bluuebunny/crossref_metadata_2025 huggingface dataset:
A putative viral defence mechanism in archaeal cells
Authors: Lillestøl Reidun , Redder Peter , Garrett Roger A. , Brügger Kim
Published: July 2009

Clusters of regularly spaced direct repeats, separated by unconserved spacer sequences, are ubiquitous in archaeal chromosomes and occur in some plasmids. Some clusters constitute around 1% of chromosomal DNA. Similarly structured clusters, generally smaller, also occur in some bacterial chromosomes. Although early studies implicated these clusters in segregation/partition functions, recent evidence suggests that the spacer sequences derive from extrachromosomal elements, and, primarily, viruses. This has led to the proposal that the clusters provide a defence against viral propagation in cells, and that both the mode of inhibition of viral propagation and the mechanism of adding spacer‐repeat units to clusters, are dependent on RNAs transcribed from the clusters. Moreover, the putative inhibitory apparatus (piRNA‐based) may be evolutionarily related to the interference RNA systems (siRNA and miRNA), which are common in eukarya. Here, we analyze all the current data on archaeal repeat clusters and provide some new insights into their diverse structures, transcriptional properties and mode of structural development. The results are consistent with larger cluster transcripts being processed at the centers of the repeat sequences and being further trimmed by exonucleases to yield a dominant, intracellular RNA species, which corresponds approximately to the size of a spacer. Furthermore, analysis of the extensive clusters of Sulfolobus solfataricus strains P1 and P2B provides support for the presence of a flanking sequence adjoining a cluster being a prerequisite for the incorporation of new spacer‐repeat units, which occurs between the flanking sequence and the cluster. An archaeal database summarizing the data will be maintained at http://dac.molbio.ku.dk/dbs/SRSR/.
Distribution, structure and diversity of “bacterial” genes encoding two‐component proteins in the Euryarchaeota
Authors: Ashby Mark K.
Published: July 2009

The publicly available annotated archaeal genome sequences (23 complete and three partial annotations, October 2005) were searched for the presence of potential two‐component open reading frames (ORFs) using gene category lists and BLASTP. A total of 489 potential two‐component genes were identified from the gene category lists and BLASTP. Two‐component genes were found in 14 of the 21 Euryarchaeal sequences (October 2005) and in neither the Crenarchaeota nor the Nanoarchaeota. A total of 20 predicted protein domains were identified in the putative two‐component ORFs that, in addition to the histidine kinase and receiver domains, also includes sensor and signalling domains. The detailed structure of these putative proteins is shown, as is the distribution of each class of two‐component genes in each species. Potential members of orthologous groups have been identified, as have any potential operons containing two or more two‐component genes. The number of two‐component genes in those Euryarchaeal species which have them seems to be linked more to lifestyle and habitat than to genome complexity, with most examples being found in Methanospirillum hungatei, Haloarcula marismortui, Methanococcoides burtonii and the mesophilic Methanosarcinales group. The large numbers of two‐component genes in these species may reflect a greater requirement for internal regulation. Phylogenetic analysis of orthologous groups of five different protein classes, three probably involved in regulating taxis, suggests that most of these ORFs have been inherited vertically from an ancestral Euryarchaeal species and point to a limited number of key horizontal gene transfer events.
Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers
Authors: Brochier-Armanet Céline , Forterre Patrick
Published: July 2009

Reverse gyrase, an enzyme of uncertain funtion, is present in all hyperthermophilic archaea and bacteria. Previous phylogenetic studies have suggested that the gene for reverse gyrase has an archaeal origin and was transferred laterally (LGT) to the ancestors of the two bacterial hyperthermophilic phyla, Thermotogales and Aquificales. Here, we performed an in‐depth analysis of the evolutionary history of reverse gyrase in light of genomic progress. We found genes coding for reverse gyrase in the genomes of several thermophilic bacteria that belong to phyla other than Aquificales and Thermotogales. Several of these bacteria are not, strictly speaking, hyperthermophiles because their reported optimal growth temperatures are below 80 °C. Furthermore, we detected a reverse gyrase gene in the sequence of the large plasmid of Thermus thermophilus strain HB8, suggesting a possible mechanism of transfer to the T. thermophilus strain HB8 involving plasmids and transposases. The archaeal part of the reverse gyrase tree is congruent with recent phylogenies of the archaeal domain based on ribosomal proteins or RNA polymerase subunits. Although poorly resolved, the complete reverse gyrase phylogeny suggests an ancient acquisition of the gene by bacteria via one or two LGT events, followed by its secondary distribution by LGT within bacteria. Finally, several genes of archaeal origin located in proximity to the reverse gyrase gene in bacterial genomes have bacterial homologues mostly in thermophiles or hyperthermophiles, raising the possibility that they were co‐transferred with the reverse gyrase gene. Our new analysis of the reverse gyrase history strengthens the hypothesis that the acquisition of reverse gyrase may have been a crucial evolutionary step in the adaptation of bacteria to high‐temperature environments. However, it also questions the role of this enzyme in thermophilic bacteria and the selective advantage its presence could provide.
Lineage‐specific partitions in archaeal transcription
Authors: Coulson Richard M. R. , Touboul Nathalie , Ouzounis Christos A.
Published: July 2009

