Computational Methods for Reconstruction and Analysis of Genome-Scale Metabolic Networks

Metabolism is the cellular subsystem responsible for generation of energy from nutrients and production of building blocks for larger macromolecules. Computational and statistical modeling of metabolism is vital to many disciplines including bioengineering, the study of diseases, drug target identification, and understanding the evolution of metabolism. In this thesis, we propose efficient computational methods for metabolic modeling. The techniques presented are targeted particularly at the analysis of large metabolic models encompassing the whole metabolism of one or several organisms. We concentrate on three major themes of metabolic modeling: metabolic pathway analysis, metabolic reconstruction and the study of evolution of metabolism. In the first part of this thesis, we study metabolic pathway analysis. We propose a novel modeling framework called gapless modeling to study biochemically viable metabolic networks and pathways. In addition, we investigate the utilization of atom-level information on metabolism to improve the quality of pathway analyses. We describe efficient algorithms for discovering both gapless and atom-level metabolic pathways, and conduct experiments with large-scale metabolic networks. The presented gapless approach offers a compromise in terms of complexity and feasibility between the previous graph-theoretic and stoichiometric approaches to metabolic modeling. Gapless pathway analysis shows that microbial metabolic networks are not as robust to random damage as suggested by previous studies. Furthermore the amino acid biosynthesis pathways of the fungal species Trichoderma reesei discovered from atom-level data are shown to closely correspond to those of Saccharomyces cerevisiae. In the second part, we propose computational methods for metabolic reconstruction in the gapless modeling framework. We study the task of reconstructing a metabolic network that does not suffer from connectivity problems. Such problems often limit the usability of reconstructed models, and typically require a significant amount of manual postprocessing. We formulate gapless metabolic reconstruction as an optimization problem and propose an efficient divide-and-conquer strategy to solve it with real-world instances. We also describe computational techniques for solving problems stemming from ambiguities in metabolite naming. These techniques have been implemented in a web-based sofware ReMatch intended for reconstruction of models for 13C metabolic flux analysis. In the third part, we extend our scope from single to multiple metabolic networks and propose an algorithm for inferring gapless metabolic networks of ancestral species from phylogenetic data. Experimenting with 16 fungal species, we show that the method is able to generate results that are easily interpretable and that provide hypotheses about the evolution of metabolism.

Electron cryo-microscopy studies of bacteriophage phi8 and archaeal virus SH1

Symmetry is a key principle in viral structures, especially the protein capsid shells. However, symmetry mismatches are very common, and often correlate with dynamic functionality of biological significance. The three-dimensional structures of two isometric viruses, bacteriophage phi8 and the archaeal virus SH1 were reconstructed using electron cryo-microscopy. Two image reconstruction methods were used: the classical icosahedral method yielded high resolution models for the symmetrical parts of the structures, and a novel asymmetric in-situ reconstruction method allowed us to resolve the symmetry mismatches at the vertices of the viruses. Evidence was found that the hexameric packaging enzyme at the vertices of phi8 does not rotate relative to the capsid. The large two-fold symmetric spikes of SH1 were found not to be responsible for infectivity. Both virus structures provided insight into the evolution of viruses. Comparison of the phi8 polymerase complex capsid with those of phi6 and other dsRNA viruses suggests that the quaternary structure in dsRNA bacteriophages differs from other dsRNA viruses. SH1 is unusual because there are two major types of capsomers building up the capsid, both of which seem to be composed mainly of single beta-barrels perpendicular to the capsid surface. This indicates that the beta-barrel may be ancestral to the double beta-barrel fold.

