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  • 151.
    Eriksson, Olof
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Ekologisk botanik.
    Niva, Mikael
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Caruso, Alexandro
    Use and abuse of reindeer range2007Bok (Övrigt vetenskapligt)
    Abstract [en]

    In consequence of variations in geology and soils, in climate, and in its wide extent in longitude, latitude and altitude, the Scandinavian mountain chain exhibits major variations in natural conditions. Nature is constantly influenced by processes that include both natural forces and human activity.

    In the early 1990s, there was an intense media debate about current damage to the montane vegetation, which many believed they could observe.

    In 1992, the World Wide Foundation for Nature, WWF, invited representatives of responsible authorities, reindeer-husbandry interests, voluntary conservation bodies and interested researchers to a conference, which, somewhat erroneously, came to be called the 'Reindeer grazing conference', but which included a spectrum of factors that can affect the montane vegetation.

    One result of this conference was that, in 1993, WWF initiated a research project, extending over several years, intended to provide information about temporal changes in montane vegetation.

    Experimental areas distributed along the Swedish mountain chain were selected: the southernmost are on Fulufjället in Dalama, and the northernmost are ea. 15 km S of Tavvavuoma in Swedish Lapland. (Some placenames are given in modern North-Saamish spelling in Appendix 2) The vegetation types studied were Grass heath, Meadow with low herbs, Dry heath, Birch forest-heath type with lichens and Birch forest-heath with mosses. These cover all major montane areas and are important grazing areas for reindeer.

    At all study sites, six adjacent plots were selected, half of which were fenced to deny access to larger herbivores, and half were left open for grazing by all herbivores. The composition of plant communities in the field, bottom and tree layer in plots was estimated in 1995-96, and re-estimated three to four years later.

    Generally, marginal or no effects of enclosure were seen on the vegetation communities, and there were no differences between vegetation types.

    Up to the end of the 19th century, travellers in the montane region, both Saami and outsiders, ocularly assessed the plant cover. As a rule, they reported a good supply of reindeer fodder plants, especially lichen species.

    From the end of the 19th century, there began to be observations of severely denuded lichen cover, especially in areas exposed to a veritable invasion of Saami and reindeer from the north-Norwegian and north-Finnish reindeer grazing areas. Incomers from those areas introduced an extensive form of reindeer husbandry, developed to suit conditions on the Finnmarksvidda and in northernmost Finland, where large reindeer herds could readily find grazing on well-demarcated headlands and islands during the snowfree season, without much supervision.

    The conflicts of interest between the incomers, and indigenous Saami who wished to carry on an intensive form of reindeer husbandry, with closely supervised herds, were great. From the beginning of the 20th century, state interventions, in the form of commissions of enquiry and field surveys, were instituted. Their aim was to resolve existing conflicts, to ensure a sustainable access to grazing, and satisfactory profitability. The results cannot be said to have been satisfactory.

  • 152.
    Eriksson Röhnisch, Kajsa
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Purification and Technical Application of a Serine Protease Inhibitor from Solanum tuberosum2016Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
  • 153.
    Eriksson Röhnisch, Kajsa
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Bygdén, Evelina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Dahlberg, Jenny
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Nerén, Isabelle
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Rylander, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Wärn, Caroline
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Östergren, Tiolina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Samband mellan virulensgener och VTEC-infektioner: Riskklassificeringssystem för VTEC2013Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
  • 154.
    Erkers, Julia
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Towards automatic smartphone analysis for point-of-care microarray assays2016Självständigt arbete på avancerad nivå (yrkesexamen), 300 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Poverty and long distances are two reasons why some people in the third world countries hasdifficulties seeking medical help. A solution to the long distances could be if the medical carewas more mobile and diagnostically tests could be performed on site in villages. A new pointof-care test based on a small blood shows promising results both in run time and mobility.However, the method still needs more advanced equipment for analysis of the resultingmicroarray. This study has investigated the potential to perform the analysis within asmartphone application, performing all steps from image capturing to a diagnostic result. Theproject was approach in two steps, starting with implementation and selection of imageanalysis methods and finishing with implementing those results into an Android application.A final application was not developed, but the results gained from this project indicates that asmartphone processing power is enough to perform heavy image analysis within a sufficientamount of time. It also imply that the resolution in the evaluated images taken with a Nexus 6together with an external macro lens most likely is enough for the whole analysis, but furtherwork must be done to ensure it.

  • 155.
    Esberg, Johannes
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    HABITATSPREFERENSER HOS SVARTMUNNAD SMÖRBULT (NEOGOBIUS MELANOSTOMUS)2017Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
  • 156.
    Euler, Nora
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    CSF biomarkers related to sleep, cognition and neuroinflammation in patients with Kleine Levin Syndrome2018Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Kleine Levin Syndrome (KLS) is a hypersomniac disease of episodic nature that affects only 1-5 per million individuals globally. In addition to extensive periods of sleep (> 20 hours) patients experience a wide range of symptoms during an episode, which occur approximately 1-12 times a year with a median of 10 days. The etiology and pathophysiology of the disease is unknown. Diagnostic criteria (The International Classification of Sleep disorders, third addition) rely solemnly on symptomatic characteristics. Misdiagnosis is unfortunately common. The potential of using hypocretin-1, amyloid-beta/tau and the IgG index in the CSF as potential disease biomarkers was investigated. Measurements were taken during the asymptomatic and/or symptomatic phase of the disease. All values were within the normal range. Lower hypocretin-1 values were observed in the asymptomatic phase compared to the symptomatic phase in two of the three patients, although not statistically significant. 

  • 157.
    Evasdotter, Liselott
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Restoration of a Rich Fen by Top Soil Removal: Temporal and Spatial Responses among Vascular Plants, Bryophytes and Land Snails during 15 years2011Självständigt arbete på avancerad nivå (magisterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Rich fens are calcareous and nutrient poor wetlands with a rich flora of orchids, sedges and mosses. As many as one hundred plant species are rich fen specialists. Many wetlands have been drained historically, and transformed to agricultural land or production forests. Today rich fens cover only 2-3% of the total mire area in Sweden. Rich fen is a rare and valuable habitat also from a European perspective and is protected in the Natura 2000-network. To increase and maintain the biodiversity and ecosystem services rich fens can offer, it is important to increase the rich fen area by restoration and management. Rich fen restoration can be carried out in different ways. In this report the restoration method of top soil removal is investigated. The method has never been tested before in Sweden and therefore it is important to evaluate the suitability of the method for further conservation work.

     

    Before restoration, the study area had been drained, used as arable land and pasture, and finally become abandoned and overgrown by tall eutrophic herbaceous vegetation. An excavator dug away the layer of nutrient rich top soil and then the site was left for spontaneous development. Adjacent to the restored area, there is a small remnant of rich fen. Monitoring of the restored area was performed during the first five years after the restoration. I repeated the monitoring after ten years, and analyzed the long-term succession of plants and snails, in comparison with the status in the reference fen.

