. Univ Tecnol Fed Parana, Bioinformat Grad Program PPGBIOINFO, Dept Comp Sci, 1640 Ave Alberto Carazzai, BR-86300000 Cornelio Procopio, PR, Brazil Univ Sao Paulo, Ribeirao Preto Med Sch, Dept Biochem & Immunol, 3900 Bandeirantes Ave, BR-14049900 Monte Alegre do Sul, SP, Brazil UNESP, Sao Paulo State Univ, Inst Biosci, Dept Bot, Av 24-A 1515, BR-13506900 Rio Claro, SP, Brazil UNESP, Sao Paulo State Univ, Inst Biosci, Dept Bot, Av 24-A 1515, BR-13506900 Rio Claro, SP, Brazil FAPESP: 2017/03052-2 CNPq: 309642/2015-9

In C. crescentus, iron metabolism is mainly controlled by the transcription factor Fur (ferric uptake regulator). Iron-bound Fur represses genes related to iron uptake and can directly activate the expression of genes for iron-containing proteins. In this work, we used total RNA sequencing (RNA-seq) of wild type C. crescentus growing in minimal medium under iron limitation and a fur mutant strain to expand the known Fur regulon, and to identify novel iron-regulated genes. The RNA-seq of cultures treated with the iron chelator 2-2-dypiridyl (DP) allowed identifying 256 upregulated genes and 236 downregulated genes, being 176 and 204 newly identified, respectively. Sixteen transcription factors and seven sRNAs were upregulated in iron limitation, suggesting that the response to low iron triggers a complex regulatory network. Notably, lexA along with most of its target genes were upregulated, suggesting that DP treatment caused DNA damage, and the SOS DNA repair response was activated in a RecA-dependent manner, as confirmed by RT-qPCR. Fluorescence microscopy assays using an oxidation-sensitive dye showed that wild type cells in iron limitation and the fur mutant were under endogenous oxidative stress, and a direct measurement of cellular H2O2 showed that cells in iron-limited media present a higher amount of endogenous H2O2. A mutagenesis assay using the rpoB gene as a reporter showed that iron limitation led to an increase in the mutagenesis rate. These results showed that iron deficiency causes C. crescentus cells to suffer oxidative stress and to activate the SOS response, indicating an increase in DNA damage.

Background Angiostrongylus vasorum is a nematode residing in the heart and pulmonary vessels of dogs and wild carnivores. In Europe the red fox is its reservoir, while only three records from wolves have been published. Angiostrongylus vasorum has a worldwide distribution, and many pieces of evidence demonstrate that it is spreading from endemic areas to new ones. In Italy, A. vasorum was reported with increasing frequency in dogs and foxes in the last decades, and now it is considered endemic throughout the country. Angiostrongylus vasorum can be asymptomatic or cause respiratory and circulatory disorders, at times causing severe disseminated infections. Methods Between February 2012 and December 2016, 25 wolves found dead in central Italy were submitted to the Istituto Zooprofilattico del Lazio e della Toscana for post-mortem examination. Samples of lungs, heart, liver, spleen, kidneys, mediastinic lymph nodes and brain were collected from each animal for histological examination. When adult and larval nematodes were microscopically seen in lungs, the other organs were processed, and five histological sections for each organ were examined. To confirm parasite identification, lung samples were submitted to a PCR-sequencing protocol targeting the ITS2 region of A. vasorum. Results Seven wolves (28.0%) harboured nematode larvae in lung sections. In two of the positive wolves, adult nematodes were visible in pulmonary arteries, in four animals larvae were also detected in other organs. DNA sequencing reactions confirmed parasite identification as A. vasorum in all the cases. Conclusions As a result of the high prevalence of A. vasorum reported in wolves in the present study, a focus of high circulation could be hypothesised in central Italy. Nevertheless, the similarly high prevalence in foxes originating from the same areas were reported in previous papers. Histopathological evidence highlights the pathogenic potential of A. vasorum in the wolf, especially in juvenile animals.

