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Book ; Online ; Thesis: Exploring the metabolic space of the genus Pseudomonas through genome-scale, constraint-based modelling

Puchałka, Jacek [Verfasser]

2008

Author's details	von Jacek Puchałka
Keywords	Biowissenschaften, Biologie ; Life Science, Biology
Subject code	sg570
Language	English
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Article ; Online: Characterizing the optimal flux space of genome-scale metabolic reconstructions through modified latin-hypercube sampling.

Chaudhary, Neha / Tøndel, Kristin / Bhatnagar, Rakesh / dos Santos, Vítor A P Martins / Puchałka, Jacek

Molecular bioSystems

2016 Volume 12, Issue 3, Page(s) 994–1005

Abstract: Genome-Scale Metabolic Reconstructions (GSMRs), along with optimization-based methods, predominantly Flux Balance Analysis (FBA) and its derivatives, are widely applied for assessing and predicting the behavior of metabolic networks upon perturbation, ... ...

Abstract	Genome-Scale Metabolic Reconstructions (GSMRs), along with optimization-based methods, predominantly Flux Balance Analysis (FBA) and its derivatives, are widely applied for assessing and predicting the behavior of metabolic networks upon perturbation, thereby enabling identification of potential novel drug targets and biotechnologically relevant pathways. The abundance of alternate flux profiles has led to the evolution of methods to explore the complete solution space aiming to increase the accuracy of predictions. Herein we present a novel, generic algorithm to characterize the entire flux space of GSMR upon application of FBA, leading to the optimal value of the objective (the optimal flux space). Our method employs Modified Latin-Hypercube Sampling (LHS) to effectively border the optimal space, followed by Principal Component Analysis (PCA) to identify and explain the major sources of variability within it. The approach was validated with the elementary mode analysis of a smaller network of Saccharomyces cerevisiae and applied to the GSMR of Pseudomonas aeruginosa PAO1 (iMO1086). It is shown to surpass the commonly used Monte Carlo Sampling (MCS) in providing a more uniform coverage for a much larger network in less number of samples. Results show that although many fluxes are identified as variable upon fixing the objective value, majority of the variability can be reduced to several main patterns arising from a few alternative pathways. In iMO1086, initial variability of 211 reactions could almost entirely be explained by 7 alternative pathway groups. These findings imply that the possibilities to reroute greater portions of flux may be limited within metabolic networks of bacteria. Furthermore, the optimal flux space is subject to change with environmental conditions. Our method may be a useful device to validate the predictions made by FBA-based tools, by describing the optimal flux space associated with these predictions, thus to improve them.
MeSH term(s)	Algorithms ; Computer Simulation ; Discriminant Analysis ; Genome ; Genome, Bacterial ; Genome, Fungal ; Metabolic Networks and Pathways ; Principal Component Analysis ; Pseudomonas aeruginosa/genetics ; Reproducibility of Results ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism
Language	English
Publishing date	2016-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2188635-0
ISSN	1742-2051 ; 1742-206X
ISSN (online)	1742-2051
ISSN	1742-206X
DOI	10.1039/c5mb00457h
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Article ; Online: Novel spontaneous deletion of artemis exons 10 and 11 in mice leads to T- and B-cell deficiency.

Barthels, Christian / Puchałka, Jacek / Racek, Tomas / Klein, Christoph / Brocker, Thomas

PloS one

2013 Volume 8, Issue 9, Page(s) e74838

Abstract: Here we describe a novel, spontaneous, 4035 basepairs long deletion in the DNA cross-link repair 1C (Dclre1c)-locus in C57BL/6-mice, which leads to loss of exons 10 and 11 of the gene encoding for Artemis, a protein involved into V(D) J-recombination of ... ...

Abstract	Here we describe a novel, spontaneous, 4035 basepairs long deletion in the DNA cross-link repair 1C (Dclre1c)-locus in C57BL/6-mice, which leads to loss of exons 10 and 11 of the gene encoding for Artemis, a protein involved into V(D) J-recombination of antigen receptors of T and B cells. While several spontaneous mutations of Artemis have been described to cause SCID in humans, in mice, only targeted deletions by knockout technology are known to cause the same phenotype so far. The deletion we observed causes a loss of Artemis function in the C57BL/6 strain and, consequently, the absence of T and B cells, in presence of normal numbers of NK cells and cells of the myeloid lineage. Thus, for the first time we present T(-)B(-)NK(+) severe combined immunodeficiency (SCID) phenotype after spontaneously occurring modification of Artemis gene in mice. Our mouse model may serve as a valuable tool to study mechanisms as well as potential therapies of SCID in humans.
MeSH term(s)	Animals ; B-Lymphocytes/immunology ; B-Lymphocytes/metabolism ; Base Sequence ; Endonucleases/genetics ; Exons ; Gene Order ; Immunophenotyping ; Mice ; Nuclear Proteins/genetics ; Phenotype ; Polymorphism, Single Nucleotide ; Sequence Deletion ; Severe Combined Immunodeficiency/genetics ; Severe Combined Immunodeficiency/immunology ; T-Lymphocytes/immunology ; T-Lymphocytes/metabolism
Chemical Substances	Nuclear Proteins ; Endonucleases (EC 3.1.-) ; Dclre1c protein, mouse (EC 3.1.-.-)
Language	English
Publishing date	2013-09-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0074838
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Article ; Online: Preference of Genetic Diagnosis of CXCR4 Mutation Compared with Clinical Diagnosis of WHIM Syndrome.

