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1.  Pegylated IFN-α regulates hepatic gene expression through transient Jak/STAT activation 
The Journal of Clinical Investigation  2014;124(4):1568-1581.
The use of pegylated interferon-α (pegIFN-α) has replaced unmodified recombinant IFN-α for the treatment of chronic viral hepatitis. While the superior antiviral efficacy of pegIFN-α is generally attributed to improved pharmacokinetic properties, the pharmacodynamic effects of pegIFN-α in the liver have not been studied. Here, we analyzed pegIFN-α–induced signaling and gene regulation in paired liver biopsies obtained prior to treatment and during the first week following pegIFN-α injection in 18 patients with chronic hepatitis C. Despite sustained high concentrations of pegIFN-α in serum, the Jak/STAT pathway was activated in hepatocytes only on the first day after pegIFN-α administration. Evaluation of liver biopsies revealed that pegIFN-α induces hundreds of genes that can be classified into four clusters based on different temporal expression profiles. In all clusters, gene transcription was mainly driven by IFN-stimulated gene factor 3 (ISGF3). Compared with conventional IFN-α therapy, pegIFN-α induced a broader spectrum of gene expression, including many genes involved in cellular immunity. IFN-induced secondary transcription factors did not result in additional waves of gene expression. Our data indicate that the superior antiviral efficacy of pegIFN-α is not the result of prolonged Jak/STAT pathway activation in hepatocytes, but rather is due to induction of additional genes that are involved in cellular immune responses.
doi:10.1172/JCI70408
PMCID: PMC3973080  PMID: 24569457
2.  Cambial activity and xylem cell development in Pinus cembra and Pinus sylvestris at their climatic limits in the Eastern Alps in 2007 
Phyton; annales rei botanicae  2011;51(2):299-313.
Summary
It has been frequently stressed that at distributional boundaries, like at the Alpine timberline and within dry inner Alpine environments, tree growth will be affected first by changing climate conditions. Climate in 2007 was characterized by the occurrence of exceptionally mild temperatures in spring (3.4 and 2.7 °C above long-term mean (LTM) at timberline and the valley sites, respectively) with an almost continuous drought period recorded in April and slightly warmer than average temperatures throughout summer (1.3 °C above LTM at both sites).
We compared temporal dynamics of cambial activity and xylem cell development in Pinus cembra at the Alpine timberline (1950 m a.s.l.) and Pinus sylvestris at a xeric inner Alpine site (750 m a.s.l.) by repeated cellular analyses of micro-cores (n = 5 trees/site). While onset of wood formation in P. sylvestris and P. cembra differed by about two weeks (12 and 27 April, respectively), maximum daily growth rates peaked on 6 May at the valley site and on 23 June at timberline. At both sites maximum tracheid production was reached prior to occurrence of more favourable climatic conditions during summer, i.e. an increase in precipitation and temperature. Xylem formation ended on 31 August and 28 October at the xeric site and at timberline, respectively.
This study demonstrates the plasticity of tree-ring formation along an altitudinal transect in response to water availability and temperature. Whether early achievement of maximum growth rates is an adaptation to cope with extreme environmental conditions prevailing at limits of tree growth needs to be analysed more closely by taking belowground carbon allocation into account.
PMCID: PMC3837289  PMID: 24273354
Alpine timberline; cambium; dry inner Alpine valley; intra-annual growth; Scots pine; Stone pine; wood anatomy; xylogenesis
3.  Susceptibility-weighted imaging at 7 T: Improved diagnosis of cerebral cavernous malformations and associated developmental venous anomalies☆☆☆ 
NeuroImage : Clinical  2012;1(1):116-120.
Background and aim
In the diagnosis of cerebral cavernous malformations (CCMs) magnetic resonance imaging is established as the gold standard. Conventional MRI techniques have their drawbacks in the diagnosis of CCMs and associated venous malformations (DVAs). The aim of our study was to evaluate susceptibility weighted imaging SWI for the detection of CCM and associated DVAs at 7 T in comparison with 3 T.
