Evolution of domain combinations in protein kinases and its implications for functional diversity

Protein kinases phosphorylating Ser/Thr/Tyr residues in several cellular proteins exert tight control over their biological functions. They constitute the largest protein family in most eukaryotic species. Protein kinases classified based on sequence similarity in their catalytic domains, cluster into subfamilies, which share gross functional properties. Many protein kinases are associated or tethered covalently to domains that serve as adapter or regulatory modules,naiding substrate recruitment, specificity, and also serve as scaffolds. Hence the modular organisation of the protein kinases serves as guidelines to their functional and molecular properties. Analysis of genomic repertoires of protein kinases in eukaryotes have revealed wide spectrum of domain organisation across various subfamilies of kinases. Occurrence of organism-specific novel domain combinations suggests functional diversity achieved by protein kinases in order to regulate variety of biological processes. In addition, domain architecture of protein kinases revealed existence of hybrid protein kinase subfamilies and their emerging roles in the signaling of eukaryotic organisms. In this review we discuss the repertoire of non-kinase domains tethered to multi-domain kinases in the metazoans. Similarities and differences in the domain architectures of protein kinases in these organisms indicate conserved and unique features that are critical to functional specialization. (C) 2009 Elsevier Ltd. All rights reserved.

Genetic regulation of flower development

Flower development provides a model system to study mechanisms that govern pattern formation in plants. Most flowers consist of four organ types that are present in a specific order from the periphery to the centre of the flower. Reviewed here are studies on flower development in two model species: Arabidopsis thaliana and Antirrhinum majus that focus on the molecular genetic analysis of homeotic mutations affecting pattern formation in the flower. Based on these studies a model was proposed that explains how three classes of regulatory genes can together control the development of the correct pattern of organs in the flower. The universality of the basic tenets of the model is apparent from the analysis of the homologues of the Arabidopsis genes from other plant species

Theoretical Studies on the Structure and Bonding of Metallacyclocumulenes, -cyclopentynes, and -cycloallenes

In this paper, we compare the electronic structure of the hafnacycloallene complex Cp(2)HfC(4)Rr'(2)R `' (5Hf), which was previously described by Erker et al., with those of the titanium, zirconium, and hafnium complexes Cp(2)M(eta(4)-RHC(4)HR) (3M; i.e. metallacyclopent-2,3,4-trienes, metallacyclocumulenes) and Cp(2)M(eta(2)-R(2)C(4)R(2)) (4M; i.e. 1-metallacyclopent-3-ynes) using density functional theory (BP86/LANL2DZ) calculations. Moreover, the eta(3)-phenylallenyl zirconocene complex 7Zr, which was synthesized by Wojcicki et al., is included for the comparison. These calculations and extended Huckel calculations show that the bonding in complex 5Hf is remarkably similar to that of complexes 4M and 7Zr. An analysis of the structural parameters and bonding reveals that the unique interaction of the internal carbon atoms along with the terminal carbon atoms with the bent-metallocene moiety is the reason for the unusual stability of these metallacycles. The molecular orbital analysis further suggests that complex 5Hf can react with another metal fragment to give the bimetallic complexes 9 and 10. The electronic structures of complexes 3M, 4M, 5Hf, and 7Zr have been comparatively studied to get a general understanding of the bonding in these metallacycles.

Confinement-deconfinement transition and spin correlations in a generalized Kitaev model

We present a spin model, namely, the Kitaev model augmented by a loop term and perturbed by an Ising Hamiltonian, and show that it exhibits both confinement-deconfinement transitions from spin liquid to antiferromagnetic/spin-chain/ferromagnetic phases and topological quantum phase transitions between gapped and gapless spin-liquid phases. We develop a fermionic resonating-valence-bonds (RVB) mean-field theory to chart out the phase diagram of the model and estimate the stability of its spin-liquid phases, which might be relevant for attempts to realize the model in optical lattices and other spin systems. We present an analytical mean-field theory to study the confinement-deconfinement transition for large coefficient of the loop term and show that this transition is first order within such mean-field analysis in this limit. We also conjecture that in some other regimes, the confinement-deconfinement transitions in the model, predicted to be first order within the mean-field theory, may become second order via a defect condensation mechanism. Finally, we present a general classification of the perturbations to the Kitaev model on the basis of their effect on it's spin correlation functions and derive a necessary and sufficient condition, within the regime of validity of perturbation theory, for the spin correlators to exhibit a long-ranged power-law behavior in the presence of such perturbations. Our results reproduce those of Tikhonov et al. [Phys. Rev. Lett. 106, 067203 (2011)] as a special case.

