Archerfish foraging success varies with immediate competition level but not group size.

Group living can lead to kleptoparasitism, the theft of resources by competitors. Under such conditions, foragers may alter their behavior to minimize competition. However, it is unclear how such behavioral changes impact foraging performance. Archerfish (Toxotes spp.) are a good model for investigating the behavioral responses to kleptoparasitism, as their hunting method (shooting waterjets at insects perched above the water) leaves them vulnerable to theft. They must hit the target prey with sufficient force to dislodge it; thus, the prey may land some distance away from the shooter. Kleptoparasitism rates increase with group size in archerfish, and individuals alter their behavior around conspecifics. We investigated whether group size affected shooting success, using 7-spot archerfish T. chatareus. We considered a fish's shot to be successful if it knocked a fly, placed on a transparent platform above the tank, into the water. The probability of shooting success was modeled as a function of group size, aiming duration, nearest neighbor distance and position, and trial number. We found no effect of group size, aiming duration, or nearest neighbor distance or position on shooting success. Shooting success increased as trials progressed, likely due to the fish becoming more familiar with the task. We also found no change in the kleptoparasitism rate between group sizes. Instead, the likelihood of the shooter consuming the prey depended on the types of competition present at the time of shooting. We suggest that archerfish shooting behavior can be influenced by the presence of conspecifics in ways not previously considered.

Dynamic changes in tumor profiling reveal intra- and inter-tumoral heterogeneity focused on an uncharacterized HER2 mutation: a case report of a young breast cancer patient.

Despite multiple recent advances in systemic therapy for metastatic breast cancer, cases which display suboptimal response to guideline-driven treatment are frequently seen in the clinic. Effective options for such patients are limited, particularly in later line of therapy, and selection of optimal treatment options is essentially empirical and based largely on considerations of previous regimens received. Comprehensive cancer profiling includes detection of genetic alterations in tissue and circulating tumor DNA (ctDNA), immunohistochemistry (IHC) from re-biopsied metastatic disease, circulating tumor cells (CTCs), gene expression analysis and pharmacogenomics. The advent of this methodology and application to metastatic breast cancer, facilitates a more scientifically informed approach to identification of optimal systemic therapy approaches independent of the restrictions implied by clinical guidelines. Here we describe a case of metastatic breast cancer where consecutive comprehensive tumor profiling reveals ongoing tumor evolution, guiding the identification of novel effective therapeutic strategies.

Optimal hematocrit theory - A review.

In humans and higher animals, a trade-off between a sufficiently high concentration of erythrocytes (hematocrit), to bind oxygen and sufficiently low blood viscosity to allow rapid blood flow has been achieved during evolution. The optimal value lies between the extreme cases of pure blood plasma, which cannot practically transport any oxygen, and 100\% hematocrit, which would imply very slow blood flow or none at all. As oxygen delivery to tissues is the main task of the cardiovascular system, it is reasonable to expect that maximum oxygen delivery has been achieved during evolution. Optimal hematocrit theory, based on this optimality principle, has been successful in predicting hematocrit values of about 0.3-0.5, which are indeed observed in humans and many animal species. Similarly, the theory can explain why higher than normal hematocrit, ranging from 0.5 to 0.7, can promote better exertional performance. Here we present a review of theoretical approaches to the calculation of the optimal hematocrit value under different conditions and discuss them in a broad physiological context. Several physiological and medical implications are outlined, e.g. in view of blood doping, temperature adaptation, and life at high altitudes.

Studying mixed-species biofilms of Candida albicans and Staphylococcus aureus using evolutionary game theory.

