Correct biological timing in Arabidopsis requires multiple light-signaling pathways.

Circadian oscillators provide rhythmic temporal cues for a range of biological processes in plants and animals, enabling anticipation of the day/night cycle and enhancing fitness-associated traits. We have used engineering models to understand the control principles of a plant's response to seasonal variation. We show that the seasonal changes in the timing of circadian outputs require light regulation via feed-forward loops, combining rapid light-signaling pathways with entrained circadian oscillators. Linear time-invariant models of circadian rhythms were computed for 3,503 circadian-regulated genes and for the concentration of cytosolic-free calcium to quantify the magnitude and timing of regulation by circadian oscillators and light-signaling pathways. Bioinformatic and experimental analysis show that rapid light-induced regulation of circadian outputs is associated with seasonal rephasing of the output rhythm. We identify that external coincidence is required for rephasing of multiple output rhythms, and is therefore important in general phase control in addition to specific photoperiod-dependent processes such as flowering and hypocotyl elongation. Our findings uncover a fundamental design principle of circadian regulation, and identify the importance of rapid light-signaling pathways in temporal control.

Nucleated polymerization with secondary pathways. I. Time evolution of the principal moments.

Self-assembly processes resulting in linear structures are often observed in molecular biology, and include the formation of functional filaments such as actin and tubulin, as well as generally dysfunctional ones such as amyloid aggregates. Although the basic kinetic equations describing these phenomena are well-established, it has proved to be challenging, due to their non-linear nature, to derive solutions to these equations except for special cases. The availability of general analytical solutions provides a route for determining the rates of molecular level processes from the analysis of macroscopic experimental measurements of the growth kinetics, in addition to the phenomenological parameters, such as lag times and maximal growth rates that are already obtainable from standard fitting procedures. We describe here an analytical approach based on fixed-point analysis, which provides self-consistent solutions for the growth of filamentous structures that can, in addition to elongation, undergo internal fracturing and monomer-dependent nucleation as mechanisms for generating new free ends acting as growth sites. Our results generalise the analytical expression for sigmoidal growth kinetics from the Oosawa theory for nucleated polymerisation to the case of fragmenting filaments. We determine the corresponding growth laws in closed form and derive from first principles a number of relationships which have been empirically established for the kinetics of the self-assembly of amyloid fibrils.

La sacra doctrina y el gnosticismo : (S. Th., I, q. 1, art. 1)

El estudio de la falsa gnosis es algo de lo cual varios pensadores católicos ya han escrito y lo siguen haciendo. Sin embargo, la consideración de este argumento a la luz del pensamiento de Santo Tomás de Aquino no es algo común. El concepto de gnosis (gnw/sij, conocimiento), en sí mismo, no significa algo peyorativo. Por el contrario, Jesucristo hace referencia a los doctores de la ley que han quitado la llave de la ciencia (Lc 11, 52). Por su parte san Pablo confiesa que «no hay sino un solo Dios y Padre, de quien proceden todas las cosas, y nosotros estamos destinados hacia él; y un solo Señor Jesucrito, por quien son todas las cosas, y nosostros también por él. Pero no en todos se halla esa ciencia (h` gnw/sij)». Este conocimiento o gnosis que toma la Revelación en la fe por regla y guía es la gnosis verdadera Nos proponemos en este trabajo realizar una lectura del art. 1º de la Iª Pars de la Suma Teológica y compararlo ante todo con el fundamento mismo de aquello que san Pablo denomina como «la mal llamada ciencia»...

Report from the Knowledge Exchange Event: Pathways to Open Scholarship

The report on the ‘Pathways to Open Scholarship’ conference, organised by Knowledge Exchange to celebrate its 10th anniversary, contains an overview of the views that invited speakers and experts in the audience expressed on Open Scholarship developments. Open Scholarship is not yet a reality of everyday research and education. The event reported on, addressed the concept of "open scholarship" by debating issues and key challenges with the aim to identify pathways forward. Four central themes which represent crucial dimensions of open scholarship have been explored: Benefits, risks and limitations of Open Scholarship; Success as a researcher; Technology; and Publishing and publication services. The report contains views, expectations, wishes and frustrations that experts have on open scholarship, as well as new and promising initiatives and approaches. The report is a starting point for future planning of KE activity and input for a range of consultation talks with respected experts and leaders in the research community in KE countries and beyond.