Postoperative soft tissue defects in the ankle area : The etiology and methods of reconstruction

The risk is obvious for soft tissue complications after operative treatment of the Achilles tendon, calcaneal bone or after ankle arthroplasty. Such complications after malleolar fractures are, however, seldom seen. The reason behind these complications is that the soft tissue in this region is tight and does not allow much tension to the wound area after surgery. Furthermore the area of operation may be damaged by swelling after the injury, or can be affected by peripheral vascular disease. While complications in this area are unavoidable, they can be diminished. This study attempts to highlight the possible predisposing factors leading to complications in these operations and on the other hand, to determine the solutions to solve soft tissue problems in this region. The study consists of five papers. The first article is a reprint on the soft tissue reconstruction of 25 patients after their complicated Achilles tendon surgeries were analysed. The second study reviews a series of 126 patients after having undergone an operative treatment of calcaneal bone fractures and analyses the complications and possible reasons behind them. The third part analyses a series of corrections of 35 soft tissue complications after calcaneal fracture operations. The fourth part reviews a series of 7 patients who had undergone complicated ankle arthroplasties. The last article presents a series of post operative lateral defects of the ankle treated with a less frequently used distally based peroneus brevis muscle flap and analyses the results. What can be conducted from these studies is that in general, the results after the correction of even severe soft tissue complications in the ankle region are good. For the small defects around the Achilles tendon, the local flaps are useful, but the larger defects are best treated with a free flap. We found that a long delay from trauma to surgery and a long operating time were predisposing factors that lead to soft tissue complications after operatively treated calcaneal bone fractures. The more severe the injury, the greater the risk for wound complication. Surprisingly, the long-term results after infected calcaneal osteosyntheses were acceptable and the calcaneal bone seems to tolerate chronic infections very well if the soft tissue is reconstructed successfully. Behind the complicated ankle arthroplasties, unexpectedly high number of cases experiencing arteriosclerosis of the lower extremity was found. These complications lead to ankle fusion but can be solved with a free flap if the vascularity is intact or can be reconstructed. For this reason a vascular examination of the lower extremity arteries of the patients going to ankle arthroplasty is strongly recommended. Moreover postoperative lateral malleolar wound infections which typically create lateral ankle defects can successfully be treated with a peroneus brevis muscle flap covered with a free skin graft.

The TRAM flap for breast reconstruction : Studies on perioperative cutaneous blood flow, vasoconstriction, and indices of obesity

Breast reconstruction is performed for 10-15 % of women operated on for breast cancer. A popular method is the TRAM (transverse rectus abdominis musculocutaneous) flap formed of the patient’s own abdominal tissue, a part of one of the rectus abdominis muscles and a transverse skin-subcutis area over it. The flap can be raised as a pedicled or a free flap. The pedicled TRAM flap, based on its nondominant pedicle superior epigastric artery (SEA), is rotated to the chest so that blood flow through SEA continues. The free TRAM flap, based on its dominant pedicle deep inferior epigastric artery (DIEA), is detached from the abdomen, transferred to the chest, and DIEA and vein are anastomosed to vessels on the chest. Cutaneous necrosis is seen in 5–60 % of pedicled TRAM flaps and in 0–15 % of free TRAM flaps. This study was the first one to show with blood flow measurements that the cutaneous blood flow is more generous in free than in pedicled TRAM flaps. After this study the free TRAM flap has exceeded the pedicled flap in popularity as a breast reconstruction method, although the free flap it is technically a more demanding procedure than the pedicled TRAM flap. In pedicled flaps, a decrease in cutaneous blood flow was observed when DIEA was ligated. It seems that SEA cannot provide sufficient blood flow on the first postoperative days. The postoperative cutaneous blood flow in free TRAM flaps was more stable than in pedicled flaps. Development of cutaneous necrosis of pedicled TRAM flaps could be predicted based on intraoperative laser Doppler flowmetry (LDF) measurements. The LDF value on the contralateral skin of the flap decreased to 43 ± 7 % of the initial value after ligation of the DIEA in flaps developing cutaneous necrosis during the next week. Endothelin-1 (ET-1) is a powerful vasoconstrictory peptide secreted by vascular endothelial cells. A correlation was found between plasma ET-1 concentrations and peripheral vasoconstriction developing during and after breast reconstructions with a pedicled TRAM flap. ET-1 was not associated with the development of cutaneous necrosis. Felodipine, a vasodilating calcium channel antagonist, had no effect on plasma ET-1 concentrations, peripheral vasoconstriction or development of cutaneous necrosis in free TRAM flaps. Body mass index and thickness of abdominal were not associated with cutaneous necrosis in pedicled TRAM flaps.

