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Genome sequence and genetic diversity of the common carp, Cyprinus carpio
A draft genome of domesticated C. carpio (strain Songpu) is presented, whose current assembly contains 52,610 protein-coding genes and approximately 92.3% coverage of its paleotetraploidized genome (2n = 100).
Quality assessment parameters for EST-derived SNPs from catfish
Stringent quality assessment measures should be used when working with EST-derived SNPs, including contigs containing four or more ESTs and the minor allele sequence frequency, to provide effective means for SNP identification in species where genome sequence resources are lacking.
Improving fatty acids production by engineering dynamic pathway regulation and metabolic control
- P. Xu, Lingyun Li, Fuming Zhang, G. Stephanopoulos, M. Koffas
- Biology, MedicineProceedings of the National Academy of Sciences
- 21 July 2014
A genetically encoded metabolic switch that enables dynamic regulation of fatty acids (FA) biosynthesis in Escherichia coli was reported, able to dynamically compensate the critical enzymes involved in the supply and consumption of malonyl-CoA and efficiently redirect carbon flux toward FA biosynthesis.
Divergent Toll-like receptors in catfish (Ictalurus punctatus): TLR5S, TLR20, TLR21.
- P. Baoprasertkul, P. Xu, E. Peatman, H. Kucuktas, Zhanjiang Liu
- Biology, MedicineFish & shellfish immunology
- 1 December 2007
To better understand these teleost adaptations to the TLR family, isolated, sequenced, and characterized the full-length cDNA and gene sequences of TLR5S, TLR20, and TLR21 from catfish as well as studied their expression pattern in tissues.
ePathBrick: a synthetic biology platform for engineering metabolic pathways in E. coli.
The development of a set of vectors compatible with BioBrick standards and its application in metabolic engineering, which allow for fine-tuning gene expression by integrating multiple transcriptional activation or repression signals into the operator region.
Convergent evolution of perenniality in rice and sorghum
- F. Hu, D. Tao, +8 authors Z.-K. Li
- Biology, MedicineProceedings of the National Academy of Sciences…
- 17 March 2003
Analysis of genes in rice and sorghum suggests that the two genes may be key regulators of rhizome development in many Poaceae, which may contribute significantly to understanding of grass evolution, advance opportunities to develop perennial cereals, and offer insights into environmentally benign weed-control strategies.
Modular optimization of multi-gene pathways for fatty acids production in E. coli.
A modular engineering approach was systematically removed metabolic pathway bottlenecks and led to significant titre improvements in a multi-gene fatty acid metabolic pathway to demonstrate a generalized approach to engineering cell factories for valuable metabolites production.
Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA.
- P. Xu, S. Ranganathan, Zachary L. Fowler, C. Maranas, M. Koffas
- Biology, MedicineMetabolic engineering
- 1 September 2011
Combined effect of the genetic interventions was found to be synergistic based on a developed analysis method that correlates genetic modification to cell phenotype, specifically the identified knockout targets and overexpression targets can cooperatively force carbon flux towards malonyl-CoA.
The warm temperature acclimation protein Wap65 as an immune response gene: its duplicates are differentially regulated by temperature and bacterial infections.
- Z. Sha, P. Xu, T. Takano, Hong Liu, J. Terhune, Zhanjiang Liu
- Biology, MedicineMolecular immunology
- 1 March 2008
The results of this study suggest that Wap65 genes are not only important for its classical role as a warm temperature acclimation protein, but more importantly, may also function as an immune response protein.
The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts
- Zhanjiang Liu, Shikai Liu, +49 authors G. Waldbieser
- Biology, MedicineNature communications
- 2 June 2016
A high-quality reference genome sequence of channel catfish is reported, providing evidence that lack of secretory calcium-binding phosphoproteins accounts for the evolutionary loss of scales in catfish and demonstrates the power of comparative subtraction of candidate genes for traits of structural significance.