Some ethical issues raised by studies of predation and aggression

This paper discusses some of the ethical issues raised by studies of predator-prey and aggressive interactions when these involve artificially-staged encounters. Such experiments call for special care in ensuring that a maximum of information is gained and a minimum of suffering caused. On the one hand, we should consider critically the theoretical importance of the question at issue, make sure that the behaviour is recorded accurately and explore the possibility of collaborative experiments. On the other hand, field studies of natural encounters should be used wherever possible. Where staged encounters are necessary, the use of model predators should be considered, the number of subjects kept to a minimum and the experiments made as short as possible.     

Sounds Modulate Males’ Aggressiveness in a Cichlid Fish

Acoustic signals are produced in many fish species during agonistic or courtship interactions. A way to test the biological role of these sounds is the use of acoustic playback experiments. However, sounds are usually associated with visual displays and playback experiments performed in fish so far, often failed to match acoustic and visual stimuli. To avoid this mismatch issue, we experimentally separated or coupled visual and acoustic channels to test the role of sounds produced during male–male aggressive interactions in a cichlid fish, Metriaclima zebra. Results show that aggressive behaviour is based on visual stimuli and that acoustic signals alone never trigger aggression. Furthermore, the association between visual and acoustic channels lowers the level of aggressiveness found when fish can only interact visually. This suggests that acoustic signals used during a dispute may complement visual displays to modulate males’ behaviour by reducing their aggressiveness and the risk of escalated fights.     

Fluorescent protein FRET: the good, the bad and the ugly

Dynamic protein interactions play a significant part in many cellular processes. A technique that shows considerable promise in elucidating such interactions is F?rster resonance energy transfer (FRET). When combined with multiple, colored fluorescent proteins, FRET permits high spatial resolution assays of protein-protein interactions in living cells. Because FRET signals are usually small, however, their measurement requires careful interpretation and several control experiments. Nevertheless, the use of FRET in cell biological experiments has exploded over the past few years. Here we describe the physical basis of FRET and the fluorescent proteins appropriate for these experiments. We also review the approaches that can be used to measure FRET, with particular emphasis on the potential artifacts associated with each approach.     

Behavioral controls of food intake

Recent conceptualizations of food intake have divided ingestive behavior into multiple distinct phases. Here, we present a temporally and operationally defined classification of ingestive behaviors. Importantly, various physiological signals including hypothalamic peptides are thought to impact these distinct behavioral phases of ingestion differently. In this review, we summarize a number of behavioral assays designed to delineate the effects of hormone and peptide signals that influence food intake on these ingestive mechanisms. Finally, we discuss two issues that we have encountered in our laboratory which may obstruct the interpretation of results from these types of studies. First, the influence of previous experience with foods used in these behavioral tests and second, the importance of the nutrient composition of the selected test foods. The important conclusion discussed here is that the behavioral analysis of ingestion is accompanied by theoretical constructs and artificial divisions of biological realities and the appreciation of this fact can only increase the opportunities of contemporary behavioral scientists to make significant and novel observations of ingestive behaviors.     

Designing experiments that aid in the identification of regulatory networks.

Predictive mathematical models of the interactions of a genetic network can provide insight into the mechanisms of gene regulation, the role of various genes within a network and how multiple genes interact leading to complex traits. However, identification of the parameters and interactions is currently a limiting step in the development of such models. This work reviews the state of the art for design of experiments in biological systems and demonstrates the need for improved design of experiments through the use of a model system. Appropriate design of experiments has a profound impact on the ability to identify a model and on the quality of resulting identified model. Key issues include the selection of appropriate input sequences (e.g. random, independent multivariate inputs) and the selection of the sampling frequencies. This work demonstrates that these issues are especially important in the identification of biochemical networks and that the traditional biochemical approach is incapable of truly identifying the behavior present in such networks.     

Solution NMR of supramolecular complexes: providing new insights into function

Solution NMR spectroscopy is an extremely powerful technology for the study of biomolecular dynamics and site-specific molecular interactions. An important limitation in the past has been molecule size, with molecular weights of targets seldom exceeding 50 kDa. New labeling technology and NMR experiments are changing this paradigm so that applications for investigating supramolecular complexes are starting to become feasible. Here we describe a strategy developed in our laboratory that involves the use of labeled methyl groups of isoleucine, leucine and valine residues in proteins as probes, along with experiments that significantly enhance the lifetimes of the resulting signals. We describe the application of these methods to a number of systems with molecular weights in the hundreds of kilodaltons.     