     

    The vegetation in the restored parts is approaching the one in the reference fen. For example, the number of rich fen specialists has increased steadily. However, the colonization of bryophytes is slow. They cover at most 20 % in the restored parts, while 80 % in the reference fen, possibly because of dispersal limitation and the fact that the restored area is drier than the reference fen. More species of herbs can be found in the restored parts than in the reference fen. Another difference is the high cover of bare soil in the restored areas, compared to none in the reference fen. Some trees and bushes are growing in the area, primarily birch (Betula pubescens) and different species of Salix. The land snails have successfully colonized the restored areas. After two years the same number of species was found in the restored area, as in the reference fen. The total number of species found in the restored areas was 26, compared to 29 in the reference fen, among them three rare rich fen indicator species.

     

    The results show how the restored site has developed from bare mineral soil to a rich fen site, approaching the species composition of the reference fen. Several species of rich fen specialists among vascular plants, bryophytes and land snails have established in the restored areas. The small rich fen close to the restored area functions as a source from where plants and animals can spread. Overall the restoration shows very positive results, going from bare soil to rich fen vegetation in only ten years.

  • 158.
    Everitt, Turid
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Karolinska Institutet, Medical Biochemistry and Biophysics/SciLifeLab.
    Utilizing data from a new, quantitative ChIP-sequencing method to investigate the dynamics of histone H3.32018Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    DNA is a key component of almost all cells, but it is not the sole determinant of the cellular functions and features. A great number of histones, transcription factors and other proteins interact with the DNA, regulating fundamental processes such as DNA accessibility and gene expression. Perturbations of these interactions are associated to a wide range of diseases. An example is the histone variant H3.3, which is normally involved in prevention of genomic rearrangements during mammalian development. Mutations in the H3.3 gene have been shown to be related to pediatric brain cancer forms. Studying this histone variant and other protein-DNA interactions is important in order to understand cellular processes as well as causes of diseases. This has commonly been done through a sequencing method called ChIP-seq, which however does not normally capture the dynamics of the interactions. Therefore a new method called MINUTE-ChIP has been developed, which in combination with a special type of pulse-chase experiment adds a time dimension to the analyses. In this project, data from this new method has been analyzed in order to investigate the dynamics of histone H3.3. In addition to calculating the rates of incorporation and release from the DNA, tools for visualizing the data in interactive plots have also been developed. These calculations and tools facilitate the interpretation of the histone H3.3 data and can in the future be used for analyzing data generated by similar experiments for other chromatin factors.

    Publikationen är tillgänglig i fulltext från 2020-01-01 12:08
  • 159.
    Fanny, Törnkvist
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    SKÖTSELPLAN FÖR NATURRESERVATET HELGES HAGE2014Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    The aim of this study was to prepare a management plan for the future nature reserve Helges hage in Eksta, Gotland. The area has a long continuity as a woodland and has been used as pasture and for selective logging. This type of forestry practices creates a dynamic, heterogeneous landscape with a rich biodiversity. In Helges hage many unusual soil fungi and two endangered grass species have been found. Grazed woodlands is one of the habitats that has decreased most in Sweden the last century as a result of the modern forestry. Helges hage has not been grazed since the 1960 and the forest understory is now overgrown by shrubs and saplings. In order to preserve the natural values of a grazed woodland it is required to reintroduce grazing and that parts of the forest is thinned in order to create a less dense forest with more light reaching the ground.

  • 160.
    Fei, Mengjie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Effect of light regime on Drosera Rotundifolia2015Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
    Abstract [en]

    The perennial carnivorous plant Drosera rotundifolia with its red leaves has interested scientists for ages. The red colour of its leaves was for long time believed to help in luring prey insects, but later studies have indicated that it might also function as an alert to pollinators and to avoid over capture of pollinators. Either of the functions is important for the carnivorous investment of D. rotundifolia. As the red colour in the leaves is determined by the accumulation of the UV-positive compound anthocyanin, it is possible that the leaf colouration is affected by the surrounding light regime. Therefore, it would be useful to understand the function of the red colouration and how it relates to the local light regime. In my study, leaf colour varied a lot under different light regimes, however with no significant pattern along light gradient. Leaf size exerted an effect on leaf colour, as smaller leaves were redder. In addition, effects of light on morphological traits were detected. With an increase of sun exposure, D. rotundifolia had higher specific leaf dry mass. Plants had larger total leaf area on plots with intermediate vascular plant vegetation height. Exposure to light and insects and nutrient conditions indicated by vascular plant height could in combination affect the growth of leaves of D. rotundifolia. Also the competition of nutrient by Sphagnum fuscum (Schimper) H. Klinggräff could be one of the factors influencing the leaf area of D. rotundifolia. Thus, this study found an effect of light on morphological traits of D. rotundifolia, but lacked evidence on colouration. Further studies could be carried out with a more detailed description of the light regime when illustrating the light effect on colouration of leaves of D. rotundifolia.

  • 161.
    Fernberg, Jenny
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Growth Dynamics, Antibiotic Susceptibility and the Effect of Sublethal Ciprofloxacin Concentrations in Susceptible and Resistant Escherichia coli in Biofilm2019Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Instead of planktonic growth in nature, many species of bacteria form biofilm to survive in harsh conditions. Although many chronic bacterial infections are caused by bacterial species in a biofilm lifestyle, previous research has focused on studying antibiotic resistance in planktonic growth. Here we used a modified MBEC assay, i.e. biofilm growth on pegs, to determine Escherichia coli biofilm inhibitory concentrations (BIC) of ciprofloxacin, streptomycin and rifampicin and to study the minimal selective concentration (MSC) for ciprofloxacin in E. coli biofilm. We could observe high inhibitory concentrations for all antibiotics in the biofilm pre-formed in media without antibiotics compared to the biofilm formed in antibiotics. We also show preliminary result indicating that sublethal concentrations of ciprofloxacin lead to the selection of ciprofloxacin resistant mutants in biofilm and that the selection level is lower than what was observed in planktonic growing E. coli. With more knowledge in how the biofilm formation precedes in different antibiotic settings, the treatment for chronic biofilm infections used today could be evaluated and changed so that the infections could be eradicated.

  • 162.
    Ferrer, Samuel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    STAIRS: Data reduction strategy on genomics2019Självständigt arbete på avancerad nivå (magisterexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Background. An enormous accumulation of genomic data has been taking place over the last ten years. This makes the activities of visualization and manual inspection, key steps in trying to understand large datasets containing DNA sequences with millions of letters. This situation has created a gap between data complexity and qualified personnel due to the need of trading between visualization, reduction capacity and exploratory functions, features rarely achieved by existing tools, such as SRA toolkit (https://www.ncbi.nlm.nih.gov/sra/docs/toolkitsoft/), for instance. A novel approach to the problem of genomic analysis and visualization was pursued in this project, by means of STrAtified Interspersed Reduction Structures (STAIRS). Result. Ten weeks of intense work resulted in novel algorithms to compress data, transform it into stairs vectors and align them. Smith–Waterman and Needleman–Wunsch algorithms have been specially modified for this purpose and the application brought about statistical performance and behavioural charts.

