Anaerobic fungal communities differ along the horse digestive tract
Mura, Erica ; Edwards, Joan ; Kittelmann, Sandra ; Kaerger, Kerstin ; Voigt, Kerstin ; Mrázek, Jakub ; Moniello, Giuseppe ; Fliegerova, Katerina - \ 2019
Fungal Biology 123 (2019)3. - ISSN 1878-6146 - p. 240 - 246.
Anaerobic fungi - Diversity - Equine hindgut - ITS1 - Uncultured
Anaerobic fungi are potent fibre degrading microbes in the equine hindgut, yet our understanding of their diversity and community structure is limited to date. In this preliminary work, using a clone library approach we studied the diversity of anaerobic fungi along six segments of the horse hindgut: caecum, right ventral colon (RVC), left ventral colon (LVC), left dorsal colon (LDC), right dorsal colon (RDC) and rectum. Of the 647 ITS1 clones, 61.7 % were assigned to genus level groups that are so far without any cultured representatives, and 38.0 % were assigned to the cultivated genera Neocallimastix (35.1 %), Orpinomyces (2.3 %), and Anaeromyces (0.6 %). AL1 dominated the group of uncultured anaerobic fungi, particularly in the RVC (88 %) and LDC (97 %). Sequences from the LSU clone library analysis of the LDC, however, split into two distinct phylogenetic clusters with low sequence identity to Caecomyces sp. (94–96 %) and Liebetanzomyces sp. (92 %) respectively. Sequences belonging to cultured Neocallimastix spp. dominated in LVC (81 %) and rectum (75.5 %). Quantification of anaerobic fungi showed significantly higher concentrations in RVC and RDC compared to other segments, which influenced the interpretation of the changes in anaerobic fungal diversity along the horse hindgut. These preliminary findings require further investigation.
Towards globally customizable ecosystem service models
Martínez-López, Javier ; Bagstad, Kenneth J. ; Balbi, Stefano ; Magrach, Ainhoa ; Voigt, Brian ; Athanasiadis, Ioannis ; Pascual, Marta ; Willcock, Simon ; Villa, Ferdinando - \ 2019
Science of the Total Environment 650 (2019). - ISSN 0048-9697 - p. 2325 - 2336.
ARIES - Cloud-based modelling - Context-aware modelling - decision making - semantic modelling - spatial multi-criteria analysis
Scientists, stakeholders and decision makers face trade-offs between adopting simple or complex approaches when modeling ecosystem services (ES). Complex approaches may be time- and data-intensive, making them more challenging to implement and difficult to scale, but can produce more accurate and locally specific results. In contrast, simple approaches allow for faster assessments but may sacrifice accuracy and credibility. The ARtificial Intelligence for Ecosystem Services (ARIES) modeling platform has endeavored to provide a spectrum of simple to complex ES models that are readily accessible to a broad range of users. In this paper, we describe a series of five “Tier 1” ES models that users can run anywhere in the world with no user input, while offering the option to easily customize models with context-specific data and parameters. This approach enables rapid ES quantification, as models are automatically adapted to the application context. We provide examples of customized ES assessments at three locations on different continents and demonstrate the use of ARIES' spatial multi-criteria analysis module, which enables spatial prioritization of ES for different beneficiary groups. The models described here use publicly available global- and continental-scale data as defaults. Advanced users can modify data input requirements, model parameters or entire model structures to capitalize on high-resolution data and context-specific model formulations. Data and methods contributed by the research community become part of a growing knowledge base, enabling faster and better ES assessment for users worldwide. By engaging with the ES modeling community to further develop and customize these models based on user needs, spatiotemporal contexts, and scale(s) of analysis, we aim to cover the full arc from simple to complex assessments, minimizing the additional cost to the user when increased complexity and accuracy are needed.
