Polymerase chain reaction for the diagnosis of bovine genital campylobacteriosis

Bovine genital campylobacteriosis is a common venereal disease of cattle; the prevalence of this disease can be underestimated mostly because of the nature of the etiological agent, the microaerobic Campylobacter fetus subspecies venerealis. The purpose of the current study was to evaluate the utilization of polymerase chain reaction (PCR) in the diagnosis of genital campylobacteriosis in samples obtained from bull prepuce aspirate, cow cervical mucus, and abomasum contents of aborted fetuses, collected into enrichment medium. Five different DNA extraction protocols were tested: thermal extraction, lysis with proteinase K, lysis with guanidine isothiocyanate, lysis with DNAzol, and lysis with hexadecyltrimethylammonium bromide (CTAB). The specificity, sensitivity, and technical application of the PCR assay were also evaluated with clinical samples and compared to bacterial isolation by standard culture. DNA extraction by the CTAB protocol provided better results in PCR, and it was able to detect 63 colony-forming units per ml of C. fetus. Out of 277 clinical samples tested, 68 (24%) were positive for Campylobacter fetus using PCR, while only 8 (2.8%) of the samples were positive by bacterial isolation in solid medium, proving the superiority of the PCR technique when compared to the standard isolation method, and providing evidence for its usefulness as a better screening test in cattle for the diagnosis of bovine genital campylobacteriosis.

Serology, polymerase chain reaction and histopathology for leptospirosis in samples collected at slaughter from dairy cows of Parnaiba region, state of Piauí, Brazil

The presence of anti leptospiral agglutinins (microscopic agglutination test - MAT) and DNA of leptospires was investigated in the kidney and urine (Polymerase Chain Reaction - PCR) in samples collected at the time of slaughter of cattle originating from the dairy basin of Parnaíba, Piauí, Brazil, as also the lesions in kidney, lung, liver, uterus, ovary and placenta (histopathology and immunohistochemistry). In the MAT, Hardjo was the predominant serovar with the highest number of reagent animals for the strain Hardjobovis/Sponselee. Anti-leptospiral antigens were scored in epithelial cells, interstitial vascular endothelium, endothelium of glomerular capillaries and Bowman's capsule of 20 positive animals. Inflammatory cells were more common in the kidney. PCR was positive in urine and kidney tissue

Supply chain performance management system

The purpose of the study is to determine general features of the supply chain performance management system, to assess the current state of performance management in the case company mills and to make proposals for improvement – how the future state of performance management system would look like. The study covers four phases which consist of theory and case company parts. Theoretical review gives understanding about performance management and measurement. Current state analysis assesses the current state of performance management in the mills. Results and proposals for improvement are derived from current state analysis and finally the conclusions with answers to research questions are presented. Supply chain performance management system consists of five areas: perfor-mance measurement and metrics, action plans, performance tracking, performance dialogue and rewards, consequences and actions. The result of the study revealed that all mills were quite average level in performance management and there is a room for improvement. Created performance improvement matrix served as a tool in assessing current performance management and could work also as a tool in the future in mapping the current state after transformation process. Limited harmonization was revealed as there were different ways to work and manage performance in the mills. Lots of good ideas existed though actions are needed to make a progress. There is also need to harmonize KPI structure.

Value added logistics in supply and demand chain : COSTFIX : New operation model for maintenance material logistics in paper industry

This research report illustrates and examines new operation models for decreasing fixed costs and transforming them into variable costs in the field of paper industry. The report illustrates two cases – a new operation model for material logistics in maintenance and an examination of forklift truck fleet outsourcing solutions. Conventional material logistics in maintenance operation is illustrated and some problems related to conventional operation are identified. A new operation model that solves some of these problems is presented including descriptions of procurement and service contracts and sources of added value. Forklift truck fleet outsourcing solutions are examined by illustrating the responsibilities of a host company and a service provider both before and after outsourcing. The customer buys outsourcing services in order to improve its investment productivity. The mechanism of how these services affect the customer company’s investment productivity is illustrated.