Patients and methods
24 patients (14 female, 10 male; median age: 38.3 y (21.1 y–69.1 y) were included in the study. Patients enrolled in the study received a 3 T and a 7 T MRI on the same day. The following sequences were applied on both field strengths: a T1 weighted 3D GRE sequence (MP-RAGE) and a SWI sequence. After obtaining the study MRIs, eleven patients underwent surgery and 13 patients were followed conservatively or were treated radio-surgically.
Results
Patients initially presented with haemorrhage (n = 4, 16.7%), seizures (n = 2, 8.3%) or other neurology (n = 18, 75.0%). For surgical resected lesions histopathological findings verified the diagnosis of CCMs. A significantly higher number of CCMs was diagnosed at 7 T SWI sequences compared with 3 T SWI (p < 0.05). Additionally diagnosed lesions on 7 T MRI were significantly smaller compared to the initial lesions on 3 T MRIs (p < 0.001). Further, more associated DVAs were diagnosed at 7 T MRI compared to 3 T MRI.
Conclusion
SWI sequences at ultra-high-field MRI improve the diagnosis of CCMs and associated DVAs and therefore add important pre-operative information.
doi:10.1016/j.nicl.2012.09.005
PMCID: PMC3757736  PMID: 24179744
CCMs, cerebral cavernous malformations; DVA, developmental venous malformation; SWI, susceptibility weighted imaging; Cerebral cavernous malformations; High field MRI; Susceptibility weighted imaging
4.  Effects of environmental conditions on onset of xylem growth in Pinus sylvestris under drought 
Tree physiology  2011;31(5):483-493.
Summary
We determined influence of environmental factors (air and soil temperature, precipitation, photoperiod) on onset of xylem growth in Scots pine (Pinus sylvestris L.) within a dry inner Alpine valley (750 m a.s.l., Tyrol, Austria) by repeatedly sampling micro-cores throughout 2007-2010 at two sites (xeric and dry-mesic) at the start of the growing season. Temperature sums were calculated in degree-days (DD) ≥ 5 °C from 1 January and 20 March, i.e. spring equinox, to account for photoperiodic control of release from winter dormancy. Threshold temperatures at which xylogenesis had a 0.5 probability of being active were calculated by logistic regression. Onset of xylem growth, which was not significantly different between the xeric and dry-mesic site, ranged from mid-April in 2007 to early May in 2008. Among most study years statistically significant differences (P < 0.05) in onset of xylem growth were detected. Mean air temperature sums calculated from 1 January until onset of xylem growth were 230 ± 44 DD (mean ± standard deviation) at the xeric and 205 ± 36 DD at the dry-mesic site. Temperature sums calculated from spring equinox until onset of xylem growth showed quite less variability during the four year study period amounting to 144 ± 10 and 137 ± 12 DD at the xeric and dry-mesic site, respectively. At both sites xylem growth was active when daily minimum, mean and maximum air temperatures were 5.3, 10.1 and 16.2 °C, respectively. Soil temperature thresholds and DD until onset of xylem growth differed significantly between sites indicating minor importance of root-zone temperature for onset of xylem growth. Although spring precipitation is known to limit radial growth in P. sylvestris exposed to dry inner Alpine climate, results of this study revealed that (i) a daily minimum air temperature threshold for onset of xylem growth in the range of 5-6 °C exists and (ii) air temperature sum rather than precipitation or soil temperature triggers start of xylem growth. Based on these findings we suggest that drought stress forces P. sylvestris to draw upon water reserves in the stem for enlargement of first tracheids after cambial resumption in spring.
doi:10.1093/treephys/tpr034
PMCID: PMC3427020  PMID: 21593011
dry inner Alpine valley; heat-sum; phenology; Scots pine; wood formation; xylogenesis
5.  Hypothermia in the operating theatre 
Critical Care  2012;16(Suppl 2):A17.
doi:10.1186/cc11275
PMCID: PMC3389477
6.  Tristetraprolin-driven regulatory circuit controls quality and timing of mRNA decay in inflammation 
Inflammatory gene activation must be rigorously controlled to ensure a rapid, but transient, response. In this work, a regulatory circuit is revealed that governs the destabilization of inflammatory mRNAs and plays an essential role in re-establishing immune homeostasis after inflammatory stimulus.
