Analyzing the temporal regulation of translation efficiency in mouse liver.

Mammalian physiology and behavior follow daily rhythms that are orchestrated by endogenous timekeepers known as circadian clocks. Rhythms in transcription are considered the main mechanism to engender rhythmic gene expression, but important roles for posttranscriptional mechanisms have recently emerged as well (reviewed in Lim and Allada (2013) [1]). We have recently reported on the use of ribosome profiling (RPF-seq), a method based on the high-throughput sequencing of ribosome protected mRNA fragments, to explore the temporal regulation of translation efficiency (Janich et al., 2015 [2]). Through the comparison of around-the-clock RPF-seq and matching RNA-seq data we were able to identify 150 genes, involved in ribosome biogenesis, iron metabolism and other pathways, whose rhythmicity is generated entirely at the level of protein synthesis. The temporal transcriptome and translatome data sets from this study have been deposited in NCBI's Gene Expression Omnibus under the accession number GSE67305. Here we provide additional information on the experimental setup and on important optimization steps pertaining to the ribosome profiling technique in mouse liver and to data analysis.

Spatial and Temporal Trends in Sunshine Duration over Western Europe

This work analyzes sunshine duration variability in the western part of Europe (WEU) over the 1938– 2004 period. A principal component analysis is applied to cluster the original series from 79 sites into 6 regions, and then annual and seasonal mean series are constructed on regional and also for the whole WEU scales. Over the entire period studied here, the linear trend of annual sunshine duration is found to be nonsignificant. However, annual sunshine duration shows an overall decrease since the 1950s until the early 1980s, followed by a subsequent recovery during the last two decades. This behavior is in good agreement with the dimming and brightening phenomena described in previous literature. From the seasonal analysis, the most remarkable result is the similarity between spring and annual series, although the spring series has a negative trend; and the clear significant increase found for the whole WEU winter series, being especially large since the 1970s. The behavior of the major synoptic patterns for two seasons is investigated, resulting in some indications that sunshine duration evolution may be partially explained by changes in the frequency of some of them

The temporal dynamics of resource use by frugivorous birds: a network approach

Ecological network patterns are influenced by diverse processes that operate at different temporal rates. Here we analyzed whether the coupled effect of local abundance variation, seasonally phenotypic plastic responses, and species evolutionary adaptations might act in concert to shape network patterns. We studied the temporal variation in three interaction properties of bird species (number of interactions per species, interaction strength, and interaction asymmetry) in a temporal sequence of 28 plant frugivore interaction networks spanning two years in a Mediterranean shrubland community. Three main hypotheses dealing with the temporal variation of network properties were tested, examining the effects of abundance, switching behavior between alternative food resources, and morphological traits in determining consumer interaction patterns. Our results demonstrate that temporal variation in consumer interaction patterns is explained by short-term variation in resource and bird abundances and seasonal dietary switches between alternative resources (fleshy fruits and insects). Moreover, differences in beak morphology are associated with differences in switching behavior between resources, suggesting an important role of foraging adaptations in determining network patterns. We argue that beak shape adaptations might determine generalist and specialist feeding behaviors and thus the positions of consumer species within the network. Finally, we provide a preliminary framework to interpret phylogenetic signal in plant animal networks. Indeed, we show that the strength of the phylogenetic signal in networks depends on the relative importance of abundance, behavioral, and morphological variables. We show that these variables strongly differ in their phylogenetic signal. Consequently, we suggest that moderate and significant phylogenetic effects should be commonly observed in networks of species interactions. Read More: http://www.esajournals.org/doi/abs/10.1890/07-1939.1

Diagnóstico espaço-temporal da ocorrência de herbicidas nas águas superficiais e sedimentos do Rio Corumbataí e principais afluentes

Residues of herbicides from sugarcane were monitored in waters and sediments of Corumbataí River and tributaries. Ametryne, atrazine, simazine, hexazinone, glyphosate, and clomazone were detected in water samples, with negligible levels of ametryne and glyphosate in sediment samples. The area of recharge of the Guarani aquifer presented the highest triazine and clomazone levels. The triazines were detected at higher levels, with atrazine above Brazil's potability and quality standards. Total herbicide levels at some sampling points were 13 times higher than the European Community potability limit. There is no Brazilian standard for ametryne, although the risk is larger due to ametryne's higher toxicity for the aquatic biota.

