Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species

High-density oligonucleotide (oligo) arrays are a powerful tool for transcript profiling. Arrays based on GeneChip® technology are amongst the most widely used, although GeneChip® arrays are currently available for only a small number of plant and animal species. Thus, we have developed a method to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species and tested the method by analysing the transcriptome of Brassica oleracea L., a species for which no GeneChip® array is available, using a GeneChip® array designed for Arabidopsis thaliana (L.) Heynh. Genomic DNA from B. oleracea was labelled and hybridised to the ATH1-121501 GeneChip® array. Arabidopsis thaliana probe-pairs that hybridised to the B. oleracea genomic DNA on the basis of the perfect-match (PM) probe signal were then selected for subsequent B. oleracea transcriptome analysis using a .cel file parser script to generate probe mask files. The transcriptional response of B. oleracea to a mineral nutrient (phosphorus; P) stress was quantified using probe mask files generated for a wide range of gDNA hybridisation intensity thresholds. An example probe mask file generated with a gDNA hybridisation intensity threshold of 400 removed > 68 % of the available PM probes from the analysis but retained >96 % of available A. thaliana probe-sets. Ninety-nine of these genes were then identified as significantly regulated under P stress in B. oleracea, including the homologues of P stress responsive genes in A. thaliana. Increasing the gDNA hybridisation intensity thresholds up to 500 for probe-selection increased the sensitivity of the GeneChip® array to detect regulation of gene expression in B. oleracea under P stress by up to 13-fold. Our open-source software to create probe mask files is freely available http://affymetrix.arabidopsis.info/xspecies/ webcite and may be used to facilitate transcriptomic analyses of a wide range of plant and animal species in the absence of custom arrays.

Density of insect-pollinated grassland plants decreases with increasing surrounding land-use intensity

Pollinator declines have raised concerns about the persistence of plant species that depend on insect pollination, in particular by bees, for their reproduction. The impact of pollinator declines remains unknown for species-rich plant communities found in temperate seminatural grasslands. We investigated effects of land-use intensity in the surrounding landscape on the distribution of plant traits related to insect pollination in 239 European seminatural grasslands. Increasing arable land use in the surrounding landscape consistently reduced the density of plants depending on bee and insect pollination. Similarly, the relative abundance of bee-pollination-dependent plants increased with higher proportions of non-arable agricultural land (e.g. permanent grassland). This was paralleled by an overall increase in bee abundance and diversity. By isolating the impact of the surrounding landscape from effects of local habitat quality, we show for the first time that grassland plants dependent on insect pollination are particularly susceptible to increasing land-use intensity in the landscape.

Delivery of crop pollination services is an insufficient argument for wild pollinator conservation

There is compelling evidence that more diverse ecosystems deliver greater benefits to people, and these ecosystem services have become a key argument for biodiversity conservation. However, it is unclear how much biodiversity is needed to deliver ecosystem services in a cost-effective way. Here we show that, while the contribution of wild bees to crop production is significant, service delivery is restricted to a limited subset of all known bee species. Across crops, years and biogeographical regions, crop-visiting wild bee communities are dominated by a small number of common species, and threatened species are rarely observed on crops. Dominant crop pollinators persist under agricultural expansion and many are easily enhanced by simple conservation measures, suggesting that cost-effective management strategies to promote crop pollination should target a different set of species than management strategies to promote threatened bees. Conserving the biological diversity of bees therefore requires more than just ecosystem-service-based arguments.

Non-bee insects are important contributors to global crop pollination

Wild and managed bees are well documented as effective pollinators of global crops of economic importance. However, the contributions by pollinators other than bees have been little explored despite their potential to contribute to crop production and stability in the face of environmental change. Non-bee pollinators include flies, beetles, moths, butterflies, wasps, ants, birds, and bats, among others. Here we focus on non-bee insects and synthesize 39 field studies from five continents that directly measured the crop pollination services provided by non-bees, honey bees, and other bees to compare the relative contributions of these taxa. Non-bees performed 25–50% of the total number of flower visits. Although non-bees were less effective pollinators than bees per flower visit, they made more visits; thus these two factors compensated for each other, resulting in pollination services rendered by non-bees that were similar to those provided by bees. In the subset of studies that measured fruit set, fruit set increased with non-bee insect visits independently of bee visitation rates, indicating that non-bee insects provide a unique benefit that is not provided by bees. We also show that non-bee insects are not as reliant as bees on the presence of remnant natural or seminatural habitat in the surrounding landscape. These results strongly suggest that non-bee insect pollinators play a significant role in global crop production and respond differently than bees to landscape structure, probably making their crop pollination services more robust to changes in land use. Non-bee insects provide a valuable service and provide potential insurance against bee population declines.

