Results 51 to 60 of about 49,031 (262)

The Codon Statistics Database: A Database of Codon Usage Bias

Molecular Biology and Evolution, 2022
Abstract We present the Codon Statistics Database, an online database that contains codon usage statistics for all the species with reference or representative genomes in RefSeq (over 15,000). The user can search for any species and access two sets of tables.
Krishnamurthy Subramanian, Bryan Payne, Felix Feyertag, David Alvarez-Ponce   +3 more
openaire   +2 more sources

Calpain small subunit homodimerization is robust and calcium‐independent

FEBS Letters, EarlyView.
Calpains dimerize via penta‐EF‐hand (PEF) domains. Using single‐molecule force spectroscopy, we measured the strength and kinetics of PEF–PEF homodimer binding. The interaction is robust, shows a transient conformational step before dissociation, and remains largely insensitive to Ca2+.
Nesha May O. Andoy, Trina Dykstra‐MacPherson, Mathias A. Bell, Peter L. Davies, Ruby May A. Sullan   +4 more
wiley   +1 more source

Codon Usage in the Iflaviridae Family Is Not Diverse Though the Family Members Are Isolated from Diverse Host Taxa

Viruses, 2019
All iflavirus members belong to the unique genus, Iflavirus, of the family, Iflaviridae. The host taxa and sequence identities of these viruses are diverse.
Sheng-Lin Shi, Run-Xi Xia
doaj   +1 more source

Peroxidasin enables melanoma immune escape by inhibiting natural killer cell cytotoxicity

Molecular Oncology, EarlyView.
Peroxidasin (PXDN) is secreted by melanoma cells and binds the NK cell receptor NKG2D, thereby suppressing NK cell activation and cytotoxicity. PXDN depletion restores NKG2D signaling and enables effective NK cell–mediated melanoma killing. These findings identify PXDN as a previously unrecognized immune evasion factor and a potential target to improve
Hsu‐Min Sung, David Bickel, Lena C. M. Krause, Daria Ezeriņa, Christian Ickes, Julian Wojtachnia, Christine S. Gibhardt, Magdalena Shumanska, Khadija Wahni, Andrea Paluschkiwitz, Julia Malo Pueyo, Ekaterina Baranova, Wim Vranken, Hedwig Stanisz, Ioana Stejerean‐Todoran, Michael P. Schön, Joris Messens, Ivan Bogeski   +17 more
wiley   +1 more source

Scaled codon usage similarity index: A comprehensive resource for crop plants

Journal of Genetic Engineering and Biotechnology
Over the past three decades species-specific codon usage bias has been used to optimize heterologous gene expression in the target host. However, synthesizing codon optimized gene for multiple species is not achievable due to the prohibitive expense of ...
Taniya Bargoti, Divya Pratap Nain, Rajesh Kumar, Amit Kumar Awasthi, Deepali Singh, Vikrant Nain   +5 more
doaj   +1 more source

Analysis of transcriptome data reveals multifactor constraint on codon usage in Taenia multiceps

BMC Genomics, 2017
Background Codon usage bias (CUB) is an important evolutionary feature in genomes that has been widely observed in many organisms. However, the synonymous codon usage pattern in the genome of T. multiceps remains to be clarified.
Xing Huang, Jing Xu, Lin Chen, Yu Wang, Xiaobin Gu, Xuerong Peng, Guangyou Yang   +6 more
doaj   +1 more source

Quantifying shifts in natural selection on codon usage between protein regions: a population genetics approach

BMC Genomics, 2022
Background Codon usage bias (CUB), the non-uniform usage of synonymous codons, occurs across all domains of life. Adaptive CUB is hypothesized to result from various selective pressures, including selection for efficient ribosome elongation, accurate ...
Alexander L. Cope, Michael A. Gilchrist
doaj   +1 more source

Identification of serum protein biomarkers for pre‐cancerous lesions associated with pancreatic ductal adenocarcinoma

Molecular Oncology, EarlyView.
This work identified serum proteins associated with pancreatic epithelial neoplasms (PanINs) and early‐stage PDAC. Proteomics screens assessed genetically engineered mice with abundant PanINs, KPC mice (Lox‐STOP‐Lox‐KrasG12D/+ Lox‐STOP‐Lox‐Trp53R172H/+ Pdx1‐Cre) before PDAC development and also early‐stage PDAC patients (n = 31), compared to benign ...
Hannah Mearns, Jaclyn S. Long, Sergio Lilla, Kelly Hodge, Marcus J. G. W. Ladds, Colin Nixon, Paula Fernández‐Palanca, Sara Zanivan, Pilar Acedo, Stephen P. Pereira, Kevin M. Ryan   +10 more
wiley   +1 more source

A general model of codon bias due to GC mutational bias.

PLoS ONE, 2010
BackgroundIn spite of extensive research on the effect of mutation and selection on codon usage, a general model of codon usage bias due to mutational bias has been lacking.
Gareth A Palidwor, Theodore J Perkins, Xuhua Xia   +2 more
doaj   +1 more source

Genetic attenuation of ALDH1A1 increases metastatic potential and aggressiveness in colorectal cancer

Molecular Oncology, EarlyView.
Aldehyde dehydrogenase 1A1 (ALDH1A1) is a cancer stem cell marker in several malignancies. We established a novel epithelial cell line from rectal adenocarcinoma with unique overexpression of this enzyme. Genetic attenuation of ALDH1A1 led to increased invasive capacity and metastatic potential, the inhibition of proliferation activity, and ultimately ...
Martina Poturnajova, Zuzana Kozovska, Ondrej Pos, Kristina Pavlov, Sachin Gulati, Peter Makovicky, Kristina Jakic, Monika Burikova, Eva Sedlackova, Barbora Svitkova, Silvia Tyciakova, Vojtech Bystry, Nicolas Blavet, Boris Tichy, Matej Hrnciar, Jaroslav Budis, Miroslav Tomas, Peter Dubovan, Georgina Kolnikova, Veronika Repaska, Nikoleta Mojzesova, Eva Zomborska, Daniel Pindak, Michal Mego, Tomas Szemes, Miroslava Matuskova   +25 more
wiley   +1 more source