Results 61 to 70 of about 215,700 (227)

GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data

Genomics, Proteomics & Bioinformatics, 2018
Interactions between chromatin segments play a large role in functional genomic assays and developments in genomic interaction detection methods have shown interacting topological domains within the genome.
Riccardo Calandrelli, Qiuyang Wu, Jihong Guan, Sheng Zhong   +3 more
doaj   +1 more source

A yeast model of 5‐oxoproline accumulation reveals a general toleration to 5‐oxoproline

FEBS Open Bio, EarlyView.
Using a yeast model, we show that even high accumulation of 5‐oxoproline causes only mild cellular stress and does not trigger oxidative stress. Instead, cells adapt by activating efflux pumps and diverse protective pathways, suggesting that previously proposed harmful effects of 5‐oxoproline may arise from indirect metabolic imbalances rather than the
Pratiksha Dubey, Vaishnavi Sanjayan, Praveen Singh, Shantanu Sengupta, Anand Kumar Bachhawat   +4 more
wiley   +1 more source

Sudden anaerobization in Amphibacillus xylanus increases intracellular labile ferrous iron and inhibits cell growth

FEBS Open Bio, EarlyView.
Abruptly changing from aerobic to anaerobic conditions (sudden anaerobization) induced growth inhibition and a significant increase in intracellular labile ferrous iron in the aerotolerant anaerobe Amphibacillus xylanus. We found that free flavins mediate efficient electron transfer from NADH to ferric iron under anaerobic conditions, suggesting that ...
Shinya Kimata, Yoichi Sakai, Keisuke Tanaka, Etsuro Yoshimura, Ken Kitano, Morio Ishikawa, Tadahiro Nakamoto, Tsutomu Takayama, Hirofumi Inoue, Kaho Nomura, Tomonori Suzuki, Masataka Uchino, Akira Abe, Youichi Niimura   +13 more
wiley   +1 more source

Aquaporin‐3 and aquaporin‐5 impact the development of pancreatic ductal adenocarcinoma spheroids

FEBS Open Bio, EarlyView.
Schematic representation of the role of aquaporin‐3 (AQP3) and aquaporin‐5 (AQP5) in pancreatic ductal adenocarcinoma (PDAC). Both proteins are upregulated in PDAC and are associated with tumor progression and metastatic potential. Silencing AQP3 or AQP5 in PDAC spheroids results in decreased diameter, area, and overall growth, underscoring their key ...
Catarina Pimpão, Diogo M. Engrácia, Graça Soveral, Filipa Mendes   +3 more
wiley   +1 more source

Application of Hi-C and other omics data analysis in human cancer and cell differentiation research

Computational and Structural Biotechnology Journal, 2021
With the development of 3C (chromosome conformation capture) and its derivative technology Hi-C (High-throughput chromosome conformation capture) research, the study of the spatial structure of the genomic sequence in the nucleus helps researchers ...
Haiyan Gong, Yi Yang, Sichen Zhang, Minghong Li, Xiaotong Zhang   +4 more
doaj   +1 more source

A Prospective Study of Individuals at Risk of Multiple Sclerosis Informs the Design of Primary Prevention Studies

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT Objective In multiple sclerosis, the optimal time for deploying a therapeutic intervention is before the central nervous system is damaged; given the success of trials treating the earliest stage of MS, the radiologically isolated syndrome, developing primary prevention strategies is an important next challenge.
Amy W. Laitinen, Ceren Tozlu, Tina Roostaei, Fatoumata Diallo, Kaho Onomichi, Jiyeon Son, Zongqi Xia, Philip L. De Jager   +7 more
wiley   +1 more source

Methods for comparative ChIA-PET and Hi-C data analysis

Methods, 2020
The three-dimensional architecture of chromatin in the nucleus is important for genome regulation and function. Advanced high-throughput sequencing-based methods have been developed for capturing chromatin interactions (Hi-C, genome-wide chromosome conformation capture) or enriching for those involving a specific protein (ChIA-PET, chromatin ...
Capurso, Dan, Tang, Zhonghui, Ruan, Yijun   +2 more
openaire   +3 more sources

FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data

Genome Biology, 2020
Chromosome conformation capture data, particularly from high-throughput approaches such as Hi-C, are typically very complex to analyse. Existing analysis tools are often single-purpose, or limited in compatibility to a small number of data formats ...
Kai Kruse, Clemens B. Hug, Juan M. Vaquerizas   +2 more
doaj   +1 more source

SPG4 and Dementia: Expanding the Clinical Spectrum

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT Objective Hereditary spastic paraplegia (HSP) is a group of disorders characterized by progressive spasticity and lower limb weakness, with mutations in SPG4/SPAST being the most common cause. Detailed studies and clinical and molecular comparisons across different populations are missing.
Emanuele Panza, Arun Meyyazhagan, Eliseo Picchi, Gustavo Ribas, Ingrid Faber, Ryosuke Miyamoto, Preethi Basavaraju, Paolo Eusebi, Haripriya Kuchi Bhotla, Mario Stasi, Fabrizio Gaudiello, Francesco Patti, Filippo Maria Santorelli, Marcondes Cavalcante França Jr, José Luiz Pedroso, Orlando Graziani Povoas Barsottini, Hélio Afonso Ghizoni Teive, Peter Henry St George‐Hyslop, Toshitaka Kawarai, Antonio Orlacchio   +19 more
wiley   +1 more source

HiCHap: a package to correct and analyze the diploid Hi-C data

BMC Genomics, 2020
Background In diploid cells, it is important to construct maternal and paternal Hi-C contact maps respectively since the two homologous chromosomes can differ in chromatin three-dimensional (3D) organization.
Han Luo, Xinxin Li, Haitao Fu, Cheng Peng   +3 more
doaj   +1 more source