Aghamohammadi, Asghar / Abolhassani, Hassan / Puchalka, Jacek / Greif-Kohistani, Naschla / Zoghi, Samaneh / Klein, Christoph / Rezaei, Nima

Journal of clinical immunology

2017 Volume 37, Issue 3, Page(s) 282–286

MeSH term(s)	Agammaglobulinemia/diagnosis ; Agammaglobulinemia/genetics ; Child, Preschool ; Female ; Humans ; Immunoglobulins, Intravenous/therapeutic use ; Immunologic Deficiency Syndromes/diagnosis ; Immunologic Deficiency Syndromes/immunology ; Male ; Mutation/genetics ; Pathology, Molecular/methods ; Receptors, CXCR4/genetics ; Warts/diagnosis ; Warts/immunology
Chemical Substances	CXCR4 protein, human ; Immunoglobulins, Intravenous ; Receptors, CXCR4
Language	English
Publishing date	2017-03-28
Publishing country	Netherlands
Document type	Case Reports ; Comparative Study ; Letter
ZDB-ID	779361-3
ISSN	1573-2592 ; 0271-9142
ISSN (online)	1573-2592
ISSN	0271-9142
DOI	10.1007/s10875-017-0387-5
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Article: Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks.

Puchałka, Jacek / Kierzek, Andrzej M

Biophysical journal

2004 Volume 86, Issue 3, Page(s) 1357–1372

Abstract: The biochemical reaction networks include elementary reactions differing by many orders of magnitude in the numbers of molecules involved. The kinetics of reactions involving small numbers of molecules can be studied by exact stochastic simulation. This ... ...

Abstract	The biochemical reaction networks include elementary reactions differing by many orders of magnitude in the numbers of molecules involved. The kinetics of reactions involving small numbers of molecules can be studied by exact stochastic simulation. This approach is not practical for the simulation of metabolic processes because of the computational cost of accounting for individual molecular collisions. We present the "maximal time step method," a novel approach combining the Gibson and Bruck algorithm with the Gillespie tau-leap method. This algorithm allows stochastic simulation of systems composed of both intensive metabolic reactions and regulatory processes involving small numbers of molecules. The method is applied to the simulation of glucose, lactose, and glycerol metabolism in Escherichia coli. The gene expression, signal transduction, transport, and enzymatic activities are modeled simultaneously. We show that random fluctuations in gene expression can propagate to the level of metabolic processes. In the cells switching from glucose to a mixture of lactose and glycerol, random delays in transcription initiation determine whether lactose or glycerol operon is induced. In a small fraction of cells severe decrease in metabolic activity may also occur. Both effects are epigenetically inherited by the progeny of the cell in which the random delay in transcription initiation occurred.
MeSH term(s)	Biochemistry/methods ; Cell Physiological Phenomena ; Computer Simulation ; Escherichia coli/physiology ; Gene Expression Regulation/physiology ; Glucose/metabolism ; Glycerol/metabolism ; Homeostasis/physiology ; Kinetics ; Lactose/metabolism ; Models, Biological ; Models, Chemical ; Multienzyme Complexes/metabolism ; Signal Transduction/physiology ; Stochastic Processes ; Time Factors
Chemical Substances	Multienzyme Complexes ; Glucose (IY9XDZ35W2) ; Lactose (J2B2A4N98G) ; Glycerol (PDC6A3C0OX)
Language	English
Publishing date	2004-03
Publishing country	United States
Document type	Comparative Study ; Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't ; Validation Studies
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/S0006-3495(04)74207-1
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Article ; Online: Multicongenic fate mapping quantification of dynamics of thymus colonization.

Ziętara, Natalia / Łyszkiewicz, Marcin / Puchałka, Jacek / Witzlau, Katrin / Reinhardt, Annika / Förster, Reinhold / Pabst, Oliver / Prinz, Immo / Krueger, Andreas

The Journal of experimental medicine

2015 Volume 212, Issue 10, Page(s) 1589–1601

Abstract: Postnatal T cell development depends on continuous colonization of the thymus by BM-derived T lineage progenitors. Both quantitative parameters and the mechanisms of thymus seeding remain poorly understood. Here, we determined the number of dedicated ... ...

