Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes

Increasingly, various ‘omics data are contributing significantly to our understanding of novel biological processes, but it has not been possible to iteratively elucidate hierarchical functions in complex phenomena. We describe a general systems biology approach called Active Interaction Mapping (AI-MAP), which elucidates the hierarchy of functions for any biological process. Existing and new ‘omics data sets can be iteratively added to create and improve hierarchical models which enhance our understanding of particular biological processes. The best datatypes to further improve an AI-MAP model are predicted computationally. We applied this approach to our understanding of general and selective autophagy, which are conserved in most eukaryotes, setting the stage for the broader application to other cellular processes of interest. In the particular application to autophagy-related processes, we uncovered and validated new autophagy and autophagy-related processes, expanded known autophagy processes with new components, integrated known non-autophagic processes with autophagy and predict other unexplored connections.     

Diffraction patterns as a tool to recognize copepods

Photographs of three species of calanoid copepods were digitized,binarized and edited to remove the debris present in the imagesand to simulate different degrees of segmentation. Twentyeightsegmented images of the three species were generated after pre-processingto obtain their digital Fourier transform or diffraction pattern.Cluster analysis was carried out for the images of the wpepodsand for their diffraction patterns to determine which set ofimages discriminated genus, species and sex of the selectedorganisms.Ihe dendrograms of the diffraction patterns had morepower of discrimination and 50% less variability. This methodis promising, but more research is necessary in order to implementan automated system for plankton identification in the nearfuture.     

Desiccation as a mitigation tool to manage biofouling risks: trials on temperate taxa to elucidate factors influencing mortality rates

The desiccation tolerance of biofouling taxa (adults and early life-stages) was determined under both controlled and ‘realistic’ field conditions. Adults of the ascidian Ciona spp. died within 24 h. Mortality in the adult blue mussel Mytilus galloprovincialis occurred within 11 d under controlled conditions, compared with 7 d when held outside. The Pacific oyster Crassostrea gigas was the most desiccation-tolerant taxon tested (up to 34 d under controlled conditions). Biofouling orientated to direct sunlight showed faster mortality rates for all the taxa tested. Mortality in Mytilus juveniles took up to 24 h, compared with 8 h for Ciona, with greater survival at the higher temperature (18.5°C) and humidity (~95% RH) treatment combination. This study demonstrated that desiccation can be an effective mitigation method for a broad range of fouling taxa, especially their early life-stages. Further work is necessary to assess risks from other high-risk species such as algae and cyst forming species.     

Fuzzy chorotypes as a conceptual tool to improve insight into biogeographic patterns

Chorotypes--statistically significant groups of coincident distribution areas--constitute biogeographic units that are fuzzy by nature. This quality has been referred to in the literature but has not been analyzed in depth or methodologically developed. The present work redefines chorotypes as fuzzy sets from a pragmatic perspective and basically focuses on the methodological and interpretative implications of this approach. The amphibian fauna in the Iberian Peninsula was used as an example to explore the fuzzy nature of chorotypes. The method on which this article is based is a widely used technique to define chorotypes. This method involves the fuzziness that is inherent to the identification between degree of similarity and degree of membership and includes a probabilistic analysis of the classification for the objective delimitation of chorotypes. The main innovation of this paper is a procedure to analyze chorotypes as fuzzy biogeographic units. A set of fuzzy parameters to deal with the biogeographic interpretation of fuzzy chorotypes is also described. A computer program has been developed and is freely available. History may be related to the degree of fuzziness of chorotypes. In our example, with amphibian distributions in Iberia, less fuzzy chorotypes could have a historical explanation, and the internal fuzziness of chorotypes increases with their distance to hypothetical Pleistocene refugia.     

