Ligand dependent intra and inter subunit communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of structure networks

Homodimeric protein tryptophanyl tRNA synthetase (TrpRS) has a Rossmann fold domain and belongs to the 1c subclass of aminoacyl tRNA synthetases. This enzyme performs the function of acylating the cognate tRNA. This process involves a number of molecules (2 protein subunits, 2 tRNAs and 2 activated Trps) and thus it is difficult to follow the complex steps in this process. Structures of human TrpRS complexed with certain ligands are available. Based on structural and biochemical data, mechanism of activation of Trp has been speculated. However, no structure has yet been solved in the presence of both the tRNA(Trp) and the activated Trp (TrpAMP). In this study, we have modeled the structure of human TrpRS bound to the activated ligand and the cognate tRNA. In addition, we have performed molecular dynamics (MD) simulations on these models as well as other complexes to capture the dynamical process of ligand induced conformational changes. We have analyzed both the local and global changes in the protein conformation from the protein structure network (PSN) of MD snapshots, by a method which was recently developed in our laboratory in the context of the functionally monomeric protein, methionyl tRNA synthetase. From these investigations, we obtain important information such as the ligand induced correlation between different residues of this protein, asymmetric binding of the ligands to the two subunits of the protein as seen in the crystal structure analysis, and the path of communication between the anticodon region and the aminoacylation site. Here we are able to elucidate the role of dimer interface at a level of detail, which has not been captured so far.

A review of IATTC research on the early life history and reproductive biology of scombrids conducted at the Achotines Laboratory from 1985 to 2005

English: For nearly a century, fisheries scientists have studied marine fish stocks in an effort to understand how the abundances of fish populations are determined. During the early lives of marine fishes, survival is variable, and the numbers of individuals surviving to transitional stages or recruitment are difficult to predict. The egg, larval, and juvenile stages of marine fishes are characterized by high rates of mortality and growth. Most marine fishes, particularly pelagic species, are highly fecund, produce small eggs and larvae, and feed and grow in complex aquatic ecosystems. The identification of environmental or biological factors that are most important in controlling survival during the early life stages of marine fishes is a potentially powerful tool in stock assessment. Because vital rates (mortality and growth) during the early life stages of marine fishes are high and variable, small changes in those rates can have profound effects on the properties of survivors and recruitment potential (Houde 1989). Understanding and predicting the factors that most strongly influence pre-recruit survival are key goals of fisheries research programs. Spanish: Desde hace casi un siglo, los científicos pesqueros han estudiado las poblaciones de peces marinos en un intento por entender cómo se determina la abundancia de las mismas. Durante la vida temprana de los peces marinos, la supervivencia es variable, y el número de individuos que sobrevive hasta las etapas transicionales o el reclutamiento es difícil de predecir. Las etapas de huevo, larval, y juvenil de los peces marinos son caracterizadas por tasas altas de mortalidad y crecimiento. La mayoría de los peces marinos, particularmente las especies pelágicas, son muy fecundos, producen huevos y larvas pequeños, y se alimentan y crecen en ecosistemas acuáticos complejos. La identificación los factores ambientales o biológicos más importantes en el control de la supervivencia durante las etapas tempranas de vida de los peces marinos es una herramienta potencialmente potente en la evaluación de las poblaciones. Ya que las tasas vitales (mortalidad y crecimiento) durante las etapas tempranas de vida de los peces marinos son altas y variables, cambios pequeños en esas tasas pueden ejercer efectos importantes sobre las propiedades de los supervivientes y el potencial de reclutamiento (Houde 1989). Comprender y predecir los factores que más afectan la supervivencia antes del reclutamiento son objetivos clave de los programas de investigación pesquera.