The phylogenetic distribution of the components comprising the transcriptional machinery in the crenarchaeal and euryarchaeal lineages of the Archaea was analyzed in a systematic manner by genome‐wide profiling of transcription complements in fifteen complete archaeal genome sequences. Initially, a reference set of transcription‐associated proteins (TAPs) consisting of sequences functioning in all aspects of the transcriptional process, and originating from the three domains of life, was used to query the genomes. TAP‐families were detected by sequence clustering of the TAPs and their archaeal homologues, and through extensive database searching, these families were assigned a function. The phylogenetic origins of archaeal genes matching hidden Markov model profiles of protein domains associated with transcription, and those encoding the TAP‐homologues, showed there is extensive lineage‐specificity of proteins that function as regulators of transcription: most of these sequences are present solely in the Euryarchaeota, with nearly all of them homologous to bacterial DNA‐binding proteins. Strikingly, the hidden Markov model profile searches revealed that archaeal chromatin and histone‐modifying enzymes also display extensive taxon‐restrictedness, both across and within the two phyla.
Cultivation of methanogens from shallow marine sediments at Hydrate Ridge, Oregon
Authors: Kendall Melissa M. , Boone David R.
Published: July 2009

Little is known about the methanogenic degradation of acetate, the fate of molecular hydrogen and formate or the ability of methanogens to grow and produce methane in cold, anoxic marine sediments. The microbes that produce methane were examined in permanently cold, anoxic marine sediments at Hydrate Ridge (44°35′ N, 125°10′ W, depth 800 m). Sediment samples (15 to 35 cm deep) were collected from areas of active methane ebullition or areas where methane hydrates occurred. The samples were diluted into enrichment medium with formate, acetate or trimethylamine as catabolic substrate. After 2 years of incubation at 4 °C to 15 °C, enrichment cultures produced methane. PCR amplification and sequencing of the rRNA genes from the highest dilutions with growth suggested that each enrichment culture contained a single strain of methanogen. The level of sequence similarity (91 to 98%) to previously characterized prokaryotes suggested that these methanogens belonged to novel genera or species within the orders Methanomicrobiales and Methanosarcinales. Analysis of the 16S rRNA gene libraries from DNA extracted directly from the sediment samples revealed phylotypes that were either distantly related to cultivated methanogens or possible anaerobic methane oxidizers related to the ANME‐1 and ANME‐2 groups of the Archaea. However, no methanogenic sequences were detected, suggesting that methanogens represented only a small proportion of the archaeal community.
AMP‐forming acetyl‐CoA synthetases in Archaea show unexpected diversity in substrate utilization
Authors: Ingram-Smith Cheryl , Smith Kerry S.
Published: July 2009

Adenosine monophosphate (AMP)‐forming acetyl‐CoA synthetase (ACS; acetate:CoA ligase (AMP‐forming), EC 6.2.1.1) is a key enzyme for conversion of acetate to acetyl‐CoA, an essential intermediate at the junction of anabolic and catabolic pathways. Phylogenetic analysis of putative short and medium chain acyl‐CoA synthetase sequences indicates that the ACSs form a distinct clade from other acyl‐CoA synthetases. Within this clade, the archaeal ACSs are not monophyletic and fall into three groups composed of both bacterial and archaeal sequences. Kinetic analysis of two archaeal enzymes, an ACS from Methanothermobacter thermautotrophicus (designated as MT‐ACS1) and an ACS from Archaeoglobus fulgidus (designated as AF‐ACS2), revealed that these enzymes have very different properties. MT‐ACS1 has nearly 11‐fold higher affinity and 14‐fold higher catalytic efficiency with acetate than with propionate, a property shared by most ACSs. However, AF‐ACS2 has only 2.3‐fold higher affinity and catalytic efficiency with acetate than with propionate. This enzyme has an affinity for propionate that is almost identical to that of MT‐ACS1 for acetate and nearly tenfold higher than the affinity of MT‐ACS1 for propionate. Furthermore, MT‐ACS1 is limited to acetate and propionate as acyl substrates, whereas AF‐ACS2 can also utilize longer straight and branched chain acyl substrates. Phylogenetic analysis, sequence alignment and structural modeling suggest a molecular basis for the altered substrate preference and expanded substrate range of AF‐ACS2 versus MT‐ACS1.
Identification of SmtB/ArsR cis elements and proteins in archaea using the Prokaryotic InterGenic Exploration Database (PIGED)
Authors: Bose Michael , Slick David , Sarto Mickey J. , Murphy Patrick , Roberts David , Roberts Jacqueline , Barber Robert D.
Published: July 2009

