Development of a species-specific polymerase chain reaction assay for Gardnerella vaginalis

The nucleotide sequence of the region between the 16S and 23S rRNA genes of the facultative anaerobic bacteriumGardnerella vaginalishas been determined, together with the 5′ proximal 500 nucleotides of the 23S rRNA gene. Regions suited for the development of specific, probe-confirmable polymerase chain reaction (PCR) assays were selected. PCR assays were evaluated with respect to sensitivity and specificity, the latter in comparison with a number ofG. vaginalisreference strains and closely related species likeBifidobacteriumspp. In an initial diagnostic study it appeared that the PCR test detectedG. vaginalisin 40% of women irrespective of their clinical status. Ten out of 11 patients suffering from bacterial vaginosis as defined on the basis of clinical parameters were carryingG. vaginalis

Evaluating the optimal portfolio of VRE capacity to be integrated into the power system A case study of Zambia

Republikken Zambia ligger i Sørlige Afrika. Som mange av sine naboland har landet en lav grad av elektrifisering, og under halvparten av befolkningen har tilgang til elektrisitet. I tillegg har det vannkraftdominerte Zambiske kraftsystemet vist seg å være sårbart for endringer i nedbør og tørke. De siste årene har lave nedbørsmengder, kombinert med økt etterspørsel etter elektrisitet, ført til et stort kraftunderskudd. Dette kraftunderskuddet har resultert i omfattende bruk av lastfrakobling. Økt integrasjon av variabel fornybar energi (VRE) har blitt foreslått som et tiltak for å diversifisere porteføljen av kraftverk i systemet. Fornybar energi kan potensielt øke forsyningssikkerheten og redusere kostnadene forbundet med elektrisitetsproduksjon. Denne avhandlingen evaluerer den optimale porteføljen av solkraft og vindkraft som kan integreres i det Zambiske kraftsystemet innen 2030. En framgangsmåte bestående av tre steg er benyttet. I det første steget analyseres historiske data fra databasen Renewables.ninja for å undersøke forventet variasjon i kraftproduksjon fra VRE og variasjoner i nedbørsmengde. Andre steg finner den optimale porteføljen av VRE gjennom simuleringer i en enkeltnode-modell av kraftsystemet i open-source softwaren PowerGAMA. Tredje steg simulerer lastflyten med den optimale porteføljen av VRE integrert i kraftnettet, for å identifisere potensielle flaskehalser i nettet. Resultatene viser at den årlige elektrisitetsproduksjonen fra sol- og vindkraft er relativt stabil, og negativt korrelert med nedbørsmengde. Elektrisitetsproduksjonen fra VRE er derfor vanligvis høyere i tørre år sammenliknet med våte år. I tillegg er produksjonen fra VRE høyest i den tørre sesongen. Dette støtter antagelsen om at økt kapasitet av VRE i kraftsystemet kan øke forsyningssikkerheten ved å diversifisere den vannkraftdominerte kraftporteføljen. Den optimale porteføljen av VRE blir i denne avhandlingen funnet som den porteføljen som minimerer systemkostnaden. En portefølje på 2100 MW, bestående av 1470 MW (70%) solkraft og 630 MW (30%) vindkraft resulterer i den laveste kostnaden, og er derfor identifisert som optimal. Dette tilsvarer en VRE-andel på 37% av forventet produksjonskapasitet i systemet i 2030. Bruker man en dynamisk verdsettelse av vann lagret i vannkraftreservoarer, eller et lavere startnivå for fyllingsgraden i reservoarer, endrer den optimale porteføljestørrelsen seg til henholdsvis 2700 MW og 3100 MW. Fordelingen mellom solkraft og vindkraft holder seg imidlertid på 70/30, som