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School of Biological Sciences

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https://hdl.handle.net/1853/70750

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College of Sciences

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Center for the Study of Systems Biology

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https://finding-aids.library.gatech.edu/agents/corporate_entities/1131

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Publication Search Results

Now showing 1 - 10 of 107

Lateral gene transfer of pandemic Vibrio parahaemolyticus genomic island genes

(Georgia Institute of Technology, 2008-12-15) Silberger, Daniel James

Vibrio parahaemolyticus is an emerging enteric pathogen. The O3:K6 serotype has become pandemic, and the genome has been sequenced for the RIMD2210633 strain of this serotype (20). The thermostabile direct hemolysin (tdh), thermostabile related hemolysin (trh), and two distinct Type III Secretion Systems (T3SS) have been implicated in virulence. Deletion studies have determined that the T3SS alone are sufficient to induce eukaryotic cell apoptosis. The T3SS loci are found within two separate genomic islands. Because genomic islands are known to be disseminated by Lateral Gene Transfer (LGT), we examined the distribution of the pandemic genomic island genes among clinical and environmental V. parahaemolyticus isolates and also among closely-related environmental Vibrio spp. using primers designed to amplify hemolysins and T3SS effectors previously characterized for V. parahaemolyticus strain RIMD2210633 (23). We also examined the distribution of a hypothetical bacteriocin, encoded by vpa1263, within another genomic island that is similar to the bacteriocins produced by Escherichia coli. Preliminary screens for the bacteriocin gene suggest that many clinical strains and some environmental strains contain vpa1263. PCR screens for the T3SS effector genes have shown that 22% of closely-related environmental Vibrio spp. contain at least one T3SS1 or one T3SS2 effector gene. Sequencing of housekeeping genes is ongoing to confirm these findings.
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

(Georgia Institute of Technology, 2008-12-12) Pandit, Shashi Bhushan ; Skolnick, Jeffrey

Background: Protein tertiary structure comparisons are employed in various fields of contemporary structural biology. Most structure comparison methods involve generation of an initial seed alignment, which is extended and/or refined to provide the best structural superposition between a pair of protein structures as assessed by a structure comparison metric. One such metric, the TM-score, was recently introduced to provide a combined structure quality measure of the coordinate root mean square deviation between a pair of structures and coverage. Using the TM-score, the TM-align structure alignment algorithm was developed that was often found to have better accuracy and coverage than the most commonly used structural alignment programs; however, there were a number of situations when this was not true. Results: To further improve structure alignment quality, the Fr-TM-align algorithm has been developed where aligned fragment pairs are used to generate the initial seed alignments that are then refined using dynamic programming to maximize the TM-score. For the assessment of the structural alignment quality from Fr-TM-align in comparison to other programs such as CE and TMalign, we examined various alignment quality assessment scores such as PSI and TM-score. The assessment showed that the structural alignment quality from Fr-TM-align is better in comparison to both CE and TM-align. On average, the structural alignments generated using Fr-TM-align have a higher TM-score (~9%) and coverage (~7%) in comparison to those generated by TM-align. Fr- TM-align uses an exhaustive procedure to generate initial seed alignments. Hence, the algorithm is computationally more expensive than TM-align. Conclusion: Fr-TM-align, a new algorithm that employs fragment alignment and assembly provides better structural alignments in comparison to TM-align. The source code and executables of Fr- TM-align are freely downloadable at: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/.
Aurora kinase inhibitors synergize with paclitaxel to induce apoptosis in ovarian cancer cells

(Georgia Institute of Technology, 2008-12-11) Scharer, Christopher D. ; Laycock, Noelani ; Osunkoya, Adeboye O. ; Logani, Sanjay ; McDonald, John F. ; Benigno, Benedict B. ; Moreno, Carlos S.

