Catching transcriptional regulation by thermostatistical modeling

Gene expression is frequently regulated by multiple transcription factors (TFs). Thermostatistical methods allow for a quantitative description of interactions between TFs, RNA polymerase and DNA, and their impact on the transcription rates. We illustrate three different scales of the thermostatistical approach: the microscale of TF molecules, the mesoscale of promoter energy levels and the macroscale of transcriptionally active and inactive cells in a cell population. We demonstrate versatility of combinatorial transcriptional activation by exemplifying logic functions, such as AND and OR gates. We discuss a metric for cell-to-cell transcriptional activation variability known as Fermi entropy. Suitability of thermostatistical modeling is illustrated by describing the experimental data on transcriptional induction of NF?B and the c-Fos protein.

N-dimensional electron in an anharmonic potential:the large-N limit

We show that the energy levels predicted by a frac(1, N)-expansion method for an N-dimensional electron in an anharmonic potential are always lower than the exact energy levels but monotonically converge toward their exact eigenstates for higher ordered corrections. The technique allows a systematic approach for quantum many body problems in a confined potential and explains the remarkable agreement of such approximate theories when compared with numerical results.

Hydrogen-terminated detonation nanodiamond:impedance spectroscopy and thermal stability studies

In this paper, we investigated the effect of hydrogen termination on the electrical properties and impedance spectra of detonation nanodiamond. The impedance spectra revealed that the hydrogen-termination process increases the electrical conductivity by four orders of magnitude at room temperature. An equivalent circuit has been proposed to correlate with the conduction mechanism. Arrhenius plot showed that there were two different activation energy levels located at 0.089 eV and 0.63 eV between 50 °C and 400 °C. The possible physical mechanism corresponding to these activation energy levels has been discussed. Hydrogen-terminated detonation nanodiamond has been further annealed at different temperatures prior to FTIR and XPS measurements in order to understand their thermal stability. The results demonstrated that the surface oxidization occurred between 100 °C and 150 °C. However, the C-H bonds could partially survive when the temperature reaches 400 °C in air. © 2013 American Institute of Physics.

Low-fat food consumption by people with diabetes decreases fat saturated fat, and cholesterol intake

This study investigated the effect of providing free-access to several fat-modified foods on dietary energy and fat intake in free-living individuals with and without diabetes mellitus. Five low/no-fat products or their regular-fat versions were provided to volunteers to take home and use for 3 days. Energy and nutrient intakes of all foods consumed were determined through a weighed food diary and by weighing the food provided before and after consumption. Fifteen individuals with diabetes and 15 case-matched controls without diabetes participated in the study. Individuals with diabetes and controls responded similarly to the fat-modified foods. In both groups there was a significant reduction in the percent of kcals and grams of fat consumed during the low-fat condition compared to the regular-fat condition (p

Organic carbon sources and their transfer in a gulf of Mexico coral reef ecosystem

Coral reefs face unprecedented threats throughout most of their range. Poorly planned coastal development has contributed increased nutrients and sewage contamination to coastal waters, smothering some corals and contributing to overgrowth by macroalgae. My approach to assessing the degree to which coral reef ecosystems have been influenced by terrestrial and anthropogenic organic carbon inputs is through the use of carbon (C) and nitrogen (N) stable isotopes and lipid biomarkers in a marine protected area, the Coral Reef System of Veracruz: Parque Nacional Sistema Arrecifal Veracruzano (PNSAV) in the southwest Gulf of Mexico. Firstly, I used a C and N stable isotope mixing model and a calculated fatty acid (FA) retention factor to reveal the primary producer sources that fuel the coral reef food web. Secondly, I used lipid classes, FA and sterol biomarkers to determine production of terrestrial and marine biogenic material of nutritional quality to pelagic and benthic organisms. Finally, I used coprostanol to determine pollutant loading from sewage in the suspended particulate matter. Results indicate that phytoplankton is the major source of essential metabolite FA for marine fish and that dietary energy from terrestrial sources such as mangroves are transferred to juvenile fish, while seagrass non-essential FA are transferred to the entire food web mainly in the rainy season. Sea urchins may be the main consumers of brown macroalgae, especially in the dry season, while surgeon fish prefer red algae in both dry and rainy seasons. C and N isotopic values and the ratio C:N suggest that fertilizer is the principal source of nitrogen to macroalgae. Thus nitrogen supply also favored phytoplankton and seagrass growth leading to a better nutritional condition and high retention of organic carbon in the food web members during the rainy season when river influence increases. However, the great star coral Montastrea cavernosa nutritional condition decreased significantly in the rainy season. The nearest river to the PNSAV was polluted in the dry season; however, a dilution effect was detected in the rainy season, when some coral reefs were contaminated. In 2013, a new treatment plant started working in the area. I would suggest monitoring δ¹⁵N and the C: N ratio in macroalgae as indicators of the nitrogen input and coprostanol as an indicator of human feces pollution in order to verify the efficiency of the new treatment plant as part of the management program of the PNSAV.

