Effects of whole-grain cereals on fecal microbiota and short-chain fatty acids in dogs: a comparison of rye, oats and wheat

Dietary fiber in dog food is reported to promote healthy gut microbiota, but few studies have investigated the effects of whole-grain cereals, which contain a variety of fiber types and other bioactive compounds. The aim of the present study was to compare the effects of diets containing whole-grain rye (RYE), oats (OAT) and wheat (WHE) on fecal microbiota and short-chain fatty acid production. Eighteen dogs were fed three experimental diets, each for four weeks, in a cross-over design. Fecal samples were collected at the end of each diet period. Analysis of 16S rRNA gene amplicons showed that family Lachnospiraceae and genus Bacteroides were the gut microbial groups most affected by diet, with lowest relative abundance following consumption of RYE and a trend for a corresponding increase in genus Prevotella_9. Fecal acetate and propionate concentrations were higher after consumption of RYE compared with OAT. In conclusion, rye had the strongest effect on gut microbiota and short-chain fatty acids, although the implications for dog gut health are not yet elucidated.

Effects of rye inclusion in dog food on fecal microbiota and short-chain fatty acids

BACKGROUND

Rye intake has been associated with beneficial effects on health in human interventions, possibly due to dietary fiber in rye. In dogs, few studies have explored the effects on health of dietary fiber in general, and rye fiber in particular. The aim of this study was to investigate how inclusion of rye, compared with wheat, influenced fecal microbiota composition, short chain fatty acids (SCFA) and apparent total tract digestibility (ATTD) in dogs. Six male Beagle dogs (mean age 4.6 years, SEM 0.95 years; mean body weight 14.6 kg, SEM 0.32 kg) were fed three experimental diets, each for 21 days, including an adaptation period of six days and with 2-2.5 months between diet periods. The diets were similar regarding energy and protein, but had different carbohydrate sources (refined wheat (W), whole grain rye (R), or an equal mixture of both (RW)) comprising 50% of total weight on a dry matter (DM) basis. The diets were baked and titanium dioxide was added for ATTD determination. Fecal samples were collected before and in the end of each experimental period. Fecal microbiota was analyzed by sequencing 16S rRNA gene amplicons and fecal SCFA by high-performance liquid chromatography. Crude protein, crude fat, neutral detergent fiber, and gross energy (GE) in food and feces were analyzed and ATTD of each was determined. Univariate and multivariate statistical methods were applied in data evaluation.

RESULTS

Faecal microbiota composition, differed depending on diet (P = 0.002), with samples collected after consumption of the R diet differing from baseline. This was primarily because of a shift in proportion of Prevotella, which increased significantly after consumption of the R diet (P < 0.001). No significant differences were found for SCFA, but there was a tendency (P < 0.06) for higher molar proportions of acetic acid following consumption of the R diet. The ATTD of crude protein, crude fat, neutral detergent fiber, and GE was lower after consumption of the R diet compared with the other diets (P < 0.05).

CONCLUSIONS

Consumption of the R diet, but not RW or W diets, was associated with specific shifts in microbial community composition and function, but also with lower ATTD.

Age Rather Than Supplementation with Oat β-Glucan Influences Development of the Intestinal Microbiota and SCFA Concentrations in Suckling Piglets

The effects of early supplementation with oat β-glucan during the suckling period on piglet gut microbiota composition, concentrations of short-chain fatty acids, and gut physiological markers were assessed. Fifty piglets from five litters, balanced for sex and birth weight, were divided within litters into two treatment groups: β-glucan and control. Piglets in the β-glucan group received the supplement three times/week from day 7 of age until weaning. Rectal swab samples were collected from 10 piglets per treatment group (balanced across litters) from week 1 to week 4, and plasma samples were collected at 1, 3, and 4 weeks of age. Additional samples of intestinal tissues and jugular and portal vein plasma were collected from 10 animals at weaning (one per treatment group and litter). The concentrations of short-chain fatty acids in plasma and the microbiota composition in rectal swabs were mainly influenced by piglet age, rather than the supplement. There were significant differences in microbiota composition between litters and several correlations between concentrations of short-chain fatty acids in plasma and specific microbial taxa in rectal swabs. Overall, β-glucan supplementation did not have any clear impact on the gut environment in suckling piglets, whereas a clear age-related pattern emerged.

Nowcasting (Short-Term Forecasting) of COVID-19 Hospitalizations Using Syndromic Healthcare Data, Sweden, 2020

We report on local nowcasting (short-term forecasting) of coronavirus disease (COVID-19) hospitalizations based on syndromic (symptom) data recorded in regular healthcare routines in Östergötland County (population ≈465,000), Sweden, early in the pandemic, when broad laboratory testing was unavailable. Daily nowcasts were supplied to the local healthcare management based on analyses of the time lag between telenursing calls with the chief complaints (cough by adult or fever by adult) and COVID-19 hospitalization. The complaint cough by adult showed satisfactory performance (Pearson correlation coefficient r>0.80; mean absolute percentage error <20%) in nowcasting the incidence of daily COVID-19 hospitalizations 14 days in advance until the incidence decreased to <1.5/100,000 population, whereas the corresponding performance for fever by adult was unsatisfactory. Our results support local nowcasting of hospitalizations on the basis of symptom data recorded in routine healthcare during the initial stage of a pandemic.

Data augmentation with Mobius transformations

Data augmentation has led to substantial improvements in the performance and generalization of deep models, and remains a highly adaptable method to evolving model architectures and varying amounts of data—in particular, extremely scarce amounts of available training data. In this paper, we present a novel method of applying Möbius transformations to augment input images during training. Möbius transformations are bijective conformal maps that generalize image translation to operate over complex inversion in pixel space. As a result, Möbius transformations can operate on the sample level and preserve data labels. We show that the inclusion of Möbius transformations during training enables improved generalization over prior sample-level data augmentation techniques such as cutout and standard crop-and-flip transformations, most notably in low data regimes.