Features of a unique intronless cluster of class I small heat shock protein genes in tandem with box C/D snoRNA genes on chromosome 6 in tomato (Solanum lycopersicum)

Physical clustering of genes has been shown in plants; however, little is known about gene clusters that have different functions, particularly those expressed in the tomato fruit. A class I 17.6 small heat shock protein (Sl17.6 shsp) gene was cloned and used as a probe to screen a tomato (Solanum lycopersicum) genomic library. An 8.3-kb genomic fragment was isolated and its DNA sequence determined. Analysis of the genomic fragment identified intronless open reading frames of three class I shsp genes (Sl17.6, Sl20.0, and Sl20.1), the Sl17.6 gene flanked by Sl20.1 and Sl20.0, with complete 5' and 3' UTRs. Upstream of the Sl20.0 shsp, and within the shsp gene cluster, resides a box C/D snoRNA cluster made of SlsnoR12.1 and SlU24a. Characteristic C and D, and C' and D', boxes are conserved in SlsnoR12.1 and SlU24a while the upstream flanking region of SlsnoR12.1 carries TATA box 1, homol-E and homol-D box-like cis sequences, TM6 promoter, and an uncharacterized tomato EST. Molecular phylogenetic analysis revealed that this particular arrangement of shsps is conserved in tomato genome but is distinct from other species. The intronless genomic sequence is decorated with cis elements previously shown to be responsive to cues from plant hormones, dehydration, cold, heat, and MYC/MYB and WRKY71 transcription factors. Chromosomal mapping localized the tomato genomic sequence on the short arm of chromosome 6 in the introgression line (IL) 6-3. Quantitative polymerase chain reaction analysis of gene cluster members revealed differential expression during ripening of tomato fruit, and relatively different abundances in other plant parts.

Infrared Spectra of Dimethylphenanthrenes in the Gas phase

Infrared spectra of atmospherically and astronomically important dimethylphenanthrenes (DMPs), namely 1,9-DMP, 2,4-DMP, and 3,9-DMP, were recorded in the gas phase from 400 to 4000 cm(-1) with a resolution of 0.5 cm(-1) at 110 degrees C using a 7.2 m gas cell. DFT calculations at the B3LYP/6-311G** level were carried out to get the harmonic and anharmonic frequencies and their corresponding intensities for the assignment of the observed bands. However, spectral assignments could not be made unambiguously using anharmonic or selectively scaled harmonic frequencies. Therefore, the scaled quantum mechanical (SQM) force field analysis method was adopted to achieve more accurate assignments. In this method force fields instead of frequencies were scaled. The Cartesian force field matrix obtained from the Gaussian calculations was converted to a nonredundant local coordinate force field matrix and then the force fields were scaled to match experimental frequencies in a consistent manner using a modified version of the UMAT program of the QCPE package. Potential energy distributions (PEDs) of the normal modes in terms of nonredundant local coordinates obtained from these calculations helped us derive the nature of the vibration at each frequency. The intensity of observed bands in the experimental spectra was calculated using estimated vapor pressures of the DMPs. An error analysis of the mean deviation between experimental and calculated intensities reveal that the observed methyl C-H stretching intensity deviates more compared to the aromatic C-H and non C-H stretching bands.