Background B cell depletion with rituximab (RTX) is approved for treatment of rheumatoid arthritis (RA) and ANCA-associated vasculitides (AAV). Recently, RTX has been shown to be effective in AAV maintenance therapy, but an optimal RTX treatment schedule is unknown and the time to B cell repopulation after RTX has not been studied. Objectives To compare kinetics of B cell repopulation after RTX treatment in AAV, RA and connective tissue diseases (CTD) to improve the design of RTX-retreatment schedules in AAV and other autoimmune diseases. Methods Retrospective single-center analysis of patients with AAV, RA or CTD treated with RTX and a follow-up of >9 months were included. B-cell-repopulation was defined as a peripheral B-cell count >0.5% and >5/μl. Prolonged B cell depletion was defined by a B cell repopulation starting later than 12 months after RTX treatment. Results 120 patients were included in the study. Sixty-six patients had AAV with 55 classified as granulomatosis with polyangiitis (GPA) or microscopic polyangiitis (MPA) and 11 as eosinophilic granulomatosis with polyangiitis (EGPA). Thirty-five patients had RA and 19 were treated with RTX because of CTD. There were no significant differences between the groups regarding age and sex. Most patients were treated with RTX 1000mg twice, two weeks apart. Cumulative CYC doses were higher in patients with AAV or CTD than in RA patients. In RA and CTD we observed a B-cell repopulation in all patients (100%) while only 33 AAV patients (50%) had started B-cell repopulation (p Conclusions In contrast to RA and CTD, in AAV RTX induces long-lasting depletion of B cells that is associated with decreased antibody production. This observation points towards potential defects in the B cell compartment in AAV and has important implications for the design of maintenance treatment schedules using RTX. Disclosure of Interest J. Thiel Consultant for: Roche, M. Rizzi: None declared, A. Troilo: None declared, U. Salzer: None declared, A. Venhoff: None declared, R. Lorenzetti: None declared, R. Voll Consultant for: Roche, N. Venhoff Consultant for: Roche

Made available in DSpace on 2018-12-11T17:32:14Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-01-01. Added 1 bitstream(s) on 2021-07-15T15:04:15Z : No. of bitstreams: 1 S1415-47572017000200217.pdf: 2227310 bytes, checksum: ff9948fb5bb58d84242606d224b5e35a (MD5) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Endogenous viral elements (EVEs) are the result of heritable horizontal gene transfer from viruses to hosts. In the last years, several EVE integration events were reported in plants by the exponential availability of sequenced genomes. Eucalyptus grandis is a forest tree species with a sequenced genome that is poorly studied in terms of evolution and mobile genetic elements composition. Here we report the characterization of E. grandis endogenous viral element 1 (EgEVE_1), a transcriptionally active EVE with a size of 5,664 bp. Phylogenetic analysis and genomic distribution demonstrated that EgEVE_1 is a newly described member of the Caulimoviridae family, distinct from the recently characterized plant Florendoviruses. Genomic distribution of EgEVE_1 and Florendovirus is also distinct. EgEVE_1 qPCR quantification in Eucalyptus urophylla suggests that this genome has moreEgEVE_1 copies than E. grandis. EgEVE_1 transcriptional activity was demonstrated by RT-qPCR in five Eucalyptus species and one intrageneric hybrid. We also identified that Eucalyptus EVEs can generate small RNAs (sRNAs),that might be involved in de novo DNA methylation and virus resistance. Our data suggest that EVE families in Eucalyptus have distinct properties, and we provide the first comparative analysis of EVEs in Eucalyptus genomes. Departamento de Botânica Instituto de Biociências Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP) Departamento de Genética Instituto de Biociências Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP) PPGBIOINFO Universidade Tecnológica Federal do Paraná Genética e Biologia Molecular Universidade Estadual de Londrina Departamento de Botânica Instituto de Biociências Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP) Departamento de Genética Instituto de Biociências Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP) CNPq: 474123/2010-3

New dietary habits have favored an ever growing popularity of Eastern country cooking style and in particular of sushi. Even though the Reg. (EU) 1379/2013 does not apply to restaurants and caterers, the Reg. (EU) 1169/2011 establishes that all the information they provided to the final consumer have to meet the transparency requirements as regards the description of the ingredients used for the preparation of food. The present study aimed at performing a molecular based survey to identify the seafood species used in the sushi preparations at the retail level. A total of 185 samples were collected from sushi venues and supermarkets and DNA barcoding, followed by a pairwise divergence and Neighbor Joining clustering analysis, was applied in order to verify the information declared at purchase. Rather than to a proper training of Food Business Operators working at the catering level, the low mislabeling rate found in this study (3.4%) could be ascribed to the standardization of the products sold in ethnic restaurants. In fact, the common practice of proposing standardized menus always relying on the same species of fish could limit the risk of mislabeling occurrence.