  • 163.
    Filek, Klara
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Contact-dependent growth inhibition in Escherichia coli EC932018Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Microorganisms live in complex communities and interact either through secreting soluble molecules or by delivering effectors in a contact dependent manner. Microbial interactions range from cooperative to competitive. Contact-dependent growth inhibition (CDI), discovered in Escherichia coli EC93, is becoming increasingly studied, as this mode of interaction seems to be widespread among proteobacteria. CDI is mediated by cdiBAI genes which encode for a two-partner secretion system; i.e. CdiB is an outer membrane protein that transports CdiA to the surface of the cell. CdiA can interact with a specific receptor on a target cell and deliver a toxin localized in its C-terminal domain to the target cell. CdiI is a small immunity protein that neutralizes the toxic effect of CdiA toxin. Recently, evidence from our research group has shown that E. coli EC93 harbours two cdi loci. The first cdi locus has been extensively studied but the role of second locus remained unknown. In this study we wanted to elucidate the activity and the role of second E. coli EC93 cdi locus in intra-strain bacterial interactions. Bacterial competitions of E. coli EC93 wild type versus E. coli EC93 targets that had deletions for one or both cdi loci showed that the second locus is indeed active in inhibiting the targets, albeit to a lesser extent than the first. The toxic activity of the second cdi-locus was neutralized specifically by the second immunity protein. The expression of both these systems is higher under carbon starvation conditions than in nutrient rich conditions. Unfortunately, we could not elucidate the mechanism of toxicity for the second cdi locus toxin. Taken together, our results show that E. coli EC93 actively uses both of its cdi loci during bacterial interactions and that these systems are more active during stressful conditions.

  • 164.
    Flinkfeldt, Linnea
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    High throughput pipeline for rapid antibiotic susceptibility testing and ID of bacteria from blood cultures2019Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Rapid and accurate species identification and antibiotic susceptibility testing are of great importance for patients with sepsis and to stop over- and misuse of antibiotics contributing to antibiotic resistance. QuickMIC™ is a rapid antibiotic susceptibility testig system based on a microfluidic technology solution developed by Gradientech that measure MICs on bacteria from positive blood culture bottles. By combining QuickMIC™ with a rapid system for detection and identification, the time to detection, identification and antibiotic susceptibiolity testing could be shortened with days compared to pipelines used today which could mean the difference of life and death for patients. The T2Bacteria® panel and T2Dx® instrument developed by T2 biosystems is an FDA-cleared test for rapid detection and identification of bacteria from whole blood based on magnetic molecular resonance technology. The time to result of the T2Dx® instrument is 3-4 hours and the time to result for QuickMIC™ is 2-4 hours. In this project, the possibilities and benefits of such a pipeline have been studied by comparison to a pipeline typically used today. Time, accuracy and practical aspects have been investigated during the project and the results are promising for future further studies.

  • 165.
    Fogelström, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    DNA barcoding of freshwater fishes in Matang, Malaysia2015Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
  • 166.
    Forngren, Sofia
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Uppsala universitet, Humanistisk-samhällsvetenskapliga vetenskapsområdet, Fakulteten för utbildningsvetenskaper, Institutionen för pedagogik, didaktik och utbildningsstudier.
    Kognitiv neurovetenskap i skolan2019Självständigt arbete på avancerad nivå (yrkesexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    Utvecklingen av nya metoder för att studera hjärnans struktur och funktion har lett till ny förståelse om kognition. Inom kognitiv neurovetenskap studeras sambandet mellan hjärnan och tänkandet, där inlärning ingår. Hur inlärning fungerar är väsentligt för att utbildning tillgodogörs. Denna litteraturstudie är baserad på delar av den kognitiva neurovetenskapen som berör olika aspekter av vad skolan och lärare kan ha nytta av för att främja elevers inlärning. Hjärnans olika funktioner kan ofta kopplas till olika regioner i hjärnan, och hippocampus samt främre hjärnbarken är två viktiga regioner för både minnesbildning samt framplockning av minnen. Främre hjärnbarken är dessutom den del av hjärnan där de exekutiva funktionerna som har stor betydelse för inlärning är lokaliserade. En viktig förutsättning för inlärning är att hjärnan är plastisk, den kan förändras både strukturellt och biokemiskt. Hjärnan är plastisk hela livet, men fram tills 25-årsåldern då hjärnan fortfarande utvecklas sker större förändringar, vilket har betydelse för såväl inlärning som beteende. Stress kan genom bland annat synaptisk plasticitet påverka inlärning på ett negativt sätt över tid, samtidigt som det även direkt hämmar vår förmåga både att lära oss och att minnas. Till exempel kan stress hämma våra exekutiva funktioner, varav arbetsminnet är en sådan funktion som är betydande för inlärning. Många ungdomar idag lider av psykisk ohälsa, och upplevelser av negativa emotioner bidrar till att hjärnan och kroppen upplever stress. För att öka elevers uppmärksamhet är det därför viktigt med ett klassrum där det är lugnt och alla känner sig trygga. Elevers uppmärksamhet och inlärning kan även påverkas genom motivation, som i hjärnan är lokaliserat i en del av belöningssystemet. Det är även förmågan att lära sig genom återkoppling, som är ett effektivt sätt att skapa inlärning. Hjärnan lär sig genom att associera ny information till tidigare lagrad kunskap, vilket är bra att tänka på framförallt när ny kunskap ska presenteras. Bra sömn och fysisk aktivitet är två faktorer som är viktiga för minnesbildningen men som kan kännas svåra att påverka som lärare, samtidigt som det inte är helt omöjligt. Även mindfulness kan implementeras och bidra till både bättre välmående och inlärning. Den kognitiva neurovetenskapen kan på flera sätt tillämpas i skolan för att främja elevers inlärning.

  • 167.
    Forngren, Sofia
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Vad säger neurobiologisk forskning om motivationens betydelse för inlärning?2018Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    Kan motivation till att lära sig gå att se genom avbildningar av hjärnan? Finns det någraneurobiologiska stöd för att det dessutom skulle kunna påverka minnesbildning? Tidigareforskning har visat att aktivering av belöningssystemet och ökade nivåer av signalsubstansendopamin kan gynna minnesbildning. I denna översiktsartikel behandlas studier som berörmotivation ur olika psykologiska aspekter och hur det påverkar det deklarativalångtidsminnet. Olika hjärnavbildningsmetoder där dopaminerga regioner och hippocampushar varit centrala, tillsammans med olika inlärningsuppgifter och psykologiska tester talar föratt motivation är en viktig faktor för inlärning. Dessutom visar flera av studierna att positivåterkoppling har en bättre effekt på inlärning jämfört med negativ återkoppling.

  • 168.
    Forslund, Annica
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Investigation of developmental neurotoxic effects of exposure to a combination of methylmercury and chlorpyrifos2018Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
  • 169.
    Forsskåhl, Sophia Katarina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Göteborg Universitet, Biomedicinska institutionen, Avdelningen för mikrobiologi och immunologi.
    Altered expression of inflammasome components in inflammatory bowel disease2019Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
    Abstract [en]

    The inflammasome complex is a multiprotein complex that may play a role in the pathogenesis of inflammatory bowel disease (IBD) by secreting the inflammatory cytokines interleukin (IL)-1β and IL-18, and inducing pyroptosis, as a response to signals through several inflammasome sensors.

