Shared KEGG pathways of icariin-targeted genes and osteoarthritis

The beneficial effects of icariin in the management of many diseases, such as chronic renal failure and heart failure, are well known. Icariin has also been shown to ameliorate osteoarthritis (OA) symptoms; however, the underlying mechanisms remain unclear. In this study, a bioinformatics analysis was performed to investigate the KEGG pathways of icariin-targeted genes involved in OA. Our study suggests that icariin plays a role in OA by regulating inflammatory cytokine production, insulin resistance, and cell survival through modulation of the NF-κB, MAPK, and Akt signaling pathways. Importantly, IKBKB, NFKBIA, MAPK8, MAPK9, and MAPK10 may be the hub genes affected by icariin when providing its beneficial effects on OA. In addition, we found that icariin decreases proinflammatory factors and inhibits chondrocyte apoptosis through suppression of the NF-κB pathway. Our study highlights a set of KEGG pathways that could explain the molecular mechanism of icariin's action on OA, suggesting that icariin could be considered as a promising therapeutic option for OA.     

Eco Cyc: encyclopedia of Escherichia coli genes and metabolism.

The EcoCyc database describes the genome and gene products of Escherichia coli, its metabolic and signal-transduction pathways, and its tRNAs. The database describes 4391 genes of E.coli, 695 enzymes encoded by a subset of these genes, 904 metabolic reactions that occur in E.coli, and the organization of these reactions into 129 metabolic pathways. The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways. EcoCyc has many references to the primary literature, and is a (qualitative) computational model of E. coli metabolism. EcoCyc is available at URL http://ecocyc. PangeaSystems.com/ecocyc/     

EcoCyc: an encyclopedia of Escherichia coli genes and metabolism.

The encyclopedia of Escherichia coli genes and metabolism (EcoCyc) is a database that combines information about the genome and the intermediary metabolism of E.coli. It describes 2034 genes, 306 enzymes encoded by these genes, 580 metabolic reactions that occur in E.coli and the organization of these reactions into 100 metabolic pathways. The EcoCyc graphical user interface allows query and exploration of the EcoCyc database using visualization tools such as genomic map browsers and automatic layouts of metabolic pathways. EcoCyc spans the space from sequence to function to allow investigation of an unusually broad range of questions. EcoCyc can be thought of as both an electronic review article, because of its copious references to the primary literature, and as an in silico model of E.coli that can be probed and analyzed through computational means.     

Sequence analysis of genes and genomes

A major step towards understanding of the genetic basis of an organism is the complete sequence determination of all genes in its genome. The development of powerful techniques for DNA sequencing has enabled sequencing of large amounts of gene fragments and even complete genomes. Important new techniques for physical mapping, DNA sequencing and sequence analysis have been developed. To increase the throughput, automated procedures for sample preparation and new software for sequence analysis have been applied. This review describes the development of new sequencing methods and the optimisation of sequencing strategies for whole genome and cDNA analysis, as well as discusses issues regarding sequence analysis and annotation.     

Classification of triplet periodicity in the DNA sequences of genes from KEGG databank

Totally, 472 288 regions of triplet periodicity were found in 578 868 genes from KEGG databank version 29 and classified. A new concept of triplet periodicity class and a measure of similarity between periodicity classes were introduced. Overall, 2520 classes were created and contained 94% of the triplet periodicity cases found. A similar correlation between the triplet periodicity and reading frame was observed for 92% of triplet periodicity regions contained in different classes. The remaining triplet periodicity regions displayed a shift of the reading frame relative to that common for the majority of genes belonging to the same triplet periodicity class. The hypothetical amino acid sequences were deduced from the periodicity regions according to the reading frame characteristic of the given triplet periodicity class. BLAST analysis demonstrated that 2660 hypothetical amino acid sequences display a statistically significant similarity to proteins from the Uni-Prot databank. It was supposed that 8% of the triplet periodicity regions contained in the classes have frameshift mutations. The triplet periodicity classes can be used to identify the coding regions in genes and to searching for frameshift mutations.     

Essence of life: essential genes of minimal genomes

Essential genes are absolutely required for cell survival. Determination of the universal minimal set of genes needed to sustain life is, therefore, expected to contribute greatly to our understanding of life at its simplest level, with applications in medicine and synthetic biology. The search for the minimal genome has led to the identification of often variable gene sets. We argue here that, based on the outcome of these analyses, it is becoming increasingly evident that some genes, and the functions encoded by them, are absolutely necessary for the survival of any living entity, whereas others can be omitted. We also examine ways of determining the minimal genome and discuss possible practical applications of a minimal cell.     

KEGG: Kyoto Encyclopedia of Genes and Genomes.

Kyoto Encyclopedia of Genes and Genomes (KEGG) is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules. The major component of KEGG is the PATHWAY database that consists of graphical diagrams of biochemical pathways including most of the known metabolic pathways and some of the known regulatory pathways. The pathway information is also represented by the ortholog group tables summarizing orthologous and paralogous gene groups among different organisms. KEGG maintains the GENES database for the gene catalogs of all organisms with complete genomes and selected organisms with partial genomes, which are continuously re-annotated, as well as the LIGAND database for chemical compounds and enzymes. Each gene catalog is associated with the graphical genome map for chromosomal locations that is represented by Java applet. In addition to the data collection efforts, KEGG develops and provides various computational tools, such as for reconstructing biochemical pathways from the complete genome sequence and for predicting gene regulatory networks from the gene expression profiles. The KEGG databases are daily updated and made freely available (http://www.genome.ad.jp/kegg/).     