Detailed finite element modelling of deep needle insertions into a soft tissue phantom using a cohesive approach

Detailed finite element modelling of needle insertions into soft tissue phantoms encounters difficulties of large deformations, high friction, contact loading and material failure. This paper demonstrates the use of cohesive elements in high-resolution finite element models to overcome some of the issues associated with these factors. Experiments are presented enabling extraction of the strain energy release rate during crack formation. Using data from these experiments, cohesive elements are calibrated and then implemented in models for validation of the needle insertion process. Successful modelling enables direct comparison of finite element and experimental force–displacement plots and energy distributions. Regions of crack creation, relaxation, cutting and full penetration are identified. By closing the loop between experiments and detailed finite element modelling, a methodology is established which will enable design modifications of a soft tissue probe that steers through complex mechanical interactions with the surrounding material.     

Methionine scanning as an NMR tool for detecting and analyzing biomolecular interaction surfaces

Methyl NMR spectroscopy is a powerful tool for studying protein structure, dynamics, and interactions. Yet difficulties with resonance assignment and the low abundance of methyl groups can preclude detailed NMR studies, particularly the determination of continuous interaction surfaces. Here we present a straightforward strategy that overcomes these problems. We systematically substituted solvent-exposed residues with reporter methionines in the expected binding site and performed chemical shift perturbation (CSP) experiments using methyl-TROSY spectra. We demonstrate the utility of this approach for the interaction between the HECT domain of the Rsp5p ubiquitin ligase and its cognate E2, Ubc4. Using these mutants, we could instantaneously assign all newly arising reporter methyl signals, determine the Ubc4 interaction surface on a per-residue basis, and investigate the importance of each individual mutation for ligand binding. Our data show that methionine scanning significantly extends the applicability, information content, and spatial resolution of methyl CSP experiments.     

Differential scanning calorimetry of a conformational transition in heavy meromyosin

We have investigated the potential use of differential scanning calorimetry (DSC) to characterize conformational changes in proteins with emphasis on a conformational change in the myosin head which may be related to the power-stroke providing force production in muscle contraction. Simulations indicate that two-state conformational transitions with enthalpy changes greater than approximately 30 kcal/mol should be observable by DSC. We present here differential scanning calorimetric studies of a predenaturation structural change in heavy meromyosin. The high concentration of protein required for these experiments leads to potential contributions from intermolecular interactions. The technical difficulties associated with studying conformational transitions by DSC are discussed.     

Aggressive Play and Communication in Rhesus Monkeys (Macaca mulatta)

One adaptive function that has been suggested for social playin higher primates is the learning, refining, or practicingof communicative skills. Despite the absence of experimentaldata, a comparison of the structure of aggressive play and communicationmay shed light on this hypothesis. The great majority of rhesusmonkey agonistic interactions are mediated by stereotyped signals.Deprivation experiments have shown that appropriate interpretationand use of such signals requires early social experience. Suchexperience seemingly must have the following characteristics:(i) The relevant agonistic signals must occur, (ii) These signalsmust regularly be paired with other stimuli for appropriateresponses to signals to be learned. Signals must produce regularresponses in other monkeys for appropriate use to be learned.Aggressive play seems to be an unpromising context in whichto learn, refine, or practice agonistic signals. These signalsare not observed in play, and the signals that do occur arerestricted to play and are not regularly paired with unconditionedstimuli.     

Influence of Nematodes on Resource Utilization by Bacteria—an in vitro Study

The positive influence of bacterial feeding nematodes on bacterial mediated processes such as organic matter mineralization and nutrient cycling is widely accepted, but the mechanisms of these interactions are not always apparent. Both transport of bacteria by nematodes, and nutritional effects caused by nematode N excretion are thought to be involved, but their relative importance is not known because of the difficulties in studying these interactions in soil. We developed a simple in vitro assay to study complex nematode/bacterial interactions and used it to conduct a series of experiments to determine the potential influence of nematode movement and nutritional effects on bacterial resource use. The system used bacterial feeding and nonfeeding insect parasitic nematodes, and luminescent bacteria marked with metabolic reporter genes. Both nutritional enhancement of bacterial activity and bacterial transport were observed and we hypothesize that in nature, the relative importance of transport is likely to be greater in bulk soil, whereas nematode excretion may have greater impact in the rhizosphere. In both cases, the ability of nematodes to enhance bacterial resource utilization has implications for soil components of biogeochemical cycling.     

