Myocardial infarction (MI) and stroke are the major causes of cardiovascular related morbidities and mortalities around the world. The prevalence of cardiovascular diseases has been increased in last decades and it is vital need of time to investigate this global problem with focus on risk population stratification. The aim of the present study is to investigate the association between individualized personality trait that is neuroticism and risk of MI and stroke has been investigated in a large population-based cohort of UK biobank.375,713 individuals (mean age: 56.24 ± 8.06) were investigated in this longitudinal study and were followed up for seven years to assess the association between neuroticism and risk of MI and stroke incidence. The neuroticism score was assessed by a 12-item questionnaire at baseline, while information related to MI and stroke events was either collected from hospital records and death registries or was self-reported by the participants. Cox proportional hazard regression adjusted for age, gender, BMI, socioeconomic status, lifestyle factors and medical histories for hypertension, diabetes and depression was used. All statistical analyses were performed using R software. In fully adjusted model, a one standard deviation increase in neuroticism score was associated with 1.05-fold increased risk for MI. (HR=1.047(1.009-1.087), p=0.015). However, no significant association was observed between neuroticism score and incident stroke as well as between neuroticism score and overall cardiovascular disease (MI and stroke combined). Results from the present study indicate that neuroticism is a risk factor for MI but not for stroke. These findings suggest that personality traits such as neuroticism may prove to be helpful in efficient risk stratification and pre-clinical diagnosis of individuals at risk for MI.

Pathway enrichment analysis is an approach extensively used when analyzing high throughput data to identify pathways enriched within a group of differentially expressed genes. Furthermore, different methods utilizing the topology of the pathway offer a unique way of analyzing and interpreting gene expression data. These methods usually offer pathway topologies with a limited number of methods and visualization of results. Also, the use of different methods individually and comparison of their results can be very cumbersome, time-consuming and prone to errors due to the need for repeated data conversion and transfer. Packages that offer a common interface to multiple methods are therefore necessary, to provide a uniform way of calling these methods or specifying parameters, and making simultaneous application of the methods easier. In this study topology-based pathway enrichment analysis was performed by using the R packages EnrichmentBrowser and ToPASeq on a time series RNA-Seq data for cardiac hypertrophy in order to compare their usability. Additionally, different topology-based enrichment analysis methods included in the packages were compared with a non-topology-based pathway enrichment analysis method as well as the combination of their results in order to assess biological insights. Regarding usability, the available instructions for how to use both EnrichmentBrowser and ToPASeq were easy to understand and apply in the R workspace. Furthermore, both packages were easy to install and adjust to various parameters. However, ToPASeq returned errors when some parameters other than the default ones were used. Also, one of the differences between the tools was the flexibility of options for visualization and interpretation of the results, where EnrichmentBrowser had clear advantages. Regarding biological insights, the methods SPIA and DEGraph produced significant pathways linked to the phenotype cardiac hypertrophy, with a clear advantage for SPIA that performed well in both tested data setups. Finally, combining results from both SPIA and GSEA (non-topology-based pathway enrichment analysis method) improved individual ranking by increasing confidence in specific target pathways and eliminating irrelevant pathways.

No description available.

Freshwater mussels (Unionida) belong to phylum Mollusca and live in freshwater habitats, such as lakes and rivers. Freshwater mussels have high capacity for water purification and play an important role in calcium recycling. There is not much information about the freshwater mussel genome due to lack of genomic sequences in the database, till now only four species have been sequenced and the only Swedish one is Margaritifera margaritifera. This study aim was to usenanopore sequencing technology to sequence the genomic DNA of a freshwater mussel. The data about the genomic sequence is helpful in identification of their species and give a better understanding towards the genomics and transcriptomics, it also could help in the development of multi-biomarker panels for an early assessment of water pollution. In this study the DNA used was extracted from the foot tissues, and different tissue homogenization methods were tested to find the best approach. The genomic DNA was sequenced by using Oxford nanopore MinION device, and the reads were assembled and polished using multiple software through bioinformatic analysis. The number of reads from sequencing the DNA covered only 13.5x of the estimated genome size of the freshwater mussel, while the required coverage for a complete genome assembly is 20x-25x or higher. Due to low coverage and fragmentation, a partial sequence of the genomic DNA was obtained. This indicates that nanopore sequencing could be used, but additional sequencing runs are needed to get enough coverage to assemble a complete genomic DNA of the freshwater mussel.

