Introduction to the CoNLL-2001 Shared Task: Clause Identification

We describe the CoNLL-2001 shared task: dividing text into clauses. We give background information on the data sets, present a general overview of the systems that have taken part in the shared task and briefly discuss their performance

Characterization of the Cyclin Dependent Kinase Complex Bur1-2 and its Interaction with RPA

Gene expression is highly regulated and interconnected to processes like mRNP processing, mRNA export as well as to DNA repair and replication. The first step of gene expression is the transcription of protein coding genes by RNA polymerase II. Transcription is controlled by general transcription factors, the phosphorylation of the C-terminal domain of Rpb1, the largest subunit of RNA polymerase II, and chromatin modifications that allow proper accessibility of the DNA. A major player in these coupling processes is the TREX complex, coupling transcription elongation to the nucleo-cytoplasmic export of the mRNP via the nuclear pore complex. Particularly, the THO subcomplex of TREX has functions in hyperrecombination, nucleotide excision repair and transcription coupled repair. A genetic screen with TREX components, performed to identify genes involved in these processes, lead to the identification of the cyclin dependent kinase Bur1. Bur1 and its cyclin Bur2 are needed for efficient transcription elongation by RNA polymerase II by regulating the methylation of histone tails. Interestingly, Bur1 interacts in vivo with RPA, a single strand DNA binding protein essential for genome stability. This biochemical interaction raised the idea of a novel interconnection between transcription, chromatin modification and genome maintenance. Mutations in the BUR1 as well as in the RFA1 gene lead to sensitivity to drugs that cause DNA damage and replication or transcription stress. Deletion of the C-terminus of Bur1, which is sufficient for the binding to RPA, also renders cells sensitive to those agents. This shows the functional significance of this protein-protein interaction in the cell upon stress induction. However, attempts to identify the DNA repair pathway Bur1 is involved in showed that mutations in BUR1 do not behave epistatic with deletions of specific pathways. This result points to a more general, maybe regulatory role of Bur1 in the response to DNA damage. It is interesting to note that mutations in BUR1 lead to increased genomic instability as they show the appearance of a higher amount and longer persistence of nuclear foci, DNA repair “factories” that contain, among other proteins, Rfa1 and Rad52. Furthermore, RFA1 mutants show decreased levels of histone H3 alone as well as lower levels of histone H3 Lysine 4 trimethylation, a mark for transcription elongation, when combined with a mutation in BUR1. The RFA1 mutant is also impaired in the expression of a β-galactosidase reporter gene, pointing to a function of RPA in transcription. Interestingly, combining BUR1 and RFA1 mutants leads to a lower susceptibility of cells to stress than one of the mutations alone. On the one hand, this could be elucidated by better growth of the double mutant strains upon stress compared to the single mutants. On the other hand, whole genome expression analysis shows that the double mutant strain clusters with the bur1 mutant whereas the rfa1 mutant does not, showing that its expression pattern is closer to the bur1 mutant. Both results show that the protein complexes have antagonistic roles as the combination of both mutations leads to a suppression phenotype based on differential gene expression. Taken together, a function of Bur1 in genome maintenance could be established, as well as an effect of RPA on transcription elongation and chromatin modification. The results provide a possibility to speculate about a coupling of transcription and genome stability mediated by the interaction of Bur1-2 with RPA

Biological aspects of an interesting fossil fish: <i>Paramblypterus duvernoyi</i> (Amblypteridae, Actinopterygii)

