Genome-scale modeling of the protein secretory machinery in yeast

The protein secretory machinery in Eukarya is involved in post-translational modification (PTMs) and sorting of the secretory and many transmembrane proteins. While the secretory machinery has been well-studied using classic reductionist approaches, a holistic view of its complex nature is lacking. Here, we present the first genome-scale model for the yeast secretory machinery which captures the knowledge generated through more than 50 years of research. The model is based on the concept of a Protein Specific Information Matrix (PSIM: characterized by seven PTMs features). An algorithm was developed which mimics secretory machinery and assigns each secretory protein to a particular secretory class that determines the set of PTMs and transport steps specific to each protein. Protein abundances were integrated with the model in order to gain system level estimation of the metabolic demands associated with the processing of each specific protein as well as a quantitative estimation of the activity of each component of the secretory machinery

Application of the Recovery Potential Screening Tool in the Matagorda Bay Watershed

The State of Texas currently contains 568 water bodies considered impaired due to excessive pollutant loading. Of these, approximately 48% are impaired due to elevated levels of fecal indicator bacteria from animals, birds and humans. Once impaired, efforts to restore water quality must be undertaken. This large number of bacteria impairments leaves the State with a sizable task ahead and presents a range of restoration challenges. Restoring all of these impaired water bodies is costly and resource intensive, thus prioritizing future water quality restoration efforts is a means to efficiently allocate available resources and achieve timely restoration results. The U.S. Environmental Protection Agency (EPA) developed the Recovery Potential Screening (RPS) tool to help prioritize water body restoration planning efforts (Norton et al. 2009). Built as a technical aid for states and government agencies, the RPS tool provides a systematic approach for comparing the relative restorability of water bodies. When employed and supplied with sufficient data, this tool can aid groups and entities considering restoration efforts determine which water bodies have the highest likelihood of successful water quality restoration based on characteristics of the local watershed (U.S. EPA 2014)

Basin Approach to Address Bacterial Impairments in Basins 15, 16, and 17

In the 2012 Texas Integrated Report and 303(d) List, approximately 48% of the 568 impaired water bodies were caused by high bacteria levels. Once a water body has been listed, the Clean Water Act requires action to be undertaken to restore water quality in that water body. Several options exist to achieve this, which include additional monitoring, a standards assessment, development of a total maximum daily load (TMDL) or development of another watershed based plan such as a watershed protection plan. Traditionally, impairments have been addressed one at a time. In order to more efficiently address similar impairments within the same basin, more efficiently distribute resources, and with the hopes of preventing future listings within the same watershed, a new basin wide approach is being implemented in the Texas River Basins 15 (Colorado – Lavaca), 16 (Lavaca), and 17 (Lavaca Guadalupe). These watersheds, collectively referred to as the Matagorda Bay watershed have five water body assessment units impaired for elevated levels of fecal indicator bacteria: Carancahua Bay, Arenosa Creek, Tres Palacios Creek and two segments of the Lavaca River. This report discusses the current and historical state of the study area and focuses on describing the physical, hydrological, climatic, and demographic conditions as well as potential sources of pollution. Information presented will be used in future water quality analysis and will assist in determining how to address bacteria impairments in the watershed. Information is compiled on a watershed level, summarizing all three basins, as well as within each basin where appropriate

PI3K/AKT is involved in mediating survival signals that rescue Ewing tumour cells from fibroblast growth factor 2-induced cell death

While in vitro studies had shown that fibroblast growth factor 2 (FGF2) can induce cell death in Ewing tumours, it remained unclear how Ewing tumour cells survive in vivo within a FGF2-rich microenvironment. Serum- and integrin-mediated survival signals were, therefore, studied in adherent monolayer and anchorage-independent colony cell cultures. In a panel of Ewing tumour cell lines, either adhesion to collagen or exposure to serum alone only had a minor protective effect against FGF2. However, both combined led to complete resistance to 5 ng ml−1 FGF2 in three of four FGF2-sensitive cell lines (RD-ES, RM-82 and WE-68), and to an increased survival as compared to other culture conditions in TC-71 cells. Inhibition studies with LY294002 demonstrated that the serum signal is mediated via the phosphoinositide 3-OH kinase/AKT pathway. Thus, Ewing tumour cells escape FGF2-induced cell death by modulating FGF2 signalling. The tumour microenvironment provides the necessary survival signals by integrin-mediated adhesion and soluble serum factor(s). These survival signals warrant further investigation as a potential resistance mechanism to other apoptosis-inducing agents in vivo

Biogeography in the air: fungal diversity over land and oceans

Biogenic aerosols are relevant for the Earth system, climate, and public health on local, regional, and global scales. Up to now, however, little is known about the diversity and biogeography of airborne microorganisms. We present the first DNA-based analysis of airborne fungi on global scales, showing pronounced geographic patterns and boundaries. In particular we find that the ratio of species richness between Basidiomycota and Ascomycota is much higher in continental air than in marine air. This may be an important difference between the 'blue ocean' and 'green ocean' regimes in the formation of clouds and precipitation, for which fungal spores can act as nuclei. Our findings also suggest that air flow patterns and the global atmospheric circulation are important for the understanding of global changes in biodiversity.Max Planck Society (MPG)Max Planck Society (MPG)LEC Geocycles in MainzLEC Geocycles in Mainzstate Rheinland-Pfalz [596]state RheinlandPfalzGerman Research Foundation [DE1161/2-1, PO1013/5-1, FOR 1525 INUIT]German Research Foundatio

Estimation of local and external contributions of biomass burning to PM2.5 in an industrial zone included in a large urban settlement

A total of 85 PM2.5 samples were collected at a site located in a large industrial zone (Porto Marghera, Venice, Italy) during a 1-year-long sampling campaign. Samples were analyzed to determine water-soluble inorganic ions, elemental and organic carbon, and levoglucosan, and results were processed to investigate the seasonal patterns, the relationship between the analyzed species, and the most probable sources by using a set of tools, including (i) conditional probability function (CPF), (ii) conditional bivariate probability function (CBPF), (iii) concentration weighted trajectory (CWT), and (iv) potential source contribution function (PSCF) analyses. Furthermore, the importance of biomass combustions to PM2.5 was also estimated. Average PM2.5 concentrations ranged between 54 and 16 μg m−3 in the cold and warm period, respectively. The mean value of total ions was 11 μg m−3 (range 1–46 μg m−3): The most abundant ion was nitrate with a share of 44 % followed by sulfate (29 %), ammonium (14 %), potassium (4 %), and chloride (4 %). Levoglucosan accounted for 1.2 % of the PM2.5 mass, and its concentration ranged from few ng m−3 in warm periods to 2.66 μg m−3 during winter. Average concentrations of levoglucosan during the cold period were higher than those found in other European urban sites. This result may indicate a great influence of biomass combustions on particulate matter pollution. Elemental and organic carbon (EC, OC) showed similar behavior, with the highest contributions during cold periods and lower during summer. The ratios between biomass burning indicators (K+, Cl−, NO3−, SO42−, levoglucosan, EC, and OC) were used as proxy for the biomass burning estimation, and the contribution to the OC and PM2.5 was also calculated by using the levoglucosan (LG)/OC and LG/PM2.5 ratios and was estimated to be 29 and 18 %, respectively