Collaborative grid infrastructure for molecular simulations: The eMinerals minigrid as a prototype integrated computer and data grid

This paper describes a prototype grid infrastructure, called the eMinerals minigrid, for molecular simulation scientists. which is based on an integration of shared compute and data resources. We describe the key components, namely the use of Condor pools, Linux/Unix clusters with PBS and IBM's LoadLeveller job handling tools, the use of Globus for security handling, the use of Condor-G tools for wrapping globus job submit commands, Condor's DAGman tool for handling workflow, the Storage Resource Broker for handling data, and the CCLRC dataportal and associated tools for both archiving data with metadata and making data available to other workers.

Self-assembly and hydrogelation of an amyloid peptide fragment

The self-assembly of a fragment of the amyloid beta peptide that has been shown to be critical in amyloid fibrillization has been studied in aqueous solution. There are conflicting reports in the literature on the fibrillization of A beta (16-20), i.e., KLVFF, and our results shed light on this. In dilute solution, self-assembly of NH2-KLVFF-COOH is strongly influenced by aromatic interactions between phenylalanine units, as revealed by UV spectroscopy and circular dichroism. Fourier transform infrared (FTIR) spectroscopy reveals beta-sheet features in spectra taken for more concentrated solutions and also dried films. X-ray diffraction and cryo-transmission electron microscopy (cryo-TEM) provide further support for beta-sheet amyloid fibril formation. A comparison of cryo-TEM images with those from conventional dried and negatively stained TEM specimens highlights the pronounced effects of sample preparation on the morphology. A comparison of FTIR data for samples in solution and dried samples also highlights the strong effect of drying on the self-assembled structure. In more concentrated phosphate-buffered saline (PBS) solution, gelation of NH2-KLVFF-COOH is observed. This is believed to be caused by screening of the electrostatic charge on the peptide, which enables beta sheets to aggregate into a fibrillar gel network. The rheology of the hydrogel is probed, and the structure is investigated by light scattering and small-angle X-ray scattering.

Development of an ex vivo human skin model for intradermal vaccination : tissue viability and Langerhans cell behaviour

The presence of resident Langerhans cells (LCs) in the epidermis makes the skin an attractive target for DNA vaccination. However, reliable animal models for cutaneous vaccination studies are limited. We demonstrate an ex vivo human skin model for cutaneous DNA vaccination which can potentially bridge the gap between pre-clinical in vivo animal models and clinical studies. Cutaneous transgene expression was utilised to demonstrate epidermal tissue viability in culture. LC response to the culture environment was monitored by immunohistochemistry. Full-thickness and split-thickness skin remained genetically viable in culture for at least 72 h in both phosphate-buffered saline (PBS) and full organ culture medium (OCM). The epidermis of explants cultured in OCM remained morphologically intact throughout the culture duration. LCs in full-thickness skin exhibited a delayed response (reduction in cell number and increase in cell size) to the culture conditions compared with split-thickness skin, whose response was immediate. In conclusion, excised human skin can be cultured for a minimum of 72 h for analysis of gene expression and immune cell activation. However, the use of split-thickness skin for vaccine formulation studies may not be appropriate because of the nature of the activation. Full-thickness skin explants are a more suitable model to assess cutaneous vaccination ex vivo.

Growth of Salmonella enteritidis in artificially contaminated eggs: the effects of inoculum size and suspending media

