LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 346

Search options

  1. Article: Editorial: Isotopic labeling approaches for exploring plant metabolism dynamics.

    Dellero, Younès / Nikoloski, Zoran

    Frontiers in plant science

    2024  Volume 14, Page(s) 1356153

    Language English
    Publishing date 2024-01-08
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2023.1356153
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  2. Book ; Online: Engineering Synthetic Metabolons: From Metabolic Modelling to Rational Design of Biosynthetic Devices

    Voll, Lars M. / Nikoloski, Zoran

    2016  

    Abstract: The discipline of Synthetic Biology has recently emerged at the interface of biology and engineering. The definition of Synthetic Biology has been dynamic over time ever since, which exemplifies that the field is rapidly moving and comprises a broad ... ...

    Abstract The discipline of Synthetic Biology has recently emerged at the interface of biology and engineering. The definition of Synthetic Biology has been dynamic over time ever since, which exemplifies that the field is rapidly moving and comprises a broad range of research areas. In the frame of this Research Topic, we focus on Synthetic Biology approaches that aim at rearranging biological parts/ entities in order to generate novel biochemical functions with inherent metabolic activity. This Research Topic encompasses Pathway Engineering in living systems as well as the in vitro assembly of biomolecules into nano- and microscale bioreactors. Both, the engineering of metabolic pathways in vivo, as well as the conceptualization of bioreactors in vitro, require rational design of assembled synthetic pathways and depend on careful selection of individual biological functions and their optimization. Mathematical modelling has proven to be a powerful tool in predicting metabolic flux in living and artificial systems, although modelling approaches have to cope with a limitation in experimentally verified, reliable input variables. This Research Topic puts special emphasis on the vital role of modelling approaches for Synthetic Biology, i.e. the predictive power of mathematical simulations for (i) the manipulation of existing pathways and (ii) the establishment of novel pathways in vivo as well as (iii) the translation of model predictions into the design of synthetic assemblies
    Keywords Engineering (General). Civil engineering (General) ; Biotechnology
    Size 1 electronic resource (130 p.)
    Publisher Frontiers Media SA
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT020090641
    ISBN 9782889199211 ; 2889199215
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  3. Article: Genome-Scale Modeling Specifies the Metabolic Capabilities of

    Wendering, Philipp / Nikoloski, Zoran

    mSystems

    2022  Volume 7, Issue 1, Page(s) e0121621

    Abstract: Rhizophagus ... ...

    Abstract Rhizophagus irregularis
    Language English
    Publishing date 2022-01-25
    Publishing country United States
    Document type Journal Article
    ISSN 2379-5077
    ISSN 2379-5077
    DOI 10.1128/msystems.01216-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  4. Article ; Online: Self- and cross-attention accurately predicts metabolite-protein interactions.

    Campana, Pedro Alonso / Nikoloski, Zoran

    NAR genomics and bioinformatics

    2023  Volume 5, Issue 1, Page(s) lqad008

    Abstract: Metabolites regulate activity of proteins and thereby affect cellular processes in all organisms. Despite extensive efforts to catalogue the metabolite-protein interactome in different organisms by employing experimental and computational approaches, the ...

    Abstract Metabolites regulate activity of proteins and thereby affect cellular processes in all organisms. Despite extensive efforts to catalogue the metabolite-protein interactome in different organisms by employing experimental and computational approaches, the coverage of such interactions remains fragmented, particularly for eukaryotes. Here, we make use of two most comprehensive collections, BioSnap and STITCH, of metabolite-protein interactions from seven eukaryotes as gold standards to train a deep learning model that relies on self- and cross-attention over protein sequences. This innovative protein-centric approach results in interaction-specific features derived from protein sequence alone. In addition, we designed and assessed a first double-blind evaluation protocol for metabolite-protein interactions, demonstrating the generalizability of the model. Our results indicated that the excellent performance of the proposed model over simpler alternatives and randomized baselines is due to the local and global features generated by the attention mechanisms. As a results, the predictions from the deep learning model provide a valuable resource for studying metabolite-protein interactions in eukaryotes.
    Language English
    Publishing date 2023-01-31
    Publishing country England
    Document type Journal Article
    ISSN 2631-9268
    ISSN (online) 2631-9268
    DOI 10.1093/nargab/lqad008
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  5. Article: Systematic comparison of local approaches for isotopically nonstationary metabolic flux analysis.

    Huß, Sebastian / Nikoloski, Zoran

    Frontiers in plant science

    2023  Volume 14, Page(s) 1178239

    Abstract: Quantification of reaction fluxes of metabolic networks can help us understand how the integration of different metabolic pathways determine cellular functions. Yet, intracellular fluxes cannot be measured directly but are estimated with metabolic flux ... ...