    This study looked at the expression of several inflammasome components in the ileum and colon of patients suffering from IBD. The inflammasome sensors NLRP1, NLRP3, AIM2 and pyrin were upregulated in whole intestinal tissue of IBD patients, particularly in the colon. NLRP6 expression was increased in the colon of Crohn's disease patients, but not ulcerative colitis patients relative to colon of controls, and was reduced in the ileum of Crohn's disease patients compared to control ileum. Expression of caspase-1 and IL-1β, but not IL-18, were also increased in ileum and colon tissue from Crohn's patients.

    To identify the cell type where inflammasome expression was altered in Crohn’s disease, transcription of inflammasome subunits in intestinal tissue enriched for epithelial cells or lamina propria (LP) cells was analysed. These analyses indicated that LP cells have greater expression of the inflammasome sensors NLRP1, NLRP3, AIM2 and pyrin relative to epithelial cells, both during disease and in control tissue. Moreover, LP cells from Crohn’s patients have higher expression level of NLRP1, AIM2 and pyrin than LP cells from controls. In contrast the inflammasome sensor NLRP6 was more highly expressed by epithelial cells relative to LP cells in general, and NLRP6 expression in LP cells from IBD patients was lower than that observed in LP cells from controls.

    The observed differential expression of inflammasome components in controls versus IBD intestine and in different cellular fractions of intestinal tissue highlight the importance of understanding the role of the inflammasome in IBD and hints at the possibility of targeting the inflammasome pathway as a future treatment strategy.

  • 170.
    Fortier-Dubois, Étienne
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Late Devonian vertebrates from Siberia: a synchrotron microtomography study of bone bed material2016Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    This is an investigation of new vertebrate fossil material from the Late Devonian locality of Ivanovka, Uryup River, Siberia. This bone bed material, circa 375 million years in age, represents a unique opportunity to fill a gap in our understanding of Late Devonian diversity, biogeography, and vertebrate evolution: Siberia, at the time, was an independent continent, and yet its fauna remains virtually unknown in comparison with the other paleocontinents, Euramerica and Gondwana. Using synchrotron microtomographic scanning, a non-destructive technique that has never, to our knowledge, been applied to bone bed material, we obtained 3D image stacks that were then modelled to yield triangle meshes representing the bones in three dimensions. These meshes could then be identified, described, and interpreted. Many of the discovered bones belong to the poorly known genus Megistolepis Obruchev 1955, potentially allowing a radical increase in knowledge regarding this taxon. Other material includes lungfish and possible fragments of limbed tetrapods, though the evidence of the latter is scarce. A discussion of the advantages and disadvantages of synchrotron microtomography for the study of bone bed material concludes the paper. 

  • 171.
    Fransson, Lina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Fine scale habitat and movement patterns of javan slow loris (Nycticebus javanicus) in Cipaganti, West Java, Indonesia2018Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Today biodiversity is rapidly decreasing and an increasing number of threatened species live in modified and human dominated landscapes. Therefore it is essential to learn more about how species cope with the changes of their habitat. The focus of this study lies on a primate species, the critically endangered Javan slow loris (Nycticebus javanicus), endemic to the densely populated island of Java, Indonesia.  In cooperation with the Little fire face project in West Java, I used a step selection function (SSF) framework, to understand how landscape structure affects the movement of Javan slow lorises within a fragmented mountain-agroforest landscape of Cipaganti, West Java.

    To investigate the movement and fine scale habitat selection of slow lorises I used one hour locations of 6 radio-collared slow lorises. The habitat and vegetation of observed and random steps was investigated in multiple variables such as presence of food trees and signs of human disturbance. For the analysis I paired observed steps (1h relocations) with 3 random habitat locations and used a conditional logistic regression to parameterize the SSF, which represents the probability of a focal slow loris to select a given step as a function of the habitat and vegetation factors surveyed. In average the slow lorises travelled about 450 m each night and most frequently they used a step length of about 0 – 50 m.

    My result reveals that slow lorises fine scale habitat selection is positively influenced by the presence of trees and tree trunk cover (indirect increasing the canopy cover and connectivity). They are also to a high extent positively affected by the presence of a feeding tree species, Calliandra calothyrsus. Surprisingly slow lorises selected steps associated with a higher number of fields (fields may indicate an increased biodiversity within the location). The results also indicate that slow lorises are limited in their movement by the presence of fields or rivers, which indicates that slow lorises are negatively influenced in their movement by a declining ability to move and forage within Cipaganti. I found no significant differences between sexes in their distance travelled.

    The recommendation for future conservation of slow lorises in Cipaganti is to prevent further habitat loss and fragmentation through activities that protect or maintain the present suitable slow loris habitat. Further research is needed to increase the knowledge of these primates’ abilities to live in this modified landscape. 

  • 172.
    Fransson, Lina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Äggläggningspreferenser för honor av väddnätfjäril, Euphydryas aurinia, på området Bälsalvret, Gotland2015Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    This study aims to get a better understanding of the oviposition-behaviour of the butterflyMarsh Fritillary (Euphydryas aurinia), in the area Bälsalvret on the Island of Gotland. Thestudy may provide helpful information to aid the conservation of the species in the area andalso provide overall knowledge about the female’s preferences when it comes to choosingmicrohabitat and host plant for their eggs.The analysis of the microhabitat preference for oviposition by the Marsh Fritillary showedthat eggs were predominantly laid on large-sized host plant individuals with a warmermicroclimate; with a preference for the rosette diameter, the length and the width of the leafand the number of Succisa pratensis individuals in the vicinity. This indicates that thefemale’s priority is to place the eggs at the most optimal place for their offspring’s survivaland growth.

  • 173.
    Fransson, Lina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Äggläggningspreferenser för honor av väddnätfjäril, Euphydryas aurinia, på området Bälsalvret, Gotland2015Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    This study aims to get a better understanding of the oviposition-behaviour of the butterfly Marsh Fritillary (Euphydryas aurinia), in the area Bälsalvret on the Island of Gotland. The study may provide helpful information to aid the conservation of the species in the area and also provide overall knowledge about the female’s preferences when it comes to choosing microhabitat and host plant for their eggs.

    The analysis of the microhabitat preference for oviposition by the Marsh Fritillary showed that eggs were predominantly laid on large-sized host plant individuals with a warmer microclimate; with a preference for the rosette diameter, the length and the width of the leaf and the number of Succisa pratensis individuals in the vicinity. This indicates that the female’s priority is to place the eggs at the most optimal place for their offspring’s survival and growth.

  • 174.
    Fredriksson, Lennie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Clustering of DNA sequence reads from repeat regions using defined nucleotide positions (DNPs)2010Studentarbete övrigt, 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Sequencing genomes with a high frequency of repeat regions is a difficult task.The aim of the project was to develop an algorithm to speed up the sequencing process of highly repetitive genome. By using specific differences between the repeats called defined nucleotide positions (DNPs), cluster DNA sequence reads into contigs. The strategy used in the development of the algorithm resulted in a quite complex algorithm. Test runs of the algorithm showed that there is still work to be done to get a desirable result.

