Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs

Framework Convention on Climate Change

Life cycle impact assessment (LCIA) translates emissions and resource extractions into a limited number of environmental impact scores by means of so-called characterisation factors. There are two mainstream ways to derive characterisation factors, i.e. at midpoint level and at endpoint level. To further progress LCIA method development, we updated the ReCiPe2008 method to its version of 2016. This paper provides an overview of the key elements of the ReCiPe2016 method. We implemented human health, ecosystem quality and resource scarcity as three areas of protection. Endpoint characterisation factors, directly related to the areas of protection, were derived from midpoint characterisation factors with a constant mid-to-endpoint factor per impact category. We included 17 midpoint impact categories. The update of ReCiPe provides characterisation factors that are representative for the global scale instead of the European scale, while maintaining the possibility for a number of impact categories to implement characterisation factors at a country and continental scale. We also expanded the number of environmental interventions and added impacts of water use on human health, impacts of water use and climate change on freshwater ecosystems and impacts of water use and tropospheric ozone formation on terrestrial ecosystems as novel damage pathways. Although significant effort has been put into the update of ReCiPe, there is still major improvement potential in the way impact pathways are modelled. Further improvements relate to a regionalisation of more impact categories, moving from local to global species extinction and adding more impact pathways. Life cycle impact assessment is a fast evolving field of research. ReCiPe2016 provides a state-of-the-art method to convert life cycle inventories to a limited number of life cycle impact scores on midpoint and endpoint level.

/pdf/recipe2016-a-harmonised-life-cycle-impact-assessment-method-igx7h71aru.pdf

ReCiPe2016: a harmonised life cycle impact assessment method at midpoint and endpoint level

The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative genomics, regulation, expression and variation data. The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome. The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics including expression data and several gene properties. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.

/pdf/the-ucsc-genome-browser-database-update-2006-2go51ivp5f.pdf

The UCSC Genome Browser Database: update 2006

The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up to a full chromosome and includes assembly data, genes and gene predictions, mRNA and EST alignments, and comparative genomics, regulation, expression and variation data. The database is optimized for fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. In the past year, 22 new assemblies and several new sets of human variation annotation have been released. New features include VisiGene, a fully integrated in situ hybridization image browser; phyloGif, for drawing evolutionary tree diagrams; a redesigned Custom Track feature; an expanded SNP annotation track; and many new display options. The Genome Browser, other tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.

/pdf/the-ucsc-genome-browser-database-update-2007-hbgc689jyw.pdf

The UCSC genome browser database: update 2007

We present results of a life cycle assessment (LCA) of Marcellus shale gas used for power generation. The analysis employs the most extensive data set of any LCA of shale gas to date, encompassing data from actual gas production and power generation operations. Results indicate that a typical Marcellus gas life cycle yields 466 kg CO2eq/MWh (80% confidence interval: 450–567 kg CO2eq/MWh) of greenhouse gas (GHG) emissions and 224 gal/MWh (80% CI: 185–305 gal/MWh) of freshwater consumption. Operations associated with hydraulic fracturing constitute only 1.2% of the life cycle GHG emissions, and 6.2% of the life cycle freshwater consumption. These results are influenced most strongly by the estimated ultimate recovery (EUR) of the well and the power plant efficiency: increase in either quantity will reduce both life cycle freshwater consumption and GHG emissions relative to power generated at the plant. We conclude by comparing the life cycle impacts of Marcellus gas and U.S. coal: The carbon footprint of Ma...

https://marcelluscoalition.org/wp-content/uploads/2013/04/es305162w.pdf

Life Cycle Greenhouse Gas Emissions and Freshwater Consumption of Marcellus Shale Gas

Selectin-Like Kinetics and Biomechanics Promote Rapid Platelet Adhesion in Flow: The GPIbα-vWF Tether Bond

http://archive.gersteinlab.org/papers/e-print/sex-devcell/reprint.pdf

Major molecular differences between mammalian sexes are involved in drug metabolism and renal function.

The ability of platelets to tether to and translocate on injured vascular endothelium relies on the interaction between the platelet glycoprotein receptor Ib alpha (GPIb/spl alpha/) and the A1 domain of von Willebrand factor (vWF-A1). We now report that the GPIb/spl alpha/-vWF-A1 tether bond displays similar kinetic attributes as the selectins including: 1) the requirement for a critical level of flow to initiate adhesion, 2) short-lived tethering events at sites of vascular injury in vivo, and 3) a fast intrinsic dissociation rate constant, k/sub off//sup 0/ (3.45 /spl plusmn/ 0.37 s/sup -1/). Values for k/sub off/, also varied exponentially (4.2 /spl plusmn/ 0.8 s/sup -1/ to 7.3 /spl plusmn/ 0.4 s/sup -1/) as a function of the force applied to the bond (from 36 to 217pN). The biological importance of rapid bond dissociation is demonstrated by kinetic characterization of the naturally occurring A1 domain mutation, I546V that results in spontaneous binding of plasma vWF to circulating platelets in flowing blood. This mutation resulted in a loss of the shear threshold phenomenon, a /spl sim/6-fold reduction in k/sub off/, but no significant alteration in the ability of the tether bond to resist shear-induced forces. Thus, flow dependent adhesion and rapid and force-dependent kinetic properties are the predominant features of the GPIb/spl alpha/-vWF-A1 tether bond.

/pdf/selectin-like-kinetics-and-biomechanics-promote-rapid-41leb9vhxi.pdf

Selectin-like kinetics and biomechanics promote rapid platelet adhesion in flow: the GPIb/spl alpha/-vWF tether bond

Botrocetin is a snake venom protein that enhances the affinity of the A1 domain of plasma von Willebrand factor (vWF) for the platelet receptor glycoprotein Ibalpha (GPIbalpha), an event that contributes to bleeding and host death. Here we describe a kinetic and crystallographic analysis of this interaction that reveals a novel mechanism of affinity enhancement. Using high-temporal-resolution microscopy, we show that botrocetin decreases the GPIbalpha off-rate two-fold in both human and mouse complexes without affecting the on-rate. The key to this behavior is that, upon binding of GPIbalpha to vWF-A1, botrocetin prebound to vWF-A1 makes no contacts initially with GPIbalpha, but subsequently slides around the A1 surface to form a new interface. This two-step mechanism and flexible coupling may prevent adverse alterations in on-rate of GPIbalpha for vWF-A1, and permit adaptation to structural differences in GPIbalpha and vWF in several prey species.

Ian J. Laurenzi

Papers

Life Cycle Greenhouse Gas Emissions and Freshwater Consumption of Marcellus Shale Gas

Selectin-Like Kinetics and Biomechanics Promote Rapid Platelet Adhesion in Flow: The GPIbα-vWF Tether Bond

Major molecular differences between mammalian sexes are involved in drug metabolism and renal function.

Selectin-like kinetics and biomechanics promote rapid platelet adhesion in flow: the GPIb/spl alpha/-vWF tether bond

The snake venom protein botrocetin acts as a biological brace to promote dysfunctional platelet aggregation