High-throughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses

Here, high-throughput sequencing was employed to reveal the highly diverse bacterial populations present in 62 Irish artisanal cheeses and, in some cases, associated cheese rinds. Using this approach, we revealed the presence of several genera not previously associated with cheese, including Faecalibacterium, Prevotella, and Helcococcus and, for the first time, detected the presence of Arthrobacter and Brachybacterium in goats' milk cheese. Our analysis confirmed many previously observed patterns, such as the dominance of typical cheese bacteria, the fact that the microbiota of raw and pasteurized milk cheeses differ, and that the level of cheese maturation has a significant influence on Lactobacillus populations. It was also noted that cheeses containing adjunct ingredients had lower proportions of Lactococcus species. It is thus apparent that high-throughput sequencing-based investigations can provide valuable insights into the microbial populations of artisanal foods.     

Cobble community DNA as a tool to monitor patterns of biodiversity within kelp forest ecosystems

Kelp forest ecosystems dominate 150,000 km of global temperate coastline, rivalling the coastal occurrence of coral reefs. Despite the astounding biological diversity and productive ecological communities associated with kelp forests, patterns of species richness and composition are difficult to monitor and compare. Crustose coralline algae are a critically important substrate for propagule settlement for a range of kelp forest species. Coralline‐covered cobbles are home to hundreds of species of benthic animals and algae and form a replicable unit for ecological assays. Here, we use DNA metabarcoding of bulk DNA extracts sampled from cobbles to explore patterns of species diversity in kelp forests of the central California coast. The data from 97 cobbles within kelp forest ecosystems at three sites in Central California show the presence of 752 molecular operational taxonomic units (MOTUs) and 53 MOTUs assigned up to the species level with >95% similarity to current databases. We are able to detect spatial patterns of important management targets such as abalone recruits, and localized abundance of sea stars in 2012. Comparison of classic ecological surveys of these sites reveals large differences in species targets for these two approaches. In order to make such comparisons more quantitative, we use Presence/Absence Metabarcoding, using the fraction of replicate cobbles showing a species as a measure of its local abundance. This approach provides a fast and repeatable survey method that can be applied for biodiversity assessments across systems to shed light on the impact of different ecological disturbances and the role played by marine protected areas.     

Spatial autocorrelation as a tool for identifying the geographical patterns of aphid annual abundance

Abstract 1 A spatial autocorrelation analysis was undertaken to investigate the spatial structure of annual abundance for the pest aphid Myzus persicae collected in suction traps distributed across north‐west Europe. 2 The analysis was applied at two different scales. The Moran index was used to estimate the degree of spatial autocorrelation at all sites within the study area (global level). The contributions of each site to the global index were identified by the use of a local indicator of spatial autocorrelation (LISA). A hierarchical cluster analysis was undertaken to highlight differences between groups of resulting correlograms. 3 Similarity between traps was shown to occur over large geographical distances, suggesting an impact of phenomena such as climatic gradients or land use types. 4 The presence of outliers and zones of similarity (hot‐spots) and of dissimilarity (cold‐spots) were identified indicating a strong impact of local effects. 5 Several groups of traps characterized by similarities in their local spatial structure (correlograms, value of Moran's I_i) also had similar values for land use variables (the area occupied by agricultural zones, forest and sea). 6 It is concluded that trap data can provide information about Myzus persicae that is representative of large geographical areas. Thus, trap data can be used to estimate the aerial abundance of this species, even if the suction traps are not regularly and densely distributed.     

Low-energy electrons inside active DNA models: A tool to elucidate the radiation action mechanisms

To postulate radiation action mechanisms and to test them by Monte Carlo simulation, a complex computer model was developed consisting of major components for the generation of a radiation spectrum, biomolecular structures, and electron track structures in liquid water. As the radiation source¹²⁵I is employed here; it is an excellent test radiation due to its exactly localized position in the DNA molecule and high biological toxicity as a consequence of the emission of short-ranging Auger electrons. A linear DNA plasmid model (Pomplun 1991) which can actively respond to radical attack (Terrissol and Pomplun 1994) has been modified into a nucleosome model representing the double-helix of DNA with 146 basepairs and more than 9000 atoms surrounding the histones. The introduction of this new target structure allows a more realistic simulation of cellular conditions. Using the model's decay accumulation aspect, the situation of many break and survival experiments can be approximated and the influence of several cellular parameters tested. As a first step, a correlation between the size of energy depositions and strand-break patterns was sought.     

