Mastergradsoppgaver i biologi (Helsefak)https://hdl.handle.net/10037/1992024-03-29T13:51:27Z2024-03-29T13:51:27ZThe use of traditional and unconventional culturing methods for the discovery of antimicrobial compounds derived from marine microorganismsBrocklesby, Charlotte Kit Munhttps://hdl.handle.net/10037/295402023-06-30T06:03:47Z2023-05-15T00:00:00ZBrocklesby, Charlotte Kit Mun<br />
The main aim is to evaluate the content of marine biofilms and different marine bacteria for antimicrobial potential.
Hypothesis: antimicrobial compounds can be produced in the presence of other bacterial species; in the context of Winogradsky columns that simulate a naturalistic environment, and in the proximity to other species in the case of marine bacterial isolates.
For this main aim and hypothesis, the following subgoals are defined:
1. Document any antimicrobial production by marine bacteria from different marine sources, using a co-culture approach.
2. Document the bacterial content of biofilm in Winogradsky columns (WC) from the seashore, using different techniques.
3. Evaluate the antibacterial production in the bacterial content from Winogradsky biofilms by performing diffusing assays, MIC assays in combinations with chromatographic methods.<br />
2023-05-15T00:00:00ZThe use of traditional and unconventional culturing methods for the discovery of antimicrobial compounds derived from marine microorganismsBrocklesby, Charlotte Kit MunThe main aim is to evaluate the content of marine biofilms and different marine bacteria for antimicrobial potential.
Hypothesis: antimicrobial compounds can be produced in the presence of other bacterial species; in the context of Winogradsky columns that simulate a naturalistic environment, and in the proximity to other species in the case of marine bacterial isolates.
For this main aim and hypothesis, the following subgoals are defined:
1. Document any antimicrobial production by marine bacteria from different marine sources, using a co-culture approach.
2. Document the bacterial content of biofilm in Winogradsky columns (WC) from the seashore, using different techniques.
3. Evaluate the antibacterial production in the bacterial content from Winogradsky biofilms by performing diffusing assays, MIC assays in combinations with chromatographic methods.UiT Norges arktiske universitetUiT The Arctic University of NorwayStensvåg, KlaraMastergradsoppgaveMaster thesisInhibition of bacterial and human zinc-metalloproteasesChaulagain, Bibekhttps://hdl.handle.net/10037/277232022-12-07T12:48:48Z2021-11-30T00:00:00ZChaulagain, Bibek<br />
Antibiotic resistance is one of the major challenges in the present era and it is drastically increasing with the increase in time because of the overuse and misuse of antibiotics. Therefore, there is a demand of new antibiotics with new modes of action or other innovative strategies to overcome bacterial infections as soon as possible. The zinc metalloproteases Themolysin (TLN), Pseudolysin (PLN) and Aureolysin (ALN) are important bacterial virulence factors and the inhibition of these bacterial virulence factors is believed to be a new treatment option of bacterial infections. However, in order to have a therapeutic value, inhibitors of these enzymes should not interfere strongly with the activity of human zinc metalloproteases.
In the present thesis, 26 compounds were tested for the inhibition of TLN, PLN, ALN and the human matrix metalloproteases-14(MMP-14). The compounds were selected from a previous virtual screening project at the research group. The inhibition of the compounds was tested by measuring the enzyme activity of PLN, TLN ALN and MMP-14 after exposure of the test compounds. The time resolved fluorescence by the use of fluorogenic substrates was used to measure the enzyme activity. The results showed that some of the compounds inhibited the enzyme activity by 30%-40% and they were not considered as slow binders as there was no significant change in activity with respect to the time. Compounds with highest rate of inhibition in enzyme assays were selected and proceed for molecular modeling studies by docking and MMGBSA calculations. The best compounds were compared with a known strong inhibitor of the zinc- metalloproteases in the molecular modeling part.<br />
2021-11-30T00:00:00ZInhibition of bacterial and human zinc-metalloproteasesChaulagain, BibekAntibiotic resistance is one of the major challenges in the present era and it is drastically increasing with the increase in time because of the overuse and misuse of antibiotics. Therefore, there is a demand of new antibiotics with new modes of action or other innovative strategies to overcome bacterial infections as soon as possible. The zinc metalloproteases Themolysin (TLN), Pseudolysin (PLN) and Aureolysin (ALN) are important bacterial virulence factors and the inhibition of these bacterial virulence factors is believed to be a new treatment option of bacterial infections. However, in order to have a therapeutic value, inhibitors of these enzymes should not interfere strongly with the activity of human zinc metalloproteases.