Anterior cruciate ligament reconstruction with special reference to magnetic resonance imaging of the postoperative outcome

Anterior cruciate ligament (ACL) tear is a common sports injury of the knee. Arthroscopic reconstruction using autogenous graft material is widely used for patients with ACL instability. The grafts most commonly used are the patellar and the hamstring tendons, by various fixation techniques. Although clinical evaluation and conventional radiography are routinely used in follow-up after ACL surgery, magnetic resonance imaging (MRI) plays an important role in the diagnosis of complications after ACL surgery. The aim of this thesis was to study the clinical outcome of patellar and hamstring tendon ACL reconstruction techniques. In addition, the postoperative appearance of the ACL graft was evaluated using several MRI sequences. Of the 175 patients who underwent an arthroscopically assisted ACL reconstruction, 99 patients were randomized into patellar tendon (n=51) or hamstring tendon (n=48) groups. In addition, 62 patients with hamstring graft ACL reconstruction were randomized into either cross-pin (n=31) or interference screw (n=31) fixation groups. Follow-up evaluation determined knee laxity, isokinetic muscle performance and several knee scores. Lateral and anteroposterior view radiographs were obtained. Several MRI sequences were obtained with a 1.5-T imager. The appearance and enhancement pattern of the graft and periligamentous tissue, and the location of bone tunnels were evaluated. After MRI, arthroscopy was performed on 14 symptomatic knees. The results revealed no significant differences in the 2-year outcome between the groups. In the hamstring tendon group, the average femoral and tibial bone tunnel diameter increased during 2 years follow-up by 33% and 23%, respectively. In the asymptomatic knees, the graft showed homogeneous and low signal intensity with periligamentous streaks of intermediate signal intensity on T2-weighted MR images. In the symptomatic knees, arthroscopy revealed 12 abnormal grafts and two meniscal tears, each with an intact graft. Among 3 lax grafts visible on arthroscopy, MRI showed an intact graft and improper bone tunnel placement. For diagnosing graft failure, all MRI findings combined gave a specificity of 90% and a sensitivity of 81%. In conclusion, all techniques appeared to improve patients' performance, and were therefore considered as good choices for ACL reconstruction. In follow-up, MRI permits direct evaluation of the ACL graft, the bone tunnels, and additional disorders of the knee. Bone tunnel enlargement and periligamentous tissue showing contrast enhancement were non-specific MRI findings that did not signify ACL deficiency. With an intact graft and optimal femoral bone tunnel placement, graft deficiency is unlikely, and the MRI examination should be carefully scrutinized for possible other causes for the patients symptoms.