Early life history studies of Yellowfin tuna, Thunnus albacares. I. Food selection of Yellowfin tuna, Thunnus albacares, larvae reared in the laboratory. II. Age validation and growth of Yellowfin tuna, Thunnus albacares, larvae reared in the laboratory

English: Food selection of first-feeding yellowfin tuna larvae was studied in the laboratory during October 1992. The larvae were hatched from eggs obtained by natural spawning of yellowfin adults held in sea pens adjacent to Ishigaki Island, Okinawa Prefecture, Japan. The larvae were fed mixed-prey assemblages consisting of size-graded wild zooplankton and cultured rotifers. Yellowfin larvae were found to be selective feeders during the first four days of feeding. Copepod nauplii dominated the diet numerically, by frequency of occurrence and by weight. The relative importance of juvenile and adult copepods (mostly cyclopoids) in the diet increased over the 4-day period. Rotifers, although they comprised 31 to 40 percent of the available forage, comprised less than 2.1 percent of the diet numerically. Prey selection indices were calculated taking into account the relative abundances of prey, the swimming speeds of yellowfin larvae and their prey, and the microscale influence of turbulence on encounter rates. Yellowfin selected for copepod nauplii and against rotifers, and consumed juvenile and adult copepods in proportion to their abundances. Yellowfin larvae may select copepod nauplii and cyclopoid juveniles and adults based on the size and discontinuous swimming motion of these prey. Rotifers may not have been selected because they were larger or because they exhibit a smooth swimming pattern. The best initial diet for the culture of yellowfin larvae may be copepod nauplii and cyclopoid juveniles and adults, due to the size, swimming motion, and nutritional content of these prey. If rotifers alone are fed to yellowfin larvae, the rotifers should be enriched with a nutritional supplement that is high in unsaturated fatty acids. Mouth size of yellowfin larvae increases rapidly within the first few days of feeding, which minimizes limitations on feeding due to prey size. Although yellowfin larvae initiate feeding on relatively small prey, they rapidly acquire the ability to add relatively large, rare prey items to the diet. This mode of feeding may be adaptive for the development of yellowfin larvae, which have high metabolic rates and live in warm mixed-layer habitats of the tropical and subtropical Pacific. Our analysis also indicates a strong potential for the influence of microscale turbulence on the feeding success of yellowfin larvae. --- Experiments designed to validate the periodicity of otolith increments and to examine growth rates of yellowfin tuna larvae were conducted at the Japan Sea-Farming Association’s (JASFA) Yaeyama Experimental Station, Ishigaki Island, Japan, in September 1992. Larvae were reared from eggs spawned by captive yellowfin enclosed in a sea pen in the bay adjacent to Yaeyama Station. Results indicate that the first increment is deposited within 12 hours of hatching in the otoliths of yellowfin larvae, and subsequent growth increments are formed dailyollowing the first 24 hours after hatching r larvae up to 16 days of age. Somatic and otolith gwth ras were examined and compared for yolksac a first-feeding larvae reared at constant water tempatures of 26�and 29°C. Despite the more rapid develo of larvae reared at 29°C, growth rates were nnificaifferent between the two treatments. Howeve to poor survival after the first four days, it was ssible to examine growth rates beyond the onset of first feeding, when growth differences may become more apparent. Somatic and otolith growth were also examined for larvae reared at ambient bay water temperatures during the first 24 days after hatching. timates of laboratory growth rates were come to previously reported values for laboratory-reared yelllarvae of a similar age range, but were lower than growth rates reported for field-collected larvae. The discrepancy between laboratory and field growth rates may be associated with suboptimal growth conditions in the laboratory. Spanish: Durante octubre de 1992 se estudió en el laboratorio la seleccalimento por larvaún aleta amarillmera alimentación. Las larvas provinieron de huevos obtenidosel desove natural de aletas amarillas adultos mantenidos en corrales marinos adyacentes a la Isla Ishigaki, Prefectura