Nutritional control of mRNA isoform expression during developmental arrest and recovery in C. elegans.

Nutrient availability profoundly influences gene expression. Many animal genes encode multiple transcript isoforms, yet the effect of nutrient availability on transcript isoform expression has not been studied in genome-wide fashion. When Caenorhabditis elegans larvae hatch without food, they arrest development in the first larval stage (L1 arrest). Starved larvae can survive L1 arrest for weeks, but growth and post-embryonic development are rapidly initiated in response to feeding. We used RNA-seq to characterize the transcriptome during L1 arrest and over time after feeding. Twenty-seven percent of detectable protein-coding genes were differentially expressed during recovery from L1 arrest, with the majority of changes initiating within the first hour, demonstrating widespread, acute effects of nutrient availability on gene expression. We used two independent approaches to track expression of individual exons and mRNA isoforms, and we connected changes in expression to functional consequences by mining a variety of databases. These two approaches identified an overlapping set of genes with alternative isoform expression, and they converged on common functional patterns. Genes affecting mRNA splicing and translation are regulated by alternative isoform expression, revealing post-transcriptional consequences of nutrient availability on gene regulation. We also found that phosphorylation sites are often alternatively expressed, revealing a common mode by which alternative isoform expression modifies protein function and signal transduction. Our results detail rich changes in C. elegans gene expression as larvae initiate growth and post-embryonic development, and they provide an excellent resource for ongoing investigation of transcriptional regulation and developmental physiology.

Structure of the adenylation domain of an NAD+-dependent DNA ligase

Background: DNA ligases catalyse phosphodiester bond formation between adjacent bases in nicked DNA, thereby sealing the nick. A key step in the catalytic mechanism is the formation of an adenylated DNA intermediate. The adenyl group is derived from either ATP (in eucaryotes and archaea) or NAD+4 (in bacteria). This difference in cofactor specificity suggests that DNA ligase may be a useful antibiotic target.

Results: The crystal structure of the adenylation domain of the NAD+-dependent DNA ligase from Bacillus stearothermophilus has been determined at 2.8 Å resolution. Despite a complete lack of detectable sequence similarity, the fold of the central core of this domain shares homology with the equivalent region of ATP-dependent DNA ligases, providing strong evidence for the location of the NAD+-binding site.

Conclusions: Comparison of the structure of the NAD+4-dependent DNA ligase with that of ATP-dependent ligases and mRNA-capping enzymes demonstrates the manifold utilisation of a conserved nucleotidyltransferase domain within this family of enzymes. Whilst this conserved core domain retains a common mode of nucleotide binding and activation, it is the additional domains at the N terminus and/or the C terminus that provide the alternative specificities and functionalities in the different members of this enzyme superfamily.

Metabolomic Profiling of In Vivo Plasma Responses to DioxinAssociated Dietary Contaminant Exposure in Rats: Implications for Identification of Sources of Animal and Human Exposure

Dioxin contamination of the food chain typically occurs when cocktails of combustion residues or polychlorinated biphenyl (PCB) containing oils become incorporated into animal feed. These highly toxic compounds are bioaccumulative with small amounts posing a major health risk. The ability to identify animal exposure to these compounds prior to their entry into the food chain may be an invaluable tool to safeguard public health. Dioxin-like compounds act by a common mode of action and this suggests that markers or patterns of response may facilitate identification of exposed animals. However, secondary co-contaminating compounds present in typical dioxin sources may affect responses to compounds. This study has investigated for the first time the potential of a metabolomics platform to distinguish between animals exposed to different sources of dioxin contamination through their diet. Sprague-Dawley rats were given feed containing dioxin-like toxins from hospital incinerator soot, a common PCB oil standard and pure 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) (normalized at 0.1 µg/kg TEQ) and acquired plasma was subsequently biochemically profiled using ultra high performance liquid chromatography (UPLC) quadropole time-of-flight-mass spectrometry (QTof-MS). An OPLS-DA model was generated from acquired metabolite fingerprints and validated which allowed classification of plasma from individual animals into the four dietary exposure study groups with a level of accuracy of 97-100%. A set of 24 ions of importance to the prediction model, and which had levels significantly altered between feeding groups, were positively identified as deriving from eight identifiable metabolites including lysophosphatidylcholine (16:0) and tyrosine. This study demonstrates the enormous potential of metabolomic-based profiling to provide a powerful and reliable tool for the detection of dioxin exposure in food-producing animals.