indikerer at dette kan være en optimal fordeling. Resultatene fra enkle lastflytanalyser viser at det eksisterende strømnettet kan håndtere integrasjonen av den optimale porteføljen av VRE, gitt den antatte plasseringen av nye kraftverk i nettet. I et teknisk perspektiv er det derfor fleksibiliteten til eksisterende vannkraftverk som vurderes som den mest kritiske faktoren for å øke andelen VRE i systemet. Studier av de tekniske konsekvensene av endrede operasjonsmønstre på vannkraftverk, som følge av innfasing av VRE, er derfor foreslått som tema for fremtidig arbeid.The Republic of Zambia is located in Southern Africa. Like many of its neighboring countries, the electrification rate is low, and less than half the population has access to electricity. Also, the hydropower-dominated Zambian power system has proven vulnerable to changes in rainfall and drought. In recent years, low rainfalls, combined with increasing electricity demand, has led to massive power shortages, resulting in load shedding. Integrating variable renewable energy (VRE) has been proposed as a measure for diversifying the generation portfolio. Renewable energy integration has the potential to increase energy security and lower system operational cost. This thesis evaluates the optimal portfolio of solar PV and wind power capacity to be integrated into the Zambian power system within 2030. A framework consisting of three steps is developed. First, the expected variations in VRE generation output and precipitation are investigated based on historical data from the Renewables.ninja database. Second, the optimal VRE portfolio is assessed through simulations in a single-node power system model in the open source software PowerGAMA. Finally, load flows are evaluated with the optimal portfolio of VRE integrated into the electricity grid, to identify potential grid constraints. The results suggest that annual electricity output from solar PV and wind power plants is relatively stable, and negatively correlated with precipitation. VRE generation is therefore usually higher in dry years, compared to wet years. Also, the electricity production from VRE is highest in the dry season. These findings support the fact that increasing the VRE penetration in the system could increase energy security by diversifying the hydro-dominated generation portfolio. The optimal VRE portfolio is found as the one minimizing the system cost. A portfolio of 2100 MW, consisting of 1470 MW (70%) solar PV capacity and 630 MW (30%) wind power capacity, provides the lowest cost, and is hence identified as optimal. This corresponds to a total VRE share of 37% of expected system generation capacity in 2030. When using a dynamic valuation of water stored in reservoirs, or a lower initial reservoir level, the optimal portfolio size changes to 2700 MW and 3100 MW, respectively. However, the distribution between solar PV and wind power capacity remains at 70/30, suggesting that this could be the optimal distribution of solar PV and wind power capacity. The results from brief load flow analyses show that the existing electricity grid is suited for integrating the optimal portfolio of VRE, given the assumed distribution of new power plants in the grid. From a technical perspective, the flexibility of existing hydropower plants is therefore considered the most critical factor for increasing the VRE penetration in the system. Evaluating the technical impacts on hydropower plants from changed operations due to VRE integration is suggested as future work