Mathematical and computational models for pain: a systematic review

OBJECTIVE

There is no single prevailing theory of pain that explains its origin, qualities, and alleviation. Although many studies have investigated various molecular targets for pain management, few have attempted to examine the etiology or working mechanisms of pain through mathematical or computational model development. In this systematic review, we identified and classified mathematical and computational models for characterizing pain.

METHODS

The databases queried were Science Direct and PubMed, yielding 560 articles published prior to January 1st, 2020. After screening for inclusion of mathematical or computational models of pain, 31 articles were deemed relevant.

RESULTS

Most of the reviewed articles utilized classification algorithms to categorize pain and no-pain conditions. We found the literature heavily focused on the application of existing models or machine learning algorithms to identify the presence or absence of pain, rather than to explore features of pain that may be used for diagnostics and treatment.

CONCLUSIONS

Although understudied, the development of mathematical models may augment the current understanding of pain by providing directions for testable hypotheses of its underlying mechanisms. Additional focus is needed on developing models that seek to understand the underlying mechanisms of pain, as this could potentially lead to major breakthroughs in its treatment.

Optimization of additive chemotherapy combinations for an in vitro cell cycle model with constant drug exposures

Proliferation of an in vitro population of cancer cells is described by a linear cell cycle model with n states, subject to provocation with m chemotherapeutic compounds. Minimization of a linear combination of constant drug exposures is considered, with stability of the system used as a constraint to ensure a stable or shrinking cell population. The main result concerns the identification of redundant compounds, and an explicit solution formula for the case where all exposures are nonzero. The orthogonal case, where each drug acts on a single and different stage of the cell cycle, leads to a version of the classic inequality between the arithmetic and geometric means. Moreover, it is shown how the general case can be solved by converting it to the orthogonal case using a linear invertible transformation. The results are illustrated with two examples corresponding to combination treatment with two and three compounds, respectively.

Quantification of true lumen helical morphology and chirality in type B aortic dissections

Chirality is a fundamental property in many biological systems. Motivated by previous observations of helical aortic blood flow, aortic tissue fibers, and propagation of aortic dissections, we introduce methods to characterize helical morphology of aortic dissections. After validation on computer-generated phantoms, the methods were applied to patients with type B dissection. For this cohort, there was a distinct bimodal distribution of helical propagation of the dissection with either achiral or exclusively right-handed chirality, with no intermediate cases or left-handed cases. This clear grouping indicates that dissection propagation favors these two modes, which is potentially due to the right-handedness of helical aortic blood flow and cell orientation. The characterization of dissection chirality and quantification of helical morphology advances our understanding of dissection pathology and lays a foundation for applications in clinical research and treatment practice. For example, the chirality and magnitude of helical metrics of dissections may indicate risk of dissection progression, help define treatment and surveillance strategies, and enable development of novel devices that account for various helical morphologies.NEW & NOTEWORTHY A novel definition of helical propagation of type B aortic dissections reveals a distinct bimodality, with the true lumen being either achiral (nonhelical) or exclusively right-handed. This right-handed chirality is consistent with anatomic and physiological phenomena such as right-handed twist during left ventricle contraction, helical blood flow, and tissue fiber direction. The helical character of aortic dissections may be useful for pathology research, diagnostics, treatment selection, therapeutic durability prediction, and aortic device design.

New Conceptual Toxicokinetic Model to Assess Synergistic Mixture Effects between the Aromatic Hydrocarbon β-Naphthoflavone and the Azole Nocodazole on the CYP1A Biomarker in a Fish Cell Line

Toxicokinetic interactions with catabolic cytochrome P450 (CYP) enzymes can inhibit chemical elimination pathways and cause synergistic mixture effects. We have created a mathematical bottom-up model for a synergistic mixture effect where we fit a multidimensional function to a given data set using an auxiliary nonadditive approach. The toxicokinetic model is based on the data from a previous study on a fish cell line, where the CYP1A enzyme activity was measured over time after exposure to various combinations of the aromatic hydrocarbon β-naphthoflavone and the azole nocodazole. To describe the toxicokinetic mechanism in this pathway and how that affects the CYP1A biomarker, the model uses ordinary differential equations. Local sensitivity and identifiability analyses revealed that all the 10 parameters estimated in the model were identified uniquely while fitting the model to the data for measuring the CYP1A enzyme activity. The model has a good prediction power and is a promising tool to test the synergistic toxicokinetic interactions between different chemicals.

Side Reactions Do Not Completely Disrupt Linear Self-Replicating Chemical Reaction Systems

A crucial question within the fields of origins of life and metabolic networks is whether or not a self-replicating chemical reaction system is able to persist in the presence of side reactions. Due to the strong nonlinear effects involved in such systems, they are often difficult to study analytically. There are however certain conditions that allow for a wide range of these reaction systems to be well described by a set of linear ordinary differential equations. In this article, we elucidate these conditions and present a method to construct and solve such equations. For those linear self-replicating systems, we quantitatively find that the growth rate of the system is simply proportional to the sum of all the rate constants of the reactions that constitute the system (but is nontrivially determined by the relative values). We also give quantitative descriptions of how strongly side reactions need to be coupled with the system in order to completely disrupt the system.

A developmentally descriptive method for quantifying shape in gastropod shells

The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods.

