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Calcium-induced aggregation of archaeal bipolar tetraether liposomes derived from the thermoacidophilic archaeon Sulfolobus acidocaldarius  [PDF]
Roby Kanichay,Lawrence T. Boni,Peter H. Cooke,Tapan K. Khan
Archaea , 2003, DOI: 10.1155/2003/603528
Abstract: Previously, we showed that the proton permeability of small unilamellar vesicles (SUVs) composed of polar lipid fraction E (PLFE) from the thermoacidophilic archaeon Sulfolobus acidocaldarius was remarkably low and insensitive to temperature (Komatsu and Chong 1998). In this study, we used photon correlation spectroscopy to investigate the time dependence of PLFE SUV size as a function of Ca2
MONITORING INTRABDOMINAL PRESSURE, Something Old, Something New, Something Borrowed…  [PDF]
Ioana Grigora?
Jurnalul de Chirurgie , 2009,
Abstract: Systematic interest in intraabdominal pressure began about two decades ago. Since than, the amount of scientific data regarding this problem have been risen exponentially. This happened due to several reasons: description of pathophysiological pathways which link intra-abdominal hypertension (IAH) to multiple organ dysfunction syndrome refinement of measurement techniques, emergence of national, international and worldwide scientific organizations dedicated to IAH and the dramatic increase in body of published papers dealing with this topic. The critical mass of this accumulation was reached and the explosive dissemination of data bursted...In conclusion, measurement of IAP is an old tool. What is new is the recognition of its importance for guiding therapy and for patient outcome. As in case of sepsis, recognition of IAH / ACS should initiate an algorithm-based approach. Something old, something new, something borrowed…
Oligomerization of Sulfolobus solfataricus signature amidase is promoted by acidic pH and high temperature  [PDF]
Anna Scotto D’Abusco,Rita Casadio,Gianluca Tasco,Laura Giangiacomo,Anna Giartosio,Valentina Calamia,Stefania Di Marco,Roberta Chiaraluce,Valerio Consalvi,Roberto Scandurra,Laura Politi
Archaea , 2005, DOI: 10.1155/2005/543789
Abstract: The recombinant amidase from the hyperthermophylic archaeon Sulfolobus solfataricus (SSAM) a signature amidase, was cloned, purified and characterized. The enzyme is active on a large number of aliphatic and aromatic amides over the temperature range 60–95 °C and at pH values between 4.0 and 9.5, with an optimum at pH 5.0. The recombinant enzyme is in the form of a dimer of about 110 kD that reversibly associates into an octamer in a pH-dependent reaction. The pH dependence of the state of association was studied using gel permeation chromatography, analytical ultracentrifugation and dynamic light scattering techniques.
Identification and Characterisation of a Novel Acylpeptide Hydrolase from Sulfolobus Solfataricus: Structural and Functional Insights  [PDF]
Marta Gogliettino, Marco Balestrieri, Ennio Cocca, Sabrina Mucerino, Mose Rossi, Mauro Petrillo, Emanuela Mazzella, Gianna Palmieri
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0037921
Abstract: A novel acylpeptide hydrolase, named APEH-3Ss, was isolated from the hypertermophilic archaeon Sulfolobus solfataricus. APEH is a member of the prolyl oligopeptidase family which catalyzes the removal of acetylated amino acid residues from the N terminus of oligopeptides. The purified enzyme shows a homotrimeric structure, unique among the associate partners of the APEH cluster and, in contrast to the archaeal APEHs which show both exo/endo peptidase activities, it appears to be a “true” aminopeptidase as exemplified by its mammalian counterparts, with which it shares a similar substrate specificity. Furthermore, a comparative study on the regulation of apeh gene expression, revealed a significant but divergent alteration in the expression pattern of apeh-3Ss and apehSs (the gene encoding the previously identified APEHSs from S. solfataricus), which is induced in response to various stressful growth conditions. Hence, both APEH enzymes can be defined as stress-regulated proteins which play a complementary role in enabling the survival of S. solfataricus cells under different conditions. These results provide new structural and functional insights into S. solfataricus APEH, offering a possible explanation for the multiplicity of this enzyme in Archaea.