Causes of malocclusion in rabbits

Bettfel är en mycket vanlig sjukdom hos det tredje vanligaste sällskapsdjuret, kaninen, och kan vålla mycket lidande. Kaninen hör till de lagomorfa djuren, hardjuren, och deras fysiologi skiljer sig från många andra däggdjurs inklusive gnagarna. Deras tänder växer hela livet och de har även en mycket effektiv kalciummetabolism. Tänderna slits konstant av den gräsbaserade födan men trots det händer det ofta att tänderna börjar växa till onormala ställningar. Bettfel kan medföra att tänderna växer ut i över eller underkäken och bildar abscesser eller växer in i tårkanalen. Kindtänder kan bilda vassa taggar som ger skador på tunga och slemhinnor. Framtänderna kan i vissa extrema fall växa ut genom kinden. Det medför att kaninerna slutar äta, går ned i vikt och får sämre hygien. Vissa kaniner går med bettfel så länge att de svälter ihjäl. För att kunna förebygga och behandla bettfel krävs att man känner till hur sjukdomen uppstod. Syftet med denna litteraturgenomgång är att titta på olika tänkbara orsaker till bettfel. Litteraturen visar att det finns fler tänkbara orsaker till bettfel. De kan enkelt delas in i hereditära och förvärvade. Den troligaste hereditära orsaken till bettfel är mandibulär prognatism som ger kaninerna underbett tillskillnad från normala kaniner som har ett litet överbett. Underbettet gör att tänderna inte slits mot varandra. Det uppkommer mycket tidigt i livet. Förvärvade bettfel kan orsakas av många saker. Några som tas upp i litteraturen är abscesser, trauma, ålder och foderrelaterade där det senare tas upp som det mest troliga även om exakt orsak fortfarande är omdiskuterat. Det finns studier som pekar på att det är fodrets struktur som är den viktigaste faktorn och att det är för lite slitage som är orsaken till att tänderna blir långa. Vidare finns det studier som visar att strukturen är mindre viktig och att det är kalcium och D-vitamininnehållet som betyder mest. Det troligaste svaret är nog att flera faktorer kan medverka till förvärvade bettfel och att felutfodring är en viktig del. Det behövs mer och större studier i ämnet för att redogöra för de exakta mekanismerna bakom bettfel och hur man bäst förebygger dem. Avelsarbete skulle kunna få bort den andel bettfel som orsakas av mandibulär prognatism. I övrigt bör kaninens kost bestå av hö eller gräs för att förebygga förvärvade bettfel. Müsli bör undvikas helt.Rabbits are the third most common animal kept as pet. They are lagomorphs and have a unique teeth physiology. They also have constantly growing teeth and a very effective calcium metabolism. This complexity also makes rabbits vulnerable to dental diseases where malocclusion is one of the most common. Rabbits that suffer from malocclusion can have upper incisors growing around and into the upper jaw causing lesions. The roots of the teeth can grow into the jaw causing abscesses and cutting of tear-ducts. The cheek teeth can grow into the tongue causing severe pain. Sometimes rabbits stop eating and eventually die from starvation. Knowing the underlying cause is crucial to be able to treat affected rabbits properly. It is also necessary when trying to prevent malocclusion from arising from the beginning. Rabbits once treated for malocclusion are most likely to need teeth trimming the rest of the life so prevention is important. This study aims to bring up and discuss different theories on causes of malocclusion in rabbits. The literature brings up a vast number of possible causes to malocclusion. They are easily categorized in hereditary and acquired causes. More uncommon causes are abscesses in the face, trauma (rabbit being stepped on or rabbit chewing on the cage metal wires) and age. The most probable causes of acquired malocclusion are diet related. It’s either caused by too low calcium content, causing metabolic bone disease, or caused by lack of abrasiveness on the constantly crowing teeth. Hereditary is most probably caused by mandibular prognathism. Affected rabbits have a longer mandibular which gives the rabbit an under bite, rabbits normally have a small overbite, and the teeth don’t line up properly and don’t get enough attrition. The exact cause of malocclusion in rabbits is not enough investigated and more studies are needed. What can be concluded is that it is important that owners give their rabbits a diet that consists of a good quality hay to prevent malocclusion. Müsli is not recommended. Breeders can reduce the risk of malocclusion by selecting for breeding only rabbits that are known to not give offspring with mandibular prognathis

Evaluation of stifle joint conformation by computed tomo-graphy and association with osteochondrosis in wild boars and domestic pigs