Traducción técnica del capítulo III del libro Advanced Data Warehouse design: from conventional to spatial and temporal applications

The proposal to work on this final project came after several discussions held with Dr. Elzbieta Malinowski Gadja, who in 2008 published the book entitled Advanced Data Warehouse Design: From Conventional to Spatial and Temporal Applications (Data-Centric Systems and Applications). The project was carried out under the technical supervision of Dr. Malinowski and the direct beneficiary was the University of Costa Rica (UCR) where Dr. Malinowski is a professor at the Department of Computer Science and Informatics. The purpose of this project was twofold: First, to translate chapter III of said book with the intention of generating educational material for the use of the UCR and, second, to venture in the field of technical translation related to data warehouse. For the first component, the goal was to generate a final product that would eventually serve as an educational tool for the post-graduate courses of the UCR. For the second component, this project allowed me to acquire new skills and put into practice techniques that have helped me not only to perfom better in my current job as an Assistant Translator of the Inter-American BAnk (IDB), but also to use them in similar projects. The process was lenggthy and required torough research and constant communication with the author. The investigation focused on the search of terms and definitions to prepare the glossary, which was the basis to start the translation project. The translation process itself was carried out by phases, so that comments and corrections by the author could be taken into account in subsequent stages. Later, based on the glossary and the translated text, illustrations had been created in the Visio software were translated. In addition to the technical revision by the author, professor Carme Mangiron was in charge of revising the non-technical text. The result was a high-quality document that is currently used as reference and study material by the Department of Computer Science and Informatics of Costa Rica.

Studying Memory Encoding to Promote Reliable Engagement of the Medial Temporal Lobe at the Single-subject Level

The medial temporal lobe (MTL)-comprising hippocampus and the surrounding neocortical regions-is a targeted brain area sensitive to several neurological diseases. Although functional magnetic resonance imaging (fMRI) has been widely used to assess brain functional abnormalities, detecting MTL activation has been technically challenging. The aim of our study was to provide an fMRI paradigm that reliably activates MTL regions at the individual level, thus providing a useful tool for future research in clinical memory-related studies. Twenty young healthy adults underwent an event-related fMRI study consisting of three encoding conditions: word-pairs, face-name associations and complex visual scenes. A region-of-interest analysis at the individual level comparing novel and repeated stimuli independently for each task was performed. The results of this analysis yielded activations in the hippocampal and parahippocampal regions in most of the participants. Specifically, 95% and 100% of participants showed significant activations in the left hippocampus during the face-name encoding and in the right parahippocampus, respectively, during scene encoding. Additionally, a whole brain analysis, also comparing novel versus repeated stimuli at the group level, showed mainly left frontal activation during the word task. In this group analysis, the face-name association engaged the HP and fusiform gyri bilaterally, along with the left inferior frontal gyrus, and the complex visual scenes activated mainly the parahippocampus and hippocampus bilaterally. In sum, our task design represents a rapid and reliable manner to study and explore MTL activity at the individual level, thus providing a useful tool for future research in clinical memory-related fMRI studies.

Perfil espacial e temporal de poluentes nas águas da represa municipal de São José do Rio Preto, São Paulo, Brasil

In this manuscript, seasonal and spatial trends of water collected from two sampling places in the Preto River in the Turvo-Grande watershed were evaluated. Water samples were collected during June/07 to July/08 and parameters sulphate, total organic carbon, ammonia, conductivity, dissolved oxygen, temperature, dissolved total solids and nitrate were quantified. Seasonal trend indicated sanitary effluents as a point source of contamination in both sampling points. Vertical trends demonstrated that the Municipal Dam was not stratified and received a diffuse source of pollutants from flooding and agriculture runoffs. It was also verified that there is relatively fast ammonia consumption kinetics having a half-life time of 1.43 h which can explain the low ammonia concentrations found in these aquatic bodies.

