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result(s) for
"Berg, Johan"
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Dissected antiporter modules establish minimal proton-conduction elements of the respiratory complex I
2024
The respiratory Complex I is a highly intricate redox-driven proton pump that powers oxidative phosphorylation across all domains of life. Yet, despite major efforts in recent decades, its long-range energy transduction principles remain highly debated. We create here minimal proton-conducting membrane modules by engineering and dissecting the key elements of the bacterial Complex I. By combining biophysical, biochemical, and computational experiments, we show that the isolated antiporter-like modules of Complex I comprise all functional elements required for conducting protons across proteoliposome membranes. We find that the rate of proton conduction is controlled by conformational changes of buried ion-pairs that modulate the reaction barriers by electric field effects. The proton conduction is also modulated by bulky residues along the proton channels that are key for establishing a tightly coupled proton pumping machinery in Complex I. Our findings provide direct experimental evidence that the individual antiporter modules are responsible for the proton transport activity of Complex I. On a general level, our findings highlight electrostatic and conformational coupling mechanisms in the modular energy-transduction machinery of Complex I with distinct similarities to other enzymes.
The mechanism of Complex I remains to be fully determined. Here, the authors used an integrative approach to show that the dissected antiporter modules of Complex I have all the essential elements required to transport protons across the membrane.
Journal Article
Challenges and Opportunities for Public Participation in Urban and Regional Planning during the COVID-19 Pandemic—Lessons Learned for the Future
by
Olufemi, Olusola
,
van den Berg, Johan
,
Pantić, Marijana
in
Charters
,
Citizen participation
,
collaborative decision making
2021
The COVID-19 pandemic has spurred significant changes in the fields of economic development, social issues, everyday life, etc. Activities that used to depend on face-to-face communication were firstly suspended and then shifted to new forms of communication. This includes the public participation process in urban and spatial planning. Therefore, this study explores the new domain developed in urban and spatial planning with regard to public participation and surmises future realms in the post-pandemic era. On the occasion of the virtual collaboration platform Cyber Agora organized by the ISOCARP (International Society of City and Regional Planners), chosen participants got together virtually to share, discuss, and compare their practical knowledge in public participation before and during COVID-19. In addition, they addressed the potential benefits of shifting from traditional to virtual participation and potential benefits in the post-COVID-19 era. Considering the collected data and understanding them in the light of the available literature, this study concludes that the application of a combined approach (using both traditional and virtual modes of participation) is recommended because it would enable a larger number and higher diversity of participants. The study also elaborates particular modes of virtual participation with the pros and cons of their use in a particular context.
Journal Article
Life cycle impact assessment in the arctic: Challenges and research needs
2017
Life cycle assessment (LCA) is increasingly used for environmental assessment of products and production processes to support environmental decision-making both worldwide and in the Arctic. However, there are several weaknesses in the impact assessment methodology in LCA, e.g., related to uncertainties of impact assessment results, absence of spatial differentiation in characterization modeling, and gaps in the coverage of impact pathways of different “archetypal” environments. Searching for a new resource base and areas for operation, marine and marine-based industries are continuously moving north, which underlines the need for better life cycle impact assessment in the Arctic, particularly to aid in industrial environmental management systems and stakeholder communications. This paper aims to investigate gaps and challenges in the application of the currently available impact assessment methods in the Arctic context. A simplified Arctic mining LCA case study was carried out to demonstrate the relevance of Arctic emissions at the midpoint and endpoint levels, as well as possible influences of the Arctic context on the impact assessment results. Results of this study showed that significant research gaps remain in Arctic-dependent life cycle impact assessment, particularly on: (i) the possible influences of the Arctic-specific features on characterization factors for impact assessment (such as seasonality, cold climate, precipitation, and marine dependence); and (ii) the coverage of impact pathways, especially on the under-addressed marine impacts and marine/near-shore dispersion processes. Addressing those identified research gaps and demand for future Arctic life cycle impact assessment could increase the credibility of LCA as an environmental decision-making support tool for Arctic industries and better support sustainable Arctic development.
Journal Article
Life Cycle Based Climate Emissions of Charcoal Conditioning Routes for the Use in the Ferro-Alloy Production
2022
Renewable reductants are intended to significantly reduce CO2 emissions from ferro-alloy production, e.g., by up to 80% in 2050 in Norway. However, charcoals provide inferior properties compared to fossil fuel-based reductants, which can hamper large replacement ratios. Therefore, conditioning routes from coal beneficiation was investigated to improve the inferior properties of charcoal, such as mechanical strength, volatile matter, CO2 reactivity and mineral matter content. To evaluate the global warming potential of renewable reductants, the CO2 emissions of upgraded charcoal were estimated by using a simplified life cycle assessment, focusing on the additional emissions by the energy demand, required chemicals and mass loss for each process stage. The combination of ash removal, briquetting and high-temperature treatment can provide a renewable coke with superior properties compared to charcoal, but concomitantly decrease the available biomass potential by up to 40%, increasing the CO2-based global warming potential of industrial produced charcoal to ≈500 kg CO2-eq. t−1 FC. Based on our assumptions, CO2 emissions from fossil fuel-based reductants can be reduced by up to 85%. A key to minimizing energy or material losses is to combine the pyrolysis and post-treatment processes of renewable reductants to upgrade industrial charcoal on-site at the metallurgical plant. Briquetting showed the largest additional global warming potential from the investigated process routes, whereas the high temperature treatment requires a renewable energy source to be sustainable.
