Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices.

Mass spectrometry-based metabolomics approaches can enable detection and quantification of many thousands of metabolite features simultaneously. However, compound identification and reliable quantification are greatly complicated owing to the chemical complexity and dynamic range of the metabolome. Simultaneous quantification of many metabolites within complex mixtures can additionally be complicated by ion suppression, fragmentation and the presence of isomers. Here we present guidelines covering sample preparation, replication and randomization, quantification, recovery and recombination, ion suppression and peak misidentification, as a means to enable high-quality reporting of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics-derived data.

The archerfish predictive C-start.

A very quick decision enables hunting archerfish to secure downed prey even when they are heavily outnumbered by competing other surface-feeding fish. Based exclusively on information that is taken briefly after the onset of prey motion, the fish select a rapid C-start that turns them right towards the later point of catch. Moreover, the C-start, and not later fin strokes, already lends the fish the speed needed to arrive at just the right time. The archerfish predictive C-starts are kinematically not distinguishable from escape C-starts made by the same individual and are among the fastest C-starts known in teleost fish. The start decisions allow the fish-for ballistically falling prey-to respond accurately to any combination of the initial variables of prey movement and for any position and orientation of the responding fish. The start decisions do not show a speed-accuracy tradeoff and their accuracy is buffered against substantial changes of environmental parameters. Here, I introduce key aspects of this high-speed decision that combines speed, complexity, and precision in an unusual way.

Removing a single neuron in a vertebrate brain forever abolishes an essential behavior.

The giant Mauthner (M) cell is the largest neuron known in the vertebrate brain. It has enabled major breakthroughs in neuroscience but its ultimate function remains surprisingly unclear: An actual survival value of M cell-mediated escapes has never been supported experimentally and ablating the cell repeatedly failed to eliminate all rapid escapes, suggesting that escapes can equally well be driven by smaller neurons. Here we applied techniques to simultaneously measure escape performance and the state of the giant M axon over an extended period following ablation of its soma. We discovered that the axon survives remarkably long and remains still fully capable of driving rapid escape behavior. By unilaterally removing one of the two M axons and comparing escapes in the same individual that could or could not recruit an M axon, we show that the giant M axon is essential for rapid escapes and that its loss means that rapid escapes are also lost forever. This allowed us to directly test the survival value of the M cell-mediated escapes and to show that the absence of this giant neuron directly affects survival in encounters with a natural predator. These findings not only offer a surprising solution to an old puzzle but demonstrate that even complex brains can trust vital functions to individual neurons. Our findings suggest that mechanisms must have evolved in parallel with the unique significance of these neurons to keep their axons alive and connected.

Archerfish vision: Visual challenges faced by a predator with a unique hunting technique.

Archerfish are well-known for their ballistic hunting behaviour, in which they shoot down aerial prey with a well-aimed jet of water. This unique hunting strategy poses several challenges for visual systems. Archerfish face significant distortion to the appearance of targets due to refraction at the air/water interface, they search for prey against a complex background of foliage, they change prey targeting behaviour as conditions change, and they must make high speed decisions to avoid competition. By studying how archerfish have overcome these challenges, we have been able to understand more about fundamental problems faced by visual systems and the mechanisms used to solve them. In some cases, such as when searching for targets, the visual capabilities of archerfish are functionally similar to those of humans, despite significant differences in neuroanatomy. In other cases, the particular challenge faced by archerfish magnifies fundamental problems generally faced by visual systems, such as recognizing objects given strong viewpoint dependent changes to appearance. The efficiency of archerfish retrieving fallen prey to avoid kleptoparasitism, demonstrates that their visual processing excels in both speed and accuracy. In this review, we attempt to provide an overview of the many facets of visually driven behaviour of archerfish, and how they have been studied. In addition to their hunting technique, archerfish are ideal for visual processing experiments as they can be quickly trained to perform a range of non-ecologically relevant tasks. Their behavioural flexibility moreover, introduces the opportunity to study how experience-dependence and choice affects visual processing.

Electric catfish hearts are not intrinsically immune to electric shocks.

