Principles of sequence-recognition in aromatic polyimides

Pyrene-based molecular tweezers show sequence-specific binding to aromatic polyimides through sterically-controlled donor-acceptor pi-stacking and hydrogen bonding; H-1 NMR spectra of tweezer-complexes with polyimides having different sequence-restrictions show conclusively that the detection of long range sequence-information results from multiple tweezer-binding at adjacent imide residues.

Solid-state NMR as a probe of anion binding: molecular dynamics and associations in a [5]polynorbornane bisurea host complexed with terephthalate

A range of solid-state NMR techniques is used to characterise a molecular host:guest complex consisting of a [5]polynorbornane bisurea host binding a terephthalate dianion guest. Detailed information is obtained on the molecular dynamics and associations from the point of view of both the host and guest molecules. The formation of the complex in the solid state is confirmed using (1)H 2D exchange NMR, and the 180° flipping of the (2)H-labelled terephthalate guest and its eventual expulsion from the complex at elevated temperatures are quantified using variable-temperature (2)H spin-echo experiments. Two-dimensional (1)H-(13)C HETCOR spectra obtained under fast magic angle spinning conditions (60 kHz) show a high resolution despite the poor crystallinity of the solid complex, and clearly reveal changes in the rigidity of the host molecule when complexed. Short-range intra- and intermolecular (1)H-(1)H proximities are also detected using 2D SQ-DQ correlation methods, providing insight into the molecular packing in the solid phase.

Male behavior of Mischocyttarus cerberus (Hymenoptera, Vespidae) during attacks on the nest by ants

The objectives of the present study were to verify if the males of the wasp Mischocyttarus cerberus participate in defense of the nest as they react to attack by ants, and to observe if they use chemical defense. First, wasps were stimulated with an empty pair of tweezers and a second stimulation was done with a pair of tweezers containing an ant, Camponotus crassus. The behaviors of the wasps were recorded and analyzed. The males can participate in defense of the nest, presenting some aggressive behaviors, even so, most of the time they ignore the stimulation, hide behind the nest and stay immobile.

Cooperative RNA Polymerase Molecules Behavior on a Stochastic Sequence-Dependent Model for Transcription Elongation

The transcription process is crucial to life and the enzyme RNA polymerase (RNAP) is the major component of the transcription machinery. The development of single-molecule techniques, such as magnetic and optical tweezers, atomic-force microscopy and single-molecule fluorescence, increased our understanding of the transcription process and complements traditional biochemical studies. Based on these studies, theoretical models have been proposed to explain and predict the kinetics of the RNAP during the polymerization, highlighting the results achieved by models based on the thermodynamic stability of the transcription elongation complex. However, experiments showed that if more than one RNAP initiates from the same promoter, the transcription behavior slightly changes and new phenomenona are observed. We proposed and implemented a theoretical model that considers collisions between RNAPs and predicts their cooperative behavior during multi-round transcription generalizing the Bai et al. stochastic sequence-dependent model. In our approach, collisions between elongating enzymes modify their transcription rate values. We performed the simulations in Mathematica® and compared the results of the single and the multiple-molecule transcription with experimental results and other theoretical models. Our multi-round approach can recover several expected behaviors, showing that the transcription process for the studied sequences can be accelerated up to 48% when collisions are allowed: the dwell times on pause sites are reduced as well as the distance that the RNAPs backtracked from backtracking sites. © 2013 Costa et al.

Simulation-based cutaneous surgical-skill training on a chicken-skin bench model in a medical undergraduate program