de Okinawa (Japón). Se alimentó a las larvas con presas mixtas de zooplancton silvestre clasificado por tamaño y rotíferos cultivados. Se descubrió que las larvas de aleta amarilla se alimentan de forma selectiva durante los cuatro primeros días de alimentación. Los nauplios de copépodo predominaron en la dieta en número, por frecuencia de ocurrencia y por peso. La importancia relativa de copépodos juveniles y adultos (principalmente ciclopoides) en la dieta aumentó en el transcurso del período de 4 días. Los rotíferos, pese a que formaban del 31 al 40% del alimento disponible, respondieron de menos del 2,1% de la dieta en número. Se calcularon índices de selección de presas tomando en cuenta la abundancia relativa de las presas, la velocidad de natación de las larvas de aleta amarilla y de sus presas, y la influencia a microescala de la turbulencia sobre las tasas de encuentro. Los aletas amarillas seleccionaron a favor de nauplios de copépodo y en contra de los rotíferos, y consumieron copépodos juveniles y adultos en proporción a su abundancia. Es posible que las larvas de aleta amarilla seleccionen nauplios de copépodo y ciclopoides juveniles y adultos con base en el tamaño y movimiento de natación discontinuo de estas presas. Es posible que no se hayan seleccionado los rotíferos a raíz de su mayor tamaño o su patrón continuo de natación. Es posible que la mejor dieta inicial para el cultivo de larvas de aleta amarilla sea nauplios de copépodo y ciclopoides juveniles y adultos, debido al tamaño, movimiento de natación, y contenido nutritivo de estas presas. Si se alimenta a las larvas de aleta amarilla con rotíferos solamente, se debería enriquecerlos con un suplemento nutritivo rico en ácidos grasos no saturados. El tamaño de la boca de las larvas de aleta amarilla aumenta rápidamente en los primeros pocos días de alimentación, reduciendo la limitación de la alimentación debida al tamaño de la presa. Pese a que las larvas de aleta amarilla inician su alimentación con presas relativamente pequeñas, se hacen rápidamente capaces de añadir presas relativamente grandes y poco comunes a la dieta. Este modo de alimentación podría ser adaptivo para el desarrollo de larvas de aleta amarilla, que tienen tasa metabólicas altas y viven en hábitats cálidos en la capa de mezcla en el Pacífico tropical y subtropical. Nuestro análisis indica también que la influencia de turbulencia a microescala es potencialmente importante para el éxito de la alimentación de las larvas de aleta amarilla. --- En septiembre de 1992 se realizaron en la Estación Experimental Yaeyama de la Japan Sea- Farming Association (JASFA) en la Isla Ishigaki (Japón) experimentos diseñados para validar la periodicidad de los incrementos en los otolitos y para examinar las tasas de crecimiento de las larvas de atún aleta amarilla. Se criaron las larvas de huevos puestos por aletas amarillas cautivos en un corral marino en la bahía adyacente a la Estación Yaeyama. Los resultados indican que el primer incremento es depositado menos de 12 horas después de la eclosión en los otolitos de las larvas de aleta amarilla, y que los incrementos de crecimiento subsiguientes son formados a diario a partir de las primeras 24 horas después de la eclosión en larvas de hasta 16 días de edad. Se examinaron y compararon las tasas de crecimiento somático y de los otolitos en larvas en las etapas de saco vitelino y de primera alimentación criadas en aguas de temperatura constante entre 26°C y 29°C. A pesar del desarrollo más rápido de las larvas criadas a 29°C, las tasas de crecimiento no fueron significativamente diferentes entre los dos tratamientos. Debido a la mala supervivencia a partir de los cuatro primeros días, no fue posibación, uando las diferencias en el crecimiento podrían hacerse más aparentes. Se examinó también el crecimiento somático y de los otolitos para larvas criadas en temperaturas de agua ambiental en la bahía durante los 24 días inmediatamente después de la eclosión. Nuestras estimaciones de las tasas de crecimiento en el laboratorio fueron comparables a valores reportados previamente para larvas de aleta amarilla de edades similares criadas en el laboratorio, pero más bajas que las tasas de crecimiento reportadas para larvas capturadas en el mar. La discrepancia entre las tasas de crecimiento en el laboratorio y el mar podría estar asociada con condiciones subóptimas de crecimiento en el lab

