Leveraging EST Evidence to Automatically Predict Alternatively Spliced Genes, Master\u27s Thesis, December 2006

Current methods for high-throughput automatic annotation of newly sequenced genomes are largely limited to tools which predict only one transcript per gene locus. Evidence suggests that 20-50% of genes in higher eukariotic organisms are alternatively spliced. This leaves the remainder of the transcripts to be annotated by hand, an expensive time-consuming process. Genomes are being sequenced at a much higher rate than they can be annotated. We present three methods for using the alignments of inexpensive Expressed Sequence Tags in combination with HMM-based gene prediction with N-SCAN EST to recreate the vast majority of hand annotations in the D.melanogaster genome. In our first method, we “piece together” N-SCAN EST predictions with clustered EST alignments to increase the number of transcripts per locus predicted. This is shown to be a sensitve and accurate method, predicting the vast majority of known transcripts in the D.melanogaster genome. We present an approach of using these clusters of EST alignments to construct a Multi-Pass gene prediction phase, again, piecing it together with clusters of EST alignments. While time consuming, Multi-Pass gene prediction is very accurate and more sensitive than single-pass. Finally, we present a new Hidden Markov Model instance, which augments the current N-SCAN EST HMM, that predicts multiple splice forms in a single pass of prediction. This method is less time consuming, and performs nearly as well as the multi-pass approach

Elastic network models capture the motions apparent within ensembles of RNA structures

The role of structure and dynamics in mechanisms for RNA becomes increasingly important. Computational approaches using simple dynamics models have been successful at predicting the motions of proteins and are often applied to ribonucleo-protein complexes but have not been thoroughly tested for well-packed nucleic acid structures. In order to characterize a true set of motions, we investigate the apparent motions from 16 ensembles of experimentally determined RNA structures. These indicate a relatively limited set of motions that are captured by a small set of principal components (PCs). These limited motions closely resemble the motions computed from low frequency normal modes from elastic network models (ENMs), either at atomic or coarse-grained resolution. Various ENM model types, parameters, and structure representations are tested here against the experimental RNA structural ensembles, exposing differences between models for proteins and for folded RNAs. Differences in performance are seen, depending on the structure alignment algorithm used to generate PCs, modulating the apparent utility of ENMs but not significantly impacting their ability to generate functional motions. The loss of dynamical information upon coarse-graining is somewhat larger for RNAs than for globular proteins, indicating, perhaps, the lower cooperativity of the less densely packed RNA. However, the RNA structures show less sensitivity to the elastic network model parameters than do proteins. These findings further demonstrate the utility of ENMs and the appropriateness of their application to well-packed RNA-only structures, justifying their use for studying the dynamics of ribonucleo-proteins, such as the ribosome and regulatory RNAs

The immune-modulating pregnancy-specific glycoproteins evolve rapidly and their presence correlates with hemochorial placentation in primates

BACKGROUND Pregnancy-specific glycoprotein (PSG) genes belong to the carcinoembryonic antigen (CEA) gene family, within the immunoglobulin gene superfamily. In humans, 10 PSG genes encode closely related secreted glycoproteins. They are exclusively expressed in fetal syncytiotrophoblast cells and represent the most abundant fetal proteins in the maternal blood. In recent years, a role in modulation of the maternal immune system possibly to avoid rejection of the semiallogeneic fetus and to facilitate access of trophoblast cells to maternal resources via the blood system has been suggested. Alternatively, they could serve as soluble pathogen decoy receptors like other members of the CEA family. Despite their clearly different domain organization, similar functional properties have also been observed for murine and bat PSG. As these species share a hemochorial type of placentation and a seemingly convergent formation of PSG genes during evolution, we hypothesized that hemochorial placentae support the evolution of PSG gene families. RESULTS To strengthen this hypothesis, we have analyzed PSG genes in 57 primate species which exhibit hemochorial or epitheliochorial placentation. In nearly all analyzed apes some 10 PSG genes each could be retrieved from genomic databases, while 6 to 24 PSG genes were found in Old World monkey genomes. Surprisingly, only 1 to 7 PSG genes could be identified in New World monkeys. Interestingly, no PSG genes were found in more distantly related primates with epitheliochorial placentae like lemurs and lorises. The exons encoding the putative receptor-binding domains exhibit strong selection for diversification in most primate PSG as revealed by rapid loss of orthologous relationship during evolution and high ratios of nonsynonymous and synonymous mutations. CONCLUSION The distribution of trophoblast-specific PSGs in primates and their pattern of selection supports the hypothesis that PSG are still evolving to optimize fetal-maternal or putative pathogen interactions in mammals with intimate contact of fetal cells with the immune system of the mother like in hemochorial placentation

Interview with Robert Zimmermann

In this interview with Julia Stringfellow, Robert Zimmermann, LU class of 1953, discusses his time as a student.https://lux.lawrence.edu/oralhistories/1020/thumbnail.jp

Coevolution of paired receptors in Xenopus carcinoembryonic antigen-related cell adhesion molecule families suggests appropriation as pathogen receptors