In the present thesis, 26 compounds were tested for the inhibition of TLN, PLN, ALN and the human matrix metalloproteases-14(MMP-14). The compounds were selected from a previous virtual screening project at the research group. The inhibition of the compounds was tested by measuring the enzyme activity of PLN, TLN ALN and MMP-14 after exposure of the test compounds. The time resolved fluorescence by the use of fluorogenic substrates was used to measure the enzyme activity. The results showed that some of the compounds inhibited the enzyme activity by 30%-40% and they were not considered as slow binders as there was no significant change in activity with respect to the time. Compounds with highest rate of inhibition in enzyme assays were selected and proceed for molecular modeling studies by docking and MMGBSA calculations. The best compounds were compared with a known strong inhibitor of the zinc- metalloproteases in the molecular modeling part.UiT Norges arktiske universitetUiT The Arctic University of Norwaysylte, ingebrigtMastergradsoppgaveMaster thesisDeterminants of Staphylococcus aureus colonization and infection: Characterization of interaction between serine-aspartate containing protein D and human Siglec11 and Siglec16Spahiu, Irahttps://hdl.handle.net/10037/270552022-10-17T08:20:16Z2021-10-15T00:00:00ZSpahiu, Ira<br />
<p><i>Staphylococcus aureus</i> is a Gram-positive opportunistic pathogen responsible for a range of infections that can lead to fatal invasive diseases such as pneumonia or osteomyelitis. Approximately 30% of the healthy adult population are persistently colonized by <i>S. aureus</i> strains in their anterior nares. The molecular mechanism underlying <i>S. aureus</i> colonization and infection during its interaction with the host is not fully understood.
<p><i>S. aureus</i> can express several virulence determinants during its interaction with the host and/or host components. One of these virulence determinants is the serine-aspartate containing protein D (SdrD). It can increase <i>S. aureus</i> ability to survive in the blood and during systemic infections. SdrD is important for <i>S. aureus</i> colonization, survival, and infection of the host.
<p>Unpublished results have demonstrated a possible interaction between SdrD and various proteins in human blood plasma. One of these proteins was identified as the human protein Siglec16. The biological functions of Siglec16 are mostly unknown however, studies show high identity between extracellular regions of Siglec11 and 16. Therefore, this study also includes the Siglec11 as a possible binding partner of the SdrD in the plasma.
<p>The aim of this thesis was to develop the biological tools which will facilitate the characterization of the biological implications of the possible interaction between SdrD and Siglec16 and/or Siglec11. The overall results show a slight progress in obtaining the tools to help in further research in characterizing the biological functions of the proteins Siglec16 and Siglec11. However, some results remain unclear and inconclusive in demonstrating a possible or significant interaction between SdrD and the Siglec proteins 11 and 16.<br />
2021-10-15T00:00:00ZDeterminants of Staphylococcus aureus colonization and infection: Characterization of interaction between serine-aspartate containing protein D and human Siglec11 and Siglec16Spahiu, Ira<p><i>Staphylococcus aureus</i> is a Gram-positive opportunistic pathogen responsible for a range of infections that can lead to fatal invasive diseases such as pneumonia or osteomyelitis. Approximately 30% of the healthy adult population are persistently colonized by <i>S. aureus</i> strains in their anterior nares. The molecular mechanism underlying <i>S. aureus</i> colonization and infection during its interaction with the host is not fully understood.
<p><i>S. aureus</i> can express several virulence determinants during its interaction with the host and/or host components. One of these virulence determinants is the serine-aspartate containing protein D (SdrD). It can increase <i>S. aureus</i> ability to survive in the blood and during systemic infections. SdrD is important for <i>S. aureus</i> colonization, survival, and infection of the host.
<p>Unpublished results have demonstrated a possible interaction between SdrD and various proteins in human blood plasma. One of these proteins was identified as the human protein Siglec16. The biological functions of Siglec16 are mostly unknown however, studies show high identity between extracellular regions of Siglec11 and 16. Therefore, this study also includes the Siglec11 as a possible binding partner of the SdrD in the plasma.