Microvascular reconstruction in extremity soft tissue sarcoma surgery

Soft tissue sarcomas (STS) are rare tumors of soft tissue occurring most frequently in the extremities. Modern treatment of extremity STS is based on limb-sparing surgery combined with radiotherapy. To prevent local recurrence, a healthy tissue margin of 2.5 cm around the resected tumor is required. This results in large defects of soft tissue and bone, necessitating the use of reconstructive surgery to achieve wound closure. When local or pedicled soft tissue flaps are unavailable, reconstruction with free flaps is used. Free flaps are elevated at a distant site, and have their blood flow restored at the recipient site through microvascular anastomosis. When limb-sparing surgery is made impossible, amputation is the only option. Proximal amputation such as forequarter amputation (FQA) causes considerable morbidity, but is nevertheless warranted for carefully selected patients for cure or palliation. 116 patients treated in 1985 - 2006 were included in the study. Of these, 93 patients treated with limb-sparing surgery and microvascular reconstructive surgery after resection of extremity STS. 25 patients who underwent FQA were also included. Patients were identified and their medical records retrospectively reviewed. In all, 105 free flap procedures were performed for 103 patients. A total of 95 curatively treated STS patients were included in survival analysis. The latissimus dorsi, used in 56% of cases, was the most frequently used free flap. Free flap success rate was 96%. There were 9% microvascular anastomosis complications and 15% wound complications. For curatively treated STS patients, local recurrence-free survival at 5 years was 73.1%, metastasis-free survival 58.3%, and overall disease-specific survival 68.9%. Functional results were good, with 75% of patients regaining normal or near-normal function after lower extremity, and 55% after upper extremity STS resection. Among curatively treated forequarter amputees, 5-year disease-free survival was 44%. In the palliatively treated group median time until disease death was 14 months. Microvascular reconstruction after extremity soft tissue sarcoma resection is safe and reliable, and produces well-healing wounds allowing early oncological treatment. Oncological outcome after these procedures is comparable to that of other extremity sarcoma patients. Functional results are generally good. Forequarter amputation is a useful treatment option for soft tissue tumors of the shoulder girdle and proximal upper extremity. When free flap coverage of extended forequarter amputation is required, the preferable flap is a fillet flap from the amputated extremity. Acceptable oncological outcome is achieved for curatively treated FQA patients. In the palliatively treated patient considerable periods of increased quality of life can be achieved.

Reconstruction of past UV radiation

Solar ultraviolet (UV) radiation has a broad range of effects concerning life on Earth. Soon after the mid-1980s, it was recognized that the stratospheric ozone content was declining over large areas of the globe. Because the stratospheric ozone layer protects life on Earth from harmful UV radiation, this lead to concern about possible changes in the UV radiation due to anthropogenic activity. Initiated by this concern, many stations for monitoring of the surface UV radiation were founded in the late 1980s and early 1990s. As a consequence, there is an apparent lack of information on UV radiation further in the past: measurements cannot tell us how the UV radiation levels have changed on time scales of, for instance, several decades. The aim of this thesis was to improve our understanding of past variations in the surface UV radiation by developing techniques for UV reconstruction. Such techniques utilize commonly available meteorological data together with measurements of the total ozone column for reconstructing, or estimating, the amount of UV radiation reaching Earth's surface in the past. Two different techniques for UV reconstruction were developed. Both are based on first calculating the clear-sky UV radiation using a radiative transfer model. The clear-sky value is then corrected for the effect of clouds based on either (i) sunshine duration or (ii) pyranometer measurements. Both techniques account also for the variations in the surface albedo caused by snow, whereas aerosols are included as a typical climatological aerosol load. Using these methods, long time series of reconstructed UV radiation were produced for five European locations, namely Sodankylä and Jokioinen in Finland, Bergen in Norway, Norrköping in Sweden, and Davos in Switzerland. Both UV reconstruction techniques developed in this thesis account for the greater part of the factors affecting the amount of UV radiation reaching the Earth's surface. Thus, they are considered reliable and trustworthy, as suggested also by the good performance of the methods. The pyranometer-based method shows better performance than the sunshine-based method, especially for daily values. For monthly values, the difference between the performances of the methods is smaller, indicating that the sunshine-based method is roughly as good as the pyranometer-based for assessing long-term changes in the surface UV radiation. The time series of reconstructed UV radiation produced in this thesis provide new insight into the past UV radiation climate and how the UV radiation has varied throughout the years. Especially the sunshine-based UV time series, extending back to 1926 and 1950 at Davos and Sodankylä, respectively, also put the recent changes driven by the ozone decline observed over the last few decades into perspective. At Davos, the reconstructed UV over the period 1926-2003 shows considerable variation throughout the entire period, with high values in the mid-1940s, early 1960s, and in the 1990s. Moreover, the variations prior to 1980 were found to be caused primarily by variations in the cloudiness, while the increase of 4.5 %/decade over the period 1979-1999 was supported by both the decline in the total ozone column and changes in the cloudiness. Of the other stations included in this work, both Sodankylä and Norrköping show a clear increase in the UV radiation since the early 1980s (3-4 %/decade), driven primarily by changes in the cloudiness, and to a lesser extent by the diminution of the total ozone. At Jokioinen, a weak increase was found, while at Bergen there was no considerable overall change in the UV radiation level.

