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Metaproteomics of complex microbial communities in biogas plants

Robert Heyer, Fabian Kohrs, Udo Reichl, Dirk Benndorf
<span title="2015-04-15">2015</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hqhbgym6bfdm5jsesxfb3g5wza" style="color: black;">Microbial Biotechnology</a> </i> &nbsp;
Reichl and D. Benndorf to identify the majority of key bacterial enzymes for the acetyl-CoA pathway.  ...  Reichl and D. Benndorf phylogenetic groups known to be involved in biomass conversion to methane were identified.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/1751-7915.12276">doi:10.1111/1751-7915.12276</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25874383">pmid:25874383</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4554464/">pmcid:PMC4554464</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/b4mgm2jffvh7pp7nr567yvszye">fatcat:b4mgm2jffvh7pp7nr567yvszye</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170815213831/http://pubman.mpdl.mpg.de/pubman/item/escidoc:2153363/component/escidoc:2182929/2153363_heyer.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/de/b1/deb1e31ab83d3f6f7b069dc246396ed620c3298e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/1751-7915.12276"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4554464" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Metaproteome analysis of sewage sludge from membrane bioreactors

Ramona Kuhn, Dirk Benndorf, Erdmann Rapp, Udo Reichl, Luigi Leonardo Palese, Alfieri Pollice
<span title="2011-05-23">2011</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fuys75pzlrec5izxlpab5g6jue" style="color: black;">Proteomics</a> </i> &nbsp;
Microbial dynamics and enzymatic activities of activated sludge processes are not completely understood yet. A better understanding about the biology is indispensable for further process optimization. Since proteins play a key role as catalysts in sludge processes, a protocol for protein extraction and analysis by 2-D PAGE was established. It is based on phenol extraction of alkaline extracts and on a subsequent precipitation with ammonium sulphate. 2-D protein patterns obtained from different
more &raquo; ... ludges collected from membrane bioreactors showedbesides common spots -significant differences. Selected proteins were identified with nano-HPLC-ESI-MS/MS. All membrane biological reactor (MBR) sludge samples investigated in this study contained elastase 3A, which implies that this human serine protease is a significant constituent of municipal wastewater. Although the identification of proteins from ammonia-oxidizing bacterium Nitrosomonas europaea was expected, the detection of a protein with homology to the marine bacterium Saprospira grandis in MBR1 was surprising.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pmic.201000590">doi:10.1002/pmic.201000590</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21604373">pmid:21604373</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/erjrhgzdxvgndaxafoygvmluju">fatcat:erjrhgzdxvgndaxafoygvmluju</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20120417180036/http://www.irsa.cnr.it:80/Docs/Archivio/Proteom_2011.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/48/14/4814a0369c25ffc0f39b6622f40ce3ee9c350070.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pmic.201000590"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