A 75-81 GHz, 14.3 dBm Peak Output Power, 21 dB Peak Gain, SiGe Power-Combining Amplifier Operating from a Single 3.3 V Supply

A compact differential 4-way power combiner with 2.3 dB loss and high common-mode rejection characteristic for use in mm-wave PAs is presented. A complete circuit comprised of a power splitter, two-stage cascode PA array, and a power combiner was implemented in SiGe technology. Measured small-signal gain of at least 17 dB was obtained from 74.5 GHz to 80.5 GHz with a peak 21 dB at 79 GHz. The prototype delivered 13.2 dBm P1dB and 14.3 dBm Psat when operated from a single 3.3 V supply at 75 GHz.

Complex Interactions between Dioxin-Like and Non-Dioxin-Like Compounds for in Vitro Cellular Responses: Implications for the Identification of Dioxin Exposure Biomarkers

Despite considerable advances in reducing the production of dioxin-like toxicants in recent years, contamination of the food chain still occasionally occurs resulting in huge losses to the agri-food sector and risk to human health through exposure. Dioxin-like toxicity is exhibited by a range of stable and bioaccumulative compounds including polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs), produced by certain types of combustion, and man-made coplanar polychlorinated biphenyls (PCBs), as found in electrical transformer oils. While dioxinergic compounds act by a common mode of action making exposure detection biomarker based techniques a potentially useful tool, the influence of co-contaminating toxicants on such approaches needs to be considered. To assess the impact of possible interactions, the biological responses of H4IIE cells to challenge by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in combination with PCB-52 and benzo-a-pyrene (BaP) were evaluated by a number of methods in this study. Ethoxyresorufin-O-deethylase (EROD) induction in TCDD exposed cells was suppressed by increasing concentrations of PCB-52, PCB-153, or BaP up to 10 mu M. BaP levels below 1 mu M suppressed TCDD stimulated EROD induction, but at higher concentrations, EROD induction was greater than the maximum observed when cells were treated with TCDD alone. A similar biphasic interaction of BaP with TCDD co-exposure was noted in the AlamarBlue assay and to a lesser extent with PCB-52. Surface enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF) profiling of peptidomic responses of cells exposed to compound combinations was compared. Cells co-exposed to TCDD in the presence of BaP or PCB-52 produced the most differentiated spectra with a substantial number of non-additive interactions observed. These findings suggest that interactions between dioxin and other toxicants create novel, additive, and non-additive effects, which may be more indicative of the types of responses seen in exposed animals than those of single exposures to the individual compounds.

A new bulk-driven input stage design for sub 1-volt CMOS op-amps

This paper presents a new design approach for a rail-to-rail bulk-driven input stage using a standard single-well (n-well in this paper) CMOS technology. This input stage can provide nearly constant transconductance and constant slew rate over the entire input common-mode voltage, operating with a wide supply voltage ranging from sub 1-volt (V/sub T0/+ 3V/sub DSsat/) to the maximum allowed for the CMOS process, as well as preventing latch-up.

Active nuclear import and cytoplasmic retention of activation-induced deaminase

The enzyme activation-induced deaminase (AID) triggers antibody diversification in B cells by catalyzing deamination and consequently mutation of immunoglobulin genes. To minimize off-target deamination, AID is restrained by several regulatory mechanisms including nuclear exclusion, thought to be mediated exclusively by active nuclear export. Here we identify two other mechanisms involved in controlling AID subcellular localization. AID is unable to passively diffuse into the nucleus, despite its small size, and its nuclear entry requires active import mediated by a conformational nuclear localization signal. We also identify in its C terminus a determinant for AID cytoplasmic retention, which hampers diffusion to the nucleus, competes with nuclear import and is crucial for maintaining the predominantly cytoplasmic localization of AID in steady-state conditions. Blocking nuclear import alters the balance between these processes in favor of cytoplasmic retention, resulting in reduced isotype class switching.

Autocyclic erosion in tidal marshes

A common mode whereby destruction of coastal lowlands occurs is frontal erosion. The edge cliffing, nonetheless, is also an inherent aspect of salt marsh development in many northwest European tidal marshes. Quite a few geomorphologists in the earlier half of the past century recognized such edge erosion as a definite repetitive stage within an autocyclic mode of marsh growth. A shift in research priorities during the past decades (primarily because of coastal management concerns, however) has resulted in an enhanced focus on sediment-flux measurement campaigns on salt marshes. This, somewhat "object-oriented" strategy hindered any further development of the once-established autocyclic growth concept, which virtually has gone into oblivion in recent times. This work makes an attempt to resurrect the notion of autocyclicity by employing its premises to address edge erosion in tidal marshes. Through a review of intertidal morphosedimentology the underlying framework for autocyclicity is envisaged. The phenomenon is demonstrated in the Holocene salt marsh plain of Moricambe basin in NW England that displays several distinct phases of marsh retreat in the form of abandoned clifflets. The suite of abandoned shorelines and terraces has been identified in detailed field mapping that followed analysis of topographic maps and aerial photographs. Vertical trends in marsh plain sediments are recorded in trenches for signs of past marsh front movements. The characteristic sea level history of the area offers an opportunity to differentiate the morphodynamic variability induced in the autocyclic growth of the marsh plain in scenarios of rising and falling sea level and the accompanied change in sediment budget. The ideas gathered are incorporated to construct a conceptual model that links temporal extent of marsh erosion to inner tidal flat sediment budget and sea level tendency. The review leads to recognition of the necessity of adopting an holistic approach in the morphodynamic investigations where marshes should be treated as a component within the "marsh-mudflat system" as each element apparently modulates evolution of the other, with an eventual linkage to subtidal channels. (C) 2009 Elsevier B.V. All rights reserved.

