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Xenbase
Xenbase is a Model Organism Database (MOD), providing informatics resources, as well as genomic and biological data on Xenopus frogs.K. Karimi et al. (2017Xenbase: a genomic, epigenomic and transcriptomic model organism database Nucleic Acids Research (NAR), gkx936 Xenbase has been available since 1999, and covers both X. laevis and X. tropicalis Xenopus varieties. As of 2013 all of its services are running on virtual machines in a private cloud environment, making it one of the first MODs to do so.K. Karimi and P.D. Vize (2014)The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud Database, doi: 10.1093/database/bau108 Other than hosting genomics data and tools, Xenbase supports the Xenopus research community though profiles for researchers and laboratories, and job and events postings. Xenbase's Software and Hardware Platform Xenbase runs in a cloud environment. Its virtual machines are running in a VMware vSphere environment on two servers, wi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Xenopus
''Xenopus'' () (Gk., ξενος, ''xenos''=strange, πους, ''pous''=foot, commonly known as the clawed frog) is a genus of highly aquatic frogs native to sub-Saharan Africa. Twenty species are currently described within it. The two best-known species of this genus are '' Xenopus laevis'' and '' Xenopus tropicalis'', which are commonly studied as model organisms for developmental biology, cell biology, toxicology, neuroscience and for modelling human disease and birth defects. The genus is also known for its polyploidy, with some species having up to 12 sets of chromosomes. Characteristics ''Xenopus laevis'' is a rather inactive creature. It is incredibly hardy and can live up to 15 years. At times the ponds that ''Xenopus laevis'' is found in dry up, compelling it, in the dry season, to burrow into the mud, leaving a tunnel for air. It may lie dormant for up to a year. If the pond dries up in the rainy season, ''Xenopus laevis'' may migrate long distances to another pond ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Xenopus Tropicalis
The western clawed frog (''Xenopus tropicalis'') is a species of frog in the family Pipidae, also known as tropical clawed frog. It is the only species in the genus ''Xenopus'' to have a diploid genome. Its genome has been sequenced, making it a significant model organism for genetics that complements the related species ''Xenopus laevis'' (the African clawed frog), a widely used vertebrate model for developmental biology. ''X. tropicalis'' also has a number of advantages over ''X. laevis'' in research, such as a much shorter generation time (<5 months), smaller size ( body length), and a larger number of eggs per spawn. It is found in , ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Xenopus Laevis
The African clawed frog (''Xenopus laevis'', also known as the xenopus, African clawed toad, African claw-toed frog or the ''platanna'') is a species of African aquatic frog of the family Pipidae. Its name is derived from the three short claws on each hind foot, which it uses to tear apart its food. The word ''Xenopus'' means 'strange foot' and ''laevis'' means 'smooth'. The species is found throughout much of Sub-Saharan Africa (Nigeria and Sudan to South Africa),Weldon; du Preez; Hyatt; Muller; and Speare (2004). Origin of the Amphibian Chytrid Fungus.' Emerging Infectious Diseases 10(12). and in isolated, introduced populations in North America, South America, Europe, and Asia. All species of the family Pipidae are tongueless, toothless and completely aquatic. They use their hands to shove food in their mouths and down their throats and a hyobranchial pump to draw or suck things in their mouth. Pipidae have powerful legs for swimming and lunging after food. They also use t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Model Organism Databases
Model organism databases (MODs) are biological databases Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genom ..., or knowledgebases, dedicated to the provision of in-depth biological data for intensively studied model organisms. MODs allow researchers to easily find background information on large sets of genes, plan experiments efficiently, combine their data with existing knowledge, and construct novel hypotheses. They allow users to analyse results and interpret datasets, and the data they generate are increasingly used to describe less well studied species. Where possible, MODs share common approaches to collect and represent biological information. For example, all MODs use the Gene Ontology (GO) to describe functions, processes and cellular locations of specific gene products. Pr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Echinobase
Echinobase is a Model Organism Database (MOD). It supports the international research community by providing a centralized, integrated web based resource to access the diverse and rich, functional genomics data of echinoderm evolution, development and gene regulatory networks. BI Arshinoff, GA Cary, K Karimi, S Foley, S Agalakov, F Delgado, VS Lotay, CJ Ku, TJ Pells, TR Beatman, E Kim, RA Cameron, PD Vize, CA Telmer, JC Croce, CA Ettensohn, VF HinmanEchinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms Nucleic Acids Research, 2021, doi:10.1093/nar/gkab1005 Genomic research data and tools are available for searching, browsing and bioinformatic analysis of genomes, genes, and transcripts. Echinobase provides a critical data sharing infrastructure for other NIH-funded projects and enhances the availability and visibility of echinoderm data to the broader biomedical research community. Su ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MiRNA
