Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.

Within the ENCODE Consortium, GENCODE aimed to accurately annotate all protein-coding genes, pseudogenes, and noncoding transcribed loci in the human genome through manual curation and computational methods. Annotated transcript structures were assessed, and less well-supported loci were systematically, experimentally validated. Predicted exon-exon junctions were evaluated by RT-PCR amplification followed by highly multiplexed sequencing readout, a method we called RT-PCR-seq. Seventy-nine percent of all assessed junctions are confirmed by this evaluation procedure, demonstrating the high quality of the GENCODE gene set. RT-PCR-seq was also efficient to screen gene models predicted using the Human Body Map (HBM) RNA-seq data. We validated 73% of these predictions, thus confirming 1168 novel genes, mostly noncoding, which will further complement the GENCODE annotation. Our novel experimental validation pipeline is extremely sensitive, far more than unbiased transcriptome profiling through RNA sequencing, which is becoming the norm. For example, exon-exon junctions unique to GENCODE annotated transcripts are five times more likely to be corroborated with our targeted approach than with extensive large human transcriptome profiling. Data sets such as the HBM and ENCODE RNA-seq data fail sampling of low-expressed transcripts. Our RT-PCR-seq targeted approach also has the advantage of identifying novel exons of known genes, as we discovered unannotated exons in ~11% of assessed introns. We thus estimate that at least 18% of known loci have yet-unannotated exons. Our work demonstrates that the cataloging of all of the genic elements encoded in the human genome will necessitate a coordinated effort between unbiased and targeted approaches, like RNA-seq and RT-PCR-seq.

Disseny i implementació d'una aplicació per a dispositius mòbils per identificar elements geològics en el terreny

En aquests treball es presenta el procés de disseny i desenvolupament d'una aplicació per a dispositius mòbils que permet millorar la localització i identificació de les zones d'allaus. L'aplicació anomenada IdAllau, té les següents funcions principals: emmagatzematge, geolocalització, fotografia, representació cartografica, realitat augmentada i recerca per proximitat. La aplicació s'ha desenvolupat amb Android i llibreries i API's de codi lliure (Osmdroid i Appunta); amb els avantatges i inconvenients que comporta treballar-hi. El resultat final és una aplicació que permetrà als tècnics identificar les zones d'allaus en el camp utilitzant principalment la realitat augmentada i la geolocalització amb cartografia temàtica

The Adoption of Technologies, Policies, and Systems for Improving Fleet Fuel Performance, 2007

The dramatic rise in fuel prices and growing environmental concerns are pressing freight transportation companies to pursue new systems and methods to improve fuel efficiency and reduce their environmental impact. While select major carriers appear to be leading efforts to adopt technologies that support a dramatic improvement in fuel performance, there appears to be little understanding as to the breadth and depth of efforts being taken by the broader motor carrier community, consisting of over 20,000 companies of all sizes. The purpose of this study was to investigate the level of adoption of technologies and policies to support improved fuel efficiency among motor carrier fleets.

07032-012 Lake MacBride Watershed Final Report

Lake Macbride is considered to be one of the top four lakes for fishing in the state of Iowa. It is widely used by the public and contributes significant economic benefits to the county. Lake Macbride is situated in the North Corridor which is one of the fastest growing areas in the state. The lake has a surface area of 940 acres and drains 16,205 acres. Lake Macbride is on the Iowa 303(d) list for excessive sediments and nutrients. In 2001, Lake Macbride State Park received over 2.5 million dollars from the Marine Fuel Tax and Fish and Wildlife Trust to install 2 silt basins and stabilize over 12 miles of shoreline in the lake. Also in 2001, the Johnson County SWCD received a WSPF allocation from DSC to address agriculture and urban runoff issues in the watershed. Section 319 funding was received in 2002 to continue watershed efforts to the present. A watershed assessment was completed in 2003 to guide watershed activities. In 2005, a TMDL was completed for the lake. Since 2001, over $645,000 dollars has been spent by landowners and funding partners to install conservation practices in the watershed. Watershed efforts have resulted in the reduction of over 4200 tons of soils from being delivered into Lake Macbride. Nutrient reductions have also occurred from the development of nutrient management plans on 2000 acres. The District is in the process of wrapping up watershed efforts on private land. A series of 13 structures is planned to be installed in the State Park over the next several years. One of the last remaining items that still needs addressed is 1,400 feet of eroding shoreline adjacent to Lake Macbride along Cottage Reserve Road. The road is under the jurisdiction of the Johnson County Board of Supervisors. Both the Board of Supervisors and the IDNR are willing to contribute substantial dollars to address the 250 tons of soil that are being directly delivered to Lake Macbride each year.