Molecular Characterization of Copper and Cadmium Resistance Determinants in the Biomining Thermoacidophilic Archaeon Sulfolobus metallicus  [PDF]
Alvaro Orell,Francisco Remonsellez,Rafaela Arancibia,Carlos A. Jerez
Archaea , 2013, DOI: 10.1155/2013/289236
Abstract: Sulfolobus metallicus is a thermoacidophilic crenarchaeon used in high-temperature bioleaching processes that is able to grow under stressing conditions such as high concentrations of heavy metals. Nevertheless, the genetic and biochemical mechanisms responsible for heavy metal resistance in S. metallicus remain uncharacterized. Proteomic analysis of S. metallicus cells exposed to 100?mM Cu revealed that 18 out of 30 upregulated proteins are related to the production and conversion of energy, amino acids biosynthesis, and stress responses. Ten of these last proteins were also up-regulated in S. metallicus treated in the presence of 1?mM Cd suggesting that at least in part, a common general response to these two heavy metals. The S. metallicus genome contained two complete cop gene clusters, each encoding a metallochaperone (CopM), a Cu-exporting ATPase (CopA), and a transcriptional regulator (CopT). Transcriptional expression analysis revealed that copM and copA from each cop gene cluster were cotranscribed and their transcript levels increased when S. metallicus was grown either in the presence of Cu or using chalcopyrite (CuFeS2) as oxidizable substrate. This study shows for the first time the presence of a duplicated version of the cop gene cluster in Archaea and characterizes some of the Cu and Cd resistance determinants in a thermophilic archaeon employed for industrial biomining. 1. Introduction Bioleaching is the biological conversion of an insoluble metal compound into a water soluble form [1, 2]. Microbe-based processes have clear economic advantages in the extraction of metals from many low-grade deposits [3], and these metal-extraction processes are usually more environmentally friendly than physical-chemical processes [3–5]. Some ores are refractory to mesophilic leaching and temperatures preferably as high as 75–85°C are required [6, 7]. At high temperatures, biomining consortia are dominated by thermoacidophilic Archaea from the genus Sulfolobus, Acidianus, and Metallosphaera [8]. Metals play an integral role in the life process of microorganisms, but at high levels both essential and nonessential metals can damage cell membranes, alter enzyme specificity, disrupt cellular functions, and damage the structure of DNA [9, 10]. Acid-leaching solutions are characterized by high metal concentrations that are toxic to most life, and as might be expected, microorganisms that grow in mineral-rich environments are, in most cases, remarkably tolerant to a wide range of metal ions [3, 11] and should possess robust metal resistance mechanisms [11–15].
Identification and Characterization of Small RNAs in the Hyperthermophilic Archaeon Sulfolobus solfataricus  [PDF]
Ning Xu, Yan Li, Ying-Tao Zhao, Li Guo, Yuan-Yuan Fang, Jian-Hua Zhao, Xiu-Jie Wang, Li Huang, Hui-Shan Guo
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0035306
Abstract: The term RNA silencing (RNA interference, RNAi) describes a set of mechanisms that regulate gene expression in eukaryotes. Small interfering RNAs (siRNA) and microRNAs (miRNAs) are two major types of RNAi-associated small RNAs (smRNAs) found in most eukaryotic organisms. Despite the presence of a plethora of non-coding RNAs longer than 50-nucleotide (nt) in length in various species of Archaea, little is known about smRNAs in archaea that resemble the 20–24-nt long smRNAs found in eukaryotes, which have been implicated in the post-transcriptional control of gene expression. Here, we report the finding of a large number of smRNAs approximatelly 20-nt in length, including phased smRNAs and potential miRNAs, from the hyperthermophilic archaeon Sulfolobus solfataricus p2 (Ssp2) based on deep sequencing. The expression of some of the miRNA candidates in Ssp2 was confirmed. Consistent with the Ssp2 hyperthermophilic properties, we found that higher temperatures more efficiently induced the production of the miRNA candidates in an in vitro system using the putative foldback precursor transcripts incubated with Ssp2 extract. Although we initially predicted putative target genes of some miRNA candidates, further analysis mapped the cleavage sites downstream of the miRNA candidate complementary regions, similar to those involved in plant miRNA-mediated TAS transcript cleavage. We also identified smRNAs from clustered, regularly interspaced, short palindromic repeat (CRISPR) loci, which play important roles in prokaryotic microbial defense systems. Archaea represent a unique life form next to Bacteria and Eukarya, and our results may provide a useful resource for further in-depth study on the regulation and evolution of smRNAs in this special organism.