|Pseudo-starvation driven energy expenditure negatively affects ovarian follicle development
Coleman, V. ; Meng, L. ; Teerds, K.J. ; Keijer, J. ; Bunschoten, J.E. ; Zhao, Y. ; Ost, M. ; Voigt, A. - \ 2018
Objective: Conditions of reduced energy availability negatively affect female fertility. We examined whether a change in whole body energy fluxes away from the ovary could affect follicular development, employing mice ectopically expressing uncoupling protein 1 in skeletal muscle (UCP1-TG). We especially addressed insulin-like growth factor 1 (IGF1), a growth factor playing an important role in the regulation of both substrate metabolism and female fertility. Methods: Female UCP1-TG and wild-type (WT) mice were killed at 12 weeks postpartum. Energy intake, expenditure, activity, body weight and length, and body composition were measured. Plasma insulin, glucose, leptin and IGF1 levels were analysed. Ovaries were serial sectioned and follicle and corpora lutea numbers were counted. IGF1 signalling was analysed by immunohistochemical staining for activation of insulin receptor substrate 1/2 (IRS1/2) and AKT. Results: UCP1-TG female mice had increased energy expenditure, reduced body size, maintained adiposity, and decreased IGF1 concentrations compared to their WT littermates. Preantral and antral follicle numbers were reduced by 40% and 60%, respectively, in UCP1-TG mice, compared to WT mice. Corpora lutea (CL) were absent in 40% of the ovaries of UCP1-TG mice. No difference in total and phospho-IRS2 immunostaining was observed between WT and UCP1-TG ovaries. Phospho-IRS1, phosho-AKT -Ser473 and -Thr308 immunostaining was present in granulosa cells of antral follicles in WT ovaries, but faint to absent in antral follicles of UCP1-TG mice.Conclusion: The reduction in circulating IGF1 levels due to ectopic expression of UCP1 leads to areduced activation of the IRS1-PI3/AKT pathway negatively affecting normal ovarian follicle development and ovulation.
Machine learning for ecosystem services
Willcock, Simon ; Martínez-López, Javier ; Hooftman, Danny A.P. ; Bagstad, Kenneth J. ; Balbi, Stefano ; Marzo, Alessia ; Prato, Carlo ; Sciandrello, Saverio ; Signorello, Giovanni ; Voigt, Brian ; Villa, Ferdinando ; Bullock, James M. ; Athanasiadis, Ioannis N. - \ 2018
Ecosystem Services 33 (2018)B. - ISSN 2212-0416 - p. 165 - 174.
ARIES - Artificial intelligence - Big data - Data driven modelling - Data science - Machine learning - Mapping - Modelling - Uncertainty, Weka
Recent developments in machine learning have expanded data-driven modelling (DDM) capabilities, allowing artificial intelligence to infer the behaviour of a system by computing and exploiting correlations between observed variables within it. Machine learning algorithms may enable the use of increasingly available ‘big data’ and assist applying ecosystem service models across scales, analysing and predicting the flows of these services to disaggregated beneficiaries. We use the Weka and ARIES software to produce two examples of DDM: firewood use in South Africa and biodiversity value in Sicily, respectively. Our South African example demonstrates that DDM (64–91% accuracy) can identify the areas where firewood use is within the top quartile with comparable accuracy as conventional modelling techniques (54–77% accuracy). The Sicilian example highlights how DDM can be made more accessible to decision makers, who show both capacity and willingness to engage with uncertainty information. Uncertainty estimates, produced as part of the DDM process, allow decision makers to determine what level of uncertainty is acceptable to them and to use their own expertise for potentially contentious decisions. We conclude that DDM has a clear role to play when modelling ecosystem services, helping produce interdisciplinary models and holistic solutions to complex socio-ecological issues.
A Pressure Test to Make 10 Molecules in 90 Days : External Evaluation of Methods to Engineer Biology
Casini, Arturo ; Chang, Fang Yuan ; Eluere, Raissa ; King, Andrew M. ; Young, Eric M. ; Dudley, Quentin M. ; Karim, Ashty ; Pratt, Katelin ; Bristol, Cassandra ; Forget, Anthony ; Ghodasara, Amar ; Warden-Rothman, Robert ; Gan, Rui ; Cristofaro, Alexander ; Borujeni, Amin Espah ; Ryu, Min Hyung ; Li, Jian ; Kwon, Yong Chan ; Wang, He ; Tatsis, Evangelos ; Rodriguez-Lopez, Carlos ; O'Connor, Sarah ; Medema, Marnix H. ; Fischbach, Michael A. ; Jewett, Michael C. ; Voigt, Christopher ; Gordon, D.B. - \ 2018
Journal of the American Chemical Society 140 (2018)12. - ISSN 0002-7863 - p. 4302 - 4316.
