Coupling GIS and LCA for biodiversity assessments of land use

Geospatial details about land use are necessary to assess its potential impacts on biodiversity. Geographic information systems (GIS) are adept at modeling land use in a spatially explicit manner, while life cycle assessment (LCA) does not conventionally utilize geospatial information. This study presents a proof-of-concept approach for coupling GIS and LCA for biodiversity assessments of land use and applies it to a case study of ethanol production from agricultural crops in California. GIS modeling was used to generate crop production scenarios for corn and sugar beets that met a range of ethanol production targets. The selected study area was a four-county region in the southern San Joaquin Valley of California, USA. The resulting land use maps were translated into maps of habitat types. From these maps, vectors were created that contained the total areas for each habitat type in the study region. These habitat compositions are treated as elementary input flows and used to calculate different biodiversity impact indicators in a second paper (Geyer et al., submitted). Ten ethanol production scenarios were developed with GIS modeling. Current land use is added as baseline scenario. The parcels selected for corn and sugar beet production were generally in different locations. Moreover, corn and sugar beets are classified as different habitat types. Consequently, the scenarios differed in both the habitat types converted and in the habitat types expanded. Importantly, land use increased nonlinearly with increasing ethanol production targets. The GIS modeling for this study used spatial data that are commonly available in most developed countries and only required functions that are provided in virtually any commercial or open-source GIS software package. This study has demonstrated that GIS-based inventory modeling of land use allows important refinements in LCA theory and practice. Using GIS, land use can be modeled as a geospatial and nonlinear function of output. For each spatially explicit process, land use can be expressed within the conventional structure of LCA methodology as a set of elementary input flows of habitat types

SIMAP: the similarity matrix of proteins

Similarity Matrix of Proteins (SIMAP) () provides a database based on a pre-computed similarity matrix covering the similarity space formed by >4 million amino acid sequences from public databases and completely sequenced genomes. The database is capable of handling very large datasets and is updated incrementally. For sequence similarity searches and pairwise alignments, we implemented a grid-enabled software system, which is based on FASTA heuristics and the Smith–Waterman algorithm. Our ProtInfo system allows querying by protein sequences covered by the SIMAP dataset as well as by fragments of these sequences, highly similar sequences and title words. Each sequence in the database is supplemented with pre-calculated features generated by detailed sequence analyses. By providing WWW interfaces as well as web-services, we offer the SIMAP resource as an efficient and comprehensive tool for sequence similarity searches

Mechanism of lignin inhibition of enzymatic biomass deconstruction

Background The conversion of plant biomass to ethanol via enzymatic cellulose hydrolysis offers a potentially sustainable route to biofuel production. However, the inhibition of enzymatic activity in pretreated biomass by lignin severely limits the efficiency of this process. Results By performing atomic-detail molecular dynamics simulation of a biomass model containing cellulose, lignin, and cellulases (TrCel7A), we elucidate detailed lignin inhibition mechanisms. We find that lignin binds preferentially both to the elements of cellulose to which the cellulases also preferentially bind (the hydrophobic faces) and also to the specific residues on the cellulose-binding module of the cellulase that are critical for cellulose binding of TrCel7A (Y466, Y492, and Y493). Conclusions Lignin thus binds exactly where for industrial purposes it is least desired, providing a simple explanation of why hydrolysis yields increase with lignin removal

Skin and hair on-a-chip: in vitro skin models versus ex vivo tissue maintenance with dynamic perfusion

Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG geförderten) Allianz- bzw. Nationallizenz frei zugänglich.This publication is with permission of the rights owner freely accessible due to an Alliance licence and a national licence (funded by the DFG, German Research Foundation) respectively.Substantial progress has been achieved over the last few decades in the development of skin equivalents to model the skin as an organ. However, their static culture still limits the emulation of essential physiological properties crucial for toxicity testing and compound screening. Here, we describe a dynamically perfused chip-based bioreactor platform capable of applying variable mechanical shear stress and extending culture periods. This leads to improvements of culture conditions for integrated in vitro skin models, ex vivo skin organ cultures and biopsies of single hair follicular units.BMBF, 0315569, GO-Bio 3: Multi-Organ-Bioreaktoren für die prädiktive Substanztestung im ChipformatDFG, GSC 203, Berlin-Brandenburg School for Regenerative Therapie

Human hair follicle eqivalents in vitro for transplantation and chip-based substance testing : From 22nd European Society for Animal Cell Technology (ESACT) Meeting on Cell Based Technologies Vienna, Austria. 15-18 May 2011