Joseph A. Schumpeter's Theory of Social and Economic Evolution : a Reconstruction and Critique

The book presents a reconstruction, interpretation and critical evaluation of the Schumpeterian theoretical approach to socio-economic change. The analysis focuses on the problem of social evolution, on the interpretation of the innovation process and business cycles and, finally, on Schumpeter s optimistic neglect of ecological-environmental conditions as possible factors influencing social-economic change. The author investigates how the Schumpeterian approach describes the process of social and economic evolution, and how the logic of transformations is described, explained and understood in the Schumpeterian theory. The material of the study includes Schumpeter s works written after 1925, a related part of the commentary literature on these works, and a selected part of the related literature on the innovation process, technological transformations and the problem of long waves. Concerning the period after 1925, the Schumpeterian oeuvre is conceived and analysed as a more or less homogenous corpus of texts. The book is divided into 9 chapters. Chapters 1-2 describe the research problems and methods. Chapter 3 is an effort to provide a systematic reconstruction of Schumpeter's ideas concerning social and economic evolution. Chapters 4 and 5 focus their analysis on the innovation process. In Chapters 6 and 7 Schumpeter's theory of business cycles is examined. Chapter 8 evaluates Schumpeter's views concerning his relative neglect of ecological-environmental conditions as possible factors influencing social-economic change. Finally, chapter 9 draws the main conclusions.

Khα1,2 hypersatellites of 3d transition metals and their photoexcitation energy dependence

Hollow atoms in which the K shell is empty while the outer shells are populated allow studying a variety of important and unusual properties of atoms. The diagram x-ray emission lines of such atoms, the K-h alpha(1,2) hypersatellites (HSs), were measured for the 3d transition metals, Z=23-30, with a high energy resolution using photoexcitation by monochromatized synchrotron radiation. Good agreement with ab initio relativistic multiconfigurational Dirac-Fock calculations was found. The measured HS intensity variation with the excitation energy yields accurate values for the excitation thresholds, excludes contributions from shake-up processes, and indicates domination near threshold of a nonshake process. The Z variation of the HS shifts from the diagram line K alpha(1,2), the K-h alpha(1)-K-h alpha(2) splitting, and the K-h alpha(1)/K-h alpha(2) intensity ratio, derived from the measurements, are also discussed with a particular emphasis on the QED corrections and Breit interaction.

Temperature-Sensitive Src-Transformed Mdck Cells nn 3d Cultures as a Model of Malignant Transformation of Epithelial Cells