Exploration of new drug delivery pathways: I. Mechanism of folate uptake in cultured human cells. II. Role of nuclear localization signal peptides in the delivery of oligonucleotide into reconstituted nuclei

The roles of the folate receptor and an anion carrier in the uptake of 5- methyltetrahydrofolate (5-MeH_4folate) were studied in cultured human (KB) cells using radioactive 5-MeH_4folate. Binding of the 5-MeH_4folate was inhibited by folic acid, but not by probenecid, an anion carrier inhibitor. The internalization of 5-MeH_4folate was inhibited by low temperature, folic acid, probenecid and methotrexate. Prolonged incubation of cells in the presence of high concentrations of probenecid appeared to inhibit endocytosis of folatereceptors as well as the anion carrier. The V_(max) and K_M values for the carrier were 8.65 ± 0.55 pmol/min/mg cell protein and 3.74 ± 0.54µM, respectively. The transport of 5-MeH4folate was competitively inhibited by folic acid, probenecid and methotrexate. The carrier dissociation constants for folic acid, probenecid and methotreate were 641 µM, 2.23 mM and 13.8 µM, respectively. Kinetic analysis suggests that 5-MeH_4folate at physiological concentration is transported through an anion carrier with the characteristics of the reduced-folate carrier after 5-MeH_4folate is endocytosed by folate receptors in KB cells. Our data with KB cells suggest that folate receptors and probenecid-sensitive carriers work in tandem to transport 5-MeH_4folate to the cytoplasm of cells, based upon the assumption that 1 mM probenecid does not interfere with the acidification of the vesicle where the folate receptors are endocytosed.

Oligodeoxynucleotides designed to hybridize to specific mRNA sequences (antisense oligonucleotides) or double stranded DNA sequences have been used to inhibit the synthesis of a number of cellular and viral proteins (Crooke, S. T. (1993) FASEB J. 7, 533-539; Carter, G. and Lemoine, N. R. (1993) Br. J. Cacer 67, 869-876; Stein, C. A. and cohen, J. S. (1988) Cancer Res. 48, 2659-2668). However, the distribution of the delivered oligonucleotides in the cell, i.e., in the cytoplasm or in the nucleus has not been clearly defined. We studied the kinetics of oligonucleotide transport into the cell nucleus using reconstituted cell nuclei as a model system. We present evidences here that oligonucleotides can freely diffuse into reconstituted nuclei. Our results are consistent with the reports by Leonetti et al. (Proc. Natl. Acad. Sci. USA, Vol. 88, pp. 2702-2706, April 1991), which were published while we were carrying this research independently. We also investigated whether a synthetic nuclear localization signal (NLS) peptide of SV40 T antigen could be used for the nuclear targeting of oligonucleotides. We synthesized a nuclear localization signal peptide-conjugated oligonucleotide to see if a nuclear localization signal peptide can enhance the uptake of oligonucleotides into reconstituted nuclei of Xenopus. Uptake of the NLS peptide-conjugated oligonucleotide was comparable to the control oligonucleotide at similar concentrations, suggesting that the NLS signal peptide does not significantly enhance the nuclear accumulation of oligonucleotides. This result is probably due to the small size of the oligonucleotide.

Design and analysis of nucleic acid reaction pathways

Nucleic acids are a useful substrate for engineering at the molecular level. Designing the detailed energetics and kinetics of interactions between nucleic acid strands remains a challenge. Building on previous algorithms to characterize the ensemble of dilute solutions of nucleic acids, we present a design algorithm that allows optimization of structural features and binding energetics of a test tube of interacting nucleic acid strands. We extend this formulation to handle multiple thermodynamic states and combinatorial constraints to allow optimization of pathways of interacting nucleic acids. In both design strategies, low-cost estimates to thermodynamic properties are calculated using hierarchical ensemble decomposition and test tube ensemble focusing. These algorithms are tested on randomized test sets and on example pathways drawn from the molecular programming literature. To analyze the kinetic properties of designed sequences, we describe algorithms to identify dominant species and kinetic rates using coarse-graining at the scale of a small box containing several strands or a large box containing a dilute solution of strands.

Origin of Th/U variations in chondritic meteorites

Isotope dilution thorium and uranium analyses of the Harleton chondrite show a larger scatter than previously observed in equilibrated ordinary chondrites (EOC). The linear correlation of Th/U with 1/U in Harleton (and all EOC data) is produced by variation in the chlorapatite to merrillite mixing ratio. Apatite variations control the U concentrations. Phosphorus variations are compensated by inverse variations in U to preserve the Th/U vs. 1/U correlation. Because the Th/U variations reflect phosphate ampling, a weighted Th/U average should converge to an improved solar system Th/U. We obtain Th/U=3.53 (1_-mean=0.10), significantly lower and more precise than previous estimates.

To test whether apatite also produces Th/U variation in CI and CM chondrites, we performed P analyses on the solutions from leaching experiments of Orgueil and Murchison meteorites.

A linear Th/U vs. 1/U correlation in CI can be explained by redistribution of hexavalent U by aqueous fluids into carbonates and sulfates.