Background: Because of ethical and medico-legal aspects involved in the training of cutaneous surgical skills on living patients, human cadavers and living animals, it is necessary the search for alternative and effective forms of training simulation. Aims: To propose and describe an alternative methodology for teaching and learning the principles of cutaneous surgery in a medical undergraduate program by using a chicken-skin bench model. Materials and Methods: One instructor for every four students, teaching materials on cutaneous surgical skills, chicken trunks, wings, or thighs, a rigid platform support, needled threads, needle holders, surgical blades with scalpel handles, rat-tooth tweezers, scissors, and marking pens were necessary for training simulation. Results: A proposal for simulation-based training on incision, suture, biopsy, and on reconstruction techniques using a chicken-skin bench model distributed in several sessions and with increasing levels of difficultywas structured. Both feedback and objective evaluations always directed to individual students were also outlined. Conclusion: The teaching of a methodology for the principles of cutaneous surgery using a chicken-skin bench model versatile, portable, easy to assemble, and inexpensive is an alternative and complementary option to the armamentarium of methods based on other bench models described. © Indian Journal of Dermatology 2013.

Modelo cinético estocástico para a transcrição considerando colisões entre as moléculas de RNA polimerase

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Determinação de parâmetros para a avaliação de carcaça em bubalinos machos no Estado do Pará

O presente estudo objetivou criar um protocolo para identificação da qualidade da carcaça de bubalinos machos abatidos no Estado do Pará. Para isso, efetuou-se o estudo em duas etapas: na primeira, utilizou-se 174 animais para a criação e implantação do protocolo de identificação da idade através do desenvolvimento dos pares de dentes incisivos e das mensurações lineares, altura de garupa e cernelha, perímetro torácico e comprimento corporal. A segunda etapa constou da comprovação do protocolo pré-estabelecido inserido dentro da avaliação das características de carcaça, através dos rendimentos de carcaça quente e fria, do traseiro, dianteiro, ponta de agulha, área de olho de lombo e espessura de gordura subcutânea de 76 animais abatidos. Verificou-se a ausência dos cantos decíduos 4º par nos animais de zero a três meses de idade. Os cantos estabeleceram-se definitivamente entre três e seis meses de idade. A partir dos seis meses de idade, os dentes incisivos decíduos estão todos presentes e estabelecidos. Aos 24 meses observou-se o início da troca dentária das pinças (1º par). Entre os 30 a 55 meses de idade ocorreu a troca dentária dos primeiros e segundos médios (2º e 3º par, respectivamente) e acima dos 55 meses, a troca dos cantos. Dos 55 aos 100 meses de idade, todos os dentes incisivos permanentes estavam estabelecidos. O peso vivo dos animais apresentou uma correlação positiva e significativa com as mensurações lineares, altura de garupa e cernelha, perímetro torácico e comprimento corporal. Dos 25,7 meses até os 30 meses de idade houve uma redução da taxa de crescimento, conseqüência da puberdade e acabamento da gordura de cobertura. A partir dos 18 meses de idade não houve diferença significativa de rendimento de carcaça quente e fria, do traseiro, da área de olho de lombo e da espessura de gordura subcutânea dos animais. O rendimento dianteiro foi maior em búfalos acima de 24 meses de idade e o rendimento de ponta de agulha foi maior para búfalos mais jovens. Concluiu-se que o início da troca dentária das pinças é a idade ideal para o abate, onde coincide com a redução da taxa de crescimento e da deposição de gordura de cobertura da carcaça.

Morfometria de rainhas do gênero ATTA (Hymenoptera: Formicidae: Myrmicinae), arquitetura interna e infecção pelo fundo parasita Escovopsis de ninhos iniciais

Pós-graduação em Ciências Biológicas (Zoologia) - IBB

Transcrição cooperativa de genes ribossomais em Escherichia coli usando um modelo estocástico e dependente de sequência

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Correlação entre os questionários dash, qualidade de vida SF-36 e avaliação física nas afecções do punho e da mão

Pós-graduação em Bases Gerais da Cirurgia - FMB

Viral contamination during sequential phacoemulsification surgeries in an experimental model