Construction of Robot Intra-modal and Inter-modal Coordination Skills by Developmental Learning

Q. Meng and M. H. Lee, 'Construction of Robot Intra-modal and Inter-modal Coordination Skills by Developmental Learning', Journal of Intelligent and Robotic Systems, 48(1), pp 97-114, 2007.

Inter-ELM evolution of the edge current density profile on the ASDEX upgrade tokamak

The sudden decrease of plasma stored energy and subsequent power deposition on the first wall of a tokamak due to edge localised modes (ELMs) is potentially detrimental to the success of a future fusion reactor. Understanding and control of ELMs is critical for the longevity of these devices and also to maximise their performance. The commonly accepted picture of ELMs posits a critical pressure gradient and current density in the plasma edge, above which coupled magnetohy drodynamic peeling-ballooning modes become unstable. Much analysis has been presented in recent years on the spatial and temporal evolution of the edge pressure gradient. However, the edge current density has typically been overlooked due to the difficulties in measuring this quantity. In this thesis, a novel method of current density recovery is presented, using the equilibrium solver CLISTE to reconstruct a high resolution equilibrium utilising both external magnetic and internal edge kinetic data measured on the ASDEX Upgrade tokamak. The evolution of the edge current density relative to an ELM crash is presented, showing that a resistive delay in the buildup of the current density is unlikely. An uncertainty analysis shows that the edge current density can be determined with an accuracy consistent with that of the kinetic data used. A comparison with neoclassical theory demonstrates excellent agreement be- tween the current density determined by CLISTE and the calculated profiles. Three ELM mitigation regimes are investigated: Type-II ELMs, ELMs sup- pressed by external magnetic perturbations, and Nitrogen seeded ELMs. In the first two cases, the current density is found to decrease as mitigation on- sets, indicating a more ballooning-like plasma behaviour. In the latter case, the flux surface averaged current density can decrease while the local current density increases, providing a mechanism to suppress both the peeling and ballooning modes.

Ocean acidification has different effects on the production of DMS and DMSP measured in cultures of Emiliania huxleyi and a mesocosm study: a comparison of laboratory monocultures and community interactions

The human-induced rise in atmospheric carbon dioxide since the industrial revolution has led to increasing oceanic carbon uptake and changes in seawater carbonate chemistry, resulting in lowering of surface water pH. In this study we investigated the effect of increasing CO2 partial pressure (pCO2) on concentrations of volatile biogenic dimethylsulfide (DMS) and its precursor dimethylsulfoniopropionate (DMSP), through monoculture studies and community pCO2 perturbation. DMS is a climatically important gas produced by many marine algae: it transfers sulfur into the atmosphere and is a major influence on biogeochemical climate regulation through breakdown to sulfate and formation of subsequent cloud condensation nuclei (CCN). Overall, production of DMS and DMSP by the coccolithophore Emiliania huxleyi strain RCC1229 was unaffected by growth at 900 matm pCO2, but DMSP production normalised to cell volume was 12% lower at the higher pCO2 treatment. These cultures were compared with community DMS and DMSP production during an elevated pCO2 mesocosm experiment with the aim of studying E. huxleyi in the natural environment. Results contrasted with the culture experiments and showed reductions in community DMS and DMSP concentrations of up to 60 and 32% respectively at pCO2 up to 3000 matm, with changes attributed to poorer growth of DMSP-producing nanophytoplankton species, including E. huxleyi, and potentially increased microbial consumption of DMSand dissolvedDMSPat higher pCO2.DMSandDMSPproduction differences between culture and community likely arise from pH affecting the inter-species responses between microbial producers and consumers.

Development and Single-Laboratory Validation of a Pseudofunctional Biosensor Immunoassay for the Detection of the Okadaic Acid Group of Toxins

A rapid analytical optical biosensor-based immunoassay was developed and validated for the detection of okadaic acid (OA) and its structurally related toxins from shellfish matrix. The assay utilizes a monoclonal antibody which binds to the OA group of toxins in order of their toxicities, resulting in a pseudofunctional assay. Single-laboratory validation of the assay for quantitative detection of OA determined that it has an action limit of 120 mu g/kg, a limit of detection of 31 mu g/kg, and a working range of 31-174 mu g/kg. The midpoint on the standard matrix calibration curve is 80 mu g/kg, half the current regulatory limit. Inter- and intra-assay studies of negative mussel samples spiked with various OA concentrations produced average coefficient of variation (CV) and standard deviation (SD) values of 7.9 and 10.1, respectively. The assay was also validated to confirm the ability to accurately codetect and quantify dinophysistoxin-1 (DTX-1), DTX-2, and DTX-3 from shellfish matrix. Alkaline hydrolysis was not required for the detection of DTX-3 from matrix. Excellent correlations with the data generated by the biosensor method and liquid chromatography/tandem mass spectrometry (LC/MS/MS) were obtained using a certified reference material (R-2 = 0.99), laboratory reference material, and naturally contaminated mussel samples (R-2 = 0.97). This new procedure could be used as a rapid screening procedure replacing animal-based tests for DSP toxins.