Unlike CI and EOC, whole rock Th/U variations in CMs are mostly due to Th variations. A Th/U vs. 1/U linear correlation suggested by previous data for CMs is not real. We distinguish 4 components responsible for the whole rock Th/U variations: (1) P and actinide-depleted matrix containing small amounts of U-rich carbonate/sulfate phases (similar to CIs); (2) CAIs and (3) chondrules are major reservoirs for actinides, (4) an easily leachable phase of high Th/U. likely carbonate produced by CAI alteration. Phosphates play a minor role as actinide and P carrier phases in CM chondrites.

Using our Th/U and minimum galactic ages from halo globular clusters, we calculate relative supernovae production rates for ²³²Th/²³⁸U and ²³⁵U/²³⁸U for different models of r-process nucleosynthesis. For uniform galactic production, the beginning of the r-process nucleosynthesis must be less than 13 Gyr. Exponentially decreasing production is also consistent with a 13 Gyr age, but very slow decay times are required (less than 35 Gyr), approaching the uniform production. The 15 Gyr Galaxy requires either a fast initial production growth (infall time constant less than 0.5 Gyr) followed by very low decrease (decay time constant greater than 100 Gyr), or the fastest possible decrease (≈8 Gyr) preceded by slow in fall (≈7.5 Gyr).

Pathways for the uptake of dissolved organic matter (DOM) by aquatic animals

In this article, pathways from freshwater and marine environments are described. DOM is defined operationally as all the organic compounds which pass through a filter of pore size 0.45 microm., those retained on the surface of the filter being particulate organic matter (POM). DOM can be taken up directly by animals by transfer across the body wall, but more commonly DOM is obtained from ingested food. Once ingested POM from food particles are broken down in the gut, small molecules of DOM are released for transfer across the gut wall. Some ingested particles are attacked by micro-organisms living in the gut, thereby making the DOM available to the host animal. The importance of the microbial loop is discussed, as well as aggregation processes between the fractions of DOM which are more obviously particulate in nature. (DBO)

Efeitos da hipóxia-isquemia perinatal sobre o comportamento motor, distribuição da Tirosina Hidroxilase na substância negra e da NADPH diaforase no hipocampo durante o desenvolvimento em ratos

A hipóxia isquemia (HI) pré-natal é uma das principais causas de mortalidade e doenças neurológicas crônicas em neonatos, que podem apresentar déficits remanentes como: retardamento, paralisia cerebral, dificuldade de aprendizado ou epilepsia. Estes prejuízos, provavelmente, estão relacionados com o atraso no desenvolvimento neural, astrogliose e com a perda de neurônios e oligodendrócitos. Déficits funcionais e cognitivos estão associados à degeneração de vias dopaminérgicas e de estruturas hipocampais. A enzima tirosina hidroxilase (TH) é a enzima limitante na síntese de dopamina e seus níveis são alterados em eventos de HI. O óxido nítrico (NO) é um gás difusível que atua modulando diferentes sistemas, participando de eventos como plasticidade sináptica e neuromodulação no sistema nervoso central e é produzido em grandes quantidades em eventos de injúria e inflamação, como é o caso da HI. O presente estudo teve por objetivos avaliar, utilizando o modelo criado por Robinson e colaboradores em 2005, os efeitos da HI sobre o comportamento motor e avaliar o desenvolvimento de estruturas encefálicas relacionadas a este comportamento como a substância negra (SN) e o complexo hipocampal. A HI foi induzida a partir do clampeamento das artérias uterinas da rata grávida, por 45 minutos no décimo oitavo dia de gestação (grupo HI). Em um grupo de fêmeas a cirurgia foi realizada, mas não houve clampeamento das artérias (grupo SHAM). A avaliação do comportamento motor foi realizada com os testes ROTAROD e de campo aberto em animais de 45 dias. Os encéfalos foram processados histologicamente nas idades de P9, P16, P23 e P90, sendo então realizada imunohistoquímica para TH e histoquímica para NADPH diaforase (NADPH-d), para avaliação do NO. Nossos resultados demonstraram redução da imunorreatividade para a TH em corpos celulares na SN aos 16 dias no grupo HI e aumento na imunorreatividade das fibras na parte reticulada aos 23 dias, com a presença de corpos celulares imunorreativos nesta região no grupo HI. Demonstramos também aumento do número de células marcadas para NADPH-d no giro dentado nos animais HI, nas idades analisadas, assim como aumento na intensidade de reação no corno de Ammon (CA1 e CA3) aos 9 dias no grupo HI, e posterior redução nesta marcação aos 23 e 90dias neste mesmo grupo. Nos testes comportamentais, observamos diminuição da atividade motora no grupo HI com uma melhora do desempenho ao longo dos testes no ROTAROD, sem entretanto atingir o mesmo nível do grupo SHAM. Os animais HI não apresentaram maior nível de ansiedade em relação ao grupo SHAM, descartando a hipótese das alterações observadas nos testes de motricidade estarem relacionadas a fatores ansiogênicos. O modelo de clampeamento das artérias uterinas da fêmea se mostrou uma ferramenta importante no estudo das alterações decorrentes do evento de HI pré-natal, por produzir diversos resultados que são similares aos ocorridos em neonatos que passam por este evento.