Purpose: To determine the incidence of Piry virus contamination among surgical instruments used with disposable accessories for phacoemulsification during sequential surgeries. Methods: An experimental model was created with 4 pigs' eyes that were contaminated with Piry virus and 4 pigs' eyes that were not contaminated. Phacoemulsification was performed on the eyes, alternating between the contaminated and non-contaminated eyes. From one surgery to another, the operating fields, gloves, scalpel, tweezers, needles, syringes, tips and bag collector from the phacoemulsification machine were exchanged; only the hand piece and the irrigation and aspiration systems were maintained. Results: In the collector bag, three samples from the contaminated eyes (3/4) were positive, and two samples from the non-contaminated (2/4) eyes were also positive; at the tip, one sample from the contaminated eyes (1/4) and two samples of the noncontaminated eyes (2/4) yielded positive results. In the irrigation system, one sample from a non-contaminated eye (1/4) was positive, and in the aspiration system, two samples from contaminated eyes (2/4) and two samples from non-contaminated eyes (2/4) were positive. In the gloves, the samples were positive in two samples from the non-contaminated eyes (2/4) and in two samples from the contaminated eyes (2/4). In the scalpel samples, three contaminated eyes (3/4) and none of the non-contaminated eyes (0/4) were positive; finally, two samples from the anterior chambers of the non-contaminated eyes gathered after surgery were positive. Conclusions: In two non-contaminated eyes, the presence of genetic material was detected after phacoemulsification surgery, demonstrating that the transmission of the genetic material of the Piry virus occurred at some point during the surgery on these non-contaminated eyes when the hand piece and irrigation and aspiration systems were reused between surgeries.

Anisotrope Kolloide aus flüssigkristallinen Polymeren

In dieser Arbeit wird die Synthese, Charakterisierung und Manipulation anisotroper Kolloide aus flüssigkristallinen Polymeren beschrieben. Um Kolloide verschiedener Größe und aus verschiedenen Polymeren zu erhalten, wurden verschiedene Techniken verwendet. Einerseits wurden Kolloide aus nematischen und smektischen Polymeren mit Durchmessern meist im Bereich von 0,5 bis 3,5 Mikrometern hergestellt. Dazu wurden 16 verschiedene Acrylat- und Methacrylatmonomere synthetisiert und mittels Dispersionspolymerisation polymerisiert. Durch Variation der Polymerisationsbedingungen wurden Kolloide verschiedener Größe und Polydispersität erhalten. Durch Saatpolymerisation konnten zudem die Kugelgrößen bei gleichbleibend geringer Polydispersität erhöht werden. Polarisationsmikroskopie zeigt, dass die meisten Kolloide mit einer Größe zwischen ca. 2 bis 4 Mikrometern eine bipolare Direktorkonfiguration haben. Einige dieser Kolloide wurden mit einer optischen Pinzette mit zirkular polarisiertem Licht eingefangen und rotiert. Zum anderen wurden verschiedene flüssigkristalline Polymere (Polysiloxane, Hauptkettenpolymere und Polyacrylate) durch den Miniemulsionsprozess in Kolloide mit Durchmessern im Bereich von ca. 50 bis 300 nm überführt. Durch Variation der Emulgator- und Polymermenge sowie der Art des Emulgators konnte die Kugelgröße beeinflusst werden. Für die Polysiloxankolloide erfolgte die Aufklärung ihrer inneren Struktur mittels TEM und Kryo-TEM, da durch das Silizium im Polymerrückgrat ohne zusätzliches Anfärben ein Kontrast vorhanden ist. Die TEM-Aufnahmen zeigen deutlich die smektische Schichtstruktur innerhalb der Kolloide aus „verdünnten“ Copolysiloxanen und sind somit der erste direkte Beweis für die Mikrophasenseparation zwischen den Mesogenen und Polysiloxanketten, die bisher basierend auf Röntgenmessungen nur indirekt vorhergesagt wurde. Für die Copolysiloxane mit 2-Ring-Mesogenen wurden zwiebelartige Strukturen und für die Copolysiloxane mit 3-Ring-Mesogenen parallele Schichtstrukturen gefunden. Im ersten Fall folgt die smektische Schichtstruktur der Kugelsymmetrie des Kolloids, im zweiten Fall dominiert die Tendenz der smektischen Schichten, sich parallel anzuordnen.