<p>The aim of this thesis was to develop the biological tools which will facilitate the characterization of the biological implications of the possible interaction between SdrD and Siglec16 and/or Siglec11. The overall results show a slight progress in obtaining the tools to help in further research in characterizing the biological functions of the proteins Siglec16 and Siglec11. However, some results remain unclear and inconclusive in demonstrating a possible or significant interaction between SdrD and the Siglec proteins 11 and 16.UiT Norges arktiske universitetUiT The Arctic University of NorwayMaster thesisMastergradsoppgaveEstablishment of an advanced flow cytometry protocol for analyzing immune cell subsets from lung cancer patientsBeyene, Sweet Yibiohttps://hdl.handle.net/10037/268222022-09-16T06:48:12Z2022-08-22T00:00:00ZBeyene, Sweet Yibio<br />
Lymphocytes are known for their role in tumor promotion and tumor suppression. T cell infiltration of the tumor microenvironment has been linked to a better prognosis and outcome in various malignancies. CD8+ T cells can eliminate cancer cells by causing them to lyse, while CD4+ T cells can be both tumor promoting and tumor suppressing. However, the prognostic impact of functional lymphocyte subtypes in non-small cell lung cancer (NSCLC) is not completely known. Therefore, the aim of this thesis was to establish a multiparametric flow cytometry protocol to explore the presence of functional lymphocyte subtypes in peripheral blood mononuclear cells from healthy donors and validate it for use in blood and tissue samples from NSCLC patients. Furthermore, the effects of cryopreservation on sample quality and lymphocyte subtype distribution were also explored.
Our study showed that the presence of selected lymphocyte subtypes can be explored in blood from NSCLC patients. However, it also showed that cryopreservation had an effect on the distribution of some lymphocyte subtypes. The blood samples that were analyzed using the CD8+ T cell subtypes panel showed a quantitative decrease of cells after cryopreservation. Similar observations were made for blood samples analyzed using the expanded lymphocyte panel. Statistical analysis showed that these differences may be attributable to the effects of cryopreservation. However, due to small sample sizes we were unable to determine whether the differences were statistically significance.
Having established this protocol, our future aim is to analyze more NSCLC patient samples, both from blood and tissue.<br />
2022-08-22T00:00:00ZEstablishment of an advanced flow cytometry protocol for analyzing immune cell subsets from lung cancer patientsBeyene, Sweet YibioLymphocytes are known for their role in tumor promotion and tumor suppression. T cell infiltration of the tumor microenvironment has been linked to a better prognosis and outcome in various malignancies. CD8+ T cells can eliminate cancer cells by causing them to lyse, while CD4+ T cells can be both tumor promoting and tumor suppressing. However, the prognostic impact of functional lymphocyte subtypes in non-small cell lung cancer (NSCLC) is not completely known. Therefore, the aim of this thesis was to establish a multiparametric flow cytometry protocol to explore the presence of functional lymphocyte subtypes in peripheral blood mononuclear cells from healthy donors and validate it for use in blood and tissue samples from NSCLC patients. Furthermore, the effects of cryopreservation on sample quality and lymphocyte subtype distribution were also explored.
Our study showed that the presence of selected lymphocyte subtypes can be explored in blood from NSCLC patients. However, it also showed that cryopreservation had an effect on the distribution of some lymphocyte subtypes. The blood samples that were analyzed using the CD8+ T cell subtypes panel showed a quantitative decrease of cells after cryopreservation. Similar observations were made for blood samples analyzed using the expanded lymphocyte panel. Statistical analysis showed that these differences may be attributable to the effects of cryopreservation. However, due to small sample sizes we were unable to determine whether the differences were statistically significance.
