Type III restriction-modification enzymes: a historical perspective

Restriction endonucleases interact with DNA at specific sites leading to cleavage of DNA. Bacterial DNA is protected from restriction endonuclease cleavage by modifying the DNA using a DNA methyltransferase. Based on their molecular structure, sequence recognition, cleavage position and cofactor requirements, restriction-modification (R-M) systems are classified into four groups. Type III R-M enzymes need to interact with two separate unmethylated DNA sequences in inversely repeated head-to-head orientations for efficient cleavage to occur at a defined location (25-27 bp downstream of one of the recognition sites). Like the Type I R-M enzymes, Type III R-M enzymes possess a sequence-specific ATPase activity for DNA cleavage. ATP hydrolysis is required for the long-distance communication between the sites before cleavage. Different models, based on 1D diffusion and/or 3D-DNA looping, exist to explain how the long-distance interaction between the two recognition sites takes place. Type III R-M systems are found in most sequenced bacteria. Genome sequencing of many pathogenic bacteria also shows the presence of a number of phase-variable Type III R-M systems, which play a role in virulence. A growing number of these enzymes are being subjected to biochemical and genetic studies, which, when combined with ongoing structural analyses, promise to provide details for mechanisms of DNA recognition and catalysis

Weichselian vegetation and palaeoenvironment in western Norway and northern Russia. Evidence from pollen analytical investigations

This thesis focuses on the vegetation history and environmental changes in western Norway and northern Russia during the last glacial period (the Weichselian). Pollen grains deposited in lakes and bogs are used as the main palaeoecological tool to reconstruct the vegetation in this period characterised by a changing climate. The work is presented in three individual papers. Paper I deals with the vegetation development on the islands Stord and Bømlo in southern Hordaland, western Norway, at the end of the Late-Weichselian/Marine Isotope Stage (MIS) 2. The two small basins studied, Vassnestjern and Dåfjordsmyr, were deglaciated around 14.6–14.5 ka BP, which is in accordance with other studied sites in the region. The pioneer vegetation was relatively sparse and characterised by snow-bed taxa like Salix, Rumex and Oxyria in addition to grasses. The vegetation became gradually denser during the Lateglacial interstadial (Bølling-Allerød). Empetrum was an important element of the vegetation from around 13.7 ka BP. At least two short-lasting (100–150 years) episodes of reduction in humus-soil vegetation are recorded within the interstadial. These cold periods have been correlated with the GI-1d (14.025–13.9 ka BP) and GI-1b (13.26–13.05 ka BP) events in the Greenland Isotope records. Responses to the Younger Dryas (YD) cooling (12.85–11.65 ka BP) are clearly reflected as an opening of vegetation and reduction in humus-soil communities. Re-establishment of heath communities followed by the development of birch forests were responses to the Holocene warming. Paper II presents pollen records from Dimnamyra and Løkjingsmyra, two small bog basins in the Sunnmøre region, western Norway. The study revealed that the outer coast of Sunnmøre was deglaciated around 15.3 ka BP, slightly earlier than previously thought. The new records from Sunnmøre are compared with the data from southern Hordaland presented in paper I, as well as other published records from western Norway and the European continent. The pioneer vegetation, characterised by snow-bed communities, was quite similar along the coast of western Norway. However, the subsequent development of extensive heath vegetation during the Lateglacial interstadial recorded in south-western Norway is almost absent further north. The vegetation was dominated by grassland, and responses to the GI-1d and GI-1b events are not detected in the Sunnmøre records. A pronounced peak in Poaceae is recorded around 12.9 ka BP, probably reflecting warmer and/or drier conditions. The YD event is clearly reflected also in the Sunnmøre records as a change towards more open vegetation and increased occurrence of snow-bed communities. Pollen-climate transfer functions were used to reconstruct mean July temperatures (Tjul) for several sites in western Norway. Extremely little variability through the Lateglacial is reconstructed for the southern sites, and YD temperatures appear to have been overestimated. The estimated temperatures of the northern sites accord better with the biostratigraphical signals of the sites. However, all sites along the transect show similar vegetational responses, and the inconsistency in the reconstructed Tjul between the sites suggests that the results from pollen-based temperature reconstructions from the Lateglacial must be interpreted with caution. The focus of paper III is the vegetation development and the glacial history of the Polar Ural Mountains, northern Russia. Sediment and palynological records are presented from the shallow Lake Gerdizty at the eastern rim of the mountain chain. Two till beds were identified in the bottom sediments of the lake. The lowermost, fine-grained till was deposited by an ice-sheet from the Siberian lowland sometime towards the end of MIS 5 or during MIS 4. This implies that the lake is not positioned outside the limits of all Weichselian (MIS 5d– 2) glaciations, as assumed when the lake was cored. The overlying, coarser sediments originate from a local ice cap that was flowing from the mountain area in the west sometime during MIS 4, i.e. after 78 ka BP, but before ~65 ka BP when lacustrine sediments started to accumulate in the basin. Throughout the Middle Weichselian/MIS 3 and the major part of the Late Weichselian/MIS 2, the landscape was characterised by open vegetation of steppe and tundra communities. Some dwarf shrubs were present in the earliest phase, but no trees were growing locally, thus indicating summer temperatures below 10 °C. When climate improved at the end of the Late Weichselian, the vegetation became denser with increasing importance of shrubs. Birch-spruce forests developed in the vicinity of Lake Gerdizty shortly after the transition to the Holocene, indicating higher summer temperatures than today