Centralized facilities for genetic engineering, or "biofoundries", offer the potential to design organisms to address emerging needs in medicine, agriculture, industry, and defense. The field has seen rapid advances in technology, but it is difficult to gauge current capabilities or identify gaps across projects. To this end, our foundry was assessed via a timed "pressure test", in which 3 months were given to build organisms to produce 10 molecules unknown to us in advance. By applying a diversity of new approaches, we produced the desired molecule or a closely related one for six out of 10 targets during the performance period and made advances toward production of the others as well. Specifically, we increased the titers of 1-hexadecanol, pyrrolnitrin, and pacidamycin D, found novel routes to the enediyne warhead underlying powerful antimicrobials, established a cell-free system for monoterpene production, produced an intermediate toward vincristine biosynthesis, and encoded 7802 individually retrievable pathways to 540 bisindoles in a DNA pool. Pathways to tetrahydrofuran and barbamide were designed and constructed, but toxicity or analytical tools inhibited further progress. In sum, we constructed 1.2 Mb DNA, built 215 strains spanning five species (Saccharomyces cerevisiae, Escherichia coli, Streptomyces albidoflavus, Streptomyces coelicolor, and Streptomyces albovinaceus), established two cell-free systems, and performed 690 assays developed in-house for the molecules.
|Future research directions to reconcile wind turbine - wildlife interactions
May, R. ; Gill, A.B. ; Koppel, Johann ; Langston, R.H.W. ; Reichenbach, Marc ; Scheidat, M. ; Smallwood, Shawn ; Voigt, C. ; Hueppop, O. ; Portman, Michelle - \ 2017
In: Wind Energy and Wildlife Interactions. - Springer International Publishing - ISBN 9783319512709 - p. 255 - 276.
Future research directions - impacts of wind farms - wildlife - animal movement decisions - mitigation hierarchy
Concurrent with the development of wind energy, research activity on wind energy generation and wildlife has evolved significantly during the last decade. This chapter presents an overview of remaining key knowledge gaps, consequent future research directions and their significance for management and planning for wind energy generation. The impacts of wind farms on wildlife are generally site-, species- and season-specific and related management strategies and practices may differ considerably between countries. These differences acknowledge the need to consider potential wildlife impacts for each wind farm project. Still, the ecological mechanisms guiding species’ responses and potential vulnerability to wind farms can be expected to be fundamental in nature. A more cohesive understanding of the causes, patterns, mechanisms, and consequences of animal movement decisions will thereby facilitate successful mitigation of impacts. This requires planning approaches that implement the mitigation hierarchy effectively to reduce risks to species of concern. At larger geographical scales, population-level and cumulative impacts of multiple wind farms (and other anthropogenic activity) need to be addressed. This requires longitudinal and multiple-site studies to identify species-specific traits that influence risk of mortality, notably from collision with wind turbines, disturbance or barrier effects. In addition, appropriate pre- and post-construction monitoring techniques must be utilized. Predictive modelling to forecast risk, while tackling spatio-temporal variability, can guide the mitigation of wildlife impacts at wind farms.
Linking demand and supply factors in identifying cultural ecosystem services of urban green infrastructures : A review of European studies
Hegetschweiler, K.T. ; Vries, Sjerp de; Arnberger, Arne ; Bell, Simon ; Brennan, Michael ; Siter, Nathan ; Olafsson, Anton Stahl ; Voigt, Annette ; Hunziker, Marcel - \ 2017
Urban Forestry and Urban Greening 21 (2017). - ISSN 1618-8667 - p. 48 - 59.
Factors influencing well-being benefits - Linkage of social and physical data - Spatially explicit - Urban forestry - Urban green space
Urban green infrastructure provides a number of cultural ecosystem services that are greatly appreciated by the public. In order to benefit from these services, actual contact with the respective ecosystem is often required. Furthermore, the type of services offered depend on the physical characteristics of the ecosystem. We conducted a review of publications dealing with demand or social factors such as user needs, preferences and values as well as spatially explicit supply or physical factors such as amount of green space, (bio)diversity, recreational infrastructure, etc. and linking demand and supply factors together. The aim was to provide an overview of this highly interdisciplinary research, to describe how these linkages are being made and to identify which factors significantly influence dependent variables such as levels of use, activities or health and well-being benefits. Commonly used methods were the combination of questionnaires with either on-site visual recording of elements or GIS data. Links between social and physical data were usually established either by using statistical tools or by overlaying different thematic maps. Compared to the large number of variables assessed in most studies, the significant effects in the end were relatively few, not consistent across the studies and largely dependent on the context they were seen in. Studies focused on aesthetic and recreational services, while spiritual, educational and inspirational services were not considered when creating links to spatially explicit ecological structures. We conclude that an improvement and harmonization of methodologies, cross-country studies and an expansion of this line of research to a wider range of services and more user groups could help clarify relationships and thereby increase applicability for urban management and planning.