First published by BioMed Central: Marx, Uwe ; Lindner, Gerd ; Wagner, Ilka ; Horland, Reyk ; Atac, Beren ; Hoffmann, Silke ; Gruchow, Mathias ; Sonntag, Frank ; Klotzbach, Udo ; Lauster, Roland: Human hair follicle equivalents in vitro for transplantation and chip-based substance testing : From 22nd European Society for Animal Cell Technology (ESACT) Meeting on Cell Based Technologies Vienna, Austria. 15-18 May 2011. - In: BMC Proceedings. - ISSN 1753-6561 (online). - 5 (2011), suppl. 8, O7. - doi:10.1186/1753-6561-5-S8-O7

Survival and prognostic factors in conventional G1 chondrosarcoma

Background Chondrosarcoma is the second most frequent malignant bone tumor. Grade I chondrosarcoma (syn.: atypical cartilaginous tumor) is classified as an intermediately and locally aggressive neoplasm and typically is treated less aggressively (i.e., by intralesional curettage). Does the data regarding local recurrence (LR) and metastatic disease justify this? Methods From 1982 to 2014, 37 consecutive patients with G1 chondrosarcoma had been resected or curetted. The margin was defined as R0 (wide resection) or R1 (marginal resection). All patients were followed for evidence of local recurrence or metastatic disease. Overall and recurrence-free survival were calculated, and various potentially prognostic factors were evaluated. Results In 23 patients (62%), the tumor was widely (R0) resected, whereas in 14 patients, (38%) the resection was marginal (R1). Overall survival was 97% after 5 years, 92% after 10 years, and 67% after 20 years. Five-year local recurrence-free survival was 96%. Ten-year local recurrence-free survival was 83%. Local recurrence-free survival showed a significant correlation to margin status but no correlation to location or age. None of the patients with local recurrence died during the follow-up. One patient had metastatic disease at initial presentation, and a further five patients developed metastatic disease during follow-up. Metastatic disease proofed to be a highly significant factor for survival but was not correlated to local recurrence. Conclusions There was no significant correlation between the outcome and the primary tumor location. Marginal resection was a risk factor for LR, but there was no significant difference in the overall survival in patients with or without LR. Metastatic disease (16%) was more common than expected from the literature and a significant predictor for poor overall survival

MafA and MafB Regulate Genes Critical to β-Cells in a Unique Temporal Manner

OBJECTIVE-Several transcription factors are essential to pancreatic islet beta-cell development, proliferation, and activity, including MafA and MafB. However, MafA and MafB are distinct from others in regard to temporal and islet cell expression pattern, with beta-cells affected by MafB only during development and exclusively by MafA in the adult. Our aim was to define the functional relationship between these closely related activators to the beta-cell. RESEARCH DESIGN AND METHODS-The distribution of MafA and MafB in the beta-cell population was determined immunohistochemically at various developmental and perinatal stages in mice. To identify genes regulated by MafB, microarray profiling was performed on wild-type and MafB(-/-) pancreata at embryonic day 18.5, with candidates evaluated by quantitative RT-PCR and in situ hybridization. The potential role of MafA in the expression of verified targets was next analyzed in adult islets of a pancreas-wide MafA mutant (termed MafA(Delta Panc)). RESULTS-MafB was produced in a larger fraction of beta-cells than MafA during development and found to regulate potential effectors of glucose sensing, hormone processing, vesicle formation, and insulin secretion. Notably, expression from many of these genes was compromised in MafA(Delta Panc) islets, suggesting that MafA is required to sustain expression in adults. CONCLUSIONS-Our results provide insight into the sequential manner by which MafA and MafB regulate islet beta-cell formation and maturation. Diabetes 59:2530-2539, 201

Neoadjuvant or adjuvant sirolimus for malignant metastatic or locally advanced perivascular epithelioid cell tumors: two case reports

Perivascular epithelioid cell tumors (PEComas) are very rare mesenchymal tumors, characterized by the presence of perivascular epithelioid cells. Despite their often benign nature, malignant variants with a locally aggressive growth pattern and even distant metastases are known. We describe two cases of malignant PEComas. The first patient had an extensive peritoneal spread and a history of multiple resections, and received the mechanistic target of rapamycin inhibitor sirolimus in a postoperative setting as maintenance therapy. The second patient presented with locally advanced disease in the iliac fossa and was treated with sirolimus in a neoadjuvant setting and achieved complete remission. Both patients have been under treatment for 18 and 52 months, respectively, and are currently in complete remission. These two cases indicate that mechanistic target of rapamycin inhibition for malignant PEComas could be a safe and successful treatment strategy in a neoadjuvant setting with an acceptable toxicity profile