Having established this protocol, our future aim is to analyze more NSCLC patient samples, both from blood and tissue.UiT Norges arktiske universitetUiT The Arctic University of NorwayAndersen, SigveBusund, Lill-Tove RasmussenMastergradsoppgaveMaster thesisThe human polyomavirus KI: A study on cell permissivity, sub-cellular localization of VP1 and presence in cerebrospinal fluid and urineLudvigsen, Maria A.https://hdl.handle.net/10037/265902022-09-02T07:32:46Z2011-11-17T00:00:00ZLudvigsen, Maria A.<br />
KI polyomavirus (KIPyV) is a relatively newly discovered human polyomavirus originally identified in respiratory tract samples. Little is known about the route of infection or transmission, and the pathogenic properties of this virus are virtually unknown. The life cycle of KIPyV has not been studied as a permissive cell system has not been identified so far. The bona fide sites of viral replication in the human body remain unknown, but indications of a respiratory or oral route of infection led us to investigate whether the A549 lung cell line was permissive to KIPyV. In this thesis we have investigated if the A549 cell line allows KIPyV propagation and if viral protein is detectable by antibodies directed against KIPyV VP1. This was performed by transfecting with KIPyV genome and analyzing the cells for mRNA expression of LT-ag and antibody detection of VP1 by western blotting. LT-ag mRNA was successfully detected by PCR but detection of KIPyV VP1 by the use of our antibody was unsuccessful. The sub-cellular localization of KIPyV VP1 protein has been investigated by confocal microscopy using EGFP-KI VP1 fusion protein. Both A549 and Vero cell line were studied and the EGFP signal localized differently in the two cell lines. In A549 cells the localization was mainly in the nucleus while in Vero cells cytoplasm localization was mostly observed. We have also examined cerebrospinal fluid from patients with suspicion of neurological diseases and urine specimens from immunocompromised patients with systemic lupus erythematosus for KIPyV DNA by nested PCR. We have indicated the presence of KIPyV VP1 DNA by nested PCR and sequencing of the PCR products.<br />
2011-11-17T00:00:00ZThe human polyomavirus KI: A study on cell permissivity, sub-cellular localization of VP1 and presence in cerebrospinal fluid and urineLudvigsen, Maria A.KI polyomavirus (KIPyV) is a relatively newly discovered human polyomavirus originally identified in respiratory tract samples. Little is known about the route of infection or transmission, and the pathogenic properties of this virus are virtually unknown. The life cycle of KIPyV has not been studied as a permissive cell system has not been identified so far. The bona fide sites of viral replication in the human body remain unknown, but indications of a respiratory or oral route of infection led us to investigate whether the A549 lung cell line was permissive to KIPyV. In this thesis we have investigated if the A549 cell line allows KIPyV propagation and if viral protein is detectable by antibodies directed against KIPyV VP1. This was performed by transfecting with KIPyV genome and analyzing the cells for mRNA expression of LT-ag and antibody detection of VP1 by western blotting. LT-ag mRNA was successfully detected by PCR but detection of KIPyV VP1 by the use of our antibody was unsuccessful. The sub-cellular localization of KIPyV VP1 protein has been investigated by confocal microscopy using EGFP-KI VP1 fusion protein. Both A549 and Vero cell line were studied and the EGFP signal localized differently in the two cell lines. In A549 cells the localization was mainly in the nucleus while in Vero cells cytoplasm localization was mostly observed. We have also examined cerebrospinal fluid from patients with suspicion of neurological diseases and urine specimens from immunocompromised patients with systemic lupus erythematosus for KIPyV DNA by nested PCR. We have indicated the presence of KIPyV VP1 DNA by nested PCR and sequencing of the PCR products.Universitetet i TromsøUniversity of TromsøMoens, UgoMaster thesisMastergradsoppgaveNon-Invasive Methods for Detection of Genetic Abnormalities in Human Embryos Cell-Free DNA Secreted from Human Embryos as an Alternative to DNA from Cell Biopsies for Genetic AnalysesFinanger, Viktoria Emeline Swatyhttps://hdl.handle.net/10037/262872022-08-19T06:02:52Z2022-05-15T00:00:00ZFinanger, Viktoria Emeline Swaty<br />
Chromosomal abnormalities are one of the main causes of implantation failure following embryo transfer in in vitro fertilization (IVF). Preimplantation genetic testing for aneuploidies (PGT-A) is time-consuming, expensive, and invasive. Non-invasive PGT-A (niPGT-A) is an alternative where secreted embryonic cell-free DNA (cfDNA) in spent culture medium (SCM) is investigated. This study aimed to investigate and prepare for the implementation of niPGT-A in the IVF-unit at UNN.
To reach this objective 36 anonymized frozen embryos were thawed, cultured and DNA from dissociated cells and SCM was extracted. Furthermore, two different analysis methods were chosen: digital droplet PCR (ddPCR) and Oxford nanopore sequencing. The latter required amplification by Repli-G in advance. ddPCR was performed to investigate genes located on chromosomes 21 (RUNX1 and BRWD1) and 18 (TCF4 and SMAD4), to identify trisomy 21.