Automatisk borrning av hål för interface av vinge och fena : En teoretisk idé för hur borrningen ska kunna automatiseras

Year 2024 U.S. Air Force will replace their current Northrop T-38 Talon aircraft trainer for pilots, and therefore they have designed the T-X program where several aircraft manufactures competes about the first order of 350 aircrafts. Boeing and Saab AB have in cooperation produced a new aircraft trainer, Boeing T-X, where Saab AB produces the rear part of the fuselage. Today two prototypes have been produced and tested to fly, but if Boeing and Saab wins the order the production has to be more effective to manage the production volume. The aircraft has two wings and two fins which are assembled via an interface with several larger holes which were partially drilled manually during the prototype manufacturing. The purpose with this thesis was to examine if the drilling of the interfaces could be automated in order to increase the production volume, regarding to economy and high tolerance - and flatness requirements. The purpose was also to determine how much of the drilling should be done in an earlier stage and how much should be done where the fuselage is assembled. To manage the time limit, delimitations were set to only make a pre-study and examine which path Saab should take when selecting a suitable solution, the time limit will not be enough for a ready solution. Different drilling methods and different machines and robots suitable for drilling were examined. Concept selection matrices were used in the work process to reach a result, where different concepts were developed and compared with each other based on the requirements. The result was to develop the CNC gantry machine concept. År 2024 kommer U.S. Air Force byta ut sina nuvarande skolflygplan Northrop T-38 Talon, och har därför startat T-X programmet där olika företag är med och tävlar om första ordern på 350 flygplan. Boeing och Saab AB har i samarbete tagit fram ett nytt skolflygplan, Boeing T-X, där Saab AB tillverkar bakre delen av flygkroppen. I dagsläget har två prototyper tillverkats och provflugits, men om Boeing och Saab får ordern måste produktionen effektiviseras för att klara av produktionshastigheten. Flygplanet har två vingar och två fenor vilka fästs via ett interface med ett fåtal större hål vilka under prototyptillverkningen till viss del har borrats manuellt. Syftet med det här exjobbet var att undersöka om borrningen av interfacen gick att automatisera för att kunna öka produktionshastigheten, med avseende på ekonomi samt höga tolerans- och planhetskrav. Syftet var också att avgöra hur mycket av borrningen som skulle göras i ett tidigare skede och hur mycket som skulle göras där flygkroppen byggs samman. För att hinna under tio veckor gjordes avgränsningar till att endast göra en förstudie och ett vägval åt Saab, och inte ta fram en färdig lösning. Olika borrningsmetoder samt maskiner och robotar lämpade för borrning undersöktes. För att komma fram till ett resultat användes under arbetet konceptutvecklingsmatriser, där olika koncept togs fram och jämfördes med varandra utifrån de krav som identifierats. Resultatet blev att utveckla CNC gantry maskin konceptet.

Automatisk borrning av hål för interface av vinge och fena : En teoretisk idé för hur borrningen ska kunna automatiseras

Year 2024 U.S. Air Force will replace their current Northrop T-38 Talon aircraft trainer for pilots, and therefore they have designed the T-X program where several aircraft manufactures competes about the first order of 350 aircrafts. Boeing and Saab AB have in cooperation produced a new aircraft trainer, Boeing T-X, where Saab AB produces the rear part of the fuselage. Today two prototypes have been produced and tested to fly, but if Boeing and Saab wins the order the production has to be more effective to manage the production volume. The aircraft has two wings and two fins which are assembled via an interface with several larger holes which were partially drilled manually during the prototype manufacturing. The purpose with this thesis was to examine if the drilling of the interfaces could be automated in order to increase the production volume, regarding to economy and high tolerance - and flatness requirements. The purpose was also to determine how much of the drilling should be done in an earlier stage and how much should be done where the fuselage is assembled. To manage the time limit, delimitations were set to only make a pre-study and examine which path Saab should take when selecting a suitable solution, the time limit will not be enough for a ready solution. Different drilling methods and different machines and robots suitable for drilling were examined. Concept selection matrices were used in the work process to reach a result, where different concepts were developed and compared with each other based on the requirements. The result was to develop the CNC gantry machine concept. År 2024 kommer U.S. Air Force byta ut sina nuvarande skolflygplan Northrop T-38 Talon, och har därför startat T-X programmet där olika företag är med och tävlar om första ordern på 350 flygplan. Boeing och Saab AB har i samarbete tagit fram ett nytt skolflygplan, Boeing T-X, där Saab AB tillverkar bakre delen av flygkroppen. I dagsläget har två prototyper tillverkats och provflugits, men om Boeing och Saab får ordern måste produktionen effektiviseras för att klara av produktionshastigheten. Flygplanet har två vingar och två fenor vilka fästs via ett interface med ett fåtal större hål vilka under prototyptillverkningen till viss del har borrats manuellt. Syftet med det här exjobbet var att undersöka om borrningen av interfacen gick att automatisera för att kunna öka produktionshastigheten, med avseende på ekonomi samt höga tolerans- och planhetskrav. Syftet var också att avgöra hur mycket av borrningen som skulle göras i ett tidigare skede och hur mycket som skulle göras där flygkroppen byggs samman. För att hinna under tio veckor gjordes avgränsningar till att endast göra en förstudie och ett vägval åt Saab, och inte ta fram en färdig lösning. Olika borrningsmetoder samt maskiner och robotar lämpade för borrning undersöktes. För att komma fram till ett resultat användes under arbetet konceptutvecklingsmatriser, där olika koncept togs fram och jämfördes med varandra utifrån de krav som identifierats. Resultatet blev att utveckla CNC gantry maskin konceptet.

