Unified Alignment of Protein-Protein Interaction Networks

Paralleling the increasing availability of protein-protein interaction (PPI) network data, several network alignment methods have been proposed. Network alignments have been used to uncover functionally conserved network parts and to transfer annotations. However, due to the computational intractability of the network alignment problem, aligners are heuristics providing divergent solutions and no consensus exists on a gold standard, or which scoring scheme should be used to evaluate them. We comprehensively evaluate the alignment scoring schemes and global network aligners on large scale PPI data and observe that three methods, HUBALIGN, L-GRAAL and NATALIE, regularly produce the most topologically and biologically coherent alignments. We study the collective behaviour of network aligners and observe that PPI networks are almost entirely aligned with a handful of aligners that we unify into a new tool, Ulign. Ulign enables complete alignment of two networks, which traditional global and local aligners fail to do. Also, multiple mappings of Ulign define biologically relevant soft clusterings of proteins in PPI networks, which may be used for refining the transfer of annotations across networks. Hence, PPI networks are already well investigated by current aligners, so to gain additional biological insights, a paradigm shift is needed. We propose such a shift come from aligning all available data types collectively rather than any particular data type in isolation from others

Selection on age of female reproduction in the marula fruit fly, Ceratitis cosyra (Walker) (Diptera: Tephritidae), decreases total antioxidant capacity and lipid peroxidation

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.Data availability: Data are available from the University of Pretoria online repository: https://doi.org/10.25403/UPresearchdata.12480569.v1The oxidative damage caused to cells by Reactive Oxygen Species (ROS) is one of several factors implicated in causing ageing. Oxidative damage may also be a proximate cost of reproductive effort that mediates the trade-off often observed between reproduction and survival. However, how the balance between oxidative damage and antioxidant protection affects life-history strategies is not fully understood. To improve our understanding, we selected on female reproductive age in the marula fruit fly, Ceratitis cosyra, and quantified the impact of selection on female and male mortality risk, female fecundity, male sperm transfer, calling and mating. Against expectations, upward-selected lines lived shorter lives and experienced some reductions in reproductive performance. Selection affected oxidative damage to lipids and total antioxidant protection, but not in the direction predicted; longer lives were associated with elevated oxidative damage, arguing against the idea that accumulated oxidative damage reduces lifespan. Greater reproductive effort was also associated with elevated oxidative damage, suggesting that oxidative damage may be a cost of reproduction, although one that did not affect survival. Our results add to a body of data showing that the relationship between lifespan, reproduction and oxidative damage is more complex than predicted by existing theories.NRF University of Pretori

An Introductory Guide to Aligning Networks Using SANA, the Simulated Annealing Network Aligner.

Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological networks holds similar promise. Biological networks generally model interactions between biomolecules such as proteins, genes, metabolites, or mRNAs. There is strong evidence that the network topology-the "structure" of the network-is correlated with the functions performed, so that network topology can be used to help predict or understand function. However, unlike sequence comparison and alignment-which is an essentially solved problem-network comparison and alignment is an NP-complete problem for which heuristic algorithms must be used.Here we introduce SANA, the Simulated Annealing Network Aligner. SANA is one of many algorithms proposed for the arena of biological network alignment. In the context of global network alignment, SANA stands out for its speed, memory efficiency, ease-of-use, and flexibility in the arena of producing alignments between two or more networks. SANA produces better alignments in minutes on a laptop than most other algorithms can produce in hours or days of CPU time on large server-class machines. We walk the user through how to use SANA for several types of biomolecular networks

An introductory guide to aligning networks using SANA, the Simulated Annealing Network Aligner

Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological {\em networks} holds similar promise. Biological networks generally model interactions between biomolecules such as proteins, genes, metabolites, or mRNAs. There is strong evidence that the network topology -- the "structure" of the network -- is correlated with the functions performed, so that network topology can be used to help predict or understand function. However, unlike sequence comparison and alignment -- which is an essentially solved problem -- network comparison and alignment is an NP-complete problem for which heuristic algorithms must be used. Here we introduce SANA, the {\it Simulated Annealing Network Aligner}. SANA is one of many algorithms proposed for the arena of biological network alignment. In the context of global network alignment, SANA stands out for its speed, memory efficiency, ease-of-use, and flexibility in the arena of producing alignments between 2 or more networks. SANA produces better alignments in minutes on a laptop than most other algorithms can produce in hours or days of CPU time on large server-class machines. We walk the user through how to use SANA for several types of biomolecular networks. Availability: https://github.com/waynebhayes/SAN

PROPER: global protein interaction network alignment through percolation matching