Protein identification pipeline for the homology-driven proteomics

Homology-driven proteomics is a major tool to characterize proteomes of organisms with unsequenced genomes. This paper addresses practical aspects of automated homology-driven protein identifications by LC-MS/MS on a hybrid LTQ orbitrap mass spectrometer. All essential software elements supporting the presented pipeline are either hosted at the publicly accessible web server, or are available for free download. (C) 2008 Elsevier B.V. All rights reserved.

Separating the wheat from the chaff: unbiased filtering of background tandem mass spectra improves protein identification

Only a small fraction of spectra acquired in LC-MS/MS runs matches peptides from target proteins upon database searches. The remaining, operationally termed background, spectra originate from a variety of poorly controlled sources and affect the throughput and confidence of database searches. Here, we report an algorithm and its software implementation that rapidly removes background spectra, regardless of their precise origin. The method estimates the dissimilarity distance between screened MS/MS spectra and unannotated spectra from a partially redundant background library compiled from several control and blank runs. Filtering MS/MS queries enhanced the protein identification capacity when searches lacked spectrum to sequence matching specificity. In sequence-similarity searches it reduced by, on average, 30-fold the number of orphan hits, which were not explicitly related to background protein contaminants and required manual validation. Removing high quality background MS/MS spectra, while preserving in the data set the genuine spectra from target proteins, decreased the false positive rate of stringent database searches and improved the identification of low-abundance proteins.

Sambandet mellan bestrykningsrecepturoch sänkningen av ytansvithet vid UV-lackning

AssiDomän tillverkar kartong till förpackningsindustrin. Inom detta område är vitheten på kartongytanen viktig parameter. För att höja intrycket av förpackningen samt skapa en skyddande yta lackas ofta förpackningen med UV-lack efter tryck. Efter lackning kan då otryckta lackade ytor uppfattas som mindre vita. För att ta reda på om bestrykningssammansättningen har betydelse har ett fem olika bestrykningar blandats. Pigmenten som använts i bestrykningarna är karbonat, kaolin och titandioxidi olika kombinationer. Kartong har sedan bestrukits med dessa och därefter lackerats med UV-lack. Lackningen har gjorts i tre olika lackmängder. Mätningar har sedan gjorts gällande framförallt vithet. Den samverkan som sker mellan ljus, materialet och dess struktur är av stor vikt för att skapa en yta med goda optiska egenskaper. Resultaten i detta försök visar att lacken påverkar de optiska egenskaperna och framförallt vitheten. De lackerade ytorna fick en gulton efter lackering vilket kan ha att göra med lackens egenskaper. Vitheten hade en något mindre minskning för den bestrykning som bestod av karbonat och titandioxid. Skillnaden var dock mycket liten då alla bestrykningar fick en sänkning av vitheten med cirka 11-13 procentenheter oberoende av utgångsvärdet i vithet för respektive bestrykning innan lackning. Positivt var att det kunde konstateras att den bestrykning som hade det högsta vithetsvärdet före lackning också hade det efter lackning med ett normalt lackpålägg vilket betyder att en hög vithet är av betydelse även om den bestrukna ytan ska lackas. Den sänkning av vitheten som sker kan ha flera tänkbara orsaker. En tänkbar orsak kan vara att lacken förstör den porösa struktur som ger den viktiga ljusspridningen i bestrykningsskiktet. Resultaten visar också att lackens egenskaper tycks vara av stor betydelse. Den gulton som framträdde efter lackning tyder på en ökad absorption av vissa ljusvåglängder. Något som också pekar på detta är att alla fem bestrykningarna fick en liknande sänkning av vitheten. För att säga exakt vad som är orsaken eller vilken kombination som påverkar vitheten mest krävs ytterliggare tester. Olika UV-lacker kan testas eftersom endast en UV-lack har använts i dessa försök. En närmare studie av gränsyta mellan UV-lacken och bestrykningsskiktet bör också göras för att se hur lacken påverkar bestrykningsskiktets struktur.

Den Moderna Synthen : Hur påverkar dess valmöjligheter det musikaliska skapandet?