MEMS based microactuator for microjet applications

The objective of this work is to confirm the possibility of utilization of PolyVinyliDeneFlouride (PVDF) films in MEMS based microactuator for microjet applications. A membrane type microactuator is designed, developed, packaged and tested. The microactuator consists of PVDF film attached to thin Silicon diaphragm. As the voltage difference is applied across it, due to the piezoelectric behaviour, it deforms primarily in d31 mode, which in turn deflects the diaphragm. Using finite element methods, coupled field analysis is carried out to optimize the dimensions of the actuator with respect to the output force and input voltage. A cavity with a square diaphragm of 1mm×1mm×5μm is realized using standard microfabrication technique. 50μm thick PVDF film, cut with special dicing saw, is glued inside the metalized cavity using low stress, conductive, room temperature cured epoxy. The 3mm×3mm×0.675mm actuator die is packaged using Chip-On-Board technique in conjunction with low temperature soldering for taking the connections. The micro-actuator is tested in both actuation and sensing mode. The developed actuator is proposed to use with micro nozzle to study the utilization in drug delivery system.

Dynamics of history-dependent epidemics in temporal networks

The structural properties of temporal networks often influence the dynamical processes that occur on these networks, e.g., bursty interaction patterns have been shown to slow down epidemics. In this paper, we investigate the effect of link lifetimes on the spread of history-dependent epidemics. We formulate an analytically tractable activity-driven temporal network model that explicitly incorporates link lifetimes. For Markovian link lifetimes, we use mean-field analysis for computing the epidemic threshold, while the effect of non-Markovian link lifetimes is studied using simulations. Furthermore, we also study the effect of negative correlation between the number of links spawned by an individual and the lifetimes of those links. Such negative correlations may arise due to the finite cognitive capacity of the individuals. Our investigations reveal that heavy-tailed link lifetimes slow down the epidemic, while negative correlations can reduce epidemic prevalence. We believe that our results help shed light on the role of link lifetimes in modulating diffusion processes on temporal networks.

Tetraphenylethene-Based Conjugated Fluoranthene: A Potential Fluorescent Probe for Detection of Nitroaromatic Compounds

This study reports the synthesis and photophysical properties of a star-shaped, novel, fluoranthene-tetraphenylethene (TFPE) conjugated luminogen, which exhibits aggregation-induced blue-shifted emission (AIBSE). The bulky fluoranthene units at the periphery prevent intramolecular rotation (IMR) of phenyl rings and induces a blueshift with enhanced emission. The AIBSE phenomenon was investigated by solvatochromic and temperature-dependent emission studies. Nanoaggregates of TFPE, formed by varying the water/THF ratio, were investigated by SEM and TEM and correlated with optical properties. The TFPE conjugate was found to be a promising fluorescent probe towards the detection of nitroaromatic compounds (NACs), especially for 2,4,6-trinitrophenol (PA) with high sensitivity and a high Stern-Volmer quenching constant. The study reveals that nanoaggregates of TFPE formed at 30 and 70% water in THF showed unprecedented sensitivity with detection limits of 0.8 and 0.5ppb, respectively. The nanoaggregates formed at water fractions of 30 and 70% exhibit high Stern-Volmer constants (K-sv=79998 and 51120m(-1), respectively) towards PA. Fluorescence quenching is ascribed to photoinduced electron transfer between TFPE and NACs with a static quenching mechanism. Test strips coated with TFPE luminogen demonstrate fast and ultra-low-level detection of PA for real-time field analysis.

Damage Localization, Sensitivity of Energy Release and the Catastrophe Transition

Large earthquakes can be viewed as catastrophic ruptures in the earth’s crust. There are two common features prior to the catastrophe transition in heterogeneous media. One is damage localization and the other is critical sensitivity; both of which are related to a cascade of damage coalescence. In this paper, in an attempt to reveal the physics underlying the catastrophe transition, analytic analysis based on mean-field approximation of a heterogeneous medium as well as numerical simulations using a network model are presented. Both the emergence of damage localization and the sensitivity of energy release are examined to explore the inherent statistical precursors prior to the eventual catastrophic rupture. Emergence of damage localization, as predicted by the mean-field analysis, is consistent with observations of the evolution of damage patterns. It is confirmed that precursors can be extracted from the time-series of energy release according to its sensitivity to increasing crustal stress. As a major result, present research indicates that the catastrophe transition and the critical point hypothesis (CPH) of earthquakes are interrelated. The results suggest there may be two cross-checking precursors of large earthquakes: damage localization and critical sensitivity.