Development and application of polymerase chain reaction test for detection of Conidiobolus lamprauges

Conidiobolomycosis is a granulomatous disease caused by the fungus Conidiobolus spp. in humans and animals. Traditional technique for diagnosis of the disease is isolation of the agent associated with the presence of typical clinical signs and pathological conditions. The aim of this study was to describe the development of a specific polymerase chain reaction (PCR) test for Conidiobolus lamprauges to detect the fungus in clinical samples. Samples from suspected animals were collected and submitted to isolation, histopathological analysis and amplification by PCR. DNA from tissues was subjected to PCR with fungi universal primers 18S rDNA gene, and specific primers were designed based on the same gene in C. lamprauges that generated products of about 540 bp and 222 bp respectively. The culture was positive in 26.6% of clinical samples. The PCR technique for C. lamprauges showed amplification of DNA from fresh tissues (80%) and paraffin sections (44.4%). In conclusion, the PCR technique described here demonstrated a high sensitivity and specificity for detection of fungal DNA in tissue samples, providing a tool for the rapid diagnosis of C. lamprauges.

Molecular diagnosis of Anaplasma marginale in cattle: quantitative evaluation of a real-time PCR (Polymerase Chain Reaction) based on msp5 gene

The rickettsia Anaplasma marginale is considered the main agent of bovine anaplasmosis. Due the nonspecific clinical signs of the anaplasmosis, the diagnosis of infection depends of laboratory confirmation. In recent years, molecular diagnostic methods have been used to detect A. marginale in cattle. However, the existence of a large number of assays of different sensitivity and cost makes the choice of an appropriate test difficult. In the present study, a real-time Polymerase Chain Reaction (PCR) based on the msp5 target gene was quantitatively assessed and compared to an end point PCR. Both reactions were subjected to sensitivity and specificity evaluation using plasmid DNA and samples from cattle experimentally infected with A. marginale. A comparative field trial of the tests was carried out using samples of cattle from a stable enzootic area for A. marginale. The real-time PCR showed a higher sensitivity than the end point PCR. This reaction (i.e. real-time PCR) was able to detect one copy of the msp5 gene in 100 ηg of plasmidial DNA, and more than 80% of its results were positive among experimentally infected animals seven days after infection. In addition, based on in silico analysis, the real-time PCR evaluated in the present study appears to be useful for the detection of A. ovis.

The effects of location, feedstock availability, and supply-chain logistics on the greenhouse gas emissions of forest-biomass energy utilization in Finland

Forest biomass represents a geographically distributed feedstock, and geographical location affects the greenhouse gas (GHG) performance of a given forest-bioenergy system in several ways. For example, biomass availability, forest operations, transportation possibilities and the distances involved, biomass end-use possibilities, fossil reference systems, and forest carbon balances all depend to some extent on location. The overall objective of this thesis was to assess the GHG emissions derived from supply and energy-utilization chains of forest biomass in Finland, with a specific focus on the effect of location in relation to forest biomass’s availability and the transportation possibilities. Biomass availability and transportation-network assessments were conducted through utilization of geographical information system methods, and the GHG emissions were assessed by means of lifecycle assessment. The thesis is based on four papers in which forest biomass supply on industrial scale was assessed. The feedstocks assessed in this thesis include harvesting residues, smalldiameter energy wood and stumps. The principal implication of the findings in this thesis is that in Finland, the location and availability of biomass in the proximity of a given energyutilization or energy-conversion plant is not a decisive factor in supply-chain GHG emissions or the possible GHG savings to be achieved with forest-biomass energy use. Therefore, for the greatest GHG reductions with limited forest-biomass resources, energy utilization of forest biomass in Finland should be directed to the locations where most GHG savings are achieved through replacement of fossil fuels. Furthermore, one should prioritize the types of forest biomass with the lowest direct supply-chain GHG emissions (e.g., from transport and comminution) and the lowest indirect ones (in particular, soil carbon-stock losses), regardless of location. In this respect, the best combination is to use harvesting residues in combined heat and power production, replacing peat or coal.