High quality colloidal crystals with different architectures and their optical properties

In this present work high quality PMMA opals with different sphere sizes, silica opals from large size spheres, multilayer opals, and inverse opals were fabricated. Highly monodisperse PMMA spheres were synthesized by surfactant-free emulsion polymerization (polydispersity ~2%). Large-area and well-ordered PMMA crystalline films with a homogenous thickness were produced by the vertical deposition method using a drawing device. Optical experiments have confirmed the high quality of these PMMA photonic crystals, e.g., well resolved high-energy bands of the transmission and reflectance spectra of the opaline films were observed. For fabrication of high quality opaline photonic crystals from large silica spheres (diameter of 890 nm), self-assembled in patterned Si-substrates a novel technique has been developed, in which the crystallization was performed by using a drawing apparatus in combination with stirring. The achievements comprise a spatial selectivity of opal crystallization without special treatment of the wafer surface, the opal lattice was found to match the pattern precisely in width as well as depth, particularly an absence of cracks within the size of the trenches, and finally a good three-dimensional order of the opal lattice even in trenches with a complex confined geometry. Multilayer opals from opaline films with different sphere sizes or different materials were produced by sequential crystallization procedure. Studies of the transmission in triple-layer hetero-opal revealed that its optical properties cannot only be considered as the linear superposition of two independent photonic bandgaps. The remarkable interface effect is the narrowing of the transmission minima. Large-area, high-quality, and robust photonic opal replicas from silicate-based inorganic-organic hybrid polymers (ORMOCER® s) were prepared by using the template-directed method, in which a high quality PMMA opal template was infiltrated with a neat inorganic-organic ORMOCER® oligomer, which can be photopolymerized within the opaline voids leading to a fully-developed replica structure with a filling factor of nearly 100%. This opal replica is structurally homogeneous, thermally and mechanically stable and the large scale (cm2 size) replica films can be handled easily as free films with a pair of tweezers.

Total nitrogen from solid phase in the Jena Experiment (Block 2 Main Experiment up to 100cm depth, year 2002)

This data set contains measurements of total nitrogen from the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. Soil sampling and analysis: Stratified soil sampling to a depth of 1m was performed before sowing in April 2002. Three independent samples per plot were taken of all plots in block 2 using a motor-driven soil column cylinder (Cobra, Eijkelkamp, 8.3 cm in diameter). Soil samples were dried at 40°C and segmented to a depth resolution of 5 cm giving 20 depth subsamples per core. All samples were analyzed independently. All soil samples were passed through a sieve with a mesh size of 2 mm. Rarely present visible plant remains were removed using tweezers. Total nitrogen concentration was analyzed on ball-milled subsamples (time 4 min, frequency 30 s-1) by an elemental analyzer at 1150°C (Elementaranalysator vario Max CN; Elementar Analysensysteme GmbH, Hanau, Germany).

Soil carbon in the Jena Experiment (all blocks Main Experiment up to 30cm depth, year 2002)

This data set contains soil carbon measurements (Organic carbon, inorganic carbon, and total carbon; all measured in dried soil samples) from the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. Soil sampling and analysis: Stratified soil sampling was performed before sowing in April 2002. Five independent samples per plot were taken using a split tube sampler with an inner diameter of 4.8 cm (Eijkelkamp Agrisearch Equipment, Giesbeek, the Netherlands). Soil samples were dried at 40°C and then segmented to a depth resolution of 5 cm giving six depth subsamples per core. All samples were analyzed independently and averaged values per depth layer are reported. Soil samples were passed through a sieve with a mesh size of 2 mm. Rarely present visible plant remains were removed using tweezers. Total carbon concentration was analyzed on ball-milled subsamples (time 4 min, frequency 30 s-1) by an elemental analyzer at 1150°C (Elementaranalysator vario Max CN; Elementar Analysensysteme GmbH, Hanau, Germany). We measured inorganic carbon concentration by elemental analysis at 1150°C after removal of organic carbon for 16 h at 450°C in a muffle furnace. Organic carbon concentration was calculated as the difference between both measurements of total and inorganic carbon.