We describe a regulatory circuit that governs the sequential destabilization of inflammatory mRNAs. This circuit limits potentially deleterious inflammatory mRNA accumulation, yet it prevents premature removal of those mRNAs that are still needed.We show that the sequential destabilization of inflammatory mRNAs is driven by the continuous inverse coupling of p38 MAPK activity profile with the mRNA-destabilizing function of tristetraprolin (TTP) during the entire inflammatory response. This control mechanism ensures that with time, the TTP-dependent mRNA decay gradually spreads resulting in cumulative elimination of 30% of inflammation-induced unstable mRNAs in macrophages.We generated mice with myeloid cell-specific TTP deletion to provide evidence for the function of this regulatory circuit in vivo. These animals are hypersensitive to LPS and display a dysbalanced cytokine production whose pattern is agreement with our model of sequential destabilization the individual mRNAs by TTP.We propose that myeloid TTP is critically involved in the re-installment of immune homeostasis after inflammatory stimulus rather than in the maintenance of steady-state immune homeostasis.
For a successful yet controlled immune response, cells need to specifically destabilize inflammatory mRNAs but prevent premature removal of those still used. The regulatory circuits controlling quality and timing in the global inflammatory mRNA decay are not understood. Here, we show that the mRNA-destabilizing function of the AU-rich element-binding protein tristetraprolin (TTP) is inversely regulated by the p38 MAPK activity profile such that after inflammatory stimulus the TTP-dependent decay is initially limited to few mRNAs. With time, the TTP-dependent decay gradually spreads resulting in cumulative elimination of one third of inflammation-induced unstable mRNAs in macrophages in vitro. We confirmed this sequential decay model in vivo since LPS-treated mice with myeloid TTP ablation exhibited similar cytokine dysregulation profile as macrophages. The mice were hypersensitive to LPS but otherwise healthy with no signs of hyperinflammation seen in conventional TTP knockout mice demonstrating the requirement for myeloid TTP in re-installment but not maintenance of immune homeostasis. These findings reveal a TTP- and p38 MAPK-dominated regulatory mechanism that is vital for balancing acute inflammation by a temporally and qualitatively controlled mRNA decay.
doi:10.1038/msb.2011.93
PMCID: PMC3737733  PMID: 22186734
immune homeostasis; inflammation; mRNA stability; p38 MAPK; tristetraprolin
7.  Animal snoRNAs and scaRNAs with exceptional structures 
RNA Biology  2011;8(6):938-946.
The overwhelming majority of small nucleolar RNAs (snoRNAs) fall into two clearly defined classes characterized by distinctive secondary structures and sequence motifs. A small group of diverse ncRNAs, however, shares the hallmarks of one or both classes of snoRNAs but differs substantially from the norm in some respects. Here, we compile the available information on these exceptional cases, conduct a thorough homology search throughout the available metazoan genomes, provide improved and expanded alignments, and investigate the evolutionary histories of these ncRNA families as well as their mutual relationships.
doi:10.4161/rna.8.6.16603
PMCID: PMC3256416  PMID: 21955586
box C/D; boxH/ACA; scaR-NA; evolution; secondary structure
8.  Climatic influences on intra-annual stem radial increment of Pinus sylvestris (L.) exposed to drought 
Trees (Berlin, Germany : West)  2010;24(5):887-898.
Within a dry inner Alpine valley in the Eastern Central Alps (750 m a.s.l., Tyrol, Austria) the influence of climate variables (precipitation, air humidity, temperature) and soil water content on intra-annual dynamics of tree-ring development was determined in Scots pine (Pinus sylvestris L.) at two sites differing in soil water availability (xeric and dry-mesic site). Radial stem development was continuously followed during 2007 and 2008 by band dendrometers and repeated micro-sampling of the developing tree rings of mature trees. Daily and seasonal fluctuations of the stem radius, which reached almost half of total annual increment, primarily reflected changes in tree water status and masked radial stem growth especially during drought periods in spring. However, temporal dynamics of intra-annual radial growth determined by both methods were found to be quite similar, when onset of radial growth in dendrometer traces was defined by the occurrence of first enlarging xylem cells. Radial increments during the growing period, which lasted from early April through early August showed statistically significant relationships with precipitation (Kendall τ = 0.234, p < 0.01, and τ = 0.184, p < 0.05, at the xeric and dry-mesic site, respectively) and relative air humidity (Pearson r = 0.290, p < 0.05, and r = 0.306, p < 0.05 at the xeric and dry-mesic site, respectively). Soil water content and air temperature had no influence on radial stem increment. Culmination of radial stem growth was detected at both study plots around mid-May, prior to occurrence of more favourable climatic conditions, i.e. an increase in precipitation during summer. We suggest that the early decrease in radial growth rate is due to a high belowground demand for carbohydrates to ensure adequate resource acquisition on the drought prone substrate.