Background: A large percentage of patients with recurrent ovarian cancer develop resistance to the taxane class of chemotherapeutics. While mechanisms of resistance are being discovered, novel treatment options and a better understanding of disease resistance are sorely needed. The mitotic kinase Aurora-A directly regulates cellular processes targeted by the taxanes and is overexpressed in several malignancies, including ovarian cancer. Recent data has shown that overexpression of Aurora-A can confer resistance to the taxane paclitaxel. Methods: We used expression profiling of ovarian tumor samples to determine the most significantly overexpressed genes. In this study we sought to determine if chemical inhibition of the Aurora kinase family using VE-465 could synergize with paclitaxel to induce apoptosis in paclitaxel-resistant and sensitive ovarian cancer cells. Results: Aurora-A kinase and TPX2, an activator of Aurora-A, are two of the most significantly overexpressed genes in ovarian carcinomas. We show that inhibition of the Aurora kinases prevents phosphorylation of a mitotic marker and demonstrate a dose-dependent increase of apoptosis in treated ovarian cancer cells. We demonstrate at low doses that are specific to Aurora-A, VE-465 synergizes with paclitaxel to induce 4.5-fold greater apoptosis than paclitaxel alone in 1A9 cells. Higher doses are needed to induce apoptosis in paclitaxel-resistant PTX10 cells. Conclusion: Our results show that VE-465 is a potent killer of taxane resistant ovarian cancer cells and can synergize with paclitaxel at low doses. These data suggest patients whose tumors exhibit high Aurora-A expression may benefit from a combination therapy of taxanes and Aurora-A inhibition.
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(Georgia Institute of Technology, 2008-12) Ter-Hovhannisyan,Vardges ; Lomsadze, Alexandre ; Chernoff, Yury O. ; Borodovsky, Mark

We describe a new ab initio algorithm, GeneMark-ES version 2, that identifies protein-coding genes in fungal genomes. The algorithm does not require a predetermined training set to estimate parameters of the underlying hidden Markov model (HMM). Instead, the anonymous genomic sequence in question is used as an input for iterative unsupervised training. The algorithm extends our previously developed method tested on genomes of Arabidopsis thaliana, Caenorhabditis elegans, and Drosophila melanogaster. To better reflect features of fungal gene organization, we enhanced the intron submodel to accommodate sequences with and without branch point sites. This design enables the algorithm to work equally well for species with the kinds of variations in splicing mechanisms seen in the fungal phyla Ascomycota, Basidiomycota, and Zygomycota. Upon self-training, the intron submodel switches on in several steps to reach its full complexity. We demonstrate that the algorithm accuracy, both at the exon and the whole gene level, is favorably compared to the accuracy of gene finders that employ supervised training. Application of the new method to known fungal genomes indicates substantial improvement over existing annotations. By eliminating the effort necessary to build comprehensive training sets, the new algorithm can streamline and accelerate the process of annotation in a large number of fungal genome sequencing projects
Bone marrow regeneration follwing tibial marrow ablation in rats is age dependent

(Georgia Institute of Technology, 2008-11-19) Fisher, Maya

Objective: Injuries to the marrow cavity result in rapid bone formation followed by regeneration of the marrow. It is not known whether this process is affected by age, although the quality of marrow is markedly different in young and old animals. To test if marrow restoration differs with age, we used the rat tibial bone marrow ablation model, which has been used to examine calcification, osteointegration of metal implants, and remodeling of bone graft substitutes. Methods: Marrow was ablated in the left tibia of seven rats (rNu/rNu) per time point. At 0,7,14,21,28,35 and 42 days post-surgery, treated tibias and contralateral tibias were harvested and fixed in buffered formalin. Both tibias were scanned using microCT and trabecular and cortical BVF/TV calculated. Mid-sagittal sections of decalcified bones were stained with H&E and BVF/TV calculated. Results: MicroCT analysis of 1-month animals showed increased bone formation on day-7 and on day-21 the marrow was restored. Increased bone was seen in 3-month animals on day-7 and day-14, but it was significantly less than in 1-month rats. By day-21, trabecular bone was reduced by 50%. 10-month animals had less trabecular bone at day-7 and 14, but bone remained in the medullary canal through day-1. Histomorphometry indicated that bone formation peaked at day-7 in 1-month rats with remodeling underway by day-14. Bone formation in 3-month rats also peaked at day-7, but restoration occurred by day-21. However, in 10-month rats, peak bone occurred on day-14, with remodeling on day-28. Conclusions: Aged animals produced less primary bone than younger animals and remodeling was initiated later. Differences in micro-CT and histomorphometric analyses may reflect a reduction in calcification of the osteoid in the 10-month old animals. (Supported by Boston Scientific, Inc.)
Discovery and characterization of KNOX proteins lacking a homeodomain, produced by alternative splicing of KNAT1-like genes in gymnosperms and angiosperms