Extracellular vesicles (EVs) are released by almost  all types of cells. EVs play an    important role in cell-to-cell communication by sending biomolecules such as mRNAs to    other cells via endocytosis. This project aims to understand the roles of EVs and their    potential application as mRNA delivery vehicles by completing two objectives. One       objective was to investigate the EVs’ roles in cell proliferation by routinely removing EVs    from cell-conditioned media, transferring stress-induced EVs to recipient epithelial cells, and examining their cell number. Another objective was to analyzethe transcriptomic expression of HUVEC cells treated with breast-cancer-derived EVs. EVs were routinely removed from the cell culture using 100 kDa filters, 15 kDa filters, or by changing to new media. The result showed that the epithelial cancer cell line grows at a lower growth rate when EVs are removed using 100 kDa filters and 15 kDa filters compared to the control. The stressinduced EV transfer experiment showed no significant difference in cell number among different stress conditions and stress-EV treatment. The transcriptomic analysis revealed 765 differentially expressed genes, which were mapped onto pathways using the IPA software. The majority of the top 10 significant pathways were associated with cancer progression. IPA’s Biomarker Filter function revealed 35 cancer biomarkers, as well as 33 putative angiogenesis biomarkers. VEGFAtargeted genes were identified, and the ones that are upregulated and located in the extracellular matrix or plasma membrane were identified as putative biomarkers for VEGFA-induced angiogenesis. The top 10-pathways suggest that the recipient HUVEC may receive cancer-related messages from the EVs. It is important to evaluate the content of EVs derived from different origins thoroughly. Cancer-derived EVs may induced angiogenesis in HUVEC, as shownpreviously, but cancer EVs might also communicate cancer signals that can cause pathological effects. Extensive studies and validation are needed to fully understand the role of EVs and their application as an mRNA delivering system.

Acute myeloid leukaemia (AML) is a heterogeneous group of myeloid lineage malignancies arising from a spectrum of mutations. AML is characterized by the uncontrolled proliferation of clonal cells, which are unable to properly differentiate into mature myeloid cells. The present day standard treatment of care for AML patients under 60 years of age is the “7+3” induction chemotherapy. The survival rate beyond 5 years has been maintained at 40%. Most AML patients older than 60 years are unable to tolerate this intensive cytotoxic induction regimen and are treated with hypomethylating drugs. The two-year relapse-free survival rate of these patients remains at 40% (exceptionally low) with a median survival of 6.5 months. Thus, novel therapeutic strategies are urgently needed to improve the overall survival of both young and elderly AML patients. Therefore, elucidating the molecular mechanisms underlying AML has been of prime importance in the development of efficacious targeted therapeutics to treat subtypes of this heterogeneous haematological malignancy. Next-generation sequencing has uncovered that the most frequently mutated class of genes in AML encode epigenetic modifiers, suggesting that alterations in the epigenetic landscape contribute to the development of AML. H3K27me3 is an epigenetic alteration of the Histone H3, one of the five principal histones involved in chromatin construction in eukaryotic cells. In refractory acute myeloid leukaemia, a study found an epigenetic relationship between the decreased abundance of the Polycomb related protein MTF2 and chemotherapy resistance. MTF2 loss hampered PRC2 complex expression and H3K27me3 deposition at numerous genes, including the major target gene MDM2, resulting in enhanced MDM2 expression, which depleted p53 and conferred chemoresistance. This study aimed to elucidate the epigenetic dysregulation in chemorefractory and chemoresponsive AML.     A systems biology methodology was utilized here. Two AML sample types were collected from the bone marrow of AML patients. The first sample (AML_4) had basal levels of the epigenetic modification H3K27me3 and basal levels of MTF2. The second sample (AML_1) had low levels of H3K27me3 and basal levels of MTF2. ATAC-seq (Assay for Transposase Accessible Chromatin with High-Throughput Sequencing) is a powerful tool for revealing chromatin accessibility across the genome. By probing hyperactive Tn5 transposase to a DNA sequence, ATAC-seq generates reads from cells representing accessible regions that correspond to nucleosome positioning and transcription factor binding sites. ATAC-seq was performed on AML_4 and AML_1. Bioinformatics analysis was conducted on the two ATAC-seq data to identify transcription factors with differential activity in each of the AML types. 36 transcription factors with significant differential activity were identified in AML_1 while 4 transcription factors were identified in AML_4. These results reveal higher epigenetic dysregulation in AML_1. These results reveal higher epigenetic dysregulation in AML_1 compared to AML_4. These transcription factors with significant activity in the different AML types would be combined with CHIP-seq and RNA-seq data thereafter used for gene regulatory network analysis of key AML genes to uncover the underlying mechanisms of the regulation of these genes.

