Análise estratigráfica do intervalo siluro-devoniano da bacia do Amazonas

O trabalho consiste na análise estratigráfica do intervalo siluro-devoniano da Bacia do Amazonas utilizando como base os conceitos da Estratigrafia Moderna, mais especificamente a sequência estratigráfica genética, proposta por Galloway (1989), a qual utiliza as superfícies de inundação marinha como os limites de uma sequência sedimentar. A principal razão para a utilização desta metodologia deve-se ao fato que o conteúdo rochoso compreendido no intervalo estudado teve a sua sedimentação relacionada às transgressões marinhas que faziam parte do contexto paleogeográfico da bacia durante o Siluriano e Devoniano. Desta forma, as superfícies de inundação máxima, representativas de eventos cronoestratigráficos, destacam-se nos perfis de raios gama e são tomadas como datum de correlação em treze poços exploratórios, os quais foram distribuídos em quatro seções (A-A, B-B, C-C e D-D) pela bacia. A análise destas seções permitiu a identificação de quatro sequências de terceira ordem (AB, BC, CD e DE), limitadas no topo e na base por superfícies de inundação marinha. Cada sequência é constituída por ciclos regressivo-transgressivos assimétricos, representados pelo trato de sistemas de mar alto e pelo trato de sistemas transgressivo. A análise destas seções integrada à interpretação de mapas estratigráficos (isópacas, isólitas e porcentagem de areias) possibilitou identificar o depocentro da bacia, bem como duas áreas principais como fonte de sedimentos arenosos (uma a oeste e outra a sul). Além disto, foi possível inferir que a comunicação marinha com o continente, durante as transgressões paleozoicas, responsável pela deposição de sedimentos pelíticos, seguiu uma orientação de norte para sul, evoluindo obliquamente em direção ao continente num trend nordeste para sudoeste. Por fim, a partir da análise cíclica em perfis de raios gama, as superfícies de inundação marinha, do intervalo Devoniano, das bacias do Amazonas e Parnaíba foram correlacionadas.

Transcriptome analysis of Neotyphodium and Epichloë grass endophytes

Large-scale gene discovery has been performed for the grass fungal endophytes Neotyphodium coenophialum, Neotyphodium lolii, and Epichloë festucae. The resulting sequences have been annotated by comparison with public DNA and protein sequence databases and using intermediate gene ontology annotation tools. Endophyte sequences have also been analysed for the presence of simple sequence repeat and single nucleotide polymorphism molecular genetic markers. Sequences and annotation are maintained within a MySQL database that may be queried using a custom web interface. Two cDNA-based microarrays have been generated from this genome resource. They permit the interrogation of 3806 Neotyphodium genes (NchipTM microarray), and 4195 Neotyphodium and 920 Epichloë genes (EndoChipTM microarray), respectively. These microarrays provide tools for high-throughput transcriptome analysis, including genome-specific gene expression studies, profiling of novel endophyte genes, and investigation of the host grass–symbiont interaction. Comparative transcriptome analysis in Neotyphodium and Epichloë was performed

Association of FOXE1 Polyalanine Repeat Region with Papillary Thyroid Cancer

CONTEXT: Polyalanine tract variations in transcription factors have been identified for a wide spectrum of developmental disorders. The thyroid transcription factor forkhead factor E1 (FOXE1) contains a polymorphic polyalanine tract with 12-22 alanines. Single-nucleotide polymorphisms (SNP) close to this locus are associated with papillary thyroid cancer (PTC), and a strong linkage disequilibrium block extends across this region. OBJECTIVE: The objective of the study was to assess whether the FOXE1 polyalanine repeat region was associated with PTC and to assess the effect of polyalanine repeat region variants on protein expression, DNA binding, and transcriptional function on FOXE1-responsive promoters. DESIGN: This was a case-control study. SETTING: The study was conducted at a tertiary referral hospital. PATIENTS AND METHODS: The FOXE1 polyalanine repeat region and tag SNP were genotyped in 70 PTC, with a replication in a further 92 PTC, and compared with genotypes in 5767 healthy controls (including 5667 samples from the Wellcome Trust Case Control Consortium). In vitro studies were performed to examine the protein expression, DNA binding, and transcriptional function for FOXE1 variants of different polyalanine tract lengths. RESULTS: All the genotyped SNP were in tight linkage disequilibrium, including the FOXE1 polyalanine repeat region. We confirmed the strong association of rs1867277 with PTC (overall P = 1 × 10(-7), odds ratio 1.84, confidence interval 1.31-2.57). rs1867277 was in tight linkage disequilibrium with the FOXE1 polyalanine repeat region (r(2) = 0.95). FOXE1(16Ala) was associated with PTC with an odds ratio of 2.23 (confidence interval 1.42-3.50; P = 0.0005). Functional studies in vitro showed that FOXE1(16Ala) was transcriptionally impaired compared with FOXE1(14Ala), which was not due to differences in protein expression or DNA binding. CONCLUSIONS: We have confirmed the previous association of FOXE1 with PTC. Our data suggest that the coding polyalanine expansion in FOXE1 may be responsible for the observed association between FOXE1 and PTC.

