The Schistosoma mansoni genome encodes thousands of long non-coding RNAs predicted to be functional at different parasite life-cycle stages

Next Generation Sequencing (NGS) strategies, like RNA-Seq, have revealed the transcription of a wide variety of long non-coding RNAs (lncRNAs) in the genomes of several organisms. In the present work we assessed the lncRNAs complement of Schistosoma mansoni, the blood fluke that causes schistosomiasis, ranked among the most prevalent parasitic diseases worldwide. We focused on the long intergenic/intervening ncRNAs (lincRNAs), hidden within the large amount of information obtained through RNA-Seq in S. mansoni (88 libraries). Our computational pipeline identified 7029 canonically-spliced putative lincRNA genes on 2596 genomic loci (at an average 2.7 isoforms per lincRNA locus), as well as 402 spliced lncRNAs that are antisense to protein-coding (PC) genes. Hundreds of lincRNAs showed traits for being functional, such as the presence of epigenetic marks at their transcription start sites, evolutionary conservation among other schistosome species and differential expression across five different life-cycle stages of the parasite. Real-time qPCR has confirmed the differential life-cycle stage expression of a set of selected lincRNAs. We have built PC gene and lincRNA co-expression networks, unraveling key biological processes where lincRNAs might be involved during parasite development. This is the first report of a large-scale identification and structural annotation of lncRNAs in the S. mansoni genome

Les occlusions neonatales au Centre National Hospitalier et Universitare (CNHU) de Cotonou : Aspects épidémiologiques, cliniques et thérapeutiques

Les occlusions nonatales (ONN), les plus frquentes des urgences chirurgicales nonatales, sont des affections graves, greves d.une forte mortalit dpassant encore 50% en Afrique tropicale. Ce travail avait pour objectifs d.tudier leurs aspects pidmiologiques, cliniques et volutifs et d.analyser les problmes poss par leur prise en charge au Centre National Hospitalier et Universitaire (CNHU) de Cotonou. Il s.agit d.une tude rtrospective vise descriptive portant sur les occlusions nonatales, l.exclusion des malformations ano-rectales. 62 dossiers d.occlusions nonatales ont t colligs reprsentant 41 % des syndromes occlusifs. L.incidence annuelle moyenne tait de 4. L.ge moyen d.admission tait de 14 ± 5 jours. La sex-ratio tait de 1,4. Le dlai d.admission tait en moyenne de 11 ± 4 jours. Aucune ONN n.a t diagnostique en priode antnatale. 50% des ONN taient des atrsies intestinales. Le dlai moyen d.intervention chirurgicale tait de 7 + 3 jours. Les complications post-opratoires, observes dans 75% des cas, taient domines par la dnutrition (55%) et les occlusions post-opratoires (22%). La mortalit globale tait de 44,2%. Elle tait plus importante chez les oprs (58,3%). Les ONN ont une frquence sous estime Cotonou. Elles sont caractrises par des retards considrables l.admission, au diagnostic et l.intervention, et de fortes, morbidit et mortalit. Cette situation est en rapport avec l.absence de diagnostic antnatal, l.inexistence de services spcialiss et performants d.Anesthsie-Ranimation et de Soins intensifs en Nonatologie et l.inexistence de couverture sociale universelle. Clinics in Mother and Child Health Vol. 3(1) 2006: 457-46

Generation of Two Paclitaxel-Resistant High-Grade Serous Carcinoma Cell Lines With Increased Expression of P-Glycoprotein

Debulking surgery followed by chemotherapy are the standard of care for high-grade serous carcinoma. After an initial good response to treatment, the majority of patients relapse with a chemoresistant profile, leading to a poor overall survival. Chemotherapy regimens used in high-grade serous carcinomas are based in a combination of classical chemotherapeutic drugs, namely, Carboplatin and Paclitaxel. The mechanisms underlying drug resistance and new drug discovery are crucial to improve patients’ survival. To uncover the molecular mechanisms of chemoresistance and test drugs capable of overcoming this resistant profile, it is fundamental to use good cellular models capable of mimicking the chemoresistant disease. Herein, we established two high-grade serous carcinoma cell lines with intrinsic resistance to Carboplatin and induced Paclitaxel resistance (OVCAR8 PTX R C and OVCAR8 PTX R P) derived from the OVCAR8 cell line. These two chemoresistant cell line variants acquired an enhanced resistance to Paclitaxel-induced cell death by increasing the drug efflux capacity, and this resistance was stable in long-term culture and following freeze/thaw cycles. The mechanism underlying Paclitaxel resistance resides in a significant increase in P-glycoprotein expression and, when this drug efflux pump was blocked with Verapamil, cells re-acquired Paclitaxel sensitivity. We generated two high-grade serous carcinoma cell lines, with a double-chemoresistant (Carboplatin and Paclitaxel) phenotype that mimics the majority of tumor recurrences in ovarian cancer context. This robust tool is suitable for preliminary drug testing towards the development of therapeutic strategies to overcome chemoresistance.This work was developed at i3S/IPATIMUP, an Associate Laboratory of the Portuguese Ministry of Science, Technology and Higher Education, and partially supported by Funda̧cao para a Cîencia e a Tecnologia (FCT). This research was supported by European Regional Development Funds (ERDF) funds through the COMPETE 2020–Operational Program for Competitiveness and Internationalization (POCI), Portugal 2020, Funda̧cao para a Cîencia e a Tecnologia (FCT)/Minist́erio da Cîencia, Tecnologia e Inova̧cao (MCTES), under the project POCI 01-0145-FEDER-029503 (PTDC/MEC-ONC/29503/2017) and CESPU (Cooperativa de Ensino Superior Politécnico e Universitário) under the project ComeTarget_CESPU_2017 (to HB). MN acknowledges FCT/MCTES and UE for financial support through a PhD fellowship (2020.04720.BD) cosponsored by Fundo Social Europeu (FSE) through Programa Operacional Regional Norte (Norte 2020)