Insectivorous bats face fragmentation and loss of suitable habitats. Bats numbers are declining in several parts of the world and scientists aim to construct distribution models that can predict occurrence, in order to understand species habitat requirements. Significant correlation has been found between species and habitat attributes but conditions differ across the world and between species. A predictive model will not work as well somewhere else. Bat occurrence in Vara, Alingsås, Vårgårda and Borås municipalities is only briefly inventoried. The aim of this study is to investigate if chosen habitat attributes affect bat occurrence in these municipalities. Inventories from wind energy establishments were used, and nine species were found. Multiple linear logistic regression analysis were used to compare species occurrence with vicinity to water, trees with special qualities “Skyddsvärda träd”, nature reserves, area of deciduous forest and urban area, and aspect. Five significant results are consistent with previous knowledge; positive effect of vicinity to skyddsvärda träd and small area of open habitats for Myotis brandtii/mustacinus and positive effect of vicinity to urban areas for Nyctalus noctula and Vespertilio murinus. Four significant results contradict known behaviour or cannot be explained. There is also a non-significant positive trend of vicinity to water for seven species. The results are unclear with low reliability. Type of bat activity is not known. Habitat requirements differ whether the area is used for roosting, hunting or transport, which is important to consider when “occurrence” is defined. Data was not collected at the same time of the year which affects both activity and species occurrence. This type of analysis along with modelling is a cost-effective way to monitor bat dispersion. Studies in other countries have found predictive correlations and this study can be improved. Therefore it should be possible to generate more accurate analyses in future Swedish studies. / Insektsätande fladdermöss hotas av fragmentering och förlust av boplatser. I flera världsdelar minskar fladdermöss i antal och forskare arbetar med att skapa modeller som förutsäger förekomst, för att förstå arters habitatkrav. Signifikanta samband har påvisats mellan arter och attribut i deras livsmiljöer men levnadsförhållanden skiljer sig mycket över världen och mellan arter. En modell kan inte antas fungera lika bra överallt. I Vara, Alingsås, Vårgårda och Borås kommuner är fladdermusförekomst endast översiktligt inventerad. Syftet med den här studien är att undersöka om utvalda miljöparametrar påverkar förekomst i nämnda kommuner. Inventeringar utförda i samband med vindkraftsutbyggnad användes, där nio arter påträffades. Arternas förekomst jämfördes genom multipel linjär logistisk regressionsanalys med avstånd till närmsta vatten, skyddsvärda träd, naturreservat samt tätort, mängden lövskog och öppen mark inom 300 meter från inventeringspunkten samt väderstreck på sluttningar. Fem signifikanta resultat kan kopplas till tidigare kända beteenden, såsom positiv effekt av närhet till skyddsvärda träd och minskande mängd öppen mark för Tajga/mustaschfladdermus (Myotis brandtii/mustacinus) och positiv effekt av närhet till tätort för Större brunfladdermus (Nyctalus noctula) och Gråskimlig fladdermus (Vespertilio murinus). Fyra signifikanta resultat strider mot arters beteenden eller inte kan förklaras. Bland icke signifikanta resultat syns en positiv trend av närhet till vatten för sju av nio arter. Resultatet spretar och tillförlitligheten är låg. Det är inte känt vilken aktivitet fladdermössen utövade under inventeringarna. Habitatkrav skiljer sig om området används som boplats, jaktmark eller förflyttningsstråk, vilket är viktigt att ta hänsyn tillvid definition av ”förekomst”. Data är dessutom insamlad under olika tider på året vilket påverkar både aktivitet och förekomst. Denna typ av analys tillsammans med modellering är ett kostnadseffektivt sätt att bevaka fladdermusförekomst. Studier i andra delar av världen har hittat tydliga samband och det finns förbättringsmöjligheter i denna metod. Därför finns förutsättningar för framtida mer precisa analyser även i Sverige.

