Copy Number Variation Shapes Genome Diversity in Arabidopsis Over Immediate Family Generational Scales

Arabidopsis thaliana is the model plant and is grown worldwide by plant biologists seeking to dissect the molecular underpinning of plant growth and development. Gene copy number variation (CNV) is a common form of genome natural diversity that is currently poorly studied in plants and may have broad implications for model organism research, evolutionary biology, and crop science. Herein, comparative genomic hybridization (CGH) was used to identify and interrogate regions of gene CNV across the A. thaliana genome. A common temperature condition used for growth of A. thaliana in our laboratory and many around the globe is 22 °C. The current study sought to test whether A. thaliana, grown under different temperature (16 and 28 °C) and stress regimes (salicylic acid spray) for five generations, selecting for fecundity at each generation, displayed any differences in CNV relative to a plant lineage growing under normal conditions. Three siblings from each alternative temperature or stress lineage were also compared with the reference genome (22 °C) by CGH to determine repetitive and nonrepetitive CNVs. Findings document exceptional rates of CNV in the genome of A. thaliana over immediate family generational scales. A propensity for duplication and nonrepetitive CNVs was documented in 28 °C CGH, which was correlated with the greatest plant stress and infers a potential CNV–environmental interaction. A broad diversity of gene species were observed within CNVs, but transposable elements and biotic stress response genes were notably overrepresented as a proportion of total genes and genes initiating CNVs. Results support a model whereby segmental CNV and the genes encoded within these regions contribute to adaptive capacity of plants through natural genome variation

Neural Network Parameterizations of Electromagnetic Nucleon Form Factors

The electromagnetic nucleon form-factors data are studied with artificial feed forward neural networks. As a result the unbiased model-independent form-factor parametrizations are evaluated together with uncertainties. The Bayesian approach for the neural networks is adapted for chi2 error-like function and applied to the data analysis. The sequence of the feed forward neural networks with one hidden layer of units is considered. The given neural network represents a particular form-factor parametrization. The so-called evidence (the measure of how much the data favor given statistical model) is computed with the Bayesian framework and it is used to determine the best form factor parametrization.Comment: The revised version is divided into 4 sections. The discussion of the prior assumptions is added. The manuscript contains 4 new figures and 2 new tables (32 pages, 15 figures, 2 tables

Structure formation in cosmologies with oscillating dark energy

{abridged} We study the imprints on the formation and evolution of cosmic structures of dynamical dark energy models, characterized by an oscillating equation of state. The redshift evolution of the equation of state parameter w(z) for dark energy is characterized by two parameters, describing the amplitude and the frequency of the oscillations. We consider six different oscillating dark energy models, each characterized by a different set of parameter values. Under the common assumption that dark energy is not clustering on the scales of interest, we study different aspects of cosmic structure formation. In particular, we self-consistently solve the spherical collapse problem. We then estimate the behavior of several cosmological observables, such as the linear growth factor, the Integrated Sachs-Wolfe (ISW) effect, the number counts of massive structures, and the matter and cosmic shear power spectra. We show that, independently of the amplitude and the frequency of the dark energy oscillations, none of the aforementioned observables show an oscillating behavior as a function of redshift. This is a consequence of the said observables' being integrals over some functions of the expansion rate over cosmic history. We also notice that deviations with respect to the expectations for a fiducial LambdaCDM cosmology are generically small, and in the majority of the cases distinguishing an oscillating dark energy model would be difficult. Exceptions to this conclusion are provided by the cosmic shear power spectrum, which for some of the models shows a difference at the level of \sim 10% over a wide range of angular scales, and the abundance of galaxy clusters, which is modified at the $\sim 10-20$ level at $z \gtrsim 0.6$ for future wide weak lensing surveys.Comment: 18 pages, 15 figures, published on MNRA

Measurement of the Longitudinal Spin Transfer to Lambda and Anti-Lambda Hyperons in Polarised Muon DIS

