Single molecule analysis of combinatorial splicing

Alternative splicing creates diverse mRNA isoforms from single genes and thereby enhances complexity of transcript structure and of gene function. We describe a method called spliceotyping, which translates combinatorial mRNA splicing patterns along transcripts into a library of binary strings of nucleic acid tags that encode the exon composition of individual mRNA molecules. The exon inclusion pattern of each analyzed transcript is thus represented as binary data, and the abundance of different splice variants is registered by counts of individual molecules. The technique is illustrated in a model experiment by analyzing the splicing patterns of the adenovirus early 1A gene and the beta actin reference transcript. The method permits many genes to be analyzed in parallel and it will be valuable for elucidating the complex effects of combinatorial splicing

A dual-tag microarray platform for high-performance nucleic acid and protein analyses

DNA microarrays serve to monitor a wide range of molecular events, but emerging applications like measurements of weakly expressed genes or of proteins and their interaction patterns will require enhanced performance to improve specificity of detection and dynamic range. To further extend the utility of DNA microarray-based approaches we present a high-performance tag microarray procedure that enables probe-based analysis of as little as 100 target cDNA molecules, and with a linear dynamic range close to 105. Furthermore, the protocol radically decreases the risk of cross-hybridization on microarrays compared to current approaches, and it also allows for quantification by single-molecule analysis and real-time on-chip monitoring of rolling-circle amplification. We provide proof of concept for microarray-based measurement of both mRNA molecules and of proteins, converted to tag DNA sequences by padlock and proximity probe ligation, respectively

Targeted resequencing of candidate genes using selector probes

Targeted genome enrichment is a powerful tool for making use of the massive throughput of novel DNA-sequencing instruments. We herein present a simple and scalable protocol for multiplex amplification of target regions based on the Selector technique. The updated version exhibits improved coverage and compatibility with next-generation-sequencing (NGS) library-construction procedures for shotgun sequencing with NGS platforms. To demonstrate the performance of the technique, all 501 exons from 28 genes frequently involved in cancer were enriched for and sequenced in specimens derived from cell lines and tumor biopsies. DNA from both fresh frozen and formalin-fixed paraffin-embedded biopsies were analyzed and 94% specificity and 98% coverage of the targeted region was achieved. Reproducibility between replicates was high (R2 = 0, 98) and readily enabled detection of copy-number variations. The procedure can be carried out in <24 h and does not require any dedicated instrumentation

ProteinSeq: High-Performance Proteomic Analyses by Proximity Ligation and Next Generation Sequencing

Despite intense interest, methods that provide enhanced sensitivity and specificity in parallel measurements of candidate protein biomarkers in numerous samples have been lacking. We present herein a multiplex proximity ligation assay with readout via realtime PCR or DNA sequencing (ProteinSeq). We demonstrate improved sensitivity over conventional sandwich assays for simultaneous analysis of sets of 35 proteins in 5 µl of blood plasma. Importantly, we observe a minimal tendency to increased background with multiplexing, compared to a sandwich assay, suggesting that higher levels of multiplexing are possible. We used ProteinSeq to analyze proteins in plasma samples from cardiovascular disease (CVD) patient cohorts and matched controls. Three proteins, namely P-selectin, Cystatin-B and Kallikrein-6, were identified as putative diagnostic biomarkers for CVD. The latter two have not been previously reported in the literature and their potential roles must be validated in larger patient cohorts. We conclude that ProteinSeq is promising for screening large numbers of proteins and samples while the technology can provide a much-needed platform for validation of diagnostic markers in biobank samples and in clinical use

Biomolecular Analysis by Dual-Tag Microarrays and Single Molecule Amplification

Padlock probes and proximity ligation are two powerful molecular tools for detection of nucleic acids and proteins, respectively. Both methods result in the formation of DNA reporter molecules upon recognition of specific target molecules. These reporter molecules can be designed to include tag sequences that can be analyzed by techniques for nucleic acid analysis. Herein, I present a dual-tag microarray (DTM) platform that is suitable for high-performance analyses of DNA reporter molecule libraries, generated by padlock and proximity probing reactions. The DTM platform was applied for analysis of mRNA transcripts using padlock probes, and of cytokines using proximity ligation. The platform drastically improved specificity of detection, and it allowed precise measurements of proteins and nucleic acids over wide dynamic ranges. The thesis also presents two techniques for multi-probe analyses of biomolecules: the triple-specific proximity ligation assay (3PLA) for protein analyses, and the spliceotyping assay for mRNA analyses. 3PLA allows highly specific measurements of as little as hundreds of target protein molecules by interrogating three target epitopes simultaneously. In spliceotyping the exon composition of individual transcripts are represented as a series of tag sequences in DNA reporter molecules, via a series of target-dependent ligation reactions. Next, the splicing patterns along individual transcripts can be revealed by amplified single molecule detection and step-wise decoding