Muscle mitochondrial stress adaptation operates independently of endogenous FGF21 action
Ost, Mario ; Coleman, Verena ; Voigt, Anja ; Schothorst, E.M. van; Keipert, Susanne ; Stelt, Inge van der; Ringel, Sebastian ; Graja, Antonia ; Ambrosi, Thomas ; Kipp, A.P. ; Jastroch, Martin ; Schulz, T.J. ; Keijer, Jaap ; Klaus, Susanne - \ 2016
Molecular Metabolism 5 (2016)2. - ISSN 2212-8778 - p. 79 - 90.
Browning - FGF21 - GDF15 - Mitochondrial disease - Muscle mitohormesis - Myokine
Objective: Fibroblast growth factor 21 (FGF21) was recently discovered as stress-induced myokine during mitochondrial disease and proposed as key metabolic mediator of the integrated stress response (ISR) presumably causing systemic metabolic improvements. Curiously, the precise cell-non-autonomous and cell-autonomous relevance of endogenous FGF21 action remained poorly understood. Methods: We made use of the established UCP1 transgenic (TG) mouse, a model of metabolic perturbations made by a specific decrease in muscle mitochondrial efficiency through increased respiratory uncoupling and robust metabolic adaptation and muscle ISR-driven FGF21 induction. In a cross of TG with Fgf21-knockout (FGF21-/-) mice, we determined the functional role of FGF21 as a muscle stress-induced myokine under low and high fat feeding conditions. Results: Here we uncovered that FGF21 signaling is dispensable for metabolic improvements evoked by compromised mitochondrial function in skeletal muscle. Strikingly, genetic ablation of FGF21 fully counteracted the cell-non-autonomous metabolic remodeling and browning of subcutaneous white adipose tissue (WAT), together with the reduction of circulating triglycerides and cholesterol. Brown adipose tissue activity was similar in all groups. Remarkably, we found that FGF21 played a negligible role in muscle mitochondrial stress-related improved obesity resistance, glycemic control and hepatic lipid homeostasis. Furthermore, the protective cell-autonomous muscle mitohormesis and metabolic stress adaptation, including an increased muscle proteostasis via mitochondrial unfolded protein response (UPRmt) and amino acid biosynthetic pathways did not require the presence of FGF21. Conclusions: Here we demonstrate that although FGF21 drives WAT remodeling, the adaptive pseudo-starvation response under elevated muscle mitochondrial stress conditions operates independently of both WAT browning and FGF21 action. Thus, our findings challenge FGF21 as key metabolic mediator of the mitochondrial stress adaptation and powerful therapeutic target during muscle mitochondrial disease.
Chapter Four : Towards an Integration of Biodiversity–Ecosystem Functioning and Food Web Theory to Evaluate Relationships between Multiple Ecosystem Services
Hines, J. ; Putten, W.H. van der; Deyn, G.B. de; Wagg, C. ; Voigt, W. ; Mulder, C. ; Weisser, W.W. ; Engel, J. ; Melian, C. ; Scheu, S. ; Birkhofer, K. ; Ebeling, A. ; Scherber, C. ; Eisenhauer, N. - \ 2015
Advances in Ecological Research 53 (2015). - ISSN 0065-2504 - p. 161 - 199.
Ecosystem responses to changes in species diversity are often studied individually. However, changes in species diversity can simultaneously influence multiple interdependent ecosystem functions. Therefore, an important challenge is to determine when and how changes in species diversity that influence one function will also drive changes in other functions. By providing the underlying structure of species interactions, ecological networks can quantify connections between biodiversity and multiple ecosystem functions. Here, we review parallels in the conceptual development of biodiversity–ecosystem functioning (BEF) and food web theory (FWT) research. Subsequently, we evaluate three common principles that unite these two research areas by explaining the patterns, concentrations, and direction of the flux of nutrients and energy through the species in diverse interaction webs. We give examples of combined BEF–FWT approaches that can be used to identify vulnerable species and habitats and to evaluate links that drive trade-offs between multiple ecosystems functions. These combined approaches reflect promising trends towards better management of biodiversity in landscapes that provide essential ecosystem services supporting human well-being.
