Det finns idag flera tusen genetiska sjukdomar som inte kan botas med hjälp av dagens läkemedelsbehandlingar. Detta är något forskarna försöker finna en lösning på. Två nya potenta genredigeringsverktyg har utvecklats och tros kunna bota och behandla många av de idag kända genetiska sjukdomarna. Detta är clustered regularly interspaced short palindromic repeats med CRISPR-associerade proteiner, CRISPR/Cas9 och prime editing. Tekniker som utvecklats från det adaptiva immunförsvaret hos prokaryoter. Både CRISPR/Cas9 och prime editing är RNA-guidade system med DNA som mål, de är även möjliga att programmera. Syftet med denna litteratursökning var att: 1) Jämföra teknikerna CRISPR/Cas9 och prime editing, 2) Undersöka vilka idag pågående kliniska prövningar som finns där någon av teknikerna används vid behandling av sjukdom. 3) Undersöka vilka sjukdomstillstånd som tros kunna botas och/eller behandlas med hjälp av någon av teknikerna samt 4) undersöka hur forskare ser på de etiska aspekterna av dessa tekniker. Information har hämtats under arbetets gång, främst från PubMed, Google och clinicaltrials.gov. Det finns idag 16 pågående studier där CRISPR/Cas9 används som behandlingsmetod. För prime editing finns det inga pågående studier. Sjukdomarna som forskarna hoppas kunna behandla med hjälp av metoderna är många, men de har kommit längst i utvecklingen av läkemedel för cancer, blodsjukdomar och ögonsjukdomar. De etiska diskussionerna har varit många och den stora frågan som diskuteras är hur tekniken skall regleras för att inte utnyttjas till sådant som potentiellt kan vara skadligt. Detta är två tekniker med hopp om nya behandlingsmetoder för genetiska sjukdomar, dock är de endast i början av sin utveckling och mer forskning och förfining av metoderna krävs innan de kan tillämpas kliniskt. / Today, there are thousands of genetic diseases that cannot be cured with the help of today's drug treatments. This is something the researchers are trying to find a solution to. Two new potent gene editing tools have been developed and are believed to be able to treat or cure many of today's genetic diseases. These are Clustered regularly interspaced short palindromic repeats with CRISPR-associated proteins, CRISPR/Cas9 and prime editing. Techniques developed from the adaptive immune system of prokaryotes. Both CRISPR/Cas9 and prime editing are RNA-guided DNA-targeted systems that are programmable. The purpose of this literature search was to: 1) compare the CRISPR/Cas9 and prime editing techniques, 2) investigate the current clinical trials in which any of the techniques are used to treat disease. 3) investigate which diseases that are believed to be cured and/or treated by using one of the techniques, and 4) investigare how researchers view the ethical aspects of these techniques. Information was gathered during a period between January to May 2020, mainly from PubMed, Google and clinicaltrials.gov. There are currently 16 ongoing studies using CRISPR/Cas9 as a treatment method. For prime editing there are no ongoing studies. The diseases that the researchers hope to be able to treat using the methods are many, but they have come the farthest in the development of a drug for cancer, blood diseases and eye diseases. There have been many discussions about the ethical side, but the big question being discussed is how the technology should be regulated so that it may not be used to harm instead of treat. These two techniques give hope of new treatment methods of genetic diseases, however, they are in the early stages of their development and more research and refinement of the methods is required before they can be applied clinically.

Purpose This project aims to explore the classification method of kinase inhibitors with five-channel cell painting image data based on the deep learning model. Methods A ResNet50 transfer learning model was used as the starting point to build the deep neural network (DNN) model, where different DNN parameters were selected to make the deep learning model more suitable for the cell painting data. Two different adaptive layers (adaptive average pooling 3D and convolution 2D) were added separately before the ResNet50 transfer learning model to adapt the five-layer cell painting image to the neural network. In addition, the skimage.transform.resize function was used to compress the five-layer cell painting image. Results The proposed deep learning model demonstrates the effectiveness in all three classification experiments. The proposed model performs particularly well in classifying among control, EGFR, PIKK and CDK kinase inhibitors families. It achieves an F1-score of 0.7764 on all four targets and has a 93\% accuracy rate in the PIKK kinase inhibitors family. The adaptive average pooling 3D layer successfully adapts the five-layer images to the model, resulting in an improved effect. The training time of the model is significantly reduced to one-fortieth by compressing the image size. Conclusion The proposed model achieved convincing effectiveness in classifying families, which showed progress in building the deep learning model to classify kinase inhibitors on five-channel cell painting data. This study also proved the feasibility of directly inputting five-channel cell painting images to DNN. In addition, the speed of the model increased sharply by compressing the image size without an obvious loss of data information.