Diagnosis of Leishmania infantum infection by Polymerase Chain Reaction in wild mammals

Visceral leishmaniasis is a chronic infectious disease caused by Leishmania infantum (synonym: Leishmania chagasi) and transmitted by the sandfly Lutzomyia longipalpis in Brazil. It is an endemic zoonosis in several regions of the country, including Belo Horizonte (State of Minas Gerais). In urban areas, the domestic dog is susceptible and considered the most important animal reservoir. However, L. infantum has been previously diagnosed in other species, including captive primates and canids. This study aimed to evaluate the presence of the agent DNA in captive animals as well as some free ranging animals from the Zoo-Botanical Foundation of Belo Horizonte by Polymerase Chain Reaction. Eighty one blood samples from primates, carnivores, ruminants, edentates, marsupial, and a monogastric herbivore were analyzed. Three primates Alouatta guariba (brown howler monkey), and two canids Speothos venaticus (bush dog) were positive, demonstrating the importance of leishmaniasis control in endemic areas for preservation of wildlife species in captivity.

Plasmodium spp. and Haemoproteus spp. infection in birds of the Brazilian Atlantic Forest detected by microscopy and polymerase chain reaction

In recent years haemosporidian infection by protozoa of the genus Plasmodium and Haemoproteus, has been considered one of the most important factors related to the extinction and/or population decline of several species of birds worldwide. In Brazil, despite the large avian biodiversity, few studies have been designed to detect this infection, especially among wild birds in captivity. Thus, the objective of this study was to analyze the prevalence of Plasmodium spp. and Haemoproteus spp. infection in wild birds in captivity in the Atlantic Forest of southeastern Brazil using microscopy and the polymerase chain reaction. Blood samples of 119 different species of birds kept in captivity at IBAMA during the period of July 2011 to July 2012 were collected. The parasite density was determined based only on readings of blood smears by light microscopy. The mean prevalence of Plasmodium spp. and Haemoproteus spp. infection obtained through the microscopic examination of blood smears and PCR were similar (83.19% and 81.3%, respectively), with Caracara plancus and Saltator similis being the most parasitized. The mean parasitemia determined by the microscopic counting of evolutionary forms of Plasmodium spp. and Haemoproteus spp. was 1.51%. The results obtained from this study reinforce the importance of the handling of captive birds, especially when they will be reintroduced into the wild.

Assessment of purchasing maturity in spare parts supply chain

To describe the change of purchasing moving from administrative to strategic function academics have put forward maturity models which help practitioners to compare their purchasing activities to industry top performers and best practices. However, none of the models aim to distinguish the purchasing maturity from the after-sales point of view, even though after-sales activities are acknowledged as a relevant source of revenue, profit and competitive advantage in most manufacturing firms. The maturity of purchasing and supply management practices have a large impact to the overall performance of the spare parts supply chain and ultimately to the value creation and relationship building for the end customer. The research was done as a case study for a European after-sales organization which is part of a globally operating industrial firm specialized in heavy machinery. The study mapped the current state of the purchasing practices in the case organization and also distinguished the relevant areas for future development. The study was based on the purchasing maturity model developed by Schiele (2007) and investigated also how applicable is the maturity model in the spare parts supply chain context. Data for the assessment was gathered using five expert interviews inside the case organization and other parties involved in the company’s spare parts supply chain. Inventory management dimension was added to the original maturity model in order to better capture the important areas in a spare parts supply chain. The added five questions were deduced from the spare parts management literature and verified as relevant areas by the case organization’s personnel. Results indicate that largest need for development in the case organization are: better collaboration between sourcing and operative procurement functions, use of installed base information in the spare parts management, training plan development for new buyers, assessment of aligned KPI’s between the supply chain parties and better defining the role of after-sales sourcing. The purchasing maturity model used in this research worked well in H&R Leading, Controlling and Inventory Management dimensions. The assessment was more difficult to conduct in the Supplier related processes, Process integration and Organizational structure –dimensions, mainly because the assessment in these sections would for some parts require more company-wide assessment. Results indicate also that the purchasing maturity model developed by Schiele (2007) captures the relevant areas in the spare parts supply as well.