Network-based integration of molecular and physiological data elucidates regulatory mechanisms underlying adaptation to high-fat diet
Derous, D. ; Kelder, T. ; Schothorst, E.M. van; Erk, M. van; Voigt, A. ; Klaus, S. ; Keijer, J. ; Radonjic, M. - \ 2015
Genes & Nutrition 10 (2015)4. - ISSN 1555-8932
obesity - disease - expression - receptor
Health is influenced by interplay of molecular, physiological and environmental factors. To effectively maintain health and prevent disease, health-relevant relations need to be understood at multiple levels of biological complexity. Network-based methods provide a powerful platform for integration and mining of data and knowledge characterizing different aspects of health. Previously, we have reported physiological and gene expression changes associated with adaptation of murine epididymal white adipose tissue (eWAT) to 5 days and 12 weeks of high-fat diet (HFD) and low-fat diet feeding (Voigt et al. in Mol Nutr Food Res 57:1423–1434, 2013. doi:10.1002/mnfr.201200671). In the current study, we apply network analysis on this dataset to comprehensively characterize mechanisms driving the short- and long-term adaptation of eWAT to HFD across multiple levels of complexity. We built a three-layered interaction network comprising enriched biological processes, their transcriptional regulators and associated changes in physiological parameters. The multi-layered network model reveals that early eWAT adaptation to HFD feeding involves major changes at a molecular level, including activation of TGF-ß signalling pathway, immune and stress response and downregulation of mitochondrial functioning. Upon prolonged HFD intake, initial transcriptional response tails off, mitochondrial functioning is even further diminished, and in turn the relation between eWAT gene expression and physiological changes becomes more prominent. In particular, eWAT weight and total energy intake negatively correlate with cellular respiration process, revealing mitochondrial dysfunction as a hallmark of late eWAT adaptation to HFD. Apart from global understanding of the time-resolved adaptation to HFD, the multi-layered network model allows several novel mechanistic hypotheses to emerge: (1) early activation of TGF-ß signalling as a trigger for structural and morphological changes in mitochondrial organization in eWAT, (2) modulation of cellular respiration as an intervention strategy to effectively deal with excess dietary fat and (3) discovery of putative intervention targets, such those in pathways related to appetite control. In conclusion, the generated network model comprehensively characterizes eWAT adaptation to high-fat diet, spanning from global aspects to mechanistic details. Being open to further exploration by the research community, it provides a resource of health-relevant interactions ready to be used in a broad range of research applications.
The misconception of ecosystem disservices : How a catchy term may yield the wrong messages for science and society
Villa, Ferdinando ; Bagstad, Kenneth J. ; Voigt, Brian ; Johnson, Gary W. ; Athanasiadis, Ioannis N. ; Balbi, Stefano - \ 2014
Ecosystem Services 10 (2014). - ISSN 2212-0416 - p. 52 - 53.
Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
Schoch, C.L. ; Robbertse, B. ; Robert, V. ; Vu, D. ; Cardinali, G. ; Irinyi, L. ; Meyer, W. ; Nilsson, R.H. ; Hughes, K. ; Miller, A.N. ; Kirk, P.M. ; Abarenkov, K. ; Aime, M.C. ; Ariyawansa, H.A. ; Bidartondo, M. ; Boekhout, T. ; Buyck, B. ; Cai, Q. ; Chen, J. ; Crespo, A. ; Crous, P.W. ; Damm, U. ; Beer, Z.W. de; Dentinger, B.T.M. ; Divakar, P.K. ; Duenas, M. ; Feau, N. ; Fliegerova, K. ; Garcia, M.A. ; Ge, Z.W. ; Griffith, G.W. ; Groenewald, J.Z. ; Groenewald, M. ; Grube, M. ; Gryzenhout, M. ; Gueidan, C. ; Guo, L. ; Hambleton, S. ; Hamelin, R. ; Hansen, K. ; Hofstetter, V. ; Hong, S.B. ; Houbraken, J. ; Hyde, K.D. ; Inderbitzin, P. ; Johnston, P.A. ; Karunarathna, S.C. ; Koljalg, U. ; Kovacs, G.M. ; Kraichak, E. ; Krizsan, K. ; Kurtzman, C.P. ; Larsson, K.H. ; Leavitt, S. ; Letcher, P.M. ; Liimatainen, K. ; Liu, J.K. ; Lodge, D.J. ; Luangsa-ard, J.J. ; Lumbsch, H.T. ; Maharachchikumbura, S.S.N. ; Manamgoda, D. ; Martin, M.P. ; Minnis, A.M. ; Moncalvo, J.M. ; Mule, G. ; Nakasone, K.K. ; Niskanen, T. ; Olariaga, I. ; Papp, T. ; Petkovits, T. ; Pino-Bodas, R. ; Powell, M.J. ; Raja, H.A. ; Redecker, D. ; Sarmiento-Ramirez, J.M. ; Seifert, K.A. ; Shrestha, B. ; Stenroos, S. ; Stielow, B. ; Suh, S.O. ; Tanaka, K. ; Tedersoo, L. ; Telleria, M.T. ; Udayanga, D. ; Untereiner, W.A. ; Dieguez Uribeondo, J. ; Subbarao, K.V. ; Vagvolgyi, C. ; Visagie, C. ; Voigt, K. ; Walker, D.M. ; Weir, B.S. ; Weiss, M. ; Wijayawardene, N.N. ; Wingfield, M.J. ; Xu, J.P. ; Yang, Z.L. ; Zhang, N. ; Zhuang, W.Y. ; Federhen, S. - \ 2014
Database : the Journal of Biological Databases and Curation 2014 (2014). - ISSN 1758-0463 - 21 p.