Microbial genome sequencing projects have revealed an apparently wide distribution of SmtB/ArsR metal‐responsive transcriptional regulators among prokaryotes. Using a position‐dependent weight matrix approach, prokaryotic genome sequences were screened for SmtB/ArsR DNA binding sites using data derived from intergenic sequences upstream of orthologous genes encoding these regulators. Sixty SmtB/ArsR operators linked to metal detoxification genes, including nine among various archaeal species, are predicted among 230 annotated and draft prokaryotic genome sequences. Independent multiple sequence alignments of putative operator sites and corresponding winged helix‐turn‐helix motifs define sequence signatures for the DNA binding activity of this SmtB/ArsR subfamily. Prediction of an archaeal SmtB/ArsR based upon these signature sequences is confirmed using purified Methanosarcina acetivorans C2A protein and electrophoretic mobility shift assays. Tools used in this study have been incorporated into a web application, the Prokaryotic InterGenic Exploration Database (PIGED; http://bioinformatics.uwp.edu/~PIGED/home.htm), facilitating comparable studies. Use of this tool and establishment of orthology based on DNA binding signatures holds promise for deciphering potential cellular roles of various archaeal winged helix‐turn‐helix transcriptional regulators.
Gene decay in archaea
Authors: van Passel M. W. J. , Smillie C. S. , Ochman H.
Published: July 2009

The gene‐dense chromosomes of archaea and bacteria were long thought to be devoid of pseudogenes, but with the massive increase in available genome sequences, whole genome comparisons between closely related species have identified mutations that have rendered numerous genes inactive. Comparative analyses of sequenced archaeal genomes revealed numerous pseudogenes, which can constitute up to 8.6% of the annotated coding sequences in some genomes. The largest proportion of pseudogenes is created by gene truncations, followed by frameshift mutations. Within archaeal genomes, large numbers of pseudogenes contain more than one inactivating mutation, suggesting that pseudogenes are deleted from the genome more slowly in archaea than in bacteria. Although archaea seem to retain pseudogenes longer than do bacteria, most archaeal genomes have unique repertoires of pseudogenes.
The genome of Hyperthermus butylicus: a sulfur‐reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 °C
Authors: Brügger Kim , Chen Lanming , Stark Markus , Zibat Arne , Redder Peter , Ruepp Andreas , Awayez Mariana , She Qunxin , Garrett Roger A. , Klenk Hans-Peter
Published: July 2009

Hyperthermus butylicus, a hyperthermophilic neutrophile and anaerobe, is a member of the archaeal kingdom Crenarchaeota. Its genome consists of a single circular chromosome of 1,667,163 bp with a 53.7% G+C content. A total of 1672 genes were annotated, of which 1602 are protein‐coding, and up to a third are specific to H. butylicus. In contrast to some other crenarchaeal genomes, a high level of GUG and UUG start codons are predicted. Two cdc6 genes are present, but neither could be linked unambiguously to an origin of replication. Many of the predicted metabolic gene products are associated with the fermentation of peptide mixtures including several peptidases with diverse specificities, and there are many encoded transporters. Most of the sulfur‐reducing enzymes, hydrogenases and electron‐transfer proteins were identified which are associated with energy production by reducing sulfur to H2S. Two large clusters of regularly interspaced repeats (CRISPRs) are present, one of which is associated with a crenarchaeal‐type cas gene superoperon; none of the spacer sequences yielded good sequence matches with known archaeal chromosomal elements. The genome carries no detectable transposable or integrated elements, no inteins, and introns are exclusive to tRNA genes. This suggests that the genome structure is quite stable, possibly reflecting a constant, and relatively uncompetitive, natural environment.
A bifunctional archaeal protein that is a component of 30S ribosomal subunits and interacts with C/D box small RNAs
Authors: Ciammaruconi Andrea , Gorini Stefania , Londei Paola
Published: July 2009

We have identified a novel archaeal protein that apparently plays two distinct roles in ribosome metabolism. It is a polypeptide of about 18 kDa (termed Rbp18) that binds free cytosolic C/D box sRNAs in vivo and in vitro and behaves as a structural ribosomal protein, specifically a component of the 30S ribosomal subunit. As Rbp18 is selectively present in Crenarcheota and highly thermophilic Euryarchaeota, we propose that it serves to protect C/D box sRNAs from degradation and perhaps to stabilize thermophilic 30S subunits.
New methods for tightly regulated gene expression and highly efficient chromosomal integration of cloned genes for Methanosarcina species
Authors: Guss Adam M. , Rother Michael , Zhang Jun Kai , Kulkkarni Gargi , Metcalf William W.
Published: July 2009

A highly efficient method for chromosomal integration of cloned DNA into Methanosarcina spp. was developed utilizing the site‐specific recombination system from the Streptomyces phage φC31. Host strains expressing the φC31 integrase gene and carrying an appropriate recombination site can be transformed with non‐replicating plasmids carrying the complementary recombination site at efficiencies similar to those obtained with self‐replicating vectors. We have also constructed a series of hybrid promoters that combine the highly expressed M. barkeri PmcrB promoter with binding sites for the tetracycline‐responsive, bacterial TetR protein. These promoters are tightly regulated by the presence or absence of tetracycline in strains that express the tetRgene. The hybrid promoters can be used in genetic experiments to test gene essentiality by placing a gene of interest under their control. Thus, growth of strains with tetR‐regulated essential genes becomes tetracycline‐dependent. A series of plasmid vectors that utilize the site‐specific recombination system for construction of reporter gene fusions and for tetracycline regulated expression of cloned genes are reported. These vectors were used to test the efficiency of translation at a variety of start codons. Fusions using an ATG start site were the most active, whereas those using GTG and TTG were approximately one half or one fourth as active, respectively. The CTG fusion was 95% less active than the ATG fusion.
Molybdate treatment and sulfate starvation decrease ATP and DNA levels in Ferroplasma acidarmanus
Authors: Baumler David J. , Hung Kai-Foong , Jeong Kwang Cheol , Kaspar Charles W.
Published: July 2009