Superconductivity, spin-glass properties, and ferromagnetism in amorphous La-Gd-Au alloys

The superconducting and magnetic properties of splat cooled amorphous alloys of composition (La_100-xGd_x)₈₀Au₂₀ (0 ≤ x ≤ 100) have been studied. The La₈₀Au₂₀ alloys are ideal type II super-conductors (critical temperature T_c = 3.5° K ). The concentration range (x less than 1) where superconductivity and spin-glass freezing n1ight coexist has been studied in detail. The spin-glass alloys (0 less than x less than 70) exhibit susceptibility maxima and thermomagnetic history effects. In the absence of complications due to crystal field and enhanced matrix effects, a phenomenological model is proposed in which the magnetic clusters are treated as single spin entities interacting via random forces using the molecular field approach. The fundamental parameters (such as the strength of the forces and the size of clusters) can be deduced from magnetization measurements. The remanent magnetization is shown to arise from an interplay of the RKKY and dipolar forces. Magnetoresistivity results are found to be consistent with the aforementioned picture. The nature of magnetic interactions in an amorphous matrix is also discussed. The moment per Gd atom (7µ_B) is found to be constant and close to that of the crystalline value throughout the concentration range investigated. Finally, a detail study is made of the critical phenomena and magnetic properties of the amorphous ferromagnet: Gd₈₀Au₂₀. The results are compared with recent theories on amorphous magnetism.

Gestão em saúde, uma perspectiva ergológica: com quantos gestos se faz uma gestão

Baseado na convicção de que trabalhar é gerir fruto das pesquisas com a perspectiva da Ergologia , procura-se nesta tese pensar gestão como um conceito ampliado, algo que todos os humanos operam ao trabalhar, e não somente como uma função exclusiva de administradores, no sentido restrito do termo (referido apenas aos chefes, diretores, etc.). Tendo como campo empírico o Sistema Único de Saúde (SUS) e investigando-se as proposições de alguns dos principais autores sobre o tema da Gestão e Planejamento em Saúde, verificou-se que uma exaustiva busca vem sendo empreendida por diversos agentes do campo da Saúde e por pesquisadores para aproximarem-se, compreenderem e desenvolverem melhor as habilidades, os conhecimentos, as competências e os dispositivos que permitiriam uma gestão mais eficiente do SUS e, mais especificamente, no âmbito de uma Unidade de Saúde Pública no Brasil. Estiveram em análise as práticas de gestão desenvolvidas em um Centro Municipal de Saúde do estado do Rio de Janeiro (Brasil), no qual o autor da tese, além das atividades de pesquisa, exercia a função de diretor geral. A tese teve como objetivo principal analisar, do ponto de vista da atividade, a dimensão gestionária do trabalho na Unidade de Saúde citada, a fim de discutir a viabilidade naquele local e, possivelmente em outras Unidades de Saúde do exercício de uma ergogestão, isto é, uma gestão com base nos princípios propostos pela Ergologia quando o ponto de vista da atividade tem cidadania no meio de trabalho. O referencial teórico constituiu-se de algumas abordagens clínicas do trabalho (Ergonomia da Atividade, Psicopatologia do Trabalho, Psicodinâmica do Trabalho e Clínica da Atividade, esta última em menor proporção) com elementos das contribuições do educador brasileiro Paulo Freire, do psicanalista inglês Donald Winnicott e do biólogo chileno Humberto Maturana, todas colocadas em sinergia dialética sob a orientação da perspectiva ergológica. No curso da investigação foram utilizados métodos e técnicas pertinentes a este quadro e que objetivaram possibilitar a aproximação e o diálogo com os protagonistas da atividade na Unidade de Saúde em análise. Destacam-se as influências da pesquisa-intervenção e da pesquisa etnográfica, sendo o principal dispositivo técnico utilizado aquele denominado Encontros sobre o Trabalho. A pesquisa empreendida, conjuntamente com a experiência concreta de gerenciamento (como diretor geral), permitiu concluir que o esforço de implantação da modalidade que se denomina ergogestão, privilegiando o ponto de vista da atividade, pôde colaborar para promover transformações positivas no cotidiano da Unidade posta em análise. Contudo, sua aceitação por um maior número de atores e seu desenvolvimento dependem do atendimento de algumas necessidades, apontadas pelo coletivo de trabalho como entraves a superar. Os achados aqui presentes podem contribuir para a construção de um patrimônio de informações acerca da Unidade. A partir desse patrimônio outras experiências de gerenciamento podem vir a se desenvolver, obtendo-se assim, cada vez maior êxito na gestão do processo de trabalho e na melhoria das condições do atendimento oferecido aos usuários.