internal transcribed spacer - arbuscular mycorrhizal fungi - ribosomal dna - interspecific hybridization - sequence analyses - species complex - identification - evolution - barcode - life
DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
Remarkably high surface visco-elasticity of adsorption layers of triterpenoid saponins
Golemanov, K. ; Tcholakova, S. ; Denkov, N. ; Pelan, E. ; Stoyanov, S.D. - \ 2013
Soft Matter 9 (2013)24. - ISSN 1744-683X - p. 5738 - 5752.
amplitude oscillatory shear - acacia-concinna saponins - steroidal saponins - beta-lactoglobulin - alkaline hydrolysate - sorbitan tristearate - interfacial rheology - tribulus-terrestris - plasma-cholesterol - panax-ginseng
Saponins are natural surfactants, with molecules composed of a hydrophobic steroid or triterpenoid group, and one or several hydrophilic oligosaccharide chains attached to this group. Saponins are used in cosmetic, food and pharmaceutical products, due to their excellent ability to stabilize emulsions and foams, and to solubilize bulky hydrophobic molecules. The foam and emulsion applications call for a better understanding of the surface properties of saponin adsorption layers, including their rheological properties. Of particular interest is the relation between the molecular structure of the various saponins and their surface properties. Here, we study a series of eight triterpenoid and three steroid saponins, with different numbers of oligosaccharide chains. The surface rheological properties of adsorption layers at the air-water interface, subjected to creep-recovery and oscillatory shear deformations, are investigated. The experiments showed that all steroid saponins exhibited no shear elasticity and had negligible surface viscosity. In contrast, most of the triterpenoid saponins showed complex visco-elastic behavior with extremely high elastic modulus (up to 1100 mN m(-1)) and viscosity (130 N s m(-1)). Although the magnitude of the surface modulus differed significantly for the various saponins, they all shared qualitatively similar rheological properties: (1) the elastic modulus was much higher than the viscous one. (2) Up to a certain critical value of surface stress, sC, the single master curve described the dependence of the creep compliance versus time. This rheological response was described well by the compound Voigt model. (3) On increasing the surface stress above sC, the compliance decreased with the applied stress, and eventually, all layers became purely viscous, indicating a loss in the layer structure, responsible for the elastic properties. The saponin extracts, showing the highest elastic moduli, were those of Escin, Tea saponins and Berry saponins, all containing predominantly monodesmosidic triterpenoid saponins. Similarly, a high surface modulus was measured for Ginsenosides extracts, containing bidesmosidic triterpenoid saponins with short sugar chains.
Short term, high fat-feeding induced changes in white adipose tissue gene expression are highly predictive for long term changes
Voigt, A. ; Agnew, K. ; Schothorst, E.M. van; Keijer, J. ; Klaus, S. - \ 2013
Molecular Nutrition & Food Research 57 (2013)8. - ISSN 1613-4125 - p. 1423 - 1434.
diet-induced obesity - epigallocatechin gallate - uncoupling protein-1 - insulin-resistance - mice - microarray - oxidation - efficiency - adipocytes - alpha
Scope - We aimed to evaluate the predictability of short-term (5 days) changes in epididymal white adipose tissue (eWAT) gene expression for long-term (12 weeks) changes induced by high-fat diet (HFD) feeding. Methods and results - Mice were fed semisynthetic diets containing 10 (low-fat diet) or 40 (HFD) energy% of fat. Global gene expression in eWAT was analyzed using microarrays and confirmed by quantitative PCR. As expected, HFD feeding resulted in increased body fat accumulation and reduced glucose tolerance after 12 weeks. A total of 4678 transcripts were significantly changed by HFD after 12 weeks and 973 after 5 days, with an overlap of 764 transcripts encoding 549 genes. Of these, 79% were downregulated and 21% were upregulated by HFD, all in the same direction and highly correlated (r2 = 0.90) between the time points. Pathway analysis showed downregulation of the main identified processes: lipid metabolism, carbohydrate metabolism, and oxidative phosphorylation. Mest (mesoderm-specific transcript) was highly upregulated, confirming its role as an early marker of fat cell expansion. Conclusion - The high predictive value of short-term gene expression changes for long-term effects of high fat feeding is a promising step to establish robust early biomarkers that could shorten animal trials to assess health-promoting food compounds.