Abstract	Postnatal T cell development depends on continuous colonization of the thymus by BM-derived T lineage progenitors. Both quantitative parameters and the mechanisms of thymus seeding remain poorly understood. Here, we determined the number of dedicated thymus-seeding progenitor niches (TSPNs) capable of supporting productive T cell development, turnover rates of niche occupancy, and feedback mechanisms. To this end, we established multicongenic fate mapping combined with mathematical modeling to quantitate individual events of thymus colonization. We applied this method to study thymus colonization in CCR7(-/-)CCR9(-/-) (DKO) mice, whose TSPNs are largely unoccupied. We showed that ∼160-200 TSPNs are present in the adult thymus and, on average, 10 of these TSPNs were open for recolonization at steady state. Preconditioning of wild-type mice revealed a similar number of TSPNs, indicating that preconditioning can generate space efficiently for transplanted T cell progenitors. To identify potential cellular feedback loops restricting thymus colonization, we performed serial transfer experiments. These experiments indicated that thymus seeding was directly restricted by the duration of niche occupancy rather than long-range effects, thus challenging current paradigms of thymus colonization.
MeSH term(s)	Animals ; Cell Lineage ; Mice, Inbred C57BL ; Mice, Knockout ; Receptors, CCR/genetics ; Receptors, CCR/metabolism ; Receptors, CCR7/genetics ; Receptors, CCR7/metabolism ; Receptors, Interleukin-17/genetics ; Stem Cells/physiology ; T-Lymphocytes/cytology ; T-Lymphocytes/physiology ; Thymocytes/physiology ; Thymus Gland/cytology ; Thymus Gland/physiology ; Thymus Gland/radiation effects
Chemical Substances	CC chemokine receptor 9 ; Ccr7 protein, mouse ; Il17r protein, mouse ; Receptors, CCR ; Receptors, CCR7 ; Receptors, Interleukin-17
Language	English
Publishing date	2015-09-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218343-2
ISSN	1540-9538 ; 0022-1007
ISSN (online)	1540-9538
ISSN	0022-1007
DOI	10.1084/jem.20142143
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Article ; Online: Author Correction: Human FCHO1 deficiency reveals role for clathrin-mediated endocytosis in development and function of T cells.

Łyszkiewicz, Marcin / Ziętara, Natalia / Frey, Laura / Pannicke, Ulrich / Stern, Marcel / Liu, Yanshan / Fan, Yanxin / Puchałka, Jacek / Hollizeck, Sebastian / Somekh, Ido / Rohlfs, Meino / Yilmaz, Tuğba / Ünal, Ekrem / Karakukcu, Musa / Patiroğlu, Türkan / Kellerer, Christina / Karasu, Ebru / Sykora, Karl-Walter / Lev, Atar /

Simon, Amos / Somech, Raz / Roesler, Joachim / Hoenig, Manfred / Keppler, Oliver T / Schwarz, Klaus / Klein, Christoph

Nature communications

2020 Volume 11, Issue 1, Page(s) 1963

Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

Abstract	An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Language	English
Publishing date	2020-04-20
Publishing country	England
Document type	Journal Article ; Published Erratum
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-020-15946-x
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Article ; Online: Human FCHO1 deficiency reveals role for clathrin-mediated endocytosis in development and function of T cells.

Simon, Amos / Somech, Raz / Roesler, Joachim / Hoenig, Manfred / Keppler, Oliver T / Schwarz, Klaus / Klein, Christoph

Nature communications

2020 Volume 11, Issue 1, Page(s) 1031

Abstract: Clathrin-mediated endocytosis (CME) is critical for internalisation of molecules across cell membranes. The FCH domain only 1 (FCHO1) protein is key molecule involved in the early stages of CME formation. The consequences of mutations in FCHO1 in humans ... ...

Abstract	Clathrin-mediated endocytosis (CME) is critical for internalisation of molecules across cell membranes. The FCH domain only 1 (FCHO1) protein is key molecule involved in the early stages of CME formation. The consequences of mutations in FCHO1 in humans were unknown. We identify ten unrelated patients with variable T and B cell lymphopenia, who are homozygous for six distinct mutations in FCHO1. We demonstrate that these mutations either lead to mislocalisation of the protein or prevent its interaction with binding partners. Live-cell imaging of cells expressing mutant variants of FCHO1 provide evidence of impaired formation of clathrin coated pits (CCP). Patient T cells are unresponsive to T cell receptor (TCR) triggering. Internalisation of the TCR receptor is severely perturbed in FCHO1-deficient Jurkat T cells but can be rescued by expression of wild-type FCHO1. Thus, we discovered a previously unrecognised critical role of FCHO1 and CME during T-cell development and function in humans.
MeSH term(s)	Animals ; CD4-Positive T-Lymphocytes/pathology ; Cell Differentiation ; Cells, Cultured ; Endocytosis/physiology ; Female ; HIV Infections/genetics ; HIV-1/pathogenicity ; Humans ; Jurkat Cells ; Loss of Function Mutation ; Lymphopenia/genetics ; Lymphopenia/pathology ; Male ; Membrane Proteins/chemistry ; Membrane Proteins/deficiency ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Mice ; Pedigree ; Receptors, Antigen, T-Cell/metabolism ; T-Lymphocytes/physiology ; T-Lymphocytes/virology
Chemical Substances	FCHO1 protein, human ; Membrane Proteins ; Receptors, Antigen, T-Cell
Language	English
Publishing date	2020-02-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-020-14809-9
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Article ; Online: Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis.