Arcabouço estratigráfico e ciclicidade deposicional dos sistemas sedimentares quaternários da plataforma sul da Bacia de Campos (RJ)

A análise sísmica de ~ 3000 km de dados sísmicos sparker de reflexão monocanal permitiu a proposição de um arcabouço estratigráfico englobando a seção rasa (~300 milisegundos) da plataforma continental sul da Bacia de Campos. Cinco sequências sísmicas foram reconhecidas (Sq1-Sq5), limitadas por superfícies erosivas de escala plataformal (superfícies S1-S5), interpretadas como sequências deposicionais formadas por oscilações glacioeustáticas e limites de sequências (discordâncias regionais) esculpidos durante longos períodos de exposição subaérea e total da plataforma, indicando condições de diminuição de nível de base e destruição parcial de espaço de acomodação sedimentar. As sequências Sq1-Sq4 são dominantemente regressivas, compostas principalmente por prismas de regressão forçada de borda de plataforma/talude superior. A sequência superficial Sq5 é constituída essencialmente de unidades retrogradantes restritas à plataforma continental, interpretadas como compondo uma sequência eminentemente transgressiva. A correlação entre dados sísmicos e cronoestratigráficos de um poço exploratório disponível na área permitiu posicionar a deposição desta sucessão estratigráfica entre o Pleistoceno Médio- Holoceno (últimos ~500 ka). Além disso, a correlação entre a base de dados com curvas globais de variações eustáticas, baseadas nas razões isotópicas de 18O (estágios isotópicos marinhos), permitiu ainda sugerir que a sucessão estratigráfica Sq1-Sq4 registra sequências regressivas de quarta ordem, refletindo deposição durante ciclos glacioeustáticos de ~ 100 -120 ka de duração e de alta amplitude de oscilação eustática (100-145m), que caracterizam o sinal eustático nos últimos ~500 ka. A sequência Sq5 seria uma sequência ainda em formação, constituída por depósitos transgressivos e de mar alto formados durante o Pleistoceno Tardio-Holoceno.