Acute spinal cord injury is often caused by collisions with motor vehicles, falls or violence. This injury could potentially lead to paraplegia or tetraplegia, causing great economic and personal loss. The patophysiology is biphasic, with primary and secondary mechanisms. Regarding secondary spinal cord injury, glutamate and interleukin-1 beta (IL-1<img src="http://www.diva-portal.org/cgi-bin/mimetex.cgi?%5Cbeta" data-classname="equation" data-title="" />) activates N-methyl-d-aspartate (NMDA)-receptors leading to prolonged excitotoxity, causing neuronal death and subsequently glial scarring. Cross-linked-hyaluronic acid gel and interleukin-1 receptor antagonist (IL-1RA) are believed to have a neuroprotective effect. The major aim of this study was to evaluate neuroprotection in the central neural system. Briefly, spinal cord slice cultures from mice (p9-12) were chemically injured with NMDA and treated with two hyaluronic acid-based gels with integrated, or added, IL1RA. RNA was extracted and transcripted to cDNA. The gene expression of Neuronal nuclear protein, <img src="http://www.diva-portal.org/cgi-bin/mimetex.cgi?%5Cbeta" data-classname="equation" data-title="" />-aktin and IL-1<img src="http://www.diva-portal.org/cgi-bin/mimetex.cgi?%5Cbeta" data-classname="equation" data-title="" /> were studies with RT-qPCR. Results showed that gel integrated with IL1RA had significant therapeutic effect, resembling undamaged cultures. Furthermore, axonal outgrowth was investigated in dorsal root ganglion (DRG) in which two preparations of the method were evaluated. Results demonstrated that changing medium every other day was more preferred, compared to adding 20 µl medium every day.  In conclusion, gels integrated with IL1RA have neuroprotective properties and in DRG preparations, medium should be changed every other day for optimal results.

If you could trap a moment of painful sorrow or a deep joy, what form would you like to keep? This project is exploring how designing with biology can allow new sets of affordances and ways of expressing and interacting with the artifacts. Hence to this idea, the researcher is exploring the concept of crystalizing tears and turning them to gold, both metaphorically and literally. Showcasing how wearable made of living things could allow us more humane, poetic, and symbiotic relationships, compare to transactional interactions we currently have with wearables based on computation. As the outcome of the project, the researcher uses a biochemical phenomenon to commemorate chapters in life. Beyond that, the researcher is opening a field of what could be possible in the context of designing with biology and biological matters, how we are going to use them, and what kind of relationship we could build, as we move from machines to organisms, from pixels to cells. In its core, the researcher desired to show that Interaction designers must become material researchers, rather than inhabiting in the realm of familiar mediums. And this is what this thesis is all about, and hopefully, it does not stop there.