MicroRNA (miRNA) are small, single-stranded, non-coding RNA molecules containing 21 to 23 nucleotides. Found in plants, animals and some viruses, miRNAs are involved in RNA silencing and post-transcriptional regulation of gene expression. miRNAs base-pair to complementary sequences in mRNA molecules, then gene silence said mRNA molecules by one or more of the following processes: (1) cleavage of mRNA strand into two pieces, (2) destabilization of mRNA by shortening its poly(A) tail, or (3) translation of mRNA into proteins. This last method of gene silencing is the least efficient of the three, and requires the aid of ribosomes. miRNAs resemble the small interfering RNAs (siRNAs) of the RNA interference (RNAi) pathway, except miRNAs derive from regions of RNA transcripts that fold back on themselves to form short hairpins, whereas siRNAs derive from longer regions of double-stranded RNA. The human genome may encode over 1900 miRNAs, although more recent analysis sugges ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Morpholino
A Morpholino, also known as a Morpholino oligomer and as a phosphorodiamidate Morpholino oligomer (PMO), is a type of oligomer molecule (colloquially, an oligo) used in molecular biology to modify gene expression. Its molecular structure contains DNA bases attached to a backbone of methylenemorpholine rings linked through phosphorodiamidate groups. Morpholinos block access of other molecules to small (~25 base) specific sequences of the base-pairing surfaces of ribonucleic acid (RNA). Morpholinos are used as research tools for reverse genetics by knocking down gene function. This article discusses only the Morpholino antisense oligomers, which are nucleic acid analogs. The word "Morpholino" can occur in other chemical names, referring to chemicals containing a six-membered morpholine ring. To help avoid confusion with other morpholine-containing molecules, when describing oligos "Morpholino" is often capitalized as a trade name, but this usage is not consistent across scientifi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Oligonucleotides
Oligonucleotides are short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, research, and forensics. Commonly made in the laboratory by solid-phase chemical synthesis, these small bits of nucleic acids can be manufactured as single-stranded molecules with any user-specified sequence, and so are vital for artificial gene synthesis, polymerase chain reaction (PCR), DNA sequencing, molecular cloning and as molecular probes. In nature, oligonucleotides are usually found as small RNA molecules that function in the regulation of gene expression (e.g. microRNA), or are degradation intermediates derived from the breakdown of larger nucleic acid molecules. Oligonucleotides are characterized by the sequence of nucleotide residues that make up the entire molecule. The length of the oligonucleotide is usually denoted by " -mer" (from Greek ''meros'', "part"). For example, an oligonucleotide of six nucleotides (nt) is a hexamer, while one of 25 nt ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SiRNA
Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded RNA at first non-coding RNA molecules, typically 20-24 (normally 21) base pairs in length, similar to miRNA, and operating within the RNA interference (RNAi) pathway. It interferes with the expression of specific genes with complementary nucleotide sequences by degrading mRNA after transcription, preventing translation. Text was copied from this source, which is available under Creative Commons Attribution 4.0 International License Structure Naturally occurring siRNAs have a well-defined structure that is a short (usually 20 to 24- bp) double-stranded RNA (dsRNA) with phosphorylated 5' ends and hydroxylated 3' ends with two overhanging nucleotides. The Dicer enzyme catalyzes production of siRNAs from long dsRNAs and small hairpin RNAs. siRNAs can also be introduced into cells by transfection. Since in principle any gene can be knocked down by a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Embryogenesis
An embryo is an initial stage of development of a multicellular organism. In organisms that reproduce sexually, embryonic development is the part of the life cycle that begins just after fertilization of the female egg cell by the male sperm cell. The resulting fusion of these two cells produces a single-celled zygote that undergoes many cell divisions that produce cells known as blastomeres. The blastomeres are arranged as a solid ball that when reaching a certain size, called a morula, takes in fluid to create a cavity called a blastocoel. The structure is then termed a blastula, or a blastocyst in mammals. The mammalian blastocyst hatches before implantating into the endometrial lining of the womb. Once implanted the embryo will continue its development through the next stages of gastrulation, neurulation, and organogenesis. Gastrulation is the formation of the three germ layers that will form all of the different parts of the body. Neurulation forms the ne ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene Expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. These products are often proteins, but in non-protein-coding genes such as transfer RNA (tRNA) and small nuclear RNA (snRNA), the product is a functional non-coding RNA. Gene expression is summarized in the central dogma of molecular biology first formulated by Francis Crick in 1958, further developed in his 1970 article, and expanded by the subsequent discoveries of reverse transcription and RNA replication. The process of gene expression is used by all known life— eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea), and utilized by viruses—to generate the macromolecular machinery for life. In genetics, gene expression is the most fundamental level at which the genotype gives rise to the phen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
