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Functional non-coding (fnc)RNAs are nucleotide sequences of varied lengths, structures, and mechanisms that ubiquitously influence gene expression and translation, genome stability and dynamics, and human health and disease. Here, to shed light on their functional determinants, we seek to exploit the evolutionary record of variation and divergence read from sequence comparisons. The approach follows the phylogenetic Evolutionary Trace (ET) paradigm, first developed and extensively validated on proteins. We assigned a relative rank of importance to every base in a study of 1070 functional RNAs, including the ribosome, and observed evolutionary patterns strikingly similar to those seen in proteins, namely, (1) the top-ranked bases clustered in secondary and tertiary structures. (2) In turn, these clusters mapped functional regions for catalysis, binding proteins and drugs, post-transcriptional modification, and deleterious mutations. (3) Moreover, the quantitative quality of these clusters correlated with the identification of functional regions. (4) As a result of this correlation, smoother structural distributions of evolutionary important nucleotides improved functional site predictions. Thus, in practice, phylogenetic analysis can broadly identify functional determinants in RNA sequences and functional sites in RNA structures, and reveal details on the basis of RNA molecular functions. As example of application, we report several previously undocumented and potentially functional ET nucleotide clusters in the ribosome. This work is broadly relevant to studies of structure-function in ribonucleic acids. Additionally, this generalization of ET shows that evolutionary constraints among sequence, structure, and function are similar in structured RNA and proteins. RNA ET is currently available as part of the ET command-line package, and will be available as a web-server.
This article was published in the following journal.
Name: PLoS computational biology
Pullulanases are well-known debranching enzymes hydrolyzing α-1,6-glycosidic linkages. To date, engineering of pullulanase is mainly focused on catalytic pocket or domain tailoring based on structure...
Trace elements have important influence on body function primarily because of the vital role they have in many physiological processes. Their alterations have been found in many disorders, including c...
The present study evaluated the phytoremediation potential of the floating macrophyte for removing trace metals from contaminated water bodies. Forty quadrats, distributed equally in eight sites (six...
N-Glycosylation is one of the most important post-translational mechanisms in eukaryotes. It plays a vital role in various biological processes such as protein folding, stability, immunogenicity of di...
The freshwater polyculture pond culturing occupied an important position in the aquaculture industry. Accumulation of trace metals was investigated in water, sediments, and fish (Carassius auratus, Cy...
Physicians know that their patients can react differently to the same medical treatment: for some of them, the drug will prove inefficient, whereas for others it might provoke side-effects...
This is a single-center, exploratory comparative pilot study to identify the most appropriate method for microbial consortia sampling from the skin. Ten subjects are expected to complete ...
It has been observed that patients on total parenteral nutrition (TPN) have high plasma chromium level. There is reason to believe that TPN solutions contain chromium and possibly other tr...
The main objective of this study is to evaluate the systemic impact of salting out of trace elements (TE) by metallic and nonmetallic implantable medical devices (IMD) and in particular th...
Cardiovascular disease (CVD) affects millions of people in the United States; each year, more people die from CVD than from any other disease. There are many dietary and lifestyle factors ...
An analytical transmission electron microscopy method using an electron microscope fitted with an energy filtering lens. The method is based on the principle that some of the ELECTRONS passing through the specimen will lose energy when they ionize inner shell electrons of the atoms in the specimen. The amount of energy loss is dependent upon the element. Analysis of the energy loss spectrum (ELECTRON ENERGY-LOSS SPECTROSCOPY) reveals the elemental composition of a specimen. It is used analytically and quantitatively to determine which, how much of, and where specific ELEMENTS are in a sample. For example, it is used for elemental mapping of PHOSPHORUS to trace the strands of NUCLEIC ACIDS in nucleoprotein complexes.
A metallic element of atomic number 30 and atomic weight 65.38. It is a necessary trace element in the diet, forming an essential part of many enzymes, and playing an important role in protein synthesis and in cell division. Zinc deficiency is associated with ANEMIA, short stature, HYPOGONADISM, impaired WOUND HEALING, and geophagia. It is known by the symbol Zn.
Local surface sites on antibodies which react with antigen determinant sites on antigens. They are formed from parts of the variable regions of FAB FRAGMENTS.
Regulatory sequences important for viral replication that are located on each end of the HIV genome. The LTR includes the HIV ENHANCER, promoter, and other sequences. Specific regions in the LTR include the negative regulatory element (NRE), NF-kappa B binding sites , Sp1 binding sites, TATA BOX, and trans-acting responsive element (TAR). The binding of both cellular and viral proteins to these regions regulates HIV transcription.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
The process of gene expression is used by eukaryotes, prokaryotes, and viruses to generate the macromolecular machinery for life. Steps in the gene expression process may be modulated, including the transcription, RNA splicing, translation, and post-tran...
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...