Milk Fever Control Principles: A Review

Three main preventive principles against milk fever were evaluated in this literature review, and the efficacy of each principle was estimated from the results of controlled investigations. Oral calcium drenching around calving apparently has a mean efficacy of 50%–60% in terms of milk fever prevention as well as prevention of milk fever relapse after intravenous treatment with calcium solutions. However, some drenches have been shown to cause lesions in the forestomacs. When using the DCAD (dietary cation-anion difference) principle, feeding rations with a negative DCAD (measured as (Na + K) – (Cl + S)) significantly reduce the milk fever incidence. Calculating the relative risk (RR) of developing milk fever from controlled experiments results in a mean RR between 0.19 and 0.35 when rations with a negative versus positive DCAD are compared. The main drawback from the DCAD principle is a palatability problem. The principle of feeding rations low in calcium is highly efficient in milk fever prevention provided the calcium intake in the dry period is kept below 20 g per day. Calculating the relative risk (RR) of developing milk fever from controlled experiments results in a very low mean RR (between 0 and 0.20) (daily calcium intake below versus above 20 g/d). The main problem in implementing the low-Ca principle is difficulties in formulating rations sufficiently low in calcium when using commonly available feeds. The use of large doses of vitamin D metabolites and analogues for milk fever prevention is controversial. Due to toxicity problems and an almost total lack of recent studies on the subject this principle is not described in detail. A few management related issues were discussed briefly, and the following conclusions were made: It is important to supply the periparturient cow with sufficient magnesium to fulfil its needs, and to prevent the dry cows from being too fat. Available information on the influence of carbohydrate intake, and on the effect of the length of the dry period and prepartum milking, is at present insufficient to include these factors in control programmes.     

ROCS: A reproducibility index and confidence score for interaction proteomics

ABSTRACT: BACKGROUND: Affinity-Purification Mass-Spectrometry (AP-MS) provides a powerful means of identifyingprotein complexes and interactions. Several important challenges exist in interpreting theresults of AP-MS experiments. First, the reproducibility of AP-MS experimental replicatescan be low, due both to technical variability and the dynamic nature of protein interactions inthe cell. Second, the identification of true protein-protein interactions in AP-MS experimentsis subject to inaccuracy due to high false negative and false positive rates. Severalexperimental approaches can be used to mitigate these drawbacks, including the use ofreplicated and control experiments and relative quantification to sensitively distinguish trueinteracting proteins from false ones. RESULTS: To address the issues of reproducibility and accuracy of protein-protein interactions, weintroduce a two-step method, called ROCS, which makes use of Indicator Proteins to selectreproducible AP-MS experiments, and of Confidence Scores to select specific protein-proteininteractions. The Indicator Proteins account for measures of protein identification as well asprotein reproducibility, effectively allowing removal of outlier experiments that contributenoise and affect downstream inferences. The filtered set of experiments is then used in theProtein-Protein Interaction (PPI) scoring step. Prey protein scoring is done by computing aConfidence Score, which accounts for the probability of occurrence of prey proteins in thebait experiments relative to the control experiment, where the significance cutoff parameter isestimated by simultaneously controlling false positives and false negatives against metrics offalse discovery rate and biological coherence respectively. In summary, the ROCS methodrelies on automatic objective criterions for parameter estimation and error-controlledprocedures. We illustrate the performance of our method by applying it to five previously published AP-MS experiments, each containing well characterized protein interactions,allowing for systematic benchmarking of ROCS. We show that our method may be used onits own to make accurate identification of specific, biologically relevant protein-proteininteractions or in combination with other AP-MS scoring methods to significantly improveinferences. CONCLUSIONS: Our method addresses important issues encountered in AP-MS datasets, making ROCS a verypromising tool for this purpose, either on its own or especially in conjunction with othermethods. We anticipate that our methodology may be used more generally in proteomicsstudies and databases, where experimental reproducibility issues arise. The method isimplemented in the R language, and is available as an R package called "ROCS", freelyavailable from the CRAN repository http://cran.r-project.org/.     

Adaptive combinatorial design to explore large experimental spaces: approach and validation

Systems biology requires mathematical tools not only to analyse large genomic datasets, but also to explore large experimental spaces in a systematic yet economical way. We demonstrate that two-factor combinatorial design (CD), shown to be useful in software testing, can be used to design a small set of experiments that would allow biologists to explore larger experimental spaces. Further, the results of an initial set of experiments can be used to seed further 'Adaptive' CD experimental designs. As a proof of principle, we demonstrate the usefulness of this Adaptive CD approach by analysing data from the effects of six binary inputs on the regulation of genes in the N-assimilation pathway of Arabidopsis. This CD approach identified the more important regulatory signals previously discovered by traditional experiments using far fewer experiments, and also identified examples of input interactions previously unknown. Tests using simulated data show that Adaptive CD suffers from fewer false positives than traditional experimental designs in determining decisive inputs, and succeeds far more often than traditional or random experimental designs in determining when genes are regulated by input interactions. We conclude that Adaptive CD offers an economical framework for discovering dominant inputs and interactions that affect different aspects of genomic outputs and organismal responses.     