Distributional (In)Congruence of Biodiversity-Ecosystem Functioning
Mulder, Christian ; Boit, Alice ; Mori, Shigeta ; Vonk, J.A. ; Dyer, Scott D. ; Faggiano, Leslie ; Geisen, Stefan ; González, Angélica L. ; Kaspari, Michael ; Lavorel, Sandra ; Marquet, Pablo A. ; Rossberg, Axel G. ; Sterner, Robert W. ; Voigt, Winfried ; Wall, Diana H. - \ 2012
In: Global Change in Multispecies Systems Part 1 / Jacob, U., Woodward, G., Academic Press Inc. (Advances in Ecological Research ) - ISBN 9780123969927 - p. 1 - 88.
The majority of research on biodiversity-ecosystem functioning in laboratories has concentrated on a few traits, but there is increasing evidence from the field that functional diversity controls ecosystem functioning more often than does species number. Given the importance of traits as predictors of niche complementarity and community structures, we (1) examine how the diversity sensu lato of forest trees, freshwater fishes and soil invertebrates might support ecosystem functioning and (2) discuss the relevance of productive biota for monophyletic assemblages (taxocenes).In terrestrial ecosystems, correlating traits to abiotic factors is complicated by the appropriate choice of body-size distributions. Angiosperm and gymnosperm trees, for example, show metabolic incongruences in their respiration rates despite their pronounced macroecological scaling. Scaling heterotrophic organisms within their monophyletic assemblages seems more difficult than scaling autotrophs: in contrast to the generally observed decline of mass-specific metabolic rates with body mass within metazoans, soil organisms such as protozoans show opposite mass-specific trends.At the community level, the resource demand of metazoans shapes multitrophic interactions. Hence, population densities and their food web relationships reflect functional diversity, but the influence of biodiversity on stability and ecosystem functioning remains less clear. We focused on fishes in 18 riverine food webs, where the ratio of primary versus secondary extinctions (hereafter, 'extinction partitioning') summarizes the responses of fish communities to primary species loss (deletions) and its consequences. Based on extinction partitioning, our high-diversity food webs were just as (or even more) vulnerable to extinctions as low-diversity food webs.Our analysis allows us to assess consequences of the relocation or removal of fish species and to help with decision-making in sustainable river management. The study highlights that the topology of food webs (and not simply taxonomic diversity) plays a greater role in stabilizing the food web and enhancing ecological services than is currently acknowledged.
Surface Shear Rheology of Saponin Adsorption Layers
Golemanov, K. ; Tcholakova, S. ; Denkov, N. ; Pelan, E. ; Stoyanov, S.D. - \ 2012
Langmuir 28 (2012)33. - ISSN 0743-7463 - p. 12071 - 12084.
physico-chemical properties - quillaja bark saponin - air-water-interface - thin liquid-films - plant saponins - chromatographic determination - phospholipid monolayers - yucca-schidigera - acid saponins - cholesterol
Saponins are a wide class of natural surfactants, with molecules containing a rigid hydrophobic group (triterpenoid or steroid), connected via glycoside bonds to hydrophilic oligosaccharide chains. These surfactants are very good foam stabiliziers and emulsifiers, and show a range of nontrivial biological activities. The molecular mechanisms behind these unusual properties are unknown, and, therefore, the saponins have attracted significant research interest in recent years. In our previous study (Stanimirova et al. Langmuir 2011, 27, 12486-12498), we showed that the triterpenoid saponins extracted from Quillaja saponaria plant (Quillaja saponins) formed adsorption layers with unusually high surface dilatational elasticity, 280 +/- 30 mN/m. In this Article, we study the shear rheological properties of the adsorption layers of Quillaja saponins. In addition, we study the surface shear rheological properties of Yucca saponins, which are of steroid type. The experimental results show that the adsorption layers of Yucca saponins exhibit purely viscous rheological response, even at the lowest shear stress applied, whereas the adsorption layers of Quillaja saponins behave like a viscoelastic two-dimensional body. For Quillaja saponins, a single master curve describes the data for the viscoelastic creep compliance versus deformation time, up to a certain critical value of the applied shear stress. Above this value, the layer compliance increases, and the adsorption layers eventually transform into viscous ones. The experimental creep recovery curves for the viscoelastic layers are fitted very well by compound Voigt rheological model. The obtained results are discussed from the viewpoint of the layer structure and the possible molecular mechanisms, governing the rheological response of the saponin adsorption layers.