Ribonucleocapsid formation of severe acute respiratory syndrome coronavirus through molecular action of the N-terminal domain of N protein

Conserved among all coronaviruses are four structural proteins: the matrix (M), small envelope (E), and spike (S) proteins that are embedded in the viral membrane and the nucleocapsid phosphoprotein (N), which exists in a ribonucleoprotein complex in the lumen. The N-terminal domain of coronaviral N proteins (N-NTD) provides a scaffold for RNA binding, while the C-terminal domain (N-CTD) mainly acts as oligomerization modules during assembly. The C terminus of the N protein anchors it to the viral membrane by associating with M protein. We characterized the structures of N-NTD from severe acute respiratory syndrome coronavirus (SARS-CoV) in two crystal forms, at 1.17 A (monoclinic) and at 1.85 A (cubic), respectively, resolved by molecular replacement using the homologous avian infectious bronchitis virus (IBV) structure. Flexible loops in the solution structure of SARS-CoV N-NTD are now shown to be well ordered around the beta-sheet core. The functionally important positively charged beta-hairpin protrudes out of the core, is oriented similarly to that in the IBV N-NTD, and is involved in crystal packing in the monoclinic form. In the cubic form, the monomers form trimeric units that stack in a helical array. Comparison of crystal packing of SARS-CoV and IBV N-NTDs suggests a common mode of RNA recognition, but they probably associate differently in vivo during the formation of the ribonucleoprotein complex. Electrostatic potential distribution on the surface of homology models of related coronaviral N-NTDs suggests that they use different modes of both RNA recognition and oligomeric assembly, perhaps explaining why their nucleocapsids have different morphologies.

Método experimental para determinação das capacitancias parasitas do motor de indução trifásico acionado por inversor MLP

A proposta deste trabalho é apresentar uma nova metodologia para determinação experimental das capacitancias parasitas do motor de indução trifásico de rotor em gaiola. As capacitancias parasitas fazem parte do circuito equivalente do motor para estudos de interferência eletromagnética causada no motor de indução em modo comum quando ele for acionado por inversor controlado por modulação por largura de pulsos (MLP). Os procedimentos propostos para o desenvolvimento deste novo método consistem em: a) determinação dos parâmetros do circuito equivalente do motor de indução trifásico, em regime permanente, através de ensaio em laboratório; b) estabelecer configurações de ligações entre o inversor MLP e o motor para medições das grandezas de interesse que são as seguintes: tensões de modo comum e de eixo, correntes de fuga e de eixo, através de circuito de medição desenvolvido para este fim; c) calcular os valores das capacitancias parasitas entre estator e carcaça do motor; estator e rotor; rotor e carcaça e de rolamento utilizando a expressão matemática da definição de capacitancia; d) utilizar o software Pspice para simular o sistema motor de indução trifásico, alimentado por inversor MLP, com os circuitos equivalentes em baixas e altas frequências; e) obter as formas de onda características do fenômeno de modo comum.

On designing linearly-tunable ultra-low voltage CMOS gm-C filters

A linearly-tunable ULV transconductor featuring excellent stability of the processed signal common-mode voltage upon tuning, critical for very-low voltage applications, is presented. Its employment to the synthesis of CMOS gm-C high-frequency and voiceband filters is discussed. SPICE data describe the filter characteristics. For a 1.3 V-supply, their nominal passband frequencies are 1.0 MHz and 3.78 KHz, respectively, with tuning rates of 12.52 KHz/mV and 0.16 KHz/m V, input-referred noise spectral density of 1.3 μV/Hz1/2 and 5.0μV/Hz1/2 and standby consumption of 0.87 mW and 11.8 μW. Large-signal distortion given by THD = 1% corresponds to a differential output-swing of 360 mVpp and 480 mVpp, respectively. Common-mode voltage deviation is less than 4 mV over tuning interval.