Automated Quantification of Diseased Thoracic Aortic Longitudinal Centerline and Surface Curvatures

Precise description of vascular morphometry is crucial to support medical device manufacturers and clinicians for improving device development and interventional outcomes. A compact and intuitive method is presented to automatically characterize the surface geometry of tubular anatomic structures and quantify surface curvatures starting from generic stereolithographic (STL) surfaces. The method was validated with software phantoms and used to quantify the longitudinal surface curvatures of 37 human thoracic aortas with aneurysm or dissection. The quantification of surface curvatures showed good agreement with analytic solutions from the software phantoms, and demonstrated better agreement as compared to estimation methods using only centerline geometry and cross-sectional radii. For the human thoracic aortas, longitudinal inner surface curvature was significantly higher than centerline curvature (0.33 ± 0.06 versus 0.16 ± 0.02 cm−1 for mean; 1.38 ± 0.48 versus 0.45 ± 0.11 cm−1 for peak; both p &lt; 0.001). These findings show the importance of quantifying surface curvatures in order to better describe the geometry and biomechanical behavior of the thoracic aorta, which can assist in treatment planning and supplying device manufactures with more precise boundary conditions for mechanical evaluation.

Dissuasive effect, information provision, and consumer reactions to the term 'Biotechnology': The case of reproductive interventions in farmed fish

Biotechnology can provide innovative and efficient tools to support sustainable development of aquaculture. It is generally accepted that use of the term 'genetically modified' causes controversy and conflict among consumers, but little is known about how using the term 'biotechnology' as a salient feature on product packaging affects consumer preferences. In an online discrete choice experiment consisting of two treatments, a set of 1005 randomly chosen Swedish consumers were surveyed about use of hormone and triploidization sterilization techniques for salmonids. The information given to the treatment group included an additional sentence stating that the triploidization technique is an application of biotechnology, while the control group received the same text but without reference to biotechnology. Analysis using a hierarchical Bayes approach revealed significant consumer reactions to the term biotechnology. When the term was included in information, variation in consumer willingness-to-pay (WTP) estimates increased significantly. Moreover, some participants were dissuaded towards an option guaranteeing no biotechnological intervention in production of fish. These results have multiple implications for research and for the food industry. For research, they indicate the importance of examining the distribution of variation in WTP estimates for more complete characterization of the effects of information on consumer behavior. For the food industry, they show that associating food with biotechnology creates more variability in demand. Initiatives should be introduced to reduce the confusion associated with the term biotechnology among consumers.

Haematological and intestinal health parameters of rainbow trout are influenced by dietary live yeast and increased water temperature

Live yeast may be a sustainable protein source in salmonid diets while exhibiting a probiotic effect to counteract environmental stressors, such as increased water temperature that is being exacerbated by climate change. The objective of this study was to evaluate the effects of feeding a high dietary inclusion of live yeast and increased water temperature on growth, haematological and intestinal physiology of rainbow trout. For six weeks, 129 g fish in 16 tanks (n = 4) were fed either a diet based on fishmeal or based on live yeast (214 g kg^-1 of diet or 7.6 log CFU g^-1 of Saccharomyces cerevisiae) that replaced 40% of fishmeal protein while fish were reared in water temperatures of either 11 °C (cold) or 18 °C (warm). Fish weights, caudal blood and proximal and distal intestines were collected and analysed. Fish fed live yeast resulted in reduced growth (SGR and WG) and higher FCR, while growth in cold and warm water was similar despite differences in TGC. However, increased mortality, plasma cortisol, and intestinal oedema and villous damage indicated fish reared in warm water were subjected to chronic stress. Temperature had a significant effect on haematocrit and red blood cell counts that resulted in significantly higher haemoglobin levels in fish kept in warm water attributed to an elevated oxygen demand. In the proximal intestine, increased temperature resulted in reduced expression of pro-inflammatory cytokines, e.g. TNFα and IL8, that were further reduced in fish fed live yeast. In addition, feeding live yeast reduced gene expression of CLD6 involved in gut barrier function, which suggests that the level of yeast was too high and masked any beneficial effects on fish health. In conclusion, feeding a high inclusion of live yeast reduced fish growth and expression of intestinal genes, while increasing the temperature from 11 to 18 °C subjected fish to chronic stress that restricted growth, suppressed innate immunity and induced intestinal damage. Replacing 40% of fishmeal protein with live yeast did not counteract negative effects caused by increased temperature, thus alternative strategies need to be explored and implemented to protect the growth and health of rainbow trout from seasonal and long-term rises in water temperature.

Exploring the Arctic Charr Intestinal Glycome: Evidence of Increased N-Glycolylneuraminic Acid Levels and Changed Host-Pathogen Interactions in Response to Inflammation

Disease outbreaks are a limiting factor for the sustainable development of the aquaculture industry. The intestinal tract is covered by a mucus layer mainly comprised by highly glycosylated proteins called mucins. Mucins regulate pathogen adhesion, growth, and virulence, and the glycans are vital for these functions. We analyzed intestinal mucin O-glycans on mucins from control and full-fat extruded soy-bean-fed (known to cause enteritis) Arctic charr using liquid chromatography-tandem mass spectrometry. In total, 56 glycans were identified on Arctic charr intestinal mucins, with a high prevalence of core-5-type and sialylated O-glycans. Disialic-acid-epitope-containing structures including NeuAcα2,8NeuAc, NeuAc(Gc)α2,8NeuGc(Ac), and NeuGcα2,8NeuGc were the hallmark of Arctic charr intestinal mucin glycosylation. Arctic charr fed with soy bean meal diet had lower (i) number of structures detected, (ii) interindividual variation, and (iii) N-glycolylneuraminic-acid-containing glycans compared with control Arctic charr. Furthermore, Aeromonas salmonicida grew less in response to mucins from inflamed Arctic charr than from the control group. The Arctic charr glycan repertoire differed from that of Atlantic salmon. In conclusion, the loss of N-glycolylneuraminic acid may be a biomarker for inflammation in Arctic char, and inflammation-induced glycosylation changes affect host-pathogen interactions.