Sulfate is a primary source of sulfur for most microbes and in some prokaryotes it is used an electron acceptor. The acidophile Ferroplasma acidarmanus (strain fer1) requires a minimum of 150 mM of a sulfate‐containing salt for growth. Sulfate is assimilated by F. acidarmanus into proteins and reduced to form the volatile organic sulfur compounds methanethiol and dimethyldisulfide. In the absence of sulfate, cell death occurs by an unknown mechanism. In this study, cell viability and genomic DNA and ATP contents of F. acidarmanus were monitored in response to the absence of sulfate or the presence of sulfate and the sulfate analog molybdate (). Cellular DNA and ATP contents were monitored as markers of cell viability. The absence of sulfate led to a decrease in viable cell numbers of greater than 7 log10 within 5 days, a > 99% reduction in genomic DNA within 3 days, and a > 60% decrease in ATP within 6 h. Likewise, cells incubated with lost viability (decreased by > 2 log10 in 5 days), extractable genomic DNA (reduction of > 60% in 2 days), and ATP (reduction of > 70 % in 2 hours). These results demonstrate that sulfate deprivation or the presence of molybdate have similar impacts on cell viability and essential biomolecules. Sulfate was coupled to cellular ATP content and maintenance of DNA integrity in F. acidarmanus, a finding that may be applicable to other acidophiles that are typically found in sulfate‐rich biotopes.
Classification and regression tree (CART) analyses of genomic signatures reveal sets of tetramers that discriminate temperature optima of archaea and bacteria
Authors: Dyer Betsey Dexter , Kahn Michael J. , LeBlanc Mark D.
Published: July 2009

Classification and regression tree (CART) analysis was applied to genome‐wide tetranucleotide frequencies (genomic signatures) of 195 archaea and bacteria. Although genomic signatures have typically been used to classify evolutionary divergence, in this study, convergent evolution was the focus. Temperature optima for most of the organisms examined could be distinguished by CART analyses of tetranucleotide frequencies. This suggests that pervasive (nonlinear) qualities of genomes may reflect certain environmental conditions (such as temperature) in which those genomes evolved. The predominant use of GAGA and AGGA as the discriminating tetramers in CART models suggests that purine‐loading and codon biases of thermophiles may explain some of the results.
Conditions for gene disruption by homologous recombination of exogenous DNA into the Sulfolobus solfataricus genome
Authors: Albers Sonja-Verena , Driessen Arnold J. M.
Published: July 2009

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.
Identification of the gene for disaggregatase from Methanosarcina mazei
Authors: Osumi Naoki , Kakehashi Yoshihiro , Matsumoto Shiho , Nagaoka Kazunari , Sakai Junichi , Miyashita Kiyotaka , Kimura Makoto , Asakawa Susumu
Published: July 2009

The gene sequences encoding disaggregatase (Dag), the enzyme responsible for dispersion of cell aggregates of Methanosarcina mazei to single cells, were determined for three strains of M. mazei (S‐6T, LYC and TMA). The dag genes of the three strains were 3234 bp in length and had almost the same sequences with 97% amino acid sequence identities. Dag was predicted to comprise 1077 amino acid residues and to have a molecular mass of 120 kDa containing three repeats of the DNRLRE domain in the C terminus, which is specific to the genus Methanosarcina and may be responsible for structural organization and cell wall function. Recombinant Dag was overexpressed in Escherichia coli and preparations of the expressed protein exhibited enzymatic activity. The RT‐PCR analysis showed that dag was transcribed to mRNA in M. mazei LYC and indicated that the gene was expressed in vivo. This is the first time the gene involved in the morphological change of Methanosarcina spp. from aggregate to single cells has been identified.
Improving low‐temperature activity of Sulfolobus acidocaldarius 2‐keto‐3‐deoxygluconate aldolase
Authors: Wolterink-van Loo Suzanne , Siemerink Marco A. J. , Perrakis Georgios , Kaper Thijs , Kengen Servé W. M. , van der Oost John
Published: July 2009

Sulfolobus acidocaldarius 2‐keto‐3‐deoxygluconate aldolase (SacKdgA) displays optimal activity at 95°C and is studied as a model enzyme for aldol condensation reactions. For application of SacKdgA at lower temperatures, a library of randomly generated mutants was screened for improved synthesis of 2‐keto‐3‐deoxygluconate from pyruvate and glyceraldehyde at the suboptimal temperature of 50 °C. The single mutant SacKdgA‐V193A displayed a threefold increase in activity compared with wild type SacKdgA. The increased specific activity at 40–60 °C of this mutant was observed, not only for the condensation of pyruvate with glyceraldehyde, but also for several unnatural acceptor aldehydes. The optimal temperature for activity of SacKdgA‐V193A was lower than for the wild type enzyme, but enzymatic stability of the mutant was similar to that of the wild type, indicating that activity and stability were uncoupled. Valine193 has Van der Waals interactions with Lysine153, which covalently binds the substrate during catalysis. The mutation V193A introduced space close to this essential residue, and the increased activity of the mutant presumably resulted from increased flexibility of Lysine153. The increased activity of SacKdgA‐V193A with unaffected stability demonstrates the potential for optimizing extremely thermostable aldolases for synthesis reactions at moderate temperatures.
pH‐, temperature‐ and ion‐dependent oligomerization of Sulfolobus solfataricus recombinant amidase: a study with site‐specific mutants
Authors: Politi Laura , Chiancone Emilia , Giangiacomo Laura , Cervoni Laura , Scotto d’abusco Anna , Scorsino Stefano , Scandurra Roberto
Published: July 2009