The equilibrium between cell proliferation, differentiation, and apoptosis is crucial for maintaining homeostasis in epithelial tissues. In order for the epithelium to function properly, individual cells must gain normal structural and functional polarity. The junctional proteins have an important role both in binding the cells together and in taking part in cell signaling. Cadherins form adherens junctions. Cadherins initiate the polarization process by first recognizing and binding the neighboring cells together, and then guiding the formation of tight junctions. Tight junctions form a barrier in dividing the plasma membranes to apical and basolateral membrane domains. In glandular tissues, single layered and polarized epithelium is folded into tubes or spheres, in which the basal side of the epithelial layer faces the outer basal membrane, and the apical side the lumen. In carcinogenesis, the differentiated architecture of an epithelial layer is disrupted. Filling of the luminal space is a hallmark of early epithelial tumors in tubular and glandular structures. In order for the transformed tumor cells to populate the lumen, enhanced proliferation as well as inhibition of apoptosis is required. Most advances in cancer biology have been achieved by using two-dimensional (2D) cell culture models, in which the cells are cultured on flat surfaces as monolayers. However, the 2D cultures are limited in their capacity to recapitulate the structural and functional features of tubular structures and to represent cell growth and differentiation in vivo. The development of three-dimensional (3D) cell culture methods enables the cells to grow and to be studied in a more natural environment. Despite the wide use of 2D cell culture models and the development of novel 3D culture methods, it is not clear how the change of the dimensionality of culture conditions alters the polarization and transformation process and the molecular mechanisms behind them. Src is a well-known oncogene. It is found in focal and adherens junctions of cultured cells. Active src disrupts cell-cell junctions and interferes with cell-matrix binding. It promotes cell motility and survival. Src transformation in 2D disrupts adherens junctions and the fibroblastic phenotype of the cells. In 3D, the adherens junctions are weakened, and in glandular structures, the lumen is filled with nonpolarized vital cells. Madin-Darby canine kidney (MDCK) cells are an epithelial cell type commonly used as a model for cell polarization. Its-src-transformed variants are useful model systems for analyzing the changes in cell morphology, and they play a role in src-induced malignant transformation. This study investigates src-transformed cells in 3D cell cultures as a model for malignant transformation. The following questions were posed. Firstly: What is the role of the composition and stiffness of the extracellular matrix (ECM) on the polarization and transformation of ts v-src MDCK cells in 3D cell cultures? Secondly: How do the culture conditions affect gene expression? What is the effect of v-src transformation in 2D and in 3D cell models? How does the shift from 2D to 3D affect cell polarity and gene expression? Thirdly: What is the role of survivin and its regulator phosphatase and tensin homolog protein (PTEN) in cell polarization and transformation, and in determining cell fate? How does their expression correlate with impaired mitochondrial function in transformed cells? In order to answer the above questions, novel methods of culturing and monitoring cells had to be created: novel 3D methods of culturing epithelial cells were engineered, enabling real time monitoring of a polarization and transformation process, and functional testing of 3D cell cultures. Novel 3D cell culture models and imaging techniques were created for the study. Attention was focused especially on confocal microscopy and live-cell imaging. Src-transformation disturbed the polarization of the epithelium by disrupting cell adhesion, and sensitized the cells to their environment. With active src, the morphology of the cell cluster depended on the composition and stiffness of the matrix. Gene expression studies revealed a broader impact of src transformation than mere continuous activity of src-kinase. In 2D cultures, src transformation altered the expression of immunological, actin cytoskeleton and extracellular matrix (ECM). In 3D, the genes regulating cell division, inhibition of apoptosis, cell metabolism, mitochondrial function, actin cytoskeleton and mechano-sensing proteins were altered. Surprisingly, changing the culture conditions from 2D to 3D affected also gene expression considerably. The microarray hit survivin, an inhibitor of apoptosis, played a crucial role in the survival and proliferation of src-transformed cells.

