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251.
252.
Doris H. Fuertinger Franz Kappel Stephan Thijssen Nathan W. Levin Peter Kotanko 《Journal of mathematical biology》2013,66(6):1209-1240
In this paper we present a model for erythropoiesis under the basic assumption that sufficient iron availability is guaranteed. An extension of the model including a sub-model for the iron dynamics in the body is topic of present research efforts. The model gives excellent results for a number of important situations: recovery of the red blood cell mass after blood donation, adaptation of the number of red blood cells to changes in the altitude of residence and, most important, the reaction of the body to different administration regimens of erythropoiesis stimulating agents, as for instance in the case of pre-surgical administration of Epoetin-α. The simulation results concerning the last item show that choosing an appropriate administration regimen can reduce the total amount of the administered drug considerably. The core of the model consists of structured population equations for the different cell populations which are considered. A key feature of the model is the incorporation of neocytolysis. 相似文献
253.
Sai Krishna C. Korada Trevor D. Johns Christopher E. Smith Nathan D. Jones Kimberly A. McCabe Charles E. Bell 《Nucleic acids research》2013,41(11):5887-5897
Escherichia coli Exonuclease I (ExoI) digests single-stranded DNA (ssDNA) in the 3′-5′ direction in a highly processive manner. The crystal structure of ExoI, determined previously in the absence of DNA, revealed a C-shaped molecule with three domains that form a central positively charged groove. The active site is at the bottom of the groove, while an extended loop, proposed to encircle the DNA, crosses over the groove. Here, we present crystal structures of ExoI in complex with four different ssDNA substrates. The structures all have the ssDNA bound in essentially the predicted manner, with the 3′-end in the active site and the downstream end under the crossover loop. The central nucleotides of the DNA form a prominent bulge that contacts the SH3-like domain, while the nucleotides at the downstream end of the DNA form extensive interactions with an ‘anchor’ site. Seven of the complexes are similar to one another, but one has the ssDNA bound in a distinct conformation. The highest-resolution structure, determined at 1.95 Å, reveals an Mg2+ ion bound to the scissile phosphate in a position corresponding to MgB in related two-metal nucleases. The structures provide new insights into the mechanism of processive digestion that will be discussed. 相似文献
254.
Daniella Ishimaru Ewan P. Plant Amy C. Sims Boyd L. Yount Jr Braden M. Roth Nadukkudy V. Eldho Gabriela C. Pérez-Alvarado David W. Armbruster Ralph S. Baric Jonathan D. Dinman Deborah R. Taylor Mirko Hennig 《Nucleic acids research》2013,41(4):2594-2608
Messenger RNA encoded signals that are involved in programmed -1 ribosomal frameshifting (-1 PRF) are typically two-stemmed hairpin (H)-type pseudoknots (pks). We previously described an unusual three-stemmed pseudoknot from the severe acute respiratory syndrome (SARS) coronavirus (CoV) that stimulated -1 PRF. The conserved existence of a third stem–loop suggested an important hitherto unknown function. Here we present new information describing structure and function of the third stem of the SARS pseudoknot. We uncovered RNA dimerization through a palindromic sequence embedded in the SARS-CoV Stem 3. Further in vitro analysis revealed that SARS-CoV RNA dimers assemble through ‘kissing’ loop–loop interactions. We also show that loop–loop kissing complex formation becomes more efficient at physiological temperature and in the presence of magnesium. When the palindromic sequence was mutated, in vitro RNA dimerization was abolished, and frameshifting was reduced from 15 to 5.7%. Furthermore, the inability to dimerize caused by the silent codon change in Stem 3 of SARS-CoV changed the viral growth kinetics and affected the levels of genomic and subgenomic RNA in infected cells. These results suggest that the homodimeric RNA complex formed by the SARS pseudoknot occurs in the cellular environment and that loop–loop kissing interactions involving Stem 3 modulate -1 PRF and play a role in subgenomic and full-length RNA synthesis. 相似文献
255.