En fallstudie i huruvida mångfalden av valmöjligheter och funktioner i en modern synth påverkar musikskapandeprocessen. Undersökningen fokuseras på att undersöka hur dagens kompositörer använder sig av ljudskapande i moderna synthar. Syftet med denna undersökning är att se om mångfald av funktioner i en modern synth påverkar musikskapandet, för att ge läsaren en tankeställare angående arbetsflödet i sitt musikskapande, så att en effektivisering av processen kan tillämpas och att om möjligt, ge rum för mera musikskapande och mindre teknikförståelse. Denna undersökning gjordes genom att genomföra ett antal intervjuer samt en kompletterande enkätundersökning. Slutstsen jag kommit fram till är att en mångfald av funktioner påverkar musikskapandet, antingen negativt eller positivt beroende på genre och kompositörens erfarenhet av synthar.

Analog eller digital summering vid mixning av ljud : Blir det någon skillnad i slutresultatet?

I denna uppsats undersöks huruvida en lyssnare kan skilja på två ljudmixar som är mixade på samma sätt men summerade på olika sätt. Den ena summeras analogt och den andra digitalt. Om så är fallet, hur tycker lyssnaren att dessa skillnader yttrar sig? Som metod fick en testpanel i ett blindtest lyssna på två olika mixar, en rocklåt och en jazzlåt, som båda fanns i både analogt och digitalt summerade versioner. Dessa fick testsubjekten sedan besvara några frågor kring och tycka till om dessa olika versioner i en kvalitativ enkätundersökning Det visade sig att skillnader uppfattades av merparten av lyssnarna. Den vanligast förekommande beskrivningen var att det var skillnad på stereobredd, djup och dynamik i mixarna beroende på hur de summerats. Även ord som klarhet, värme och tydlighet förekom. Testpanelen var överlag även väldigt bra på att gissa vilken version som var summerad på vilket sätt. Dessa gissningar verkar i på många fall vara baserad på den förutfattade meningen att analogt borde vara bättre. Det är ganska tydligt att detta forskningsarbete i mångt och mycket är en fallstudie för just de variabler som förekom (märke på den analoga summeraren, ljudkvalité på de inspelade ljudet, programmaterial med mera). Fler tester och undersökningar behövs för att kunna dra generella slutsatser.

Källkritik på Internet : En kvalitativ studie av den källkritiska medvetenheten hos gymnasieelever på samhällsprogrammet

This essay is an ideographic study over the capacity of high school students to use the Internet with source criticism, and their attitudes towards this media. It’s a qualitative study whose main purpose is to seek out how the students reflect upon the problems facing them when searching facts and information over the internet.The focus group is six 18 year old high school students, who are studying in a normal sized town in the middle of Sweden, and are about to finish their studies in the program for social sciences. The study was made through interviews, one on one with the students,The results of the analysis have shown that even if students not necessarily use a pre meditated method when searching for information over the internet, they do have a basic understanding of the matter, especially concerning the nature of the source, who published it and why. Not all students made any thorough comparison with other, already established media, such as TV or books, but the analysis made it clear that they more or less deliberately saw the established media as more trustworthy in general. Individuals publishing on the internet, such as bloggers and Wikipedia, are seen with the utmost skepticism while public institutions such as universities and public service TV, are generally trusted as being honest and objective, also when publishing on the internet.

Kriminalitetens geografi : vardagsbrottslighetens spatiala fördelning i Borlänge

The aim of this thesis is to describe and analyze the geographical distribution of everyday criminality in the town of Borlänge during the year 2002 and to analyze which measures to be taken in the physical social planning to decrease this everyday criminality there. The term everyday criminality is here to be understood as those categories of crime that appear most frequently in the records of reports to the police every year. Here two kinds of crime have been in focus, thefts from cars and office burglary.In fulfilling this aim two main questions have been answered. The first one is how the everyday criminality was distributed geographically in the town of Borlänge during the year 2002. The second one is which measures to be taken in the physical social planning to decrease this everyday criminality in the town of Borlänge.In order to answer the first question a spatial autocorrelation analysis, Local Moran LISA has been used. This method is based on the measurement Moran´s I and shows the spatial autocorrelation for every single location. To answer the second question three different theories of crime prevention through environmental design have been studied and applied in the analysis. These are Jane Jacobs’ ideas about ”the living city”, Oscar Newman´s ideas about ”defensible space” and Ronald V. Clarke´s theories about crime prevention.The major conclusions that can be drawn from this thesis are that the risk of being exposed to thefts from cars, during the analyzed time period, was highest in Centrum and Hagalund and their surroundings. The lowest risk of being exposed to this type of crime was found in Domnarvet and Islingby, during the year 2002. The highest risk of being a victim of the crime office burglary was found in Hagalund and its surroundings and in the single area of Kvarnsveden. The corresponding lowest risk was found in Lergärdet and its surroundings and in Norra Backa and Kupolen. The measures that should be taken in order to decrease these types of criminality can be divided into overall changes and place-specific changes. When it comes to the crime thefts from cars a more attractive central business district, a better view of parking lots from nearby buildings, dividing of larger parking lot zones into smaller ones, migration of hidden parking lots and stronger access control to parking lots where problems with this kind of crime have occurred have been suggested as overall changes. The corresponding place-specific changes are to remove vegetation that is blocking the view, better lighting and to put up signs with information about increased risk of exposure to crime at parking lots with the most problems. To decrease the amount of office burglaries overall changes as to create a better view of the area from nearby surroundings, move bigger office compartments or divide them into smaller units, rebuild characteristic buildings and increase security by strengthening the access control to offices with these kinds of problems could be useful. Finally there are possibilities to decrease office burglary by using place-specific measures as surveillance cameras combined with signs containing information about these, high fences and better lighting around the buildings where a higher risk of being exposed to this kind of criminality is present.