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.
Existence of Fixed Point Results in G‐Metric Spaces
Authors: Mustafa Zead , Shatanawi Wasfi , Bataineh Malik
Published: July 2009

The purpose of this paper is to prove the existence of fixed points
of contractive mapping defined on G‐metric space where the completeness is
replaced with weaker conditions. Moreover, we showed that these conditions
do not guarantee the completeness of G‐metric spaces.
Novel FTLRNN with Gamma Memory for Short-Term and Long-Term Predictions of Chaotic Time Series
Authors: Badjate Sanjay L. , Dudul Sanjay V.
Published: July 2009

Multistep ahead prediction of a chaotic time series is a difficult task that has attracted increasing interest in the recent years. The interest in this work is the development of nonlinear neural network models for the purpose of building multistep chaotic time series prediction. In the literature there is a wide range of different approaches but their success depends on the predicting performance of the individual methods. Also the most popular neural models are based on the statistical and traditional feed forward neural networks. But it is seen that this kind of neural model may present some disadvantages when long-term prediction is required. In this paper focused time-lagged recurrent neural network (FTLRNN) model with gamma memory is developed for different prediction horizons. It is observed that this predictor performs remarkably well for short-term predictions as well as medium-term predictions. For coupled partial differential equations generated chaotic time series such as Mackey Glass and Duffing, FTLRNN-based predictor performs consistently well for different depths of predictions ranging from short term to long term, with only slight deterioration after k is increased beyond 50. For real-world highly complex and nonstationary time series like Sunspots and Laser, though the proposed predictor does perform reasonably for short term and medium-term predictions, its prediction ability drops for long term ahead prediction. However, still this is the best possible prediction results considering the facts that these are nonstationary time series. As a matter of fact, no other NN configuration can match the performance of FTLRNN model. The authors experimented the performance of this FTLRNN model on predicting the dynamic behavior of typical Chaotic Mackey-Glass time series, Duffing time series, and two real-time chaotic time series such as monthly sunspots and laser. Static multi layer perceptron (MLP) model is also attempted and compared against the proposed model on the performance measures like mean squared error (MSE), Normalized mean squared error (NMSE), and Correlation Coefficient (r). The standard back-propagation algorithm with momentum term has been used for both the models.
A Comprehensive Review of Immunosuppression Used for Liver Transplantation
Authors: Mukherjee Sandeep , Mukherjee Urmila
Published: July 2009

Since liver transplantation was approved for the treatment of end stage liver disease, calcineurin inhibitors (CNI's) have played a critical role in the preservation of allograft function. Unfortunately, these medications cause a variety of Side effects such as diabetes, hypertension and nephrotoxicity which in turn result in significant morbidity and reduced quality of life. A variety of newer immunosuppressants have been evaluated over the last decade in an attempt to either substitute for CNI's or use with reduced dose CNI's while still preserving allograft function However, current data does not recommend complete cessation of CNI's due to unacceptably high rates of allograft rejection. As these medications have their own unique adverse effects, a careful assessment on their risks and benefits is essential, particularly when additive or synergistic effects with CNI's may occur. Furthermore, the impact of these newer medications on the risk of hepatitis C recurrence and progression remains to be elucidated. Controlled trials are urgently required to assist transplant physicians with choosing the optimum immunosuppressive regimen for their patients. This review will discuss commonly used immunosuppressants prescribed in liver transplantation, emerging therapties and where appropriate, the impact of these medications on the recurrence of hepatitis C after liver transplantation.
Effects of Cytochrome P450 Inhibitors on Itraconazole and Fluconazole Induced Cytotoxicity in Hepatocytes
Authors: Somchit Nhareet , Ngee Chong Sock , Yaakob Azhar , Ahmad Zuraini , Zakaria Zainul Amiruddin
Published: July 2009