Post orthodontic effects of SARPE on sleep-disordered breathing in young adults as observed in a sleep laboratory

Introduction: L’expansion palatine du maxillaire a beaucoup d’effets positifs sur la respiration et la qualité du sommeil, mais peu d'études ont examiné ces données sur des adultes ayant dépassé l’âge permettant de bénéficier d'une expansion palatine conventionnelle. Le but de cette recherche est d’évaluer la stabilité de l’EPRAC (expansion palatine rapide assistée chirurgicalement) et son effet sur les troubles respiratoires après l’ablation des appareils orthodontiques. Méthodes: Neuf patients (Âge moyen 21, entre 16-39 ans) nécessitant une EPRAC ont passé des nuits dans un laboratoire de sommeil, et ce avant l’EPRAC, après l’EPRAC, et après l’ablation des appareils fixes. Les radiographies céphalométriques postéroantérieures ainsi que les modèles d’étude ont été pris pendant ces trois périodes de temps. Résultats: L’analyse des modèles d’étude a démontré une récidive significative au niveau des distances inter-molaires et inter-canines au niveau du maxillaire seulement. Les analyses céphalométriques ont démontré une récidive au niveau de la largeur maxillaire. Aucun changement important n'a été observé dans les stades de sommeil, mais une réduction importante dans l’index de ronflement a été notée. De plus, il y avait moins de changements entre les stades de sommeil. Conclusions: La récidive squelettique est minime et cliniquement non significative. Par contre, les changements dans les distances intermolaires et intercanines sont cliniquement importants. Il semble également qu'une EPRAC ait un effet positif sur la qualité de sommeil par la réduction de l’indice de ronflement ainsi que sur la diminution des changements entre les stades de sommeil.

Inter-relação da modulação gênica entre triidotironina(T3) e estradiol(E2) em cultura primária de adrenocarcinoma de mama

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

Inter-relação: citros, porta-enxerto, doença e ácaro da leprose em plantas submetidas a estresse hídrico e nutricional

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Alterações do ventrículo esquerdo e suas inter-relações com a monitorização ambulatorial de pressão arterial em pacientes tratados por hemodiálise crônica

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Laboratory testes with quality data in Dentistry

In laboratory tests, just following the manufacturer’s instructions of materials or equipments may not be enough to obtain reliable data. Thus, intra and inter-examiners studies may be required. The aim of this study was to illustrate the application of the Intraclass Correlation Coefficient (r) in a study related to the color changing and hardness of composite resin conducted by two examiners. The color and hardness of 10 specimens of composite resin were evaluated by a colorimetric spectrophotometer and hardness tester, respectively, at two different times. Two trained examiners performed two measurements with an interval of one week. Specimens were stored in artificial saliva at 37±1ºC for 7 days. The Intraclass Correlation was used for analysis of intra and inter-examiner reproducibility. The intra-examiner reproducibility was 0.79, 0.44 and 0.76 for L, a and b color coordinates for the examiner 1 and 0.84, 0.23, 0.21 for examiner 2. For hardness, r-values were 0.00 and 0.23 for the examiner 1 and 2, respectively, showing unsatisfactory agreement on color and hardness evaluation for both examiners. It was noted that only the observation of protocol for use of equipment and examiners training were not sufficient to collect reliable information. Thus, adjustments in the experimental protocol were made and devices were produced to standardize the measurements. The reproducibility study was performed again. For examiner 1, values as 0.90, 0.59 and 0.79 were verified for L, a and b coordinates and, for examiner 2 were obtained values of 0.90, 0.75, 0.95. In relation to hardness, r-values of 0.75 and 0.71 were obtained for examiners 1 and 2, respectively. The inter-examiner reproducibility was 0.86, 0.87, 0.91 for L, a and b coordinates and 0.79 for hardness. It was concluded that intra and inter-examiner calibration is essential for obtaining quality measurements in laboratory tests.

