Land Use in LCA: Including Regionally Altered Precipitation to Quantify Ecosystem Damage

The incorporation of soil moisture regenerated by precipitation, or green water, into life cycle assessment has been of growing interest given the global importance of this resource for terrestrial ecosystems and food production. This paper proposes a new impact assessment model to relate land and water use in seasonally dry, semiarid, and arid regions where precipitation and evapotranspiration are closely coupled. We introduce the Precipitation Reduction Potential midpoint impact representing the change in downwind precipitation as a result of a land transformation and occupation activity. Then, our end-point impact model quantifies terrestrial ecosystem damage as a function of precipitation loss using a relationship between woody plant species richness, water and energy regimes. We then apply the midpoint and end-point models to the production of soybean in Southeastern Amazonia which has resulted from the expansion of cropland into tropical forest, with noted effects on local precipitation. Our proposed cause-effect chain represents a complementary approach to previous contributions which have focused on water consumption impacts and/or have represented evapotranspiration as a loss to the water cycle

Two Structural Motifs within Canonical EF-Hand Calcium-Binding Domains Identify Five Different Classes of Calcium Buffers and Sensors

<div><p>Proteins with EF-hand calcium-binding motifs are essential for many cellular processes, but are also associated with cancer, autism, cardiac arrhythmias, and Alzheimer's, skeletal muscle and neuronal diseases. Functionally, all EF-hand proteins are divided into two groups: (1) calcium sensors, which function to translate the signal to various responses; and (2) calcium buffers, which control the level of free Ca²⁺ ions in the cytoplasm. The borderline between the two groups is not clear, and many proteins cannot be described as definitive buffers or sensors. Here, we describe two highly-conserved structural motifs found in all known different families of the EF-hand proteins. The two motifs provide a supporting scaffold for the DxDxDG calcium binding loop and contribute to the hydrophobic core of the EF hand domain. The motifs allow more precise identification of calcium buffers and calcium sensors. Based on the characteristics of the two motifs, we could classify individual EF-hand domains into five groups: (1) Open static; (2) Closed static; (3) Local dynamic; (4) Dynamic; and (5) Local static EF-hand domains.</p></div

Example interactions within cluster I.

<p>(A) and (B) illustrate two types of interactions between the flanking α-helices I and IV (cluster I in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109287#pone-0109287-g001" target="_blank">Figure 1</a>). The interactions occur <i>via</i> amino acids at positions -X+1, X-4 and -Z+1, which are also shown as black circles in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109287#pone-0109287-g001" target="_blank">Figures 1A and 1C</a> and highlighted in black in the alignment in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109287#pone-0109287-g001" target="_blank">Figure 1B</a>. Because in cluster I, positions X-4 and -Z+1 are purely aromatic (Φ) in all EF-hand representative structures, cluster I is called aromatic. (C) Contains the description of interactions for the eleven EF-hand fold representatives. The pattern “(-X+1)_helixIV^<u>CH-π</u> Φ(X-4)_helixI<u>^CH-π</u> Φ(-Z+1)_helixIV<u>^{weak HB}</u> (-X+1)_helixIV” indicates a circular interaction, where a side-chain atom of the –X+1 residue from the flanking α-helix IV forms a CH-π interaction with the ring of the X-4 aromatic amino acid from helix I, which, in turn, forms a CH-π interaction with the ring of the –Z+1 aromatic amino acid from helix IV, which interacts with the initial –X+1 residue from the flanking α-helix IV by means of a weak CH-O hydrogen bond.</p

List of eleven non-redundant, representative calcium-bound X-ray and NMR protein complexes, which represent eleven different families of EF-hand domains.

