De novo Transcriptome Assemblies of Rana (Lithobates) catesbeiana and Xenopus laevis Tadpole Livers for Comparative Genomics without Reference Genomes

In this work we studied the liver transcriptomes of two frog species, the American bullfrog (Rana (Lithobates) catesbeiana) and the African clawed frog (Xenopus laevis). We used high throughput RNA sequencing (RNA-seq) data to assemble and annotate these transcriptomes, and compared how their baseline expression profiles change when tadpoles of the two species are exposed to thyroid hormone. We generated more than 1.5 billion RNA-seq reads in total for the two species under two conditions as treatment/control pairs. We de novo assembled these reads using Trans-ABySS to reconstruct reference transcriptomes, obtaining over 350,000 and 130,000 putative transcripts for R. catesbeiana and X. laevis, respectively. Using available genomics resources for X. laevis, we annotated over 97% of our X. laevis transcriptome contigs, demonstrating the utility and efficacy of our methodology. Leveraging this validated analysis pipeline, we also annotated the assembled R. catesbeiana transcriptome. We used the expression profiles of the annotated genes of the two species to examine the similarities and differences between the tadpole liver transcriptomes. We also compared the gene ontology terms of expressed genes to measure how the animals react to a challenge by thyroid hormone. Our study reports three main conclusions. First, de novo assembly of RNA-seq data is a powerful method for annotating and establishing transcriptomes of non-model organisms. Second, the liver transcriptomes of the two frog species, R. catesbeiana and X. laevis, show many common features, and the distribution of their gene ontology profiles are statistically indistinguishable. Third, although they broadly respond the same way to the presence of thyroid hormone in their environment, their receptor/signal transduction pathways display marked differences

Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies

New generation sequencing technologies offer unique opportunities and challenges for re-sequencing studies. In this article, we focus on re-sequencing experiments using the Solexa technology, based on bacterial artificial chromosome (BAC) clones, and address an experimental design problem. In these specific experiments, approximate coordinates of the BACs on a reference genome are known, and fine-scale differences between the BAC sequences and the reference are of interest. The high-throughput characteristics of the sequencing technology makes it possible to multiplex BAC sequencing experiments by pooling BACs for a cost-effective operation. However, the way BACs are pooled in such re-sequencing experiments has an effect on the downstream analysis of the generated data, mostly due to subsequences common to multiple BACs. The experimental design strategy we develop in this article offers combinatorial solutions based on approximation algorithms for the well-known max n-cut problem and the related max n-section problem on hypergraphs. Our algorithms, when applied to a number of sample cases give more than a 2-fold performance improvement over random partitioning

Joint analysis of coastal altimetry and high-frequency (HF) radar data: observability of seasonal and mesoscale ocean dynamics in the Bay of Biscay

Land-based coastal high-frequency (HF) radar systems provide operational measurements of coastal surface currents (within 1–3&thinsp;m depth) with high spatial (300&thinsp;m–10&thinsp;km) and temporal ( ≤ 1&thinsp;h) sampling resolutions, while the near-continuous altimetry missions provide information, from 1993 until today, on geostrophic currents in the global ocean with typical along-track and temporal sampling resolutions of  &gt; 7&thinsp;km and  &gt; 9 days, respectively. During the last years, the altimetry community has made a step forward in improving these data in the coastal area, where the data present lower quality than in the open ocean. The combination of HF radar and altimetry measurements arises as a promising strategy to improve the continuous monitoring of the coastal area (e.g. by expanding the measurements made by HF radars to adjacent areas covered by the altimetry or by validating/confirming improvements brought by specific coastal algorithms or new altimeter missions). A first step towards this combination is the comparison of both data sets in overlapping areas.In this study, a HF radar system and two Jason-2 satellite altimetry products with different processing are compared over the period from 1 January 2009 to 24 July 2015. The results provide an evaluation of the performance of different coastal altimetry data sets within the study area and a better understanding of the ocean variability contained in the HF radar and altimetry data sets. Both observing systems detect the main mesoscale processes within the study area (the Iberian Poleward Current and mesoscale eddies), and the highest correlations between radar and altimetry (up to 0.64) occur in the slope where the Iberian Poleward Current represents a significant part of the variability in the circulation. Besides, the use of an Ekman model, to add the wind-induced current component to the altimetry-derived geostrophic currents, increases the agreement between both data sets (increasing the correlation by around 10&thinsp;%).</p

Development Of PLC Based Prototype Data Acquisition And Control System For Laboratory Type Gasifiers