The longitudinal polarisation transfer from muons to lambda and anti-lambda hyperons, D_LL, has been studied in deep inelastic scattering off an unpolarised isoscalar target at the COMPASS experiment at CERN. The spin transfers to lambda and anti-lambda produced in the current fragmentation region exhibit different behaviours as a function of x and xF . The measured x and xF dependences of D^lambda_LL are compatible with zero, while D^anti-lambda_LL tends to increase with xF, reaching values of 0.4 - 0.5. The resulting average values are D^lambda_LL = -0.012 +- 0.047 +- 0.024 and D^anti-lambda_LL = 0.249 +- 0.056 +- 0.049. These results are discussed in the frame of recent model calculations.Comment: 13 pages, 7 figure

Observation of a J^PC = 1-+ exotic resonance in diffractive dissociation of 190 GeV/c pi- into pi- pi- pi+

The COMPASS experiment at the CERN SPS has studied the diffractive dissociation of negative pions into the pi- pi- pi+ final state using a 190 GeV/c pion beam hitting a lead target. A partial wave analysis has been performed on a sample of 420000 events taken at values of the squared 4-momentum transfer t' between 0.1 and 1 GeV^2/c^2. The well-known resonances a1(1260), a2(1320), and pi2(1670) are clearly observed. In addition, the data show a significant natural parity exchange production of a resonance with spin-exotic quantum numbers J^PC = 1-+ at 1.66 GeV/c^2 decaying to rho pi. The resonant nature of this wave is evident from the mass-dependent phase differences to the J^PC = 2-+ and 1++ waves. From a mass-dependent fit a resonance mass of 1660 +- 10+0-64 MeV/c^2 and a width of 269+-21+42-64 MeV/c^2 is deduced.Comment: 7 page, 3 figures; version 2 gives some more details, data unchanged; version 3 updated authors, text shortened, data unchange

Perspectives on utilization of edible coatings and nano-laminate coatings for extension of postharvest storage of fruits and vegetables

It is known that in developing countries, a large quantity of fruit and vegetable losses results at postharvest and processing stages due to poor or scarce storage technology and mishandling during harvest. The use of new and innovative technologies for reducing postharvest losses is a requirement that has not been fully covered. The use of edible coatings (mainly based on biopolymers) as a postharvest technique for agricultural commodities has offered biodegradable alternatives in order to solve problems (e.g., microbiological growth) during produce storage. However, biopolymer-based coatings can present some disadvantages such as: poor mechanical properties (e.g., lipids) or poor water vapor barrier properties (e.g., polysaccharides), thus requiring the development of new alternatives to solve these drawbacks. Recently, nanotechnology has emerged as a promising tool in the food processing industry, providing new insights about postharvest technologies on produce storage. Nanotechnological approaches can contribute through the design of functional packing materials with lower amounts of bioactive ingredients, better gas and mechanical properties and with reduced impact on the sensorial qualities of the fruits and vegetables. This work reviews some of the main factors involved in postharvest losses and new technologies for extension of postharvest storage of fruits and vegetables, focused on perspective uses of edible coatings and nano-laminate coatings.María L. Flores-López thanks Mexican Science and Technology Council (CONACYT, Mexico) for PhD fellowship support (CONACYT Grant Number: 215499/310847). Miguel A. Cerqueira (SFRH/BPD/72753/2010) is recipient of a fellowship from the Fundação para a Ciência e Tecnologia (FCT, POPH-QREN and FSE Portugal). The authors also thank the FCT Strategic Project of UID/ BIO/04469/2013 unit, the project RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462) and the project ‘‘BioInd Biotechnology and Bioengineering for improved Industrial and AgroFood processes,’’ REF. NORTE-07-0124-FEDER-000028 Co-funded by the Programa Operacional Regional do Norte (ON.2 – O Novo Norte), QREN, FEDER. Fundação Cearense de Apoio ao Desenvolvimento Científico e Tecnológico – FUNCAP, CE Brazil (CI10080-00055.01.00/13)