Journal Article
Lipid Composition Affects the Efficiency in the Functional Reconstitution of the Cytochrome c Oxidase
by
Brzezinski, Peter
,
Berg, Johan
,
Heberle, Joachim
in
Bacterial Proteins - chemistry
,
Binding sites
,
Cytochrome
2020
The transmembrane protein cytochrome c oxidase (CcO) is the terminal oxidase in the respiratory chain of many aerobic organisms and catalyzes the reduction of dioxygen to water. This process maintains an electrochemical proton gradient across the membrane hosting the oxidase. CcO is a well-established model enzyme in bioenergetics to study the proton-coupled electron transfer reactions and protonation dynamics involved in these processes. Its catalytic mechanism is subject to ongoing intense research. Previous research, however, was mainly focused on the turnover of oxygen and electrons in CcO, while studies reporting proton turnover rates of CcO, that is the rate of proton uptake by the enzyme, are scarce. Here, we reconstitute CcO from R. sphaeroides into liposomes containing a pH sensitive dye and probe changes of the pH value inside single proteoliposomes using fluorescence microscopy. CcO proton turnover rates are quantified at the single-enzyme level. In addition, we recorded the distribution of the number of functionally reconstituted CcOs across the proteoliposome population. Studies are performed using proteoliposomes made of native lipid sources, such as a crude extract of soybean lipids and the polar lipid extract of E. coli, as well as purified lipid fractions, such as phosphatidylcholine extracted from soybean lipids. It is shown that these lipid compositions have only minor effects on the CcO proton turnover rate, but can have a strong impact on the reconstitution efficiency of functionally active CcOs. In particular, our experiments indicate that efficient functional reconstitution of CcO is strongly promoted by the addition of anionic lipids like phosphatidylglycerol and cardiolipin.
Journal Article
Cloning of the astaxanthin synthase gene from Xanthophyllomyces dendrorhous (Phaffia rhodozyma) and its assignment as a β-carotene 3-hydroxylase/4-ketolase
by
Sandmann, Gerhard
,
van den Berg, Johan
,
Setoguchi, Yutaka
in
Amino Acid Sequence
,
astaxanthin
,
Astaxanthin synthase
2006
A gene has been cloned from Xanthophyllomyces dendrorhous by complementation of astaxanthin formation in a β-carotene accumulating mutant. It consists of 3,166 bp and contains 17 introns. For the β-carotene mutant ATCC 96815, a single point mutation in the splicing sequence of intron 8 was found. The resulting improper splicing of the mRNA results in an inactive protein. The cDNA of this β-carotene oxygenase encodes a cytochrome P450 monooxygenase belonging to the 3A subfamily. P450-specific domains were identified including a cytochrome P450 and an oxygen binding motif. Electrons are provided by a cytochrome P450 reductase. Functional characterization of the enzyme by genetic modification of X. dendrorhous demonstrated that this P450 monooxygenase is multifunctional catalyzing all steps from β-carotene to astaxanthin formation by oxygenation of carbon 3 and 4. The reaction sequence is first 4-ketolation of β-carotene followed by 3-hydroxylation. A hydroxylation mechanism at allylic carbon atoms has been proposed for the generation of 4-keto and 3-hydroxy groups at both β-ionone ends.
Journal Article
Trends in Tissue Engineering for Blood Vessels
2012
Over the years, cardiovascular diseases continue to increase and affect not only human health but also the economic stability worldwide. The advancement in tissue engineering is contributing a lot in dealing with this immediate need of alleviating human health. Blood vessel diseases are considered as major cardiovascular health problems. Although blood vessel transplantation is the most convenient treatment, it has been delimited due to scarcity of donors and the patient’s conditions. However, tissue-engineered blood vessels are promising alternatives as mode of treatment for blood vessel defects. The purpose of this paper is to show the importance of the advancement on biofabrication technology for treatment of soft tissue defects particularly for vascular tissues. This will also provide an overview and update on the current status of tissue reconstruction especially from autologous stem cells, scaffolds, and scaffold-free cellular transplantable constructs. The discussion of this paper will be focused on the historical view of cardiovascular tissue engineering and stem cell biology. The representative studies featured in this paper are limited within the last decade in order to trace the trend and evolution of techniques for blood vessel tissue engineering.
Journal Article
Effect factors for marine invasion impacts on biodiversity
by
Gjedde, Philip
,
Verones, Francesca
,
Pettersen, Johan Berg
in
artificial intelligence
,
Assessments
,
Bias
2024
Purpose
Marine vertebrate populations have halved in the past decades, and invasive species are a major driver for this loss. While many model the spread of invasive species, a model to assess impacts of marine invasions, after introduction, has hitherto been missing. We present the first regionalized effect factors for marine invasions. These factors gauge differences in biodiversity impacts after invasions, enabling life cycle impact assessments to highlight biodiversity impacts from invasive species.