化德群和土门群沉积岩碎屑锆石研究：对华北克拉通基底及元古宙盆地演化的指示意义

The Huade Group, consisting of low-grade and un-metamorphosed sedimentary rocks with no volcanic interlayer, is located at the northern margin of the North China craton and adjoining the south part of the Central Asian Orogenic Belt. It is east to the Paleo- to Meso-Proterozoic Bayan Obo and Zhaertai-Langshan rifts and northwest to the Paleo- to Neo-proterozoic Yanshan aulacogen, in which the typical Changcheng, Jixian and Qingbaikou systems are developed. The Huade Group are mainly composed of pebbly sandstones, sandstones, greywackes，shales，calc-silicate rocks and limestones, partly undergoing low-grade metamorphism and being changed to meta-sandstones, schists, phyllites, slates and crystalline limestones or marbles. The stratigraphic sequences show several cycles of deposition. Each of them developed coarse clastic rocks – interbedded fine clastic rocks and pelites from bottom upward or from coarse clastic rocks to interbedded fine clastic rocks and pelites to carbonate rocks. The Tumen Group outcrop sporadically around or west to the Tanlu faults in western Shandong. They are mainly composed of pebbly sandstones, sandstones, shales and limestones. This thesis deals with the characteristics of petrology, geochemistry and sedimentary of the Huade Group and the Tumen Group, and discusses the LA-ICP-MS and SIMS U-Pb ages, Hf isotope and trace element composition of the detrital zircons from 5 meta-sandstone samples of the Huade Group and 3 sandstone samples of the Tumen Group. The age populations of the detrital zircons from the Huade Group are mainly ~2.5 Ga and ~1.85 Ga, and there are also minor peaks at ~2.0 Ga, ~1.92 Ga and ~1.73 Ga. Most of the detrital zircon grains of 2.47-2.57 Ga and a few of 1.63-2.03 Ga have Hf crust model ages of 2.7-3.0 Ga, and most of the detrital zircon grains of 1.63-2.03 Ga have Hf crust model ages of 2.35-2.7 Ga, with a peak at 2.54 Ga. The main age peaks of the detrital zircons from the Tumen Group are ~2.5 Ga、~1.85 Ga, 1.57 Ga, 1.5 Ga, 1.33 Ga and 1.2 Ga. Different samples from the Tumen Group have distinct Hf isotopic characteristics. Detrital zircon grains of ~2.52 Ga from one sandstone sample have 2.7-3.2 Ga Hf crust model ages, whereas zircon grains of 1.73-2.02 Ga and 2.31-2.68 Ga from another sample have Hf crust model ages of 2.95-3.55 Ga. Detrital zircon grains of Mesoproterozoic ages have Paleoproterozoic (1.7-2.25 Ga) crust model ages. Through detailed analyses of the detrital zircons from the Huade and Tumen Group and comparison with those from the sedimentary rocks of similar sedimentary ages, the thesis mainly reaches the following conclusions: 1. The youngest age peaks of the detrital zircons of 1.73 Ga constrains the sedimentary time of the Huade Group from late Paleoproterozoic to Mesoproterozoic. 2. The age peaks of detrital zircons of the Huade Group correspond to the significant Precambrian tectonic-thermal events of the North China craton. The basement of the North China craton is the main provenance of the Huade Group, of which the intermediate to high grade metamorphic sedimentary rocks are dominant and provide mainly 1.85-1.92 Ga sediments. 3. The Huade basin belongs to the North China craton and it is suggested that the northern boundary of the North China craton should be north to the Huade basin. 4. The stratigraphic characteristics indicate the Huade Group formed in a stable shallow-hypabyssal sedimentary basin. The rock association and sedimentary time of the Huade Group are similar to those of the Banyan Obo Group and the Zhaertai Group, and they commonly constitute late Paleoproterozoic to Mesoproterozoic continental margin basins along the northern margin of the North China craton. 5. The continental margin basins would have initiated coeval with the Yanshan and Xiong’er aulacogens. 6. The ages of the detrital zircons from the Tumen Group and the Penglai Group at Shandong peninsula and the Yushulazi Group at south Liaoning are similar, so their sedimentary time is suggested to be Neoproterozoic，coeval with the Qingbaikou system. The detrital zircon ages of 1.0-1.2 Ga from the Tumen Group, the Penglai Group and the Yushulazi Group indicate that there have being 1.0-1.2 Ga magmatic activities at the eastern margin of the North China craton. 7. The U-Pb age populations of the detrital zircons from the late Paleoproterozoic to Neoproterozoic sedimentary rocks suggest that the main Precambrian tectonic-thermal events of the North China craton happened at ~2.5 Ga and ~1.85 Ga. But the events at 2.7 Ga and 1.2 Ga are also of great significance. Hf isotope characteristics indicate that the significant crust growth periods of the North China craton are 2.7-3.0 Ga and ~2.5 Ga.

Synapsing variable length crossover: An algorithm for crossing and comparing variable length genomes

The Synapsing Variable Length Crossover (SVLC) algorithm provides a biologically inspired method for performing meaningful crossover between variable length genomes. In addition to providing a rationale for variable length crossover it also provides a genotypic similarity metric for variable length genomes enabling standard niche formation techniques to be used with variable length genomes. Unlike other variable length crossover techniques which consider genomes to be rigid inflexible arrays and where some or all of the crossover points are randomly selected, the SVLC algorithm considers genomes to be flexible and chooses non-random crossover points based on the common parental sequence similarity. The SVLC Algorithm recurrently "glues" or synapses homogenous genetic sub-sequences together. This is done in such a way that common parental sequences are automatically preserved in the offspring with only the genetic differences being exchanged or removed, independent of the length of such differences. In a variable length test problem the SVLC algorithm is shown to outperform current variable length crossover techniques. The SVLC algorithm is also shown to work in a more realistic robot neural network controller evolution application.