Variabilidade espacial e temporal de parâmetros físico-químicos nos rios Turvo, Preto e Grande no estado de São Paulo, Brasil

This work aims to study spatial and seasonal variability of some chemical-physical parameters in the Turvo/Grande watershed, São Paulo State, Brazil. Water samples were taken monthly, 2007/07-2008/11, from fourteen sampling stations sited along the Turvo, Preto and Grande Rivers and its main tributaries. The Principal Component Analysis and hierarchical cluster analysis showed two distinct groups in this watershed, the first one associated for the places more impacted by domestic effluent (lower levels of dissolved oxygen in the studied region). The sampling places located to downstream (Turvo and Grande rivers) were discriminate by diffuse source of pollutants from flooding and agriculture runoffs in a second group.

APARATO ELETROQUÍMICO PARA SISTEMA DE AQUISIÇÃO DE DADOS MULTICANAL COM RESOLUÇÃO ESPAÇO-TEMPORAL

Spatiotemporal pattern formation in reaction-transport systems takes place spontaneously when the system is kept far from thermodynamic equilibrium. Targets, reaction fronts, waves, spirals, spots and stripes are some typical examples of selforganized structuring. In electrochemical systems, monitoring spatiotemporal patterns of potential in the solid/liquid interface can be done by the use of equally distributed microprobes located close to the working electrode. However, the physical size of each probe can limit the spatial resolution and alter mass transport properties. In contrast, the direct measurement of discrete electrodes does not suffer from this limitation and allows the accurate manipulation of the spatial coupling through changes in resistors connected to the electric circuit. In this paper, the development of an electrochemical setup for multichannel data acquisition with spatiotemporal resolution is described, especially to monitor low levels of currents usually observed in the electro-oxidation of small organic molecules.

Análise da curva de progresso temporal da vassoura-de-bruxa do cupuaçuzeiro

A evolução de lançamentos e de flores de cupuaçuzeiro (Theobroma grandiflorum) com sintomas de vassoura-de-bruxa e a produção de basidiocarpos do patógeno (Crinipellis perniciosa) foram monitoradas em plantas enxertada e não-enxertadas de um campo experimental no município de Belém, PA. Modelos epidemiológicos (logístico, Gompertz, e as somas logístico + logístico e Gompertz + Gompertz) foram ajustados a curvas de progresso da doença bianuais (1993 e 1994 para incidência da doença em lançamentos e basidiocarpos produzidos nesses lançamentos) e anuais (1994), para incidência da doença em flores e basidiocarpos produzidos nessas flores. A soma de duas equações logísticas apresentou bom ajuste aos dados bianuais e o modelo logístico, aos dados anuais. O início da manifestação dos sintomas esteve, geralmente, associado ao período seco enquanto que a produção de basidiocarpos coincidiu com o período chuvoso. A maior emissão de vassouras-de-bruxa ocorreu de julho a outubro e a maior frutificação, entre maio e julho.

Temporal progress of southern rust in maize under different environmental conditions

The progress of the severity of southern rust in maize (Zea mays) caused by Puccinia polysora was quantified in staggered plantings in different geographical areas in Brazil, from October to May, over two years (1995-1996 and 1996-1997). The logistic model, fitted to the data, better described the disease progress curves than the Gompertz model. Four components of the disease progress curves (maximum disease severity; area under the disease progress curve, AUDPC; area under the disease progress curve around the inflection point, AUDPCi; and epidemic rate) were used to compare the epidemics in different areas and at different times of planting. The AUDPC, AUDPCi, and the epidemic rate were analyzed in relation to the weather (temperature, relative humidity, hours of relative humidity >90%, and rainfall) and recorded during the trials. Disease severity reached levels greater than 30% in Piracicaba and Guaíra in the plantings between December and January. Lower values of AUDPC occurred in later plantings at both locations. The epidemic rate was positively correlated (P < 0.05) with the mean daily temperatures and negatively correlated with hours of relative humidity >90%. The AUDPC was not correlated with any weather variable. The AUDPCi was negatively related to both variables connected to humidity, but not to rain. Long periods (mostly >13 h day-1) of relative humidity >90% (that corresponded to leaf wetness) occurred in Castro. Severity of southern rust in maize has always been low in Castro, thus the negative correlations between disease and the two humidity variables.