Comparison of average larval fish vertical distributions among species exhibiting different transport pathways on the southeast United States continental shelf

Water currents are vertically structured in many marine systems and as a result, vertical movements by fish larvae and zooplankton affect horizontal transport (Power, 1984). In estuaries, the vertical movements of larvae with tidal periods can result in their retention or ingress (Fortier and Leggett, 1983; Rijnsdorp et al., 1985; Cronin and Forward, 1986; Forward et al., 1999). On the continental shelf, the vertical movements of organisms interact daily and ontogenetically with depth-varying currents to affect horizontal transport (Pillar et al., 1989; Barange and Pillar, 1992; Cowen et al., 1993, 2000; Batchelder et al., 2002).

Termocronologia (U-Th)He e reativação da margem continental do sudeste do Brasil: seção Serra da Mantiqueira - Gráben da Guanabara

A evolução da margem continental do sudeste do Brasil tem sido discutida por diversos autores desde meados do século passado até os dias atuais, especialmente no contexto da origem e evolução dos escarpamentos e das bacias tafrogênicas. Buscou-se contribuir com novos dados sobre a evolução da área a partir da aplicação da termocronologia de baixa temperatura (U-Th)/He em apatita, que oferece uma sensibilidade significativa para registrar movimentações tectônicas na crosta superior. Foi possível obter idades em 107 cristais de apatita de 18 amostras do embasamento coletadas no perfil com orientação NW-SE, numa seção entre a Serra da Mantiqueira e o Gráben da Guanabara. As idades corrigidas variam entre 250,1 8,7 Ma e 43,5 1,9 Ma (2 σ) e as não corrigidas entre 174,13 3,03 Ma e 27,07 0,60 Ma (1 σ). O Neocretáceo, o Eocretáceo e o Paleoceno são os principais registros no conjunto de dados, em ordem de importância. No Neocretáceo, o intervalo entre 83,6 e 72,1 Ma (Campaniano) representa o maior destaque nos registros termocronológicos, embora os outros registros (Maastrichtiano e Santoniano) também estejam presentes e sejam importantes. As idades do Neocretáceo destacam a importância dos eventos tectonomagmáticos e soerguimento regional na história térmica dessa área, inclusive com idades (~86 Ma) atribuídas ao contexto de soerguimento da Serra do Mar. As idades do Eocretáceo indicam o registro de eventos térmicos mais antigos, vinculados à evolução pré-rifte. Já os dados do Paleoceno estariam associados ao evento de reativação responsável pela implantação do sistema de riftes continentais (~65 Ma) e as idades do Eoceno, restritas à borda de falha da bacia de Resende (49,7 Ma e 43,5 Ma), à reativação do sistema de riftes nessa área. A dispersão de idades foi interpretada como efeito dos danos de radiação já que muitos grãos apresentam correlação entre idade e concentração de urânio (eU). Os padrões de tempo-temperatura (t-T), definidos a partir dos modelos HeFTy calibrados para o modelo de difusão que considera os efeitos de danos de radiação nos cristais, registraram eventos de resfriamento rápido, os quais mostram correlação direta com episódios de reativação e soerguimento na margem continental e com registros nas bacias continentais e marginais. O padrão de aumento das idades com a elevação, assim como da costa em direção ao interior é observado, mas mostra-se alterado pela ocorrência de idades mais jovens associadas à complexa evolução dessa margem continental com desnivelamentos de blocos vinculados à tectônica pós-rift, numa situação que ressalta a influência dos episódios de reativação. As estimativas de denudação total variam entre 1,2 e 2,8 km. As taxas de erosão variam entre 15,2 e 35,3 m/Ma. A evolução da área indica não apenas a influência de um evento específico mas, possivelmente, uma combinação de episódios que se alternaram e/ou atuaram em conjunto em determinados períodos. Os eventos de reativação mais antigos, combinados com os mais recentes, exibem os seus remanescentes na paisagem (serras da Mantiqueira e do Mar e os grábens e bacias sedimentares) e assumem papel fundamental na evolução da área. Os registros de tais episódios podem ser observados nas histórias térmicas das rochas e nos depósitos correlativos nas bacias sedimentares marginais e intracontinentais.