| 1. |
- Andersson, Sandra, et al.
(författare)
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The Transcriptomic and Proteomic Landscapes of Bone Marrow and Secondary Lymphoid Tissues
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:12, s. e115911-
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Tidskriftsartikel (refereegranskat)abstract
- Background: The sequencing of the human genome has opened doors for global gene expression profiling, and the immense amount of data will lay an important ground for future studies of normal and diseased tissues. The Human Protein Atlas project aims to systematically map the human gene and protein expression landscape in a multitude of normal healthy tissues as well as cancers, enabling the characterization of both housekeeping genes and genes that display a tissue-specific expression pattern. This article focuses on identifying and describing genes with an elevated expression in four lymphohematopoietic tissue types (bone marrow, lymph node, spleen and appendix), based on the Human Protein Atlas-strategy that combines high throughput transcriptomics with affinity-based proteomics. Results: An enriched or enhanced expression in one or more of the lymphohematopoietic tissues, compared to other tissue-types, was seen for 693 out of 20,050 genes, and the highest levels of expression were found in bone marrow for neutrophilic and erythrocytic genes. A majority of these genes were found to constitute well-characterized genes with known functions in lymphatic or hematopoietic cells, while others are not previously studied, as exemplified by C19ORF59. Conclusions: In this paper we present a strategy of combining next generation RNA-sequencing with in situ affinity-based proteomics in order to identify and describe new gene targets for further research on lymphatic or hematopoietic cells and tissues. The results constitute lists of genes with enriched or enhanced expression in the four lymphohematopoietic tissues, exemplified also on protein level with immunohistochemical images.
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| 2. |
- Asp, Michaela, et al.
(författare)
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A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart
- 2019
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Ingår i: Cell. - : CELL PRESS. - 0092-8674 .- 1097-4172. ; 179:7, s. 1647-
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Tidskriftsartikel (refereegranskat)abstract
- The process of cardiac morphogenesis in humans is incompletely understood. Its full characterization requires a deep exploration of the organ-wide orchestration of gene expression with a single-cell spatial resolution. Here, we present a molecular approach that reveals the comprehensive transcriptional landscape of cell types populating the embryonic heart at three developmental stages and that maps cell-type-specific gene expression to specific anatomical domains. Spatial transcriptomics identified unique gene profiles that correspond to distinct anatomical regions in each developmental stage. Human embryonic cardiac cell types identified by single-cell RNA sequencing confirmed and enriched the spatial annotation of embryonic cardiac gene expression. In situ sequencing was then used to refine these results and create a spatial subcellular map for the three developmental phases. Finally, we generated a publicly available web resource of the human developing heart to facilitate future studies on human cardiogenesis.
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| 3. |
- Borgström, Sara, 1977-
(författare)
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Urban shades of green : Current patterns and future prospects of nature conservation in urban landscapes
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Urban nature provides local ecosystem services such as absorption of air pollutants, reduction of noise, and provision of places for recreation, and is therefore crucial to urban sustainable development. Nature conservation in cities is also part of the global effort to halt biodiversity decline. Urban landscapes, however, display distinguishing social and ecological characteristics and therefore the implementation of nature conservation frameworks into cities, requires reconsideration of what nature to preserve, for whom and where. The aim of this thesis was to examine the current urban nature conservation with special focus on formally protected areas, and discuss their future role in the urban landscape. A social-ecological systems approach was used as framework and both quantitative and qualitative methods were applied. The studies were performed at local to regional scales in the southern part of Sweden. Four key questions were addressed: i) What are the characteristics of nature conservation in urban landscapes? ii) How does establishment of nature conservation areas affect the surrounding urban landscape? iii) In what ways are spatial and temporal scales recognized in practical management of nature conservation areas? and iv) How can the dichotomy of built up and nature conservation areas be overcome in urban planning? Nature reserves in urban, compared to rural landscapes were in general fewer, but larger and included a higher diversity of land covers. They were also based on a higher number and different kinds of objectives than rural nature reserves. Urbanisation adjacent to nature reserves followed the general urbanisation patterns in the cities and no additional increase in urban settlements could be detected. In general, there was a lack of social and ecological linkages between the nature conservation areas and the urban landscape and practical management showed a limited recognition of cross-scale interactions and meso-scales. Such conceptual and physical isolation risks decreasing the public support for nature conservation, cause biodiversity decline, and hence impact the generation of ecosystem services. A major future challenge is therefore to transform current conservation strategies to become a tool where urban nature is perceived, planned and managed as valuable and integrated parts of the city. To enable social-ecological synergies, future urban planning should address proactive approaches together with key components like active enhancement of multifunctional landscapes, cross-scale strategies and border zone management.
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| 4. |
- Braniste, Viorica, et al.
(författare)
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The gut microbiota influences blood-brain barrier permeability in mice
- 2014
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Ingår i: Science Translational Medicine. - : American Association for the Advancement of Science. - 1946-6234 .- 1946-6242. ; 6:263, s. 263ra158-
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Tidskriftsartikel (refereegranskat)abstract
- Pivotal to brain development and function is an intact blood-brain barrier (BBB), which acts as a gatekeeper to control the passage and exchange of molecules and nutrients between the circulatory system and the brain parenchyma. The BBB also ensures homeostasis of the central nervous system (CNS). We report that germ-free mice, beginning with intrauterine life, displayed increased BBB permeability compared to pathogen-free mice with a normal gut flora. The increased BBB permeability was maintained in germ-free mice after birth and during adulthood and was associated with reduced expression of the tight junction proteins occludin and claudin-5, which are known to regulate barrier function in endothelial tissues. Exposure of germ-free adult mice to a pathogen-free gut microbiota decreased BBB permeability and up-regulated the expression of tight junction proteins. Our results suggest that gut microbiota-BBB communication is initiated during gestation and propagated throughout life.