Mixed-species biofilms of Candida albicans and Staphylococcus aureus pose a significant clinical challenge due to their resistance to the human immune system and antimicrobial therapy. Using evolutionary game theory and nonlinear dynamics, we analyse the complex interactions between these organisms to understand their coexistence in the human host. We determine the Nash equilibria and evolutionary stable strategies of the game between C. albicans and S. aureus and point out different states of the mixed-species biofilm. Using replicator equations we study the fungal-bacterial interactions on a population level. Our focus is on the influence of available nutrients and the quorum sensing molecule farnesol, including the potential therapeutic use of artificially added farnesol. We also investigate the impact of the suggested scavenging of C. albicans hyphae by S. aureus. Contrary to common assumptions, we confirm the hypothesis that under certain conditions, mixed-species biofilms are not universally beneficial. Instead, different Nash equilibria occur depending on encountered conditions (i.e. varying farnesol levels, either produced by C. albicans or artificially added), including antagonism. We further show that the suggested scavenging of C. albicans' hyphae by S. aureus does not influence the overall outcome of the game. Moreover, artificially added farnesol strongly affects the dynamics of the game, although its use as a medical adjuvant (add-on medication) may pose challenges.

How Plant Toxins Cause Early Larval Mortality in Herbivorous Insects: An Explanation by Modeling the Net Energy Curve.

Plants store chemical defenses that act as toxins against herbivores, such as toxic isothiocyanates (ITCs) in Brassica plants, hydrolyzed from glucosinolate (GLS) precursors. The fitness of herbivorous larvae can be strongly affected by these toxins, causing immature death. We modeled this phenomenon using a set of ordinary differential equations and established a direct relationship between feeding, toxin exposure, and the net energy of a larva, where the fitness of an organism is proportional to its net energy according to optimal foraging theory. Optimal foraging theory is widely used in ecology to model the feeding and searching behavior of organisms. Although feeding provides energy gain, plant toxins and foraging cause energy loss for the larvae. Our equations explain that toxin exposure and foraging can sharply reduce larval net energy to zero at an instar. Since herbivory needs energy, the only choice left for a larva is to stop feeding at that time point. If that is significantly earlier than the end of the last instar stage, the larva dies without food. Thus, we show that plant toxins can cause immature death in larvae from the perspective of optimal foraging theory.

Selection pressure by specialist and generalist insect herbivores leads to optimal constitutive plant defense. A mathematical model.

Brassicaceae plants have the glucosinolate-myrosinase defense system, jointly active against herbivory. However, constitutive glucosinolate (GLS) defense is observed to occur at levels that do not deter all insects from feeding. That prompts the question of why Brassicaceae plants have not evolved a higher constitutive defense. The answer may lie in the contrasting relationship between plant defense and host plant preference of specialist and generalist herbivores. GLS content increases a plant's susceptibility to specialist insects. In contrast, generalists are deterred by the plant GLSs. Although GLSs can attract the natural enemies (predators and parasitoids) of these herbivores, enemies can reduce herbivore pressure to some extent only. So, plants can be overrun by specialists if GLS content is too high, whereas generalists can invade the plants if it is too low. Therefore, an optimal constitutive plant defense can minimize the overall herbivore pressure. To explain the optimal defense theoretically, we model the contrasting host selection behavior of insect herbivores and the emergence of their natural enemies by non-autonomous ordinary differential equations, where the independent variable is the plant GLS concentration. From the model, we quantify the optimal amount of GLSs, which minimizes total herbivore (specialists and generalists) pressure. That quite successfully explains the evolution of constitutive defense in plants from the perspective of optimality theory.

Statistical analysis of synonymous and stop codons in pseudo-random and real sequences as a function of GC content.

Knowledge of the frequencies of synonymous triplets in protein-coding and non-coding DNA stretches can be used in gene finding. These frequencies depend on the GC content of the genome or parts of it. An example of interest is provided by stop codons. This is relevant for the definition of Open Reading Frames. A generic case is provided by pseudo-random sequences, especially when they code for complex proteins or when they are non-coding and not subject to selection pressure. Here, we calculate, for such sequences and for all 25 known genetic codes, the frequency of each amino acid and stop codon based on their set of codons and as a function of GC content. The amino acids can be classified into five groups according to the GC content where their expected frequency reaches its maximum. We determine the overall Shannon information based on groups of synonymous codons and show that it becomes maximum at a percent GC of 43.3% (for the standard code). This is in line with the observation that in most fungi, plants, and animals, this genomic parameter is in the range from 35 to 50%. By analysing natural sequences, we show that there is a clear bias for triplets corresponding to stop codons near the 5'- and 3'-splice sites in the introns of various clades.