Common variable immunodeficiency (CVID) is a rare primary immune deficiency (1:25000) in which patients have a reduction in antibody production and very low titres in one or more of their Ig isotypes, (IgG, IgA and sometimes IgM). This disease can cause different symptoms such as: bronchiectasis, chronic lung disease and even autoimmunity, polyclonal lymphocytic infiltration, lymphoma and death. The underlying causes of CVID are still largely unknown but studies show that different factors like primary B-cell dysfunctions, defects in T cells and antigen-presenting cells are involved. Quantitative analysis of gene expression is of high importance in understanding the molecular mechanisms underlying this diseases´ genome regulation. Next-generation RNA-seq has enabled researchers to analyse both coding and non-coding regions of RNA, and therefore has made it possible to identify differentially expressed genes in large-scale data, especially in polygenic diseases like CVID. The aim for this study was to identify the differentially expressed genes between CVID patients and healthy donors to identify important genes and molecular mechanisms underlying this diseases´ genome regulation. For this matter, whole genome RNA-seq analysis was performed on RNA isolated from sorted peripheral blood naïve and CD27bright memory B cells from healthy donors (n=7) and CVID patients (n=5). The RNA-seq data for the samples was collected and undergone several bioinformatical and analytical steps to be processed. After quality control and trimming, the data files were assembled to the human genome. Then, the transcriptomic data of the CVID patients was compared with the healthy donors to identify differentially expressed genes (DEGs). From this study, it was found that PAX5, ETS1, POU2AF1, SPIB, BACH 2, EBF1 and PRDM1 play an important role on regulation of the B cells and especially this disease. Also, the Ikaros family, toll-like receptors and a number of chemokine and cytokine receptors were found out to have high importance regarding CVID.

Single cell RNA technology is a recent technical advancement used to understand the cancertumorgenicity at single cell resolution. In this study we have analyzed the scRNA data from thenon-small cell lung cancer (NSCLC) dataset to facilitate the early identification of NSCLCsubtypes namely, squamous cell carcinoma (SCC) and adenocarcinoma (AC). Non-immunecells, have a major role in tumorigenesis of the malignant tumors, in early stages. Therefore,we have analyzed the major non-immune cells, namely endothelial cells and fibroblast cellsfrom the GSE127465 dataset using SEURAT pipeline. Dimensionality reduction analysis andcluster analysis indicate that AC and SCC subtypes of NSCLC have different fibroblastcompositions. Differential gene expression analysis indicates that AC tumours have shownelevated content of MGP/PTGDS and INMT/MFAP4 fibroblast cells, whereas squamous cellcarcinoma showed an elevated content of COL6A1/COL6A2 and FNDC1/COL12A1 fibroblastcells. The statistical analysis shows that the clustering is statistically significant and not anartefact. Given that the tumour microenvironment is highly dynamic, in this study we haveattempted to understand the tumour microenvironment by scRNA analysis of non-immune cellsat single cell resolution.

Staphylococcus aureus are bacterial pathogens causing infectious diseases. Methicillin-resistant S. aureus, or MRSA, carry the mecA or mecC genes generating resistance to β-lactam antibiotics. MRSA is problematic to treat and crucial to rapidly detect while current diagnostic workflows are time-consuming. DNA sequencing offers an alternative to existing methods. Illumina, the leading sequencing platform, is time-consuming and generates short reads. The Oxford Nanopore Technologies MinION presents rapid sequencing protocols, generating long reads at reduced accuracy. Here, the MinION device was evaluated to rapidly identify and differentiate between MRSA and non-MRSA isolates, with estimations on turn-around-times for clinical implementation.DNA extracted from 12 bacterial isolates were sequenced on the MinION. The automated workflow for raw MinION reads EPI2ME called taxonomy and resistance genes. MinION reads and corresponding Illumina reads were also assembled with Unicycler with short-read, long-read and hybrid assembly, and analyzed with the Center for Genomic Epidemiology bioinformatic tools. MinION and Illumina reads analyzed with the 1928 Diagnostics S. aureus pipelines were also compared. All tools correctly identified mecA in confirmed MRSA isolates, and mecC in an unconfirmed isolate. Similar results in terms of species, virulence and resistance genes were observed. Strain typing was problematic for MinION reads compared to Illumina, due to increased error rates. The minimum estimated turn-around-time for the MinION in this project, from library preparation, was approximately 6.5 hours to 7.5 hours per sample. Although further investigations are required, the MinION offers an intriguing alternative to current methods for identifying MRSA, aiding in rapid diagnosis and treatment.