Molecular evolution: Codes,clocks, genes and genomes

The discoveries, advancements and continuing controversies in the field of molecular evolution are reviewed. Topics summarized are (1) the evolution of the genetic code, (2) gene evolution including the demonstration of homology, estimation of sequence divergence, phylogenetic trees, the molecular clock and the origin of genes and gene families by various genetic mechanisms, and (3) eukaryotic genome evolution, including the highly repeated satellite sequences, the interspersed and potentially mobile repeated sequences and the unique sequence fraction of the genome.     

Denitrifying genes in bacterial and Archaeal genomes

Denitrification, the reduction of nitrate or nitrite to nitrous oxide or dinitrogen, is the major mechanism by which fixed nitrogen returns to the atmosphere from soil and water. Although the denitrifying ability has been found in microorganisms belonging to numerous groups of bacteria and Archaea, the genes encoding the denitrifying reductases have been studied in only few species. Recent investigations have led to the identification of new classes of denitrifying reductases, indicating a more complex genetic basis of this process than previously recognized. The increasing number of genome sequencing projects has opened a new way to study the genetics of the denitrifying process in bacteria and Archaea. In this review, we summarized the current knowledge on denitrifying genes and compared their genetic organizations by using new sequences resulting from the analysis of finished and unfinished microbial genomes with a special attention paid to the clustering of genes encoding different classes of reductases. In addition, some evolutionary relationships between the structural genes are presented.     

Phylogeny of early land plants: insights from genes and genomes

A large body of evidence from molecular systematic studies has confirmed the charophytic origin of land plants, and clarified monophyly of many lineages in charophytes and land plants. These studies have also identified liverworts as the earliest land plants, and the lycopods as the extant sister group to all other vascular plants. Two traditionally defined groups-bryophytes and pteridophytes-are now recognized as early grades of land plant evolution. However, several problems that complicate the use of sequence data in reconstructing plant phylogeny have become apparent; reconstruction of an accurate land plant phylogeny will require analysis of sequences of multiple genes and genomic structural characters of all three genomes.     

Classification of triplet periodicity in DNA sequences of genes taken from KEGG databank

We conducted classification for 472,288 regions of triplet periodicity found in 578,868 genes from release 29 of KEGG databank. A new concept of triplet periodicity class and a measure of similarity between them are introduced. Totally 2520 classes were created that contain 94% of found triplet periodicity. For 92% of triplet periodicity regions contained in classes an identical linkage of triplet periodicity to reading frame is observed. For the rest triplet periodicity cases a shift between reading frame of a gene and reading frame common for majority of genes contained in a class of triplet periodicity was observed. These periodicity regions were encoded into hypothetical amino acid sequences in accordance with reading frame built by triplet periodicity class. By BLAST program it was shown that 2660 hypothetical amino acid sequences have statistically significant similarity with proteins from UniProt databank. We suppose that 8% of triplet periodicity regions that joined classes mutated by means of reading frame shift. Created classes of triplet periodicity can be used for identification of coding regions of genes as well as for searching for mutations arisen from reading frame shift.     

The inheritance of organelle genes and genomes: patterns and mechanisms.

Unlike nuclear genes and genomes, the inheritance of organelle genes and genomes does not follow Mendel's laws. In this mini-review, I summarize recent research progress on the patterns and mechanisms of the inheritance of organelle genes and genomes. While most sexual eukaryotes show uniparental inheritance of organelle genes and genomes in some progeny at least part of the time, increasing evidence indicates that strictly uniparental inheritance is rare and that organelle inheritance patterns are very diverse and complex. In contrast with the predominance of uniparental inheritance in multicellular organisms, organelle genes in eukaryotic microorganisms, such as protists, algae, and fungi, typically show a greater diversity of inheritance patterns, with sex-determining loci playing significant roles. The diverse patterns of inheritance are matched by the rich variety of potential mechanisms. Indeed, many factors, both deterministic and stochastic, can influence observed patterns of organelle inheritance. Interestingly, in multicellular organisms, progeny from interspecific crosses seem to exhibit more frequent paternal leakage and biparental organelle genome inheritance than those from intraspecific crosses. The recent observation of a sex-determining gene in the basidiomycete yeast Cryptococcus neoformans, which controls mitochondrial DNA inheritance, has opened up potentially exciting research opportunities for identifying specific molecular genetic pathways that control organelle inheritance, as well as for testing evolutionary hypotheses regarding the prevalence of uniparental inheritance of organelle genes and genomes.     

GeneOrder: comparing the order of genes in small genomes

MOTIVATION: The recent rapid rise in the availability of whole genome DNA sequence data has led to bottlenecks in their complete analysis. Specifically, there is a need for software tools that will allow mining of gene and putative gene data at a whole genome level. These new tools will complement the current set already in use for studying specific aspects of individual genes and putative genes in detail. A key software challenge is to make them user-friendly, without losing their flexibility and capability for use in research. RESULTS: The creation of GeneOrder-a web-based interactive, computational tool-allows researchers to compare the order of genes in two genomes. It has been tested on full genome sequence data for viruses, mitochondria and chloroplasts that were obtained from the NCBI GenBank database. It is accessible at http://www.bif.atcc.org/GENEOrder/index.html. GeneOrder prepares the comparison in table form, listing the order of similar genes. Hyperlinks are provided from this output; these lead to the 'Protein Coding Regions' in the NCBI database.