Lactobacillus reuteri strains protect epithelial barrier integrity of IPEC-J2 monolayers from the detrimental effect of enterotoxigenic Escherichia coli

Lactobacillus reuteri is an inhabitant of the gastrointestinal (GI) tract of mammals and birds and several strains of this species are known to be effective probiotics. The mechanisms by which L. reuteri confers its health‐promoting effects are far from being fully understood, but protection of the mucosal barrier is thought to be important. Leaky gut is a state of abnormal intestinal permeability with implications for the pathophysiology of various gastrointestinal disorders. Enterotoxigenic Escherichia coli (ETEC) can invade the intestinal mucosa and induce changes in barrier function by producing enterotoxin or by direct invasion of the intestinal epithelium. Our hypothesis was that L. reuteri can protect the mucosal barrier, and the goal of the study was to challenge this hypothesis by monitoring the protective effect of L. reuteri strains on epithelial dysfunction caused by ETEC. Using an infection model based on the porcine intestinal cell line IPEC‐J2, it was demonstrated that pretreatment of the cells with human‐derived L. reuteri strains (ATCC PTA 6475, DSM 17938 and 1563F) and a rat strain (R2LC) reduced the detrimental effect of ETEC in a dose‐dependent manner, as monitored by permeability of FITC‐dextran and transepithelial electrical resistance (TEER). Moreover, the results revealed that ETEC upregulated proinflammatory cytokines IL‐6 and TNFα and decreased expression of the shorter isoform of ZO‐1 (187 kDa) and E‐cadherin. In contrast, pretreatment with L. reuteri DSM 17938 and 1563F downregulated expression of IL‐6 and TNFα, and led to an increase in production of the longer isoform of ZO‐1 (195 kDa) and maintained E‐cadherin expression. Interestingly, expression of ZO‐1 (187 kDa) was preserved only when the infected cells were pretreated with strain 1563F. These findings demonstrate that L. reuteri strains exert a protective effect against ETEC‐induced mucosal integrity disruption.

Good-bye slippage - a new fusion to tackle bandage slippage on the foot

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A new stocking compression system with a low well-defined resting pressure and a high working pressure

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Dietary live yeast and increased water temperature influence the gut microbiota of rainbow trout

AIMS

The objective was to determine the effects of dietary substitution of fishmeal (FM) with live yeast and increasing water temperature on the diversity and composition of gut microbiota in rainbow trout.

METHODS AND RESULTS

Fish were fed either FM or yeast (Saccharomyces cerevisiae) and reared in water temperatures of either 11°C (cold) or 18°C (warm) for 6 weeks. Luminal content and mucosa were collected from the distal gut and the load, diversity and species abundance of yeast and bacteria were analysed using agar plating, MALDI-TOF and rRNA gene amplicon sequencing. Yeast in the gut of fish fed FM were represented by S. cerevisiae, Rhodotorula spp. and Debaryomyces hansenii, while fish fed yeast contained 4-5 log higher CFU per g of yeast that were entirely represented by S. cerevisiae. For gut bacteria, sequencing of 16S rRNA gene amplicons using Illumina MiSeq showed lower bacterial diversity and abundance of lactic acid bacteria, especially Lactobacillus, in fish reared in warm rather than cold water. Fish fed yeast had similar bacterial diversity and lower abundance of Leuconostocaceae and Photobacterium compared with fish fed FM.

CONCLUSIONS

Feeding live yeast mainly increased yeast load in the gut, while increased water temperature significantly altered the gut microbiota of rainbow trout in terms of bacterial diversity and abundance.

SIGNIFICANCE AND IMPACT OF THE STUDY

Live yeast can replace 40% of FM without disrupting bacteria communities in the gut of rainbow trout, while increased water temperature due to seasonal fluctuations and/or climate change may result in a gut dysbiosis that may jeopardize the health of farmed fish.

A Lagrangian cylindrical coordinate system for characterizing dynamic surface geometry of tubular anatomic structures

Vascular morphology characterization is useful for disease diagnosis, risk stratification, treatment planning, and prediction of treatment durability. To quantify the dynamic surface geometry of tubular-shaped anatomic structures, we propose a simple, rigorous Lagrangian cylindrical coordinate system to monitor well-defined surface points. Specifically, the proposed system enables quantification of surface curvature and cross-sectional eccentricity. Using idealized software phantom examples, we validate the method's ability to accurately quantify longitudinal and circumferential surface curvature, as well as eccentricity and orientation of eccentricity. We then apply the method to several medical imaging data sets of human vascular structures to exemplify the utility of this coordinate system for analyzing morphology and dynamic geometric changes in blood vessels throughout the body. Graphical abstract Pointwise longitudinal curvature of a thoracic aortic endograft surface for systole and diastole, with their absolute difference.

Impact of anticipation in dynamical systems

Many animals, including humans, have predictive capabilities and, presumably, base their behavioral decisions-at least partially-upon an anticipated state of their environment. We explore a minimal version of this idea in the context of particles that interact according to a pairwise potential. Anticipation enters the picture by calculating the interparticle forces from linear extrapolations of the particle positions some time τ in the future. Simulations show that for intermediate values of τ, compared to a transient time scale defined by the potential and the initial conditions, the particles form rotating clusters in which the particles are arranged in a hexagonal pattern. Analysis of the system shows that anticipation induces energy dissipation and we show that the kinetic energy asymptotically decays as 1/t. Furthermore, we show that the angular momentum is not necessarily conserved for τ>0, and that asymmetries in the initial condition therefore can cause rotational movement. These results suggest that anticipation could play an important role in collective behavior, since it may induce pattern formation and stabilizes the dynamics of the system.

