DCG and bar chart for DNA topoisomerase III.

<p>(A) DCG for DNA topoisomerase III for the movement between structural pair: 1I7D, chain A, and 1D6M, chain A. (B) Decomposition of the DCG determines the number of instances in each of the four types of elemental contact-changes, “maintained”, “exchanged-partner”, “exchanged-pair” and “new”, which are displayed in a bar chart.</p

Illustrations of the ambiguity in decomposing a DCG into the elemental “exchange-partner” DCGs.

<p>Filled circles indicate residues, those coloured blue are from domain A and those coloured red from domain B. A contact is indicated by a broken line. (A) Top: residues 3 and 4 on domain B slide on residues 1 and 2 on domain A. This can be interpreted as either residue 4 sliding on the surface provided by 1 and 2 or residue 1 sliding on the surface provided by 3 and 4. Bottom: for the associated DCG the elemental “exchange-partner” DCGs are indicated by the green lines but only one can be selected as they should not overlap. (B) Top: residues 4 and 5 on domain B slide on residues 1, 2 and 3 on domain A. Bottom: there are two decomposition possibilities of the DCG indicated by the green lines, one with two non-overlapping elemental “exchange-partner” DCGs (left), and the other with one non-overlapping elemental “exchange-partner” DCG (right).</p

Motifs in DCG's indicating possible mechanism.

<p>Each filled circle or ellipse indicates a residue with domain A residues coloured blue and domain B residue red. Touching circles or ellipses indicate a contact. The graphs with squares and arrows are the associated DCGs. (A) “Multiple new.” A residue moves from having no contacts in one conformation to having multiple contacts in the other conformation. (B) “Linear Interlocking.” This might occur when there is a “shear” movement according to Gerstein et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081224#pone.0081224-Gerstein1" target="_blank">[4]</a>. The interlocking side chains are depicted in a sequence of doubly linked nodes in the DCG suggesting strong bonds that cannot be broken. (C) “Anchoring residue.” Here a single residue maintains contact with a number of other residues from the other domain, acting possibly as an anchor. (D) “Linear slide.” Here residues slide relative to each other each making at most one contact in both conformations. The DCG depicts a set of singly connected nodes arranged linearly. (E) “Branched slide.” Here one residue makes a single contact in one conformation but two contacts in the other giving a branched DCG. (F) “Multiple-to-Multiple slide.” A residue moves from having multiple contacts with a set of residues in one conformation to multiple contacts with another set of residues in the other conformation. The DCG is clearly suggestive of this process. (G) “Closed-cycle slide.” If the domains have a twisting movement as depicted on the left the DCG will have a closed cycle. (H) “Multiple see-saw.” A see-saw movement as depicted on the left will have a DCG with edge-arrows that clearly suggest a see-saw movement.</p

The five model domain movements and their corresponding elemental DCGs.

<p>Conformation 1 is on the left and conformation 2 on the right with domain A in blue and domain B in red. (A) The “no contact” contact-change implies that the domains are “free” to move. The graph is empty in this case. (B) The “new” contact-change implies an “open-closed” domain movement. In this case the elemental DCG shows a contact between the two domains in conformation 2 as indicated by the edge-arrow pointing from domain B to domain A. (C) The “maintained” case implies the domains are “anchored” and the associated DCG is a doubly-linked motif. (D) The “exchange-partner” contact-change is where a residue, here on domain B, makes a contact with a residue on domain A in conformation 1 and a contact with a different residue on domain A in conformation 2. This implies a model “sliding-twist” movement whereby domain B slides on the surface provided by domain A. The elemental DCG provides a visual metaphor for this movement with arrows indicating a movement away the contacting residue on domain A in conformation 1 (upper blue node) towards the contacting residue on domain A in conformation 2 (lower blue node). (E) The “exchanged-pair” contact-change and its associated model “see-saw” movement. The DCG clearly depicts this kind of see-saw movement.</p

Numbers in each class.

<p>Numbers in each class.</p

Table_1_Production Characteristics and Optimization of Mitigation Mussel Culture.DOCX

Bivalve environmental services have become a focal point for their inherent role in the management of eutrophication, while active cultivation has become increasingly acknowledged as a mechanism for integrated nutrient reduction. In recent years, cultivation practices designed specifically for nutrient extraction have emerged; “mitigation culture.” While modeling efforts have been able to describe expanded potential of these services, only a single commercial pilot scale, real-world demonstration, has been documented. Over two production seasons (2017–2018), the optimization of nutrient extractive potential of mussels (Mytilus edulis) at full commercial-scale was evaluated by first testing multiple density configurations of conventional longline-spat collector setups and potential harvest times, then by comparing different cultivation technologies at three farms. Potential biomass volumes of 770–1700 t with longlines and 2100–2600 t on nets was demonstrated in full-scale production (18.8 ha), yielding 0.6–1.27 t N ha–1 and 0.04–0.1 t P ha–1, and 1.63–2.0 t N ha–1 and 0.1–0.12 t P ha–1 respectively. In general, 1 t of harvested mitigation mussels will yield 13.7 kg N and 0.9 kg P. Winter harvests exhibited higher yields (103–124%) than early spring harvests on optimized configurations, favoring an abbreviated production season. Production potential was similar between sites, despite differing environmental conditions, indicating eutrophic waters are suitable for expanded mitigation production. This study presents for the first-time production data of mitigation mussels utilizing different configurations and technologies to maximize yield and nutrient extraction potential.</p

Supplementary information 1_LA_SA Togashi dataset

Huber Value dataset for 183 evergreen angiosperm trees in Australi

Additional file 5: of Alternative polyadenylation factors link cell cycle to migration

Alternative splicing with quiescence. (XLSX 136 kb

Additional file 12: of Alternative polyadenylation factors link cell cycle to migration

Isoform-specific half-lives with quiescence. (XLSX 40 kb

Additional file 11: of Alternative polyadenylation factors link cell cycle to migration

Differential expression with quiescence and knockdown. (XLSX 160 kb