Game-theoretical description of the go-or-grow dichotomy in tumor development for various settings and parameter constellations.

A medically important feature of several types of tumors is their ability to "decide" between staying at a primary site in the body or leaving it and forming metastases. The present theoretical study aims to provide a better understanding of the ultimate reasons for this so-called "go-or-grow" dichotomy. To that end, we use game theory, which has proven to be useful in analyzing the competition between tumors and healthy tissues or among different tumor cells. We begin by determining the game types in the Basanta-Hatzikirou-Deutsch model, depending on the parameter values. Thereafter, we suggest and analyze five modified variants of the model. For example, in the basic model, the deadlock game, Prisoner's Dilemma, and hawk-dove game can occur. The modified versions lead to several additional game types, such as battle of the sexes, route-choice, and stag-hunt games. For some game types, all cells are predicted to stay on their original site ("grow phenotype"), while for other types, only a certain fraction stay and the other cells migrate away ("go phenotype"). If the nutrient supply at a distant site is high, all the cells are predicted to go. We discuss our predictions in terms of the pros and cons of caloric restriction and limitations of the supply of vitamins or methionine. Our results may help devise treatments to prevent metastasis.

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.

Reinhart Heinrich: In memoriam of an exceptional scholar.

In the Mathematical Biology community, Reinhart Heinrich (1946-2006) is well-known as one of the founders of Metabolic Control Analysis. Moreover, he made significant contributions to the modelling of erythrocyte metabolism and signal transduction cascades, optimality principles in metabolism, theoretical membrane biophysics and other topics. Here, the historical context of his scientific work is outlined and numerous personal memories of the scholarship of, and cooperation with, Reinhart Heinrich are narrated. Attention is drawn again to the pros and cons of normalized and non-normalized control coefficients. The role of the Golden Ratio in a dynamic optimization problem in genetic regulation of metabolism is discussed. Overall, this article is aimed at keeping alive the memory of a unique university teacher, researcher and friend.

Recordings in an integrating central neuron reveal the mode of action of isoeugenol.

Although isoeugenol is one of the most widely used anesthetics in fish, its actual mode of action and thus its applicability for particular interventions is poorly understood. Here we determined effects of isoeugenol on various aspects of sensory and neural function, taking advantage of intracellular in vivo recordings in a uniquely suited identified neuron, the Mauthner neuron in the brain of goldfish. We show that isoeugenol strongly affects hearing and vision, but sensitivity and time course of action differed largely in these two senses. The action potential, chemical and electric synaptic transmission at the central neuron were not affected at low but efficient anesthesia. Effects seen at high concentration thereby do not support current views of how isoeugenol might act on central neurons. We show that isoeugenol is highly useful to anesthetize fish for handling, but that in more severe treatment its application needs to be carefully adapted to task.

Accurate prostate cancer detection based on enrichment and characterization of prostate cancer specific circulating tumor cells.

BACKGROUND: The low specificity of serum PSA resulting in the inability to effectively differentiate prostate cancer from benign prostate conditions is a persistent clinical challenge. The low sensitivity of serum PSA results in false negatives and can miss high-grade prostate cancers. We describe a non-invasive test for detection of prostate cancer based on functional enrichment of prostate adenocarcinoma associated circulating tumor cells (PrAD-CTCs) from blood samples followed by their identification by immunostaining for pan-cytokeratins (PanCK), prostate specific membrane antigen (PSMA), alpha methyl-acyl coenzyme-A racemase (AMACR), epithelial cell adhesion molecule (EpCAM), and common leucocyte antigen (CD45). METHODS: Analytical validation studies were performed to establish the performance characteristics of the test using VCaP prostate cancer cells spiked into healthy donor blood (HDB). The clinical performance characteristics of the test were evaluated in a case-control study with 160 known prostate cancer cases and 800 healthy males, followed by a prospective clinical study of 210 suspected cases of prostate cancer. RESULTS: Analytical validation established analyte stability as well as acceptable performance characteristics. The test showed 100% specificity and 100% sensitivity to differentiate prostate cancer cases from healthy individuals in the case control study and 91.2% sensitivity and 100% specificity to differentiate prostate cancers from benign prostate conditions in the prospective clinical study. CONCLUSIONS: The test accurately detects PrAD-CTCs with high sensitivity and specificity irrespective of stage, serum PSA or Gleason score, which translates into low risks of false negatives or overdiagnosis. The high accuracy of the test could offer advantages over PSA based prostate cancer detection.