Non-quantized minimum free energy in untranslated region exons

In an attempt to improve automated gene prediction in the untranslated region of a gene, we completed an in-depth analysis of the minimum free energy for 8,689 sub-genetic DNA sequences. We expanded Zhang's classification model and classified each sub-genetic sequence into one of 27 possible motifs. We calculated the minimum free energy for each motif to explore statistical features that correlate to biologically relevant sub-genetic sequences. If biologically relevant sub-genetic sequences fall into distinct free energy quanta it may be possible to characterize a motif based on its minimum free energy. Proper characterization of motifs can lead to greater understanding in automated genefinding, gene variability and the role DNA structure plays in gene network regulation.

Our analysis determined: (1) the average free energy value for exons, introns and other biologically relevant sub-genetic sequences, (2) that these subsequences do not exist in distinct energy quanta, (3) that introns exist however in a tightly coupled average minimum free energy quantum compared to all other biologically relevant sub-genetic sequence types, (4) that single exon genes demonstrate a higher stability than exons which span the entire coding sequence as part of a multi-exon gene and (5) that all motif types contain a free energy global minimum at approximately nucleotide position 1,000 before reaching a plateau. These results should be relevant to the biochemist and bioinformatician seeking to understand the relationship between sub-genetic sequences and the information behind them.

Microfacies and sequence stratigraphy of the Amapa Formation, Late Paleocene to Early Eocene, Foz do Amazonas Basin, Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Seqüência Ordovício-Siluriana e Devoniana no Flanco Norte da Bacia do Paraná

Two stratigraphic sequences characterize the basal units of the Paraná basin. The Ordovician-Silurian sequence overlie directly the Neoproterozoic basement and consists of a 55m-thick unit of coarse-grained sandstones, diamictites, fossiliferous shales and fine-grained micaceous sandstones. The Alto Garças Formation constitutes the base of the sequence and is made of coarse-grained, massive and reddish sandstones associated with conglomeratic lenses. Diamictites with pebbles of diverse composition in siltic and arenaceous matrix were deposited during the Ordovician-Silurian glaciation. Whenever the basal sandstones are absent, the diamictites directly overlie the basement. The diamictites were previously included in the Vila Maria Formation. However our study revealed that they are part of the Iapó Formation. A transgressive event following the glaciation is marked by the deposition of the Vila Maria Formation, which is characterized by fossiliferous (mollusks, brachiopods, cryptospores and microplankton) and laminated shales and siltstones, grading upward to fine-grained micaceous sandstones with hummocky cross stratification. Layers containing trace fossils (Anthrophycus) occur at the transition between the siltstones and the sandstones. The Devonian sequence is represented by 80-170 meters thick sandstones of the Furnas Formation (lower unit) and a sucession of sandstones, siltstones and shales of the Ponta Grossa Formation (upper unit). Unlike other areas of the Paraná Basin, the Ponta Grossa Formation is characterized by coarsening-upward succession beginning with fine sandstones and grading upward to coarse and very-coarse sandstone beds. Cretaceous modifying tectonics affected the Paleozoic sequences, which are cut by a series of faults, in some cases showing displacements greater than 500 meters.

A formação Irati (Grupo Passa Dois, Permiano, Bacia do Paraná) no furo de sondagem FP-01-PR (Sapopema, PR)

Pós-graduação em Geologia Regional - IGCE

Estratigrafia de seqüências das formações Serra Alta, Teresina e Rio do Rasto (permiano, Bacia do Paraná) na porção nordeste do Paraná e centro-sul de São Paulo

Pós-graduação em Geologia Regional - IGCE

Análise tectono-estratigráfica das sequências permotriassica e jurocretácea da bacia Chacoparanense Uruguaia (Cuenca Norte)

Pós-graduação em Geologia Regional - IGCE