BACKGROUND: In mammals, CEACAM1 and closely related members represent paired receptors with similar extracellular ligand-binding regions and cytoplasmic domains with opposing functions. Human CEACAM1 and CEACAM3 which have inhibitory ITIM/ITSM and activating ITAM-like motifs, respectively, in their cytoplasmic regions are such paired receptors. Various bacterial pathogens bind to CEACAM1 on epithelial and immune cells facilitating both entry into the host and down-regulation of the immune response whereas interaction with granulocyte-specific CEACAM3 leads to their uptake and destruction. It is unclear whether paired CEACAM receptors also exist in other vertebrate clades. RESULTS: We identified more than 80 ceacam genes in Xenopus tropicalis and X. laevis. They consist of two subgroups containing one or two putative paired receptor pairs each. Analysis of genomic sequences of paired receptors provide evidence that their highly similar ligand binding domains were adjusted by recent gene conversion events. In contrast, selection for diversification is observed among inhibitory receptor orthologs of the two frogs which split some 60 million years ago. The allotetraploid X. laevis arose later by hybridization of two closely related species. Interestingly, despite the conservation of the genomic landscape surrounding the homeologous ceacam loci only one locus resembles the one found in X. tropicalis. From the second X. laevis locus more than 80 % of the ceacam genes were lost including 5 of the 6 paired receptor genes. This suggests that once the gene for one of the paired receptors is lost the remaining gene cluster degrades rapidly probably due to lack of selection pressure exerted by pathogens. CONCLUSIONS: The presence of paired receptors and selection for diversification suggests that also in amphibians CEACAM1-related inhibitory proteins are or were used as pathogen receptors

Large spheres motion in a non homogeneous turbulent flow

We investigate the dynamics of very large particles freely advected in a turbulent von Karman flow. Contrary to other experiments for which the particle dynamics is generally studied near the geometrical center of the flow, we track the particles in the whole experiment volume. We observe a strong influence of the mean structure of the flow that generates an unexpected large-scale sampling effect for the larger particles studied; contrary to neutrally buoyant particles of smaller yet finite sizes that exhibit no preferential concentration in homogeneous and isotropic turbulence (Fiabane et al., Phys. Rev. E 86(3), 2012). We find that particles whose diameter approaches the flow integral length scale explore the von Karman flow non-uniformly, with a higher probability to move in the vicinity of two tori situated near the poloidal neutral lines. This preferential sampling is quite robust with respect to changes of any varied parameters: Reynolds number, particle density and particle surface roughness

Tracking the dynamics of translation and absolute orientation of a sphere in a turbulent flow

We study the 6-dimensional dynamics -- position and orientation -- of a large sphere advected by a turbulent flow. The movement of the sphere is recorded with 2 high-speed cameras. Its orientation is tracked using a novel, efficient algorithm; it is based on the identification of possible orientation `candidates' at each time step, with the dynamics later obtained from maximization of a likelihood function. Analysis of the resulting linear and angular velocities and accelerations reveal a surprising intermittency for an object whose size lies in the integral range, close to the integral scale of the underlying turbulent flow

Playing Muller Games in a Hurry

This work studies the following question: can plays in a Muller game be stopped after a finite number of moves and a winner be declared. A criterion to do this is sound if Player 0 wins an infinite-duration Muller game if and only if she wins the finite-duration version. A sound criterion is presented that stops a play after at most 3^n moves, where n is the size of the arena. This improves the bound (n!+1)^n obtained by McNaughton and the bound n!+1 derived from a reduction to parity games

MAVENs: Motion analysis and visualization of elastic networks and structural ensembles

<p>Abstract</p> <p>Background</p> <p>The ability to generate, visualize, and analyze motions of biomolecules has made a significant impact upon modern biology. Molecular Dynamics has gained substantial use, but remains computationally demanding and difficult to setup for many biologists. Elastic network models (ENMs) are an alternative and have been shown to generate the dominant equilibrium motions of biomolecules quickly and efficiently. These dominant motions have been shown to be functionally relevant and also to indicate the likely direction of conformational changes. Most structures have a small number of dominant motions. Comparing computed motions to the structure's conformational ensemble derived from a collection of static structures or frames from an MD trajectory is an important way to understand functional motions as well as evaluate the models. Modes of motion computed from ENMs can be visualized to gain functional and mechanistic understanding and to compute useful quantities such as average positional fluctuations, internal distance changes, collectiveness of motions, and directional correlations within the structure.</p> <p>Results</p> <p>Our new software, MAVEN, aims to bring ENMs and their analysis to a broader audience by integrating methods for their generation and analysis into a user friendly environment that automates many of the steps. Models can be constructed from raw PDB files or density maps, using all available atomic coordinates or by employing various coarse-graining procedures. Visualization can be performed either with our software or exported to molecular viewers. Mixed resolution models allow one to study atomic effects on the system while retaining much of the computational speed of the coarse-grained ENMs. Analysis options are available to further aid the user in understanding the computed motions and their importance for its function.</p> <p>Conclusion</p> <p>MAVEN has been developed to simplify ENM generation, allow for diverse models to be used, and facilitate useful analyses, all on the same platform. This represents an integrated approach that incorporates all four levels of the modeling process - generation, evaluation, analysis, visualization - and also brings to bear multiple ENM types. The intension is to provide a versatile modular suite of programs to a broader audience. MAVEN is available for download at <url>http://maven.sourceforge.net</url>.</p