Métodos de extração de fósforo e micronutrientes em latossolos com uso de energia ultrassônica

Assessing the soil nutrient availability to plants under lab conditions is one of the main challenges to Soil Fertility and Chemistry, due to the complex behavior and the interaction of the soil properties. Many extractant solutions associated with mechanical forms of agitation have been proposed, showing different correlations with plant growth and nutrients absorption. Using ultrasonic energy is a agitation procedure of the soil:extractant solution suspension (based on the cavitation phenomenon). It allows the establishment of relations between the amount of extracted nutrient and the ultrasonic energy level. Thus, this work aims: to evaluate the effect of cavitation intensity on the extraction of P, Zn, Cu, Mn and Fe in soil samples from five Latosols under different uses around Uberlândia and Uberaba, Minas Gerais State; to obtain extracting curves as function of ultrasonic energy levels; and to obtain an index from extracting curves to expresses the nutrient retention by the soil solid phase. A soil-solution suspension (ratio 1:10) was sonicated using a probe ultrasound equipment under different combinations of power and time: i) 30 W for 35, 70, 140 and 280 s; ii) 50 W for 21, 42, 84 and 168 s; and iii) 70 W for 15, 30, 60 and 120 s. The extractant solutions used were Mehlich-1 (for all elements), Olsen and distilled water for P. After each sonication, P concentration was quantified by molybdenum blue colorimetric method and Zn, Cu, Mn and Fe by flame atomic absorption spectrophotometry. The cavitation intensity did not affect the P extraction, only the total energy applied. The P extraction was influenced by extractant solution, decreasing as follows: Mehlich-1>Olsen>water. In cultivated Latosols, the P extraction increased linearly with ultrasonic energy, and the slope of the 1:1 linear regression reflects the P retention in the soil. The Zn and Fe extractions were influenced only by total energy applied. Mn and Cu extractions were influenced by both cavitation intensity and total ultrasonic energy. Soils containing similar amounts of P, Cu, Zn, Mn, and Fe may have a different extraction rate. Likewise, soils containing different amounts of those elements may have the same extraction rate.

Exoenzimas em rações de frangos de corte

The study aimed to evaluate performance, relative weight of the small intestine, digestibility and deposition of minerals in the bone of broilers supplemented with enzymatic complex (carbohydrases and phytase) in sorghum-based diets or sorghum and millet. In the experiments based of sorghum and sorghum and millet were used 912 day-old male and female Hubbard Flex chicks (50:50) were distributed in a completely randomized design in a 2x2 factorial arrangement (Feed Control base Sorghum (Contcs); FeedReducedbase Sorghum (RedS); Feed Control base sorghum + Enzymatic Complex (Contcs + Enz);. Feed reduced base sorghum + Enzymatic Complex (RedS + Enz) in the study of feed basis of sorghum and millet the design was similar (Feed Control base sorghum + millet ( ContSM); Reduced feed based on Millet + Sorghum (RedSM); Feed Control based Sorghum + Millet + EnzimaticComplex (ContSM + Enz); Reduced Feed base Sorghum+ Millet + Enzimatic Complex (RedSM + Enz). At 35 and 42 days of age were determined performance data: feed intake (CR), body weight (BW), feed conversion (FC), viability (VIAB), relative weight of the small intestine and deposition of minerals in the bone. The digestibility was evaluated sorghum grain size (crushed and whole) with and without exoenzimatico complex. They used 32 birds, eight birds per treatment, in periods from 17 to 21 (initial) and 31 to 35 days of age (fattening). The exoenzimático complex used in feed favored the weight gain results, feed conversion and bone mineralization when compared to a control diet not added to enzymes, demonstrating its effect on non-starch polysaccharides and phosphorus phytic present as anti-nutritional factors in these diets, increasing the digestibility and supply of metabolizable energy, essential amino acids, methionine and lysine and calcium and phosphorus for bone formation. It is concluded that a safe strategy for inclusion in feed is based on the reduction of energy levels, essential amino acids, methionine and lysine and calcium and phosphorus in the expected result of the constant activity of the enzymes of this exoenzimático complex.