Several seroconversions occurring in 2002 among sentinel cattle during the bluetongue-vaccination campaign in Lazio and Tuscany (central Italy) led to the suspicion of vaccine-virus circulation. Therefore in 2003, 17 seroconverting sentinel herds were investigated for the characteristics of the virus involved. From these farms, 91 unvaccinated animals and 57 Culicoides pools were tested for the presence of the bluetongue vaccine virus (serotype-2) or other strains. The presence of vaccine virus serotype-2 was confirmed by PCR followed by restriction analysis in the whole blood of 17 unvaccinated sentinel cattle and 12 pools of Culicoides imicola or C. obsoletus. Of the 17 herds, five were positive only for vaccine virus serotype-2, four were positive for other strains and two for both the vaccine and other strains; the remaining premises were virologicaly negative. The vaccine virus serotype-2 also was detected in areas not included in the vaccination campaign.

In 2001 and 2002, 235 outbreaks of bluetongue were observed in the Lazio and Tuscany regions of central Italy. During entomological surveillance Culicoides imicola , the main vector of bluetongue virus in the Mediterranean region, was detected in only 14 of 28 municipalities affected by outbreaks; Culicoides obsoletus was the most abundant species, contributing 83 per cent of individuals in catches, whereas C imicola contributed only 2 per cent. In affected municipalities the maximum catch of C obsoletus was 18,000 specimens, compared with 54 of C imicola . In October 2002 bluetongue virus serotype 2 was isolated from a single pool of wild-caught, non-blood-engorged parous C obsoletus inoculated on to BHK-21 cells. Its identity was confirmed by reverse transcriptase-PCR.

Inactivation of ribosomes by gelonin, a ribosome-inactivating protein with RNA N-glycosidase activity on 28 S rRNA, requires macromolecular cofactors present in post-ribosomal supernatants. One of these cofactors has been purified from a rat liver extract and identified as an RNA about 70 nt long which in sequence analysis shows a high level of similarity with mammalian (bovine) tRNA(Trp). The pattern of the sequencing gel is consistent with the co-existence in the preparation of two 3′-immature tRNA(Trp) species, missing only A75, or both A75 and C74. In the presence of ATP, CTP and tRNA nucleotidyltransferase, the gelonin-stimulating RNA is a good acceptor of tryptophan. An oligodeoxynucleotide complementary to positions 55 to 72 of mammalian (bovine) tRNA(Trp) hybridizes with the gelonin-stimulating RNA as demonstrated by gel mobility shift and ribonuclease H digestion. The oligodeoxynucleotide-directed ribonuclease H treatment also abolishes the gelonin-promoting activity of crude preparations of RNA, giving strong evidence that the only active RNA is a tRNA(Trp)-like molecule.

Background and study aims: Endoscopic submucosal dissection (ESD) has been proposed for large colorectal lesions, due to the high risk of recurrence following endoscopic mucosal resection. However, data on the efficacy and safety of colorectal ESD are still controversial. The aim of the current systematic review was to assess the efficacy and safety of colorectal ESD. Methods: A detailed Medline search of papers published during the period 1999 – 2010 was performed, using the search terms “Endoscopic submucosal dissection,” “Colorectal neoplasia,” “Colon,” or “Rectum.” Published studies that evaluated ESD for colorectal lesions were assessed using well-defined inclusion/exclusion criteria, including histological confirmation and surgery for complications. The process was independently performed by two authors. Forest plots on primary (i. e. histologically verified R0 resection and surgery for ESD complications) and secondary end-points were produced based on random-effect models. Heterogeneity was assessed using the I2 statistic. Risk for within-study bias was also ascertained. Results: A total of 22 studies (20 Asian, two European) provided data on 2841 ESD-treated lesions. The per-lesion summary estimate of R0 resection rate was 88 % (95 %CI 82 % – 92 %; I2 = 91 %). At meta-regression, carcinoid vs. non-carcinoid series (R0 93 % vs. 87 %; P = 0.04) and Asian vs. European series (R0 88 % vs. 65 %; P = 0.03) appeared to explain the detected heterogeneity. The per-lesion summary estimate of surgery for ESD complications was 1 % (95 %CI 0 % – 1 %) with a moderate degree of heterogeneity (I2 = 49 %). However, subgrouping of these results according to histological tumor types was not available in the reviewed studies. Conclusions: ESD appeared to be an extremely effective technique to achieve R0 resection of large colorectal lesions. The very low rate of surgery for complications also shows the potential safety of this approach.