The embryos were viable, with DNA present in every sample, having a mean of 1.289 ng/l throughout the samples. Repli-G was used to amplify five of the embryos, which gave a mean of 2099.29 ng/l, resulting in over a thousandfold increase in concentration. The amplified samples were then sequenced, which resulted in a blocked run and limited output, with the numbers of reads generated ranging from 7607 to 90 632. Yet, a consensus sequence was generated from the cfDNA found in the SCM sample of embryo 18, which was found to match the human genome. The samples run on ddPCR had a detection of genes involved in trisomy 21, with 11 out of 18 samples having positive droplets generated for the probes targeting the genes located on chromosome 21. The starting concentrations ranged from 0.599 copies/l to 4.35 copies/l in the samples with positive droplets detected. There was, however, a lack of detection on the probes targeting the genes located on chromosome 18.
In conclusion, further investigation into both nanopore sequencing and ddPCR is necessary to validate their clinical relevance, however, the possibility of using cfDNA as an alternative to cell biopsies to screen the embryos is promising.<br />
2022-05-15T00:00:00ZNon-Invasive Methods for Detection of Genetic Abnormalities in Human Embryos Cell-Free DNA Secreted from Human Embryos as an Alternative to DNA from Cell Biopsies for Genetic AnalysesFinanger, Viktoria Emeline SwatyChromosomal abnormalities are one of the main causes of implantation failure following embryo transfer in in vitro fertilization (IVF). Preimplantation genetic testing for aneuploidies (PGT-A) is time-consuming, expensive, and invasive. Non-invasive PGT-A (niPGT-A) is an alternative where secreted embryonic cell-free DNA (cfDNA) in spent culture medium (SCM) is investigated. This study aimed to investigate and prepare for the implementation of niPGT-A in the IVF-unit at UNN.
To reach this objective 36 anonymized frozen embryos were thawed, cultured and DNA from dissociated cells and SCM was extracted. Furthermore, two different analysis methods were chosen: digital droplet PCR (ddPCR) and Oxford nanopore sequencing. The latter required amplification by Repli-G in advance. ddPCR was performed to investigate genes located on chromosomes 21 (RUNX1 and BRWD1) and 18 (TCF4 and SMAD4), to identify trisomy 21.
The embryos were viable, with DNA present in every sample, having a mean of 1.289 ng/l throughout the samples. Repli-G was used to amplify five of the embryos, which gave a mean of 2099.29 ng/l, resulting in over a thousandfold increase in concentration. The amplified samples were then sequenced, which resulted in a blocked run and limited output, with the numbers of reads generated ranging from 7607 to 90 632. Yet, a consensus sequence was generated from the cfDNA found in the SCM sample of embryo 18, which was found to match the human genome. The samples run on ddPCR had a detection of genes involved in trisomy 21, with 11 out of 18 samples having positive droplets generated for the probes targeting the genes located on chromosome 21. The starting concentrations ranged from 0.599 copies/l to 4.35 copies/l in the samples with positive droplets detected. There was, however, a lack of detection on the probes targeting the genes located on chromosome 18.
In conclusion, further investigation into both nanopore sequencing and ddPCR is necessary to validate their clinical relevance, however, the possibility of using cfDNA as an alternative to cell biopsies to screen the embryos is promising.UiT Norges arktiske universitetUiT The Arctic University of NorwayNystad, MonaHentemann, MarthaMastergradsoppgaveMaster thesisEvaluation of the performance of two prediction models, the IrisPlex and the novel EC12 model, for eye colour predictions in a Norwegian population.Kjersem, Mariannehttps://hdl.handle.net/10037/254602022-06-13T21:35:38Z2020-06-12T00:00:00ZKjersem, Marianne<br />
Biological material obtained from a crime scene is used to generate DNA-profile by typing short tandem repeat (STR) markers. However, if the STR-profile do not match the DNA profile of suspects or from a crime DNA database, the investigation can go towards typing markers that can estimate externally visible characteristics (EVCs). EVCs can function as a “biological witness” and thus aid a police investigation.