Cd44v6 high membranous expression is a predictive marker of therapy response in gastric cancer patients

In gastric cancer (GC), biomarkers that define prognosis and predict treatment response remain scarce. We hypothesized that the extent of CD44v6 membranous tumor expression could predict prognosis and therapy response in GC patients. Two GC surgical cohorts, from Portugal and South Korea (n = 964), were characterized for the extension of CD44v6 membranous immuno-expression, clinicopathological features, patient survival, and therapy response. The value of CD44v6 expression in predicting response to treatment and its impact on prognosis was determined. High CD44v6 expression was associated with invasive features (perineural invasion and depth of invasion) in both cohorts and with worse survival in the Portuguese GC cohort (HR 1.461; 95% confidence interval 1.002–2.131). Patients with high CD44v6 tumor expression benefited from conventional chemotherapy in addition to surgery (p < 0.05), particularly those with heterogeneous CD44v6-positive and-negative populations (CD44v6_3+) (p < 0.007 and p < 0.009). Our study is the first to identify CD44v6 high membranous expression as a potential predictive marker of response to conventional treatment, but it does not clarify CD44v6 prognostic value in GC. Importantly, our data support selection of GC patients with high CD44v6-expressing tumors for conventional chemotherapy in addition to surgery. These findings will allow better stratification of GC patients for treatment, potentially improving their overall survival.This work was funded by FEDER-Fundo Europeu de Desenvolvimento Regional funds through the COMPETE 2020–Operacional Programme for Competitiveness and Internationalization (POCI), Portugal 2020, and by Portuguese funds through FCT–Fundação para a Ciência e a Tecnologia/Ministério da Ciência, Tecnologia e Inovação in the framework of the project “Institute for Research and Innovation in Health Sciences” (POCI-01-0145-FEDER-007274). This work was also financed by the projects NORTE-01-0145-FEDER-000003 and NORTE-01-0145-FEDER-000029, supported by the Norte Portugal Regional Programme (NORTE 2020) under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF); project POCI-01-0145-FEDER-016390 and SAICTPAC/0022/2015, funded by ERDF, POCI, and FCT; project PTDC/CTM-NAN/120958/2010, from FCT; and by project PTDC/BTM-TEC/30164/2017 funded by ERDF funds through the COMPETE 2020–POCI, Portugal 2020, and by FCT. Salary support to G.M.A. by PTDC/BTM-TEC/30164/2017 project; C.P. was supported by the grant SFRH/BD/113031/2015 from FCT

Time-Fractional Optimal Control of Initial Value Problems on Time Scales

We investigate Optimal Control Problems (OCP) for fractional systems involving fractional-time derivatives on time scales. The fractional-time derivatives and integrals are considered, on time scales, in the Riemann--Liouville sense. By using the Banach fixed point theorem, sufficient conditions for existence and uniqueness of solution to initial value problems described by fractional order differential equations on time scales are known. Here we consider a fractional OCP with a performance index given as a delta-integral function of both state and control variables, with time evolving on an arbitrarily given time scale. Interpreting the Euler--Lagrange first order optimality condition with an adjoint problem, defined by means of right Riemann--Liouville fractional delta derivatives, we obtain an optimality system for the considered fractional OCP. For that, we first prove new fractional integration by parts formulas on time scales.Comment: This is a preprint of a paper accepted for publication as a book chapter with Springer International Publishing AG. Submitted 23/Jan/2019; revised 27-March-2019; accepted 12-April-2019. arXiv admin note: substantial text overlap with arXiv:1508.0075

Sialic Acid Glycobiology Unveils Trypanosoma cruzi Trypomastigote Membrane Physiology.