Osteokondros (OC) är ett stort problem för slaktsvinsindustrin då det är mycket vanligt förekommande, och ger ekonomiskt bortfall för uppfödaren. Dessutom uppvisar djuren klinisk hälta till följd av ledsmärta. Störst problem har rapporterats hos ekologiskt uppfödda grisar. En orsak till att sjukdomen är svår att förstå är dess multifaktoriella patogenes som fortfarande inte är helt utredd i alla dess stadier. Det är visat att nekros av viktiga kärl i tillväxtbrosket hos unga djur är orsaken men vilka bakomliggande faktorer som är orsaken till kärlnekrosen är inte helt utrett. En teori som diskuterats är att nekrosen skulle bero på ledens anatomiska utseende vilket påverkar belastningen och då ger ett ökat tryck i vissa fokala vävnadsdelar av leden. Det har även diskuterats om en för snabb tillväxt skulle resultera i för stort tryck på det känsliga tillväxtbrosket och att därmed trauma skulle kunna vara orsaken till att små fokala nekroser i tillväxtbrosket förvärras och blir allvarliga skador. Vildsvin uppvisar inga eller mycket milda OC förändringar, men hos tamsvin är frekvensen mycket hög. Syftet med arbetet är att utreda om det finns anatomiska skillnader mellan vildsvin och tamsvin samt om det finns skillnader mellan tamsvin som fått olika OC-graderingar för att se om det finns ett samband mellan anatomisk konformation och OC-utveckling. Arbetet bestod av datortomografiska (DT) bilder av knäleden från 38 vildsvin och 42 tamsvin i åldern 6-18 månader respektive 5,5-6,5 månader. Tamsvinen var uppfödda under omständigheter som liknar KRAVs regler och vildsvinen frilevande och benen inskickade av jägare. I DT-bilder av benen standardiserades sedan benens position i bildhanteringsprogram och flera olika anatomiska längder och vinklar mättes i knäleden. Olika mätmetoder utprovades för att hitta den mest optimala. Alla leder graderades även på förekomst av OC med hjälp av DT. Mätvärden och gradering undersöktes med de statistiska testen ”Two sample T-test”, ”MannWhitney U test”, ”ANOVA one way” och ”Kruskal-Wallis test by ranks” för att se om det fanns några skillnader mellan vildsvin och tamsvin och för att se om det fanns något samband mellan anatomisk konformation och OC-grad hos tamsvin. Alla utom ett av tamsvinen hade OC, inga vildsvin hade OC och alla mätvärden skiljde sig mellan tam- och vildsvin. Ett mätvärde visade ett samband med allvarlighetsgraden av OC i tamsvin. Det värdet var tibias längd där allvarligare OC påvisades ju kortare benet var. Den höga OC-frekvensen i knäleden hos tamsvinen i arbetet stämmer väl överens med tidigare studier där tamsvin visar en mycket hög OC-frekvens i knä- och hasled medan OC hos vildsvin sällan rapporteras. De uppvisade skillnaderna i ledkonformation mellan tam- och vildsvin antyder ett samband mellan ledens anatomi och OC-graden vilket skulle kunna tyda på att ledens utformning kan påverka OC-utveckling. Resultatet att tibias längd var kortare hos tamsvin med allvarligare OC skulle också kunna förklaras med att OC-skadan påverkar benets längd och/eller ger sekundära ledförändringar till följd av en störd bentillväxt. Fler studier behövs för att helt verifiera resultatet och det vore av stort värde om det går att följa det levande djuret och registrera de tidiga förändringarna och hur OC-utvecklingen framskrider, för att särskilja orsaker från sekundära ledförändringar.SUMMARY Osteochondrosis (OC) is a major and common problem in the slaughter pig industry and results economic loss to the breeder. Affected animals exhibit clinical lameness due to joint pain and the frequency of OC is reported to be highest in organically reared free-range pigs. One reason why the disease is difficult to understand is its multifactorial pathogenesis which is still not fully understood. It has been shown that necrosis of important blood vessels in the growth cartilage of young animals is a cause of OC but the underlying factors that are the cause of the vascular necrosis are not completely understood. One theory is that the necrosis might depend on the anatomical shape of the joint, which affects the loading and could give rise to increased pressure in certain focal regions of the joint. It has also been discussed whether excessively rapid growth rates could result in excessive pressure on the sensitive growth cartilage and that trauma could be the reason why small focal necrosis in the growth cartilage worsens and becomes serious damage. Wild boars show no or only very mild OC changes, but in domestic pigs the frequency of OC is very high. The purpose of this work is to investigate whether there are anatomical differences between wild boars and domestic pigs and whether there are differences between domestic pigs that have received different OC grades to see if there is a connection between anatomical conformation and OC development. The work consisted of computer tomographic (CT) images of the knee joint from 38 wild boars and 42 domestic pigs aged 6-18 months and 5.5-6.5 months. The domestic pigs were bred under circumstances similar to KRAV's guidelines. The wild boars was free-living and the joints were collected by hunters. In CT images of the legs, the position of the legs was standardized with image processing software and several different anatomical lengths and angles were measured in the knee joints. Different measurement methods were tested to find the most optimal method. All joints were also graded regarding the presence of OC using the CT images. Measurements and grades were examined with the statistical tests "Two sample T-tests", "Mann-Whitney U test", "ANOVA one way" and "Kruskal-Wallis test by ranks" to see if there were any differences between wild boars and domestic pigs and to see if there was any correlation between anatomical conformation and the severity of OC degree in the domestic pig. All but one of the domestic pigs had OC, no wild boar had OC and there were statistical differences between all measured values between domestic pig and wild boar. The length of the tibia showed a correlation with the severity of OC in domestic swine, with more severe OC was detected in domestic pigs with shorter tibias. The high OC frequency in the knee joint of the domestic pigs in the work is well in line with previous studies where domestic pigs show a very high OC frequency in the knee and hock while OC in wild boar is rarely reported. The differences detected in conformation between the wild boars and domestic pigs suggests a connection between the joint's anatomy and the OC degree and might indicate that the joint conformation can affect OC development. The finding that domestic pigs with more severe OC have shorter tibias might be explained by the fact that the OC damage also affects the length of the tibia and / or that as a result of the disease in the joint there is disturbance of the tibia bone growth. More studies are needed to fully verify the outcome and it would be of great value if it is possible to follow the live animal and record the early changes and how the OC development progresses, to distinguish causes from secondary joint changes