Nathan P. Coussens Ryo Hayashi Patrick H. Brown Lakshmi Balagopalan Andrea Balbo Itoro Akpan Jon C. D. Houtman Valarie A. Barr Peter Schuck Ettore Appella Lawrence E. Samelson 《Molecular and cellular biology》2013,33(21):4140-4151
The adapter molecules SLP-76 and LAT play central roles in T cell activation by recruiting enzymes and other adapters into multiprotein complexes that coordinate highly regulated signal transduction pathways. While many of the associated proteins have been characterized, less is known concerning the mechanisms of assembly for these dynamic and potentially heterogeneous signaling complexes. Following T cell receptor (TCR) stimulation, SLP-76 is found in structures called microclusters, which contain many signaling complexes. Previous studies showed that a mutation to the SLP-76 C-terminal SH2 domain nearly abolished SLP-76 microclusters, suggesting that the SH2 domain facilitates incorporation of signaling complexes into microclusters. S. C. Bunnell, A. L. Singer, D. I. Hong, B. H. Jacque, M. S. Jordan, M. C. Seminario, V. A. Barr, G. A. Koretzky, and L. E. Samelson, Mol. Cell. Biol., 26:7155–7166, 2006). Using biophysical methods, we demonstrate that the adapter, ADAP, contains three binding sites for SLP-76, and that multipoint binding to ADAP fragments oligomerizes the SLP-76 SH2 domain in vitro. These results were complemented with confocal imaging and functional studies of cells expressing ADAP with various mutations. Our results demonstrate that all three binding sites are critical for SLP-76 microcluster assembly, but any combination of two sites will partially induce microclusters. These data support a model whereby multipoint binding of SLP-76 to ADAP facilitates the assembly of SLP-76 microclusters. This model has implications for the regulation of SLP-76 and LAT microclusters and, as a result, T cell signaling. 相似文献
256.
The intensity of competitive interactions between fishes is partly determined by prey use and ontogenetic niche shifts. In a wetland where distinct habitat shifts are missing we compared prey use of three generalist benthivorous sunfishes to look for evidence of ontogenetic, interspecific, and “seasonal” variation in prey composition. Diet analysis revealed evidence of diet ontogeny in warmouth (Lepomis gulosus, 30–152 mm standard length, SL), but not in bluespotted sunfish (Enneacanthus gloriosus, 30–47 mm SL) or dollar sunfish (Lepomis marginatus, 30–60 mm SL). Bluespotted and dollar sunfishes consumed small dipteran and amphipod prey and had similar diets in both seasons suggesting a potential for strong interspecific competition. In the dry season, warmouth shifted from using smaller insect prey to larger decapod and fish prey with increasing size. This shift to prey types that were little used by the other species reduced dietary niche overlap with the other sunfishes. After drought and re-flooding (in the wet season), decapods and small fish were less abundant in the wetland and the warmouth ontogenetic shift was less distinct. When matched for gape width, prey composition differed between warmouth and both dollar and bluespotted sunfishes in the wet season, suggesting differences in sunfish foraging modes, but prey use differences were less clear in the dry season when prey were abundant. Both warmouth ontogenetic diet shifts and seasonal variation in prey use (probably mediated by prey abundance) had strong influences on diet overlap and therefore the potential for intra- and interspecific competition between sunfishes in this wetland ecosystem. 相似文献
257.
Stephanie Waters Sanjana Luther Torsten Joerger Gary P. Richards E. Fidelma Boyd Michelle A. Parent 《Microbiology and immunology》2013,57(4):323-328
Vibrio parahaemolyticus is the most common cause of bacterial, seafood‐related illness in the USA. Currently, there is a dearth of published reports regarding immunity to infection with this pathogen. Here, production of both pro‐ and anti‐inflammatory cytokines by V. parahaemolyticus‐infected RAW 264.7 murine macrophages was studied. It was determined that this infection results in increased concentrations of IL‐1α, IL‐6, TNF‐α and IL‐10. Additionally, decreases in cell surface TLR2 and TLR4 and increases in T‐cell co‐stimulatory molecules CD40 and CD86 were discovered. The data presented here begin to identify the immune variables required to eliminate V. parahaemolyticus from infected host tissues. 相似文献
258.