Use of Remote Sensing for Collection of Data Elements for Linear Referencing Systems, 2001

This report evaluates the use of remotely sensed images in implementing the Iowa DOT LRS that is currently in the stages of system architecture. The Iowa Department of Transportation is investing a significant amount of time and resources into creation of a linear referencing system (LRS). A significant portion of the effort in implementing the system will be creation of a datum, which includes geographically locating anchor points and then measuring anchor section distances between those anchor points. Currently, system architecture and evaluation of different data collection methods to establish the LRS datum is being performed for the DOT by an outside consulting team.

FY'15 Biodiesel Fuel Revolving Fund Expenditures Report

Pursuant to Iowa Code section 307.20, the biodiesel fuel revolving fund (Fund) was created and is to be used to purchase biodiesel fuel for use in the Department of Transportation’s vehicles. The act directed that the Fund receive money from the sale of EPAct credits banked by the DOT on the effective date of the act, monies appropriated by the General Assembly, and any other monies obtained or accepted by the DOT for deposit in the Fund. This report is of the expenditures made from the Fund during FY 2015.

2016 Registered Flex Fuel Vehicles

Iowa Code section 452A.33(3) requires a report regarding flexible fuel vehicles registered in Iowa. The report includes the number of flexible fuel vehicles according to year of manufacture; the number of passenger vehicles according to year of manufacture; and the number of light pickup trucks according to the year of manufacture.

Presentació: Elements per a la comprensió crítica de la reforma de l'ensenyament secundari

La reforma de l'ensenyament secundari ha estat i és encara un tema polèmic, controvertit. En sentir crítiques referents a l'estat actual de l'ensenyament secundari per part de professionals procedents de sectors deis diferents estaments educatius, tant si aquestes crítiques són favorables a la reforma com si no ho són, és fàcil percebre un ambient general de preocupació. Davant d'aquest ambient, cal pensar que alguna cosa no deu acabar d'anar bé perquè s'hagi creat un clima de descontent tan generalitzat.

Functional analysis of cis- and trans-acting elements of the Candida albicans CDR2 promoter with a novel promoter reporter system.

Azole resistance in Candida albicans can be mediated by the upregulation of the ATP binding cassette transporter genes CDR1 and CDR2. Both genes are regulated by a cis-acting element called the drug-responsive element (DRE), with the consensus sequence 5'-CGGAWATCGGATATTTTTTT-3', and the transcription factor Tac1p. In order to analyze in detail the DRE sequence necessary for the regulation of CDR1 and CDR2 and properties of TAC1 alleles, a one-hybrid system was designed. This system is based on a P((CDR2))-HIS3 reporter system in which complementation of histidine auxotrophy can be monitored by activation of the reporter system by CDR2-inducing drugs such as estradiol. Our results show that most of the modifications within the DRE, but especially at the level of CGG triplets, strongly reduce CDR2 expression. The CDR2 DRE was replaced by putative DREs deduced from promoters of coregulated genes (CDR1, RTA3, and IFU5). Surprisingly, even if Tac1p was able to bind these putative DREs, as shown by chromatin immunoprecipitation, those from RTA3 and IFU5 did not functionally replace the CDR2 DRE. The one-hybrid system was also used for the identification of gain-of-function (GOF) mutations either in TAC1 alleles from clinical C. albicans isolates or inserted in TAC1 wild-type alleles by random mutagenesis. In all, 17 different GOF mutations were identified at 13 distinct positions. Five of them (G980E, N972D, A736V, T225A, and N977D) have already been described in clinical isolates, and four others (G980W, A736T, N972S, and N972I) occurred at already-described positions, thus suggesting that GOF mutations can occur in a limited number of positions in Tac1p. In conclusion, the one-hybrid system developed here is rapid and powerful and can be used for characterization of cis- and trans-acting elements in C. albicans.