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.

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.

Accurate Screening for Early-Stage Breast Cancer by Detection and Profiling of Circulating Tumor Cells.

BACKGROUND: The early detection of breast cancer (BrC) is associated with improved survival. We describe a blood-based breast cancer detection test based on functional enrichment of breast-adenocarcinoma-associated circulating tumor cells (BrAD-CTCs) and their identification via multiplexed fluorescence immunocytochemistry (ICC) profiling for GCDFP15, GATA3, EpCAM, PanCK, and CD45 status. METHODS: The ability of the test to differentiate BrC cases (N = 548) from healthy women (N = 9632) was evaluated in a case-control clinical study. The ability of the test to differentiate BrC cases from those with benign breast conditions was evaluated in a prospective clinical study of women (N = 141) suspected of BrC. RESULTS: The test accurately detects BrAD-CTCs in breast cancers, irrespective of age, ethnicity, disease stage, grade, or hormone receptor status. Analytical validation established the high accuracy and reliability of the test under intended use conditions. The test detects and differentiates BrC cases from healthy women with 100% specificity and 92.07% overall sensitivity in a case-control study. In a prospective clinical study, the test shows 93.1% specificity and 94.64% overall sensitivity in differentiating breast cancer cases (N = 112) from benign breast conditions (N = 29). CONCLUSION: The findings reported in this manuscript support the clinical potential of this test for blood-based BrC detection.

Case Report: Extensive Tumor Profiling in Primary Neuroendocrine Breast Cancer Cases as a Role Model for Personalized Treatment in Rare and Aggressive Cancer Types.

Neuroendocrine breast cancer (NEBC) is a rare entity accounting for <0.1% of all breast carcinomas and <0.1% of all neuroendocrine carcinomas. In most cases treatment strategies in NEBC are empirical in absence of prospective trial data on NEBC cohorts. Herein, we present two case reports diagnosed with anaplastic and small cell NEBC. After initial therapies failed, comprehensive tumor profiling was applied, leading to individualized treatment options for both patients. In both patients, targetable alterations of the PI3K/AKT/mTOR pathway were found, including a PIK3CA mutation itself and an STK11 mutation that negatively regulates the mTOR complex. The epicrisis of the two patients exemplifies how to manage rare and difficult to treat cancers and how new diagnostic tools contribute to medical management.

Circulating tumor cell assay to non-invasively evaluate PD-L1 and other therapeutic targets in multiple cancers.

Biomarker directed selection of targeted anti-neoplastic agents such as immune checkpoint inhibitors, small molecule inhibitors and monoclonal antibodies form an important aspect of cancer treatment. Immunohistochemistry (IHC) analysis of the tumor tissue is the method of choice to evaluate the presence of these biomarkers. However, a significant barrier to biomarker testing on tissue is the availability of an adequate amount of tissue and need for repetitive sampling due to tumor evolution. Also, tumor tissue testing is not immune to inter- and intra-tumor heterogeneity. We describe the analytical and clinical validation of a Circulating Tumor Cell (CTC) assay to accurately assess the presence of PD-L1 22C3 and PD-L1 28.8, ER, PR and HER2, from patients with solid tumors to guide the choice of suitable targeted therapies. Analytically, the test has high sensitivity, specificity, linearity and precision. Based on a blinded case control study, the clinical sensitivity and specificity for PD-L1 (22C3 and 28.8) was determined to be 90% and 100% respectively. The clinical sensitivity and specificity was 83% and 89% for ER; 80% and 94% for PR; 63% and 89% for HER2 (by ICC); and 100% and 92% for HER2 (by FISH), respectively. The performance characteristics of the test support its suitability and adaptability for routine clinical use.