In this work the IrisPlex prediction model and a novel prediction model, EC12, were evaluated in 521 samples from the Norwegian population. A PCR-SBE-CE assay amplifying the fourteen SNPs included in the two models was optimised at Section of Forensic Genetics, Copenhagen, Denmark before it was established at Centre of Forensic Genetics, Tromsø, Norway.
IrisPlex showed high prediction accuracy for blue and brown eye colour (AUC-value of 0.84 and 0.94, respectively). However, the model did not perform good in prediction of intermediate eye colour (AUC-value of 0.6), which represented 24% of the Norwegian population and thus all these individuals were incorrectly predicted.
Comparison of EC12 and an adjusted IrisPlex model (IP NO) showed a small increase in correct predictions from 72% to 75%, respectively. A higher prediction accuracy for all eye colours were observed for the EC12 model, with AUC-value of 0.84 (blue), 0.97 (brown) and 0.68 (intermediate), while IP NO obtained AUC-values of 0.81 (blue), 0.93 (brown) and 0.59 (intermediate). This increase may imply that the additionally SNPs included in this model has an improving effect on eye colour prediction. However, the prediction of intermediate eye colour was still not good, indicating the importance of further phenotypic investigation of this category.<br />
2020-06-12T00:00:00ZEvaluation of the performance of two prediction models, the IrisPlex and the novel EC12 model, for eye colour predictions in a Norwegian population.Kjersem, MarianneBiological material obtained from a crime scene is used to generate DNA-profile by typing short tandem repeat (STR) markers. However, if the STR-profile do not match the DNA profile of suspects or from a crime DNA database, the investigation can go towards typing markers that can estimate externally visible characteristics (EVCs). EVCs can function as a “biological witness” and thus aid a police investigation.
In this work the IrisPlex prediction model and a novel prediction model, EC12, were evaluated in 521 samples from the Norwegian population. A PCR-SBE-CE assay amplifying the fourteen SNPs included in the two models was optimised at Section of Forensic Genetics, Copenhagen, Denmark before it was established at Centre of Forensic Genetics, Tromsø, Norway.
IrisPlex showed high prediction accuracy for blue and brown eye colour (AUC-value of 0.84 and 0.94, respectively). However, the model did not perform good in prediction of intermediate eye colour (AUC-value of 0.6), which represented 24% of the Norwegian population and thus all these individuals were incorrectly predicted.
Comparison of EC12 and an adjusted IrisPlex model (IP NO) showed a small increase in correct predictions from 72% to 75%, respectively. A higher prediction accuracy for all eye colours were observed for the EC12 model, with AUC-value of 0.84 (blue), 0.97 (brown) and 0.68 (intermediate), while IP NO obtained AUC-values of 0.81 (blue), 0.93 (brown) and 0.59 (intermediate). This increase may imply that the additionally SNPs included in this model has an improving effect on eye colour prediction. However, the prediction of intermediate eye colour was still not good, indicating the importance of further phenotypic investigation of this category.UiT Norges arktiske universitetUiT The Arctic University of NorwayOlsen, Gunn-HegeMjølsnes Savo, NinaBørsting, ClausJanssen, KirstinBerg, ThomasMastergradsoppgaveMaster thesisAnalysis of 30 Y-chromosomal STR markers in the Norwegian populationStøtvig, Ingridhttps://hdl.handle.net/10037/251802022-05-19T06:07:49Z2019-05-15T00:00:00ZStøtvig, Ingrid<br />
Autosomal STR-analysis is the standard method of DNA-typing in casework. However, there are forensic sample types that may contain a large fraction of female DNA and a minimal fraction of male DNA. The male fraction may not be successfully amplified using autosomal STR-analysis because it “drowns” in the female fraction. However, the analysis of male-specific YSTR markers may circumvent this obstacle.
The purpose of this study was to analyze YSTR markers in the Norwegian population. Two analysis kits based on different technologies, capillary electrophoresis and next generation sequencing, were used. Both fragment length and sequence information was obtained for YSTR alleles. The fragment length-based information is collected to be included in a reference database of YSTR haplotypes that can be used to calculate the statistical weight of the evidence upon a DNA-profile match.