Radiative rates for E1, E2, M1, and M2 transitions in S-like to F-like tungsten ions (W LIX to W LXVI)

Calculations of energy levels, radiative rates and lifetimes are reported for eight ions of tungsten, i.e. S-like (W LIX) to F-like (W LXVI). A large number of levels have been considered for each ion and extensive configuration interaction has been included among a range of configurations. For the calculations, the general-purpose relativistic atomic structure package (. grasp) has been adopted, and radiative rates (as well as oscillator strengths and line strengths) are listed for all E1, E2, M1, and M2 transitions of the ions. Comparisons have been made with earlier available experimental and theoretical energies, although these are limited to only a few levels for most ions. Therefore for additional accuracy assessments, particularly for energy levels, analogous calculations have been performed with the flexible atomic code (. fac).

Radiative rates for E1, E2, M1, and M2 transitions in Br-like ions with 43≤Z≤50

Energies and lifetimes are reported for the eight Br-like ions with 43≤Z≤50, namely Tc IX, Ru X, Rh XI, Pd XII, Ag XIII, Cd XIV, In XV, and Sn XVI. Results are listed for the lowest 375 levels, which mostly belong to the 4s²4p⁵, 4s²4p⁴4ℓ, 4s4p⁶,4s²4p⁴5ℓ, 4s²4p³4d², 4s4p⁵4ℓ, and 4s4p⁵5ℓ configurations. Extensive configuration interaction among 39 configurations (generating 3990 levels) has been considered and the general-purpose relativistic atomic structure package (grasp) has been adopted for the calculations. Radiative rates are listed for all E1, E2, M1, and M2 transitions involving the lowest 375 levels. Previous experimental and theoretical energies are available for only a few levels of three, namely Ru X, Rh XI and Pd XII. Differences with the measured energies are up to 4% but the present results are an improvement (by up to 0.3 Ryd) in comparison to other recently reported theoretical data. Similarly for radiative rates and lifetimes, prior results are limited to those involving only 31 levels of the 4s²4p⁵, 4s²4p⁴4d, and 4s4p⁶ configurations for the last four ions. Moreover, there are generally no discrepancies with our results, although the larger calculations reported here differ by up to two orders of magnitude for a few transitions.

Radiative rates for E1, E2, M1, and M2 transitions in F-like ions with 37≤Z≤53

Calculations of energy levels, radiative rates and lifetimes are reported for 17 F-like ions with 37≤Z≤53. For brevity, results are only presented among the lowest 113 levels of the 2s²2p⁵, 2s2p⁶, 2s²2p⁴3ℓ, 2s2p⁵3ℓ, and 2p⁶3ℓ configurations, although the calculations have been performed for up to 501 levels in each ion. The general-purpose relativistic atomic structure package (grasp) has been adopted for the calculations, and radiative rates (along with oscillator strengths and line strengths) are listed for all E1, E2, M1, and M2 transitions of the ions. Comparisons are made with earlier available experimental and theoretical energies, although these are limited to only a few levels for most ions. Therefore for additional accuracy assessments, particularly for energy levels, analogous calculations have been performed with the Flexible Atomic Code (fac), for up to 72 259 levels. Limited previous results are available for radiative rates for comparison purposes, and no large discrepancy is observed for any transition and/or ion.