Longitudinal Course of Clinical Lung Clearance Index in Children with Cystic Fibrosis.

RATIONALE While lung clearance index (LCI) is a sensitive marker of small airway disease in individuals with cystic fibrosis (CF), less is known about longitudinal changes in LCI during routine clinical surveillance. OBJECTIVES To describe the longitudinal course of LCI in children with CF during routine clinical surveillance and assess influencing factors. METHODS Children with CF aged 3-18 years performed LCI measurements every 3 months as part of routine clinical care between 2011 and 2018. We recorded clinical data at every visit. We used a multilevel mixed-effect model to determine changes in LCI over time and identify clinical factors that influence LCI course. MEASUREMENTS AND MAIN RESULTS We collected LCI from 1204 visits (3603 trials) in 78 participants, of which 907 visits had acceptable LCI data. The average unadjusted increase in LCI for the entire population was 0.29 LCI units·year-1 (95% CI 0.20-0.38). The increase in LCI was more pronounced in adolescence, with 0.41 units·year-1 (95% CI 0.27-0.54). Colonisation with either Pseudomonas aeruginosa or Aspergillus fumigatus, pulmonary exacerbations, CF-related diabetes, and bronchopulmonary aspergillosis were associated with a higher increase in LCI over time. Adjusting for clinical risk factors reduced the increase in LCI over time to 0.24 LCI units·year-1 (95% CI 0.16-0.33). CONCLUSION LCI measured during routine clinical surveillance is associated with underlying disease progression in children with CF. An increased change in LCI over time should prompt further diagnostic intervention

Effects of elexacaftor/tezacaftor/ivacaftor therapy in children with cystic fibrosis - a comprehensive assessment using lung clearance index, spirometry, and functional and structural lung MRI.

BACKGROUND With improvement in supportive therapies and the introduction of cystic fibrosis transmembrane conductance regulator (CFTR)-modulator treatment in patients with cystic fibrosis (CF), milder disease courses are expected. Therefore, sensitive parameters are needed to monitor disease course and effects of CFTR-modulators. Functional lung MRI using matrix-pencil decomposition (MP-MRI) is a promising tool for assessing ventilation and perfusion quantitatively. This study aimed to assess the treatment effect of elexacaftor/tezacaftor/ivacaftor combination regimen (ELX/TEZ/IVA) on measures of structural and functional lung abnormalities. METHODS 24 children with CF underwent lung function tests (multiple breath washout, spirometry), functional and structural MRI twice (one year apart) before and once after at least two weeks (mean 4.7 ± 2.6 months) on ELX/TEZ/IVA. Main outcomes were changes (Δ) upon ELX/TEZ/IVA in lung function, defect percentage of ventilation (VDP) and perfusion (QDP), defect distribution index of ventilation and perfusion (DDIV, DDIQ), and Eichinger score. Statistical analyses were performed using paired t-tests and multilevel regression models with bootstrapping. RESULTS We observed a significant improvement in lung function, structural and functional MRI parameters upon ELX/TEZ/IVA treatment (mean; 95%-CI): ΔLCI2.5 (TO) -0.84 (-1.62 to -0.06); ΔFEV1 (z-score) 1.05 (0.56 to 1.55); ΔVDP (% of impairment) -6.00 (-8.44 to -3.55); ΔQDP (% of impairment) -3.90 (-5.90 to -1.90); ΔDDIV -1.38 (-2.22 to -0.53); ΔDDIQ -0.31 (-0.73 to 0.12); ΔEichinger score -3.89 (-5.05 to -2.72). CONCLUSIONS Besides lung function tests, functional and structural MRI is a suitable tool to monitor treatment response of ELX/TEZ/IVA therapy, and seems promising as outcome marker in the future