Results 111 to 120 of about 78,844 (296)

Computational methods for ribosome profiling data analysis

WIREs RNA, 2019
AbstractSince the introduction of the ribosome profiling technique in 2009 its popularity has greatly increased. It is widely used for the comprehensive assessment of gene expression and for studying the mechanisms of regulation at the translational level.
Stephen J. Kiniry, Audrey M. Michel, Pavel V. Baranov   +2 more
openaire   +3 more sources

Analyzing the temporal regulation of translation efficiency in mouse liver

Genomics Data, 2016
Mammalian physiology and behavior follow daily rhythms that are orchestrated by endogenous timekeepers known as circadian clocks. Rhythms in transcription are considered the main mechanism to engender rhythmic gene expression, but important roles for ...
Peggy Janich, Alaaddin Bulak Arpat, Violeta Castelo-Szekely, David Gatfield   +3 more
doaj   +1 more source

Transcriptional profiling of colicin-induced cell death of Escherichia coli MG1655 identifies potential mechanisms by which bacteriocins promote bacterial diversity [PDF]

, 2004
We report the transcriptional response of Escherichia coli MG1655 to damage induced by colicins E3 and E9, bacteriocins that kill cells through inactivation of the ribosome and degradation of chromosomal DNA, respectively. Colicin E9 strongly induced the
Hinton, Jay C. D., James, Richard, Kleanthous, Colin, Moore, Geoffrey R., Rolfe, Matthew, Thompson, Arthur, WALKER, DANIEL   +6 more
core   +2 more sources

Multicohort Validation of Gut Microbiome Signatures for Cholangiocarcinoma Diagnosis and Functional Characterization of Bifidobacterium Pseudocatenulatum

Advanced Science, EarlyView.
This study analyzes gut bacteria in cholangiocarcinoma patients, revealing distinct microbial signatures that enable accurate disease detection. Species‐based diagnostic models achieved over 98% accuracy in identifying cholangiocarcinoma and distinguished it from other liver diseases. The research demonstrates that specific beneficial bacteria suppress
Benchen Rao, Jianwen Jiang, Ruiqing Zhang, Dongya Zhang, Chenchen Zhang, Ang Li, Haifeng Lu, Hua Zhang, Lin Zhou, Wenzhi Guo, Peihao Wen, Jianfeng Xue, Jie Pan, Tuerganaili Aji, Zhou Lan, Xianzhi Jiang, Shusen Zheng, Zujiang Yu, Zhigang Ren   +18 more
wiley   +1 more source

Revealing nascent proteomics in signaling pathways and cell differentiation. [PDF]

, 2018
Regulation of gene expression at the level of protein synthesis is a crucial element in driving how the genetic landscape is expressed. However, we are still limited in technologies that can quantitatively capture the immediate proteomic changes that ...
Burlingame, Alma L, Chalkley, Robert J, Forester, Craig M, Oses-Prieto, Juan A, Phillips, Nancy J, Ruggero, Davide, Urisman, Anatoly, Zhang, Li, Zhao, Qian   +8 more
core   +1 more source

Intracellular Aβ42 Sequestration by a Serine Protease Mitigates Neurotoxicity in a Drosophila Alzheimer's Disease Model

Advanced Science, EarlyView.
Emerging evidence suggests that intraneuronal Aβ accumulation represents an early pathogenic event in Alzheimer's disease (AD). Using Drosophila AD model, this study shows that a nonsecreted serine protease Yip7 physically interacts with Aβ. This causes intraneuronal Aβ accumulation but surprisingly reduces the associated neurotoxicity, arguing that ...
Jingyun Su, Meng Yang, Xinfeng Wang, Pa Wu, Zongzhao Zhai   +4 more
wiley   +1 more source

Bioenergy Cropping Reduces the Spatiotemporal Scaling of Soil Bacterial Biodiversity

Advanced Science, EarlyView.
Consistent with patterns observed in plant and animal communities, soil bacterial communities exhibit significant species–time–area and phylogenetic–time–area relationships independent of nested structure. Bioenergy cropping significantly reduces the spatiotemporal scaling rates, particularly in sandy loam soils.
Zhencheng Ye, Jialiang Kuang, Colin T. Bates, Arthur Escalas, Daliang Ning, Liyou Wu, Suo Liu, Sihang Deng, Jiesi Lei, Xiangwen Chen, Jennifer Pett‐Ridge, Malay Saha, Lauren Hale, Gangsheng Wang, Renmao Tian, Ying Fu, Yu Tang, Mary Firestone, Jizhong Zhou, Yunfeng Yang   +19 more
wiley   +1 more source

Reduced Maintenance DNA Methylation Thresholds Enable Sensitive Reporter Assays for UHRF1 and DNMT1 Inhibition

Advanced Science, EarlyView.
The authors engineer colorectal cancer cells with reduced redundancy of UHRF1 and DNMT1, key DNA methylation maintenance factors, lowering the maintenance threshold and sensitizing cells to inhibition. They develop reporter assays driven by endogenous tumor‐suppressor gene promoters with enhanced sensitivity and dynamic range to demethylating drugs ...
Cuicui Xia, Ying Cui, Jiongliang Wang, Wenjing Bai, Danyang Wang, Yao Chen, Huahui Guo, Liangyi Zong, Bing Qin, Xintong Cai, Jie Wang, Jing Huang, Scott B. Rothbart, Zufeng Guo, Stephen B. Baylin, Xiangqian Kong   +15 more
wiley   +1 more source

riboviz: analysis and visualization of ribosome profiling datasets

BMC Bioinformatics, 2017
Background Using high-throughput sequencing to monitor translation in vivo, ribosome profiling can provide critical insights into the dynamics and regulation of protein synthesis in a cell.
Oana Carja, Tongji Xing, Edward W. J. Wallace, Joshua B. Plotkin, Premal Shah   +4 more
doaj   +1 more source

Template-directed biopolymerization: tape-copying Turing machines

, 2012
DNA, RNA and proteins are among the most important macromolecules in a living cell. These molecules are polymerized by molecular machines. These natural nano-machines polymerize such macromolecules, adding one monomer at a time, using another linear ...
Chowdhury, Debashish, Sharma, Ajeet K.
core   +1 more source