Several loci overlap between the two kits, and the concordance based on fragment length was high. Forensic parameters were calculated for both kits in order to evaluate the analytical power. Sequencing leads to an increase in allele variants, and many of the allele variants found are apparently novel.<br />
2019-05-15T00:00:00ZAnalysis of 30 Y-chromosomal STR markers in the Norwegian populationStøtvig, IngridAutosomal STR-analysis is the standard method of DNA-typing in casework. However, there are forensic sample types that may contain a large fraction of female DNA and a minimal fraction of male DNA. The male fraction may not be successfully amplified using autosomal STR-analysis because it “drowns” in the female fraction. However, the analysis of male-specific YSTR markers may circumvent this obstacle.
The purpose of this study was to analyze YSTR markers in the Norwegian population. Two analysis kits based on different technologies, capillary electrophoresis and next generation sequencing, were used. Both fragment length and sequence information was obtained for YSTR alleles. The fragment length-based information is collected to be included in a reference database of YSTR haplotypes that can be used to calculate the statistical weight of the evidence upon a DNA-profile match.
Several loci overlap between the two kits, and the concordance based on fragment length was high. Forensic parameters were calculated for both kits in order to evaluate the analytical power. Sequencing leads to an increase in allele variants, and many of the allele variants found are apparently novel.UiT Norges arktiske universitetUiT The Arctic University of NorwayJanssen, KirstinOlsen, Gunn-HegeBerg, ThomasMastergradsoppgaveMaster thesisThe prognostic significance of miR-17-5p and miR-20a-5p in prostate cancerIngebriktsen, Lise Martinehttps://hdl.handle.net/10037/251772022-05-19T06:07:44Z2019-05-15T00:00:00ZIngebriktsen, Lise Martine<br />
Prostate cancer accounts for extensive mortality and is the second most frequent cancer type occurring in men, acknowledged as a severe health problem globally. In Norway, Prostate cancer is the most common form of cancer in men, and around 5.000 patients are diagnosed each year. Using in situ hybridization, we examined the in situ tissue distribution of miR-17-5p and miR-20a-5p in prostate cancer tissue and their potential functions as biomarkers, and assessed their prognostic value from our cohort of 535 prostate cancer patients. We retrospectively evaluated the prognostic impact of marker expression in the clinical outcome Biochemical failure, Clinical failure, and Prostate cancer death by utilizing survival analyses. In addition, we correlated the microRNAs miR-17-5p and miR-20a-5p with the proliferation marker Ki-67. Reducing over-treatment in PCa patients have for many years been an ongoing concern. This controversy underlines the need for more personalized diagnosis and treatment of these patients, whereas miRNAs as biomarkers proposes as promising candidates. miR-17-5p and miR-20a-5p, which are members of the miR-17-92 cluster that are known to act as oncomiRs, may have potential as prognostic biomarkers in prostate cancer, and a possible value in future treatment of prostate cancer.<br />
2019-05-15T00:00:00ZThe prognostic significance of miR-17-5p and miR-20a-5p in prostate cancerIngebriktsen, Lise MartineProstate cancer accounts for extensive mortality and is the second most frequent cancer type occurring in men, acknowledged as a severe health problem globally. In Norway, Prostate cancer is the most common form of cancer in men, and around 5.000 patients are diagnosed each year. Using in situ hybridization, we examined the in situ tissue distribution of miR-17-5p and miR-20a-5p in prostate cancer tissue and their potential functions as biomarkers, and assessed their prognostic value from our cohort of 535 prostate cancer patients. We retrospectively evaluated the prognostic impact of marker expression in the clinical outcome Biochemical failure, Clinical failure, and Prostate cancer death by utilizing survival analyses. In addition, we correlated the microRNAs miR-17-5p and miR-20a-5p with the proliferation marker Ki-67. Reducing over-treatment in PCa patients have for many years been an ongoing concern. This controversy underlines the need for more personalized diagnosis and treatment of these patients, whereas miRNAs as biomarkers proposes as promising candidates. miR-17-5p and miR-20a-5p, which are members of the miR-17-92 cluster that are known to act as oncomiRs, may have potential as prognostic biomarkers in prostate cancer, and a possible value in future treatment of prostate cancer.UiT Norges arktiske universitetUiT The Arctic University of NorwayRichardsen, ElinBusund, Lill-ToveMastergradsoppgaveMaster thesisCharacterization of commensal enterococcal membrane vesicles and their cytotoxic effect on various host cellsBhandari, Ishanhttps://hdl.handle.net/10037/251572022-05-18T09:48:51Z2020-05-14T00:00:00ZBhandari, Ishan<br />