Based on three-dimensional models of the skull and body of Paramblypterus duvernoyi, function of the feeding apparatus and potential of locomotion are interpreted. Compared to most other lower actinopterygians, certain modified features regarding the suspensory apparatus, snout bones, gape, dermohyal and suborbital region, and palaloquadrate-maxillary chamber, are present in P. duvernyoi. These features suggest an increased versatility of the skull and/or enlargement of underlying muscles, thus improving the ability of food uptake. The weak, pin-like teeth present in P. duvernoyi suggest a main diet of small or soft-bodied planktonic or benthic invertebrate organisms. Axial locomotion of P. duvernoyi appears to lie within the range of moderate swimming speeds. P. duvernoyi probably had a flat belly indicating that this species lived close to the bottom. Anhand drei-dimensionaler Modelle des Schädels und Körpers von Paramblypterus duvernoyi werden Funktionsweise des Ernährungsapparates und Möglichkeiten der Fortbewegung interpretiert. Im Vergleich mit anderen basalen Actinopterygiern erscheint die Schädelrekonstruktion von P. duvernoyi hinsichtlich des Suspensoriums. der Schnauzenknochen, der Mundöffnung, des Dermohyal- und Suborbitalbereiches, sowie der Palatoquadratum-Maxillare-Kammer abgeleitet. Dies deutet auf eine erhöhte Beweglichkeit in diesen Bereichen und/oder eine Vergrößerung der darunter liegenden Muskeln hin, was vorteilhaft für die Nahrungsaufnahme ist. Die schmalen, stiftförmigen Zähne von P. duvernoyi deuten auf eine Ernährung von kleineren oder weichkörperigen benthischen und planktischen Invertebraten hin. Vermutlich zeichnete sich die axiale Fortbewegungsweise von Paramblypterus durch mäßige mittlere Schwimmgeschwindigkeit aus. Der Bauch von P. duvernoyi war wahrscheinlich abgeflacht, was darauf hinweist, dass diese Art bodenbezogen gelebt hat. doi:10.1002/mmng.20010040109</a

Charge-Exchange Collision Dynamics and Ion Engine Grid Geometry Optimization

The development of a new three-dimensional model for determining the absolute energy distribution of ions at points corresponding to spacecraft surfaces to the side of an ion engine is presented. The ions resulting from elastic collisions, both charge-exchange (CEX) and direct, between energetic primary ions and thermal neutral xenon atoms are accounted for. Highly resolved energy distributions of CEX ions are found by integration over contributions from all points in space within the main beam formed by the primary ions. The sputtering rate due to impingement of these ions on a surface is calculated. The CEX ions that obtain significant energy (10 eV or more) in the collision are responsible for the majority of the sputtering, though this can depend on the specific material being sputtered. In the case of a molybdenum surface located 60 cm to the side of a 30 cm diameter grid, nearly 90% of the sputtering is due to the 5% of ions with the highest collision exit energies. Previous models that do not model collision energetics cannot predict this. The present results agree with other models and predict that the majority of the ion density is due to collisions where little to no energy is transferred. The sputtering model is combined with a grid-structure model in an optimization procedure where the sputtering rate at specified locations is minimized by adjustment of parameters defining the physical shape of the engine grids. Constraints are imposed that require that the deflection of the grid under a specified load does not exceed a maximum value, in order to ensure survivability of the grids during launch. To faciliate faster execution of the calculations, simplifications based on the predicted behavior of the CEX ions are implemented. For diametrically opposed sputtering locations, a rounded barrel-vault shape reduces the expected sputtering rate by up to 30% in comparison to an NSTAR-shaped grid.</p

Memory-Based Shallow Parsing

We present memory-based learning approaches to shallow parsing and apply these to five tasks: base noun phrase identification, arbitrary base phrase recognition, clause detection, noun phrase parsing and full parsing. We use feature selection techniques and system combination methods for improving the performance of the memory-based learner. Our approach is evaluated on standard data sets and the results are compared with that of other systems. This reveals that our approach works well for base phrase identification while its application towards recognizing embedded structures leaves some room for improvement

American Square Dance Vol. 37, No. 4 (Apr. 1982)

