Co-dependence between trypanosome nuclear lamina components in nuclear stability and control of gene expression

The nuclear lamina is a filamentous structure subtending the nuclear envelope and required for chromatin organization, transcriptional regulation and maintaining nuclear structure. The trypanosomatid coiled-coil NUP-1 protein is a lamina component functionally analogous to lamins, the major lamina proteins of metazoa. There is little evidence for shared ancestry, suggesting the presence of a distinct lamina system in trypanosomes. To find additional trypanosomatid lamina components we identified NUP-1 interacting proteins by affinity capture and mass-spectrometry. Multiple components of the nuclear pore complex (NPC) and a second coiled-coil protein, which we termed NUP-2, were found. NUP-2 has a punctate distribution at the nuclear periphery throughout the cell cycle and is in close proximity to NUP-1, the NPCs and telomeric chromosomal regions. RNAi-mediated silencing of NUP-2 leads to severe proliferation defects, gross alterations to nuclear structure, chromosomal organization and nuclear envelope architecture. Further, transcription is altered at telomere-proximal variant surface glycoprotein (VSG) expression sites (ESs), suggesting a role in controlling ES expression, although NUP-2 silencing does not increase VSG switching. Transcriptome analysis suggests specific alterations to Pol I-dependent transcription. NUP-1 is mislocalized in NUP-2 knockdown cells and vice versa, implying that NUP-1 and NUP-2 form a co-dependent network and identifying NUP-2 as a second trypanosomatid nuclear lamina component

On Modular Invariance and 3D Gravitational Instantons

We study the modular transformation properties of Euclidean solutions of 3D gravity whose asymptotic geometry has the topology of a torus. These solutions represent saddle points of the grand canonical partition function with an important example being the BTZ black hole, and their properties under modular transformations are inherited from the boundary conformal field theory encoding the asymptotic dynamics. Within the Chern Simons formulation, classical solutions are characterised by specific holonomies describing the wrapping of the gauge field around cycles of the torus. We find that provided these holonomies transform in an appropriate manner, there exists an associated modular invariant grand canonical partition function and that the spectrum of saddle points naturally includes a thermal bath in $AdS_3$ as discussed by Maldacena and Strominger. Indeed, certain modular transformations can naturally be described within classical bulk dynamics as mapping between different foliations with a "time" coordinate along different cycles of the asymptotic torus.Comment: 14 pages, RevTeX, typos corrected, to appear in Phys. Rev.

QiSampler: evaluation of scoring schemes for high-throughput datasets using a repetitive sampling strategy on gold standards

<p>Abstract</p> <p>Background</p> <p>High-throughput biological experiments can produce a large amount of data showing little overlap with current knowledge. This may be a problem when evaluating alternative scoring mechanisms for such data according to a gold standard dataset because standard statistical tests may not be appropriate.</p> <p>Findings</p> <p>To address this problem we have implemented the QiSampler tool that uses a repetitive sampling strategy to evaluate several scoring schemes or experimental parameters for any type of high-throughput data given a gold standard. We provide two example applications of the tool: selection of the best scoring scheme for a high-throughput protein-protein interaction dataset by comparison to a dataset derived from the literature, and evaluation of functional enrichment in a set of tumour-related differentially expressed genes from a thyroid microarray dataset.</p> <p>Conclusions</p> <p>QiSampler is implemented as an open source R script and a web server, which can be accessed at <url>http://cbdm.mdc-berlin.de/tools/sampler/</url>.</p

The Effect of Viticultural Climate on Red and White Wine Typicity - Characterization in Ibero-American grape-growing regions

Aim: This study is part of a CYTED (Ibero-American Program for Science, Technology and Development) project on vitivinicultural zoning. The objective was to characterize the effect of viticultural climate on red and white wine typicity in the macro Ibero-American viticultural region. Methods and results: The climate of 46 grape-growing regions in 6 Ibero-American countries (Argentina, Bolivia, Brazil, Chile, Spain and Portugal) was characterized using the three viticultural climate index of the Geoviticulture MCC System: the Heliothermal index HI, the Cool Night index CI and the Dryness index DI. The main sensory characteristics frequently observed in representative red and white wines of each of these regions were described by enology experts in the respective countries: intensity of colour, aroma, aroma-ripe fruit, body-palate concentration, alcohol, tannins (for red wines) and acidity as well as persistence on the palate. The data were submitted to a correlation analysis of the variables and Principal Component Analysis (PCA). Conclusion: The typicity of red and white wines was correlated with the HI, CI and DI viticultural climate indexes from the MCC System. The main wine sensory variables affected by viticultural climate were identified. Significance and impact of the study : The results can be used to project the potential impacts of climate change on wine sensory characteristics

L'effet du climat viticole sur la typicité des vins blancs: caractérisation au niveau des régions viticoles ibéro-américaines.