Bu araştırmada farklı tip gazlaştırıcılar üzerine monte edilerek gazlaştırma süreçlerinin izlenmesini sağlayacak PLC kontrollü bir veri toplama ve kontrol sistemi gerçekleştirilmiştir. Sistem, modüler yapıda olup genişletilmeye uygun analog ve dijital giriş/çıkış modülleri ile donatılmıştır. Araştırmada gerçekleştirilen prototip sistem ile termokupllar, yük hücreleri ve basınç sensörleri gibi farklı tip algılayıcılardan gelen analog ve dijital veriler algılanabilmektedir. Ayrıca PLC’nin analog çıkış kanallarından gönderilen sinyaller ile reaktörler üzerindeki fan, motor ve oransal vanaların kontrolleri sağlanarak çalışma hızları denetlenebilmektedir. Geliştirilen prototip veri toplama ve kontrol sistemi ile laboratuvar ölçekli bir gazlaştırıcıda gerçekleştirilen gazlaştırma süreçleri, bir operatör paneli üzerinden takip edilirken, süreç değişkenleri 60s periyot ile USB belleğe kaydedilebilmektedir. Sistem, genişleme modülleri ile donatılarak endüstriyel amaçlı büyük tesislerin kontrolü için de kullanılabilecek mimari yapıya sahiptir. Geliştirilen sistemin başarısı yürütülen deneysel çalışmalar ile test edilmiş ve elde edilen sıcaklık, basınç, debi ve kütle değişimi grafikleri metin içerisinde sunulmuştur.In this research, a PLC controlled data acquisition and control system has been designed which is installed on different types of gasifiers to monitor the gasification processes. It is a modular system and equipped with analog and digital input / output expansion modules. The prototype system in the research can detect analogue and digital data coming from different types of sensors such as thermocouples, load cells and pressure sensors. In addition, operating speeds of the fans, motors and proportional valves on the reactors can be controlled by providing signals from the analog output channels of the PLC. With the developed prototype data acquisition and control system, the process variables can be saved to USB memory with 60 s period and monitored on a HMI touch panelduring gasification processes performed in a laboratory scale gasifier. By equipping with expansion modules, this system can be used to control large industrial plants. The developed system has been tested successfully in experimental studies and the obtained graphs of temperature, pressure, flow and mass change are presented in the text

Coherent Pair Production by Photons in the 20-170 GeV Energy Range Incident on Crystals and Birefringence

The cross section for coherent pair production by linearly polarised photons in the 20-170 GeV energy range was measured for photon aligned incidence on ultra-high quality diamond and germanium crystals. The theoretical description of coherent bremsstrahlung and coherent pair production phenomena is an area of active theoretical debate and development. However, under our experimental conditions, the theory predicted the combined cross section and polarisation experimental observables very well indeed. In macroscopic terms, our experiment measured a birefringence effect in pair production in a crystal. This study of this effect also constituted a measurement of the energy dependent linear polarisation of photons produced by coherent bremsstrahlung in aligned crystals. New technologies for manipulating high energy photon beams can be realised based on an improved understanding of QED phenomena at these energies. In particular, this experiment demonstrates an efficient new polarimetry technique. The pair production measurements were done using two independent methods simultaneously. The more complex method using a magnet spectrometer showed that the simpler method using a multiplicity detector was also viable.Comment: 10 pages, 13 figures, 1 table, REVTeX4 two column, Version for publicatio

Linear to Circular Polarisation Conversion using Birefringent Properties of Aligned Crystals for Multi-GeV Photons

We present the first experimental results on the use of a thick aligned Si crystal acting as a quarter wave plate to induce a degree of circular polarisation in a high energy linearly polarised photon beam. The linearly polarised photon beam is produced from coherent bremsstrahlung radiation by 178 GeV unpolarised electrons incident on an aligned Si crystal, acting as a radiator. The linear polarisation of the photon beam is characterised by measuring the asymmetry in electron-positron pair production in a Ge crystal, for different crystal orientations. The Ge crystal therefore acts as an analyser. The birefringence phenomenon, which converts the linear polarisation to circular polarisation, is observed by letting the linearly polarised photons beam pass through a thick Si quarter wave plate crystal, and then measuring the asymmetry in electron-positron pair production again for a selection of relative angles between the crystallographic planes of the radiator, analyser and quarter wave plate. The systematics of the difference between the measured asymmetries with and without the quarter wave plate are predicted by theory to reveal an evolution in the Stokes parameters from which the appearance of a circularly polarised component in the photon beam can be demonstrated. The measured magnitude of the circularly polarised component was consistent with the theoretical predictions, and therefore is in indication of the existence of the birefringence effect.Comment: 12 pages, 12 figures, 1 table, REVTeX4 two column, Version for publicatio