High-cell-density cultivations to increase MVA virus production

Daniel Vázquez-Ramírez, Yvonne Genzel, Ingo Jordan, Volker Sandig, Udo Reichl
<span title="2018-02-09">2018</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wqdavxmwkrh4ndbs3jgtlylvmq" style="color: black;">Vaccine</a> </i> &nbsp;
Increasing the yield and the productivity in cell culture-based vaccine manufacturing using high-cell-density (HCD) cultivations faces a number of challenges. For example, medium consumption should be low to obtain a very high concentration of viable host cells in an economical way but must be balanced against the requirement that accumulation of toxic metabolites and limitation of nutrients have to be avoided. HCD cultivations should also be optimized to avoid unwanted induction of apoptosis
more &raquo; ... autophagy during the early phase of virus infection. To realize the full potential of HCD cultivations, a rational analysis of the cultivation conditions of the appropriate host cell line together with the optimal infection conditions for the chosen viral vaccine strain needs to be performed for each particular manufacturing process. We here illustrate our strategy for production of the modified vaccinia Ankara (MVA) virus isolate MVA-CR19 in the avian suspension cell line AGE1.CR.pIX at HCD. As a first step we demonstrate that the adjustment of the perfusion rate strictly based on the measured cell concentration and the glucose consumption rate of cells enables optimal growth in a 0.8 L bioreactor equipped with an ATF2 system. Concentrations up to 57 × 106 cells/mL (before infection) were obtained with a viability exceeding 95%, and a maximum specific cell growth rate of 0.019 h-1 (doubling time = 36.5 h). However, not only the cell-specific MVA-CR19 virus yield but also the volumetric productivity was reduced compared to infections at conventional-cell-density (CCD). To facilitate optimization of the virus propagation phase at HCD, a larger set of feeding strategies was analyzed in small-scale cultivations using shake flasks. Densities up to 63 × 106 cells/mL were obtained at the end of the cell growth phase applying a discontinuous perfusion mode (semi-perfusion) with the same cell-specific perfusion rate as in the bioreactor (0.060 nL/(cell d)). At this cell concentration, a medium exchange at time of infection was required to obtain expected virus yields during the first 24 h after infection. Applying an additional fed-batch feeding strategy during the whole virus replication phase resulted in a faster virus titer increase during the first 36 h after infection. In contrast, a semi-continuous virus harvest scheme improved virus accumulation and recovery at a rather later stage of infection. Overall, a combination of both fed-batch and medium exchange strategies resulted in similar cell-specific virus yields as those obtained for CCD processes but 10-fold higher MVA-CR19 titers, and four times higher volumetric productivity.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.vaccine.2017.10.112">doi:10.1016/j.vaccine.2017.10.112</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29433897">pmid:29433897</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7115588/">pmcid:PMC7115588</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/znx4umljfrhq3jksavu4wv3ijy">fatcat:znx4umljfrhq3jksavu4wv3ijy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200313071805/https://pure.mpg.de/rest/items/item_2548092_11/component/file_3017745/content" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/02/e0/02e0b64aa636ba6908680489dafb924fc0470589.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.vaccine.2017.10.112"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7115588" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Impact of different influenza cultivation conditions on HA N-Glycosylation

Jana V Roedig, Erdmann Rapp, Yvonne Genzel, Udo Reichl
<span title="">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/noie53zo7fdytpet5j552fhwny" style="color: black;">BMC Proceedings</a> </i> &nbsp;
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1753-6561-5-s8-p113">doi:10.1186/1753-6561-5-s8-p113</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22373320">pmid:22373320</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3284982/">pmcid:PMC3284982</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2g7mzomtpraftpgtuzveteopta">fatcat:2g7mzomtpraftpgtuzveteopta</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170818062355/http://pubman.mpdl.mpg.de/pubman/item/escidoc:1755642/component/escidoc:1755641/573928_bmc_proc_2011.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f4/05/f40566adbe02f7863f8af2d5859b5fe1591447e2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1753-6561-5-s8-p113"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3284982" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Parameter Identification Of Time-Delay Systems: A Flatness Based Approach

René Schenkendorf, Udo Reichl, Michael Mangold
<span title="">2012</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p3wtlm3j2fedxitkuu4bs3scau" style="color: black;">IFAC Proceedings Volumes</a> </i> &nbsp;
The use of mathematical models is widely established in various fields of application. To name but a few of their major applications, mathematical models can improve the controller design of complex technical systems or are able to facilitate the understanding of highly complex biochemical systems. No matter what mathematical models are used for, however, they fail to perform the intended task if they are badly parameterized. In general, during the process of parameterization one tries to make
more &raquo; ... ifferences between simulation results and measurement data as small as possible. Under the assumption of a suitable model candidate this is done by choosing optimal model parameters. Unfortunately, the majority of used models cannot be solved analytically. For example, many dynamical processes are described by systems of ordinary differential equations (ODEs). Usually, analytical solutions do not exist. Although quite efficient numerical routines are available they usually slow down the parameterization process dramatically. The situation is even more demanding if one has to deal with processes that are described by delay differential equations (DDEs). Commonly, standard DDE solvers show a lack of efficiency as well as of robustness, i.e., they are likely to fail to solve the underlying DDE system. Consequently, it would be of great benefit to eliminate any need of numerical ODE/DDE solvers. Here, the concept of flat inputs comes into play. The key aspect is to transform the DDE system into an algebraic input/output representation, i.e., the inputs of the system are expressed analytically by the outputs and derivatives thereof. Now, the objective of parameterization is to minimize differences between these flat inputs and the physical inputs of the related process. As no numerical DDE solver is involved there is a significant speedup of the parameter identification step. In addition, the presented approach is closely linked to optimal experimental design for parameter identification. In particular, the reformulation of the cost function also affects parameter sensitivities. Using the same measurement data it is possible that previously insensitive model parameters become sensitive. To check this, global parameter sensitivities are determined by Sobol' Indices of first order. All results are demonstrated for the example of a mathematical model of the influenza A virus production.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3182/20120215-3-at-3016.00029">doi:10.3182/20120215-3-at-3016.00029</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5a7jmz3w3jdqbprduh3gc3c4fq">fatcat:5a7jmz3w3jdqbprduh3gc3c4fq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170706110738/http://pubman.mpdl.mpg.de/pubman/item/escidoc%3A1753036/component/escidoc%3A2213901/1753036_schenkendorf.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/de/b6/deb6384977d45a2804864f1238071bb02d5147a6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3182/20120215-3-at-3016.00029"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