A low-voltage programmable-gain CMOS amplifier with very-low temperature-drift

A new topology for a LVLP variable-gain CMOS amplifier is presented. Input- and load-stage are built around triode-transconductors so that voltage-gain is fully defined by a linear relationship involving only device-geometries and biases. Excellent gain-accuracy, temperature-insensitivity; and wide range of programmability, are thus achieved. Moreover, adaptative biasing improves the common-mode voltage stability upon gain-adjusting. As an example, a 0-40dB programmablegain audio-amplifier is designed. Its performance is supported by a range of simulations. For VDD=1.8V and 20dB-nominal gain, one has Av=19.97dB, f3db=770KHz and quiescent dissipation of 378μW. Over temperatures from -25°C to 125°C, the 0. ldB-bandwidth is 52KHz. Dynamic-range is optimized to 57.2dB and 42.6dB for gains of 20dB and 40dB, respectively. THD figures correspond to -60.6dB@Vout= 1Vpp and -79.7dB@Vout= 0.5 Vpp. A nearly constant bandwidth for different gains is also attained.

A low-voltage triode-MOSFET four-quadrant multiplier with optimized current-efficiency

A low-voltage, low-power four-quadrant analog multiplier with optimized current-efficiency is presented. Its core corresponds to a pseudodifferential cascode, gain-boosting triode-transconductor. According to a low-voltage 1.2μm CMOS n-well process, operand differential-amplitudes are 1.0Vpp and 0.32Vpp for a 1.3V-supply. Common-mode voltages are properly chosen to maximize current-efficiency to 58%. Total quiescent dissipation is 260μW. A range of PSPICE simulation supports theoretical analysis. Excellent linearity is observed on dc characteristic. Assuming a ±0.5% mismatch on (W/L) and VTH THD at full-scale is 0.93% and 1.42%, for output frequencies of 1MHz and 10MHz, respectively.

A simplified method for determining the high frequency induction motor equivalent electrical circuit parameters to be used in EMI effect

The aim of this paper is to present a simple method for determining the high frequency parameters of a three-phase induction motor to be used in studies involving variable speed drives with PWM three-phase inverters, in which it is necessary to check the effects caused to the motor by the electromagnetic interference, (EMI) in the differential mode, as well as in the common mode. The motor parameters determination is generally performed in adequate laboratories using accurate instruments, such as very expensive RLC bridges. The method proposed here consists in the identification of the motor equivalent electrical circuit parameters in rated frequency and in high frequency through characteristic tests in the laboratory, together with the use of characteristic equations and curves, shown in the references to be mentioned for determining the motor high frequency parasite capacitances and also through system simulations using dedicated software, like Pspice, determining the characteristic waveforms involved in the differential and common mode phenomena, comparing and validating the procedure through published papers [01].

Estudo e desenvolvimento de um protótipo para redução da interferência de modo comum usando balanceamento dinâmico de impedância aplicado em biosensores e sensores eletroresistivos

A interferência eletromagnética causada pela linha de energia elétrica afeta negativamente os sinais de instrumentos eletrônicos, especialmente aqueles com baixos níveis de amplitude. Este tipo de interferência é conhecida como interferência de modo comum. Existem muitos métodos e arquiteturas utilizadas para minimizar a influência deste fenômeno de interferência em instrumentos eletrônicos, o mais comum dos quais é a utilização de filtros rejeita banda. Este trabalho apresenta: a análise, desenvolvimento, protótipo e teste de uma nova arquitetura de filtro com característica reconfigurável para instrumentos biomédicos e medição de dados de fluxo em fluido de alta complexidade, com objetivo de reduzir a interferência de modo comum e preservar as componentes do sinal útil na mesma faixa de frequência do ruído, utilizando a técnica de equilíbrio dinâmico de impedância. Além disso, este trabalho pode ser usado em qualquer sistema de medição que também sofra interferência na frequência da linha de alimentação (50/60 Hz, no Brasil e na França, 60 Hz nos Estados Unidos da América). Os blocos de circuitos foram modelados matematicamente e a função de transferência global do circuito fechado foi gerada. Em seguida, o projeto foi descrito e simulado na língua VHDL_AMS e também em um software de simulação eletrônica, usando blocos de componentes discretos, com e sem realimentação. Após análise teórica dos resultados da simulação, um circuito protótipo foi construído e testado usando como entrada um sinal obtido a partir de eletrodos de ECG e Eletrodos Eletroresistivos. Os resultados experimentais do circuito condizem com os da simulação: uma redução de ruído de 98,7% foi obtida em simulações utilizando um sinal sinusoidal, e uma redução de 92% foi realizada utilizando eletrodos de ECG em testes experimentais. Os mesmos testes em eletrodos Eletroresistivos, obtendo o maior valor de 80,3% de redução (durante análise de 3 casos). Em ambos os casos, o sinal útil foi preservado. O método e a sua arquitetura pode ser aplicado para atenuar as interferências que ocorrem na mesma banda de frequência das componentes do sinal útil, preservando ao mesmo tempo estes sinais.