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CAIcal: A combined set of tools to assess codon usage adaptation
Springer Science and Business Media LLC - Tập 3 - Trang 1-8 - 2008
The Codon Adaptation Index (CAI) was first developed to measure the synonymous codon usage bias for a DNA or RNA sequence. The CAI quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set. We describe here CAIcal, a web-server available at
http://genomes.urv.es/CAIcal......
Deep learning-assisted high-content screening identifies isoliquiritigenin as an inhibitor of DNA double-strand breaks for preventing doxorubicin-induced cardiotoxicity
Springer Science and Business Media LLC - Tập 18 - Trang 1-19 - 2023
Anthracyclines including doxorubicin are essential components of many cancer chemotherapy regimens, but their cardiotoxicity severely limits their use. New strategies for treating anthracycline-induced cardiotoxicity (AIC) are still needed. Anthracycline-induced DNA double-strand break (DSB) is the major cause of its cardiotoxicity. However, DSB-based drug screening for AIC has not been performed ......
CRISPR transcript processing: a mechanism for generating a large number of small interfering RNAs
Springer Science and Business Media LLC - Tập 7 - Trang 1-11 - 2012
CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated sequences) is a recently discovered prokaryotic defense system against foreign DNA, including viruses and plasmids. CRISPR cassette is transcribed as a continuous transcript (pre-crRNA), which is processed by Cas proteins into small RNA molecules (crRNAs) that are responsible for defense against invading viruse......
Relating underrepresented genomic DNA patterns and tiRNAs: the rule behind the observation and beyond
Springer Science and Business Media LLC - Tập 5 - Trang 1-16 - 2010
One of the central problems of post-genomic biology is the understanding of regulatory network of genes. Traditionally the problem is approached from the protein-DNA interaction perspective. In recent years various types of noncoding RNAs appeared on the scene as new potent players of the game. The exact role of these molecules in gene expression control is mostly unknown at present, while their i......
A new family of hybrid virophages from an animal gut metagenome
Springer Science and Business Media LLC - Tập 10 - Trang 1-9 - 2015
Search of metagenomics sequence databases for homologs of virophage capsid proteins resulted in the discovery of a new family of virophages in the sheep rumen metagenome. The genomes of the rumen virophages (RVP) encode a typical virophage major capsid protein, ATPase and protease combined with a Polinton-type, protein primed family B DNA polymerase. The RVP genomes appear to be linear molecules, ......
Consequences of cell-to-cell P-glycoprotein transfer on acquired multidrug resistance in breast cancer: a cell population dynamics model
Springer Science and Business Media LLC - Tập 6 Số 1 - Trang 1-18 - 2011
Cancer is a proliferation disease affecting a genetically unstable cell population, in which molecular alterations can be somatically inherited by genetic, epigenetic or extragenetic transmission processes, leading to a cooperation of neoplastic cells within tumoural tissue. The efflux protein P-glycoprotein (P-gp) is overexpressed in many cancer cells and has known capacity to confer multidrug re......
A novel superfamily containing the β-grasp fold involved in binding diverse soluble ligandsAbstract Background Domains containing the β-grasp fold are utilized in a great diversity of physiological functions but their role, if any, in soluble or small molecule ligand recognition is poorly studied. Results Using sensitive sequence and structure similarity searche...
Springer Science and Business Media LLC - - 2007
Phylogenetic analysis reveals wide distribution of globin X
Springer Science and Business Media LLC - Tập 6 - Trang 1-5 - 2011
The vertebrate globin gene repertoire consists of seven members that differ in terms of structure, function and phyletic distribution. While hemoglobin, myoglobin, cytoglobin, and neuroglobin are present in almost all gnathostomes examined so far, other globin genes, like globin X, are much more restricted in their phyletic distribution. Till today, globin X has only been found in teleost fish and......
Tissue-specific roles of peroxisomes revealed by expression meta-analysis
Springer Science and Business Media LLC - Tập 19 - Trang 1-14 - 2024
Peroxisomes are primarily studied in the brain, kidney, and liver due to the conspicuous tissue-specific pathology of peroxisomal biogenesis disorders. In contrast, little is known about the role of peroxisomes in other tissues such as the heart. In this meta-analysis, we explore mitochondrial and peroxisomal gene expression on RNA and protein levels in the brain, heart, kidney, and liver, focusin......
Intron losses and gains in the nematodesAbstract
Background
The evolution of spliceosomal introns has been widely studied among various eukaryotic groups. Researchers nearly reached the consensuses on the pattern and the mechanisms of intron losses and gains across eukaryotes. However, according to previous studies that analyzed a few gen... ...
Springer Science and Business Media LLC - - 2022
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