Comparing reverse complementary genomic words based on their distance distributions and frequencies

In this work we study reverse complementary genomic word pairs in the human DNA, by comparing both the distance distribution and the frequency of a word to those of its reverse complement. Several measures of dissimilarity between distance distributions are considered, and it is found that the peak dissimilarity works best in this setting. We report the existence of reverse complementary word pairs with very dissimilar distance distributions, as well as word pairs with very similar distance distributions even when both distributions are irregular and contain strong peaks. The association between distribution dissimilarity and frequency discrepancy is explored also, and it is speculated that symmetric pairs combining low and high values of each measure may uncover features of interest. Taken together, our results suggest that some asymmetries in the human genome go far beyond Chargaff's rules. This study uses both the complete human genome and its repeat-masked version.Comment: Post-print of a paper accepted to publication in "Interdisciplinary Sciences: Computational Life Sciences" (ISSN: 1913-2751, ESSN: 1867-1462

Segmentation of DNA into coding and noncoding regions based on inter-STOP symbols distances

In this study we set to explore the potentialities of the inter-genomic symbols distance for finding the coding regions in DNA sequences. We use the distance between STOP symbols in the DNA sequence and a chi-square statistic to evaluate the nonhomogeneity of the three possible reading frames. The results of this exploratory study suggest that inter-STOP symbols distance has strong ability to discriminate coding regions.publishe

Dissimilar Symmetric Word Pairs in the Human Genome

In this work we explore the dissimilarity between symmetric word pairs, by comparing the inter-word distance distribution of a word to that of its reversed complement. We propose a new measure of dissimilarity between such distributions. Since symmetric pairs with different patterns could point to evolutionary features, we search for the pairs with the most dissimilar behaviour. We focus our study on the complete human genome and its repeat-masked version.Comment: Submitted 13-Feb-2017; accepted, after a minor revision, 17-Mar-2017; 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB 2017, Porto, Portugal, 21-23 June, 201

An analysis of symmetric words in human DNA: adjacent vs non-adjacent word distances

It is important to develop methods for nding DNA sites with high potencial for the formation of hairpin/cruciform structures. In a previous work, we studied the distances between adjacent reversed complement words (symmetric words), and we observed that for some words some distances were favored. In the work presented here, we extended the study to the distance between non-adjacent reversed complement words and we observed strong periodicity in the distance distribution of some words. This may be an indication of potential for the formation of hairpin/cruciform structures.publishe

Ataques de traça da uva Lobesia botrana em diferentes castas das regiões dos Vinhos Verdes e Douro

The European grape berry moth Lobesia botrana Denis & Schiffermüller (Lepidoptera: Tortricidae) is responsible for direct losses due to the damage cause to the grapes and indirect losses by allowing access to the grey mould Botrytis cinerea Pers. In some varieties – as Touriga Franca – the attacks are always more intensive than with other varieties. In this work, bio-assays have been performed to test the oviposition’s behaviour of L. botrana female. Three varieties of Vinhos Verdes region – Arinto, Loureiro and Trajadura – and three varieties of Douro region – Barroca, Touriga Franca, Touriga Nacional – have been tested. Only Touriga Franca presented significantly difference being more attractive. The bio-assays partially elucidate field observations and denounce a possible existence of alelochemicals in grapes berries

Noncommutative effects in astrophysical objects: a survey

The main implications of noncommutativity over astrophysical objects are examined. Noncommutativity is introduced through a deformed dispersion relation $E^{2}=p^{2}c^{2}(1+\lambda E)^{2} + m^{2}c^{4}$ and the relevant thermodynamical quantities are calculated using the grand canonical ensemble formalism. These results are applied to simple physical models describing main-sequence stars, white-dwarfs and neutron stars. The stability of main-sequence stars and white dwarfs is discussed.Comment: 10 pages. Talk presented by C. Z. at the "First Mediterranean Conference on Classical and Quantum Gravity", Kolymbari (Crete, Greece), September 14-18, 2009. To appear in the Proceeding

Fluorescent patterning of paper through laser engraving

While thermal treatment of paper can lead to the formation of aromatic structures via hydrothermal treatment (low temperature) or pyrolysis (high temperature), neither of these approaches allow patterning the substrates. Somewhere in between these two extremes, a handful of research groups have used CO2 lasers to pattern paper and induce carbonization. However, none of the previously reported papers have focused on the possibility to form fluorescent derivatives via laser-thermal engraving. Exploring this possibility, this article describes the possibility of using a CO2 laser engraver to selectively treat paper, resulting in the formation of fluorescent compounds, similar to those present on the surface of carbon dots. To determine the most relevant variables controlling this process, 3 MM chromatography paper was treated using a standard 30 W CO2 laser engraver. Under selected experimental conditions, a blue fluorescent pattern was observed when the substrate was irradiated with UV light (365 nm). The effect of various experimental conditions (engraving speed, engraving power, and number of engraving steps) was investigated to maximize the fluorescence intensity. Through a comprehensive characterization effort, it was determined that 5-(hydroxymethyl)furfural and a handful of related compounds were formed (varying in amount) under all selected experimental conditions. To illustrate the potential advantages of this strategy, that could complement those applications traditionally developed from carbon dots (sensors, currency marking, etc.), a redox-based optical sensor for sodium hypochlorite was developed.Fil: Clark, Kaylee M.. Clemson University; Estados UnidosFil: Skrajewski, Lauren. Clemson University; Estados UnidosFil: Benavidez, Tomás Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentina. Clemson University; Estados UnidosFil: Mendes, Letícia F.. Universidade de Sao Paulo; BrasilFil: Bastos, Erick L.. Universidade de Sao Paulo; BrasilFil: Dörr, Felipe A.. Universidade de Sao Paulo; BrasilFil: Sachdeva, Rakesh. Clemson University; Estados UnidosFil: Ogale, Amod A.. Clemson University; Estados UnidosFil: Paixão, Thiago R. L. C.. Universidade de Sao Paulo; BrasilFil: Garcia, Carlos D.. Clemson University; Estados Unido