Functional responses and scaling in predator-prey interactions of marine fishes: contemporary issues and emerging concepts

Predator-prey interactions are a primary structuring force vital to the resilience of marine communities and sustainability of the world's oceans. Human influences on marine ecosystems mediate changes in species interactions. This generality is evinced by the cascading effects of overharvesting top predators on the structure and function of marine ecosystems. It follows that ecological forecasting, ecosystem management, and marine spatial planning require a better understanding of food web relationships. Characterising and scaling predator-prey interactions for use in tactical and strategic tools (i.e. multi-species management and ecosystem models) are paramount in this effort. Here, we explore what issues are involved and must be considered to advance the use of predator-prey theory in the context of marine fisheries science. We address pertinent contemporary ecological issues including (1) the approaches and complexities of evaluating predator responses in marine systems; (2) the 'scaling up' of predator-prey interactions to the population, community, and ecosystem level; (3) the role of predator-prey theory in contemporary fisheries and ecosystem modelling approaches; and (4) directions for the future. Our intent is to point out needed research directions that will improve our understanding of predator-prey interactions in the context of the sustainable marine fisheries and ecosystem management.     

Nutritional Modulation of Somatotropic Axis-cytokine Relationships in Cattle: A Brief Review

The objective of this review is to summarize data on the interrelationships that exist between nutrition, the endocrine system and their modulation of plasma tumor necrosis factor-α responses to endotoxin in cattle. During stress, intake of nutrients often is compromised and a percentage of available nutrients are diverted away from growth processes to stabilize other physiological processes of a higher survival priority. Management practices that minimize the magnitude and duration of disease stress will aid in speeding the return to homeostatic equilibrium. However, the shift away from growth during stress is almost inevitable as a mechanism to survive. Some degree of control and management of the metabolic cost of disease stress involves understanding the integration of nutritional, endocrine and immune signals by cells and working with the natural homeostatic processes. Endocrine hormones and immune system cytokine signals participate in redirecting nutrient use during disease stress. In an intricate interplay, hormones and cytokines regulate, modify and modulate each other's production and tissue interactions to alter metabolic priorities. Levels of dietary protein and energy intake affect patterns of hormones and cytokines in the blood after endotoxin challenge and further modulate the biological actions of many of these regulatory effectors. In vivo, administration of growth hormone to young calves has significant effects to decrease the many specific physiological responses to endotoxemia. Many aspects of nutrition can attenuate or facilitate this effect.     

Causal relationships between frequency bands of extracellular signals in visual cortex revealed by an information theoretic analysis

Characterizing how different cortical rhythms interact and how their interaction changes with sensory stimulation is important to gather insights into how these rhythms are generated and what sensory function they may play. Concepts from information theory, such as Transfer Entropy (TE), offer principled ways to quantify the amount of causation between different frequency bands of the signal recorded from extracellular electrodes; yet these techniques are hard to apply to real data. To address the above issues, in this study we develop a method to compute fast and reliably the amount of TE from experimental time series of extracellular potentials. The method consisted in adapting efficiently the calculation of TE to analog signals and in providing appropriate sampling bias corrections. We then used this method to quantify the strength and significance of causal interaction between frequency bands of field potentials and spikes recorded from primary visual cortex of anaesthetized macaques, both during spontaneous activity and during binocular presentation of naturalistic color movies. Causal interactions between different frequency bands were prominent when considering the signals at a fine (ms) temporal resolution, and happened with a very short (ms-scale) delay. The interactions were much less prominent and significant at coarser temporal resolutions. At high temporal resolution, we found strong bidirectional causal interactions between gamma-band (40–100 Hz) and slower field potentials when considering signals recorded within a distance of 2 mm. The interactions involving gamma bands signals were stronger during movie presentation than in absence of stimuli, suggesting a strong role of the gamma cycle in processing naturalistic stimuli. Moreover, the phase of gamma oscillations was playing a stronger role than their amplitude in increasing causations with slower field potentials and spikes during stimulation. The dominant direction of causality was mainly found in the direction from MUA or gamma frequency band signals to lower frequency signals, suggesting that hierarchical correlations between lower and higher frequency cortical rhythms are originated by the faster rhythms.