Hubble parameter data constraints on dark energy

We use Hubble parameter versus redshift data from Stern, et al(2010) and Gazta\~{n}aga, et al (2009) to place constraints on model parameters of constant and time-evolving dark energy cosmological models. These constraints are consistent with (through not as restrictive as) those derived from supernova Type Ia magnitude-redshift data. However, they are more restrictive than those derived from galaxy cluster angular diameter distance, and comparable with those from gamma-ray burst and lookback time data. A joint analysis of the Hubble parameter data with more restrictive baryon acoustic oscillation peak length scale and supernova Type Ia apparent magnitude data favors a spatially-flat cosmological model currently dominated by a time-independent cosmological constant but does not exclude time-varying dark energy.Comment: 7 pages, 9 figures, 2 tables, Accepted for publication in PL

Phase I study of epirubicin, cisplatin and capecitabine plus matuzumab in previously untreated patients with advanced oesophagogastric cancer

To evaluate the safety, tolerability, efficacy, pharmacokinetics and pharmacodynamics of the humanised antiepidermal growth factor receptor monoclonal antibody matuzumab combined with epirubicin, cisplatin and capecitabine (ECX) in patients as first-line treatment for advanced oesophagogastric cancer that express epidermal growth factor receptor (EGFR). This was a phase I dose escalation study of matuzumab at 400 and 800 mg weekly and 1200 mg every 3 weeks combined with ECX (epirubicin 50 mg m−2, cisplatin 60 mg m−2 on day 1 and capecitabine 1000 mg m−2 daily). Patients were treated until disease progression, unacceptable toxicity or for a maximum of eight cycles. Twenty-one patients were treated with matuzumab at three different dose levels (DLs) combined with ECX. The main dose-limiting toxicity (DLT) was grade 3 lethargy at 1200 mg matuzumab every 3 weeks and thus 800 mg matuzumab weekly was the maximum-tolerated dose (MTD). Other common toxicities included rash, nausea, stomatitis and diarrhoea. Pharmacokinetic evaluation demonstrated that the coadministration of ECX did not alter the exposure of matuzumab. Pharmacodynamic studies on skin biopsies demonstrated inhibition of the EGFR pathway. Objective response rates of 65% (95% confidence interval (CI): 43–82), disease stabilisation of 25% (95% CI: 11–47) and a disease control rate (CR+PR+SD) of 90% were achieved overall. The MTD of matuzumab in combination with ECX was 800 mg weekly, and at this DL it was well-tolerated and showed encouraging antitumour activity. At the doses evaluated in serial skin biopsies, matuzumab decreased phosphorylation of EGFR and MAPK, and increased phosphorylation of STAT-3

A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes

BACKGROUND: Observed co-expression of a group of genes is frequently attributed to co-regulation by shared transcription factors. This assumption has led to the hypothesis that promoters of co-expressed genes should share common regulatory motifs, which forms the basis for numerous computational tools that search for these motifs. While frequently explored for yeast, the validity of the underlying hypothesis has not been assessed systematically in mammals. This demonstrates the need for a systematic and quantitative evaluation to what degree co-expressed genes share over-represented motifs for mammals. RESULTS: We identified 33 experiments for human and mouse in the ArrayExpress Database where transcription factors were manipulated and which exhibited a significant number of differentially expressed genes. We checked for over-representation of transcription factor binding sites in up- or down-regulated genes using the over-representation analysis tool oPOSSUM. In 25 out of 33 experiments, this procedure identified the binding matrices of the affected transcription factors. We also carried out de novo prediction of regulatory motifs shared by differentially expressed genes. Again, the detected motifs shared significant similarity with the matrices of the affected transcription factors. CONCLUSIONS: Our results support the claim that functional regulatory motifs are over-represented in sets of differentially expressed genes and that they can be detected with computational methods