Effects of dietary yeast inclusion and acute stress on post-prandial whole blood profiles of dorsal aorta-cannulated rainbow trout

Yeast is a potential alternative to fish meal in diets for farmed fish, yet replacing more than 50 % of fish meal results in reduced fish growth. In a 4-week experiment, 15 rainbow trout (Oncorhynchus mykiss) were cannulated and fed three diets each week: 30 % fish meal as a control (FM); 60 % replacement of fish meal protein, on a digestible basis, with Saccharomyces cerevisiae (SC); and 60 % replacement with Wickerhamomyces anomalus and S. cerevisiae mix (WA). Blood was collected at 0, 3, 6, 12 and 24 h after feeding. In the final week, fish were exposed to a 1-min netting stressor to evaluate possible diet-stress interactions. Significant increases in pH, TCO₂, HCO₃ and base excess were found after fish were fed the SC and WA diets compared with FM, which elevated blood alkaline tides. Yeast ingredients had lower buffering capacity and ash content than fish meal, which explained the increase in alkaline tides. In addition, fish fed the WA diet had significantly reduced erythrocyte area and fish fed SC and WA diets had increased mean corpuscular haemoglobin levels, indicating haemolytic anaemia. Higher levels of nucleic acid in yeast-based diets and potentially higher production of reactive oxygen species were suspected of damaging haemoglobin, which require replacement by smaller immature erythrocytes. Acute stress caused the expected rise in cortisol and glucose levels, but no interaction with diet was found. These results show that replacing 60 % of fish meal protein with yeasts can induce haemolytic anaemia in rainbow trout, which may limit yeast inclusion in diets for farmed fish.

An innovative compression system providing low, sustained resting pressure and high, efficient working pressure

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Estimating the probability of coexistence in cross-feeding communities

The dynamics of many microbial ecosystems are driven by cross-feeding interactions, in which metabolites excreted by some species are metabolised further by others. The population dynamics of such ecosystems are governed by frequency-dependent selection, which allows for stable coexistence of two or more species. We have analysed a model of cross-feeding based on the replicator equation, with the aim of establishing criteria for coexistence in ecosystems containing three species, given the information of the three species' ability to coexist in their three separate pairs, i.e. the long term dynamics in the three two-species component systems. The triple-system is studied statistically and the probability of coexistence in the species triplet is computed for two models of species interactions. The interaction parameters are modelled either as stochastically independent or organised in a hierarchy where any derived metabolite carries less energy than previous nutrients in the metabolic chain. We differentiate between different modes of coexistence with respect to the pair-wise dynamics of the species, and find that the probability of coexistence is close to 12 for triplet systems with three pair-wise coexistent pairs and for the so-called intransitive systems. Systems with two and one pair-wise coexistent pairs are more likely to exist for random interaction parameters, but are on the other hand much less likely to exhibit triplet coexistence. Hence we conclude that certain species triplets are, from a statistical point of view, rare, but if allowed to interact are likely to coexist. This knowledge might be helpful when constructing synthetic microbial communities for industrial purposes.

Cadmium and mercury exposure over time in Swedish children

PURPOSE

Knowledge about changes in exposure to toxic metals over time remains very sparse, in particular for children, the most vulnerable group. Here, we assessed whether a reduction in environmental pollution with cadmium (Cd) and mercury (Hg) caused a change in exposure over time. In total, 1257 children (age 4-9) in two towns in Sweden were sampled once in 1986-2013. Blood concentrations of Cd (b-Cd; n=1120) and Hg (b-Hg; n=560) were determined.

RESULTS

The median b-Cd was 0.10 (geometric mean 0.10; range 0.010-0.61) μg/L and b-Hg was 0.91 (geometric mean 0.83; range 0.021-8.2) μg/L. Children living close to a smelter had higher b-Cd and b-Hg than those in urban and rural areas. There was no sex difference in b-Cd or b-Hg, and b-Cd and b-Hg showed no significant accumulation by age. b-Cd decreased only slightly (0.7% per year, p<0.001) over the study period. In contrast, b-Hg did show a clear decrease over the study period (3% per year, p<0.001).

CONCLUSIONS

The exposure to Cd was very low but still might increase the risk of disease later in life. Moreover, b-Cd only showed a minor decrease, indicating that Cd pollution should be further restricted. b-Hg was relatively low and decreasing, probably because of reduced use of dental amalgam and lower Hg intake from fish. The b-Cd and b-Hg levels decreased much less than the levels of lead in the blood as previously found in the same children.

Strategies for structuring interdisciplinary education in Systems Biology: an European perspective

Systems Biology is an approach to biology and medicine that has the potential to lead to a better understanding of how biological properties emerge from the interaction of genes, proteins, molecules, cells and organisms. The approach aims at elucidating how these interactions govern biological function by employing experimental data, mathematical models and computational simulations. As Systems Biology is inherently multidisciplinary, education within this field meets numerous hurdles including departmental barriers, availability of all required expertise locally, appropriate teaching material and example curricula. As university education at the Bachelor's level is traditionally built upon disciplinary degrees, we believe that the most effective way to implement education in Systems Biology would be at the Master's level, as it offers a more flexible framework. Our team of experts and active performers of Systems Biology education suggest here (i) a definition of the skills that students should acquire within a Master's programme in Systems Biology, (ii) a possible basic educational curriculum with flexibility to adjust to different application areas and local research strengths, (iii) a description of possible career paths for students who undergo such an education, (iv) conditions that should improve the recruitment of students to such programmes and (v) mechanisms for collaboration and excellence spreading among education professionals. With the growing interest of industry in applying Systems Biology approaches in their fields, a concerted action between academia and industry is needed to build this expertise. Here we present a reflection of the European situation and expertise, where most of the challenges we discuss are universal, anticipating that our suggestions will be useful internationally. We believe that one of the overriding goals of any Systems Biology education should be a student's ability to phrase and communicate research questions in such a manner that they can be solved by the integration of experiments and modelling, as well as to communicate and collaborate productively across different experimental and theoretical disciplines in research and development.