Background The alignment of protein-protein interaction (PPI) networks enables us to uncover the relationships between different species, which leads to a deeper understanding of biological systems. Network alignment can be used to transfer biological knowledge between species. Although different PI-network alignment algorithms were introduced during the last decade, developing an accurate and scalable algorithm that can find alignments with high biological and structural similarities among PPI networks is still challenging. Results In this paper, we introduce a new global network alignment algorithm for PPI networks called PROPER. Compared to other global network alignment methods, our algorithm shows higher accuracy and speed over real PPI datasets and synthetic networks. We show that the PROPER algorithm can detect large portions of conserved biological pathways between species. Also, using a simple parsimonious evolutionary model, we explain why PROPER performs well based on several different comparison criteria. Conclusions We highlight that PROPER has high potential in further applications such as detecting biological pathways, finding protein complexes and PPI prediction. The PROPER algorithm is available at http://proper.epfl.ch

Selection on female reproductive schedules in the marula fly, Ceratitis cosyra (Diptera : Tephritidae) affects dietary optima for female reproductive traits but not lifespan

Introduction: A changing environment can select on life-history traits and trade-offs in a myriad of ways. For example, global warming may shift phenology and thus the availability of host-plants. This may alter selection on survival and fertility schedules in herbivorous insects. If selection on life-histories changes, this may in turn select for altered nutrient intake, because the blend of nutrients organisms consume helps determine the expression of life-history traits. However, we lack empirical work testing whether shifts in the timing of oviposition alter nutrient intake and life-history strategies. Methods: We tested in the marula fruit fly, Ceratitis cosyra, how upward-selection on the age of female oviposition, in comparison with laboratory adapted control flies, affects the sex-specific relationship between protein and carbohydrate intake and life-history traits including lifespan, female lifetime egg production and daily egg production. We then determined the macronutrient ratio consumed when flies from each selection line and sex were allowed to self-regulate their intake. Results: Lifespan, lifetime egg production and daily egg production were optimised at similar protein to carbohydrate (P:C) ratios in flies from both selection lines. Likewise, females and males of both lines actively defended similar nutrient intake ratios (control =1:3.6 P:C; upward-selected = 1:3.2 P:C). Discussion: Our results are comparable to those in non-selected C. cosyra, where the optima for each trait and the self-selected protein to carbohydrate ratio observed were nearly identical. The nutrient blend that needs to be ingested for optimal expression of a given trait appeared to be well conserved across laboratory adapted and experimentally selected populations. These results suggest that in C. cosyra, nutritional requirements do not respond to a temporal change in oviposition substrate availability

Oligocene reefal deposits in the Pisang Ridge and the origin of the Lucipara Block (Banda Sea, eastern Indonesia)

International audienceIn 1998 we dredged early Oligocene/late Oligocene boundary, shallow-water reefal deposits and pelagic, early Pliocene muds in the submerged Pisang Ridge. The shallow-water deposits were identified as moderate- to low-energy coral-reef depositional environments, which confirms that the PisangRidg e belonged to the continental to continental-arc Lucipara Block which also includes the TukangBesi, Lucipara and Rama ridges. On the basis of these findings, it was possible to reconstruct parts of the general geological evolution of the Lucipara Block, which drifted away from northern Irian Jaya duringmid- Miocene times and collided with the Kolonodale Block during the late Miocene. A late-early Oligocene calc alkaline volcanic arc developed in the Weber Trough area, then uplifted to a shallow-water position at the early–late Oligocene boundary in the Pisang Ridge. Late Oligocene–early Miocene metamorphism subsequently developed, prior to the deposition of early Miocene coral reefs in the Rama Ridge. Locally, late Miocene metamorphism was identified in the Lucipara Ridge, prior to the latest Miocene–Pliocene general drowning and the splitting of the Lucipara Block into several small blocks throughout the Banda Sea region

From commodity to money : The rise of silver coinage around the Ancient Mediterranean (sixth–first centuries bce)

The reasons why the Western Mediterranean, especially Carthage and Rome, resisted monetization relative to the Eastern Mediterranean are still unclear. We address this question by combining lead (Pb) and silver (Ag) isotope abundances in silver coinage from the Aegean, Magna Graecia, Carthage and Roman Republic. The clear relationships observed between 109Ag/107Ag and 208Pb/206Pb reflect the mixing of silver ores or silver objects with Pb metal used for cupellation. The combined analysis of Ag and Pb isotopes reveals important information about the technology of smelting. The Greek world extracted Ag and Pb from associated ores, whereas, on the Iberian Peninsula, Carthaginians and Republican-era Romans applied Phoenician cupellation techniques and added exotic Pb to Pb-poor Ag ores. Massive Ag recupellation is observed in Rome during the Second Punic War. After defeating the Carthaginians and the Macedonians in the late second century bce, the Romans brought together the efficient, millennium-old techniques of silver extraction of the Phoenicians, who considered this metal a simple commodity, with the monetization of the economy introduced by the Greeks