Growth profiles of two isolates of Salmonella enteritidis phage type (PT) 4 inoculated into either the albumen of whole shell eggs or into separated albumen were found to be markedly affected by the size of the inoculum and the composition of the medium used to suspend the cells prior to inoculation. Using our model with an inoculum of two cells, multiplication of the Salmonella was not seen in 93% of eggs held at 20 degreesC for 8 days. In approximately 7% of eggs, however, growth occurred during the 8 days of storage. If the inoculum equaled or exceeded 25 cells per egg when eggs were subsequently stored at 20 degreesC, or 250 cells per egg when eggs were stored at 30 degreesC, high levels of growth of Salmonella in the egg occurred significantly more frequently than when the inoculum was two cells. High levels of growth were also seen more frequently if the inoculum was suspended in buffered peptone water or maximal recovery diluent rather than in phosphate buffered saline. Growth of Salmonella in separated albumen occurred very infrequently (1.1% of samples) at low inoculum levels and did not become significant until the inoculum was 250 cells or greater. Growth in the albumen was unaffected by the composition of the suspending medium. Provided that the inoculum was approximately 2 cells per egg and the bacteria were suspended in PBS, observed growth profiles of S. enteritidis inoculated into the albumen of whole eggs resembled those in naturally contaminated eggs. (C) 2001 Elsevier Science B.V. All rights reserved.

Concurrent recordings of bladder afferents from multiple nerves using a microfabricated PDMS microchannel electrode array

In this paper we present a compliant neural interface designed to record bladder afferent activity. We developed the implant's microfabrication process using multiple layers of silicone rubber and thin metal so that a gold microelectrode array is embedded within four parallel polydimethylsiloxane (PDMS) microchannels (5 mm long, 100 μm wide, 100 μm deep). Electrode impedance at 1 kHz was optimized using a reactive ion etching (RIE) step, which increased the porosity of the electrode surface. The electrodes did not deteriorate after a 3 month immersion in phosphate buffered saline (PBS) at 37 °C. Due to the unique microscopic topography of the metal film on PDMS, the electrodes are extremely compliant and can withstand handling during implantation (twisting and bending) without electrical failure. The device was transplanted acutely to anaesthetized rats, and strands of the dorsal branch of roots L6 and S1 were surgically teased and inserted in three microchannels under saline immersion to allow for simultaneous in vivo recordings in an acute setting. We utilized a tripole electrode configuration to maintain background noise low and improve the signal to noise ratio. The device could distinguish two types of afferent nerve activity related to increasing bladder filling and contraction. To our knowledge, this is the first report of multichannel recordings of bladder afferent activity.

Evaluation of an elastomer based gold microelectrode array for neural recording applications

We are reporting on the fabrication and electrical characterization of a novel elastomer based micro-cuff neural interface. Electrodes are gold (Au) tracks of sub-100nm thickness and are thermally evaporated on a 0.5 mm thick polydimethylsiloxane (PDMS) substrate. We investigate how electrode area and immersion in phosphate buffered saline (PBS) at 37°C influence electrode impedance. A microfluidic channel is bonded to the electrode array to form the cuff. In an acute, in-vivo, proof-of-principle recording, the device is capable of detecting light stroking and pinch of a hind leg of an anaesthetized rat.

Determination of the embedded thermo-optical expansion coefficients of PbTe and ZnSe thin film infrared multilayers

This paper reports the first derived thermo-optical properties for vacuum deposited infrared thin films embedded in multilayers. These properties were extracted from the temperature-dependence of manufactured narrow bandpass filters across the 4-17 µm mid-infrared wavelength region. Using a repository of spaceflight multi-cavity bandpass filters, the thermo-optical expansion coefficients of PbTe and ZnSe were determined across an elevated temperature range 20-160 ºC. Embedded ZnSe films showed thermo-optical properties similar to reported bulk values, whilst the embedded PbTe films of lower optical density, deviate from reference literature sources. Detailed knowledge of derived coefficients is essential to the multilayer design of temperature-invariant narrow bandpass filters for use in non-cooled infrared detection systems. We further present manufacture of the first reported temperature-invariant multi-cavity narrow bandpass filter utilizing PbS chalcogenide layer material.

