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893. Rule-based design of plant expression vectors using GenoCADAnna Coll Rius, Kristina Gruden, Mandy L. Wilson, Jean Peccoud, 2015, original scientific article Abstract: Plant synthetic biology requires software tools to assist on the design of complex multi-genic expression plasmids. Here a vector design strategy to express genes in plants is formalized and implemented as a grammar in GenoCAD, a Computer-Aided Design software for synthetic biology. It includes a library of plant biological parts organized in structural categories and a set of rules describing how to assemble these parts into large constructs. Rules developed here are organized and divided into three main subsections according to the aim of the final construct: protein localization studies, promoter analysis and protein-protein interaction experiments. The GenoCAD plant grammar guides the user through the design while allowing users to customize vectors according to their needs. Therefore the plant grammar implemented in GenoCAD will help plant biologists take advantage of methods from synthetic biology to design expression vectors supporting their research projects.
Keywords: plasmid construction, plant genetics, gene expression
Published in DiRROS: 26.07.2024; Views: 334; Downloads: 169
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894. Interference of overlapping insect vibratory communication signalsMiguel Borges, Andrej Čokl, Alenka Žunič Kosi, Meta Virant-Doberlet, Raúl Alberto Laumann, Maria Carolina Blassioli Moraes, 2015, original scientific article Abstract: Plants limit the range of insect substrate-borne vibratory communication by their architecture and mechanical properties that change transmitted signal time, amplitude and frequency characteristics. Stinkbugs gain higher signal-to-noise ratio and increase communication distance by emitting narrowband low frequency vibratory signals that are tuned with transmission properties of plants. The objective of the present study was to investigate hitherto overlooked consequences of duetting with mutually overlapped narrowband vibratory signals. The overlapped vibrations of the model stinkbug species Eushistus heros, produced naturally or induced artificially on different plants, have been analysed. They represent female and male strategies to preserve information within a complex masked signal. The brown stinkbugs E. heros communicate with species and gender specific vibratory signals that constitute characteristic duets in the calling, courtship and rivalry phases of mating behaviour. The calling female pulse overlaps the male vibratory response when the latency of the latter is shorter than the duration of the female triggering signal or when the male response does not inhibit the following female pulse. Overlapping of signals induces interference that changes their amplitude pattern to a sequence of regularly repeated pulses in which their duration and the difference between frequencies of overlapped vibrations are related inversely. Interference does not occur in overlapped narrow band female calling pulses and broadband male courtship pulse trains. In a duet with overlapped signals females and males change time parameters and increase the frequency difference between signals by changing the frequency level and frequency modulation pattern of their calls.
Keywords: vibratory communication signals, overlapping
Published in DiRROS: 26.07.2024; Views: 393; Downloads: 594
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895. The groundwater invertebrate fauna of the Channel IslandsAnton Brancelj, Lee R. F. D. Knight, Bernd Hänfling, Colin Cheney, 2015, original scientific article Abstract: The Channel Islands are a small archipelago of British dependencies just off the coast of Normandy at the western end of the English Channel. There were only three records for stygobitic Crustacea [Niphargus fontanus Bate, 1859 and N. kochianus Bate, 1859 from Jersey and N. aquilex Schiődte, 1855 from Guernsey] from the archipelago and no systematic survey has been carried out of the islands for their groundwater fauna till present. Recently sampling was carried out in wells, boreholes and springs on the four largest islands, Jersey, Guernsey, Alderney and Sark during February 2012. Niphargus aquilex was widespread across all four islands and did not appear to be restricted to any particular geology. Niphargus ladmiraulti was present in large numbers in a single borehole on Jersey, the first record of this species from the archipelago. Niphargus kochianus was collected from two sites on Alderney and the syncarid Antrobathynella stammeri (Jakobi, 1954) from two sites on the west coast of Jersey. The records for A. stammeri are new for the Channel Islands and possibly represent the first records of this species from the French bio-geographical area. The presence of N. fontanus on the islands was not confirmed. Several species of stygophilic Cyclopoida were also recorded during the survey along with epigean freshwater invertebrate taxa, which were mostly present in springs and shallow wells close to surface streams.