Glycoprotein Interactions in the Assembly of Hantaviruses

Hantaviruses are one of the five genera of the vector-borne virus family Bunyaviridae. While other members of the family are transmitted via arthropods, hantaviruses are carried and transmitted by rodents and insectivores. Occasional transmission to humans occurs via inhalation of aerosolized rodent excreta. When transmitted to man hantaviruses cause hemorrhagic fever with renal syndrome (HFRS, in Eurasia, mortality ~10%) and hantavirus cardiopulmonary syndrome (HCPS, in the Americas, mortality ~40%). The single-stranded, negative-sense RNA genome of hantaviruses is in segments S, M and L that respectively encode for nucleocapsid (N), glycoproteins Gn and Gc, and RNA-dependent RNA-polymerase (RdRp or L protein). The genome segments, encapsidated by N protein to form ribonucleoprotein (RNP), are enclosed inside a lipid envelope decorated by spikes formed of Gn and Gc. The focus of this study was to understand the mechanisms and interactions through which the virion is formed and maintained. We observed that when extracted from virions both Gn and Gc favor homo- over hetero-oligomerization. The minimal glycoprotein complexes extracted from virion by detergent were observed, by using ultracentrifugation and gel filtration, to be tetrameric Gn and homodimeric Gc. These results led us to suggest a model where tetrameric Gn complexes are interconnected through homodimeric Gc units to form the grid-like surface architecture described for hantaviruses. This model was found to correlate with the three-dimensional (3D) reconstruction of virion surface created using cryo-electron tomography (cryo-ET). The 3D-density map showed the spike complex formed of Gn and Gc to be 10 nm high and to display a four-fold symmetry with dimensions of 15 nm times 15 nm. This unique square-shaped complex on a roughly round virion creates a hitch for the assembly, since a sphere cannot be broken into rectangles. Thus additional interactions are likely required for the virion assembly. In cryo-ET we observed that the RNP makes occasional contacts to the viral membrane, suggesting an interaction between the spike and RNP. We were able to demonstrate this interaction using various techniques, and showed that both Gn and Gc contribute to the interaction. This led us to suggest that in addition to the interactions between Gn and Gc, also the interaction between spike and RNP is required for assembly. We found galectin-3 binding protein (referred to as 90K) to co-purify with the virions and showed an interaction between 90K and the virion. Analysis of plasma samples taken from patients hospitalized for Puumala virus infection showed increased concentrations of 90K in the acute phase and the increased 90K level was found to correlate with several parameters that reflect the severity of acute HFRS. The results of these studies confirmed, but also challenged some of the dogmas on the structure and assembly of hantaviruses. We confirmed that Gn and RNP do interact, as long assumed. On the other hand we demonstrated that the glycoproteins Gn and Gc exist as homo-oligomers or appear in large hetero-oligomeric complexes, rather than form primarily heterodimers as was previously assumed. This work provided new insight into the structure and assembly of hantaviruses.

Grad–Shafranov Reconstruction of Magnetic Clouds: Overview and Improvements

The Grad–Shafranov reconstruction is a method of estimating the orientation (invariant axis) and cross section of magnetic flux ropes using the data from a single spacecraft. It can be applied to various magnetic structures such as magnetic clouds (MCs) and flux ropes embedded in the magnetopause and in the solar wind. We develop a number of improvements of this technique and show some examples of the reconstruction procedure of interplanetary coronal mass ejections (ICMEs) observed at 1 AU by the STEREO, Wind, and ACE spacecraft during the minimum following Solar Cycle 23. The analysis is conducted not only for ideal localized ICME events but also for non-trivial cases of magnetic clouds in fast solar wind. The Grad–Shafranov reconstruction gives reasonable results for the sample events, although it possesses certain limitations, which need to be taken into account during the interpretation of the model results.

3D MHD simulations of subsurface convection in OB stars

During their main sequence evolution, massive stars can develop convective regions very close to their surface. These regions are caused by an opacity peak associated with iron ionization. Cantiello et al. (2009) found a possible connection between the presence of sub-photospheric convective motions and small scale stochastic velocities in the photosphere of early-type stars. This supports a physical mechanism where microturbulence is caused by waves that are triggered by subsurface convection zones. They further suggest that clumping in the inner parts of the winds of OB stars could be related to subsurface convection, and that the convective layers may also be responsible for stochastic excitation of non-radial pulsations. Furthermore, magnetic fields produced in the iron convection zone could appear at the surface of such massive stars. Therefore subsurface convection could be responsible for the occurrence of observable phenomena such as line profile variability and discrete absorption components. These phenomena have been observed for decades, but still evade a clear theoretical explanation. Here we present preliminary results from 3D MHD simulations of such subsurface convection.