Benchmarking a modified version of the civ3 nonrelativistic atomic-structure code within Na-like-tungsten R -matrix calculations

In this work we explore the validity of employing a modified version of the nonrelativistic structure code civ3 for heavy, highly charged systems, using Na-like tungsten as a simple benchmark. Consequently, we present radiative and subsequent collisional atomic data compared with corresponding results from a fully relativistic structure and collisional model. Our motivation for this line of study is to benchmark civ3 against the relativistic grasp0 structure code. This is an important study as civ3 wave functions in nonrelativistic R-matrix calculations are computationally less expensive than their Dirac counterparts. There are very few existing data for the W LXIV ion in the literature with which we can compare except for an incomplete set of energy levels available from the NIST database. The overall accuracy of the present results is thus determined by the comparison between the civ3 and grasp0 structure codes alongside collisional atomic data computed by the R-matrix Breit-Pauli and Dirac codes. It is found that the electron-impact collision strengths and effective collision strengths computed by these differing methods are in good general agreement for the majority of the transitions considered, across a broad range of electron temperatures.

Population inversion between the sup(3)Hsub(4) and the sup(3)Fsub(4) excited states of Tmsup(3+) investigated by means of numerical solutions of the rate equations system in Tmsup(3+)-doped and Tmsup(3+), Hosup(3+)-codoped fluoride glasses

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Self-Assembled InAs/GaAs Quantum Dot Solar Cells

Our work focuses on experimental and theoretical studies aimed at establishing a fundamental understanding of the principal electrical and optical processes governing the operation of quantum dot solar cells (QDSC) and their feasibility for the realization of intermediate band solar cell (IBSC). Uniform performance QD solar cells with high conversion efficiency have been fabricated using carefully calibrated process recipes as the basis of all reliable experimental characterization. The origin for the enhancement of the short circuit current density (Jsc) in QD solar cells was carefully investigated. External quantum efficiency (EQE) measurements were performed as a measure of the below bandgap distribution of transition states. In this work, we found that the incorporation of self-assembled quantum dots (QDs) interrupts the lattice periodicity and introduce a greatly broadened tailing density of states extending from the bandedge towards mid-gap. A below-bandgap density of states (DOS) model with an extended Urbach tail has been developed. In particular, the below-bandgap photocurrent generation has been attributed to transitions via confined energy states and background continuum tailing states. Photoluminescence measurement is used to measure the energy level of the lowest available state and the coupling effect between QD states and background tailing states because it results from a non-equilibrium process. A basic I-V measurement reveals a degradation of the open circuit voltage (Voc) of QD solar cells, which is related to a one sub-bandgap photon absorption process followed by a direct collection of the generated carriers by the external circuit. We have proposed a modified Shockley-Queisser (SQ) model that predicts the degradation of Voc compared with a reference bulk device. Whenever an energy state within the forbidden gap can facilitate additional absorption, it can facilitate recombination as well. If the recombination is non-radiative, it is detrimental to solar cell performance. We have also investigated the QD trapping effects as deep level energy states. Without an efficient carrier extraction pathway, the QDs can indeed function as mobile carriers traps. Since hole energy levels are mostly connected with hole collection under room temperature, the trapping effect is more severe for electrons. We have tried to electron-dope the QDs to exert a repulsive Coulomb force to help improve the carrier collection efficiency. We have experimentally observed a 30% improvement of Jsc for 4e/dot devices compared with 0e/dot devices. Electron-doping helps with better carrier collection efficiency, however, we have also measured a smaller transition probability from valance band to QD states as a direct manifestation of the Pauli Exclusion Principle. The non-linear performance is of particular interest. With the availability of laser with on-resonance and off-resonance excitation energy, we have explored the photocurrent enhancement by a sequential two-photon absorption (2PA) process via the intermediate states. For the first time, we are able to distinguish the nonlinearity effect by 1PA and 2PA process. The observed 2PA current under off-resonant and on-resonant excitation comes from a two-step transition via the tailing states instead of the QD states. However, given the existence of an extended Urbach tail and the small number of photons available for the intermediate states to conduction band transition, the experimental results suggest that with the current material system, the intensity requirement for an observable enhancement of photocurrent via a 2PA process is much higher than what is available from concentrated sun light. In order to realize the IBSC model, a matching transition strength needs to be achieved between valance band to QD states and QD states to conduction band. However, we have experimentally shown that only a negligible amount of signal can be observed at cryogenic temperature via the transition from QD states to conduction band under a broadband IR source excitation. Based on the understanding we have achieved, we found that the existence of the extended tailing density of states together with the large mismatch of the transition strength from VB to QD and from QD to CB, has systematically put into question the feasibility of the IBSC model with QDs.

