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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 that includes a complete set of utilities related
with the CAI....
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 ligands
Springer Science and Business Media LLC - - 2007
AbstractBackgroundDomains 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.ResultsUsing sensitive sequence
and structure similarity searches we identify a novel superfamily containing the
β-grasp fold. They are found in a diverse set of proteins that include the
animal ...
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 nematodes
Springer Science and Business Media LLC - - 2022
Abstract 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 genes or
genomes, Nematoda seems to be an eccentric group. Results Taking advantage of
the recent accum...
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