  • 175.
    Fridman, Belinda
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Process development for the production of a therapeutic Affibody® Molecule2014Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Recently HER3, member of the epidermal growth factor receptor family (EGFR), has been found to play a crucial role in the development of resistance towards inhibitors that are given to patients with HER1- and HER2-driven cancers. As HER3 is up-regulated or over-activated in several types of human cancers, it is of outmost importance that new innovative drugs target its oncologic activity.

    The Affibody® Molecule Z08698 inhibits the heregulin induced signalling of HER3 with high affinity (KD~50 pM). As the Affibody® Molecule is small, has high solubility and outstanding folding kinetics, an effective penetration of tumour tissue is suggested together with a rationalized manufacturing process. Further coupling to an albumin binding domain (ABD) expands the plasma half-life of the molecule, hence increasing the molecule's potential of serving as a therapeutic.

    A process development for production of Z08698-VDGS-ABD094 has been established, where the molecule is efficiently produced in the E. coli host strain BL21(DE3), through a T7 based expression system. Cultivations were performed with a fed-batch fermentation process and the conditions were further optimized in order to obtain highest expression, while avoiding undesirable modifications like gluconoylations. By employing Design of experiments in combination with multivariate data analysis, a production process resulting in ~3.5 g product/ l culture could be verified. Moreover, thermolysis was evaluated as a suitable method for cell disruption, enabling an easy and cost-effective manufacturing process of the ABD fused Affibody® Molecule.

  • 176.
    Frieberg, Kim
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Effects of effluent wastewater in developing zebrafish (Danio rerio)2018Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Traditional wastewater treatment is known not to be specifically designed to eliminate the new generation of chemical residues that ends up in the sewage system. Polluted wastewatereffluent therefore reaches the aquatic environment possibly causing adverse effects in aquatic wildlife. The effects of effluent water from five Swedish sewage treatment plants sampled on 6 occasions 2017, were studied in developing zebrafish (Danio rerio). The study included morphological, physiological and behavioural endpoints. Overall there were few effectswhere deviations from control animals could be seen in the exposed zebrafish. The overall outcome of this assessment was that the wastewater effluent had no consistent effects on the early development of zebrafish. The consequences of continuous low-level exposure duringthe whole life-cycle of wild fish are presently unknown and further studies are needed to evaluate potential risks.

  • 177.
    Gabriel Antonio, Ascue Avalos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Analysis of the response of Lactococcus lactis towards sublethal alcohol concentrations2013Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    In this study, I analyzed the Lactococcus lactis subspecies cremoris MG1363 stress response at sub-lethal alcohol levels during exponential growth phase at transcriptomics, proteomics, metabolomics levels. Ethanol, 1-butanol, 1-hexanol were the selected alcohols. Manganese- transporter- and arginine catabolic pathway genes were up-regulated by all alcohols suggesting they evoked oxidative and acidic stress. ATP manganese transporter genes, histidine- and galactose genes were also up-regulated. Purine- and pyrimidine synthesis genes were down-regulated. HPLC analysis displayed decreased biomass yield and glycolytic flux, suggesting increased glycolytic energy production and slowed down overall enzymatic rate. Proteomics analysis displayed differential expressed proteins associated with heat and oxidative stress.

  • 178.
    Garbergs, Hanna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Extraction of therapeutic proteins from dried blood spots and their analysis on Gyrolab2011Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    A method for extraction of therapeutic proteins from dried blood spots (DBS) followed by quantification on Gyrolab(TM) has been developed. The method makes it possible to measure the concentration of the analyte in the range 100-6000 ng/mL. The procedure can generate full analytical information from 15 μL blood originally sampled from a subject. The modest sample requirements allows for sampling a full pre-clinical pharmacokinetic profile from a single mouse. This may allow for reduced usage of animals during preclinical development of new therapeutic proteins in accordance with the 3R’s, replace, refine and reduce.

  • 179.
    Gevorgyan, Arusjak
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Development of a phylogenomic framework for the krill2018Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Over the last few decades, many krill stocks have declined in size and number,likely as a consequence of global climate change (Siegel 2016). A major risk factoris the increased level of carbon dioxide (CO2) in the ocean. A collapse of the krillpopulation has the potential to cause disruption of the ocean ecosystem, as krill arethe main connection between primary producers such as phytoplankton and largeranimals (Murphy et al. 2012). The aim of this project is to produce the firstphylogenomic framework with help of powerful comparative bioinformatics andphylogenomic methods in order to find and analyse the genes that help krill adaptto its environment. Problem with these studies is that we still do not have access toa reference genome sequence of any krill species. To strengthen and increase trustin our studies two different pipelines were performed, each with different OrthologyAssessment Toolkits (OATs), Orthograph and UPhO, in order to establish orthologyrelationships between transcripts/genes. Since UPhO produces well-supportedtrees where the majority of the gene trees match the species tree, it isrecommended as the proper OATs for generating a robust molecular phylogeny ofkrill. The second aim with his project was to estimate the level of positive selectionin E. superba in order to lay a foundation about level of selection acting on proteincodingsequences in krill. As expected, the level of selection was quite high in E.superba, which indicates that krill are adapted to the changing environment bypositive selection rather than natural genetic drift.

  • 180.
    Ghalib, Sara
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Holmberg, Daniel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Lundén, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Rudström, Karin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Zachrisson, Jana
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Nya lysande detektionstekniker: Undersökning hur Gyros känsliga instrument kan bli ännu känsligare2011Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    Immunoassayer är en väldigt vanlig metod för koncentrationsbestämning av biomolekyler. Denna metod nyttjar antikroppars affinitet för vissa analyter. I detta projekt har det undersökts om Gyros AB:s detektionsinstrument kan göras känsligare. Flera förslag har tagits fram genom efterforskning i artiklar och intervjuer med personer insatta inom området.

    De metoder som projektgruppen valt att presentera för företaget är enzymbaserad immunoassay med fluorescerande substrat samt multipel inmärkning av antikroppar, vilket vi tror kommer bidra till att försärka den fluorescerande signalen. Immobilisering av antikroppar med hjälp av traptavidin är ytterligare ett framtaget förbättringsförslag som syftar till att bidra med starkare och förlängd immobilisering av antikroppar till den fasta fasen i immunoassay. Flertalet andra metoder har undersökts såsom detektion med hjälp av radioaktivitet och kemiluminiscens. Inga fortsatta studier gjordes på grund av svårigheter att anpassa metoderna till de nuvarande instrumenten.

    Vi tror att de förslag på metodförbättringar som vi föreslår kan förbättra känsligheten på Gyros mätningar om de implementeras på den nuvarande plattformen.