Background Broth microdilution (BMD) is a gold-standard reference method to determine minimum inhibitory concentration (MIC) of antibiotics. For this, a standardized concentration of bacterial inoculum (2e5–8e5 colony-forming units, CFU/ml) is added to progressively higher concentrations of antibiotics. Bacteria stop growing at a particular antibiotic concentration termed MIC. Like other assays, various biological and/or technical factors can affect BMD results.   Aims To investigate the effects of inoculum concentration (5e4–5e6 CFU/ml), growth-medium concentration (cation-adjusted Mueller-Hinton Broth (CAMHB)), ranging 0.5x to 2x (1x as standard)) and age (&lt;6-months or &gt;1-year old) of fastidious medium on MIC results. And to compare BMD results using 5 different brands of CAMHBs and 1 cation-non-adjusted MH-broth (non-CAMHB).   Methods 12 isolates of bacteria (gram-positive (n=3), gram-negative(n=5), fastidious isolates (n=7)) and custom-made antibiotics-containing plates for gram-positive (11 antibiotics) or gram-negative bacteria (10 antibiotics) were used. Overnight-grown colonies were used to prepare BMD solutions (MH-broth + inoculum +/- fastidious) which were plated on antibiotic-plates as well as diluted prior to plating on agar-plates. Antibiotic- and agar-plates were incubated (18–20hr, 35°C) and used to determine MICs (following European Committee on Antimicrobial Susceptibility Testing instructions) and actual number of viable bacteria in BMD solutions, respectively.   Results Increasing inoculum concentration increased MICs of all antibiotics except cefoxitin. Piperacillin–tazobactam, levofloxacin, benzylpenicillin and ampicillin were especially sensitive to increase in inoculum and showed a 4-fold increase in &gt;50% isolates. MICs for tobramycin, tigecycline and gentamicin increased by 2-fold in &gt;50% isolates every time MH-broth concentration increased. Age of fastidious medium had no decipherable pattern of effects on MIC. All MH-broths gave similar results except when testing daptomycin which gave higher MICs with non-CAMHB compared to CAMHB.    Conclusion This research reveals some technical factors affecting MIC results. These results could help define parameters for automated BMD-performing-systems. However, this research shows only trends as more replicates are needed to determine statistically significant results.

Autoimmuna sjukdomar är en samling komplexa, kroniska, inflammatoriska sjukdomstillstånd som kännetecknas av dysreglering av immunsystemet, vilket resulterar i inflammation och skada av vävnader, celler och organ. Dessa sjukdomar har en betydande inverkan på individens livskvalitet och bidrar ofta till ökad dödsrisk där komorbiditeter föreligger. Emellertid medför den varierande symptombilden för olika autoimmuna sjukdomar betydande utmaningar för att uppnå noggrann diagnos, prognos och utvärdering av behandling. Det finns därför ett påtagligt behov av att upptäcka nya biomarkörer.  I denna studie utfördes en omfattande analys av 944 plasmaprover med hjälp av OlinkR Explore-plattformen, vilket genererade data för 1463 unika proteiner. Baserat på uttrycksdata identifierades proteiner förknippade med de sex utvalda autoimmuna sjukdomarna multipel skleros, myosit, reumatoid artrit, systemisk skleros, Sjögrens sjukdom och systemisk lupus erythematosus samt några av deras definierade subgrupper. Dessa potentiella biomarkörer kommer eventuellt att underlätta tidig diagnos, sjukdomsdifferentiering och prognos. Flertalet av dessa proteiner har ännu aldrig kopplats till de här specifika sjukdomarna i litteraturen, särskilt inte från plasmaprover, vilket ger spännande nya perspektiv för biomarkörsutveckling. Det är dock av största vikt att genomföra robusta valideringsstudier i oberoende kohorter.  Sammanfattningsvis belyser våra resultat den potentiella brukbarheten hos dessa proteomiska plasmabiomarkörer för att förbättra tidig sjukdomsdetektering, karakterisering av subgrupper och sjukdomsdifferentiering att stimulera. Förhoppningsvis kan dessa resultat stimulera till vidare forskning inom området för biomarkörer och potentiella framsteg inom individbaserad medicin. / Autoimmune diseases are complex, chronic, inflammatory conditions characterized by dysregulation of the immune system, resulting in inflammation and damage to various tissues, cells and organs. These diseases significantly impact individuals’ quality of life and often contribute to increased mortality risk in the presence of comorbidities. However, due to the diverse array of symptoms associated with different autoimmune diseases, accurate diagnosis, prognosis, and treatment evaluation pose significant challenges. Thus, there is a pressing need for the discovery of novel biomarkers.  In this study, a comprehensive analysis of 944 plasma samples using the OlinkR Explore platform was conducted, generating data on 1463 unique proteins. Based on the expression data, associated proteins were identified for six selected autoimmune diseases, namely multiple sclerosis, myositis, rheumatoid arthritis, systemic sclerosis, Sjögren’s syndrome, and systemic lupus erythematosus, as well as some of their defined subgroups. These are prospective biomarkers and have the potential to aid in early diagnosis, therapeutic intervention, subgroup identification, disease differentiation, and disease prognosis. Notably, some of these proteins have not been previously associated with the specific diseases in the existing literature, especially not in plasma samples, thereby offering intriguing new perspectives for biomarker development. However, it is of great importance to conduct robust validation studies in independent cohorts to confirm the outcomes of this study.  In summary, our findings highlight the potential utility of these proteomic plasma biomarkers in improving the early detection, subgroup characterization, and disease differentiation of autoimmune diseases. The identification of these proteins will hopefully stimulate further investigation in the field of biomarker research and potential advancements in personalized medicine.