High voltage electric shocks cause life threatening cardiac injuries such as sudden cardiac standstill or severe myocardial injury. Here, we analysed the physiology of the heart of the strongly electric catfish (Malapterurus beninensis) that stuns prey with high-voltage shocks but is immune to its own, as well as external, high-voltage shocks. Neither a detailed analysis of the electrocardiogram nor the structure of the heart indicated a specialized cardiac conduction system. Using a suitable perfusion system, we discovered that, despite its immunity in vivo, the explanted heart of electric catfish can readily be activated by external electrical currents and is equally sensitive to electric shock-induced arrhythmias as similar-sized goldfish hearts. The surprise thus is that the electric catfish has a vulnerable heart that requires to be protected by highly efficient but presently unknown means.

Dynamic optimization reveals alveolar epithelial cells as key mediators of host defense in invasive aspergillosis.

Aspergillus fumigatus is an important human fungal pathogen and its conidia are constantly inhaled by humans. In immunocompromised individuals, conidia can grow out as hyphae that damage lung epithelium. The resulting invasive aspergillosis is associated with devastating mortality rates. Since infection is a race between the innate immune system and the outgrowth of A. fumigatus conidia, we use dynamic optimization to obtain insight into the recruitment and depletion of alveolar macrophages and neutrophils. Using this model, we obtain key insights into major determinants of infection outcome on host and pathogen side. On the pathogen side, we predict in silico and confirm in vitro that germination speed is an important virulence trait of fungal pathogens due to the vulnerability of conidia against host defense. On the host side, we found that epithelial cells, which have been underappreciated, play a role in fungal clearance and are potent mediators of cytokine release. Both predictions were confirmed by in vitro experiments on established cell lines as well as primary lung cells. Further, our model affirms the importance of neutrophils in invasive aspergillosis and underlines that the role of macrophages remains elusive. We expect that our model will contribute to improvement of treatment protocols by focusing on the critical components of immune response to fungi but also fungal virulence traits.

Bioinformatics Analysis of the Periodicity in Proteins with Coiled-Coil Structure-Enumerating All Decompositions of Sequence Periods.

A coiled coil is a structural motif in proteins that consists of at least two α-helices wound around each other. For structural stabilization, these α-helices form interhelical contacts via their amino acid side chains. However, there are restrictions as to the distances along the amino acid sequence at which those contacts occur. As the spatial period of the α-helix is 3.6, the most frequent distances between hydrophobic contacts are 3, 4, and 7. Up to now, the multitude of possible decompositions of α-helices participating in coiled coils at these distances has not been explored systematically. Here, we present an algorithm that computes all non-redundant decompositions of sequence periods of hydrophobic amino acids into distances of 3, 4, and 7. Further, we examine which decompositions can be found in nature by analyzing the available data and taking a closer look at correlations between the properties of the coiled coil and its decomposition. We find that the availability of decompositions allowing for coiled-coil formation without putting too much strain on the α-helix geometry follows an oscillatory pattern in respect of period length. Our algorithm supplies the basis for exploring the possible decompositions of coiled coils of any period length.

The Definition of Open Reading Frame Revisited.

The term open reading frame (ORF) is of central importance to gene finding. Surprisingly, at least three definitions are in use. We discuss several molecular biological and bioinformatics aspects, and we recommend using the definition in which an ORF is bounded by stop codons.

Efficient high-voltage protection in the electric catfish.

For thousands of years, starting with detailed accounts from ancient Egypt, the African electric catfish (Malapteruridae) has been renowned for its ability to hunt and to defend itself with powerful electric shocks. Surprisingly, the degree to which electric catfish are protected against their own or external electric shocks, how specific any protection would be to the species-specific waveform and whether a discharging catfish has to actively prepare for the onset of its high-voltage discharges has never been analysed. Here, we used digital high-speed video to record catfish during their own discharges or as they were exposed to external discharges, employing goldfish to carefully calibrate the efficiency of all discharges. Electric catfish show a remarkable degree of protection against high voltages: both self-produced and external electric shocks that heavily affected control goldfish failed to evoke involuntary muscle contraction or to affect sensorimotor processing. Even a commercial electrofishing device, set to efficiently immobilise and narcotise fish, failed to have any effect on the electric catfish. Our findings rule out several protective mechanisms and demonstrate a highly efficient and versatile shielding whose nature is presently unclear.

Archerfish coordinate fin maneuvers with their shots.