There are many studies in the world that characterize the effect of the climate on grape composition and wine characteristics and typicity concerning different viticultural regions. However, the same is not true concerning studies in a worldwide scale to characterize this effect considering different climate types. This study is part of a CYTED (Ibero-American Program for Science, Technology and Development) project in vitivinicultural zoning. The objective was to characterize the effect of the viticultural climate on white wine typicity on the macro Ibero-American viticultural region. The methodology used 46 grape-growing regions in 6 Ibero-American countries: Argentina, Bolivia, Brazil, Chile, Portugal and Spain. The viticultural climate of each region was characterized by the 3 viticultural climate index of the Geoviticulture MCC System (1): HI (Heliothermal index), CI (Cool night index) and DI (Dryness index). The main sensory characteristics observed frequently in representative white wines produced with grapes of each of these 46 grape-growing regions were described by enologists in the respective countries, using the methodology of Zanus & Tonietto (2). The sensory description concerned the intensity of perception of Color (Cou), Aroma - Intensity (Ar), Aroma - Ripe Fruit (Ar-Fm), Body ? Palate Concentration (Con), Alcohol (Al) and Acidity (Ac). The Persistence in Mouth (Per) was also evaluated. The data were submitted to a correlation analysis of the variables and to a Principal Component Analysis (PCA). The results showed that the typicity of the white wines was correlated with the viticultural climate indexes HI, CI and DI from MCC System. The main wine sensory variables affected by viticultural climate are identified

Height and timing of growth spurt during puberty in young people living with vertically acquired HIV in Europe and Thailand.

OBJECTIVE: The aim of this study was to describe growth during puberty in young people with vertically acquired HIV. DESIGN: Pooled data from 12 paediatric HIV cohorts in Europe and Thailand. METHODS: One thousand and ninety-four children initiating a nonnucleoside reverse transcriptase inhibitor or boosted protease inhibitor based regimen aged 1-10 years were included. Super Imposition by Translation And Rotation (SITAR) models described growth from age 8 years using three parameters (average height, timing and shape of the growth spurt), dependent on age and height-for-age z-score (HAZ) (WHO references) at antiretroviral therapy (ART) initiation. Multivariate regression explored characteristics associated with these three parameters. RESULTS: At ART initiation, median age and HAZ was 6.4 [interquartile range (IQR): 2.8, 9.0] years and -1.2 (IQR: -2.3 to -0.2), respectively. Median follow-up was 9.1 (IQR: 6.9, 11.4) years. In girls, older age and lower HAZ at ART initiation were independently associated with a growth spurt which occurred 0.41 (95% confidence interval 0.20-0.62) years later in children starting ART age 6 to 10 years compared with 1 to 2 years and 1.50 (1.21-1.78) years later in those starting with HAZ less than -3 compared with HAZ at least -1. Later growth spurts in girls resulted in continued height growth into later adolescence. In boys starting ART with HAZ less than -1, growth spurts were later in children starting ART in the oldest age group, but for HAZ at least -1, there was no association with age. Girls and boys who initiated ART with HAZ at least -1 maintained a similar height to the WHO reference mean. CONCLUSION: Stunting at ART initiation was associated with later growth spurts in girls. Children with HAZ at least -1 at ART initiation grew in height at the level expected in HIV negative children of a comparable age

The OTELO survey: faint end of the luminosity function of [O_(II)]3727 emitters at ‹z›=1.43

Aims. In this paper, we aim to study the main properties and luminosity function (LF) of the [O II]3727 emitters detected in the OTELO survey in order to characterise the star formation processes in low-mass galaxies at z ∼ 1.43 and to constrain the faint-end of the LF. Methods. Here, we describe the selection method and analysis of the emitters obtained from narrow-band scanning techniques. In addition, we present several relevant properties of the emitters and discuss the selection biases and uncertainties in the determination of the LF and the star formation rate density (SFRD). Results. We confirmed a total of 60 sources from a preliminary list of 332 candidates as [O II]3727 emitters. Approximately 93% of the emitters have masses in the range of 10^(8) < M*/M⊙ < 10^(9). All of our emitters are classified as late-type galaxies, with a lower value of (u − v) when compared with the rest of the emitters of the OTELO survey. We find that the cosmic variance strongly affects the normalisation (ϕ*) of the LF and explains the discrepancy of our results when compared with those obtained from surveys of much larger volumes. However, we are able to determine the faint-end slope of the LF, namely, α = −1.42 ± 0.06, by sampling the LF down to ∼1 dex lower than in previous works. We present our calculation of the SFRD of our sample and compare it to the value obtained in previous studies from the literature