Keywords: fauna, groundwater, stygobitic
Published in DiRROS: 26.07.2024; Views: 285; Downloads: 189
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896. Analysis of glioblastoma patients' plasma revealed the presence of microRNAs with a prognostic impact on survival and those of viral originKlemen Zupančič, Helena Motaln, Miomir Knežević, Urška Verbovšek, Marjan Koršič, Tamara Lah Turnšek, Primož Rožman, Matjaž Jeras, Matjaž Hren, Kristina Gruden, Andrej Blejec, Matija Veber, Ana Herman, Andrej Porčnik, Vid Podpečan, 2015, original scientific article Abstract: Background
Glioblastoma multiforme (GBM) is among the most aggressive cancers with a poor prognosis in spite of a plethora of established diagnostic and prognostic biomarkers and treatment modalities. Therefore, the current goal is the detection of novel biomarkers, possibly detectable in the blood of GBM patients that may enable an early diagnosis and are potential therapeutic targets, leading to more efficient interventions.
Experimental Procedures
MicroRNA profiling of 734 human and human-associated viral miRNAs was performed on blood plasma samples from 16 healthy individuals and 16 patients with GBM, using the nCounter miRNA Expression Assay Kits.
Results
We identified 19 miRNAs with significantly different plasma levels in GBM patients, compared to the healthy individuals group with the difference limited by a factor of 2. Additionally, 11 viral miRNAs were found differentially expressed in plasma of GBM patients and 24 miRNA levels significantly correlated with the patients’ survival. Moreover, the overlap between the group of candidate miRNAs for diagnostic biomarkers and the group of miRNAs associated with survival, consisted of ten miRNAs, showing both diagnostic and prognostic potential. Among them, hsa miR 592 and hsa miR 514a 3p have not been previously described in GBM and represent novel candidates for selective biomarkers. The possible signalling, induced by the revealed miRNAs is discussed, including those of viral origin, and in particular those related to the impaired immune response in the progression of GBM.
Conclusion
The GBM burden is reflected in the alteration of the plasma miRNAs pattern, including viral miRNAs, representing the potential for future clinical application. Therefore proposed biomarker candidate miRNAs should be validated in a larger study of an independent cohort of patients
Keywords: microRNAs, glioblastoma multiforme, biomarkers, RNA extraction, viral disease diagnosis
Published in DiRROS: 26.07.2024; Views: 340; Downloads: 153
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897. A MSFD complementary approach for the assessment of pressures, knowledge and data gaps in Southern European Seas: The PERSEUS experienceAlenka Malej, Alessandro Crise, H. Kaberi, J. Ruiz, 2015, original scientific article Abstract: PERSEUS project aims to identify the most relevant pressures exerted on the ecosystems of the Southern European Seas (SES), highlighting knowledge and data gaps that endanger the achievement of SES Good Environmental Status (GES) as mandated by the Marine Strategy Framework Directive (MSFD). A complementary approach has been adopted, by a meta-analysis of existing literature on pressure/impact/knowledge gaps summarized in tables related to the MSFD descriptors, discriminating open waters from coastal areas. A comparative assessment of the Initial Assessments (IAs) for five SES countries has been also independently performed. The comparison between meta-analysis results and IAs shows similarities for coastal areas only. Major knowledge gaps have been detected for the biodiversity, marine food web, marine litter and underwater noise descriptors. The meta-analysis also allowed the identification of additional research themes targeting research topics that are requested to the achievement of GES
Keywords: morje, plankton, PERSEUS, MSFD, kvaliteta morskega okolja, evropske direktive, okoljski indikatorji, Marine Strategy Framework Directive, Southern European Seas, Good Environmental status, PERSEUS project, Initial assessment
Published in DiRROS: 26.07.2024; Views: 303; Downloads: 202
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898. Host range and symptomatology of Pepino mosaic virus strains occurring in EuropeDag-Ragnar Blystad, René van der Vlugt, Ana Alfaro-Fernández, María del Carmen Córdoba, Gábor Bese, Dimitrinka Hristova, Henryk Pospieszny, Nataša Mehle, Maja Ravnikar, Laura Tomassoli, Christina Varveri, Steen Lykke Nielsen, 2015, original scientific article Abstract: Pepino mosaic virus (PepMV) has caused great concern in the greenhouse tomato industry after it was found causing a new disease in tomato in 1999. The objective of this paper is to investigate alternative hosts and compare important biological characteristics of the three PepMV strains occurring in Europe when tested under different environmental conditions. To this end we compared the infectivity and symptom development of three, well characterized isolates belonging to three different PepMV strains, EU-tom, Ch2 and US1, by inoculating them on tomato, possible alternative host plants in the family Solanaceae and selected test plants. The inoculation experiments were done in 10 countries from south to north in Europe. The importance of alternative hosts among the solanaceous crops and the usefulness of test plants in the biological characterization of PepMV isolates are discussed. Our data for the three strains tested at 10 different European locations with both international and local cultivars showed that eggplant is an alternative host of PepMV. Sweet pepper is not an important host of PepMV, but potato can be infected when the right isolate is matched with a specific cultivar. Nicotiana occidentalis 37B is a useful indicator plant for PepMV studies, since it reacts with a different symptomatology to each one of the PepMV strains.