Archerfish down a variety of aerial prey from a range of distances using water jets that they adjust to the size and distance of their prey. We describe here that characteristic rapid fin maneuvers, most notably of the pectoral and pelvic fins, are precisely coordinated with the release of the jet. We discovered these maneuvers in two fish, the jets of which had been characterized in detail, that had been trained to shoot from fixed positions at targets at different heights and that remained stable during their shots. Based on the findings in these individuals, we examined shooting-associated fin movement in 28 further archerfish of two species that could shoot from freely chosen positions at targets at different heights. Slightly before the onset of the water jet, at a time when the shooter remains stable, the pectoral fins of all shooters switched from asynchronous low-amplitude beating to a synchronized rapid forward flap. The onset and duration of the forward and subsequent backward flap were robust across all individuals and shooting angles but depended on target height. The pelvic fins were slowly adducted at the start of the jet and stopped moving after its release. All other fins also showed a characteristic sequence of activation, some starting ∼0.5 s before the shot. Our findings suggest that shooting-related fin maneuvers are needed to stabilize the shooter, and that these maneuvers are an important component in the precise and powerful far-distance shooting in archerfish.

Trends in mathematical modeling of host-pathogen interactions.

Pathogenic microorganisms entail enormous problems for humans, livestock, and crop plants. A better understanding of the different infection strategies of the pathogens enables us to derive optimal treatments to mitigate infectious diseases or develop vaccinations preventing the occurrence of infections altogether. In this review, we highlight the current trends in mathematical modeling approaches and related methods used for understanding host-pathogen interactions. Since these interactions can be described on vastly different temporal and spatial scales as well as abstraction levels, a variety of computational and mathematical approaches are presented. Particular emphasis is placed on dynamic optimization, game theory, and spatial modeling, as they are attracting more and more interest in systems biology. Furthermore, these approaches are often combined to illuminate the complexities of the interactions between pathogens and their host. We also discuss the phenomena of molecular mimicry and crypsis as well as the interplay between defense and counter defense. As a conclusion, we provide an overview of method characteristics to assist non-experts in their decision for modeling approaches and interdisciplinary understanding.

Recording from an Identified Neuron Efficiently Reveals Hazard for Brain Function in Risk Assessment.

Modern societies use a continuously growing number of chemicals. Because these are released into the environment and are taken up by humans, rigorous (but practicable) risk assessment must precede the approval of new substances for commerce. A number of tests is applicable, but it has been very difficult to efficiently assay the effect of chemicals on communication and information processing in vivo in the adult vertebrate brain. Here, we suggest a straightforward way to rapidly and accurately detect effects of chemical exposure on action potential generation, synaptic transmission, central information processing, and even processing in sensory systems in vivo by recording from a single neuron. The approach is possible in an identified neuron in the hindbrain of fish that integrates various sources of information and whose properties are ideal for rapid analysis of the various effects chemicals can have on the nervous system. The analysis uses fish but, as we discuss here, key neuronal functions are conserved and differences can only be due to differences in metabolism or passage into the brain, factors that can easily be determined. Speed and efficiency of the method, therefore, make it suitable to provide information in risk assessment, as we illustrate here with the effects of bisphenols on adult brain function.

Accuracy Bounds and Measurements of a Contactless Permittivity Sensor for Gases Using Synchronized Low-Cost mm-Wave Frequency Modulated Continuous Wave Radar Transceivers.

A primary concern in a multitude of industrial processes is the precise monitoring of gaseous substances to ensure proper operating conditions. However, many traditional technologies are not suitable for operation under harsh environmental conditions. Radar-based time-of-flight permittivity measurements have been proposed as alternative but suffer from high cost and limited accuracy in highly cluttered industrial plants. This paper examines the performance limits of low-cost frequency-modulated continuous-wave (FMCW) radar sensors for permittivity measurements. First, the accuracy limits are investigated theoretically and the Cramér-Rao lower bounds for time-of-flight based permittivity and concentration measurements are derived. In addition, Monte-Carlo simulations are carried out to validate the analytical solutions. The capabilities of the measurement concept are then demonstrated with different binary gas mixtures of Helium and Carbon Dioxide in air. A low-cost time-of-flight sensor based on two synchronized fully-integrated millimeter-wave (MMW) radar transceivers is developed and evaluated. A method to compensate systematic deviations caused by the measurement setup is proposed and implemented. The theoretical discussion underlines the necessity of exploiting the information contained in the signal phase to achieve the desired accuracy. Results of various permittivity and gas concentration measurements are in good accordance to reference sensors and measurements with a commercial vector network analyzer (VNA). In conclusion, the proposed radar-based low-cost sensor solution shows promising performance for the intended use in demanding industrial applications.