Effects of Lactobacillus johnsonii and Lactobacillus reuteri on gut barrier function and heat shock proteins in intestinal porcine epithelial cells

Heat shock proteins (HSPs) are a set of highly conserved proteins that can serve as intestinal gate keepers in gut homeostasis. Here, effects of a probiotic, Lactobacillus rhamnosus GG (LGG), and two novel porcine isolates, Lactobacillus johnsonii strain P47-HY and Lactobacillus reuteri strain P43-HUV, on cytoprotective HSP expression and gut barrier function, were investigated in a porcine IPEC-J2 intestinal epithelial cell line model. The IPEC-J2 cells polarized on a permeable filter exhibited villus-like cell phenotype with development of apical microvilli. Western blot analysis detected HSP expression in IPEC-J2 and revealed that L. johnsonii and L. reuteri strains were able to significantly induce HSP27, despite high basal expression in IPEC-J2, whereas LGG did not. For HSP72, only the supernatant of L. reuteri induced the expression, which was comparable to the heat shock treatment, which indicated that HSP72 expression was more stimulus specific. The protective effect of lactobacilli was further studied in IPEC-J2 under an enterotoxigenic Escherichia coli (ETEC) challenge. ETEC caused intestinal barrier destruction, as reflected by loss of cell–cell contact, reduced IPEC-J2 cell viability and transepithelial electrical resistance, and disruption of tight junction protein zonula occludens-1. In contrast, the L. reuteri treatment substantially counteracted these detrimental effects and preserved the barrier function. L. johnsonii and LGG also achieved barrier protection, partly by directly inhibiting ETEC attachment. Together, the results indicate that specific strains of Lactobacillus can enhance gut barrier function through cytoprotective HSP induction and fortify the cell protection against ETEC challenge through tight junction protein modulation and direct interaction with pathogens.

Importance of plasticity and local adaptation for coping with changing salinity in coastal areas: a test case with barnacles in the Baltic Sea

Background

Salinity plays an important role in shaping coastal marine communities. Near-future climate predictions indicate that salinity will decrease in many shallow coastal areas due to increased precipitation; however, few studies have addressed this issue. The ability of ecosystems to cope with future changes will depend on species’ capacities to acclimatise or adapt to new environmental conditions. Here, we investigated the effects of a strong salinity gradient (the Baltic Sea system – Baltic, Kattegat, Skagerrak) on plasticity and adaptations in the euryhaline barnacle Balanus improvisus. We used a common-garden approach, where multiple batches of newly settled barnacles from each of three different geographical areas along the Skagerrak-Baltic salinity gradient were exposed to corresponding native salinities (6, 15 and 30 PSU), and phenotypic traits including mortality, growth, shell strength, condition index and reproductive maturity were recorded.

Results

We found that B. improvisus was highly euryhaline, but had highest growth and reproductive maturity at intermediate salinities. We also found that low salinity had negative effects on other fitness-related traits including initial growth and shell strength, although mortality was also lowest in low salinity. Overall, differences between populations in most measured traits were weak, indicating little local adaptation to salinity. Nonetheless, we observed some population-specific responses – notably that populations from high salinity grew stronger shells in their native salinity compared to the other populations, possibly indicating adaptation to differences in local predation pressure.

Conclusions

Our study shows that B. improvisus is an example of a true brackish-water species, and that plastic responses are more likely than evolutionary tracking in coping with future changes in coastal salinity.

Expression of heat shock proteins 27 and 72 correlates with specific commensal microbes in different regions of porcine gastrointestinal tract

The gastrointestinal (GI) tract of mammals is inhabited by trillions of microorganisms, resulting in exceedingly complex networking. The interaction between distinct bacterial species and the host immune system is essential in maintaining homeostasis in the gut ecosystem. For instance, the gut commensal microbiota dictates intestinal mucosa maturation and its abundant immune components, such as cytoprotective heat shock proteins (HSP). Here we examined physiological expression of HSP in the normal porcine GI tract and found it to be gut region- and cell type-specific in response to dietary components, microbes, and microbial metabolites to which the mucosa surface is exposed. Correlations between HSP72 expression and ileal Lactobacillus spp. and colonic clostridia species, and between HSP27 expression and uronic acid ingestion, were important interplays identified here. Thus this study provides novel insights into host-microbe interactions shaping the immune system that are modifiable by dietary regime.

Stochastic differential equations as a tool to regularize the parameter estimation problem for continuous time dynamical systems given discrete time measurements

In this paper we consider the problem of estimating parameters in ordinary differential equations given discrete time experimental data. The impact of going from an ordinary to a stochastic differential equation setting is investigated as a tool to overcome the problem of local minima in the objective function. Using two different models, it is demonstrated that by allowing noise in the underlying model itself, the objective functions to be minimized in the parameter estimation procedures are regularized in the sense that the number of local minima is reduced and better convergence is achieved. The advantage of using stochastic differential equations is that the actual states in the model are predicted from data and this will allow the prediction to stay close to data even when the parameters in the model is incorrect. The extended Kalman filter is used as a state estimator and sensitivity equations are provided to give an accurate calculation of the gradient of the objective function. The method is illustrated using in silico data from the FitzHugh-Nagumo model for excitable media and the Lotka-Volterra predator-prey system. The proposed method performs well on the models considered, and is able to regularize the objective function in both models. This leads to parameter estimation problems with fewer local minima which can be solved by efficient gradient-based methods.

Chicory (Cichorium intybus L.) and cereals differently affect gut development in broiler chickens and young pigs

