Background: In the nematode Caenorhabditis elegans the conserved Ins/IGF-1 signaling pathway regulates many biological processes including life span, stress response, dauer diapause and metabolism. Detection of differentially expressed genes may contribute to a better understanding of the mechanism by which the Ins/IGF-1 signaling pathway regulates these processes. Appropriate normalization is an essential prerequisite for obtaining accurate and reproducible quantification of gene expression levels. The aim of this study was to establish a reliable set of reference genes for gene expression analysis in C. elegans.
“What is the O2 concentration in a normoxic cell culture incubator?” This and other frequently asked questions in hypoxia research will be answered in this review. Our intention is to give a simple introduction to the physics of gases that would be helpful for newcomers to the field of hypoxia research. We will provide background knowledge about questions often asked, but without straightforward answers. What is O2 concentration, and what is O2 partial pressure? What is normoxia, and what is hypoxia? How much O2 is experienced by a cell residing in a culture dish in vitro vs in a tissue in vivo? By the way, the O2 concentration in a normoxic incubator is 18.6%, rather than 20.9% or 20%, as commonly stated in research publications. And this is strictly only valid for incubators at sea level.
Comparative genomic studies have led to the recent identification of several novel globin types in the Metazoa. They have revealed a surprising evolutionary diversity of functions beyond the familiar O(2) supply roles of hemoglobin and myoglobin. Here we report the discovery of a hitherto unrecognized family of proteins with a unique modular architecture, possessing an N-terminal calpain-like domain, an internal, circular permuted globin domain, and an IQ calmodulin-binding motif. Putative orthologs are present in the genomes of many metazoan taxa, including vertebrates. The calpain-like region is homologous to the catalytic domain II of the large subunit of human calpain-7. The globin domain satisfies the criteria of a myoglobin-like fold but is rearranged and split into two parts. The recombinantly expressed human globin domain exhibits an absorption spectrum characteristic of hexacoordination of the heme iron atom. Molecular evolutionary analyses indicate that this chimeric globin family is phylogenetically ancient and originated in the common ancestor to animals and choanoflagellates. In humans and mice, the gene is predominantly expressed in testis tissue, and we propose the name "androglobin" (Adgb). Expression is associated with postmeiotic stages of spermatogenesis and is insensitive to experimental hypoxia. Evidence exists for increased gene expression in fertile compared with infertile males.
Although most globins, including the N-terminal domains within chimeric proteins such as flavohemoglobins and globin-coupled sensors, exhibit a 3͞3 helical sandwich structure, many bacterial, plant, and ciliate globins have a 2͞2 helical sandwich structure. We carried out a comprehensive survey of globins in the genomes from the three kingdoms of life. Bayesian phylogenetic trees based on manually aligned sequences indicate the possibility of past horizontal globin gene transfers from bacteria to eukaryotes. BLASTP searches revealed the presence of 3͞3 single-domain globins related to the globin domains of the bacterial and fungal flavohemoglobins in many bacteria, a red alga, and a diatom. Iterated PSI-BLAST searches based on groups of globin sequences found that only the single-domain globins and flavohemoglobins recognize the eukaryote 3͞3 globins, including vertebrate neuroglobins, ␣-and -globins, and cytoglobins. The 2͞2 globins recognize the flavohemoglobins, as do the globin coupled sensors and the closely related single-domain protoglobins. However, the 2͞2 globins and the globin-coupled sensors do not recognize each other. Thus, all globins appear to be distributed among three lineages: (i) the 3͞3 plant and metazoan globins, single-domain globins, and flavohemoglobins; (ii) the bacterial 3͞3 globin-coupled sensors and protoglobins; and (iii) the bacterial, plant, and ciliate 2͞2 globins. The three lineages may have evolved from an ancestral 3͞3 or 2͞2 globin. Furthermore, it appears likely that the predominant functions of globins are enzymatic and that oxygen transport is a specialized development that accompanied the evolution of metazoans.evolution ͉ sequences T hirty years ago, our knowledge of globin sequences was limited to vertebrate ␣-and -globins, myoglobins (Mbs), and the symbiotic Hbs of legume plants. The ensuing years brought the discovery of 3͞3 nonsymbiotic plant Hbs (NsHbs) in plants, symbiotic Hbs in plants other than legumes, and chimeric f lavohemoglobins (FHbs), which are comprised of an Nterminal globin linked to an FAD reductase domain, in bacteria and yeasts (1-8). Concurrently, globins shorter than normal (Ͻ130 aa), the ''truncated'' Hbs, were observed in protozoa and bacteria (9, 10), and globins longer than normal (Ͼ150 aa), which aligned with the truncated Hbs, were found in green alga (11) and plants (12). The crystal structures of these globins (13-15) exhibited a novel globin fold comprised of a 2͞2 helical sandwich secondary structure. The recent rapid accumulation of genomic information has resulted in the discoveries of new types of globins, including the 3͞3 neuroglobins (Ngbs) and 3͞3 cytoglobins (Cygbs) believed to occur in all vertebrates (16), and of globins in organisms in which their presence had not been suspected, such as nematodes (17), an insect (18), and a urochordate (19). Furthermore, genomic data brought to light the existence of 3͞3 single-domain globins (SDgbs), which aligned with the globin domain of the FHbs (20). A class of generegulating, chimeric...
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