Short- and long-term anxiogenic effects induced by a single injection of subconvulsant doses of pilocarpine in rats: investigation of the putative role of hippocampal pathways

Behavioral consequences of convulsive episodes are well documented, but less attention was paid to changes that occur in response to subconvulsant doses of drugs. We investigated short- and long-term effects of a single systemic injection of a subconvulsant dose of pilocarpine on the behavior of rats as evaluated in the elevated plus maze. Pilocarpine induced an anxiogenic-like profile 24 h later, and this effect persisted for up to 3 months (% of time spent on open arms at 24 h, control = 35.47 +/- 3.23; pilocarpine 150 = 8.2 +/- 2.6; 3 months, control = 31.9 +/- 5.5; pilocarpine 150 = 9.3 +/- 4.9). Temporary inactivation of fimbria-fornix with lidocaine 4% promoted an anxiolytic-like effect per se, suggesting a tonic control of this pathway on the modulation of anxiety-related behaviors. Lidocaine also reduced the anxiogenic-like profile of animals tested 1 month after pilocarpine treatment (% of time spent on open arms, saline + phosphate-buffered saline (PBS) = 31.7 + 3.7; saline + lidocaine = 54.4 + 4.7; pilocarpine + PBS = 10.3 + 4.1; pilocarpine + lidocaine = 40.1 + 9.1). To determine whether the anxiogenic-like effect was mediated by septal region or by direct hippocampal projections to the diencephalon, the neural transmission of post-commissural fornix was blocked, and a similar reduction in the anxiogenic-like effect of pilocarpine was observed. Our findings suggest that a single systemic injection of pilocarpine may induce long-lasting anxiogenic-like behavior in rats, an effect that appears to be mediated, in part, through a direct path from hippocampus to medial hypothalamic sites involved in fear responses.

Xyloglucan nano-aggregates: Physico-chemical characterisation in buffer solution and potential application as a carrier for camptothecin, an anti-cancer drug

In this work, native xyloglucan was extracted from Tamarindus indica seeds (XGT), and its properties in phosphate buffer solution (PBS) were evaluated in comparison with a commercial tamarind kernel powder (TKP). The physico-chemical characteristics of the polysaccharides such as molar mass, critical concentration and intrinsic viscosity were determined. Furthermore, using spectroscopic and microscopy techniques, it was observed that the XGs tested can be considered macromolecules able to aggregate as nano-entities of 60-140 nm. The XGT tended to an ordered and compact spherical conformation determined by the Huggins constant, circular dichroism, atomic force microscopy and transmission electron microscopy. After the determination of the properties in PBS the XGs, at concentrations of 25% above their critical aggregation concentration, were used to encapsulate camptothecin, an anti-cancer drug. The XGT sample showed an encapsulation efficiency of 42% and first-order drug delivery kinetics. These results demonstrated the importance of knowledge of the physico-chemical properties of polysaccharides, for example, to better conduct their biotechnological applications as drug carriers. (C) 2010 Elsevier Ltd. All rights reserved.

Under flow impedimetric measurements using magnetic particles for label-free detection affinity target

The necessity to adapt sensors based on electrochemical techniques for high throughput analysis control increases the interest to develop new analytical systems able to perform measurements under buffer now. In this report we explored the possibility of employing a new system to make impedimetric measurements to detect the interaction between proteins and small molecules. The well-known biotin-streptavidin interaction was adopted to evaluate the proposed assembly. This system allows us to perform experiments under flow. Magnetic beads functionalized with streptavidin were used and first characterized using AFM and FTIR. Non-faradic impedance spectroscopy allowed the detection of the biotin-streptavidin interaction. Using our new system and under a flow of PBS buffer, 5 10-5 M of biotin was detected with a stable signal. (c) 2007 Elsevier B.V. All rights reserved.