Detta projekt genomfördes på företaget Sangair som för närvarande utvecklar medicinsk utrustning för att behandla bakteriemi med ozon. Bakteriemi uppstår när bakterier hamnar i blodomloppet, vilket kan trigga sepsis och septisk chock, med potentiellt dödligt utfall om obehandlat. För närvarande används antibiotika för att behandla bakteriemi, men det ökande hotet med antibiotikaresistens världen över innebär att forskare behöver hitta nya vägar för att behandla bakteriemi. Som en del av Sangairs utveckling gjordes en undersökning för att se hur bakterier påverkas av ozon. Projektet syftade till att 1) utveckla en metod för att detektera lysering av bakterier och 2) använda metoden för att se om ozon hade lyserande effekt på model-organismen Escherichia coli. För att testa metoden transformerades stam BL21 av E. coli med en pUC-19 plasmid för att producera beta-galaktosidas. Proteinets aktivitet mättes sedan i sonikerade bakterier, vilket visade att det var en effekitiv metod för att lysera bakterier och sedan mäta aktiviteten. För att undersöka om ozon hade en lyserande effekt, och samtidigt bestämma om man kunde mäta protein fann man att det optimala experimentella upplägget var att använde en ozonkoncentration på 6 g/m3, ett gasflöde på 5 ml/min och ett vätskeflöde på 25 ml/min. Resultatet från studien indikerade att ozon har en lyserande effekt, men fler studier behövs göras för att verifiera resultatet. Man undersökte också om detektionen av Beta-galaktosidas kunde förbättras genom att tillsätta Bovin serumalbumin (BSA) för att inhibera resterande ozon i prover som annars skulle kunna inaktivera Beta-galaktosidas. Resultaten indikerade dock inte någon effekt. Som ett sista experiment mättes även endotoxiner som frigjordes vid behandling, och det visade sig att när bakterier behandlas med ozon frigörs lipopolysackarider (LPS) och peptidoglykaner, vilket också kan tyda på lysis. / This project was conducted at Sangair. The company is currently developing a medical device aimed at treating bacteremia with ozone. Bacteremia is a condition that occurs when bacteria enters the bloodstream, and can trigger sepsis and septic shock, potentially leading to death if untreated. Antibiotics have traditionally been the way to treat bacteremia, but the looming threat of antibiotic resistance worldwide threatens this way of treatment, and research into novel approaches to eradicate the bacteria needs to be done. As part of Sangairs development, an investigation was done to see how ozone interacts with bacteria. The project aimed to 1) develop a method to detect bacterial lysis and 2) use the method to detect if ozone had a lysing effect on the bacterial model organism Escherechia coli. To test the method, the BL21 strain of  E. coli was transformed with the pUC-19 plasmid to produce the reporter enzyme Beta-galactosidase. The Beta-galactosidase activity was then measured in a supernatant of sonicated bacteria, which confirmed the suitability of the method to detect bacteria cell lysis. To be able to see if ozone had a lysing effect, while still being able to measure Beta-galactosidase, it was found that the optimal setup for this was using an ozone concentration of 6 g/m3, a gas flow of 5 ml/min and a liquid flow of 25 ml/min. The results acquired with this setup indicated that ozone had a lysing effect on E. coli but more studies are needed to verify this. It was further investigated if Beta-galactosidase detection could be improved by addition of bovine serum albumin (BSA) to quench residual ozone in the samples, but the results showed that it did not have any effect on the Beta-galactosidase enzymatic activity. As a final experiment, endotoxins that were released upon treatment were also measured, and it was found that when bacteria are treated with ozone, lipopolysaccharides (LPS) and peptidoglycans are released, further confirming lysis of the bacterial cells.