Mergers and Acquisitions - Motives, Success factors, Due diligence &amp; the Integration phase : A qualitative study concucted on three listed Swedish companies

Background: In year 2021 M&amp;A deals accounted for 5.1 trillion US dollars which crushed the last record of 4.1 trillion US dollars. The strategy of creating shareholder value by acquiring, merging or through other restructuring activities is accelerating at an increasing pace. An already extensive research within M&amp;A are supplemented by the day. Still, existing research has difficulty explaining in-depth why M&amp;A deals tend to fail.   Purpose: The aim this thesis is to form an in-depth understanding of the M&amp;A process with investigations and comparisons of motives for and success factors of mergers and acquisitions. The objective is also to describe the due diligence process and its impact on the integration phase with the ambition to provide additional aspects and differentiating explanations from the ones already established.   Method: By highlighting theorists view on motives, success factors, due diligence and importance of an integration strategy within M&amp;A the question occurs, how does some of the companies active within M&amp;A reason in this subject? The reasoning has been studied empirically through interviews with three respondents with significant positions at three different companies listed at the Swedish stock market and active within M&amp;A. To contribute to an in-depth understanding of our research aim interviews were held to create discussions beyond only answering our research questions.   Empirical results and analysis: The empirical result received from our interviews has been compiled to present the thoughts and the discussions with our respondents. The analysis partly discusses the similarities and differences between the theorists and our respondents. Further the analysis wants to contribute to in-depth understanding of the company’s thoughts and opinions within our research aim.     Conclusion: The study indicates a variation of motives of acquiring another company. The empirical findings and the theoretical framework suggest a wider product range, personal benefits for managers, increased market power and improved economic performance as the most prominent motives. Asking theorists and our respondents of what different motives there are of acquiring other companies may consequently result in different responses. A significant factor determining whether a transaction has been successful or not are accomplishments of the financial objectives. The empirical results also indicate that synergy effects and integration goals could be considered relevant success factors as well. Theorists claim that the success factors vary greatly depending on who is being asked but agrees with the empirical findings of a repetitive success factor when asking a manager being increased revenue and profitability. Due diligence conducted by the acquirer prior to an acquisition also varies greatly depending on the reason for acquiring and the extent of the target company. However, the empirical investigation exhibits three aspects always being included which is an assessment of accounting, financial and legal aspects. Issues concerning the integration phase is incorporated in only one of the three studied company’s due diligence processes. This company allocates a separate team executing both the due diligence and the post- acquisition integration of the targeted company. Considering integrational aspects in the due diligence phase entails assessments of hiring conditions, IT infrastructure and financial reporting. The empirical findings are fragmented concerning considerations of integration already in the due diligence phase but is unanimous that a smooth integration is of utmost importance for the success of the transaction

Mergers and Acquisitions - Motives, Success factors, Due diligence &amp; the Integration phase : A qualitative study concucted on three listed Swedish companies

Background: In year 2021 M&amp;A deals accounted for 5.1 trillion US dollars which crushed the last record of 4.1 trillion US dollars. The strategy of creating shareholder value by acquiring, merging or through other restructuring activities is accelerating at an increasing pace. An already extensive research within M&amp;A are supplemented by the day. Still, existing research has difficulty explaining in-depth why M&amp;A deals tend to fail.   Purpose: The aim this thesis is to form an in-depth understanding of the M&amp;A process with investigations and comparisons of motives for and success factors of mergers and acquisitions. The objective is also to describe the due diligence process and its impact on the integration phase with the ambition to provide additional aspects and differentiating explanations from the ones already established.   Method: By highlighting theorists view on motives, success factors, due diligence and importance of an integration strategy within M&amp;A the question occurs, how does some of the companies active within M&amp;A reason in this subject? The reasoning has been studied empirically through interviews with three respondents with significant positions at three different companies listed at the Swedish stock market and active within M&amp;A. To contribute to an in-depth understanding of our research aim interviews were held to create discussions beyond only answering our research questions.   Empirical results and analysis: The empirical result received from our interviews has been compiled to present the thoughts and the discussions with our respondents. The analysis partly discusses the similarities and differences between the theorists and our respondents. Further the analysis wants to contribute to in-depth understanding of the company’s thoughts and opinions within our research aim.     Conclusion: The study indicates a variation of motives of acquiring another company. The empirical findings and the theoretical framework suggest a wider product range, personal benefits for managers, increased market power and improved economic performance as the most prominent motives. Asking theorists and our respondents of what different motives there are of acquiring other companies may consequently result in different responses. A significant factor determining whether a transaction has been successful or not are accomplishments of the financial objectives. The empirical results also indicate that synergy effects and integration goals could be considered relevant success factors as well. Theorists claim that the success factors vary greatly depending on who is being asked but agrees with the empirical findings of a repetitive success factor when asking a manager being increased revenue and profitability. Due diligence conducted by the acquirer prior to an acquisition also varies greatly depending on the reason for acquiring and the extent of the target company. However, the empirical investigation exhibits three aspects always being included which is an assessment of accounting, financial and legal aspects. Issues concerning the integration phase is incorporated in only one of the three studied company’s due diligence processes. This company allocates a separate team executing both the due diligence and the post- acquisition integration of the targeted company. Considering integrational aspects in the due diligence phase entails assessments of hiring conditions, IT infrastructure and financial reporting. The empirical findings are fragmented concerning considerations of integration already in the due diligence phase but is unanimous that a smooth integration is of utmost importance for the success of the transaction

Reporäntans effekt på ett fastighetsaktieindex : En eventstudie på OMX Stockholm Real Estate GI.