Conditions for gene disruption by homologous recombination of exogenous DNA into the Sulfolobus solfataricus genome  [PDF]
Sonja-Verena Albers,Arnold J. M. Driessen
Archaea , 2008, DOI: 10.1155/2008/948014
Abstract: The construction of directed gene deletion mutants is an essential tool in molecular biology that allows functional studies on the role of genes in their natural environment. For hyperthermophilic archaea, it has been difficult to obtain a reliable system to construct such mutants. However, during the past years, systems have been developed for Thermococcus kodakarensis and two Sulfolobus species, S. acidocaldarius and derivatives of S. solfataricus 98/2. Here we describe an optimization of the method for integration of exogenous DNA into S. solfataricus PBL 2025, an S. solfataricus 98/2 derivative, based on lactose auxotrophy that now allows for routine gene inactivation.
Genome-Scale Reconstruction and Analysis of the Metabolic Network in the Hyperthermophilic Archaeon Sulfolobus Solfataricus  [PDF]
Thomas Ulas, S. Alexander Riemer, Melanie Zaparty, Bettina Siebers, Dietmar Schomburg
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0043401
Abstract: We describe the reconstruction of a genome-scale metabolic model of the crenarchaeon Sulfolobus solfataricus, a hyperthermoacidophilic microorganism. It grows in terrestrial volcanic hot springs with growth occurring at pH 2–4 (optimum 3.5) and a temperature of 75–80°C (optimum 80°C). The genome of Sulfolobus solfataricus P2 contains 2,992,245 bp on a single circular chromosome and encodes 2,977 proteins and a number of RNAs. The network comprises 718 metabolic and 58 transport/exchange reactions and 705 unique metabolites, based on the annotated genome and available biochemical data. Using the model in conjunction with constraint-based methods, we simulated the metabolic fluxes induced by different environmental and genetic conditions. The predictions were compared to experimental measurements and phenotypes of S. solfataricus. Furthermore, the performance of the network for 35 different carbon sources known for S. solfataricus from the literature was simulated. Comparing the growth on different carbon sources revealed that glycerol is the carbon source with the highest biomass flux per imported carbon atom (75% higher than glucose). Experimental data was also used to fit the model to phenotypic observations. In addition to the commonly known heterotrophic growth of S. solfataricus, the crenarchaeon is also able to grow autotrophically using the hydroxypropionate-hydroxybutyrate cycle for bicarbonate fixation. We integrated this pathway into our model and compared bicarbonate fixation with growth on glucose as sole carbon source. Finally, we tested the robustness of the metabolism with respect to gene deletions using the method of Minimization of Metabolic Adjustment (MOMA), which predicted that 18% of all possible single gene deletions would be lethal for the organism.
Natural language processing: she needs something old and something new (maybe something borrowed and something blue, too)  [PDF]
Karen Sparck Jones
Computer Science , 1995,
Abstract: Given the present state of work in natural language processing, this address argues first, that advance in both science and applications requires a revival of concern about what language is about, broadly speaking the world; and second, that an attack on the summarising task, which is made ever more important by the growth of electronic text resources and requires an understanding of the role of large-scale discourse structure in marking important text content, is a good way forward.
pH-, temperature- and ion-dependent oligomerization of Sulfolobus solfataricus recombinant amidase: a study with site-specific mutants  [PDF]
Laura Politi,Emilia Chiancone,Laura Giangiacomo,Laura Cervoni,Anna Scotto d’abusco,Stefano Scorsino,Roberto Scandurra
Archaea , 2009, DOI: 10.1155/2009/280317
Abstract: Recombinant amidase from Sulfolobus solfataricus occurred as a dimer of 110 kDa comprising identical subunits. Only dimers were present at pHs above 7.0, but with decreasing pH, dimers associated into octamers, with complete oligomerization occurring at pH 3.0. Oligomerization showed reversible temperature-dependence, with octamer formation increasing with temperature from 36 °C to between 70 and 80° C. Increasing salt concentrations, favored dissociation of the octamers. Among the three investigated factors affecting the dimer–octamer equilibrium, the most important was pH. Among four mutants obtained by site-specific mutagenesis and selection for pH and temperature sensitivity, the T319I and D487N mutant amidases, like that of the native Sulfolobus solfataricus, responded to changes in pH and temperature with a conformational change affecting the dimer–octamer equilibrium. The Y41C and L34P mutant amidases were unaffected by pH and temperature, remaining always in the dimeric state. The differences among mutants in protein conformation must be related to the position of the introduced mutation. Although the L34P and Y41C mutations are located in the helical region 33–48 (LLKLQLESYERLDSLP), which is close to the amino-terminal segment of the protein, the T319I mutation is located in a strand on the surface of the protein, which is far from, and opposite to, the amino-terminal segment. The D487N mutation is located in the center of the protein, far distant from the 33–48 segment. These observations suggest that the segment of the protein closest to the amino-terminus plays a key role in the association of dimers into octamers.
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