Utvärdering av kvalité och dess behov inom förprovtryck

It always has been a need for the abiltiy to create color proofs. When an error occurs late in the production process, itis allways complicated and difficult to correct the error. In this project, digital proofs been made and discussions havebeen held with several people in the printing industry, in order to examine how well excisting digital proofs, meet thedemand of the market. And how close the digital proofs can come to the actual printsheat from the press. The study hasbeen shown that the one thing that has had the most influence on the outcome for the quality of a digital proof, is theprintshop operator’s knowledge about color management and proofing systems. Many advertising agencies in the graphicindustry think rasterised proofs are not necessesary and expensive. Therefor they prefer a cheaper alternative, whichdoesn’t show colors as well as the rasterised proof, but well enough to be content with it. There are a good awarenessconcerning lack of communication between printshop, reproduction and advertising agency. Advertising agencies thinkthat printshop rarely listen to what they have to say, while the printshop think that the advertising agency doesn’t understandwhat they are trying to tell them. The outcome of the printed proofs in this study can’t be representive for howgood digital proofs are conducted in regular basis in the industry. The divergence between the print press sheat and thedigital proof that was made was bigger than expected. This shows that implementation of ICC profiles in a color managementflow, not alone is the answer to making perfect digital proofs. There are so many other issues that has to be examined,like color management software, measure tools and correct color management module. In order to make a perfectproof, you have to look at the whole picture. In the end, the human eye finally has the last word on wheather theproof is good or not.

Systemutveckling med ett eTjänsteperspektiv : en eTjänstemetod för utveckling av kundfokuserade eTjänster

Göran Hultgren är författaren till eTjänster som social interaktion via användning av IT-system (2007), vilken är en praktisk teori som syftar till att vara till hjälp vid analyser av eTjänster. Eftersom Hultgrens avhandling går ut på att analysera befintliga eTjänster saknas det riktlinjer för hur teorin kan tillämpas praktiskt under utvecklingen av nya eTjänster. Syftet med dennauppsats är att ta fram en systemutvecklingsmetod utifrån den praktiska eTjänsteteorin.eTjänstemetoden som vi tagit fram är baserad på en litteraturstudie av Hultgrens avhandling.Metoden består av ett antal steg som man kan följa vid utvecklingen av en eTjänsten. Den skall inte ses som en fullständig systemutvecklingsmetod utan skall fungera snarare som enkompletteringsmetod som syftar till att ett eTjänsteperspektiv behålls under hela utvecklingen.Vi hade som uppdrag av SkiBar System AB att utveckla ett community där vi kunde testa våreTjänstemetod under utvecklingen. Metoden visade sig vara ett bra sätt att behålla ett eTjänsteperspektiv,det vill säga att alla communitys tjänster syftade till att höja värdet för kunden.

Behaviour of Surface Defects in Wire Rod Rolling

Defects are often present in rolled products, such as wire rod. The markets demand for wire rod without any defects has increased. In the final wire rod products, defects originating from the steel making, casting, pre-rolling of billets and during the wire rod rolling can appear. In this work, artificial V-shaped longitudinal surface cracks has been analysed experimentally and by means of FEM. The results indicate that the experiments and FEM calculations show the same tendency except in two cases, where instability due to a fairly “round” false round bars disturbed the experiment. FE studies in combination with practical experiments are necessary in order to understand the behaviour of the material flows in the groove and to explain whether the crack will open up as a V-shape or if it will be closed as an I-shape.