Denna studie kommer undersöka reaktionerna i ett fastighetsaktieindex eftertillkännagivandet av en förändring i den svenska reporäntan. Studien kommer atttillämpa en kvantitativ metod för att besvara och sammanfatta formuleradefrågeställningar. Uppsatsens metodik följer förfaranden i enlighet med eneventstudie där reporäntebesluten är huvudeventet. Riksbankens beslut avseende reporäntan kan ske i två riktningar, en ökning avreporäntan eller en minskning av reporäntan. I vissa fall består reporäntanoförändrad vilket studien också tar i beaktning. Därmed finns det tre tänkbara beslutvilket innebär att undersökningen behövde konstrueras i enlighet med detta. Såledessamlades data in för 61 tillkännagivanden gällande reporäntan varav 14 avsågräntesänkning, 8 räntehöjningar och 39 oförändrade beslut. Vidare samlades data inför det valda fastighetsaktieindexet för varje event för att utföra beräkningar ochgenomföra tester på tre olika signifikansnivåer. Eventfönstret består av elva dagar,fem dagar innan eventdagen, fem dagar efter eventdagen och själva eventdagen. Tidigare forskning tillsammans med de slutgiltiga resultaten av testerna ochberäkningarna presenteras för att bistå diskussionen och besvara studiens syfte.Högsta uppmätta reaktionen vid beräkningen av den abnormala avkastningen visadesig vara vid ett tillfälle när Riksbanken beslutar sig för att höja reporäntan.Presenterade diagram och tabeller lämnar en del att önska eftersom den genomfördaundersökningen enbart inkluderar 8 räntehöjningar och 14 räntesänkningar. Testerutförda på den abnormala avkastningen är därmed något tvetydiga i jämförelse medtester utförda på den kumulativa genomsnittliga abnormala avkastningen. Dethögsta värde uppmätt för den kumulativa genomsnittliga abnormala avkastningavser besluten om en räntesänkning. T-testen för dessa värden påvisar en statistisksignifikans med en sannolikhet på 99 procent.

Reporäntans effekt på ett fastighetsaktieindex : En eventstudie på OMX Stockholm Real Estate GI.

Denna studie kommer undersöka reaktionerna i ett fastighetsaktieindex eftertillkännagivandet av en förändring i den svenska reporäntan. Studien kommer atttillämpa en kvantitativ metod för att besvara och sammanfatta formuleradefrågeställningar. Uppsatsens metodik följer förfaranden i enlighet med eneventstudie där reporäntebesluten är huvudeventet. Riksbankens beslut avseende reporäntan kan ske i två riktningar, en ökning avreporäntan eller en minskning av reporäntan. I vissa fall består reporäntanoförändrad vilket studien också tar i beaktning. Därmed finns det tre tänkbara beslutvilket innebär att undersökningen behövde konstrueras i enlighet med detta. Såledessamlades data in för 61 tillkännagivanden gällande reporäntan varav 14 avsågräntesänkning, 8 räntehöjningar och 39 oförändrade beslut. Vidare samlades data inför det valda fastighetsaktieindexet för varje event för att utföra beräkningar ochgenomföra tester på tre olika signifikansnivåer. Eventfönstret består av elva dagar,fem dagar innan eventdagen, fem dagar efter eventdagen och själva eventdagen. Tidigare forskning tillsammans med de slutgiltiga resultaten av testerna ochberäkningarna presenteras för att bistå diskussionen och besvara studiens syfte.Högsta uppmätta reaktionen vid beräkningen av den abnormala avkastningen visadesig vara vid ett tillfälle när Riksbanken beslutar sig för att höja reporäntan.Presenterade diagram och tabeller lämnar en del att önska eftersom den genomfördaundersökningen enbart inkluderar 8 räntehöjningar och 14 räntesänkningar. Testerutförda på den abnormala avkastningen är därmed något tvetydiga i jämförelse medtester utförda på den kumulativa genomsnittliga abnormala avkastningen. Dethögsta värde uppmätt för den kumulativa genomsnittliga abnormala avkastningavser besluten om en räntesänkning. T-testen för dessa värden påvisar en statistisksignifikans med en sannolikhet på 99 procent.