Itraconazole and fluconazole have been reported to induce hepatotoxicity in patients. The present study was designed to investigate the role of cytochrome P450 inhibitors, SKF 525A, and curcumin pretreatment on the cytotoxicity of antifungal drugs fluconazole and itraconazole. For 3 consecutive days, female rats were administered daily SKF 525A or curcumin (5 and 25 mg/kg). Control rats received an equivalent amount of dosed vehicle. The animals were anaesthetized 24 hours after receiving the last dose for liver perfusion. Hepatocytes were then exposed to various concentrations of antifungal drugs. In vitro incubation of hepatocytes with itraconazole revealed significantly lower viability when compared to fluconazole as assessed by lactate dehydrogenase, aspartate aminotransferase and alanine aminotransferase activities. The cytotoxicity of itraconazole was enhanced when incubated with hepatocytes pretreated with SKF 525A. SKF 525A had no effects on the cytotoxicity of fluconazole. Curcumin failed to either increase or decrease the cytotoxicity of both antifungal drugs. ATP levels also showed significant decrease in both itraconazole and fluconazole incubated hepatocytes. However, SKF 525A pretreated hepatocytes had significantly lower ATP levels after itraconazole incubations. Collectively, these results confirm the involvement of cytochrome P450 in the cytoprotection in itraconazole induced hepatocyte toxicity. Differences of the effects of SKF 525A on the cytotoxicity induced by itraconazole and fluconazole may be due to the differences on the metabolism of each antifungal drug in vivo.
Localized States in Bi‐Pattern Systems
Authors: Bortolozzo U. , Clerc M. G. , Haudin F. , Rojas R. G. , Residori S.
Published: July 2009

We present a unifying description of localized states observed in systems with coexistence of two spatially periodic states, called bi‐pattern systems. Localized states are pinned over an underlying lattice that is either a self‐organized pattern spontaneously generated by the system itself, or a periodic grid created by a spatial forcing. We show that localized states are generic and require only the coexistence of two spatially periodic states. Experimentally, these states have been observed in a nonlinear optical system. At the onset of the spatial bifurcation, a forced one‐dimensional amplitude equation is derived for the critical modes, which accounts for the appearance of localized states. By numerical simulations, we show that localized structures persist on two‐dimensional systems and exhibit different shapes depending on the symmetry of the supporting patterns.
Many nonuniversal archaeal ribosomal proteins are found in conserved gene clusters
Authors: Wang Jiachen , Dasgupta Indrani , Fox George E.
Published: July 2009

The genomic associations of the archaeal ribosomal proteins, (r‐proteins), were examined in detail. The archaeal versions of the universal r‐protein genes are typically in clusters similar or identical and to those found in bacteria. Of the 35 nonuniversal archaeal r‐protein genes examined, the gene encoding L18e was found to be associated with the conserved L13 cluster, whereas the genes for S4e, L32e and L19e were found in the archaeal version of the spc operon. Eleven nonuniversal protein genes were not associated with any common genomic context. Of the remaining 19 protein genes, 17 were convincingly assigned to one of 10 previously unrecognized gene clusters. Examination of the gene content of these clusters revealed multiple associations with genes involved in the initiation of protein synthesis, transcription or other cellular processes. The lack of such associations in the universal clusters suggests that initially the ribosome evolved largely independently of other processes. More recently it likely has evolved in concert with other cellular systems. It was also verified that a second copy of the gene encoding L7ae found in some bacteria is actually a homolog of the gene encoding L30e and should be annotated as such.
Potentiation of Cannabinoid-Induced Cytotoxicity in Mantle Cell Lymphoma through Modulation of Ceramide Metabolism
Authors: Gustafsson Kristin , Sander Birgitta , Bielawski Jacek , Hannun Yusuf A. , Flygare Jenny
Published: July 2009

Ceramide levels are elevated in mantle cell lymphoma (MCL) cells following treatment with cannabinoids. Here, we investigated the pathways of ceramide accumulation in the MCL cell line Rec-1 using the stable endocannabinoid analogue R(+)-methanandamide (R-MA). We further interfered with the conversion of ceramide into sphingolipids that promote cell growth. Treatment with R-MA led to increased levels of ceramide species C16, C18, C24, and C24:1 and transcriptional induction of ceramide synthases (CerS) 3 and 6. The effects were attenuated using SR141716A, which has high affinity to cannabinoid receptor 1 (CB1). The CB1-mediated induction of CerS3 and CerS6 mRNA was confirmed using Win-55,212-2. Simultaneous silencing of CerS3 and CerS6 using small interfering RNA abrogated the R-MA-induced accumulation of C16 and C24. Inhibition of either of the enzymes serine palmitoyl transferase, CerS, and dihydroceramide desaturase within the de novo ceramide pathway reversed ceramide accumulation and cell death induced by R-MA treatment. To enhance the cytotoxic effect R-MA, sphingosine kinase-1 and glucosylceramide synthase, enzymes that convert ceramide to the pro-proliferative sphingolipids sphingosine-1-phospate and glucosylceramide, respectively, were inhibited. Suppression of either enzyme using inhibitors or small interfering RNA potentiated the decreased viability, induction of cell death, and ceramide accumulation induced by R-MA treatment. Our findings suggest that R-MA induces cell death in MCL via CB1-mediated up-regulation of the de novo ceramide synthesis pathway. Furthermore, this is the first study were the cytotoxic effect of a cannabinoid is enhanced by modulation of ceramide metabolism. (Mol Cancer Res 2009;7(7):1086–98)
β-Arrestin/Ral Signaling Regulates Lysophosphatidic Acid–Mediated Migration and Invasion of Human Breast Tumor Cells
Authors: Li Timothy T. , Alemayehu Mistre , Aziziyeh Adel I. , Pape Cynthia , Pampillo Macarena , Postovit Lynne-Marie , Mills Gordon B. , Babwah Andy V. , Bhattacharya Moshmi
Published: July 2009