Thermodynamic constraints for identifying elementary flux modes.

Metabolic pathway analysis is a key method to study metabolism and the elementary flux modes (EFMs) is one major concept allowing one to analyze the network in terms of minimal pathways. Their practical use has been hampered by the combinatorial explosion of their number in large systems. The EFMs give the possible pathways at steady state, but the real pathways are limited by biological constraints. In this review, we display three different methods that integrate thermodynamic constraints in terms of Gibbs free energy in the EFMs computation.

Hunting in archerfish - an ecological perspective on a remarkable combination of skills.

Archerfish are well known for using jets of water to dislodge distant aerial prey from twigs or leaves. This Review gives a brief overview of a number of skills that the fish need to secure prey with their shooting technique. Archerfish are opportunistic hunters and, even in the wild, shoot at artificial objects to determine whether these are rewarding. They can detect non-moving targets and use efficient search strategies with characteristics of human visual search. Their learning of how to engage targets can be remarkably efficient and can show impressive degrees of generalization, including learning from observation. In other cases, however, the fish seem unable to learn and it requires some understanding of the ecological and biophysical constraints to appreciate why. The act of shooting has turned out not to be of a simple all-or-none character. Rather, the fish adjust the volume of water fired according to target size and use fine adjustments in the timing of their mouth opening and closing manoeuvre to adjust the hydrodynamic stability of their jets to target distance. As soon as prey is dislodged and starts falling, the fish make rapid and yet sophisticated multi-dimensional decisions to secure their prey against many intraspecific and interspecific competitors. Although it is not known why and how archerfish evolved an ability to shoot in the first place, I suggest that the evolution of shooting has strongly pushed the co-evolution of diverse other skills that are needed to secure a catch.

Rapid depth perception in hunting archerfish. I. The predictive C-starts use an independent estimate of target height.

Archerfish dislodge aerial prey with water jets and use their predictive C-starts to secure it. Their C-starts turn the fish to the later point of impact and set the speed so that the fish arrive just in time. The starts are adjusted on the basis of information on speed, direction, timing and horizontal start position of prey movement - sampled during less than 100 ms after prey starts falling. Presently, it is unclear whether one essential parameter, the initial height of prey, can also be determined during this brief sampling time. Shooters and probably also observing bystanders already know target height - used to hit and to shape their jets - and would simply have to feed this information into their C-start circuitry. We challenged archerfish by launching initially invisible prey objects either from the expected height level, at which the fish were looking and at which they fired shots, or from more lateral positions and a lower or higher initial height. The arrangement was designed so that an analysis of the direction and the linear speed chosen by the starting fish could determine whether the C-start information is based on the expected height or on the actual height, which can be detected only after hidden prey has begun falling. Our findings demonstrate that the fish quickly estimate initial height during the initial falling phase of prey and do not simply use the expected height level to which they were cued.

Rapid depth perception in hunting archerfish. II. An analysis of potential cues.

Based on the initial movement of falling prey, hunting archerfish select a C-start that turns them right to where their prey is going to land and lends the speed to arrive simultaneously with prey. Our companion study suggested that the information sampled in less than 100 ms also includes the initial height of falling prey. Here, we examine which cues the fish might be using to gauge height so quickly. First, we show that binocular cues are not required: C-starts that either could or could not have used binocular information were equally fast and precise. Next, we explored whether the fish were using simplifying assumptions about the absolute size of their prey or its distance from a structured background. However, experiments with unexpected changes from the standard conditions failed to cause any errors. We then tested the hypothesis that the fish might infer depth from accommodation or from cues related to blurring in the image of their falling prey. However, the fish also determined the height of 'fake flies' correctly, even though their image could never be focused and their combined size and degree of blurring should have misled the fish. Our findings are not compatible with the view that archerfish use a flexible combination of cues. They also do not support the view that height is gauged relative to structures in the vicinity of starting prey. We suggest that these fish use an elaborate analysis of looming to rapidly gauge initial height.