<p>All of the structures share the same fold (Fold: EF Hand-like) and belong to the same EF-hand fold superfamily (Superfamily: EF-hand) (from SCOP <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109287#pone.0109287-Andreeva1" target="_blank">[48]</a>).</p><p>List of eleven non-redundant, representative calcium-bound X-ray and NMR protein complexes, which represent eleven different families of EF-hand domains.</p

Five distinguishable groups of EF-hand domains based on the degree of structural rearrangements within clusters I and II, and the inter-cluster interactions that take place upon calcium binding: (1) Open Static (open domain conformation and no conformational changes); (2) Closed Static (closed domain conformation and no conformational changes); (3) Local Dynamic (simultaneous conformational changes in clusters I and II and the entire domain); (4) Dynamic (only global conformational changes, but not in clusters I and II); and (5) Local Static (stable open domain conformation, conformational changes only in clusters I and II, but not the entire domain).

<p>Domain level conformational changes, are shown by the small (“closed” domains) and large (“open” domains) distance between clusters I and II (triangles, ellipses and inverted triangles). Domain types (3) and (4) do undergo domain opening, while domain types (1), (2) and (5) do not. The conformation of the domains of type (2) remains “closed”, while the conformation the domains of types (1) and (5) remains open. Local conformational changes in clusters I and II are shown by normal triangles (compact conformation of cluster I), inverted triangles (compact conformation of cluster II), and ellipses (less compact, more open conformation of cluster II). The conformation of cluster I does not change in all of the known structures and is the same in buffers and sensors, such as in calbindin 9K, calmodulin and troponin C. The conformation of cluster II does change from being less compact to more compact in the domains of types (3) and (5). In group (4), EF-hand domains undergo domain opening, but the conformations of the conserved clusters I and II remain intact.</p

Classification of contact atoms, or targets.

<p>The target classification was adopted from the previous work of Rantanen et al. (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049216#s1" target="_blank">Introduction</a>) while some classes were excluded. As in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049216#pone-0049216-t002" target="_blank">Table 2</a>, the classes are not renumbered for the consistency of notation.</p

Effects of calcium binding on the conformation of all EF-hand domains, whose structures are known in the <i>apo</i>-form and with bound Ca²⁺ ions, and target protein ligands (where they exist).

<p>The RMSD values between the <i>apo</i>-form and the protein with bound Ca²⁺ ions and the target ligand, are calculated using the back-bone atoms of the amino acids of the clusters, and separately, using all heavy atoms of the same amino acids. The RMSD data are shown for the superposition of clusters I and II separately (groups A–C), and for superposition of the two clusters, cluster I/cluster II, simultaneously (groups D and E).</p><p>*While groups A–C coincide between <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109287#pone-0109287-t003" target="_blank">Tables 3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109287#pone-0109287-t004" target="_blank">4</a>, the RMSD calculations (this table) between clusters I and II were made only for the protein structures where the conformation of cluster II does not change upon calcium binding, and thus, proteins from group C were not included in D and E. This was done in order to observe only the inter-cluster conformational change.</p><p>Effects of calcium binding on the conformation of all EF-hand domains, whose structures are known in the <i>apo</i>-form and with bound Ca²⁺ ions, and target protein ligands (where they exist).</p

Prior densities for model parameters.

<p>Prior densities for model parameters.</p

Hierarchies from model trained with data that excludes the additive-type ligands.

<p>These are relating to example 1. Reference points and : comparison of contact atom frequencies with model based probabilities for fragment classes <b>f2</b>, <b>f5</b>, <b>f11</b> and <b>f22</b>. Hierarchy is given by the calculated probabilities, which are represented as circles. The circles are joined with a line to illustrate tendencies among target classes. The bars represent the fractions of target atoms belonging to a particular class. Both sum to one over target classes. Also shown are standard errors for both the frequencies and the model based probabilities (joined with lines and centered around the mean values). The contact atom counts in reference data for <b>f2</b>, <b>f5</b>, <b>f11</b> and <b>f22</b> are 111, 67, 1 and 6, respectively.</p

Prior probabilities for fragment classes used in this study.

<p>Classes C3 to C9.</p