MPA_Pathway_Tool: User-friendly, automatic assignment of microbial community data on metabolic pathways [article]

Daniel Walke, Kay Schallert, Prasanna Ramesh, Dirk Benndorf, Emanuel Lange, Udo Reichl, Robert Heyer
<span title="2021-07-09">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Motivation: Taxonomic and functional characterization of microbial communities from diverse environments such as the human gut or biogas plants by multi-omics methods plays an ever more important role. Researchers assign all identified genes, transcripts, or proteins to biological pathways to better understand the function of single species and microbial communities. However, due to the versatility of microbial metabolism and a still increasing number of new biological pathways, linkage to
more &raquo; ... ard pathway maps such as the KEGG (Kyoto Encyclopedia of Genes and Genomes) central carbon metabolism is often problematic. Results: We successfully implemented and validated a new user-friendly, stand-alone web application, the MPA_Pathway_Tool. It consists of two parts, called Pathway-Creator and Pathway-Calculator. The Pathway-Creator enables an easy setup of user-defined pathways with specific taxonomic constraints. The Pathway-Calculator automatically maps microbial community data from multiple measurements on selected pathways and visualizes the results. Availability and Implementation: The MPA_Pathway_Tool is implemented in Java and ReactJS. It is freely available on http://mpa-pathwaymapper.ovgu.de/. Further documentation and the complete source code are available on GitHub (https://github.com/danielwalke/MPA_Pathway_Tool). Contact: daniel.walke@ovgu.de, heyer@mpi-magdeburg.mpg.de
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.07.07.450993">doi:10.1101/2021.07.07.450993</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ealgfytdfbaa3kgchjhfuxnybe">fatcat:ealgfytdfbaa3kgchjhfuxnybe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210715071319/https://www.biorxiv.org/content/biorxiv/early/2021/07/09/2021.07.07.450993.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/4b/de/4bde5ee30a01240eb9a44fb49eefc79233eccbc9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.07.07.450993"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Site-specificO-Glycosylation Analysis of Human Blood Plasma Proteins