Determination of epinephrine in urine using multi-walled carbon nanotube modified with cobalt phthalocyanine in a paraffin composite electrode

This paper describes the development, electrochemical characterization and utilization of a cobalt phthalocyanine (CoPc), modified multi-walled carbon nanotube (MWCNT), and paraffin composite electrode for the quantitative determination of epinephrine (EP) in human urine samples. The electrochemical profile of the proposed composite electrode was analyzed by differential pulse voltammetry (DPV) that showed a shift of the oxidation peak potential of EP at 175 mV to less positive value, compared with a paraffin/graphite composite electrode without CoPc. DPV experiments in PBS at pH 6.0 were performed to determine EP without any previous step of extraction, clean-up, and derivatization, in the range from 1.33 to 5.50 mu mol L(-1), with a detection limit of 15.6 nmol L(-1) (2.86) of EP in electrolyte prepared with purified water. The lifetime of the proposed sensors was at least over 1000 determinations with 1.7 and 3.1 repeatability and reproducibility relative standard deviations, respectively. Human urine samples without any purification step were successfully analyzed under the standard addition method using paraffin/MWCNT/CoPc composite electrode. (C) 2010 Elsevier B.V. All rights reserved.

Transporte espermático e resposta inflamatória na égua após a inseminação com diferentes concentrações de espermatozóides.

Normalmente, após a cobertura ou a inseminação artificial de éguas, ocorre uma endometrite aguda transitória em resposta ao sêmen e bactérias no útero. O objetivo deste estudo foi verificar se o transporte espermático e a intensidade da reação inflamatória uterina, 2h, 4h ou 24h após a inseminação com sêmen resfriado, são influenciados pela concentração espermática na dose inseminante. Para tal, foram utilizadas 192 éguas em cio, com folículo dominante ≥35 mm, sem crescimento bacteriano e livres de PMNs aos exames uterinos complementares. As éguas foram distribuídas aleatoriamente em grupos e inseminadas com 20 ml contendo 100x106 (n=30), 500x106 (n=27) ou 1000x106 (n=31) espermatozóides diluídos em solução de 3 ml de plasma seminal e 17 ml de leite desnatado, refrigerado e armazenado por 18 a 22 horas, ou infundidas com 20 ml de plasma seminal (n=33), ou com 20 ml de leite desnatado (n=38). As éguas foram abatidas duas, quatro ou 24h após as inseminações ou infusões. O grupo controle (n=33) não recebeu nenhum tratamento. Os ovidutos foram separados do útero, sendo útero e ovidutos lavados separadamente com PBS. Uma amostra do lavado de cada oviduto foi examinada para contagem de espermatozóides e uma amostra de cada lavado uterino foi utilizada para contagem de leucócitos. Após as lavagens, foi retirada uma amostra de endométrio para exame histopatológico. As éguas inseminadas e infundidas apresentaram reação inflamatória significativamente maior que as éguas do grupo controle, no decorrer das 24 horas. A reação inflamatória foi significativamente maior nas éguas inseminadas que nas infundidas. A reação inflamatória apresentou correlação com a concentração espermática (r=0,389). O número de éguas apresentando espermatozóides nos ovidutos não foi diferente nos grupos inseminados. Concluiu-se que componentes da dose inseminante provocam uma resposta inflamatória, sendo esta tanto mais severa e de resolução mais rápida, quanto maior for a concentração espermática. Por outro lado, até as quatro horas pós-inseminação, o transporte espermático independe da concentração espermática utilizada.

Controle da diarréia suína no período de aleitamento através do fornecimento de gemas de ovos de galinhas hiperimunizadas contra Escherichia coli suína