La problemàtica psicopedagògica a secundària : alguns elements de particular incidència actual

Aquest article presenta una breu anàlisi de la situació actual de l’Educació Secundària, centrada en vuit punts: els continguts curriculars, els mètodes d’ensenyament-aprenentatge, la motivació de l’alumnat, la motivació del professorat, l’avaluació, la tutoria de grup, la tutoria individual i les relacions escola-família. Com a pistes de futur assenyala cinc aspectes: els espais de trobada escola-família, concretar els valors i conviccions de pares i mestres, l’actuació dels equips interdisciplinaris, la valoració multidimensional del progrés dels alumnes i el rellançament de la tutoria.

Elements diagnòstics en medicina interna. Una experiència d'ensenyament no presencial

La docencia no presencial permite ahorro de tiempo y de desplazamientos para los alumnos, de manera que contribuye a disminuir el coste de la docencia.

Epigenetic regulatory elements associate with specific histone modifications to prevent silencing of telomeric genes.

In eukaryotic cells, transgene expression levels may be limited by an unfavourable chromatin structure at the integration site. Epigenetic regulators are DNA sequences which may protect transgenes from such position effect. We evaluated different epigenetic regulators for their ability to protect transgene expression at telomeres, which are commonly associated to low or inconsistent expression because of their repressive chromatin environment. Although to variable extents, matrix attachment regions (MARs), ubiquitous chromatin opening element (UCOE) and the chicken cHS4 insulator acted as barrier elements, protecting a telomeric-distal transgene from silencing. MARs also increased the probability of silent gene reactivation in time-course experiments. Additionally, all MARs improved the level of expression in non-silenced cells, unlike other elements. MARs were associated to histone marks usually linked to actively expressed genes, especially acetylation of histone H3 and H4, suggesting that they may prevent the spread of silencing chromatin by imposing acetylation marks on nearby nucleosomes. Alternatively, an UCOE was found to act by preventing deposition of repressive chromatin marks. We conclude that epigenetic DNA elements used to enhance and stabilize transgene expression all have specific epigenetic signature that might be at the basis of their mode of action.

Energiansäästökohteiden kartoitus konepajateollisuuden yrityksessä

Tämän diplomityön tavoitteena on kartoittaa Vaahto Oy:n Hollolan tehtaan energiankulutus ja energiansäästökohteet. Ensin tutkittiin tehtaan energiankulutus ja energiankulutuksen jakautuminen. Tutkimuksessa käytettiin saatavilla olevia kulutustietoja, luettiin konekirjoja sekä haastateltiin tehtaan työntekijöitä. Lisäksi tehdashallien lämmityslaitteiden hyötysuhteet mitattiin. Tutkimuksen päätavoite oli selvittää, miksi tehtaan lämmitysenergiankulutus on kasvanut ja kannattaisiko rakennusten lämmittämiseen käyttää vaihtoehtoista lämmitysmuotoa öljylämmitykselle. Potentiaalisista energiansäästökohteista tehtiin investointilaskelmat ja toimenpide-ehdotukset. Kannattaviksi toimenpiteiksi tutkimuksessa todettiin: lämmityspolttoaineen vaihtaminen maakaasuun, nosto-ovien hankkiminen, paineilmaverkon huolto, paineilmakompressorin lämmöntalteenotto, tehdastilojen sisälämpötilan tarkastus ja työnjohtotilojen ilmanvaihdon käyntiaikojen muutos. Toimenpiteillä arvioidaan vuotuisten energiakustannusten pienenevän noin 34 000 euroa. Toimenpiteiden toteuttamisen arvioidaan maksavan 135 000 ¤, mistä lämmitysjärjestelmän vaihdon osuus on 100 000 ¤.