Marcus Hoffmann, Kristina Marx, Udo Reichl, Manfred Wuhrer, Erdmann Rapp
<span title="2015-11-23">2015</span> <i title="American Society for Biochemistry &amp; Molecular Biology (ASBMB)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/63atlvwyorhorfip35rcvk6bey" style="color: black;">Molecular &amp; Cellular Proteomics</a> </i> &nbsp;
Site-specific glycosylation analysis is key to investigate structure-function relationships of glycoproteins, e.g. in the context of antigenicity and disease progression. The analysis, though, is quite challenging and time consuming, in particular for O-glycosylated proteins. In consequence, despite their clinical and biopharmaceutical importance, many human blood plasma glycoproteins have not been characterized comprehensively with respect to their O-glycosylation. Here, we report on the
more &raquo; ... pecific O-glycosylation analysis of human blood plasma glycoproteins. To this end pooled human blood plasma of healthy donors was proteolytically digested using a broadspecific enzyme (Proteinase K), followed by a precipitation step, as well as a glycopeptide enrichment and fractionation step via hydrophilic interaction liquid chromatography, the latter being optimized for intact O-glycopeptides carrying short mucin-type core-1 and -2 O-glycans, which represent the vast majority of O-glycans on human blood plasma proteins. Enriched O-glycopeptide fractions were subjected to mass spectrometric analysis using reversedphase liquid chromatography coupled online to an ion trap mass spectrometer operated in positive-ion mode. Peptide identity and glycan composition were derived from lowenergy collision-induced dissociation fragment spectra acquired in multistage mode. To pinpoint the O-glycosylation sites glycopeptides were fragmented using electron transfer dissociation. Spectra were annotated by database searches as well as manually. Overall, 31 O-glycosylation sites and regions belonging to 22 proteins were identified, the majority being acute-phase proteins. Strikingly, also 11 novel O-glycosylation sites and regions were identified. In total 23 O-glycosylation sites could be pinpointed. Interestingly, the use of Proteinase K proved to be particularly beneficial in this context. The identified O-glycan compositions most probably correspond to mono-and disialylated core-1 mucin-type O-glycans (T-antigen). The developed workflow allows the identification and characterization of the major population of the human blood plasma O-glycoproteome and our results provide new insights, which can help to unravel structure-function relationships. The data were deposited to Proteome-Xchange PXD003270. Molecular & Cellular Proteomics
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1074/mcp.m115.053546">doi:10.1074/mcp.m115.053546</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26598643">pmid:26598643</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4739677/">pmcid:PMC4739677</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6qk5t2rbufa33j7vm5gyrok66i">fatcat:6qk5t2rbufa33j7vm5gyrok66i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190220123450/http://pdfs.semanticscholar.org/232b/a41ebb5b3e11e3295b377caad4dca6fe1f4e.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/23/2b/232ba41ebb5b3e11e3295b377caad4dca6fe1f4e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1074/mcp.m115.053546"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4739677" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Flow cytometric monitoring of influenza A virus infection in MDCK cells during vaccine production

Josef Schulze-Horsel, Yvonne Genzel, Udo Reichl
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rxfgte5g2bcizdvltz5dfdp7zi" style="color: black;">BMC Biotechnology</a> </i> &nbsp;
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6750-8-45">doi:10.1186/1472-6750-8-45</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18447925">pmid:18447925</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2408585/">pmcid:PMC2408585</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sao3fw63hvd7ze3tybnna3p7xi">fatcat:sao3fw63hvd7ze3tybnna3p7xi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20080530092232/http://www.biomedcentral.com/content/pdf/1472-6750-8-45.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/58/9d/589dfadd696eeb894c9756642bb9a64d2c838bf4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6750-8-45"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408585" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Bioreactor concepts for cell culture-based viral vaccine production

Lilí Esmeralda Gallo–Ramírez, Alexander Nikolay, Yvonne Genzel, Udo Reichl
<span title="2015-07-15">2015</span> <i title="Informa UK Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cyy7c7cvpvdqvf2wmucsqs6s6i" style="color: black;">Expert Review of Vaccines</a> </i> &nbsp;
Vaccine 2014;32(48):6485-92 Review Gallo-Ramírez, Nikolay, Genzel & Reichl Expert Rev. Vaccines 14(9), (2015)  ...  Genzel Y, Fischer M, Reichl U. Serum-free influenza virus production avoiding washing steps and medium exchange in large-scale microcarrier culture. Vaccine 2006;24(16): 3261-72 37.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1586/14760584.2015.1067144">doi:10.1586/14760584.2015.1067144</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26178380">pmid:26178380</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/udrgnc4q7re3bgxatgp4xpcrda">fatcat:udrgnc4q7re3bgxatgp4xpcrda</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201107084123/https://pure.mpg.de/rest/items/item_2176268_8/component/file_3242995/content" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/80/5b/805b2ed7e1588a3f273c62b59e95c8b2b4e1b3ce.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1586/14760584.2015.1067144"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Effect of influenza virus infection on key metabolic enzyme activities in MDCK cells

