Land use in life cycle assessment

As human population is continuously increasing, productive land is becoming even more limited resource for biomass production. Land use and land use change cause various environmental impacts. At the moment the focus is on land use related greenhouse gas emissions, but changes in carbon cycles and storages, soil quality and soil net productivity, and loss of biodiversity are growing in importance. Additionally, changes in land use and land cover also affect water quality and availability. Currently, land use related terminology is diverse, and the methodologies to assess the impacts of land use and land use change are still partly under development. The aim of this study was to discuss how land use induced environmental impacts can be taken into consideration in the life cycle assessment (LCA).  This report summarises the results of the FINLCA project’s (Life Cycle Assessment Framework and Tools for Finnish Companies) two tasks (WP 2.1 land use and WP 5.2 biomaterials). The study was conducted in co-operation with the Finnish Environment Institute (SYKE) and VTT Technical Research Centre of Finland. As a result, we show that it is possible to make land use impact assessment with LCA. Indicators are available for climate impacts and for all the other identified land use impact categories (resource depletion, soil quality, and biodiversity). However, limited land use related data reduces the reliability of the results. Most widely used life cycle impact assessment (LCIA) methods (e.g. ReCiPe, CML or EI99) cover only one aspect of land use induced environmental impacts. Additionally, some of the land use indicator results are difficult to understand and communicate. From the company perspective, we considered that accounting of land occupation (m2a) and transformation (m2 from and to) is a good starting point together with the relatively simple ecological footprint indicator for productive land occupation (resource depletion). A more comprehensive and challenging approach to land use impact assessment in LCA is to include all three impact categories and add the SOC/SOM indicator for soil quality impacts and EDP or PDF indicator for biodiversity. In case no quantitative assessment can be done, we propose that companies would map their raw materials’ origins. Even a qualitative assessment related to products’ life cycles would help to identify if there are any potential land use or direct and indirect land use change risks

Creating highly specific nucleases by fusion of active restriction endonucleases and catalytically inactive homing endonucleases

Zinc-finger nucleases and TALE nucleases are produced by combining a specific DNA-binding module and a non-specific DNA-cleavage module, resulting in nucleases able to cleave DNA at a unique sequence. Here a new approach for creating highly specific nucleases was pursued by fusing a catalytically inactive variant of the homing endonuclease I-SceI, as DNA binding-module, to the type IIP restriction enzyme PvuII, as cleavage module. The fusion enzymes were designed to recognize a composite site comprising the recognition site of PvuII flanked by the recognition site of I-SceI. In order to reduce activity on PvuII sites lacking the flanking I-SceI sites, the enzymes were optimized so that the binding of I-SceI to its sites positions PvuII for cleavage of the composite site. This was achieved by optimization of the linker and by introducing amino acid substitutions in PvuII which decrease its activity or disturb its dimer interface. The most specific variant showed a more than 1000-fold preference for the addressed composite site over an unaddressed PvuII site. These results indicate that using a specific restriction enzyme, such as PvuII, as cleavage module, offers an alternative to the otherwise often used catalytic domain of FokI, which by itself does not contribute to the specificity of the engineered nuclease

PENGARUH KEADILAN ORGANISASI DENGAN MEDIASI STRATEGI KOPING TERHADAP BURNOUT PADA PEKERJA SOSIAL DINAS SOSIAL

Penelitian ini bertujuan untuk mengetahui apakah ada pengaruh keadilan organisasi dengan mediasi strategi koping terhadap burnout  pada pekerja sosial dinas  sosial. Subyek penelitian sebanyak 119 pekerja sosial Dinas Sosial. Data penelitian dikumpulkan dengan empat skala, yaitu skala keadilan organisasi, skala startegi koping berfokus kepada masalah, skala strategi koping berfokus pada emosi dan skala burnout. Data dianalisis dengan  menggunakan structural equation model (SEM). Hasil penelitian menyatakan bahwa  Keadilan organisasi (distributif, prosedural, interaksional) dengan mediasi strategi koping berpengaruh signifikan terhadap burnout dengan nilai β masing-masing -0.250, 0.203 dan 0.153 dengan p masing-masing 0.000, 0.02  dan 0.011. Temuan ini memberikan peluang  bagi peneliti berikutnya untuk menyelidiki lebih lanjut tentang keadilan organisasi melalui strategi lainnya terhadap burnout pada pekerja sosial dinas sosial

Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses

For a very long time, Type II restriction enzymes (REases) have been a paradigm of ORFans: proteins with no detectable similarity to each other and to any other protein in the database, despite common cellular and biochemical function. Crystallographic analyses published until January 2008 provided high-resolution structures for only 28 of 1637 Type II REase sequences available in the Restriction Enzyme database (REBASE). Among these structures, all but two possess catalytic domains with the common PD-(D/E)XK nuclease fold. Two structures are unrelated to the others: R.BfiI exhibits the phospholipase D (PLD) fold, while R.PabI has a new fold termed ‘half-pipe’. Thus far, bioinformatic studies supported by site-directed mutagenesis have extended the number of tentatively assigned REase folds to five (now including also GIY-YIG and HNH folds identified earlier in homing endonucleases) and provided structural predictions for dozens of REase sequences without experimentally solved structures. Here, we present a comprehensive study of all Type II REase sequences available in REBASE together with their homologs detectable in the nonredundant and environmental samples databases at the NCBI. We present the summary and critical evaluation of structural assignments and predictions reported earlier, new classification of all REase sequences into families, domain architecture analysis and new predictions of three-dimensional folds. Among 289 experimentally characterized (not putative) Type II REases, whose apparently full-length sequences are available in REBASE, we assign 199 (69%) to contain the PD-(D/E)XK domain. The HNH domain is the second most common, with 24 (8%) members. When putative REases are taken into account, the fraction of PD-(D/E)XK and HNH folds changes to 48% and 30%, respectively. Fifty-six characterized (and 521 predicted) REases remain unassigned to any of the five REase folds identified so far, and may exhibit new architectures. These enzymes are proposed as the most interesting targets for structure determination by high-resolution experimental methods. Our analysis provides the first comprehensive map of sequence-structure relationships among Type II REases and will help to focus the efforts of structural and functional genomics of this large and biotechnologically important class of enzymes

Characterization and crystal structure of the type IIG restriction endonuclease RM.BpuSI

A type IIG restriction endonuclease, RM.BpuSI from Bacillus pumilus, has been characterized and its X-ray crystal structure determined at 2.35Å resolution. The enzyme is comprised of an array of 5-folded domains that couple the enzyme's N-terminal endonuclease domain to its C-terminal target recognition and methylation activities. The REase domain contains a PD-x15-ExK motif, is closely superimposable against the FokI endonuclease domain, and coordinates a single metal ion. A helical bundle domain connects the endonuclease and methyltransferase (MTase) domains. The MTase domain is similar to the N6-adenine MTase M.TaqI, while the target recognition domain (TRD or specificity domain) resembles a truncated S subunit of Type I R–M system. A final structural domain, that may form additional DNA contacts, interrupts the TRD. DNA binding and cleavage must involve large movements of the endonuclease and TRD domains, that are probably tightly coordinated and coupled to target site methylation status

Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA

The restriction endonuclease EcoRV can rapidly locate a short recognition site within long non-cognate DNA using ‘facilitated diffusion’. This process has long been attributed to a sliding mechanism, in which the enzyme first binds to the DNA via nonspecific interaction and then moves along the DNA by 1D diffusion. Recent studies, however, provided evidence that 3D translocations (hopping/jumping) also help EcoRV to locate its target site. Here we report the first direct observation of sliding and jumping of individual EcoRV molecules along nonspecific DNA. Using fluorescence microscopy, we could distinguish between a slow 1D diffusion of the enzyme and a fast translocation mechanism that was demonstrated to stem from 3D jumps. Salt effects on both sliding and jumping were investigated, and we developed numerical simulations to account for both the jump frequency and the jump length distribution. We deduced from our study the 1D diffusion coefficient of EcoRV, and we estimated the number of jumps occurring during an interaction event with nonspecific DNA. Our results substantiate that sliding alternates with hopping/jumping during the facilitated diffusion of EcoRV and, furthermore, set up a framework for the investigation of target site location by other DNA-binding proteins