Dietary fiber, resistant to host-mediated digestion in the small intestine due to lack of endogenous enzymes, impacts many facets of animal health and is associated with gut development especially in young monogastrics. Furthermore, it can be used as in-feed antibiotic alternative. Chicory (Cichorium intybus L.) forage with high content of pectin (uronic acids as building blocks) is a novel class of dietary fiber that is chemically different from cereal grains (with high content of arabinoxylans). In the present study, we investigated effects of dietary inclusion of chicory forage on digestibility, gut morphology and microbiota in broilers and young pigs. In the chicken experiment, 160 1-d old broiler chicks were fed 3 nutritionally balanced diets for 30 d including a cereal-based diet and 2 diets with part of the cereals substituted with 60 and 120 g/kg chicory forage (CF60 and CF120), whereas in the pig experiment, 18 seven-wk old Yorkshire pigs were fed 3 diets for 18 d including a cereal-based diet and 2 diets with 80 and 160 g/kg chicory forage inclusion (CF80 and CF160). Our results showed that young pigs were capable to utilize chicory forage well with higher total tract apparent digestibility (TTAD) of all fiber fractions, particularly uronic acid, compared with the control (P < 0.01). In contrast, a decreased TTAD of all fiber fractions was observed in chickens fed on diet CF120 (P < 0.05). Moreover, diet induced changes in gut morphology were observed in the large intestine of chickens. The alteration of cecal mucosal thickness was further positively correlated with TTAD of non-starch polysaccharides (NSP) and its constituent sugars (P < 0.05). In addition, in pigs, terminal restriction fragment length polymorphism (T-RFLP) analysis of intestinal microbiota revealed substantial dietary effects (cereal control diet vs. chicory forage inclusion) on the relative abundance of 2 dominant bacterial phylotypes (Prevotella sp. vs. Roseburia sp.) respectively (P < 0.05). In conclusion, our data showed that chicory forage (Cichorium intybus L.), a novel dietary fiber source in animal nutrition, have potential beneficial properties as fiber ingredient in diets for both pigs and chickens.

Cross-feeding dynamics described by a series expansion of the replicator equation

Understanding how ecosystems evolve and how they respond to external perturbations is critical if we are to predict the effects of human intervention. A particular class of ecosystems whose dynamics are poorly understood are those in which the species are related via cross-feeding. In these ecosystems the metabolic output of one species is being used as a nutrient or energy source by another species. In this paper we derive a mathematical description of cross-feeding dynamics based on the replicator equation. We show that under certain assumptions about the system (e.g., high flow of nutrients and time scale separation), the governing equations reduce to a second-order series expansion of the replicator equation. By analysing the case of two and three species we derive conditions for co-existence and show under which parameter conditions one can expect an increase in mean fitness. Finally, we discuss how the model can be parameterised from experimental data.

Expression of heat shock protein 27 in gut tissue of growing pigs fed diets without and with inclusion of chicory fiber

The physiological expression of cytoprotective heat shock protein 27 (Hsp27) in the gut was investigated in eighteen 7-wk-old pigs fed one of 3 fiber-rich diets for 18 d. The diets were a cereal-based control diet and a cereal-based diet with inclusion of either 80 g/kg chicory forage (CF80) or chicory root (CR80). Immunohistochemical staining showed that Hsp27 was expressed in all the samples from ileum and colon. The expression was most intensive in the apical intestinal epitheliums in close contact with luminal contents and lighter in crypt cells. The ileal Peyer's patches showed a strong expression of Hsp27, which was highly correlated with Hsp27 expression in the ileal epithelial cells (P = 0.003). The frequency of ileal Hsp27 expression with the most intensive staining was distributed higher in pigs fed chicory forage diet (CF80, 25%) followed by chicory root diet (CR80, 16.7%) and the control (11.1%). In proximal colon, the frequency of expression showed a similar pattern for the different diets. The intestinal microbiota profile was characterized with the intention to find correlations to heat shock protein (Hsp) expression in pig gastrointestinal (GI) tract and showed that the distal ileum and proximal colon encompass its own unique microbial profile. However, no significant relationship was found between gut microbiota diversity and Hsp27 expression. These indicate that Hsp27 expression in the porcine gut could be associated with specific dietary fiber components but not the overall microbiota diversity.

Inclusion of chicory (Cichorium intybus L.) in pigs' diets affects the intestinal microenvironment and the gut microbiota

The content and composition of prebiotic plant fiber in the diet is important in promoting gut-related health. This study investigated the effects of the dietary inclusion of chicory forage and roots on the intestinal microenvironment of pigs. Thirty-seven-week-old pigs were fed 1 of 5 diets for 18 days, including a cereal-based control diet and 4 diets with the inclusion of 80 and 160 g kg(-1) of body weight chicory forage (CF80 and CF160), 80 g kg(-1) chicory root (CR80), and a mix of 80 g kg(-1) forage and 80 g kg(-1) chicory root (CFR). The animals maintained good performance and health irrespective of diet. Bacterial community structure and diversity in ileal and colonic samples was assessed using terminal restriction fragment length polymorphism (T-RFLP), combined with cloning and sequencing. Samples clustered perfectly according to gut segment with a higher bacterial diversity in colon than ileum. Distal ileum was dominated by lactic acid bacteria (LAB), and the relative amount of this group was increased by the CF160 and CFR diets. The colonic bacterial community was dominated by butyrate-producing bacteria and Prevotella. The increased relative abundance of butyrate-producing bacteria in the colon was positively correlated with the molar proportion of acetic acid and furthermore linked to the chicory forage diets (CF80 and CF160). Diets including chicory roots (CR80 and CFR) were correlated with a higher colonic abundance of Megasphaera elsdenii. The fermentation products and pH in digesta responded to diet type and were correlated with shifts in the microbiota, showing that chicory influences the intestinal microenvironment of pigs.

Effect of space in the game "war of attrition"

Spatial dynamics has in many cases been invoked as a mechanism that can promote the evolution of coexistence and cooperation, although the precise conditions for this to occur have not yet been characterised. In an effort to address this question we have analyzed an alternative version of the theoretical game "war of attrition," which exhibits unusual behavior: The well-mixed system exhibits quasistationary coexistence and a relaxation time that scales exponentially with the system size, while the spatial system shows a relaxation time that is considerably smaller and scales with a power α≈1.4 of the system size. Further, the spatial system exhibits a first-order phase transition in the strategy distribution at a consolation prize of k≈1/3. Close to this point the relaxation time diverges with an exponent γ≈1.2. This analysis shows that the effect of space is highly dependent on the type of game considered.

Growth performance, digestibility, and gut development of broiler chickens on diets with inclusion of chicory (Cichorium intybus L.)