Robert Janke, Yvonne Genzel, Maria Wetzel, Udo Reichl
<span title="">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/noie53zo7fdytpet5j552fhwny" style="color: black;">BMC Proceedings</a> </i> &nbsp;
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1753-6561-5-s8-p129">doi:10.1186/1753-6561-5-s8-p129</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22373286">pmid:22373286</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3284985/">pmcid:PMC3284985</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/j2aeaykbjje3pp2k346rwlyldm">fatcat:j2aeaykbjje3pp2k346rwlyldm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170816080357/https://bmcproc.biomedcentral.com/track/pdf/10.1186/1753-6561-5-S8-P129?site=bmcproc.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b9/a0/b9a0ecb03588775e05184e6898b1247b61a639da.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1753-6561-5-s8-p129"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3284985" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The avian cell line AGE1.CR.pIX characterized by metabolic flux analysis

Verena Lohr, Oliver Hädicke, Yvonne Genzel, Ingo Jordan, Heino Büntemeyer, Steffen Klamt, Udo Reichl
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rxfgte5g2bcizdvltz5dfdp7zi" style="color: black;">BMC Biotechnology</a> </i> &nbsp;
In human vaccine manufacturing some pathogens such as Modified Vaccinia Virus Ankara, measles, mumps virus as well as influenza viruses are still produced on primary material derived from embryonated chicken eggs. Processes depending on primary cell culture, however, are difficult to adapt to modern vaccine production. Therefore, we derived previously a continuous suspension cell line, AGE1.CR.pIX, from muscovy duck and established chemically-defined media for virus propagation. Results: To
more &raquo; ... er understand vaccine production processes, we developed a stoichiometric model of the central metabolism of AGE1.CR.pIX cells and applied flux variability and metabolic flux analysis. Results were compared to literature dealing with mammalian and insect cell culture metabolism focusing on the question whether cultured avian cells differ in metabolism. Qualitatively, the observed flux distribution of this avian cell line was similar to distributions found for mammalian cell lines (e.g. CHO, MDCK cells). In particular, glucose was catabolized inefficiently and glycolysis and TCA cycle seem to be only weakly connected. Conclusions: A distinguishing feature of the avian cell line is that glutaminolysis plays only a minor role in energy generation and production of precursors, resulting in low extracellular ammonia concentrations. This metabolic flux study is the first for a continuous avian cell line. It provides a basis for further metabolic analyses to exploit the biotechnological potential of avian and vertebrate cell lines and to develop specific optimized cell culture processes, e.g. vaccine production processes.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6750-14-72">doi:10.1186/1472-6750-14-72</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25077436">pmid:25077436</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4124504/">pmcid:PMC4124504</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/753dz6nhtvdfhlmgqilvi364ga">fatcat:753dz6nhtvdfhlmgqilvi364ga</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180721135732/https://bmcbiotechnol.biomedcentral.com/track/pdf/10.1186/1472-6750-14-72?site=bmcbiotechnol.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2d/ac/2dacd80d3cf5bd3eea0d1e142d85ed2656d6c28d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6750-14-72"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4124504" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

MOESM1 of Predicting compositions of microbial communities from stoichiometric models with applications for the biogas process

Sabine Koch, Dirk Benndorf, Karen Fronk, Udo Reichl, Steffen Klamt
<span title="2016-12-15">2016</span> <i title="Figshare"> Figshare </i> &nbsp;
Additional file 1. Investigation of proton translocation stoichiometries in D. vulgaris
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6084/m9.figshare.c.3623327_d3.v1">doi:10.6084/m9.figshare.c.3623327_d3.v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xutfgarr2jbjxmltpkd5efvd2a">fatcat:xutfgarr2jbjxmltpkd5efvd2a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200216122204/https://s3-eu-west-1.amazonaws.com/pstorage-npg-968563215/7127204/13068_2016_429_MOESM1_ESM.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1e/15/1e15057d2e2307c9a36127d436fe517e9ff1fb86.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6084/m9.figshare.c.3623327_d3.v1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> figshare.com </button> </a>