    Abstract Quantification of reaction fluxes of metabolic networks can help us understand how the integration of different metabolic pathways determine cellular functions. Yet, intracellular fluxes cannot be measured directly but are estimated with metabolic flux analysis (MFA) that relies on the patterns of isotope labeling of metabolites in the network. For metabolic systems, typical for plants, where all potentially labeled atoms effectively have only one source atom pool, only isotopically nonstationary MFA can provide information about intracellular fluxes. There are several global approaches that implement MFA for an entire metabolic network and estimate, at once, a steady-state flux distribution for all reactions with identifiable fluxes in the network. In contrast, local approaches deal with estimation of fluxes for a subset of reactions, with smaller data demand for flux estimation. Here we present a systematic comparative review and benchmarking of the existing local approaches for isotopically nonstationary MFA. The comparison is conducted with respect to the required data and underlying computational problems solved on a synthetic network example. Furthermore, we benchmark the performance of these approaches in estimating fluxes for a subset of reactions using data obtained from the simulation of nitrogen fluxes in the
    Language English
    Publishing date 2023-06-06
    Publishing country Switzerland
    Document type Systematic Review
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2023.1178239
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  6. Article ; Online: Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection.

    Mbebi, Alain J / Nikoloski, Zoran

    PLoS computational biology

    2023  Volume 19, Issue 7, Page(s) e1010832

    Abstract: Despite extensive research efforts, reconstruction of gene regulatory networks (GRNs) from transcriptomics data remains a pressing challenge in systems biology. While non-linear approaches for reconstruction of GRNs show improved performance over simpler ...

    Abstract Despite extensive research efforts, reconstruction of gene regulatory networks (GRNs) from transcriptomics data remains a pressing challenge in systems biology. While non-linear approaches for reconstruction of GRNs show improved performance over simpler alternatives, we do not yet have understanding if joint modelling of multiple target genes may improve performance, even under linearity assumptions. To address this problem, we propose two novel approaches that cast the GRN reconstruction problem as a blend between regularized multivariate regression and graphical models that combine the L2,1-norm with classical regularization techniques. We used data and networks from the DREAM5 challenge to show that the proposed models provide consistently good performance in comparison to contenders whose performance varies with data sets from simulation and experiments from model unicellular organisms Escherichia coli and Saccharomyces cerevisiae. Since the models' formulation facilitates the prediction of master regulators, we also used the resulting findings to identify master regulators over all data sets as well as their plasticity across different environments. Our results demonstrate that the identified master regulators are in line with experimental evidence from the model bacterium E. coli. Together, our study demonstrates that simultaneous modelling of several target genes results in improved inference of GRNs and can be used as an alternative in different applications.
    MeSH term(s) Algorithms ; Escherichia coli/genetics ; Gene Regulatory Networks/genetics ; Systems Biology/methods ; Gene Expression Profiling ; Saccharomyces cerevisiae/genetics
    Language English
    Publishing date 2023-07-31
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1010832
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  7. Article ; Online: Model-driven insights into the effects of temperature on metabolism.

    Wendering, Philipp / Nikoloski, Zoran

    Biotechnology advances

    2023  Volume 67, Page(s) 108203

    Abstract: Temperature affects cellular processes at different spatiotemporal scales, and identifying the genetic and molecular mechanisms underlying temperature responses paves the way to develop approaches for mitigating the effects of future climate scenarios. A ...

    Abstract Temperature affects cellular processes at different spatiotemporal scales, and identifying the genetic and molecular mechanisms underlying temperature responses paves the way to develop approaches for mitigating the effects of future climate scenarios. A systems view of the effects of temperature on cellular physiology can be obtained by focusing on metabolism since: (i) its functions depend on transcription and translation and (ii) its outcomes support organisms' development, growth, and reproduction. Here we provide a systematic review of modelling efforts directed at investigating temperature effects on properties of single biochemical reactions, system-level traits, metabolic subsystems, and whole-cell metabolism across different prokaryotes and eukaryotes. We compare and contrast computational approaches and theories that facilitate modelling of temperature effects on key properties of enzymes and their consideration in constraint-based as well as kinetic models of metabolism. In addition, we provide a summary of insights from computational approaches, facilitating integration of omics data from temperature-modulated experiments with models of metabolic networks, and review the resulting biotechnological applications. Lastly, we provide a perspective on how different types of metabolic modelling can profit from developments in machine learning and models of different cellular layers to improve model-driven insights into the effects of temperature relevant for biotechnological applications.
    MeSH term(s) Temperature ; Metabolic Networks and Pathways/genetics ; Phenotype ; Models, Biological
    Language English
    Publishing date 2023-06-20
    Publishing country England
    Document type Systematic Review ; Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 47165-3
    ISSN 1873-1899 ; 0734-9750
    ISSN (online) 1873-1899
    ISSN 0734-9750
    DOI 10.1016/j.biotechadv.2023.108203
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 3730: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  8. Article ; Online: Toward mechanistic modeling and rational engineering of plant respiration.

    Wendering, Philipp / Nikoloski, Zoran

    Plant physiology

    2023  Volume 191, Issue 4, Page(s) 2150–2166

    Abstract: Plant respiration not only provides energy to support all cellular processes, including biomass production, but also plays a major role in the global carbon cycle. Therefore, modulation of plant respiration can be used to both increase the plant yield ... ...