Monthly square dance magazine that began publication in 1945

The role of H2A-H2B dimers in the mechanical stability of nucleosomes

Eukaryotic genomes are densely compacted into chromatin, so that they can be contained in the nucleus. Despite the tight packaging genes need to be accessible for normal metabolic activities to occur, such as transcription, repair and replication. These processes are regulated by a vast number of proteins but also by the level of compaction of chromatin. The translocation of motor proteins along DNA produces torsional stress which in turn alters chromatin compaction both upstream and downstream. Few single-molecule studies have investigated the behaviour of nucleosomes when subjected to torsion. The inability to measure the applied torque though represented a major limitation to those reports. The implementation of the rotor bead assay, which allows to directly measure the torque applied in magnetic tweezers experiments, has been hindered by a difficult sample preparation procedure. In order to overcome this limitation an efficient protocol for the insertion of chemical or structural modifications in long DNA substrates was developed. This was then further expanded to allow the introduction of labels in multiple loci and/or both strands and has been used successfully in a number of studies. Furthermore this is the first report of tensile experiments performed on nucleosomes with a histone variant. H2AvD nucleosomes were studied due to the interest in the biological role of H2A.Z-family proteins. Interestingly, the variant nucleosomes appear to bind less DNA and to be evicted from the DNA at lower forces than those observed for canonical nucleosomes. These findings show an important role for the H2A-H2B dimers in the mechanical stability of nucleosomes. Furthermore these results are in agreement with recently proposed models of a dynamic nucleosome, in contrast to the long-standing view of nucleosomes as static structures.:Abstract Table of contents 1 Introduction 1.1 The transforming principle 1.2 Chromatin 1.2.1 Nucleosomes 1.2.2 The 30 nm fibre: a mirage? 1.2.3 Histone code 1.3 Histone variant H2A.Z 1.3.1 H2A.Z and transcription 1.4 Single molecule studies of chromatin 1.4.1 Chromatin under tension 1.4.2 Open nucleosome 1.4.3 Twisted chromatin 1.5 Single molecule techniques 1.5.1 Atomic force microscopy 1.5.2 F\u7foerster resonance energy transfer 1.5.3 Magnetic tweezers 1.5.4 Worm-like chain model 2 Aims of the project 3 Cut and paste method for internal DNA labelling 3.1 Introduction 3.2 Experimental design 3.3 Results 3.3.1 Sequence design and cloning 3.3.2 Labelling and religation efficiency 3.3.3 Structural modifications 3.3.4 Labelling of multiple loci 3.3.5 Opposite-strand labelling 3.4 Discussion 4 Reconstituting chromatin 4.1 Long array of NPSs 4.1.1 Polymer physics applied to molecular cloning 4.1.2 Preventing homologous recombination 4.2 Expression and purification of histone proteins 4.2.1 Protein expression 4.2.2 Inclusions bodies 4.2.3 Histone purification 4.2.4 Octamer reconstitution and isolation 4.2.5 H2AvD 4.3 Reconstitution of nucleosomal arrays and biochemical analysis 4.3.1 Reconstitution procedure 4.3.2 Biochemical analysis 4.4 Tweezers construct with nucleosomes 5 Eviction of nucleosomes 5.1 Nucleosome eviction 5.1.1 A two-stage process 5.1.2 Chromatin fibres 5.1.3 Reassembly of nucleosomes 5.1.4 Distinct populations within nucleosome eviction events 5.1.5 Nicked and supercoilable nucleosomal arrays 5.2 Eviction of H2AvD-nucleosomes 5.2.1 H2AvD-nucleosomes bind less inner turn DNA 5.2.2 H2AvD-nucleosomes evict at lower forces 5.2.3 Likelihood of nucleosome reassembly 5.2.4 Gradual weakening of nucleosomes 5.2.5 Analysis software NucleoStep 5.3 Towards a rotor-bead assay on chromatin 5.4 Discussion 5.4.1 Nucleosome eviction in two stages 5.4.2 The fate of dimers in single molecule experiments 5.4.3 Structural origin and biological relevance of the mechanical properties of H2AvD-nucleosomal core particles 5.4.4 Monolithic or dynamic nucleosomes 6 Conclusions Bibliography Appendix 6.1 Internal labelling Procedure 6.1.1 Cloning 6.1.2 Nicking & cutting 6.1.3 The replace reaction 6.1.4 Purification 6.1.5 Ligation (optional) 6.1.6 Opposite strand labelling 6.1.7 Assessing the results of the labelling reaction 6.2 Chromatin reconstitution 6.2.1 Long array of NPSs 6.2.2 Expression and purification of histone proteins 6.2.3 Reconstitution of nucleosomal arrays and biochemical characterization 6.2.4 Simple Phenol:chloroform isolation of DNA 6.3 Magnetic tweezers experiments 6.3.1 Flow cell assembly 6.3.2 Functionalization of flow cells 6.3.3 Magnetic tweezers and rotor bead measurements 6.3.4 Force calibration List of Figures List of Tables List of publications Acknowledgements Declaration of originalit