Austin Boyd 《Historical Biology》2013,25(1-2):1-15
The mid-Pleistocene Kolymbia Flora of Rhodes, Greece occurs in the Lindos Bay Clay facies group of the Rhodes Formation and was deposited in a marine setting at about a depth of 200 m. Recorded in the flora are the youngest presence of Glyptostrobus in the eastern Mediterranean, an extinct species of Pinus very similar to the modern relict Pinus canariensis, and a new species of the disjunct Cedrus. These taxa indicate that some relict plant taxa existed on Rhodes later than previously recognised. The late presence of Taxodiaceae in the eastern Mediterranean may demerit its usefulness for determining the Pliocene–Pleistocene boundary. The finding of Liquidambar, Zelkova and Fagus in the flora supports the idea of Rhodes, and possibly the eastern Mediterranean, as a refugium during the mid-Pleistocene. Similar fossil assemblages should be found in adjacent Turkey because the Lindos Bay Clay records an extensive marine transgression probably resulting from graben tectonics that lead to the ultimate separation of Rhodes from mainland Turkey. 相似文献
259.
Evelyn Armstrong Kenneth G Boyd Anthony Pisacane Christopher J Peppiatt J Grant Burgess 《Biofouling》2013,29(2-4):215-224
Ecological problems associated with current antifouling technologies have increased interest in the natural strategies that marine organisms use to keep their surfaces clean and free from fouling. Bacteria isolated from living surfaces in the marine environment have been shown to produce chemicals that are potential antifoulants. Active compounds from the cells and culture supernatant of two bacterial strains, FS‐55 and NudMB50–11, isolated from surface of the seaweed, Fucus serratus, and the nudibranch, Archidoris pseudoargus, respectively, were extracted using solid phase extraction. The extracts were combined with acrylic base paint resin and assayed for antifouling activity by measuring their ability to inhibit the growth of fouling bacteria. These formulations were found to be active against fouling bacteria isolated from marine surfaces. The formulation of antifouling paints that incorporate marine microbial natural products is reported here for the first time. This is a significant advance towards the production of an environmentally friendly antifouling paint that utilises a sustainable supply of natural biodegradable compounds. 相似文献
260.
Vascular endothelial growth factor (VEGF), is expressed in the vicinity of sprouting vessels and its receptor (VEGF-R2/Flk-1/kdr) on the angioblasts and new vessels, and both are required for vasculogenesis and angiogenesis. VEGFR2, also called as KDR or Flk-1, is identified as an early marker for endothelial cell progenitors, whose expression is restricted to endothelial cells in vivo. VEGFR2 consists of extracellular (7-Ig-like sub-domains), transmembrane and cytoplasmic domains. In order to understand the structure–functional relationship and signal transduction process of VEGFR2, we have examined their amino acid sequences from a wide range of species including mammals, birds, Zebrafish and also computed the phylogenetic tree, secondary and domain structures. Phylogeny constructed using Maximum Parsimony tree software MEGA-5 version suggested an interesting sequence similarity between Zebrafish and Gallus, closeness between human, rat, horse and pig. Strong homology in amino acids sequences was observed between the species, such as human, Macaca mulatta, gorilla, etc, and small variations in Zebrafish and zebrafinch. The Arg and Asp residues which are involved in forming salt bridges are evolutionarily conserved from Zebrafish to human in D7 domain of VEGFR2, indicating their functional importance in VEGFR activity. Amino acids, tyrosine in the extracellular loops and cysteines involved in disulphide bridges of VEGFR2, are highly conserved suggesting their importance during ligand binding, the details of which will be discussed. 相似文献