A total of 256 broiler chickens (1 d old) were used in a 32-d growth trial to study the effects of chicory (Cichorium intybus L.) forage and root inclusion on growth performance, digestibility, and gut development. The chicory forage originated from 2 harvests (June and September) and was included at 60 and 120 g/kg. The chicory root was included alone at 60 g/kg or together with chicory forage, from both harvests, in equal amounts (60 g/kg). The cereal-based control diet and 7 experimental diets were fed to each of 4 pens of chickens (8 chickens/pen). A higher BW gain and lower feed conversion ratio were found at 13 d of age in chickens fed the 60 g/kg chicory forage diet (P ≤ 0.05), whereas performance did not differ between the control and 60 g/kg chicory root diets. In contrast, a lower performance and digestibility of DM, organic matter, and AME as well as a thinner cecal mucosa layer were found for the 120 g/kg chicory forage diet (P ≤ 0.05). No diet effects on organ parameters or on pH of cecum digesta were detected. The soluble nonstarch polysaccharides fractions of chicory forage did not have any major negative effects on performance and gut development, and chicory forage from the September harvest was seen to have a higher nutritional value than that from the June harvest. Thus, results from the current study suggest that chicory forage is a potentially useful fiber-rich feed ingredient with high palatability for broiler chickens.

Exposure to cadmium and persistent organochlorine pollutants and its association with bone mineral density and markers of bone metabolism on postmenopausal women

Environmental contaminants such as cadmium and persistent organochlorine pollutants have been proposed as risk factors of osteoporosis, and women may be at an increased risk. To assess associations between exposure to cadmium and two different POPs (2,2',4,4',5,5'-hexachlorobiphenyl CB-153, 1,1-dichloro-2,2-bis(p-chlorophenyl)-ethylene p,p'-DDE), on one hand, and bone effects, on the other, in a population-based study among postmenopausal (60-70 years) Swedish women with biobanked blood samples. The study included 908 women and was designed to have a large contrast of bone mineral densities, measured with a single photon absorptiometry technique in the non-dominant forearm. Biochemical markers related to bone metabolism were analyzed in serum. Exposure assessment was based on cadmium concentrations in erythrocytes and serum concentrations of CB-153 and p,p'-DDE. Cadmium was negatively associated with bone mineral density and parathyroid hormone, positively with the marker of bone resorption. However, this association disappeared after adjustment for smoking. The major DDT metabolite (p,p'-DDE) was positively associated with bone mineral density, an association which remained after adjustment for confounders, but the effect was weak. There was no evidence that the estrogenic congener (CB-153) was associated with any of the bone markers. In conclusion, no convincing associations were observed between cadmium and POPs, on one hand, and bone metabolism markers and BMD, on the other.

Gene divergence and pathway duplication in the metabolic network of yeast and digital organisms

We have studied the metabolic gene-function network in yeast and digital organisms evolved in the artificial life platform Avida. The gene-function network is a bipartite network in which a link exists between a gene and a function (pathway) if that function depends on that gene, and can also be viewed as a decomposition of the more traditional functional gene networks, where two genes are linked if they share any function. We show that the gene-function network exhibits two distinct degree distributions: the gene degree distribution is scale-free while the pathway distribution is exponential. This is true for both yeast and digital organisms, which suggests that this is a general property of evolving systems, and we propose that the scale-free gene degree distribution is due to pathway duplication, i.e. the development of a new pathway where the original function is still retained. Pathway duplication would serve as preferential attachment for the genes, and the experiments with Avida revealed precisely this; genes involved in many pathways are more likely to increase their connectivity. Measuring the overlap between different pathways, in terms of the genes that constitute them, showed that pathway duplication also is a likely mechanism in yeast evolution. This analysis sheds new light on the evolution of genes and functionality, and suggests that function duplication could be an important mechanism in evolution.

Morphometric study on the characteristic external features of normal and abnormal human embryos

The embryonic period is characterized by organogenesis and accompanying dynamic changes in external features. The measurement of human embryos has been limited to whole body dimensions, such as crown-rump length. More detailed measurements would add quantitative information about these characteristic events and provide a better understanding of normal and abnormal embryonic development. In the present study, we defined axes, landmarks, and measurements for human embryos, and measured 250 externally normal human embryos at Carnegie stages 14-23 (6.5-29.3 mm in crown-rump length, approximately 5-8 weeks of estimated ovulation age) that were fixed in Bouin's solution and preserved in 10% formalin solution. The axes, landmarks, and measurements defined for human embryos are corresponding to those in human and primate fetuses. The whole body, head, face, and extremities were measured using a scale attached to a dissecting microscope. Axial length, head height plus ear-shoulder length plus trunk height, was designated as a new measurement of the whole body, which is comparable with crown-rump length. Approximate standards of these measurements were obtained. The ratios of some measurements to trunk height and between the different parts were also obtained, and several different developmental patterns were recognized. The reproducibility of each measurement was evaluated by measuring 50 specimens three times each at intervals of one or two months. As a pilot study for the application of the proposed measurements, 84 human embryos with external anomalies, including holoprosencephaly, anomalies of extremities, and pharyngeal arch anomalies, were measured using the same method, and a few tendencies characteristic to holoprosencephaly were noticed.

The emergence of overlapping scale-free genetic architecture in digital organisms

We have studied the evolution of genetic architecture in digital organisms and found that the gene overlap follows a scale-free distribution, which is commonly found in metabolic networks of many organisms. Our results show that the slope of the scale-free distribution depends on the mutation rate and that the gene development is driven by expansion of already existing genes, which is in direct correspondence to the preferential growth algorithm that gives rise to scale-free networks. To further validate our results we have constructed a simple model of gene development, which recapitulates the results from the evolutionary process and shows that the mutation rate affects the tendency of genes to cluster. In addition we could relate the slope of the scale-free distribution to the genetic complexity of the organisms and show that a high mutation rate gives rise to a more complex genetic architecture.