Studio dei semiochimici coinvolti nelle interazioni intra- e inter-specifiche in Gonocerus acuteangulatus (Goeze) (Heteroptera: Coreidae) in vista di un loro impiego nella difesa del nocciolo.

Gonocerus acuteangulatus (Hemiptera: Coreidae) è considerato uno dei principali fitofagi del nocciolo, in grado di causare con l’attività trofica pesanti perdite quali-quantitative di produzione. Nel triennio sono state quindi condotte indagini sulla bioetologia di G. acuteangulatus volte a: I) studiare comportamento alimentare ed effetti sulla produzione corilicola, II) identificare i feromoni e valutarne l’attività mediante biosaggi fisiologici e comportamentali in laboratorio, semi-campo e campo, III) rilevare le piante ospiti alternative al nocciolo. Mediante isolamento di adulti del coreide su rami di nocciolo con frutti è stata confermata l’assenza di correlazione fra entità del danno e numerosità degli individui presenti in corileto. Dalle analisi sensoriali su nocciole sane e danneggiate è emerso che le alterazioni causate delle punture di nutrizione sono rese più evidenti da conservazione e tostatura. Variazioni di tempi e temperature di tostatura potrebbero mitigare gli effetti del cimiciato. Nello studio dei feromoni, G. acuteangulatus, molto mobile nell’ambiente, è risultato poco adatto ai biosaggi in condizioni artificiali, come quelle in olfattometro e semi-campo. Le femmine sono tuttavia apparse attrattive per adulti di entrambi i sessi, mentre la miscela feromonale sintetizzata ha mostrato un’azione attrattiva, seppure non costante. Pertanto, ulteriori ripetizioni sono necessarie per convalidare questi risultati preliminari, modificando le condizioni di saggio in relazione alle caratteristiche della specie. Infine è stata accertata la preferenza del fitofago per alcune specie vegetali rispetto al nocciolo. Nel corso del triennio, popolazioni molto consistenti di G. acuteangulatus sono state rilevate su bosso, ciliegio di Santa Lucia, rosa selvatica, sanguinello, spino cervino, in corrispondenza del periodo di comparsa e maturazione dei frutti. Nell’impostazione di una strategia di difesa a basso impatto ambientale, l’attrattività di queste piante, in sinergia con eventuali feromoni di aggregazione, potrebbe essere utilmente sfruttata, per mantenere il coreide lontano dalla coltura.

Three-dimensional imaging core laboratory of the endovascular aneurysm repair trials: validation of methodology

OBJECTIVE: The aim of this study was to establish and validate a three-dimensional imaging protocol for the assessment of Computed Tomography (CT) scans of abdominal aortic aneurysms in UK EVAR trials patients. Quality control and repeatability of anatomical measurements is important for the validity of any core laboratory. METHODS: Three different observers performed anatomical measurements on 50 preoperative CT scans of aortic aneurysms using the Vitrea 2 three-dimensional post-imaging software in a core laboratory setting. We assessed the accuracy of intra and inter observer repeatability of measurements, the time required for collection of measurements, 3 different levels of automation and 3 different automated criteria for measurement of neck length. RESULTS: None of the automated neck length measurements demonstrated sufficient accuracy and it was necessary to perform checking of the important automated landmarks. Good intra and limited inter observer agreement were achieved with three-dimensional assessment. Complete assessment of the aneurysm and iliacs took an average (SD) of 17.2 (4.1) minutes. CONCLUSIONS: Aortic aneurysm anatomy can be assessed reliably and quickly using three-dimensional assessment but for scans of limited quality, manual checking of important landmarks remains necessary. Using a set protocol, agreement between observers is satisfactory but not as good as within observers.

Background pathology of the ovary in a laboratory population of zebrafish Danio rerio

Adult zebrafish Danio rerio originating from one stock used as control animals in a toxicological study were examined histopathologically for the occurrence of spontaneous lesions in the gonads. While no histopathological changes were seen in the testes, the ovaries showed lesions consisting mainly of acute granulomatous inflammation with increased atresia and the presence of egg debris in the ovarian parenchyma and in the oviduct. Since infectious agents could not be detected and the fish were not exposed to toxicants, we consider these lesions as spontaneous alterations of the ovaries.