Immune function, gene expression, blood indices and performance in transition dairy cows affected by diet and inflammation

The transition period is associated with the peak incidence of production problems, metabolic disorders and infectious diseases in dairy cows (Drackley, 1999). During this time the cow’s immune system seems to be weakened; it is apparent that metabolic challenges associated with the onset of lactation are factors capable of affecting immune function. However, the reasons for this state are not entirely clear (Goff, 2006). The negative energy balance associated with parturition leads to extensive mobilization of fatty acids stored in adipose tissue, thus, causing marked elevations in blood non-esterified fatty acids (NEFA) and B-hydroxybutyrate (BHBA) concentrations (Drackley et al., 2001). Prepartal level of dietary energy can potentially affect adipose tissue deposition and, thus, the amount of NEFA released into blood and available for metabolism in liver (Drackley et al., 2005). The current feeding practices for pregnant non-lactating cows has been called into question because increasing amounts of moderate-to-high energy diets (i.e. those more similar to lactation diets in the content of energy) during the last 3 wk postpartum have largely failed to overcome peripartal health problems, excessive body condition loss after calving, or declining fertility (Beever, 2006). Current prepartal feeding practices can lead to elevated intakes of energy, which can increase fat deposition in the viscera and upon parturition lead to compromised liver metabolism (Beever, 2006, Drackley et al., 2005). Our general hypothesis was that overfeeding dietary energy during the dry period, accompanied by the metabolic challenges associated with the onset of lactation would render the cow’s immune function less responsive early postpartum. The chapters in this dissertation evaluated neutrophil function, metabolic and inflammation indices and gene expression affected by the plane of dietary energy prepartum and an early post-partum inflammatory challenge in dairy cows. The diet effect in this experiment was transcendental during the transition period and potentially during the entire lactation. Changes in energy balance were observed and provided a good model to study the challenges associated with the onset of lactation. Overall the LPS model provided a consistent response representing an inflammation incident; however the changes in metabolic indices were sudden and hard to detect in most of the cases during the days following the challenge. In general overfeeding dietary energy during the dry period resulted in a less responsive immune function during the early postpartum. In other words, controlling the dietary energy prepartum has more benefits for the dairy cow during transition.

Effects of gamma and electron beam irradiation in the antioxidante potential of methanolic extracts and infusions of Arenaria Montana L

Irradiation is a methodology qualified for dry ingredients preservation or decontamination and can be performed using various radiation sources and energy levels in accordance with the objectives to be achieved [1]. Electron beam irradiation is used mainly for food products with low density, while gamma irradiation is mainly used for large volumes [2]. Arenaria Montana L. has a high antioxidant potential and richness in bioactive phytochemicals. It is used in Portuguese traditional medicine, acting therapeutically as an anti-inflammatory and diuretic plant [3]. The aim of this work was to evaluate the effects of gamma and electron beam irradiation at different doses (I and 10 kGy) in the antioxidant activity of A. montana. Free radicals scavenging activity, reducing power and lipid peroxidation inhibition properties of its methanolic extracts and infusions were evaluated. Through a global analysis, it was concluded that the antioxidant activity proved to be higher in methanolic extracts in comparison with the infusions, where it decreased with increasing irradiation dose regardless of the technology used (gamma or electron beam). For methanolic extracts, electron beam resulted in increased antioxidant activity while gamma irradiation caused a decrease in these extracts. Thus, the antioxidant potential is variable depending not only on the type of radiation and the dose applied, but also on the solvent used in the preparation of the extracts (methanol or water).