Trypanosoma cruzi, the flagellate protozoan agent of Chagas disease or American trypanosomiasis, is unable to synthesize sialic acids de novo. Mucins and trans-sialidase (TS) are substrate and enzyme, respectively, of the glycobiological system that scavenges sialic acid from the host in a crucial interplay for T. cruzi life cycle. The acquisition of the sialyl residue allows the parasite to avoid lysis by serum factors and to interact with the host cell. A major drawback to studying the sialylation kinetics and turnover of the trypomastigote glycoconjugates is the difficulty to identify and follow the recently acquired sialyl residues. To tackle this issue, we followed an unnatural sugar approach as bioorthogonal chemical reporters, where the use of azidosialyl residues allowed identifying the acquired sugar. Advanced microscopy techniques, together with biochemical methods, were used to study the trypomastigote membrane from its glycobiological perspective. Main sialyl acceptors were identified as mucins by biochemical procedures and protein markers. Together with determining their shedding and turnover rates, we also report that several membrane proteins, including TS and its substrates, both glycosylphosphatidylinositol-anchored proteins, are separately distributed on parasite surface and contained in different and highly stable membrane microdomains. Notably, labeling for α(1,3)Galactosyl residues only partially colocalize with sialylated mucins, indicating that two species of glycosylated mucins do exist, which are segregated at the parasite surface. Moreover, sialylated mucins were included in lipid-raft-domains, whereas TS molecules are not. The location of the surface-anchored TS resulted too far off as to be capable to sialylate mucins, a role played by the shed TS instead. Phosphatidylinositol-phospholipase-C activity is actually not present in trypomastigotes. Therefore, shedding of TS occurs via microvesicles instead of as a fully soluble form

Comparative analysis of the lambda-interferons IL-28A and IL-29 regarding their transcriptome and their antiviral properties against hepatitis C virus.

Specific differences in signaling and antiviral properties between the different Lambda-interferons, a novel group of interferons composed of IL-28A, IL-28B and IL-29, are currently unknown. This is the first study comparatively investigating the transcriptome and the antiviral properties of the Lambda-interferons IL-28A and IL-29. Expression studies were performed by microarray analysis, quantitative PCR (qPCR), reporter gene assays and immunoluminometric assays. Signaling was analyzed by Western blot. HCV replication was measured in Huh-7 cells expressing subgenomic HCV replicon. All hepatic cell lines investigated as well as primary hepatocytes expressed both IFN-λ receptor subunits IL-10R2 and IFN-λR1. Both, IL-28A and IL-29 activated STAT1 signaling. As revealed by microarray analysis, similar genes were induced by both cytokines in Huh-7 cells (IL-28A: 117 genes; IL-29: 111 genes), many of them playing a role in antiviral immunity. However, only IL-28A was able to significantly down-regulate gene expression (n = 272 down-regulated genes). Both cytokines significantly decreased HCV replication in Huh-7 cells. In comparison to liver biopsies of patients with non-viral liver disease, liver biopsies of patients with HCV showed significantly increased mRNA expression of IL-28A and IL-29. Moreover, IL-28A serum protein levels were elevated in HCV patients. In a murine model of viral hepatitis, IL-28 expression was significantly increased. IL-28A and IL-29 are up-regulated in HCV patients and are similarly effective in inducing antiviral genes and inhibiting HCV replication. In contrast to IL-29, IL-28A is a potent gene repressor. Both IFN-λs may have therapeutic potential in the treatment of chronic HCV

Pulmonary cryptococcosis induces chitinase in the rat

<p>Abstract</p> <p>Background</p> <p>We previously demonstrated that chronic pulmonary infection with <it>Cryptococcus neoformans </it>results in enhanced allergic inflammation and airway hyperreactivity in a rat model. Because the cell wall of <it>C. neoformans </it>consists of chitin, and since acidic mammalian chitinase (AMCase) has recently been implicated as a novel mediator of asthma, we sought to determine whether such infection induces chitinase activity and expression of AMCase in the rat.</p> <p>Methods</p> <p>We utilized a previously-established model of chronic <it>C. neoformans </it>pulmonary infection in the rat to analyze the activity, expression and localization of AMCase.</p> <p>Results</p> <p>Our studies indicate that intratracheal inoculation of <it>C. neoformans </it>induces chitinase activity within the lung and bronchoalveolar lavage fluid of infected rats. Chitinase activity is also elicited by pulmonary infection with other fungi (e.g. <it>C. albicans</it>), but not by the inoculation of dead organisms. Enhanced chitinase activity reflects increased AMCase expression by airway epithelial cells and alveolar macrophages. Systemic cryptococcosis is not associated with increased pulmonary chitinase activity or AMCase expression.</p> <p>Conclusion</p> <p>Our findings indicate a possible link between respiratory fungal infections, including <it>C. neoformans</it>, and asthma through the induction of AMCase.</p