  • 181.
    Gillnäs, Sara
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Evolution of the synovial joints in Osteichthyes: Cells displaying functional similarities to synoviocytes in zebrafish Danio rerio2019Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Synovial joints enable frictionless movement between the adjacent bones. Lubricating fluid enclosed within the joint reduce the pressure to allow free movement. Previously synovial joints have been associated with a terrestrial life and have mainly been studied in tetrapods, such as mammals and chicken, under the assumption that the joint did not evolve before animals adapted to a life on land. However, a recent study described the production and function of lubricin in the jaw and pectoral fin joints in ray-finned fishes, such as zebrafish, suggesting previous assumption to be questionable. The current study aim to further investigate the jaw joints in the ray-finned zebrafish, by examininge the morphology and presence of specific cell types, called synoviocytes, associated with the synovial joint. The synoviocytes are divided into two groups: macrophage-like cells and fibroblast-like cells. Tissue sections were histologically investigated with nuclear staining and immunohistochemically with antibodies to chondroitin sulphate (CS-56) and uridine diphosphoglucose dehydrogenase (UDPGD, UGDH) to investigate the presence of fibroblast-like cells. Small and circular cells were observed in the joint line and surrounding cartilage nascent to the joint. These cells could not be identified as chondrocytes or part of the perichondrium, and their UDPGD activity witness on similarities to the fibroblast-like cells. UDPGD is associated to the synthesis of hyaluronan (HA) which plays a key role in joint cavitation, hence, suggesting functional similarities in the development of zebrafish jaw joint to synovial joints. Furthermore a double transgenic zebrafish, fli1:EGFP/mpeg1:mCherry, was used to examine the presence of macrophages within the joint area. Macrophages were observed on the surface of the jaw joint in close association with blood vessels but did not show signs of incorporation within the joint. These results present further similarities of joints in ray-finned fish to the synovial joint but also the need to further examine similarities in order to understand the development and evolution of the joints. The possibility to implement the zebrafish model would facilitate future studies on the healthy synovial joint as well the diseases related to it.   

    Publikationen är tillgänglig i fulltext från 2021-09-20 08:44
  • 182.
    Gkanatsiou, Eleni
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. The Sahlgrenska Academy, Department of Psychiatry and Neurochemistry.
    Development of an assay to monitor the role of Serum Amyloid P-component in Alzheimer's Disease2016Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Alzheimer’s Disease is the most common form of dementia, affecting 48 million people worldwide. Despite this fact, only 45% of the patients have received the diagnose. The reason behind this is the fact that the cause of the disease is still unclear. Several hypotheses have been suggested, with main focus in the imbalance between the production and the clearance of Αβ in the brain (formation of plaques) or hyperphosphorylation of the tau protein (formation of tangles). In order to have a better understanding of what is actually happening in the brain, more biomarkers need to be developed. Keeping this in mind, we tried to develop a method to monitor the protein levels of SAP in the brain. SAP is a glycoprotein, normally produced by the liver in acute phase immune responses. SAP has been correlated with AD in the 1980s and quite recently it has been shown that SAP is elevated in AD patients, but not in individuals with plaques and no dementia. For this reason, we developed a mass spectrometry based targeted quantification method for monitoring SAP in the brain, as well as C9, a blood contamination reference protein. Our method is robust enough to be further used in large studies, in order to investigate the role of SAP in AD.

  • 183.
    Gkanatsiou, Eleni
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Analytisk kemi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Mass Spectrometry Based Proteomics: Toward understanding neuropathic pain2016Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    The aim of this project was to get insight into mass spectrometry based proteomics, get familiarized with novel techniques, and obtain the operating skills with modern Orbitrap mass spectrometers. In order to achieve this, the proteome changes in neuropathic pain responses corresponding to nerve injury side in individual rat’s spinal cord were explored. We focused in protein identification and quantification of the expressed proteins in 3 different set of samples, SNL, Sham and Naive rats. 

  • 184.
    Glaros, Anastasios
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Data-driven Definition of Cell Types Based on Single-cell Gene Expression Data2016Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
  • 185.
    Gonzalez Gaarslev, Natalia
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    A genomic exploration of Chlamydiae in marine sponges2019Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
  • 186.
    Govind, Shakira
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Crystallisation using cross-seeding2017Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
  • 187.
    Granström, Karin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    MicroRNAs' potential in monitoring depression and anxiety2018Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Publikationen är tillgänglig i fulltext från 2020-05-31 07:37
  • 188.
    Gras, Konrad
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Giertta Adler, Julia
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Jansson, Caroline
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Niva, Ted
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Nordmark, Adrian
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Standardisering av diagnostiska tester genom utveckling av kopplingskemier för sjukdomsspecifika markörer2016Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    Diagnostiska tester som tillverkas av företaget Thermo Fisher Scientific baseras på microarrayteknologi. Dessa tester används för diagnostik av allergi och autoimmunitet. Genom immobilisering av specifika antigener på en microarrayyta kan man detektera sjukdomsspecifika antikroppar i patientprover. Antikropparna kommer att binda in till de immobiliserade antigenerna och kan sedan detekteras med hjälp av fluorescens.

    Ett problem som Thermo Fisher Scientific har haft med sina diagnostiska tester är att de ibland visar felaktiga resultat. Detta problem orsakas av ospecifik bindning av antikroppar till antigenerna samt felaktig orientering på antigenerna. Syftet med denna rapport är att presentera förslag på kopplingskemier som kan användas för optimering av diagnostiska tester, med fokus på att eliminera felaktiga resultat. Detta har uppnåtts genom en studie av relevant vetenskaplig litteratur samt kontakt och intervjuer med experter inom olika vetenskapliga områden. För utvärdering av de undersökta kopplingskemierna skapades en lista med kriterier, där kemiernas bindningsspecificitet och standardiserbarhet låg i fokus.

    Vi identifierade 21 stycken kopplingskemier ifrån litteraturstudier och analyser. Sju av dessa uppfyller alla kriterier som vi och beställaren Thermo Fisher Scientific har satt upp och därför rekommenderas dessa som lämpliga för diagnostiska test. Vi anser att dessa sju är likvärdiga vad gäller nyttan och användbarheten inom diagnostik.

  • 189.
    Greaves, Deanne
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences.
    Population biology and ecology in the rare and endangered Hapalopilus croceus.2017Självständigt arbete på avancerad nivå (masterexamen), 80 poäng / 120 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Landscape management has altered the population dynamics of many species residing in old growth ecosystems. As a result, fragmentations in residual old oak habitats in Sweden have led to the decline of endangered and long-lived polypores including the bright orange Hapalopilus croceus. Since little is known about this species, the aim was to investigate its growth, mating, and population biology using molecular and ecological methods. Specifically, what its growth patterns are, what its mating type is, and whether there is genetic variation among sampled populations in Sweden and the Baltic area. Fruiting body samples were collected from 34 localities in Sweden and 6 localities in neighboring Baltic States. Heterokaryotic mycelia were then cultivated from these samples and the genomes sequenced. 42 single-spore isolates from SLU's culture bank were also revived and cultured. These homokaryons were then crossed to determine mating type. Mating type was examined using morphological observations and calculated via mating matrix. To examine growth rate and establishment, H. croceus mycelia were grown in comparison to Fomitopsis pinicola mycelia. To explore the population biology, the potential for gene flow was analyzed among Swedish and Baltic isolates. As a result, H. croceus was found to be slow growing, exhibit a tetra polar mating type, and with limited genetic variation in the Baltic Sea area. Its slow growth could provide a possible insight into colonization strategy, whereas its multiallelic mating system could possibly increase outcrossing in the future. Minimal genetic variation could result from previous connectivity between oaks, where the fungus may have outbred readily and colonized more hosts, maintaining a more uniform genetic structure. However, recent habitat alteration has not been analyzed for this species, nor has community interaction among other fungi and fruiting dynamics. Thus, further examination of these factors would help expand this study and possibly provide conservation and management guidelines for future projects.

