Therefore in this book I will consider genes as DNA sequences encoding information for functional products, be it proteins or RNA molecules. (wikipedia.org)
The understanding of this process has been studied by the application of high-throughput sequencing technologies, which grants a better assessment of the different microbial taxa and their genes involved in this microbial succession. (frontiersin.org)
All archaeal and many bacterial genomes contain Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) and variable arrays of the CRISPR-associated ( cas ) genes that have been previously implicated in a novel form of DNA repair on the basis of comparative analysis of their protein product sequences. (biomedcentral.com)
It is proposed that unique inserts of CRISPR, some of which are homologous to fragments of bacteriophage and plasmid genes, function as prokaryotic siRNAs (psiRNA), by base-pairing with the target mRNAs and promoting their degradation or translation shutdown. (biomedcentral.com)
Sequencing the genomes of multiple, taxonomically diverse eukaryotes enables in-depth comparative-genomic analysis which is expected to help in reconstructing ancestral eukaryotic genomes and major events in eukaryotic evolution and in making functional predictions for currently uncharacterized conserved genes. (biomedcentral.com)
Transcriptome studies of wild type Haloferax cells and the deletion mutant revealed up-regulation of six genes in the deletion strain, showing that the sRNA has a clearly defined function. (uni-stuttgart.de)
Eukaryotes1
During protein synthesis, ribosomes become stalled on polyproline-containing sequences, unless they are rescued in archaea and eukaryotes by the initiation factor 5A (a/eIF-5A) and in bacteria by the homologous protein EF-P. While a structure of EF-P bound to the 70S ribosome exists, structural insight into eIF-5A on the 80S ribosome has been lacking. (cipsm.de)
Genome2
Thus, the manuscript from Guiglielmoni et al will be an almost intemporal one (up to the next sequencing revolution at last), and as they advocated for a more informed genome database, I think we should consider a rolling benchmarking system (tools, genome and sequence dataset) allowing to keep the performance of the tools up-to-date, and to propose the best set of assembly tools for a given type of genome. (peercommunityin.org)
To date, hundreds of candidate structured RNAs have been predicted using informatic approaches that search for motif structures in genomic sequence data. (biomedcentral.com)
article{marchfelder2021small, abstract = {The function and mode of action of small regulatory RNAs is currently still understudied in archaea. (uni-stuttgart.de)
Gene9
The Mendelian gene is a basic unit of heredity and the molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. (wikipedia.org)
A gene can acquire mutations in their sequence, leading to different variants, known as alleles, in the population. (wikipedia.org)
The molecular gene definition is more commonly used across biochemistry, molecular biology, and most of genetics - the gene that's described in terms of DNA sequence. (wikipedia.org)
We define a gene as a DNA sequence that is transcribed. (wikipedia.org)
A gene is a DNA sequence that codes for a diffusible product. (wikipedia.org)
Sequence homology is an indication of the genetic relatedness of different organisms and gene function. (lookformedical.com)
Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. (lookformedical.com)
Here we cloned and characterized the Pfu RNA ligase encoded by the PF0353 gene in the hyperthermophilic archaea Pyrococcus furiosus. (bvsalud.org)
Diseases1
Some genetic traits are instantly visible, such as eye color or the number of limbs, and some are not, such as blood type, the risk for specific diseases, or the thousands of basic biochemical processes that constitute life. (wikipedia.org)
Protein1
Selected portions of the DNA nucleotide sequence are copied into a corresponding RNA nucleotide sequence, which either encodes a protein (if it is an mRNA) or forms a 'structural' RNA, such as a transfer RNA (tRNA) or ribosomal RNA (rRNA) molecule. (wikipedia.org)
Regulatory1
The region of DNA which borders the 3' end of a transcription unit and where a variety of regulatory sequences are located. (lookformedical.com)
Molecules1
Dicer cleaves long dsRNA molecules into short, 21-22 nucleotide duplexes which are subsequently unwound by the RISC to yield mature siRNAs. (biomedcentral.com)
Ligation1
5'-Adenylated oligonucleotides (AppOligos) are widely used for single-stranded DNA/RNA ligation in next-generation sequencing (NGS) applications such as microRNA (miRNA) profiling. (bvsalud.org)
Genomic2
The genomic sequences of ten geographically and phenotypically diverse clinical isolates of M. catarrhalis were determined and analyzed together with two publicly available genomes. (biomedcentral.com)
For around 20 that remained uncharacterized, functions were predicted by in-depth sequence analysis and examination of genomic context. (biomedcentral.com)
In the halophilic archaeon H. volcanii a plethora of sRNAs have been identified, however, in-depth functional analysis is missing for most of them. (uni-stuttgart.de)
Approaches1
This huge and exhaustive review starts with an overview of the current sequencing technologies, followed by the theory of the different approaches for assembly and their implementation. (peercommunityin.org)
Long2
TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. (lookformedical.com)
Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. (lookformedical.com)
System2