The Mauthner cell in a fish with top-performance and yet flexibly tuned C-starts. I. Identification and comparative morphology.

Archerfish use two powerful C-starts: one to escape threats, the other to secure prey that they have downed with a shot of water. The two C-starts are kinematically equivalent and variable in both phases, and the predictive C-starts - used in hunting - are adjusted in terms of the angle of turning and the final linear speed to where and when their prey will hit the water surface. Presently, nothing is known about the neural circuits that drive the archerfish C-starts. As the starting point for a neuroethological analysis, we first explored the presence and morphology of a pair of Mauthner cells, which are key cells in the teleost fast-start system. We show that archerfish have a typical Mauthner cell in each medullary hemisphere and that these send by far the largest axons down the spinal cord. Stimulation of the spinal cord caused short-latency all-or-none field potentials that could be detected even at the surface of the medulla and that had the Mauthner cell as its only source. The archerfish's Mauthner cell is remarkably similar morphologically to that of equally sized goldfish, except that the archerfish's ventral dendrite is slightly longer and its lateral dendrite thinner. Our data provide the necessary starting point for the dissection of the archerfish fast-start system and of any role potentially played by its Mauthner cell in the two C-start manoeuvres. Moreover, they do not support the recently expressed view that Mauthner cells should be reduced in animals with highly variable fast-start manoeuvres.

The Mauthner cell in a fish with top-performance and yet flexibly tuned C-starts. II. Physiology.

The parallel occurrence in archerfish of fine-tuned and yet powerful predictive C-starts as well as of kinematically identical escape C-starts makes archerfish an interesting system to test hypotheses on the roles played by the Mauthner cells, a pair of giant reticulospinal neurons. In this study, we show that the archerfish Mauthner cell shares all hallmark physiological properties with that of goldfish. Visual and acoustic inputs are received by the ventral and lateral dendrite, respectively, and cause complex postsynaptic potentials (PSPs) even in surgically anaesthetised fish. PSP shape did not indicate major differences between the species, but simple light flashes caused larger PSPs in archerfish, often driving the cell to fire an action potential. Probing archerfish in the classical tests for feedback inhibition, established in the Mauthner-associated networks in goldfish, revealed no differences between the two species, including the indications for electrical and chemical synaptic components. Also, the established hallmark experiments on feed-forward inhibition showed no differences between the goldfish and archerfish Mauthner system. Extending these experiments to visual stimuli also failed to detect any differences between the two species and suggested that acoustical and visual input cause feed-forward inhibition, the magnitude, time course and duration of which match that of the respective PSPs in both archerfish and goldfish. Our findings question simple views on the role of the Mauthner cell and suggest that the archerfish Mauthner cell should be a good system to explore the function of these giant neurons in more sophisticated C-start behaviours.

From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints.

Elementary flux modes (EFMs) emerged as a formal concept to describe metabolic pathways and have become an established tool for constraint-based modeling and metabolic network analysis. EFMs are characteristic (support-minimal) vectors of the flux cone that contains all feasible steady-state flux vectors of a given metabolic network. EFMs account for (homogeneous) linear constraints arising from reaction irreversibilities and the assumption of steady state; however, other (inhomogeneous) linear constraints, such as minimal and maximal reaction rates frequently used by other constraint-based techniques (such as flux balance analysis [FBA]), cannot be directly integrated. These additional constraints further restrict the space of feasible flux vectors and turn the flux cone into a general flux polyhedron in which the concept of EFMs is not directly applicable anymore. For this reason, there has been a conceptual gap between EFM-based (pathway) analysis methods and linear optimization (FBA) techniques, as they operate on different geometric objects. One approach to overcome these limitations was proposed ten years ago and is based on the concept of elementary flux vectors (EFVs). Only recently has the community started to recognize the potential of EFVs for metabolic network analysis. In fact, EFVs exactly represent the conceptual development required to generalize the idea of EFMs from flux cones to flux polyhedra. This work aims to present a concise theoretical and practical introduction to EFVs that is accessible to a broad audience. We highlight the close relationship between EFMs and EFVs and demonstrate that almost all applications of EFMs (in flux cones) are possible for EFVs (in flux polyhedra) as well. In fact, certain properties can only be studied with EFVs. Thus, we conclude that EFVs provide a powerful and unifying framework for constraint-based modeling of metabolic networks.