  • 190.
    Grero, Dhanya
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Cytotoxicity of Vγ9Vδ2 T cells towards Colon Cancer Cells2014Självständigt arbete på avancerad nivå (magisterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Immunotherapies for cancer are widely studied at present. We are currently studying a specific form of “Vγ9Vδ2 T cells” found in the peripheral blood of healthy donors that can be used for the killing of HT-29 colon cancer cells. In order to determine the cytotoxicity of effectors, Vγ9Vδ2 T cells towards target cells, HT-29, it is important to first evaluate the absolute number of Vγ9Vδ2 T cells in a mixed cell population, and next to determine the phenotypic characterization, their activity and cytotoxicity in the presence of target cells. A flow cytometry and bead based assay was developed to evaluate the absolute number of Vγ9Vδ2 T cells in a mixed cell population. Peripheral Blood Mononuclear Cells (PBMCs) were surface stained with monoclonal antibodies (MoAbs) conjugated to fluorochromes that are cross reactive to cell surface markers such as CD3 (T Lymphocytes), γδ2 and were mixed with fluorophore beads. In these assays, no washes and centrifugation steps were performed after the cell surface staining and bead addition. The absolute cell counts were evaluated based on referencing a known concentration of beads. In addition, quantification assays were also performed to measure the cell and bead loss on surface staining that included washes and centrifugation steps and thus found a higher percentage loss of cells than beads. Immunophenotyping assays with four color staining were performed to monitor the phenotypic differentiation of effector cells based on cell surface markers CD27 and CD45RA. Only the naïve (CD27+CDRA+) and terminally differentiated effector memory (CD27-CD45RA+) were identified on the assays performed using Vγ9Vδ2 T cells of different donors. A flow cytometry based cytotoxicity (FCC) assay was completed to monitor the effector cell activity (CD69+) in the presence and absence of target cells and also the cytotoxicity was measured based on % specific lysis of target cells at four different effector to target (E:T) cell ratios. Only preliminary data were obtained for the FCC assay and the development is still in progress.  

  • 191.
    Groh, Selina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Patterns of diversification in osteostracan evolution2014Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
  • 192.
    Gunnarsdóttir, Fríða Björk
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Department of Oncology-Pathology, Karolinska Instututet.
    T cell reactivity to melanoma Tumor-Associated Antigens before and after surgical removal of metastases2017Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Background: Melanoma the most immunogenic cancer type and metastatic melanoma has poor prognosis. Currently, there are hardly any peripheral blood biomarkers that allow for identification of patient’s prognosis or survival. With most recent advances in melanoma treatment associated with immune based therapy, it is crucial to understand better how the immune system reacts to treatment.

    Purpose: The main objective of this project was to compare the reactivity of the T cells of patients with stage III or IV metastatic melanoma to tumor associated antigens, before and after surgery where metastatic lesions were removed. This could provide a better insight into the interaction between tumor and T cells.

    Methods: Peripheral blood mononuclear cells were isolated from blood samples taken before and after surgery. Cells were stimulated over the course of two weeks with overlapping peptide pools of three known melanoma antigens: MelanA, NY-ESO-1 and Cripto-1. After 12 days, the cells were re-stimulated and analyzed using multicolor flow cytometry. CD4 and CD8 positive cells were analyzed for cytokine production, comparing the re-stimulated cells to a negative non re-stimulated control. This gave a set of paired nominal data for each patient, pre and post-surgery. McNemar’s test was used to analyze changes before and after surgery, and Kaplan-Meier analysis were used to investigate correlation between cell reactivity and cytokine production with progression free survival.

    Results: Surgical removal of metastatic lesions changes reactivity of T cells to MelanA, NY-ESO-1 and Cripto-1. Cripto-1 showed a significant increase in both combined CD4 and CD8 response as well as in exclusive cell type response. We also observed that certain cytokine production patterns correlated with progression from stage III to stage IV melanoma.

    Conclusions: We show here that surgical removal of metastases amplifies the immune response of melanoma patients. This may provide insight into the complexity of the correlation between cytokine secretion profiles and a favorable immune response to metastatic melanoma.

  • 193.
    Gunnarsson, Ingólfur Bragi
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap.
    Synthetic biology in cyanobacteria: Expression of [FeFe] hydrogenases, their maturation systems and construction of broad-host-range vectors2011Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
  • 194.
    Gustafsson, Anna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Ryman, Helena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Lind, Simon
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Schytt-Winberg, Petter
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Hagelby Edström, Tim
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Nyberg, Erica
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Metodförslag för rening av nativt hemagglutinin från influensavirus2013Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    Hemagglutinin är ett transmembranprotein som finns i membranet hos influensaviruset. Detta protein avgör virusets infektiösa förmåga. För att förstå influensaviruset bättre och kunna hitta nya detektionsmetoder för aktiva influensavirus krävs en första framrening av proteinet. Målet med denna studie är därför att överlämna ett protokoll till beställaren med fullständig process på hur hemagglutinin kan renas fram från aktiva virus.

    Resultatet har erhållits genom en omfattande litteraturstudie där information har samlats från skriftliga och elektroniska källor, samt via intervjuer med sakkunniga forskare.

    Processen att rena fram hemagglutinin börjar med kultivering av virus i cellinjen MDCK följt av virusisolering med hjälp av centrifugering. Virusmembranet löses sedan upp och det membranbundna hemagglutininet solubiliseras. Därefter isoleras hemagglutinin från proteinlösningen med hjälp av anjonbyteskromotografi. För att påvisa närvaron av aktivt hemagglutinin utförs en HA-assay där provet tillförs på röda blodkroppar, varpå agglutination kan observeras.

    Vi menar de förslagna metoderna utgör en produktionsväg för att rena hemagglutinin från aktiva virus i nativ form. MEtoderna är valda eftersom de har få och enkla steg, vilket gör proceduren säkrare, något som vi lagt stor vikt vid. Alla valda metoder presterar väl med avseende på säkerhet och bör, då de utförs på korrekt sätt enligt alla säkerhetsföreskrifter, inte utsätta handhavaren, allmänheten eller miljön för någon risk.