Microbacterium luticocti sp. nov., isolated from sewage sludge compost

Strain SC-087BT, isolated from sewage sludge compost during a study of bacterial diversity in composts, was characterized. The isolate was a Gram-positive, short rod that was motile, catalase- and oxidase-negative and able to grow at 27–45 6C, pH 5.5–9.7 and in up to 10% NaCl. The peptidoglycan was of the B2b type, containing the characteristic amino acids ornithine, homoserine and hydroxyglutamic acid. The muramic acid residues of the peptidoglycan were partially glycolylated. The major cell-wall sugar was mannose; traces of xylose were also detected. The predominant fatty acids, comprising more than 70% of the total, were anteiso-C17 : 0 and anteiso-C15 : 0, the major respiratory quinone was menaquinone-12 (MK-12) and the G+C content of the genomic DNA was 72 mol%. Based on analysis of the 16S rRNA gene sequence, the closest phylogenetic neighbours of strain SC-087BT were members of the family Microbacteriaceae, showing sequence similarity values of around 96% with members of the species Microbacterium barkeri (96.0 %), Microbacterium gubbeenense (95.6 %) and Microbacterium indicum (95.7 %). The chemotaxonomic and phenotypic traits analysed supported the inclusion of this strain within the genus Microbacterium and the proposal of a novel species. The name Microbacterium luticocti sp. nov. is proposed and the type strain is SC-087BT (5DSM 19459T5CCUG 54537T)

Multilocus sequence typing supports the hypothesis that Ochrobactrum anthropi displays a human-associated subpopulation

<p>Abstract</p> <p>Background</p> <p><it>Ochrobactrum anthropi </it>is a versatile bacterial species with strains living in very diverse habitats. It is increasingly recognized as opportunistic pathogen in hospitalized patients. The population biology of the species particularly with regard to the characteristics of the human isolates is being investigated. To address this issue, we proposed a polyphasic approach consisting in Multi-Locus Sequence Typing (MLST), multi-locus phylogeny, genomic-based fingerprinting by pulsed-field gel electrophoresis (PFGE) and antibiotyping.</p> <p>Results</p> <p>We tested a population of 70 <it>O. anthropi </it>clinical (n = 43) and environmental (n = 24) isolates as well as the type strain <it>O. anthropi </it>ATCC49188^Tand 2 strains of <it>Ochrobactrum lupini </it>and <it>Ochrobactrum cytisi </it>isolated from plant nodules. A Multi-Locus Sequence Typing (MLST) scheme for <it>O. anthropi </it>is proposed here for the first time. It was based on 7 genes (3490 nucleotides) evolving mostly by neutral mutations. The MLST approach suggested an epidemic population structure. A major clonal complex corresponded to a human-associated lineage since it exclusively contained clinical isolates. Genomic fingerprinting separated isolates displaying the same sequence type but it did not detect a population structure that could be related to the origin of the strains. None of the molecular method allowed the definition of particular lineages associated to the host-bacteria relationship (carriage, colonisation or infection). Antibiotyping was the least discriminative method.</p> <p>Conclusion</p> <p>The results reveal a human-associated subpopulation in our collection of strains. The emergence of this clonal complex was probably not driven by the antibiotic selective pressure. Therefore, we hypothesise that the versatile species <it>O. anthropi </it>could be considered as a human-specialized opportunistic pathogen.</p