Improving the Supply Chain Performance Management System in a Finnish paper mill

This Master’s Thesis studies performance management system and its benefits, risks and costs. Objective of the thesis is to describe and evaluate currently used supply chain performance management system (SCPMS) in a Finnish paper mill and its interfaces with its business unit’s SCPMS. As a result, the host company has improvement road map for improving its SCPMS. Used SCPMS in the host company and its interfaces to business unit’s SCPMS are described based on interviews held in the host company and the business unit. Evaluation of the host company’s SCPMS is based on literature study. For improvement road map, three areas in need of improvements are chosen. The study shows the need of high level top management commitment in successful performance management system implementation and usage, especially when the system is deployed to lower levels in the organization.

Kysyntä-toimitusketjun synkronointi epävarman kysynnän ja tarjonnan toimintaympäristössä

Kysynnän ja tarjonnan epävarmuudet ovat nykyisin arkipäivää useilla toimialoilla. Elämme epävarmuuden suhteen ennen näkemättömiä aikoja, minkä on arvioitu jatkuvan myös tulevaisuudessa. Yritysten tilauskannat ovat lyhyitä, ja tilaukset viivästyvät tai peruuntuvat kokonaan. Toisaalta tarjonnan epävarmuudet aiheuttavat asiakasyrityksille haasteita esimerkiksi toimitusmyöhästymisten muodossa. Tuotannon ollessa hajaantunut verkostoihin yksittäisten yritysten toiminta ja päätökset vaikuttavat toisten verkostoyritysten toimintaan. Tämän takia epävarmuuden aiheuttamista muutoksista ja poikkeamista tulisi tiedottaa kumppaniyrityksiä, jotta kaikki pysyisivät samalla kellotaajuudella. Operatiivisen ja taktisen tiedon jakaminen on nykyisissä toimitusketjuissa jo arkipäivää, mutta yritysten välisistä rajapinnoista löytyy edelleen kehitettävää. Riittävästä ei kiinnitetä huomiota vastaanottajan kykyyn ja tapaan hyödyntää informaatiota – varsinkaan muutostilanteissa. Ajan/nopeuden ollessa yhä tärkeämpi kilpailutekijä informaation ajoituksella on kriittinen merkitys kysyntä-toimitusketjujen kokonaissuorituskykyyn. Toisin sanoen, millä ajanhetkellä tietoa tulisi jakaa, jotta kumppani pystyisi hyödyntämään saamaansa tietoa mahdollisimman hyvin. Kysyntä-toimitusketjun synkronoinnilla tarkoitetaan tässä väitöstutkimuksessa nimenomaan aikatekijään keskittymistä yritysten välisessä päätöksenteossa ja informaation jakamisessa toimitusketjun kokonaissuorituskyvyn parantamiseksi. Tutkimus kytkeytyy toimitusketjukoordinoinnin tieteelliseen keskusteluun. Koordinointiteorian keskeinen osa ovat riippuvuussuhteet, joita johdetaan koordinointimekanismien avulla. Kysyntätoimitusketjun synkronointia on mallinnettu aikaisemmin VOP-OPP-mallin (Value Offering Point – Order Penetration Point) ja sen johdannaisten avulla. Näissä malleissa asiakasyrityksen kysyntäketju ja toimittajayrityksen toimitusketju ovat keskinäisessä riippuvuussuhteessa, jota johdetaan päätöksenteon synkronoinnin ja informaation jakamisen koordinointimekanismeilla. VOP-OPP-malli johdannaisineen eivät kuitenkaan huomioi epävarman toimintaympäristön vaikutuksia synkronointiin. Näissä malleissa informaation ainoana laatudimensiona tarkasteltava aikatekijä on liian kapea-alainen näkökulma synkronointiin epävarmassa ympäristössä. Lisäksi nämä mallit keskittyvät vain yksisuuntaiseen, kysyntälähtöiseen, synkronointiin jättäen huomioimatta tarjontalähtöisen synkronoinnin. Aikatekijä- ja kokonaissuorituskykypainotustensa takia VOP-OPP-malli tarjosi kuitenkin hyvän lähtöfilosofian uusien synkronointimallien kehittämiseen. Väitöstutkimus toteutettiin hypoteettis-deduktiivisena tapaustutkimuksena, jossa ensin luotiin kirjallisuuden perusteella uudet teoreettiset synkronointimalliehdotukset. Tämän jälkeen ehdotusten toimivuutta arvioitiin käytännön kysyntä-toimitusketjuissa. Tutkimuksen uutuusarvo liittyy kysyntä-toimitusketjun synkronoinnin keskeisten piirteiden systeemiseen mallintamiseen epävarmassa toimintaympäristössä. Kontribuutiona esitetään kysyntä-toimitusketjun synkronoinnin moniulotteinen kokonaismalli, joka sisältää koordinointimekanismeina päätöksenteon synkronoinnin, informaation läpinäkyvyyden sekä asiakas- ja toimittajapään joustot. Tiedon vaihtoa mallissa tarkastellaan kaksisuuntaisesti – kysyntä- ja tarjontalähtöisesti. Informaation laatudimensioina mallissa ovat informaation ajoitus, luotettavuus ja tarkkuus. Kokonaismalli sisältää kolme alimallia: Demand Visibility Point – Demand Penetration Point (DVP-DPP) on kysyntälähtöisen synkronoinnin malli, Supply Visibility Point – Supply Information Penetration Point (SVP-SIPP) on tarjontalähtöisen synkronoinnin malli ja Integroitu DVP-DPP - SVP-SIPP-malli kytkee edellä mainitut mallit toisiinsa. Näissä alimalleissa informaation eri luokkia ovat tilausta edeltävä, tilaukseen liittyvä, tilauksen jälkeinen ja sovitun toimitusajankohdan jälkeinen kysyntä- ja tarjontatieto. Käytännön hyödyntämisen näkökulmasta mallit toimivat ns. mentaalitason koordinointimekanismeina, joiden tarkoitus on herättää toimitusketjukumppanit tavoittelemaan kokonaissuorituskyvyn parantamista oman edun tavoittelemisen sijasta. Tutkimuksen päärajoitteena on sen keskittyminen ainoastaan kahdenvälisiin yhteistyösuhteisiin, mikä tarjoaa nykyisessä verkostoituneessa toimintaympäristössä varsin kapean kuvan käytännön synkronointihaasteisiin.