  • 195.
    Gustafsson, Magnus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Ekotoxikologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Toxicity studies on bone tissue from sheep grazing on a pasture treated with sewage sludge2008Självständigt arbete på avancerad nivå (magisterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    In this study, femur bones and serum from rams and ewes (Ovis aries) bred on pastures fertilized twice annually with sewage sludge (2.25 tonnes dry matter/ha) or on control pastures were analysed. The control pastures was treated with conventional inorganic fertilizer. Both rams and ewes were exposed during development in utero, from conception, and after birth, during lactation, to weaning at 4 months of age. After that the rams were moved to pastures not fertilized with sewage sludge. The ewes, however, were retained on pastures treated with sewage sludge. The animals were slaughtered at 18 months of age and the femur bone was dissected. The peripheral Quantitative Computed Tomography (pQCT) and three-point bending test analyses of the femur bone were evaluated. In rams, the total bone mineral density (BMD) at the metaphyseal part of femur was significantly greater (10.5 %, p<0.05) in treated than control animals. Treated animals also exhibited a reduction in the total cross sectional area (CSA, 11.5 %, p<0.05), the trabecular CSA (17.1 %, p<0.05) and the periosteal circumference (5.7 %, p<0.05). Analysis of the mid-diaphyseal part revealed multiple effects e.g. the total BMD (13.8 %, p<0.05) increased significantly whereas the total CSA (12.1 %, p<0.05) and the marrow cavity (25.8 %, p<0.05) were significantly reduced in the treated rams. The threepoint bending test of the ram femur at the mid-diaphyseal part revealed an increased stiffness (6.4 %, p<0.05) in treated animals. In ewes, the trabecular bone mineral content (BMC) at the metaphyseal part of femur was significantly increased (41.6 %, p<0.05) in the treated ewes. pQCT analysis of the mid-diaphyseal part showed no adverse effects in the treated ewes. Femurs from treated ewes showed a reduction in the load at failure (17.3 %, p<0.05) and stiffness (10.7 %, p<0.05). The serum levels of the bone formation marker BAP, the bone resorption marker CTX and the vitamin D marker 25-OH D did not differ between exposed and control animals, neither for rams nor for ewes. In conclusion, this study shows that exposure to sewage sludge disrupt bone tissue homeostasis in sheep. As the rams were only exposed via placental transfer and mother’s milk, the obtained effects; increased cortical thickness, decreased circumference and decreased marrow cavity must be considered as developmental effects. The increase in femoral trabecular BMC in the ewes is thought likely to be attributable to estrogenic influences in the sludge.

  • 196.
    Gustafsson, Rickard
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Habitatval, migrations- och furageringsaktivitet samt homing hos gädda (Esox lucius) härstammande från Österby myr, Gotland.2014Självständigt arbete på grundnivå (kandidatexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    In this study the spawning migration activity, habitat choice (depth and temperature), foraging activity, duration of stay in the spawning site and homing-behavior was studied for anadromous pike (Esox lucius) in the wetland Österby myr, Gotland.

    The spawning migration was concentrated to dusk and dawn, a homing behavior was confirmed and there was no significant difference between sexes with respect to duration of stay. A difference in habitat choice and small variation in foraging activity between individuals was established.

  • 197.
    Gusén, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Environmental variation and phenotypic plasticity: The effect of water visibility on body pigmentation in perch (Perca fluviatilis L.)2010Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Phenotypic plasticity is defined as an organism’s ability to express differentphenotypes depending on the environment. Predation is one of the key forces inecology and can indirectly cause a change of the phenotype in fish populations.Pigmentation change in order to match the background is one type of camouflage usedin fish and other organisms. Moreover, pigmentation might depend on environmentalconditions such as turbidity and water colour that affect the light spectrum and thusthe visibility in the water. The phenotypic variation in body pigmentation of perch(Perca fluviatilis L.) has rarely been studied to this date. In this study, I examined ifbody pigmentation of perch varied between different environments and betweenstructurally different habitats (littoral/pelagic). I tested long-term (phenotypicplasticity) and short-term (physiological-behavioural) changes in pigmentation byusing long-term pre-treatments and short-term aquarium experiments. Differences instructurally-diverse habitats were investigated in an extensive field study.Furthermore, experimental results were compared to data from the field. The resultsshow that pigmentation is determined by environmental factors, such as water colouror turbidity, and by structural complexity. Since fishes adapted their pigmentation totheir visual environment, pigmentation is likely used as predator avoidancemechanism in perch. Moreover, it was demonstrated that the environmentally-inducedpigmentation pattern determines the magnitude of short-term pigmentation in perch.

  • 198.
    Gärdemalm Niemi, Matilda
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Rydberg Öhrling, Sara
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Stam, Emma
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Establishment of Technical Life Science Consulting Services in a Local Government Market2019Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    This master thesis evaluates the possibility for Semcon AB to establish a business within the public sector of Uppsala. The need and prerequisites for technical life science consultant services has been investigated by interviewing experts in their field. The study is explanatory and contributes with an understanding of the current situation and the outlook for consultants in in the public sector, with Region Uppsala as the targeted customer.

    The results show that the need for consultants lies within IT, logistics, medtech, and construction. A consultant should preferably have a combination of these competences. Another possibility is to aid the public sector with the difficulties in specifying the requirements of a procurement. There are different ways of establishing a business with Region Uppsala. Either by a framework agreement, as a subcontractor, or by innovation procurement.

    One aspect of successful collaboration between a consultant company and the public sector is the attitudes toward consultants. The result indicates generally positive attitudes. Despite this a concern of knowledge disappearing when the assignment is finished exists. Therefore, transparency as well as constant feedback and evaluation is highly important.

  • 199.
    Götmar, Gustav
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Ytbioteknik, Centrum för ytbioteknik.
    Fornstedt, Torgny
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Retention Mechanism of ß-blockers on an immobilized Cellulase. Relative Importance of the Hydrophobic and Ionic Contributions to their Enantioselectivity and Nonselective Interactions2000Ingår i: Analytical Chemistry, Vol. 72, s. 3908-3915Artikel i tidskrift (Refereegranskat)
  • 200.
    Haars, Jonathan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Inheritance patterns of mitochondrial DNA in Drosophila paulistorum: substantial paternal transmission and the possible role of mitochondria in speciation2019Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Direct studies of speciation are possible in the superspecies complex of Drosophila paulistorum, which consists of six different semispecies undergoing incipient speciation. Strict maternal inheritance of mitochondria is the most common pattern of mitochondrial inheritance in animals. Here I show that paternal transmission of mitochondrial DNA occurs in the heteroplasmic Orinocan semispecies and is not limited to hybrid offspring. Inheritance of one mitotype is mainly maternal while the other is mainly paternal; a highly unusual pattern of mitochondrial inheritance. I used absolute quantification real-time PCR on DNA extracted from eggs and imagoes from the Amazonian and Orinocan semispecies, as well as hybrids between these two semispecies. In crosses performed between F1 hybrids with a combination of mitotypes not found in any of the parents, no F2 hybrids were acquired. One possible explanation for this is that differences in mitotypes and inheritance patterns of mitochondrial DNA may cause incompatibilities between the genomes of D. paulistorum. This may be one cause of hybrid inviability and genetic isolation between semispecies, a necessary part of the speciation process. This further complicates the story of the ongoing speciation process in the D. paulistorum superspecies complex, which offers much to learn about speciation, mitochondrial inheritance and interactions between multiple genomes in the same organism.

    Publikationen är tillgänglig i fulltext från 2021-01-23 12:00
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