Mänsklig utforskning av månen och Mars innebär stora utmaningar för människans fysiologi och hälsa på grund av de unika miljöfaktorer som följer av långvariga rymduppdrag. Rymdbiologiska experiment har blivit ett viktigt verktyg för att studera effekterna som mikrogravitation och rymdstrålning har på levande organismer, i syfte att förstå och minska dessa utmaningar. Sådana experiment ger forskarna möjlighet att få insikt i rymduppdragens inverkan på människans fysiologi och utveckla strategier för att motverka eventuella skadliga effekter. Dessutom ger rymdbiologiska experiment möjlighet att öka vår förståelse av grundläggande biologiska processer, inklusive mikrogravitationens effekter på celldifferentiering och vävnadsregeneration, med potentiella tillämpningar för både rymdforskning och för att förbättra människors hälsa på jorden. Särskilt studier av mikrogravitationens effekter på hjärncellerna har potentiella konsekvenser för neurodegenerativa sjukdomar som Alzheimers och Parkinsons sjukdom. Genom att analysera data som genererats från hjärnor hos möss som skickats ut i rymden med en ny R-mjukvara, ArchR, är det möjligt att belysa de mekanismer som ligger till grund för förändringar i hjärnans funktion och beteende hos astronauter under långvariga rymduppdrag. Genom att förstå dessa mekanismer kan man utveckla nya terapeutiska metoder för att behandla eller till och med förebygga dessa sjukdomstillstånd. Fortsatta investeringar i rymdbiologisk forskning är avgörande för att garantera säkerheten och framgången för framtida, långvariga rymdforskningsuppdrag för människor. Genom att integrera avancerad teknik, t.ex. användning av spatiell transkriptomik eller sekvensering med encellsupplösning, kan en omfattande förståelse av komplexa biologiska system tolkas. De potentiella fördelarna med rymdbiologisk forskning sträcker sig längre än till att bara förstå effekterna av rymdfärder på människans fysiologi, med konsekvenser för grundläggande biologiska processer och behandling av en rad neurologiska sjukdomar. / Human exploration of the Moon and Mars poses significant challenges to human physiology and health due to the unique environmental factors that accompany long-duration space missions. Space biology experiments have emerged as an essential tool for studying the effects of microgravity and space radiation on living organisms, in order to understand and mitigate these challenges. Such experiments provide researchers with the opportunity to gain insights into the impacts of prolonged exposure to outer space on human physiology, and develop strategies to counteract any harmful effects. Additionally, space biology experiments offer the potential to enhance our understanding of fundamental biological processes, including the effects of microgravity on cell differentiation and tissue regeneration, with potential applications for both space exploration and improving human health on Earth. Previous research indicated the regulation of similar biomarkers, studying the effects of microgravity on brain cells could offer valuable insights into the potential impact on neurodegenerative conditions such as Alzheimer’s and Parkinson’s diseases. By analyzing data generated from the brains of mice that have been sent to space with a new R-software tool called ArchR, it is possible to elucidate the mechanisms underlying changes in brain function and behavior in astronauts during long-duration space missions. Understanding these mechanisms can inform the development of new therapeutic approaches to treating or even preventing these conditions. Continued investment in space biology research is critical to ensuring the safety and success of future long-term human space exploration missions. By integrating advanced technologies, such as the use of spatial transcriptomics or sequencing at the single-cell resolution, comprehensive understanding of complex biological systems can be interpreted. The potential benefits of space biology research extend beyond just understanding the effects of spaceflight on human physiology, with implications for fundamental biological processes and the treatment of a range of neurological diseases.