Supplier Delivery Quality Evaluation in Maintenance Supporting Spare Part Business

The focus of this thesis is the issues related to the operational purchasing level supply chain process. Due to this limitation, the physical product quality issues do not belong to the primary concerns of this thesis, whereas the bilateral processes between the supplier and the purchasing organizations are of interest. Also, the issues related to the delivery timing are excluded from the study. Because the perspective is on the issues involved in the supply chain operations, the bilateral communication issues between supplier representative and purchaser are also considered.

Corn and soybean yields as affected by cover crops and herbicide timing under no-tillage system

To achieve better results in the no-tillage system (NTS), it is important to properly manage the cover crop prior to planting by using herbicides, usually glyphosate. The effect of glyphosate on plant coverage is slow, and plants take a few days to die completely. Thus, when applying the herbicide on the same day of planting soybean or corn, cover crops are still alive and standing, causing initial shading on seedlings of the crop and delaying its establishment. Therefore, this study aimed to evaluate the effect of distinct cover crops and their timing of desiccation prior to planting soybean or corn, on crop yield and yield components. Two experiments were installed, one for soybean and another for corn. Each experiment consisted in combining three cover crops (Brachiaria brizantha, common bean or millet) chemically desiccated at two timings before planting the crop (15 or 0 days before planting) under no-tillage system (NTS). Experiments were installed in a completely randomized block design with five replications. Brachiaria brizantha produced the highest amount of biomass; common bean and millet as cover crops allowed higher soybean grain yields; herbicide application under common bean, millet and Brachiaria brizantha 15 days before planting soybean allowed higher crop grain yields; desiccation timing of common bean did not affect corn grain yield; Brachiaria brizantha should be desiccated 15 days before planting corn to allow maximum grain yield; when millet was used as a cover crop, glyphosate application at planting of corn allowed the highest grain yield.