doi:10.1007/s00468-010-0458-1
PMCID: PMC3191526  PMID: 22003269
Dendrometer; Drought; Dry inner Alpine valley; Pinus sylvestris; Radial growth; Xylem cell analysis
9.  Temporal dynamics of non-structural carbohydrates and xylem growth in Pinus sylvestris exposed to drought 
Wood formation requires a continuous supply of carbohydrates for structural growth and metabolism. In the montane belt of the central Austrian Alps we monitored the temporal dynamics of xylem growth and non-structural carbohydrates (NSC) in stem sapwood of Pinus sylvestris L. during the growing season 2009, which was characterized by exceptional soil dryness within the study area. Soil water content dropped below 10 % at the time of maximum xylem growth end of May. Histological analyses have been used to describe cambial activity and xylem growth. Determination of NSC was performed using specific enzymatic assays revealing that total NSC ranged from 0.8 to 1.7 % dry matter throughout the year. Significant variations (P < 0.05) of the size of the NSC pool were observed during the growing season. Starch showed persistent abundance throughout the year reaching a maximum shortly before onset of late wood formation in mid-July. Seasonal dynamics of NSC and xylem growth suggest that (i) high sink activity occurred at start of the growing season in spring and during late wood formation in summer and (ii) there was no particular shortage in NSC, which caused P. sylvestris to draw upon stem reserves more heavily during drought in 2009.
doi:10.1139/x11-085
PMCID: PMC3191854  PMID: 22003262
10.  Long-term changes in tree-ring – climate relationships at Mt. Patscherkofel (Tyrol, Austria) since the mid 1980s 
Trees (Berlin, Germany : West)  2008;22(1):31-40.
Although growth limitation of trees at Alpine and high-latitude timberlines by prevailing summer temperature is well established, loss of thermal response of radial tree growth during last decades has repeatedly been addressed. We examined long-term variability of climate-growth relationships in ring width chronologies of Stone pine (Pinus cembra L.) by means of moving response functions (MRF). The study area is situated in the timberline ecotone (c. 2000 – 2200 m a.s.l.) on Mt. Patscherkofel (Tyrol, Austria). Five site chronologies were developed within the ecotone with constant sample depth (≥ 19 trees) throughout most of the time period analysed. MRF calculated for the period 1866-1999 and 1901-1999 for c. 200 and c. 100 yr old stands, respectively, revealed that mean July temperature is the major and long-term stable driving force of Pinus cembra radial growth within the timberline ecotone. However, since the mid 1980s, radial growth in timberline and tree line chronologies strikingly diverges from the July temperature trend. This is probably a result of extreme climate events (e.g. low winter precipitation, late frost) and/or increasing drought stress on cambial activity. The latter assumption is supported by a < 10 % increase in annual increments of c. 50 yr old trees at the timberline and at the tree line in 2003 compared to 2002, when extraordinary hot and dry conditions prevailed during summer. Furthermore, especially during the second half of the 20th century, influence of climate variables on radial growth show abrupt fluctuations, which might also be a consequence of climate warming on tree physiology.
doi:10.1007/s00468-007-0166-7
PMCID: PMC3083837  PMID: 21532976
Climate warming; moving response function; Pinus cembra; temperature sensitivity; tree ring
11.  Temporal dynamic of wood formation in Pinus cembra along the alpine treeline ecotone and the effect of climate variables 
Trees (Berlin, Germany : West)  2009;23(3):623-635.