The lipid mediator lysophosphatidic acid (LPA) plays a role in cancer progression and signals via specific G protein–coupled receptors, LPA1-3. LPA has been shown to enhance the metastasis of breast carcinoma cells to bone. However, the mechanisms by which LPA receptors regulate breast cancer cell migration and invasion remain unclear. Breast cancer cell proliferation has been shown to be stimulated by Ral GTPases, a member of the Ras superfamily. Ral activity can be regulated by the multifunctional protein β-arrestin. We now show that HS578T and MDA-MB-231 breast cancer cells and MDA-MB-435 melanoma cells have higher expression of β-arrestin 1 mRNA compared with the nontumorigenic mammary MCF-10A cells. Moreover, we found that the mRNA levels of LPA1, LPA2, β-arrestin 2, and Ral GTPases are elevated in the advanced stages of breast cancer. LPA stimulates the migration and invasion of MDA-MB-231 cells, but not of MCF-10A cells, and this is mediated by pertussis toxin–sensitive G proteins and LPA1. However, ectopic expression of LPA1 in MCF-10A cells caused these cells to acquire an invasive phenotype. Gene knockdown of either β-arrestin or Ral proteins significantly impaired LPA-stimulated migration and invasion. Thus, our data show a novel role for β-arrestin/Ral signaling in mediating LPA-induced breast cancer cell migration and invasion, two important processes in metastasis. (Mol Cancer Res 2009;7(7):1064–77)
DNA Repair and Resistance of Gliomas to Chemotherapy and Radiotherapy
Authors: Frosina Guido
Published: July 2009

The importance of DNA repair as a resistance mechanism in gliomas, the most aggressive form of brain tumor, is a clinically relevant topic. Recent studies show that not all cells are equally malignant in gliomas. Certain subpopulations are particularly prone to drive tumor progression and resist chemo- and radiotherapy. Those cells have been variably named cancer stem cells or cancer-initiating cells or tumor-propagating cells, owing to their possible (but still uncertain) origin from normal stem cells. Although DNA repair reduces the efficacy of chemotherapeutics and ionizing radiation toward bulk gliomas, its contribution to resistance of the rare glioma stem cell subpopulations is less clear. Mechanisms other than DNA repair (in particular low proliferation and activation of the DNA damage checkpoint response) are likely main players of resistance in glioma stem cells and their targeting might yield significant therapeutic gains. (Mol Cancer Res 2009;7(7):989–99)
Distinct Early Signaling Events Resulting From the Expression of the PRKAG2 R302Q Mutant of AMPK Contribute to Increased Myocardial Glycogen
Authors: Folmes Karalyn D. , Chan Anita Y.M. , Koonen Debby P.Y. , Pulinilkunnil Thomas C. , Baczkó István , Hunter Beth E. , Thorn Stephanie , Allard Michael F. , Roberts Robert , Gollob Michael H. , Light Peter E. , Dyck Jason R.B.
Published: July 2009

Background—

Humans with an R302Q mutation in AMPKγ
2
(the
PRKAG2
gene) develop a glycogen storage cardiomyopathy characterized by a familial form of Wolff-Parkinson-White syndrome and cardiac hypertrophy. This phenotype is recapitulated in transgenic mice with cardiomyocyte-restricted expression of AMPKγ
2
R302Q. Although considerable information is known regarding the consequences of harboring the γ
2
R302Q mutation, little is known about the early signaling events that contribute to the development of this cardiomyopathy.

Methods and Results—

To distinguish the direct effects of γ
2
R302Q expression from later compensatory alterations in signaling, we used transgenic mice expressing either the wild-type AMPKγ
2
subunit (TGγ
2
WT) or the mutated form (TGγ
2
R302Q), in combination with acute expression of these proteins in neonatal rat cardiomyocytes. Although acute expression of γ
2
R302Q induces AMPK activation and upregulation of glycogen synthase and AS160, with an associated increase in glycogen content, AMPK activity, glycogen synthase activity, and AS160 expression are reduced in hearts from TGγ
2
R302Q mice, likely in response to the existing 37-fold increase in glycogen. Interestingly, γ
2
WT expression has similar, yet less marked effects than γ
2
R302Q expression in both cardiomyocytes and hearts.

Conclusions—

Using acute and chronic models of γ
2
R302Q expression, we have differentiated the direct effects of the γ
2
R302Q mutation from eventual compensatory modifications. Our data suggest that expression of γ
2
R302Q induces AMPK activation and the eventual increase in glycogen content, a finding that is masked in hearts from transgenic adult mice. These findings are the first to highlight temporal differences in the effects of the PRKAG2 R302Q mutation on cardiac metabolic signaling events.
Activation and Signaling by the AMP-Activated Protein Kinase in Endothelial Cells
Authors: Fisslthaler Beate , Fleming Ingrid
Published: July 2009