Results on the Coherent Interaction of High Energy Electrons and Photons in Oriented Single Crystals

The CERN-NA-59 experiment examined a wide range of electromagnetic processes for multi-GeV electrons and photons interacting with oriented single crystals. The various types of crystals and their orientations were used for producing photon beams and for converting and measuring their polarisation. The radiation emitted by 178 GeV unpolarised electrons incident on a 1.5 cm thick Si crystal oriented in the Coherent Bremsstrahlung (CB) and the String-of-Strings (SOS) modes was used to obtain multi-GeV linearly polarised photon beams. A new crystal polarimetry technique was established for measuring the linear polarisation of the photon beam. The polarimeter is based on the dependence of the Coherent Pair Production (CPP) cross section in oriented single crystals on the direction of the photon polarisation with respect to the crystal plane. Both a 1 mm thick single crystal of Germanium and a 4 mm thick multi-tile set of synthetic Diamond crystals were used as analyzers of the linear polarisation. A birefringence phenomenon, the conversion of the linear polarisation of the photon beam into circular polarisation, was observed. This was achieved by letting the linearly polarised photon beam pass through a 10 cm thick Silicon single crystal that acted as a "quarter wave plate" (QWP) as suggested by N. Cabibbo et al.Comment: Presented at International workshop "Relativistic Channeling and Related Coherent Phenomena", Frascati (Rome) 23-26 March 200

Exploring community perceptions in preparation for a randomised controlled trial of biofortified flour in Pakistan

Background: Biofortification of staple food crops may be a cost-effective and sustainable approach to reducing micronutrient deficiencies in resource-poor settings with low dietary diversity. However, its success depends on uptake by the local population. This paper presents formative research conducted in a remote, rural community in North West Pakistan, prior to commencing a randomised controlled trial to test the effectiveness of consuming zinc-biofortified wheat flour for alleviating zinc deficiency. It explored local community members’ knowledge, understanding and attitudes towards biofortification and views on members of their community taking part in the trial. Methods: Four focus group discussions were conducted with male and female community members (separately for cultural reasons) and four in-depth interviews were conducted with Jirga members—respected male elders. Participation was limited to households that were ineligible for the trial so that we could explore the perspectives of community members who were not influenced by the incentives of the trial. Focus group participants were selected at community events for transparency. Data collection took place at the local school and homes of Jirga members. Thematic analysis was undertaken, using a combination of deductive and inductive approaches to identify key themes. Results: A total of 47 men and women participated in this study. Participants reported clear motivation to access and consume more nutritious flour, believing this would bring health benefits, particularly to women and children. Trusted members of the local community, including Jirga members and female health workers, should be involved in providing information on biofortified flour (and the trial) to increase levels of awareness and acceptance. Without their involvement, there is a risk that biofortified flour would be mistrusted. The cost of flour is the main factor affecting purchasing decisions, and biofortified flour will need to be cost-competitive to achieve widespread uptake in marginalised, rural communities. Conclusion: This formative study generated rich, qualitative data from a range of community stakeholders to improve the understanding of important barriers and facilitators to the widespread acceptability and adoption of biofortified wheat. Implementation research such as this will inform future decision-making in relation to scaling up biofortified wheat in Pakistan

Coherent bremsstrahlung, boherent pair production, birefringence and polarimetry in the 20-170 GeV energy range using aligned crystals

The processes of coherent bremsstrahlung (CB) and coherent pair production (CPP) based on aligned crystal targets have been studied in the energy range 20-170 GeV. The experimental arrangement allowed for measurements of single photon properties of these phenomena including their polarization dependences. This is significant as the theoretical description of CB and CPP is an area of active theoretical debate and development. With the theoretical approach used in this paper both the measured cross sections and polarization observables are predicted very well. This indicates a proper understanding of CB and CPP up to energies of 170 GeV. Birefringence in CPP on aligned crystals is applied to determine the polarization parameters in our measurements. New technologies for high energy photon beam optics including phase plates and polarimeters for linear and circular polarization are demonstrated in this experiment. Coherent bremsstrahlung for the strings-on-strings (SOS) orientation yields a larger enhancement for hard photons than CB for the channeling orientations of the crystal. Our measurements and our calculations indicate low photon polarizations for the high energy SOS photons.Comment: 23 pages, 27 figures, 2 tables, REVTeX4 two column