Keywords: Pepino mosaic virus, potexvirus, strains, host plants, test plants
Published in DiRROS: 26.07.2024; Views: 265; Downloads: 231
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899. BioMinerJoachim Selbig, Kristina Gruden, Michal Or-Guil, Christian Schichor, Chris Bauer, Karol Stec, Alexander Glintschert, Johannes Schuchhardt, 2015, original scientific article Abstract: Personalized medicine is promising a revolution for medicine and human biology in the 21st century. The scientific foundation for this revolution is accomplished by analyzing biological high-throughput data sets from genomics, transcriptomics, proteomics, and metabolomics. Currently, access to these data has been limited to either rather simple Web-based tools, which do not grant much insight or analysis by trained specialists, without firsthand involvement of the physician. Here, we present the novel Web-based tool “BioMiner,” which was developed within the scope of an international and interdisciplinary project (SYSTHER†) and gives access to a variety of high-throughput data sets. It provides the user with convenient tools to analyze complex cross-omics data sets and grants enhanced visualization abilities. BioMiner incorporates transcriptomic and cross-omics high-throughput data sets, with a focus on cancer. A public instance of BioMiner along with the database is available at http://systherDB.microdiscovery.de/, login and password: “systher”; a tutorial detailing the usage of BioMiner can be found in the Supplementary File.
Keywords: data mining, multiomics data integration, biomarker detection, pathway visualization, personalized medicine, cancer
Published in DiRROS: 26.07.2024; Views: 276; Downloads: 205
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900. Survey results on nucleic acid tests of infectious diseases : present status and need for rapid and near-patient diagnosticsJörg Neukammer, Martin Hussels, Andreas Kummrow, Alison S. Devonshire, Carole A. Foy, Jim F. Huggett, Helen C. Parkes, Jana Žel, Mojca Milavec, Heinz Schimmel, Wolfgang Unger, Müslüm Akgöz, Timothy D. McHugh, Viktorija Tomič, Hans-Peter Grunert, Heinz Zeichhardt, 2015, original scientific article Abstract: This survey discusses current and emerging isothermal and rapid polymerase chain reaction (PCR) based nucleic acid amplification methods for near-patient diagnostics.
To assess the clinical need of rapid diagnostics for infectious diseases based on nucleic acid tests (NATs) we performed and analysed a questionnaire among laboratories participating in corresponding INSTAND ring trials for external quality assurance. The questions concerning new amplification technologies like isothermal nucleic acid amplification, potentially suited to significantly decrease turnaround times, were complemented by questions to evaluate the present status of NATs. Besides end-users, companies were also addressed by sending out a manufacturer specific questionnaire.
Analysis of the answers from 48 laboratories in 14 European countries revealed that a much shorter turnaround time is requested for selected pathogens compared to about 2 h or longer when applying temperature cycling amplification, i.e. PCR. In this context, most frequently mentioned were methicillin-resistant Staphylococcus aureus (MRSA), norovirus, influenza A and B viruses, cytomegalovirus (CMV) as well as hepatitis B virus (HBV) and hepatitis C virus (HCV). At present, 8% of the laboratories having participated in this survey apply isothermal amplification of nucleic acids to identify infectious pathogens.
Keywords: nucleic acid tests, infectious diseases, virus detection, bacteria detection, isothermal nucleic acid amplification, status report, questionnaire, NAT, PCR
Published in DiRROS: 26.07.2024; Views: 403; Downloads: 372
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