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| 5. |
- Dubaric, Ervin, et al.
(författare)
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Resolution and noise properties of scintillator coated X-ray detectors
- 2001
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - 0168-9002 .- 1872-9576. ; 466:1, s. 178-182
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Tidskriftsartikel (refereegranskat)abstract
- The imaging properties of X-ray pixel detectors depend on the quantum efficiency of X-rays, the generated signal of each X-ray photon and the distribution of the generated signal between pixels. In a scintillator coated device the signal is generated both by X-ray photons captured in the scintillator and by X-ray photons captured directly in the semiconductor. The Signal-to-Noise Ratio in the image is then a function of the number of photons captured in each of these processes and the yield, in terms of electron-hole pairs produced in the semiconductor, of each process. The spatial resolution is primarily determined by the light spreading within the scintillator. In a pure semiconductor detector the signal is generated by one process only. The Signal-to-Noise Ratio in the image is proportional to the number of X-ray photons captured within the sensitive layer. The spatial resolution is affected by the initial charge cloud generated in the semiconductor and any diffusion of carriers between the point of interaction and the readout electrode. In this paper we discuss the theory underlying the imaging properties of scintillator coated X-ray imaging detectors. The model is verified by simulations using MCNP and by experimental results. The results from the two-layer detector are compared with those from a pure semiconductor X-ray detector.
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| 6. |
- Eck, Joakim A.T., et al.
(författare)
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Pressure Evolution in Ceramic Stopper in a Liquid Metal Continuous Casting Simulator
- 2022
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Ingår i: 8th International Congress on the Science and Technology of Steelmaking, ICS 2022. - : Association for Iron and Steel Technology. ; , s. 398-402
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Konferensbidrag (refereegranskat)abstract
- Stopper controls see considerable use in Continuous Casting (CC) throughput control. The flow regulation results in a narrow gap between the stopper and the SEN throat which can result in considerable under-pressures. Large pressure gradients across the refractory material lead to air infiltration through joints and porous refractory material which result in oxidation and corresponding issues such as inclusions, clogging, with adverse effect on product quality. Improving the CC process makes it necessary to understand how the pressure evolves in the continuous caster. Swerim and SSAB investigated the pressure in the argon line of a ceramic stopper for different casting conditions in a liquid metal continuous casting simulator. The results showed a narrow operational region for positive pressures in stopper and an occurrence of considerably low pressures at levels down to -741 mbar relative pressure. At these under-pressures the risk for air infiltration, and thus product issues, is considerable.
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| 7. |
- Laytragoon-Lewin, Nongnit, et al.
(författare)
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Human papillomavirus (HPV), DNA aberrations and cell cycle progression in anal squamous cell carcinoma patients
- 2007
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Ingår i: Anticancer Research. - 0250-7005 .- 1791-7530. ; 27:6C, s. 4473-4479
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Tidskriftsartikel (refereegranskat)abstract
- Human papillomavirus (HP) infections of the genital tract are sexually transmitted and prevalent worldwide. In this study, the role of HPV in 72 patients with anal squamous cell carcinoma was investigated. Patients and Methods: Polymerase chain reaction (PCR) in combination with in situ hybridization was used to identify HPV-DNA in the patients biopsies. The HPV typing was conducted by pyrosequencing. Cell cycle and DNA content were analysed by cytometry. Results: Ninety percent of the carcinoma biopsies carried high-risk oncogenic HPV in their malignant cells. Eighty-one percent of these demonstrated a single infection with HPV16, 18 or 33 and 19% were double infected with HPV16 and HPV18 Accumulations of viral genes were seen at the necrotic area of the tumours. The HPV genome in the tumour cell influenced significant the host cell cycle progression, but not DNA aberrations. Within these patients, HPV status in the malignant cells was not found to be associated with patient survival time. Conclusion: High-risk oncogenic HPV may play an important role in the initiation of host cell proliferation in anal squamous cell carcinoma. However, infection with HPV may not have any direct influence itself on the clinical outcome of these patients considering the treatments currently available.
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| 8. |
- Lázár, Enikő, et al.
(författare)
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Spatial Dynamics of the Developing Human Heart
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Heart development relies on a topologically defined interplay between a diverse array of cardiac cells. We finely curated spatial and single-cell measurements with subcellular imaging-based transcriptomics validation to explore spatial dynamics during early human cardiogenesis. Analyzing almost 80,000 individual cells and 70,000 spatially barcoded tissue regions between the 5.5th and 14th postconceptional weeks, we identified 31 coarse- and 72 fine-grained cell states and mapped them to highly resolved cardiac cellular niches. We provide novel insight into the development of the cardiac pacemaker-conduction system, heart valves, and atrial septum, and decipher heterogeneity of the hitherto elusive cardiac fibroblast population. Furthermore, we describe the formation of cardiac autonomic innervation and present the first spatial account of chromaffin cells in the fetal human heart. In summary, our study delineates the cellular and molecular landscape of the developing heart’s architecture, offering links to genetic causes of heart disease.
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