We determined the temporal dynamic of cambial activity and xylem development of stone pine (Pinus cembra L.) throughout the treeline ecotone. Repeated micro-sampling of the developing tree ring was carried out during the growing seasons 2006 and 2007 at the timberline (1950 m a.s.l.), treeline (2110 m a.s.l.) and within the krummholz belt (2180 m a.s.l.) and the influence of climate variables on intra-annual wood formation was determined.
At the beginning of both growing seasons, highest numbers of cambial and enlarging cells were observed at the treeline. Soil temperatures at time of initiation of cambial activity were c. 1.5 °C higher at treeline (open canopy) compared to timberline (closed canopy), suggesting that a threshold root-zone temperature is involved in triggering onset of above ground stem growth.
The rate of xylem cell production determined in two weekly intervals during June through August 2006-2007 was significantly correlated with air temperature (temperature sums expressed as degree-days and mean daily maximum temperature) at the timberline only. Lack of significant relationships between tracheid production and temperature variables at the treeline and within the krummholz belt support past dendroclimatological studies that more extreme environmental conditions (e.g., wind exposure, frost desiccation, late frost) increasingly control tree growth above timberline.
Results of this study revealed that spatial and temporal (i.e. year-to-year) variability in timing and dynamic of wood formation of Pinus cembra is strongly influenced by local site factors within the treeline ecotone and the dynamics of seasonal temperature variation, respectively.
PMCID: PMC3078619  PMID: 21509148
Cambium; intra-annual growth; Pinus cembra; temperature; tracheid production
12.  Effects of climate variables on intra-annual stem radial increment in Pinus cembra (L.) along the alpine treeline ecotone 
Annals of forest science  2009;66(5):503.
Within the alpine treeline ecotone tree growth is increasingly restricted by extreme climate conditions. Although intra-annual stem growth recorded by dendrometers can be linked to climate, stem diameter increments in slow-growing subalpine trees are masked by changes in tree water status.We tested the hypothesis that intra-annual radial stem growth in Pinus cembra is influenced by different climate variables along the treeline ecotone in the Austrian Alps. Dendrometer traces were compared with dynamics of xylem cell development to date onset of cambial activity and radial stem growth in spring.Daily fluctuations in stem radius reflected changes in tree water status throughout the treeline ecotone. Extracted daily radial increments were significantly correlated with air temperature at the timberline and treeline only, where budburst, cambial activity and enlargement of first tracheids also occurred quite similarly. A close relationship was detected between radial increment and number of enlarging tracheids throughout the treeline ecotone.We conclude that (i) the relationship between climate and radial stem growth within the treeline ecotone is dependent on a close coupling to atmospheric climate conditions and (ii) initiation of cambial activity and radial growth in spring can be distinguished from stem re-hydration by histological analysis.
doi:10.1051/forest/2009038
PMCID: PMC3059571  PMID: 21423861
dendrometer; Pinus cembra; radial increment; treeline ecotone; xylem formation
13.  Photosynthetic temperature adaptation of Pinus cembra within the timberline ecotone of the Central Austrian Alps 
Annals of forest science  2010;67(2):201.
Temperature is suggested to determine the upper limit of tree life. Therefore, future climate warming may be of importance for tree distribution within the European Alps, where low temperatures limit carbon metabolism.
We focused on the effects of air and soil temperature on net photosynthesis (Pn) of Pinus cembra an evergreen climax species of the timberline ecotone of the Central Austrian Alps. Light response and temperature response curves were estimated along an altitudinal gradient ranging from the forest limit up to the krummholz limit in both summer and fall.
In general, Pn was significantly lower in fall as compared to summer. Nevertheless, independent from season mean Pn values tended to increase with elevation and were positively correlated with root zone temperatures. The specific leaf area by contrast declined with increasing elevation. Furthermore, the temperature optimum of net photosynthesis declined with increasing elevation and was positively correlated with the mean maximum air temperature of the 10 days prior the date of measurement.