Specific hypothetical schemes are developed for the functioning of the predicted prokaryotic siRNA system and for the formation of new CRISPR units with unique inserts encoding psiRNA conferring immunity to the respective newly encountered phages or plasmids. (biomedcentral.com)
It appears most likely that CASS is a prokaryotic system of defense against phages and plasmids that functions via the RNAi mechanism. (biomedcentral.com)
this covariation suggests that when one nucleotide of a predicted structured motif undergoes mutation, a compensatory mutation of the complementary base-pairing nucleotide is also observed, preserving the overall structure [ 3 , 4 ]. (biomedcentral.com)
Specific1
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. (lookformedical.com)
Data1
Here we use atomistic molecular dynamics (MD) simulations in combination with data clustering methods and quantum chemical calculations to probe principles underlying proton reduction as well as proton and sodium transport in Mbh from the hyperthermophilic archaeon Pyrococcus furiosus. (bvsalud.org)
Human1
DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom. (lookformedical.com)
Bacteria9
Archaea, together with Bacteria, represent the two main divisions of life on Earth, with many of the defining characteristics of the more complex eukaryotes tracing their origin to evolutionary innovations first made in their archaeal ancestors. (biomedcentral.com)
AN - infection: coord IM with GRAM-NEGATIVE BACTERIAL INFECTIONS (IM) HN - 2004 MH - Achromobacter xylosoxidans UI - D042441 MN - B3.440.400.425.117.24.950 MN - B3.660.75.27.30.950 MS - The type species of gram negative, aerobic bacteria in the genus ACHROMOBACTER. (nih.gov)
Genomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss. (biomedcentral.com)
Thus, the prevailing mode of evolution in bacteria and archaea is genome contraction, which is partially compensated by the gain of new gene families via horizontal gene transfer. (biomedcentral.com)
Reconstruction of evolution for groups of closely related bacteria and archaea reveals an extremely rapid and highly variable flux of genes in evolving microbial genomes, demonstrates that extensive gene loss and horizontal gene transfer leading to innovation are the two dominant evolutionary processes, and yields robust estimates of the supergenome size. (biomedcentral.com)
Comparative genomics of bacteria and archaea (collectively, prokaryotes) reveals extensive variation of gene repertoires, which is thought to reflect a highly dynamic regime of genome evolution [ 1 ]-[ 6 ]. (biomedcentral.com)
All evolutionary reconstructions performed with widely different groups of bacteria and archaea infer various combinations of vertical inheritance, gene loss and gain. (biomedcentral.com)
In this study, we reconstructed 103 metagenome-assembled genomes (MAGs), including 102 bacteria and one archaea, from four vessels on international voyages. (bvsalud.org)
Anaerobic2
Metabolic reconstruction revealed that, like cultured members of the Mollicutes , these 'NB1-n' representatives lack a tricarboxylic acid cycle and instead use anaerobic fermentation of simple sugars for substrate level phosphorylation. (nature.com)
AN - infection: coord IM with GRAM-NEGATIVE BACTERIAL INFECTIONS (IM) HN - 2004 MH - Acidianus UI - D041541 MN - B7.75.725.725.30 MS - A genus of facultatively anaerobic coccoid ARCHAEA, in the family SULFOLOBACEAE. (nih.gov)
Proteins1
As early as the 1980s, it was noticed that some archaea possess proteins and structures similar to eukaryotic histones and nucleosomes [ 12 , 13 ]. (biomedcentral.com)
Genomes3
Metagenomic sequencing of deep-sea methane seep sediments resulted in the assembly of two genomes from a Tenericutes -affiliated clade currently known as 'NB1-n' (SILVA taxonomy) or 'RF3' (Greengenes taxonomy). (nature.com)
These findings are compatible with the observation of the overall deletion bias in the evolution of prokaryotic (as well as eukaryotic) genomes [ 32 ],[ 33 ]. (biomedcentral.com)
Advances in sequencing technologies and bioinformatics tools have dramatically increased the recovery rate of microbial genomes from metagenomic data. (bvsalud.org)
Collectively1
The most abundant phyla in WTR samples were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes, collectively representing 92.77-97.8% of the total bacterial sequences. (bvsalud.org)
Molecular3
The Mendelian gene is a basic unit of heredity and the molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. (wikipedia.org)
The molecular gene definition is more commonly used across biochemistry, molecular biology, and most of genetics - the gene that's described in terms of DNA sequence. (wikipedia.org)
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. (lookformedical.com)
Structures1
Francis Howell Central High School, Missouri: Are there any scientists designing novel organs/body structures or cell types? (nih.gov)
Diversity1
Statistical analysis of microbial profiles indicated that water source played a significant role in microbial community structure, diversity, and richness, however coagulant type did not. (bvsalud.org)
Archaea were only discovered as a separate branch of the tree of life in the 1970s [ 1 ], yet it was noticed very early on that they share a number of common features with the more organizationally complex eukaryotes, especially in the organization of their information processing cellular machinery. (biomedcentral.com)
Variable1
Bacterial 16S variable region 4 (V4) was amplified and sequenced using Illumina MiSeq sequencing. (bvsalud.org)
Main1
One of the most notable such features is nucleosomal chromatin, although archaeal histones and chromatin differ significantly from those of eukaryotes, not all archaea possess histones and it is not clear if histones are a main packaging component for all that do. (biomedcentral.com)