Neural activity in the mouse claustrum in a cross-modal sensory selection task

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Characterizing the balance-dexterity task as a concurrent bipedal task to investigate trunk control during dynamic balance

The purpose of the study was to characterize the Balance-Dexterity Task as a means to investigate a concurrent bipedal lower-extremity task and trunk control during dynamic balance. The task combines aspects of single-limb balance and the lower-extremity dexterity test by asking participants to stand on one limb while compressing an unstable spring with the contralateral limb to an individualized target force. Nineteen non-disabled participants completed the study, and performance measures for the demands of each limb – balance and dexterous force control – as well as kinematic and electromyographic measures of trunk control were collected. Given five practice trials, participants achieved compression forces ranging from 100 to 139 N (mean 121.2 ± 12.3 N), representing 14.4–23.0% of body weight (mean 18.7 ± 2.4%), which were then presented as target forces during test trials. Dexterous force control coefficient of variation and average magnitude of the center of pressure (COP) resultant velocity were associated such that greater variability in force control was accompanied by greater COP velocity (R = 0.598, p = 0.007). Trunk coupling, quantified as the coefficient of determination (R²) of a frontal plane thorax and pelvis angle-angle plot, varied independently of any measure of balance or dexterous force control. The Balance-Dexterity Task is a continuous, dynamic balance task where bipedal coordination and trunk coupling can be concurrently observed and studied.     

Techniques to elucidate the conformation of prions

Proteinaceous infectious particles(prions) are unique pathogens as they are devoid of any coding nucleic acid.Whilst it is assumed that prion disease is transmitted by a misfolded isoform of the cellular prion protein, the structural insight of prions is still vague and research for high resolution structural information of prions is still ongoing. In this review, techniques that may contribute to the clarification of the conformation of prions are presented and discussed.     

Relaxation as a cognitive task

In the present experiment the instruction to relax was given to awake highly (Highs) and non hypnotizable subjects (Lows), while their heart rate, respirogram and skin resistance were recorded together with electroencephalogram, electroculogram and corrugator electromiogram. At the beginning of the experiment, Highs exhibited no significant difference in heart rate (HR), respiratory frequency (RF) and heart rate variability (HRV) with respect to Lows, but showed a higher EEG alpha and theta1 power. During the session, both groups decreased their heart rate, but changes were significant only in Lows, which increased significantly also the parasympathetic component of their HRV (high frequency, HF). In both groups, EEG showed alpha, beta2 and theta2 power decrements; theta1 activity decreased only in Lows, while gamma power increased in Highs and decreased in Lows. Results suggest that Highs and Lows used different cognitive strategies in the elaboration of the relaxation request and that Highs performed the task through a higher integrative activity.     

Sorting and pooling strategy: a novel tool to map a virus proteome for CD8 T-cell epitopes

Human cytomegalovirus (CMV) is a major cause of morbidity in immunocompromised individuals. However, no efficient vaccine has been developed to date. Identification of T-cell target proteins and epitopes is crucial not only for developing a successful immunization strategy, but also for new approaches using adoptive transfer of antigen-specific T-cells. The CMV genome has more than 200 open reading frames potentially coding for as many proteins. Here, we describe a robust, fast, and simple SPOT synthesis strategy, which allowed us to micro-synthesize every possible CD8 T-cell epitope in the entire potential CMV proteome. So far, 9069 of these peptides have been tested in an ex vivo T-cell stimulation assay. As well as confirming a number of previously known epitopes, we identified several new ones.