Foi estudado o efeito das gemas de ovos de aves hiperimunizadas contra Escherichia coli patogênica para suínos sobre a imunidade passiva (IP) de leitões recém-nascidos em uma unidade produtora de leitões (UPL). Foram avaliados densidade ótica do ELISA (DO), peso corporal (PC) e ocorrência de diarréia diária (OcD) em 137 leitões recém-nascidos oriundos de 25 fêmeas primíparas não vacinadas contra E. coli. De cada fêmea, foram separados 6 leitões recémnascidos de ambos os sexos, excluindo-se os mais leves e os mais pesados, divididos em 3 tratamentos e 2 repetições. A análise estatística para DO e PC foi realizada através de ANOVA, a comparação de médias entre tratamentos pelo Lsmeans e o teste do qui-quadradro para a OcD. As gemas estavam armazenadas à -5ºC, in natura e, minutos antes do fornecimento, foram descongeladas e diluídas em 15 mL de uma solução tampão (PBS). Os tratamentos foram fornecidos via oral, tendo sido os seguintes: T1: 2mL de PBS (controle) em 2 doses, a primeira ao nascer e a segunda 2 horas após o nascimento; T2: 2mL de gemas de ovos com título de 100.000 de anticorpos (IgY) contra E. coli em 2 doses, ao nascer e 2 horas após o nascimento; T3: idem ao T2, além de 2mL de gema de 3 em 3 dias até os leitões completarem 12 dias de idade. Foram realizadas duas coletas de sangue em 1 leitão/tratamento/porca: a primeira às 24 horas e a segunda aos 14 dias de idade. O título de IgY contra E. coli dos soros foi determinado por ELISA. A DO do ELISA dos leitões de T2 e T3 foi significativamente maior às 24 horas e aos 14 dias em relação ao controle (P≤0,0001). T3, T2 e T1 permaneceram 87, 79 e 72,5% do tempo estudado sem diarréia (P≤X20,0001). Os animais de T3 foram significativamente mais pesados do que os do T1 (P≤0,08), mas não diferiram de T2. Os resultados deste estudo sugerem que o uso de gemas de aves hiperimunizadas contra E. coli age efetivamente na prevenção da diarréia dos leitões e o seu uso contínuo é mais vantajoso do que o fornecimento somente ao nascer.

Estudos sobre a ação de leucócitos no endométrio de éguas.