Análise da tectônica de colocação de diques cretácicos na região de São Sebastião, SP

O trabalho foi desenvolvido no litoral norte do estado de São Paulo, onde ocorrem boas exposições de rochas intrusivas da porção meridional do Enxame de Diques da Serra do Mar, de idade eocretácica. O objetivo principal da dissertação é caracterizar os regimes tectônicos associados à colocação e à deformação de diques máficos na área de São Sebastião (SP) e sua distribuição espacial, a partir de interpretações de imagens de sensores remotos, análise de dados estruturais de campo e descrição petrográfica das rochas ígneas. A área apresenta grande complexidade no tocante ao magmatismo, uma vez que ocorrem diques de diabásios toleítico e alcalino, lamprófiro e rochas alcalinas félsicas como fonolitos, traquitos e sienitos, estes sob a forma diques, sills e plugs. Os diabásios toleíticos tem idades em torno 134 Ma, correlatas com o início do rifteamento sul-atlântico, enquanto que as rochas alcalinas datam de 86 Ma e estão relacionadas com um magmatismo intraplaca posterior. Os lineamentos estruturais orientam-se majoritariamente na direção ENE-WSW, paralela às foliações metamórficas e zonas de cisalhamento observadas no campo e descritas na literatura, referentes ao Domínio Costeiro da Faixa Ribeira. Os diques se orientam na direção NE-SW, com azimute semelhante porém ângulos de mergulho discordantes da foliação em grande parte da área, onde as foliações são de baixo ângulo. Um segundo conjunto de lineamentos orientado NW-SE ocorre como um importante conjunto de fraturas que cortam tanto as rochas do embasamento proterozóico quanto as rochas alcalinas neocretácicas. Diques com esta orientação são escassos. Um terceiro conjunto NNE-SSW ocorre na porção oeste da área, associado à presença de diques de diabásio que por vezes mostram indicadores de movimentação sinistral. A análise cinemática dos diques mostra um predomínio de distensão pura durante sua colocação, com um tensor de compressão mínima de orientação NW-SE, ortogonal ao principal trend dos diques. Componentes direcionais, por vezes ambíguas, são comumente observadas, com um discreto predomínio de componente sinistral. O mesmo padrão cinemático é observado para os diques toleíticos e para os alcalinos, sugerindo que o campo de tensões local pouco variou durante o Cretáceo. Embora o embasamento não tenha sido diretamente reativado durante a colocação dos diques, sua anisotropia pode ter controlado de certa forma a orientação do campo de tensões local durante o Cretáceo. Os mapas geofísicos da bacia de Santos existentes na literatura sugerem certo paralelismo entre as estruturas observadas na área de estudo e aquelas interpretadas na bacia. As estruturas NNE-SSW são paralelas ao trend das sub-bacias e ao gráben de Merluza, enquanto que as estruturas NW-SE são paralelas a zonas de transferência descritas na literatura.