Thus, our findings appear to reflect a long-term adaptation of the photosynthetic apparatus of Pinus cembra to the general temperature conditions with respect to elevation combined with a short term acclimation to the prevailing temperature regime.
doi:10.1051/forest/2009094
PMCID: PMC3047779  PMID: 21379394
net photosynthesis; temperature; cembran pine; timberline ecotone; global warming
14.  Effects of atmospheric and climate change at the timberline of the Central European Alps 
Annals of forest science  2009;66(4):402.
This review considers potential effects of atmospheric change and climate warming within the timberline ecotone of the Central European Alps. After focusing on the impacts of ozone (O3) and rising atmospheric CO2 concentration, effects of climate warming on the carbon and water balance of timberline trees and forests will be outlined towards conclusions about changes in tree growth and treeline dynamics.Presently, ambient ground-level O3 concentrations do not exert crucial stress on adult conifers at the timberline of the Central European Alps. In response to elevated atmospheric CO2 Larix decidua showed growth increase, whereas no such response was found in Pinus uncinata. Overall climate warming appears as the factor responsible for the observed growth stimulation of timberline trees.Increased seedling re-establishment in the Central European Alps however, resulted from invasion into potential habitats rather than upward migration due to climate change, although seedlings will only reach tree size upon successful coupling with the atmosphere and thus loosing the beneficial microclimate of low stature vegetation.In conclusion, future climate extremes are more likely than the gradual temperature increase to control treeline dynamics in the Central European Alps.
doi:10.1051/forest/2009023
PMCID: PMC3047780  PMID: 21379395
Alpine timberline; treeline; global warming; CO2; ozone; water balance; carbon gain
15.  Impact of drought on the temporal dynamics of wood formation in Pinus sylvestris 
Tree physiology  2010;30(4):490-501.
Summary
We determined the temporal dynamics of cambial activity and xylem cell differentiation of Scots pine (Pinus sylvestris L.) within a dry inner Alpine valley (750 m asl, Tyrol, Austria), where radial growth is strongly limited by drought in spring. Repeated micro-sampling of the developing tree ring of mature trees was carried out during 2 contrasting years at two study plots that differ in soil water availability (xeric and dry-mesic site).
In 2007, when air temperature at the beginning of the growing season in April exceeded the long-term mean by 6.4 °C, cambial cell division started in early April at both study plots. A delayed onset of cambial activity of c. 2 wk was found in 2008, when average climate conditions prevailed in spring, indicating that resumption of cambial cell division after winter dormancy is temperature-controlled. Cambial cell division consistently ended about the end of June/early July in both study years. Radial enlargement of tracheids started almost 3 wk earlier in 2007 compared with 2008 at both study plots. At the xeric site, the maximum rate of tracheid production in 2007 and 2008 was reached in early and mid-May, respectively, and c. 2 wk later, at the dry-mesic site. Since in both study years, more favorable growing conditions (i.e., an increase in soil water content) were recorded during summer, we suggest a strong sink competition for carbohydrates to mycorrhizal root and shoot growth. Wood formation stopped c. 4 wk earlier at the xeric compared with the dry-mesic site in both years, indicating a strong influence of drought stress on cell differentiation. This is supported by radial widths of earlywood cells, which were found to be significantly narrower at the xeric than at the dry-mesic site (P < 0.05).
Repeated cellular analyses during the two growing seasons revealed that, although spatial variability in the dynamics and duration of cell differentiation processes in Pinus sylvestris exposed to drought is strongly influenced by water availability, the onset of cambial activity and cell differentiation is controlled by temperature.
doi:10.1093/treephys/tpq003
PMCID: PMC3046340  PMID: 20197285
Cambium; dry inner Alpine valley; intra-annual growth; Scots pine; tracheid production; xylogenesis
16.  AREsite: a database for the comprehensive investigation of AU-rich elements 
Nucleic Acids Research  2010;39(Database issue):D66-D69.