Venös tromboembolism (VTE) inkluderar både djup ventrombos (DVT) och lungemboli (PE) och är en vanlig och komplex kardiovaskulär sjukdom med allvarliga kortsiktiga och långsiktiga komplikationer. I dagens kliniska praxis skulle diagnoseringen av VTE gynnas av en plasmaproteinpanel som antingen kan utesluta fall av akut VTE på egen hand eller komplettera den nuvarande biomarkören D-dimer, som i sig är begränsad av låg specificitet. På grund av den höga återfallsfrekvensen och de allvarliga post-syndromen skulle en plasmaproteinpanel som kan bedöma risken för återkommande VTE underlätta för kliniker i efterbehandlingsbeslut. Mot denna bakgrund syftade denna studie till att föreslå två separata plasmaproteinpaneler, en för att utesluta akuta VTE-patienter och en annan för att bedöma risken för återkommande VTE. Med 1463 unika plasmaproteiner screenades plasmaproteomet hos 194 individer från två undergrupper av venös tromboembolism-biomarkörstudien (VEBIOS), närmare bestämt VEBIOS ER och VEBIOS Coag, med hjälp av proximity extension assay (PEA). Både genuttryck (DE) -analys och maskininlärning (ML) -algoritmer användes för att identifiera signifikanta respektive viktiga proteiner. För akut VTE identifierades 10 signifikanta proteiner genom DE, samt en panel bestående av fem proteiner tillsammans med D-dimer hade tillsammans en area under kurvan (AUC) på 0,97 genom ML. För återkommande VTE identifierades inga signifikanta proteiner och den bästa proteinpanelen hade en AUC på 0,62. Vissa av dessa proteiner har tidigare rapporterats vara associerade med VTE och vissa inte, vilket resulterar i ortogonal validering eller påvisande av en potentiell ny biomarkör. Sammanfattningsvis hittades flera intressanta plasmaproteiner som potentiellt skulle kunna användas för att utesluta fall av akut VTE. GP1BA och S100A12 var särskilt intressanta då de var återkommande som högt ansenliga enligt DE och ML. Resultaten från denna studie kommer förhoppningsvis bidra till forskningen gällande förbättrad diagnos av VTE-patienter genom användning av plasmaproteinmarkörer och argumentationen för ytterligare undersökningar för dessa identifierade plasmaproteiner. / Venous thromboembolism (VTE) is a common and complex cardiovascular disorder with serious short- and long-term complications, comprising both deep vein thrombosis (DVT) and pulmonary embolism (PE). In current clinical practice, diagnosis of acute VTE would greatly benefit from a plasma protein panel that can exclude cases of VTE on its own or complement the current biomarker, D-dimer, which is limited by low specificity. Because of the high recurrence rate and serious post-syndromes, a protein panel that can assess the risk of VTE recurrence would help clinicians in post-treatment decision-making. Hence, this study sought out to propose two separate plasma biomarker panels, one to exclude acute VTE patients and another to risk-assess VTE recurrence.  To accomplish this, 1463 unique plasma proteins were used to investigate the plasma proteome of 194 individuals from two subgroups of the venous thromboembolism biomarker study (VEBIOS), specifically VEBIOS ER and VEBIOS Coag, using proximity extension assay (PEA). Both differential expression (DE) analysis and machine learning (ML) algorithms were used to find significant and important proteins respectively. For acute VTE, 10 significant proteins were identified through DE, and a panel of five proteins together with D-dimer had together an area under the curve (AUC) of 0.97 through ML. For VTE recurrency, no significant proteins were identified, and the best protein panel had an AUC of 0.62. Some of these proteins have previously been reported as associated to VTE and some not, resulting in some orthogonal validation or novelty. In summary, several interesting plasma proteins were found that could potentially be used to exclude cases of VTE in an acute setting. GP1BA and S100A12 were particularly interesting as they performed well in both DE and ML. The results in this study will hopefully aid the research of improving diagnosis of VTE patients using plasma biomarkers, strengthening the claim and further investigations for these identified plasma proteins.

Stem cell therapy and transplantation is a quickly evolving field with many clinical applications. However, several problems need to be overcome before they can be applied on an allogenic scale, and among them is ensuring of the purity of the applied differentiated stem cell culture. Separation using magnetic beads which attach to the wanted cells has proven to be an effective and easy method to separate them from a sample. An important factor with the method is the choice of specific surface antigens on the beads which determines how well the beads are attached to the cell.  This report will provide some fact of the immunotherapy and some of the most important stem cells and their differentiation to an active cell. It will be elucidated which cytokines are important for differentiation, and current clinical studies in the immunotherapeutic field of stem cells and their useful surface antigens. Furthermore, regenerative medicine using stem cells will be covered. A brief overview mesenchymal and induced pluripotent stem cells, their biological markers, and their various uses. Specific projects using regenerative medicine will be described and an overview of ever-expanding market for regenerative medicine will also be included.