As endometrites bacterianas são uma das principais causas de infertilidade na égua. Entre os tratamentos utilizados nesta patologia, estão as infusões uterinas de plasma homólogo acrescido de leucócitos e a infusão de leucócitos heterólogos criopreservados. O presente trabalho teve por objetivo realizar testes in vivo e in vitro, que foram descritos em dois artigos. No primeiro artigo, objetivou-se avaliar in vitro a quimiotaxia dos leucócitos eqüinos em relação a diferentes quimioatraentes, bem como sua vitalidade e produção de radicais livres de oxigênio (ROS) pós-descongelamento. No experimento 1, testou-se dextrose em concentrações de 0, 1, 2 e 6%, acrescida ou não de interleucina-8 (IL-8), como quimioatraente para leucócitos eqüinos suspensos em salina fosfatada tamponada (PBS) ou em R3F; no experimento 2, testou-se plasma homólogo ou heterólogo, a 3% (com ou sem IL-8), 10, 30, 60 e 90%, como quimioatraente; no experimento 3, foi testada a quimiotaxia de leucócitos íntegros em relação a diferentes quantidades de leucócitos lisados. O experimento 4 avaliou a vitalidade e a geração de ROS pelos leucócitos após o descongelamento, comparando quatro graus de diluição em NaCl e PBS. Concluiu-se que a dextrose não apresenta bom efeito quimioatraente para leucócitos eqüinos. Dentre as concentrações de plasma utilizadas, concentrações de plasma homólogo entre 10% e 60% apresentam bom efeito quimiotático. Já o plasma heterólogo apresentou boa atração de leucócitos quando em concentrações de 10% e de 30% Na concentração de 10x106/mL, os leucócitos lisados foram capazes de atrair leucócitos em proporção semelhante à da IL-8. Com relação aos testes-pós-descongelamento, células ressuspendidas em PBS ou NaCl apresentam vitalidade e geração de radicais livres de oxigênio semelhantes, quando incubados por até 15 minutos. No segundo artigo, realizaram-se testes in vivo compararando cinco tratamentos em éguas, em estro, experimentalmente infectadas com Streptococcus equi subsp.zooepidemicus. Foram utilizadas 25 éguas, 20 consideradas resistentes, e 5 éguas susceptíveis à endometrite. Após 24 horas, os animais foram submetidos a exame clínico, bacteriológico e citológico. Com a presença de quadro clínico de endometrite, as éguas eram submetidas a um dos seguintes tratamentos: 1-Infusão de 120mL de plasma homológo com de leucócitos frescos; 2-– Infusão de 4 mL contendo 800 x 106 leucócitos íntegros, congelados; 3-Leucócitos lisados - Infusão de 4 mL contendo 800 x 106 leucócitos lisados; 4- IL-8- Infusão de 4 mL contendo 25 ng/mL de IL-8 congelada; 5-Controle – Infusão de 4 mL de meio R3F congelado. Os exames clínico, bacteriológico e citológico foram realizados diariamente até o sétimo dia pós-infecção, ou até a eliminação da bactéria, ou até a ausência de neutrófilos no esfregaço citológico. Após os exames, as éguas receberam o tratamento designado, sendo estes realizados diariamente até a ausência de crescimento bacteriano no exame microbiológico ou por, no máximo, quatro dias. No sétimo dia, todas as éguas foram tratadas com infusão intra-uterina de 5.000.000 UI de penicilina G potássica cristalina. Após o término de um tratamento, aguardava-se cerca de sete dias para a reinfecção, num outro ciclo, quando um outro tratamento era aplicados. Todas as éguas foram submetidas a todos os tratamentos, perfazendo um total de 125 infecções experimentais num delineamento experimental do tipo Quadrado Latino. Não se observaram diferenças significativas no tempo de eliminação bacteriana nas éguas resistentes. Entretanto, nas éguas susceptíveis, observou-se uma cura bacteriana mais rápida quando as éguas foram tratadas com leucócitos frescos, leucócitos congelados e leucócitos lisados, em relação às tratadas com IL-8 e as do grupo controle. Concluiu-se que o efeito bactericida dos leucócitos viáveis ou lisados, associados ou não à presença de fatores de opsonização do plasma, foi o responsável pela cura bacteriológica e que o efeito quimioatraente de neutrófilos, plasma, restos celulares e IL-8 não influiu no tempo de eliminação bacteriana.

Ocorrência da infecção por Toxoplasma gondii e avaliação da imunização em caprinos do sertão do cabugi, Rio Grande do Norte

Toxoplasmosis is one zoonosis caused by Toxoplasma gondii protozoan. Goats, amongst the production animals, are one of the species most susceptible to this parasite, being one them main involved agents in ovine and goat abortions, determining great economic losses and implications for public health, since the presence it parasite in the products of goat origin, consist in one of the main sources of infection for the man. In this study 244 blood samples in 8 farms situated in 4 cities from the Sertão do Cabugi region, Rio Grande do Norte State, northeast of Brazil and, tested by ELISA assay. The results had shown a prevalence of 47.13% for anti- T. gondii antibodies and a significant association between positivity and variable evaluated as age, locality and property. The IgG avidity assay evaluated in 115 positive samples was carried to discriminate acute and chronic infection. Twelve samples (10.4%) had presented antibodies of low avidity while 103 (89.6%) presented high avidity antibodies; indicating that most of the animals was precocious exposure to the parasite. Significant difference was verified only for the variable sex. We also evaluate the capacity of recombinant adenoviruses codifying SAG1, SAG2, SAG3 and CMV in inducing activation of specific immune response in goat. These 109 animals received 109 pfu of the AdSAG1, AdSAG2, AdSAG3, AdCMV or PBS in vaccine protocol with 3 immunizations. Serum samples of the each animal, before and after mmunization, had been submitted to the ELISA. The results demonstrate that the immunizations had induced the production of IgG antibodies specific against T. gondii proteins