AREsite is an online resource for the detailed investigation of AU-rich elements (ARE) in vertebrate mRNA 3′-untranslated regions (UTRs). AREs are one of the most prominent cis-acting regulatory elements found in 3′-UTRs of mRNAs. Various ARE-binding proteins that possess RNA stabilizing or destabilizing functions are recruited by sequence-specific motifs. Recent findings suggest an essential role of the structural mRNA context in which these sequence motifs are embedded. AREsite is the first database that allows to quantify the structuredness of ARE motif sites in terms of opening energies and accessibility probabilities. Moreover, we also provide a detailed phylogenetic analysis of ARE motifs and incorporate information about experimentally validated targets of the ARE-binding proteins TTP, HuR and Auf1. The database is publicly available at: http://rna.tbi.univie.ac.at/AREsite.
doi:10.1093/nar/gkq990
PMCID: PMC3013810  PMID: 21071424
17.  Invertebrate 7SK snRNAs 
Journal of Molecular Evolution  2008;66(2):107-115.
7SK RNA is a highly abundant noncoding RNA in mammalian cells whose function in transcriptional regulation has only recently been elucidated. Despite its highly conserved sequence throughout vertebrates, all attempts to discover 7SK RNA homologues in invertebrate species have failed so far. Here we report on a combined experimental and computational survey that succeeded in discovering 7SK RNAs in most of the major deuterostome clades and in two protostome phyla: mollusks and annelids. Despite major efforts, no candidates were found in any of the many available ecdysozoan genomes, however. The additional sequence data confirm the evolutionary conservation and hence functional importance of the previously described 3′ and 5′ stem-loop motifs, and provide evidence for a third, structurally well-conserved domain.
doi:10.1007/s00239-007-9052-6
PMCID: PMC2755741  PMID: 18193315
7SK RNA; Polymerase III transcription; Noncoding RNA; Lophotrochozoans
18.  RNAalifold: improved consensus structure prediction for RNA alignments 
BMC Bioinformatics  2008;9:474.
Background
The prediction of a consensus structure for a set of related RNAs is an important first step for subsequent analyses. RNAalifold, which computes the minimum energy structure that is simultaneously formed by a set of aligned sequences, is one of the oldest and most widely used tools for this task. In recent years, several alternative approaches have been advocated, pointing to several shortcomings of the original RNAalifold approach.
Results
We show that the accuracy of RNAalifold predictions can be improved substantially by introducing a different, more rational handling of alignment gaps, and by replacing the rather simplistic model of covariance scoring with more sophisticated RIBOSUM-like scoring matrices. These improvements are achieved without compromising the computational efficiency of the algorithm. We show here that the new version of RNAalifold not only outperforms the old one, but also several other tools recently developed, on different datasets.
Conclusion
The new version of RNAalifold not only can replace the old one for almost any application but it is also competitive with other approaches including those based on SCFGs, maximum expected accuracy, or hierarchical nearest neighbor classifiers.
doi:10.1186/1471-2105-9-474
PMCID: PMC2621365  PMID: 19014431
19.  The Vienna RNA Websuite 
Nucleic Acids Research  2008;36(Web Server issue):W70-W74.
The Vienna RNA Websuite is a comprehensive collection of tools for folding, design and analysis of RNA sequences. It provides a web interface to the most commonly used programs of the Vienna RNA package. Among them, we find folding of single and aligned sequences, prediction of RNA–RNA interactions, and design of sequences with a given structure. Additionally, we provide analysis of folding landscapes using the barriers program and structural RNA alignments using LocARNA. The web server together with software packages for download is freely accessible at http://rna.tbi.univie.ac.at/.
doi:10.1093/nar/gkn188
PMCID: PMC2447809  PMID: 18424795
20.  Strategies for measuring evolutionary conservation of RNA secondary structures 
BMC Bioinformatics  2008;9:122.
Background
Evolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. Since almost all of the available methods used for prediction and annotation of non-coding RNA genes rely on this evolutionary signature, accurate measures for structural conservation are essential.
Results
We systematically assessed the ability of various measures to detect conserved RNA structures in multiple sequence alignments. We tested three existing and eight novel strategies that are based on metrics of folding energies, metrics of single optimal structure predictions, and metrics of structure ensembles. We find that the folding energy based SCI score used in the RNAz program and a simple base-pair distance metric are by far the most accurate. The use of more complex metrics like for example tree editing does not improve performance. A variant of the SCI performed particularly well on highly conserved alignments and is thus a viable alternative when only little evolutionary information is available. Surprisingly, ensemble based methods that, in principle, could benefit from the additional information contained in sub-optimal structures, perform particularly poorly. As a general trend, we observed that methods that include a consensus structure prediction outperformed equivalent methods that only consider pairwise comparisons.