The AMP-activated protein kinase (AMPK) was initially identified as the kinase that phosphorylates the 3-hydroxy 3-methylglutaryl coenzyme A reductase, the rate-limiting enzyme for cholesterol biosynthesis. As the name suggests, the AMPK is activated by increased intracellular concentrations of AMP, and is generally described as a “metabolite-sensing kinase” and when activated initiates steps to conserve cellular energy. Although there is a strong link between the activity of the AMPK and metabolic control in muscle cells, the activity of the AMPK in endothelial cells can be regulated by stimuli that affect cellular ATP levels, such as hypoxia as well as by fluid shear stress, Ca
2+
-elevating agonists, and hormones such as adiponectin. To date the AMPK in endothelial cells has been implicated in the regulation of fatty acid oxidation, small G protein activity and nitric oxide production as well as inflammation and angiogenesis. Moreover, there is evidence indicating that the activation of the AMPK may help to prevent the vascular complications associated with the metabolic syndrome.
Cultural and Biological Determinants in the Evaluation of Urban Green Spaces
Authors: Home Robert , Bauer Nicole , Hunziker Marcel
Published: July 2009

Dramatically increasing urbanization is observable worldwide and brings pressure on space within urban areas as the built environment intensifies. Considerable evidence suggests that contact with nature is important for city dwellers, although it is not known whether residents’ appreciation of the forms of urban green spaces is constant across different contexts. More specifically, it has not yet been shown whether our appreciation of nature is innate and inherently human, is cultural and something that we learn, or is a mixture of both. This article describes an exploratory study consisting of 17 interviews carried out in Zurich, Switzerland. Kelly’s repertory grid technique is used to identify preferred urban landscapes, which were contrasted with identified rejected landscapes. Principle components analysis and multidimensional scaling reveal a clear separation of cultural and biological modes of landscape assessment in some respondents. The research contributes to an understanding of the meanings of urban green spaces, which would in turn provide planners with a tool to match urban natural resource management with the needs of residents.
Effect of Ceramics on the Physical and Thermo-physiological Performance of Warm-up Suit
Authors: Myoung Hee Shim  , Chung Hee Park  , Heun Sup Shim
Published: July 2009

The purpose of this study was to develop a warm-up suit that is comfortable as well as having a good thermal performance. Heat-insulating water vapor-permeable fabrics for warm-up suit were developed by applying ceramic powders to hydrophilic polyurethane films, which were then incorporated into textiles. Two types of ceramic compounds were used in this study: MU-4N and RT-3. The infrared emissivity was 92.6 for MU-4N and 94.8 for RT-3. In order to evaluate the effectiveness of using ceramics in a warm-up suit, we examined the effects of ceramics on selected variables: thermo-physiological properties of the clothing systems (using thermal manikin), and thermo-physiological responses and subjective sensations of human subjects. The infrared emissivity of textiles increased when ceramics were added to the film laminate. Ceramics slightly increased the thermal insulation value and decreased the water vapor transmission rate. The thermal manikin test also showed that ceramics enhanced the thermal insulation of the clothing system without increasing the evaporative resistance. The microclimate temperature was kept higher when subjects wore the warm-up suit with ceramics.
Surface Morphology and Properties of Bombyx mori Silk Fibroin Fiber Treated with I 2-KI Aqueous Solution
Authors: Majibur Rahman Khan Md. , Gotoh Yasuo , Morikawa Hideaki , Miura Mikihiko
Published: July 2009

The surface morphology, thermal and mechanical properties of Bombyx mori silk fibroin (SF) fiber treated with a 1.23 N iodine-potassium iodide (I2-KI) aqueous solution were investigated using scanning electron microscopy (SEM), atomic force microscopy (AFM), differential scanning calorimetry, thermogravimetric analysis, and tensile measurements to clarify the effects of the iodine treatment. SEM and AFM analyses indicated that the SF fiber surface became rougher by the absorption of polyiodide ions. The mechanical properties of iodinated SF showed an increase in Young’s modulus, and strain remained constant although ultimate tensile strength slightly decreased. The thermal stability of SF molecules was greatly enhanced by iodine treatment. Iodinated SF fibers should be an attractive candidate for biomedical applications such as for producing antimicrobial filters, iodine containing wound-healing anion exchange fibers, etc.
Cluster-Spun Yarn — A New Concept in Composite Yarn Spinning
Authors: Gharahaghaji Ali Akbar , Zargar Elham Naghash , Ghane Mohammad , Hossaini Abdolkarim
Published: July 2009

The aim of this work is to explore a new method for producing spun yarn on a modified ring spinning system which is called “clusterspun yarn”. Here, we describe the effects of the clustering of polyester multifilaments on the internal structure and properties of a composite yarn. Cotton fibers and polyester multifilaments were spun into 19 Ne cluster and core-spun yarns at five different twist levels. These yarns were then tested to compare their properties, including tenacity, elongation, and evenness. Surface morphology and structural variations of cluster and core-spun yarns were studied by scanning electron microscopy. Microtome and image-processing methods have been used to study the structure and packing of fibers in the cross-section of yarns. The results show that the special structure of a cluster-spun yarn results in pronounced enhancement in the structural mechanics and yarn properties. The statistical analysis results indicate that the tenacity and breaking elongation of cluster-spun yarn is significantly more than that in core-spun yarn. The results show that the twist factor at about 3.9(α e) gives the optimum properties. In addition, lower twist is needed to produce quality yarn in cluster-spun yarns as compared with normal core-spun yarns.