BIOCLAIMS standard diet (BIOsd): a reference diet for nutritional physiology
Hoevenaars, F.P.M. ; Schothorst, E.M. van; Horakova, O. ; Voigt, A. ; Rossmeisl, M. ; Pico, C. ; Caimari, A. ; Kopecky, J. ; Klaus, S. ; Keijer, J. - \ 2012
Genes & Nutrition 7 (2012)3. - ISSN 1555-8932 - p. 399 - 404.
laboratory-animal diets - gene-expression - fat oxidation - mice - energy - rats - metabolism
Experimental replication is fundamental for practicing science. To reduce variability, it is essential to control sources of variation as much as possible. Diet is an important factor that can influence many processes and functional outcomes in studies performed with rodent models. This is especially true for, but not limited to, nutritional studies. To compare functional effects of different nutrients, it is important to use standardized, semi-purified diets. Here, we propose and describe a standard reference diet, the BIOCLAIMS standard diet. The diet is AIN-93 based, but further defined with dietary and experimental requirements taken into account that allow for experiments with bioactive food components and natural (non-expensive) labeling. This diet will be implemented by two European research consortia, Mitofood and BIOCLAIMS, to ensure inter-laboratory comparability.
In vitro fermentation of various carbohydrate-rich feed ingredients combined with chyme from pigs
Bauer, E. ; Wiliams, B.A. ; Voigt, C. ; Mosenthin, R. ; Verstegen, M.W.A. - \ 2010
Archives of Animal Nutrition 64 (2010)5. - ISSN 1745-039X - p. 394 - 411.
fatty-acid production - gastrointestinal-tract - microbial activity - diet composition - growing pigs - large-intestine - chicory roots - ileum chyme - boar taint - gut
Increased carbohydrate fermentation, compared with protein fermentation, could benefit gut health. In two in vitro experiments, the effect of carbohydrate-rich feed ingredients on fermentation characteristics of ileal chyme from pigs was assessed, using the cumulative gas production technique. Ingredients of the first experiment included gums, inulins, pectins, transgalacto-oligosaccharides, lactose and xylan. In the second experiment, a gum, pectin and transgalacto-oligosaccharides were added at different starting weights, to determine their effects on fermentation characteristics of chyme, in relation to differences in the carbohydrate concentrations. In comparison to fermentation of chyme alone, added carbohydrates led to higher total gas production (p <0.05), faster maximum rate of gas production (except for xylan) (p <0.05), and a decreased branched-chain fatty acids to straight chain fatty acids ratio (BCR) (p <0.05). In the second experiment, for all carbohydrate ingredients, the BCR decreased with increasing starting weights (p <0.05). If these supplemented dietary carbohydrates were to reach the terminal ileum of the living animal, carbohydrate fermentation in the large intestine could be stimulated, which is known to have beneficial effects on host health.
High-resolution methods for fluorescence retrieval from space
Mazzoni, M. ; Falorni, P. ; Verhoef, W. - \ 2010
Optics Express 18 (2010)15. - ISSN 1094-4087 - p. 15649 - 15663.
chlorophyll fluorescence - leaf - reflectance - vegetation - prospect - canopy
The retrieval from space of a very weak fluorescence signal was studied in the O2A and O2B oxygen atmospheric absorption bands. The accuracy of the method was tested for the retrieval of the chlorophyll fluorescence and reflectance terms contributing to the sensor signal. The radiance at the top of the atmosphere was simulated by means of a commercial radiative-transfer program at a high resolution (0.1 cm-1). A test data set was generated in order to simulate sun-induced chlorophyll fluorescence at the top of the canopy. Reflectance terms were spectrally modeled using cubic splines and fluorescence by means of the sum of two Voigt functions. Sensor radiance residual minimization was performed in the presence of a multiplicative noise, thus ensuring that the sensor simulations were realistic. The study, which focused on the possibility of retrieving fluorescence with an accuracy better than 10%, was performed for instrument resolutions ranging from about 0.4 cm-1 to 2 cm-1 in order to test the algorithm for the characteristics of existing and planned hyper-spectral sensors. The algorithm was also used to retrieve fluorescence in the single O2A band at the OCO and TANSO-FTS instrument spectral resolutions
The nature of a network concept: urban networks, from imagination to outcome
Hagens, J.E. - \ 2005
In: The dream of a GREATER Europe. Book of abstracts 2005 AESOP congress, Vienna, Austria, 13-17 July 2005. - Vienna (Austria) : Vienna Univ.of Technology/Osterreich.Kunst-und Kulturverlag - ISBN 9783854372783 - p. 80 - 81.