Metaproteomics of activated sludge from a wastewater treatment plant - A pilot study

Sebastian Püttker, Fabian Kohrs, Dirk Benndorf, Robert Heyer, Erdmann Rapp, Udo Reichl
<span title="2015-08-20">2015</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fuys75pzlrec5izxlpab5g6jue" style="color: black;">Proteomics</a> </i> &nbsp;
peptides was mainly attributed to redundant assignments of peptides to highly 119 conserved proteins from different species, e.g. chaperones, elongation factors or keratins as discussed 120 by Benndorf and Reichl  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pmic.201400559">doi:10.1002/pmic.201400559</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26201837">pmid:26201837</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/t6ytpxarwvhj3afelep7j5ben4">fatcat:t6ytpxarwvhj3afelep7j5ben4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170921211834/http://pubman.mpdl.mpg.de/pubman/item/escidoc:2176273/component/escidoc:2264241/MS_2176273_puettker.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5f/d8/5fd856cc170d88c2f02041520677f2a7924ecddf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pmic.201400559"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Coexistence in the chemostat as a result of metabolic by-products

Julia Heßeler, Julia K. Schmidt, Udo Reichl, Dietrich Flockerzi
<span title="2006-07-04">2006</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kngnkwdthrbili3232uvzfjyyi" style="color: black;">Journal of Mathematical Biology</a> </i> &nbsp;
Classical chemostat models assume that competition is purely exploitative and mediated via a common, limiting and single resource. However, in laboratory experiments with pathogens related to the genetic disease Cystic Fibrosis, species specific properties of production, inhibition and consumption of a metabolic by-product, acetate, were found. These assumptions were implemented into a mathematical chemostat model which consists of four nonlinear ordinary differential equations describing two
more &raquo; ... ecies competing for one limiting nutrient in an open system. We derive classical chemostat results and find that our basic model supports the competitive exclusion principle, the bistability of the system as well as stable coexistence. The analytical results are illustrated by numerical simulations performed with experimentally measured parameter values. As a variant of our basic model, mimicking testing of antibiotics for therapeutic treatments in mixed cultures instead of pure ones, we consider the introduction of a lethal inhibitor, which cannot be eliminated by Coexistence in the chemostat as a result of metabolic by-products 557 one of the species and is selective for the stronger competitor. We discuss our theoretical results in relation to our experimental model system and find that simulations coincide with the qualitative behavior of the experimental result in the case where the metabolic by-product serves as a second carbon source for one of the species, but not the producer.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00285-006-0012-3">doi:10.1007/s00285-006-0012-3</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16819650">pmid:16819650</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/aasbeg2wgzad7msaiucqgusn5y">fatcat:aasbeg2wgzad7msaiucqgusn5y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20091127232200/http://omnibus.uni-freiburg.de:80/~jh94/paper/chemostat_jmb06.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/31/6d/316d78c3e2a1ff2438d82d5ba0e195799eece7fb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00285-006-0012-3"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Elements in the Development of a Production Process for Modified Vaccinia Virus Ankara

Ingo Jordan, Verena Lohr, Yvonne Genzel, Udo Reichl, Volker Sandig
<span title="2013-11-01">2013</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/bzjhgcq36jerhe5h6hpr7zf344" style="color: black;">Microorganisms</a> </i> &nbsp;
The production of several viral vaccines depends on chicken embryo fibroblasts or embryonated chicken eggs. To replace this logistically demanding substrate, we created continuous anatine suspension cell lines (CR and CR.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/microorganisms1010100">doi:10.3390/microorganisms1010100</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27694766">pmid:27694766</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5029493/">pmcid:PMC5029493</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cuygh7twgraxplbdygg4lh6geu">fatcat:cuygh7twgraxplbdygg4lh6geu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170706121106/http://pubman.mpdl.mpg.de/pubman/item/escidoc%3A1852440/component/escidoc%3A1858550/1852440_jordan.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fa/4f/fa4f8308180704ed4a66eb669d850feb06f32420.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/microorganisms1010100"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5029493" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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