Forest disturbance and growth processes are reflected in the geographical distribution of large canopy gaps across the Brazilian Amazon

Canopy gaps are openings in the forest canopy resulting from branch fall and tree mortality events. The geographical distribution of large canopy gaps may reflect underlying variation in mortality and growth processes. However, a lack of data at the appropriate scale has limited our ability to study this relationship until now. We detected canopy gaps using a unique LiDAR dataset consisting of 650 transects randomly distributed across 2500 km(2) of the Brazilian Amazon. We characterized the size distribution of canopy gaps using a power law and we explore the variation in the exponent, alpha. We evaluated how the alpha varies across the Amazon, in response to disturbance by humans and natural environmental processes that influence tree mortality rates. We observed that South-eastern forests contained a higher proportion of large gaps than North-western, which is consistent with recent work showing greater tree mortality rates in the Southeast than the Northwest. Regions characterized by strong wind gust speeds, frequent lightning and greater water shortage also had a high proportion of large gaps, indicating that geographical variation in alpha is a reflection of underlying disturbance processes. Forests on fertile soils were also found to contain a high proportion of large gaps, in part because trees grow tall on these sites and create large gaps when they fall; thus, canopy gap analysis picked up differences in growth as well as mortality processes. Finally, we found that human-modified forests had a higher proportion of large gaps than intact forests, as we would expect given that these forests have been disturbed. Synthesis. The proportion of large gaps in the forest canopy varied substantially over the Brazilian Amazon. We have shown that the trends can be explained by geographical variation in disturbance and growth. The frequency of extreme weather events is predicted to increase under climate change, and changes could lead to greater forest disturbance, which should be detectable as an increased proportion of large gaps in intact forests.Peer reviewe

Phenotypic plasticity in sargassum forests may not counteract projected biomass losses along a broad latitudinal gradient

Phenotypic plasticity and local adaptation can adjust individual responses to environmental changes across species' ranges. Studies addressing the implications of such traits have been underrepresented in the marine environment. Sargassum cymosum represents an ideal model to test phenotypic plasticity, as populations along the southwestern Atlantic Ocean display a sharp decrease in abundance toward distributional range limits. We (1) characterized the macroecological environment of S. cymosum across a latitudinal gradient, (2) evaluated potential differences in ecophysiological adjustments (biomass, photosynthetic pigments, phenolic compounds, total soluble sugars and proteins, and carbon-nitrogen-CN-content), and (3) tested for differences in thermal tolerance based on time series analyses produced from the present to contrasting representative concentration pathways scenarios (RCP) of future climate changes. Our results showed distinct macroecological environments, corresponding to tropical and warm temperate conditions, driving biomass and ecophysiological adjustments of S. cymosum. Populations from the two environments displayed contrasting thermal tolerances, with tropical individuals better coping with thermal stress when compared to more temperate ones (lethal temperatures of 33 degrees C vs. 30 degrees C); yet both populations lose biomass in response to increasing thermal stress while increasing secondary metabolites (for example, carotenoids and phenolic compounds) and decrease chlorophyll's content, Fv/Fm, total soluble sugars concentration and CN ratio, owing to oxidative stress. Despite evidence for phenotypic plasticity, significant future losses might occur in both tropical and warm temperate populations, particularly under the no mitigation RCP scenario, also known as the business as usual (that is, 8.5). In this context, broad compliance with the Paris Agreement might counteract projected impacts of climate change, safeguarding Sargassum forests in the years to come.This study was supported by grants from Boticario Foundation, FAPESC-Foundation Support Research and Innovation in the State of Santa Catarina, Capes Higher Education Personnel Improvement Coordination, CNPq-National Council for Scientific and Technological Development, Petrobras Ambiental, REBENTOS-Habitat monitoring network coastal Benthic and ProspecMar-Islands Sustainable Prospecting in Ocean Islands: Biodiversity, Chemistry, Ecology and Biotechnology, Rede Coral Vivo, REDEALGAS, a Pew Marine Fellowship, the Foundation for Science and Technology (FCT) of Portugal via SFRH/BSAB/150485/2019, SFRH/BD/144878/2019, UID/Multi/04326/2019, PTDC/BIA-CBI/6515/2020 and the transitional norm DL57/2016/CP1361/CT0035. LPG received a doctorate scholarship (88882.438723/2019-01) from Capes. CFDG thanks CNPq grants PQ-309658/2016-0and306304/2019-8. PAH thanks CAPES-Senior Visitor, CAPESPrInt 310793/2018-01, CNPq-PVE 407365/2013-3, CNPq-Universal 426215/2016-8 and CNPq-PQ308537/2019-0. GK received a master's scholarship from CAPES.info:eu-repo/semantics/submittedVersio