Zobrazeno 1 - 10
of 189
pro vyhledávání: '"Karsten Zengler"'
Publikováno v:
PLoS Computational Biology, Vol 19, Iss 10, p e1011594 (2023)
Bacteroides fragilis is a universal member of the dominant commensal gut phylum Bacteroidetes. Its fermentation products and abundance have been linked to obesity, inflammatory bowel disease, and other disorders through its effects on host metabolic
Externí odkaz:
https://doaj.org/article/69db30e075964b218d68f7dd6aa08c8a
Autor:
Chien-Ting Li, Richard Eng, Cristal Zuniga, Kai-Wen Huang, Yiqun Chen, Karsten Zengler, Michael J. Betenbaugh
Publikováno v:
npj Systems Biology and Applications, Vol 9, Iss 1, Pp 1-12 (2023)
Abstract Algal cultivations are strongly influenced by light and dark cycles. In this study, genome-scale metabolic models were applied to optimize nutrient supply during alternating light and dark cycles of Chlorella vulgaris. This approach lowered
Externí odkaz:
https://doaj.org/article/1e41f77ea2984fdfa8b947b68040102d
Autor:
Diego Tec-Campos, Camila Posadas, Juan D Tibocha-Bonilla, Deepan Thiruppathy, Nathan Glonek, Cristal Zuñiga, Alejandro Zepeda, Karsten Zengler
Publikováno v:
PLoS Computational Biology, Vol 19, Iss 8, p e1011371 (2023)
The purple non-sulfur bacterium Rhodopseudomonas palustris is recognized as a critical microorganism in the nitrogen and carbon cycle and one of the most common members in wastewater treatment communities. This bacterium is metabolically extremely ve
Externí odkaz:
https://doaj.org/article/44445c019fd54c239c6288d340b88ca4
Autor:
Juan D. Tibocha-Bonilla, Cristal Zuñiga, Asama Lekbua, Colton Lloyd, Kevin Rychel, Katie Short, Karsten Zengler
Publikováno v:
npj Systems Biology and Applications, Vol 8, Iss 1, Pp 1-12 (2022)
Abstract Bacillus subtilis is a well-characterized microorganism and a model for the study of Gram-positive bacteria. The bacterium can produce proteins at high densities and yields, which has made it valuable for industrial bioproduction. Like other
Externí odkaz:
https://doaj.org/article/66bae66e8d24405387d8acba0caea2aa
Publikováno v:
BMC Bioinformatics, Vol 23, Iss 1, Pp 1-13 (2022)
Abstract Background Genome-scale metabolic reconstruction tools have been developed in the last decades. They have helped to reconstruct eukaryotic and prokaryotic metabolic models, which have contributed to fields, e.g., genetic engineering, drug di
Externí odkaz:
https://doaj.org/article/a5dcf9102cc34cdea0652b5941e51913
Autor:
Cameron Martino, Livia S. Zaramela, Bei Gao, Mallory Embree, Janna Tarasova, Seth J. Parker, Yanhan Wang, Huikuan Chu, Peng Chen, Kuei-Chuan Lee, Daniela Domingos Galzerani, Jivani M. Gengatharan, Asama Lekbua, Maxwell Neal, Rob Knight, Hidekazu Tsukamoto, Christian M. Metallo, Bernd Schnabl, Karsten Zengler
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-11 (2022)
Chronic alcohol use is associated with intestinal bacterial overgrowth and dysbiosis, but the contribution of ethanol is unclear. Here, using mouse models, the authors find that ethanol is not directly metabolized by the gut microbiota, and that indu
Externí odkaz:
https://doaj.org/article/292675b6fc0d412ca90d9a63b7406e41
Autor:
Joanna Coker, Kateryna Zhalnina, Clarisse Marotz, Deepan Thiruppathy, Megan Tjuanta, Gavin D’Elia, Rodas Hailu, Talon Mahosky, Meagan Rowan, Trent R. Northen, Karsten Zengler
Publikováno v:
mSystems, Vol 7, Iss 6 (2022)
ABSTRACT Microbial soil communities form commensal relationships with plants to promote the growth of both parties. The optimization of plant-microbe interactions to advance sustainable agriculture is an important field in agricultural research. Howe
Externí odkaz:
https://doaj.org/article/a861daaf267d4e86b110b260584c2897
synDNA—a Synthetic DNA Spike-in Method for Absolute Quantification of Shotgun Metagenomic Sequencing
Publikováno v:
mSystems, Vol 7, Iss 6 (2022)
ABSTRACT Microbiome studies have the common goal of determining which microbial taxa are present, respond to specific conditions, or promote phenotypic changes in the host. Most of these studies rely on relative abundance measurements to drive conclu
Externí odkaz:
https://doaj.org/article/452e62cdad074fd0b3173b0669cfd58a
Autor:
Daniel Hakim, Stephen Wandro, Karsten Zengler, Livia S. Zaramela, Brent Nowinski, Austin Swafford, Qiyun Zhu, Se Jin Song, Antonio Gonzalez, Daniel McDonald, Rob Knight
Publikováno v:
mSystems, Vol 7, Iss 5 (2022)
ABSTRACT Assigning taxonomy remains a challenging topic in microbiome studies, due largely to ambiguity of reads which overlap multiple reference genomes. With the Web of Life (WoL) reference database hosting 10,575 reference genomes and growing, the
Externí odkaz:
https://doaj.org/article/eecc9545c0544bd6bcd9a83695bfda89
Autor:
Morgan M. Severn, Michael R. Williams, Ali Shahbandi, Zoie L. Bunch, Laurie M. Lyon, Amber Nguyen, Livia S. Zaramela, Daniel A. Todd, Karsten Zengler, Nadja B. Cech, Richard L. Gallo, Alexander R. Horswill
Publikováno v:
mBio, Vol 13, Iss 3 (2022)
ABSTRACT Staphylococcus hominis is frequently isolated from human skin, and we hypothesize that it may protect the cutaneous barrier from opportunistic pathogens. We determined that S. hominis makes six unique autoinducing peptide (AIP) signals that
Externí odkaz:
https://doaj.org/article/d4ba64cd5ebc4fd394a77411c3ce3fc8