    Abstract Plant respiration not only provides energy to support all cellular processes, including biomass production, but also plays a major role in the global carbon cycle. Therefore, modulation of plant respiration can be used to both increase the plant yield and mitigate the effects of global climate change. Mechanistic modeling of plant respiration at sufficient biochemical detail can provide key insights for rational engineering of this process. Yet, despite its importance, plant respiration has attracted considerably less modeling effort in comparison to photosynthesis. In this update review, we highlight the advances made in modeling of plant respiration, emphasizing the gradual but important change from phenomenological to models based on first principles. We also provide a detailed account of the existing resources that can contribute to resolving the challenges in modeling plant respiration. These resources point at tangible improvements in the representation of cellular processes that contribute to CO2 evolution and consideration of kinetic properties of underlying enzymes to facilitate mechanistic modeling. The update review emphasizes the need to couple biochemical models of respiration with models of acclimation and adaptation of respiration for their effective usage in guiding breeding efforts and improving terrestrial biosphere models tailored to future climate scenarios.
    MeSH term(s) Plant Breeding ; Plants ; Climate Change ; Photosynthesis ; Respiration ; Cell Respiration ; Carbon Dioxide ; Plant Leaves
    Chemical Substances Carbon Dioxide (142M471B3J)
    Language English
    Publishing date 2023-02-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 208914-2
    ISSN 1532-2548 ; 0032-0889
    ISSN (online) 1532-2548
    ISSN 0032-0889
    DOI 10.1093/plphys/kiad054
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Bonn / Germany

    Z 1193: Show issues

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  9. Article ; Online: Prediction and integration of metabolite-protein interactions with genome-scale metabolic models.

    Habibpour, Mahdis / Razaghi-Moghadam, Zahra / Nikoloski, Zoran

    Metabolic engineering

    2024  Volume 82, Page(s) 216–224

    Abstract: Metabolites, as small molecules, can act not only as substrates to enzymes, but also as effectors of activity of proteins with different functions, thereby affecting various cellular processes. While several experimental techniques have started to ... ...

    Abstract Metabolites, as small molecules, can act not only as substrates to enzymes, but also as effectors of activity of proteins with different functions, thereby affecting various cellular processes. While several experimental techniques have started to catalogue the metabolite-protein interactions (MPIs) present in different cellular contexts, characterizing the functional relevance of MPIs remains a challenging problem. Computational approaches from the constrained-based modeling framework allow for predicting MPIs and integrating their effects in the in silico analysis of metabolic and physiological phenotypes, like cell growth. Here, we provide a classification of all existing constraint-based approaches that predict and integrate MPIs using genome-scale metabolic networks as input. In addition, we benchmark the performance of the approaches to predict MPIs in a comparative study using different features extracted from the model structure and predicted metabolic phenotypes with the state-of-the-art metabolic networks of Escherichia coli and Saccharomyces cerevisiae. Lastly, we provide an outlook for future, feasible directions to expand the consideration of MPIs in constraint-based modeling approaches with wide biotechnological applications.
    MeSH term(s) Metabolic Networks and Pathways/genetics ; Phenotype ; Models, Biological
    Language English
    Publishing date 2024-02-15
    Publishing country Belgium
    Document type Journal Article ; Review
    ZDB-ID 1470383-x
    ISSN 1096-7184 ; 1096-7176
    ISSN (online) 1096-7184
    ISSN 1096-7176
    DOI 10.1016/j.ymben.2024.02.008
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 6288: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  10. Article ; Online: Protein constraints in genome-scale metabolic models: Data integration, parameter estimation, and prediction of metabolic phenotypes.

    Ferreira, Maurício Alexander de Moura / Silveira, Wendel Batista da / Nikoloski, Zoran

    Biotechnology and bioengineering

    2024  Volume 121, Issue 3, Page(s) 915–930

    Abstract: Genome-scale metabolic models provide a valuable resource to study metabolism and cell physiology. These models are employed with approaches from the constraint-based modeling framework to predict metabolic and physiological phenotypes. The prediction ... ...

    Abstract Genome-scale metabolic models provide a valuable resource to study metabolism and cell physiology. These models are employed with approaches from the constraint-based modeling framework to predict metabolic and physiological phenotypes. The prediction performance of genome-scale metabolic models can be improved by including protein constraints. The resulting protein-constrained models consider data on turnover numbers (k
    MeSH term(s) Metabolic Networks and Pathways ; Models, Biological ; Kinetics
    Language English
    Publishing date 2024-01-04
    Publishing country United States
    Document type Systematic Review ; Journal Article ; Review
    ZDB-ID 280318-5
    ISSN 1097-0290 ; 0006-3592
    ISSN (online) 1097-0290
    ISSN 0006-3592
    DOI 10.1002/bit.28650
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.B 960: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

To top