Methods
Alien species are species that are introduced by humans to ecosystems where they are not native. We combine data from the IUCN red list and the MarINvaders database to identify the potentially disappeared fraction of native species within each marine coastal ecoregion after alien introduction. The effect factors indicate the biodiversity impact from invasions per alien introduction. However, the IUCN red list has a performance bias between taxonomic groups, and both the IUCN and the harmonized citizen science data from MarINvaders have a geographic observer’s bias. We address some of this bias by evaluating the number of threatened species per number of assessed species, as well as including machine-learning derived data for data deficient species.
Results and discussion
The resulting regional effect factors demonstrate high effects of invasions at high latitudes, which is in line with other findings. Our approach is founded on continuously growing citizen science data and so reflects the biases and uncertainties that follow with this uneven way of data sampling. On the other hand, the continuous data collection by citizen scientists will improve data coverage and thus improve the model. Vice versa, the model itself may be motivation for citizens scientists to collect more data.
Conclusion
The effect of marine invasions presented herein reflects current global information on the issue viewed in a perspective relevant for life cycle impact assessments. The developed effect factors can be used for further assessments that will aid decision-making for policies, industries, and consumers to work towards minimizing impacts of marine invasions and are developed to be compatible with different relevant fate factors.
Journal Article
Swedish-Norwegian co-operation in the treatment of three hypothermia victims
by
Karlsen, Øystein
,
Skjærvold, Nils K
,
Berg, Nils Johan
in
Accidental hypothermia
,
Accidents
,
Adolescent
2017
Background
Accidental hypothermia with cardiac arrest represents a challenge for pre-hospital rescuers as well as in-hospital staff. For pre-hospital personnel, the main focus is to get the patient to the correct destination without unnecessary delay. For in-hospital personnel early information is vital to assess the possibility for resuscitation with extracorporeal re-warming. The challenge is augmented when rescuers must cross national borders to reach and/or deliver the patients. We present a case where three adolescent boys suffered severe hypothermia after a canoeing accident in Sweden.
Case presentation
Three 14-year-old boys were canoeing a mountain lake close to the Norwegian border when their boat capsized and they all fell into the cold water. The rescue operation was hampered by rough weather conditions, and immersion times spanned from 63 to 125 min. Flight times from the scene of accident to the nearest ECMO center in Norway (Trondheim) and Sweden (Umeå) were about 30 and 90 min respectively. Two of the victims showed no vital signs after retrieval from the water and had extremely low body temperatures. They were brought to Trondheim University Hospital where they were resuscitated successfully with extracorporeal re-warming. Unable to be weaned from ECMO in the initial phase, both patients were retrieved by mobile ECMO teams to Karolinska University Hospital, from where they were discharged to their homes with good outcomes, although with some sequelae. A third victim with moderate to severe hypothermia without cardiac arrest was treated at a local hospital, from where he after a short stay was discharged without physical sequelae.
Conclusion
These cases are a reminder of the traditional mantra that «no one is dead until warm and dead». Good communication between pre- and in-hospital staff can be vital for optimizing patient treatment when handling victims of severe hypothermia, and especially when there is multiple victims. Communication between neighboring countries, but even neighboring regions within the same country, can be challenging. We encourage regions similar to ours to review protocols regarding hypothermia management, making them more robust before incidents like this take place.
Journal Article
Genes involved in carotene synthesis and mating in Blakeslea trispora
by
Ramírez-Medina, Humberto
,
van den Berg, Johan A
,
Cerdá-Olmedo, Enrique
in
Acetic acid
,
Amplified fragment length polymorphism
,
Base Sequence
2008
Mating of Blakeslea trispora and other molds of the order Mucorales requires the interaction of mycelia of opposite sex, (+) and (-), leading to the development of specialized structures and to an enhanced accumulation of β-carotene. Industry obtains β-carotene by co-cultivating appropriate strains of Blakeslea (“mated cultures”). Gene transcription in single and mated cultures was assayed by cDNA-AFLP, a technique to observe the differential expression of subsets of mRNA fragments. Overexpression in mated cultures is about ten times more frequent than underexpression. We obtained and sequenced fragments of 97 candidate genes that appeared to be overexpressed during mating and confirmed four of them by reverse transcription and real-time PCR. Comparisons with gene sequences from other organisms suggest functions in carotene biosynthesis (4 genes), energy metabolism (8), cell wall synthesis (1), transfer of acetyl groups (1), and regulatory processes (10). Sodium acetate inhibited sexual overexpression in about two-thirds of the candidate genes and acted as a signal with broad effects on the metabolism and the morphology of mated cultures. Our work offers new materials for the study of carotene biosynthesis and its regulation and for the improvement of carotene production with Mucorales.
Journal Article