Conclusion
Structural conservation can be measured accurately with relatively simple and intuitive metrics. They have the potential to form the basis of future RNA gene finders, that face new challenges like finding lineage specific structures or detecting mis-aligned sequences.
doi:10.1186/1471-2105-9-122
PMCID: PMC2335298  PMID: 18302738
21.  The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures 
Nucleic Acids Research  2007;35(Web Server issue):W335-W338.
Many non-coding RNA genes and cis-acting regulatory elements of mRNAs contain RNA secondary structures that are critical for their function. Such functional RNAs can be predicted on the basis of thermodynamic stability and evolutionary conservation. We present a web server that uses the RNAz algorithm to detect functional RNA structures in multiple alignments of nucleotide sequences. The server provides access to a complete and fully automatic analysis pipeline that allows not only to analyze single alignments in a variety of formats, but also to conduct complex screens of large genomic regions. Results are presented on a website that is illustrated by various structure representations and can be downloaded for local view. The web server is available at: rna.tbi.univie.ac.at/RNAz.
doi:10.1093/nar/gkm222
PMCID: PMC1933143  PMID: 17452347
22.  U7 snRNP-specific Lsm11 protein: dual binding contacts with the 100 kDa zinc finger processing factor (ZFP100) and a ZFP100-independent function in histone RNA 3′ end processing 
Nucleic Acids Research  2005;33(7):2106-2117.
The 3′ cleavage generating non-polyadenylated animal histone mRNAs depends on the base pairing between U7 snRNA and a conserved histone pre-mRNA downstream element. This interaction is enhanced by a 100 kDa zinc finger protein (ZFP100) that forms a bridge between an RNA hairpin element upstream of the processing site and the U7 small nuclear ribonucleoprotein (snRNP). The N-terminus of Lsm11, a U7-specific Sm-like protein, was shown to be crucial for histone RNA processing and to bind ZFP100. By further analysing these two functions of Lsm11, we find that Lsm11 and ZFP100 can undergo two interactions, i.e. between the Lsm11 N-terminus and the zinc finger repeats of ZFP100, and between the N-terminus of ZFP100 and the Sm domain of Lsm11, respectively. Both interactions are not specific for the two proteins in vitro, but the second interaction is sufficient for a specific recognition of the U7 snRNP by ZFP100 in cell extracts. Furthermore, clustered point mutations in three phylogenetically conserved regions of the Lsm11 N-terminus impair or abolish histone RNA processing. As these mutations have no effect on the two interactions with ZFP100, these protein regions must play other roles in histone RNA processing, e.g. by contacting the pre-mRNA or additional processing factors.
doi:10.1093/nar/gki516
PMCID: PMC1075925  PMID: 15824063
23.  Long-Term Productive Human Immunodeficiency Virus Infection of CD1a-Sorted Myeloid Dendritic Cells 
Journal of Virology  2005;79(1):602-608.
Myeloid, CD1a-sorted dendritic cells (MDC) productively replicated human immunodeficiency virus strains encoding envelope genes of either primary X4R5 or R5 strains for up to 45 days. Cell-free supernatant collected from long-term infected MDC, which had been exposed to an X4R5 virus 45 days earlier, was still infectious when placed over activated T cells. These data imply that DC can act as a persistent reservoir of infectious virus.
doi:10.1128/JVI.79.1.602-608.2005
PMCID: PMC538684  PMID: 15596853
24.  Impact of N-Chlorotaurine on Viability and Production of Secreted Aspartyl Proteinases of Candida spp. 
N-Chlorotaurine, an endogenous long-lived oxidant, demonstrated fungicidal activity against Candida spp. and a postantifungal effect. Secreted aspartyl proteinases, important fungal virulence factors, proved to be a first target of impact. These results provide support for the topical application of N-chlorotaurine as an antimicrobial agent in yeast infections.
doi:10.1128/AAC.46.6.1996-1999.2002
PMCID: PMC127226  PMID: 12019124

Results 1-24 (24)