Dinâmica temporal da Clorose Variegada dos Citros em três regiões do Estado de São Paulo

Este trabalho objetivou esclarecer se o progresso da Clorose Variegada dos Citros (CVC) diferia entre três regiões de São Paulo, distintas quanto à incidência da CVC em citrus (Citrus spp.). Foram avaliadas três áreas, Noroeste, Centro e Sul de São Paulo, durante dois anos, em avaliações quinzenais, quando eram mapeadas as plantas sintomáticas. Tentou-se o ajuste de nove modelos ao progresso da doença, além do ajuste de três modelos a segmentos das curvas originais. Foram estimadas também as diferenciais e as diferenciais secundárias de cada curva de progresso. Apenas quando as curvas foram divididas é que foram obtidos bons ajustes aos modelos de progresso. A diferencial (velocidade da doença) e diferencial secundária (aceleração do aparecimento de novas plantas doentes) apresentaram diversos picos ao longo do tempo. Esses picos ocorreram em meses de Primavera e Verão. Levanta-se aqui a hipótese de que os picos de diferencial - incomuns na quantidade encontrada - estejam relacionados a determinados picos de emissão de brotações, já que as novas brotações são o local preferido de alimentação dos vetores de Xylella fastidiosa.

Geoestatística como metodologia para estudar a dinâmica espaço-temporal de doenças associadas a Colletotrichum spp. transmitidos por sementes

Objetivou-se no presente trabalho caracterizar o progresso espaço-temporal da severidade da antracnose do feijoeiro comum e da ramulose do algodoeiro por meio da Geoestatística. Os experimentos foram conduzidos no campo, durante o período das águas, em diferentes épocas. Sementes inoculadas pelo método da restrição hídrica foram semeadas no centro de parcelas experimentais constituindo fonte de inóculo do tipo ponto. Foram realizadas semanalmente seis avaliações da severidade das doenças com base em escalas de notas. Pelos modelos de semivariograma isotrópicos esféricos e gaussianos ajustados aos dados, verificou-se o padrão de distribuição agregado e a dependência espacial de ambos os patossistemas. Com o mapeamento da severidade das doenças pelo método da krigagem ordinária em blocos, verificou-se menor severidade das doenças nos primeiros estádios, com aumento gradual ao longo do tempo. A antracnose apresentou formação inicial de focos de inóculo secundário, além do foco com inóculo inicial, que coalesceram com o tempo. A severidade da ramulose diminuiu gradualmente de forma radial e contínua do centro da parcela para as extremidades, com maior capacidade de infecção de plantas vizinhas, quando comparada à antracnose, possivelmente pela maior agressividade do patógeno e hábito de crescimento arbustivo do algodoeiro.

Análise temporal da sarna da macieira nas cultivares Royal Gala e Fuji sob os sistemas convencional e orgânico de produção

A sarna da macieira, causada por Venturia inaequalis, é uma das principais doenças da cultura. Devido à grande preocupação com os riscos de contaminação ambiental e intoxicação humana, o cultivo orgânico surge como uma alternativa, buscando preservar a qualidade do produto final em relação ao sistema convencional. Com o objetivo de avaliar a epidemiologia da sarna da macieira nos sistemas convencional e orgânico de produção, foi empregada a técnica de análise da dinâmica temporal, nas cultivares Royal Gala e Fuji, nas condições edafo-climáticas do Sul do Brasil. A incidência foi quantificada semanalmente, gerando 16 mapas em cada sistema de produção e quinzenalmente, a severidade da doença foi avaliada em 100 folhas, distribuídas em quatro ramos, de acordo com escala diagramática específica, com 12 repetições. Foram plotadas curvas de progresso da doença e as epidemias comparadas em relação a) início do aparecimento dos sintomas (IAS); b) tempo para atingir a máxima intensidade da doença (TAMID); c) valor máximo de severidade da doença (y max) e d) área abaixo da curva de progresso da doença (AACPD). Os dados de incidência foram analisados por meio de análise de regressão linear simples, ajustados para três modelos empíricos, Logístico, Monomolecular e Gompertz. As cultivares avaliadas foram suscetíveis à V. inaequalis, com diferenças significativas entre as cultivares e entre os sistemas de produção. Houve maiores níveis de intensidade de doença e taxa de progresso da doença (r) no sistema orgânico que no sistema convencional de produção, sendo que o modelo mais apropriado para descrever a curva de progresso da doença foi o Logístico.