Enterococcus are a group of bacteria growing on different environmental condition behaving as a commensal as well as opportunistic pathogen. Among the enterococci, Enterococcus faecium is recently emerged as a nosocomial multi-resistance pathogen especially in the severely ill and immunocompromised patients causing a wide range of diseases like endocarditis, bacteraemia and urinary tract infections. Membrane vesicles are released by these bacteria and are the membranous structure carrying different proteins and some virulence factors. This present study focuses on the isolation of membrane vesicles released by the commensal E. faecium E1007, to study the morphological characteristics and measure the host responses in different cells. First in preliminary observations, E. faecium E1007 was grown on different cultural plates and their colony characteristics were observed. Gram staining from blood agar and growth curve of E. faecium in BHI medium was monitored. E. faecium grown on BHI from both exponential and stationary growth phase releases membrane vesicles which were further purified using the density gradient centrifuge. The purified vesicles were analysed by Transmission electron microscope that showed their broad size range from 30-182 nm and 20-174 nm in stationary and exponential phases respectively and they look small circular structures. Dynamic light scattering shows an average size of 55.1 nm in crude and 100.1 nm in OptiPrep samples exponential growth phase whereas 73.7 nm in crude and 114 nm in OptiPrep samples from Stationary growth phase. The proteomic analysis shows a total of 1160, 1012, 497 proteins from Stationary growth phase OptiPrep fractions 1, 2 and 3 respectively, 425 proteins from Stationary growth phase crude samples, 362 proteins from exponential phase OptiPrep and 1044 proteins from exponential phase crude samples. Membrane vesicles were inoculated in HaCaT cells, CaCo-2 cells and neutrophil cells at different concentration and cytotoxicity in these cells were observed. Membrane vesicles from E. faecium E1007 showed high toxic to HaCaT cells and Neutrophil cells but not cytotoxic to CaCo-2 cells. This study provides a better understanding of Gram-positive E. faecium membrane vesicles and their cytotoxic nature to different host cells.<br />
2020-05-14T00:00:00ZCharacterization of commensal enterococcal membrane vesicles and their cytotoxic effect on various host cellsBhandari, IshanEnterococcus are a group of bacteria growing on different environmental condition behaving as a commensal as well as opportunistic pathogen. Among the enterococci, Enterococcus faecium is recently emerged as a nosocomial multi-resistance pathogen especially in the severely ill and immunocompromised patients causing a wide range of diseases like endocarditis, bacteraemia and urinary tract infections. Membrane vesicles are released by these bacteria and are the membranous structure carrying different proteins and some virulence factors. This present study focuses on the isolation of membrane vesicles released by the commensal E. faecium E1007, to study the morphological characteristics and measure the host responses in different cells. First in preliminary observations, E. faecium E1007 was grown on different cultural plates and their colony characteristics were observed. Gram staining from blood agar and growth curve of E. faecium in BHI medium was monitored. E. faecium grown on BHI from both exponential and stationary growth phase releases membrane vesicles which were further purified using the density gradient centrifuge. The purified vesicles were analysed by Transmission electron microscope that showed their broad size range from 30-182 nm and 20-174 nm in stationary and exponential phases respectively and they look small circular structures. Dynamic light scattering shows an average size of 55.1 nm in crude and 100.1 nm in OptiPrep samples exponential growth phase whereas 73.7 nm in crude and 114 nm in OptiPrep samples from Stationary growth phase. The proteomic analysis shows a total of 1160, 1012, 497 proteins from Stationary growth phase OptiPrep fractions 1, 2 and 3 respectively, 425 proteins from Stationary growth phase crude samples, 362 proteins from exponential phase OptiPrep and 1044 proteins from exponential phase crude samples. Membrane vesicles were inoculated in HaCaT cells, CaCo-2 cells and neutrophil cells at different concentration and cytotoxicity in these cells were observed. Membrane vesicles from E. faecium E1007 showed high toxic to HaCaT cells and Neutrophil cells but not cytotoxic to CaCo-2 cells. This study provides a better understanding of Gram-positive E. faecium membrane vesicles and their cytotoxic nature to different host cells.UiT Norges arktiske universitetUiT The Arctic University of NorwayWagner, TheresaMastergradsoppgaveMaster thesis