Agent-based modelling of iron cycling bacteria provides a framework for testing alternative environmental conditions and modes of action.

Iron-reducing and iron-oxidizing bacteria are of interest in a variety of environmental and industrial applications. Such bacteria often co-occur at oxic-anoxic gradients in aquatic and terrestrial habitats. In this paper, we present the first computational agent-based model of microbial iron cycling, between the anaerobic ferric iron (Fe3+)-reducing bacteria Shewanella spp. and the microaerophilic ferrous iron (Fe2+)-oxidizing bacteria Sideroxydans spp. By including the key processes of reduction/oxidation, movement, adhesion, Fe2+-equilibration and nanoparticle formation, we derive a core model which enables hypothesis testing and prediction for different environmental conditions including temporal cycles of oxic and anoxic conditions. We compared (i) combinations of different Fe3+-reducing/Fe2+-oxidizing modes of action of the bacteria and (ii) system behaviour for different pH values. We predicted that the beneficial effect of a high number of iron-nanoparticles on the total Fe3+ reduction rate of the system is not only due to the faster reduction of these iron-nanoparticles, but also to the nanoparticles' additional capacity to bind Fe2+ on their surfaces. Efficient iron-nanoparticle reduction is confined to pH around 6, being twice as high than at pH 7, whereas at pH 5 negligible reduction takes place. Furthermore, in accordance with experimental evidence our model showed that shorter oxic/anoxic periods exhibit a faster increase of total Fe3+ reduction rate than longer periods.

MALDI mass spectrometry imaging workflow for the aquatic model organisms Danio rerio and Daphnia magna.

Lipids play various essential roles in the physiology of animals. They are also highly dependent on cellular metabolism or status. It is therefore crucial to understand to which extent animals can stabilize their lipid composition in the presence of external stressors, such as chemicals that are released into the environment. We developed a MALDI MS imaging workflow for two important aquatic model organisms, the zebrafish (Danio rerio) and water flea (Daphnia magna). Owing to the heterogeneous structure of these organisms, developing a suitable sample preparation workflow is a highly non-trivial but crucial part of this work and needs to be established first. Relevant parameters and practical considerations in order to preserve tissue structure and composition in tissue sections are discussed for each application. All measurements were based on high mass accuracy enabling reliable identification of imaged compounds. In zebrafish we demonstrate that a detailed mapping between histology and simultaneously determined lipid composition is possible at various scales, from extended structures such as the brain or gills down to subcellular structures such as a single axon in the central nervous system. For D. magna we present for the first time a MALDI MSI workflow, that demonstrably maintains tissue integrity during cryosectioning of non-preserved samples, and allows the mapping of lipids in the entire body and the brood chamber inside the carapace. In conclusion, the lipid signatures that we were able to detect with our method provide an ideal basis to analyze changes caused by pollutants in two key aquatic model organisms.

Connexins evolved after early chordates lost innexin diversity.

Gap junction channels are formed by two unrelated protein families. Non-chordates use the primordial innexins, while chordates use connexins that superseded the gap junction function of innexins. Chordates retained innexin-homologs, but N-glycosylation prevents them from forming gap junctions. It is puzzling why chordates seem to exclusively use the new gap junction protein and why no chordates should exist that use non-glycosylated innexins to form gap junctions. Here, we identified glycosylation sites of 2388 innexins from 174 non-chordate and 276 chordate species. Among all chordates, we found not a single innexin without glycosylation sites. Surprisingly, the glycosylation motif is also widespread among non-chordate innexins indicating that glycosylated innexins are not a novelty of chordates. In addition, we discovered a loss of innexin diversity during early chordate evolution. Most importantly, lancelets, which lack connexins, exclusively possess only one highly conserved innexin with one glycosylation site. A bottleneck effect might thus explain why connexins have become the only protein used to form chordate gap junctions.