Oberhardt, Matthew A / Puchałka, Jacek / Martins dos Santos, Vítor A P / Papin, Jason A

PLoS computational biology

2011 Volume 7, Issue 3, Page(s) e1001116

Abstract: In the past decade, over 50 genome-scale metabolic reconstructions have been built for a variety of single- and multi- cellular organisms. These reconstructions have enabled a host of computational methods to be leveraged for systems-analysis of ... ...

Abstract	In the past decade, over 50 genome-scale metabolic reconstructions have been built for a variety of single- and multi- cellular organisms. These reconstructions have enabled a host of computational methods to be leveraged for systems-analysis of metabolism, leading to greater understanding of observed phenotypes. These methods have been sparsely applied to comparisons between multiple organisms, however, due mainly to the existence of differences between reconstructions that are inherited from the respective reconstruction processes of the organisms to be compared. To circumvent this obstacle, we developed a novel process, termed metabolic network reconciliation, whereby non-biological differences are removed from genome-scale reconstructions while keeping the reconstructions as true as possible to the underlying biological data on which they are based. This process was applied to two organisms of great importance to disease and biotechnological applications, Pseudomonas aeruginosa and Pseudomonas putida, respectively. The result is a pair of revised genome-scale reconstructions for these organisms that can be analyzed at a systems level with confidence that differences are indicative of true biological differences (to the degree that is currently known), rather than artifacts of the reconstruction process. The reconstructions were re-validated with various experimental data after reconciliation. With the reconciled and validated reconstructions, we performed a genome-wide comparison of metabolic flexibility between P. aeruginosa and P. putida that generated significant new insight into the underlying biology of these important organisms. Through this work, we provide a novel methodology for reconciling models, present new genome-scale reconstructions of P. aeruginosa and P. putida that can be directly compared at a network level, and perform a network-wide comparison of the two species. These reconstructions provide fresh insights into the metabolic similarities and differences between these important Pseudomonads, and pave the way towards full comparative analysis of genome-scale metabolic reconstructions of multiple species.
MeSH term(s)	Algorithms ; Biotechnology/methods ; Computational Biology/methods ; Computer Simulation ; Databases, Factual ; Gene Expression Regulation, Bacterial/physiology ; Genome ; Genome, Bacterial ; Metabolic Networks and Pathways/genetics ; Phenotype ; Pseudomonas/genetics ; Reproducibility of Results ; Software ; Species Specificity
Language	English
Publishing date	2011-03-31
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; 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.1001116
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Article: Differential diagnosis in ulcerative colitis in an adolescent: Chronic granulomatous disease needs extra attention.

Kotlarz, Daniel / Egritas Gurkan, Odul / Haskologlu, Zehra Sule / Ekinci, Ozgur / Aksu Unlusoy, Aysel / Gürcan Kaya, Neslihan / Puchalka, Jacek / Klein, Cristoph / Dalgic, Buket

World journal of gastrointestinal pathophysiology

2017 Volume 8, Issue 2, Page(s) 87–92

Abstract: Chronic granulomatous disease (CGD) is a primary immune deficiency that is commonly diagnosed under the age of 5 years (95%) and is rarely seen in adulthood. CGD may manifest as inflammatory bowel disease (IBD) in childhood. Without proper diagnosis, ... ...

Abstract	Chronic granulomatous disease (CGD) is a primary immune deficiency that is commonly diagnosed under the age of 5 years (95%) and is rarely seen in adulthood. CGD may manifest as inflammatory bowel disease (IBD) in childhood. Without proper diagnosis, these patients may be monitored for years as IBD; some may even be regarded as steroid-resistant ulcerative colitis (UC) and end up having a colectomy. In this case report, we described a patient who had been followed-up for years as UC and subsequently underwent colectomy, but was finally diagnosed in adulthood as primary immune deficiency.
Language	English
Publishing date	2017-03-01
Publishing country	United States
Document type	Case Reports
ZDB-ID	2583474-5
ISSN	2150-5330
ISSN	2150-5330
DOI	10.4291/wjgp.v8.i2.87
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