The Interplay between Natural Selection and Susceptibility to Melanoma on Allele 374F of SLC45A2 Gene in a South European Population

We aimed to study the selective pressures interacting on SLC45A2 to investigate the interplay between selection and susceptibility to disease. Thus, we enrolled 500 volunteers from a geographically limited population (Basques from the North of Spain) and by resequencing the whole coding region and intron 5 of the 34 most and the 34 least pigmented individuals according to the reflectance distribution, we observed that the polymorphism Leu374Phe (L374F, rs16891982) was statistically associated with skin color variability within this sample. In particular, allele 374F was significantly more frequent among the individuals with lighter skin. Further genotyping an independent set of 558 individuals of a geographically wider population with known ancestry in the Spanish population also revealed that the frequency of L374F was significantly correlated with the incident UV radiation intensity. Selection tests suggest that allele 374F is being positively selected in South Europeans, thus indicating that depigmentation is an adaptive process. Interestingly, by genotyping 119 melanoma samples, we show that this variant is also associated with an increased susceptibility to melanoma in our populations. The ultimate driving force for this adaptation is unknown, but it is compatible with the vitamin D hypothesis. This shows that molecular evolution analysis can be used as a useful technology to predict phenotypic and biomedical consequences in humans.

Filogenia de Mycalina Hajdu, van Soest & Hooper, 1994 (Poecilosclerida, Demospongiae): dados morfológicos e moleculares

principalmente pelo baixo grau de complexidade de especialização, escassez de caracteres distintivos e a elevada plasticidade morfológica. A partir do século XIX emergiram classificações mais robustas. O que conhecemos hoje como Ordem Poecilosclerida só começou a ser delineado pela iniciativa de Zittel (1878) com o reconhecimento de Monaxonida, ou seja, reconhecimento de um padrão de simetria nas categorias de espículas. Ridley e Dendy (1887) apresentaram uma nova classificação para as esponjas do grupo Monaxonida utilizada por Topsent (1894) para criação da Familia Poeciloscleridae, eregida a ordem por este último autor em 1928, enfatizando a presença das quelas como microscleras. Posteriormente, van Soest (1984) e Bergquist e Fromont (1988) empreenderam discussões dessa classificação com base em uma perspectiva filogenética. Uma classificação robusta e de consenso só foi conseguida a partir dos trabalhos de Hajdu e colaboradores (1994a, 1994b) e Hajdu (1994, 1995), com o estabelecimento das Subordens: Mycalina, Myxillina e Microcionina. Apesar disso, as relações internas das famílias da Subordem Mycalina permaneciam com dúvidas, principalmente no tocante à inclusão de Podospongiidae, Isodictyidae, e a relação de Poecilosclerida com a Ordem Haplosclerida. Neste trabalho foi proposto a revisão da classificação da Subordem Mycalina com base em dados morfológicos e moleculares. Foram feitas análises filogenéticas em três níveis taxonômicos, espécie, gênero e família, com base em dados morfológicos. Além disso, foi feita uma análise filogenética molecular utilizando sequências parciais da subunidade maior do RNA ribossomal (LSU do RNAr). As amostras de Mycalina foram amplificadas via PCR e posteriormente sequenciadas. Com base nestes resultados foi concluído que: as Familias Cladorhizidae, Guitarridae, Mycalidae e Hamacanthidae são monofiléticas. Para esta última foi confirmada a série de transformação sigmancistra > cirtancistra > diâncistra > clavidisco. A posição da Familia Podospongiidae dentro de Mycalina está bem corroborada, porém, precisa ser melhor estudada com dados moleculares para determinar, ou não, o seu monofiletismo. A Familia Esperiopsidae precisa ser melhor estudada com base em dados morfológicos e o gênero Amphilectus precisa ser revisado, provavelmente uma parte deste estaria melhor alocado em Haplosclerida junto com Isodictyidae. A Familia Desmacellidae não é monofilética, bem como Biemna e Neofibularia, provavelmente, não são Poecilosclerida e deveriam ser transferidas para uma posição próxima de Tetractinellida. Desmacella provavelmente é uma Mycalina com posição basal na Subordem. Os demais gêneros precisam ser estudados com base em dados moleculares. A Ordem Haplosclerida provavelmente é o grupo irmão de Poecilosclerida e a série de transformação sigmas > quelas foi confirmada com base em dados morfológicos e moleculares. A Subordem Mycalina não é monofilética como definida em Hajdu e van Soest (2002a). Palavras-chave: Sistemática. Porifera. Evolução.