(Georgia Institute of Technology, 2008-11-17) Sheth, Mili

Homeobox genes encode homeodomain (HD) proteins which function as transcription factors and play an important role in plant and animal development by controlling cell specification and pattern formation. (Knotted1 in Arabidopsis thaliana) KNAT1-like mRNAs referred to as PtKN1(HD+) and mRNA sequences which lack HD region referred as PtKN1(hd-) were cloned from embryos of loblolly pine (Pinus taeda L.). Production of PtKN1(hd-) mRNAs is developmentally regulated and their encoded protein is abundant in mature pine embryos. Both forms of PtKN1 are produced by the same gene which has 5 exons; the regulatory dynamic is between cleavage-polyadenylation or termination within intron 3 to produce PtKN1 mRNA lacking HD sequences and splicing of exon 3 to exon 4 which excludes the 3'UTR/exon3 sequence to create an mRNA which encodes a HD. KNAT1 mRNA in Arabidopsis which lacks HD sequences was identified and characterized. While KNAT1 has been studied for many years, this is the first report of a KNAT1 mRNA lacking HD. KNAT1 mRNA lacking HD sequences was identified for the RS1 gene of maize, a monocotyledon. This is the first report of splicing of KNAT1 genes to produce mRNAs lacking HD sequences. The phenomenon appears to be ubiquitous as it is observed in gymnosperms, and both dicotyledonous and monocotyledonous angiosperms.
Unsupervised and semi-supervised training methods for eukaryotic gene prediction

(Georgia Institute of Technology, 2008-11-17) Ter-Hovhannisyan, Vardges

This thesis describes new gene finding methods for eukaryotic gene prediction. The current methods for deriving model parameters for gene prediction algorithms are based on curated or experimentally validated set of genes or gene elements. These training sets often require time and additional expert efforts especially for the species that are in the initial stages of genome sequencing. Unsupervised training allows determination of model parameters from anonymous genomic sequence with. The importance and the practical applicability of the unsupervised training is critical for ever growing rate of eukaryotic genome sequencing. Three distinct training procedures are developed for diverse group of eukaryotic species. GeneMark-ES is developed for species with strong donor and acceptor site signals such as Arabidopsis thaliana, Caenorhabditis elegans and Drosophila melanogaster. The second version of the algorithm, GeneMark-ES-2, introduces enhanced intron model to better describe the gene structure of fungal species with posses with relatively weak donor and acceptor splice sites and well conserved branch point signal. GeneMark-LE, semi-supervised training approach is designed for eukaryotic species with small number of introns. The results indicate that the developed unsupervised training methods perform well as compared to other training methods and as estimated from the set of genes supported by EST-to-genome alignments. Analysis of novel genomes reveals interesting biological findings and show that several candidates of under-annotated and over-annotated fungal species are present in the current set of annotated of fungal genomes.
Natural selection governs local, but not global, evolutionary gene coexpression networks in Caenorhabditis elegans

(Georgia Institute of Technology, 2008-11-13) Jordan, I. King ; Katz, Lee S. ; Denver, Dee R. ; Streelman, J. Todd

Background. Large-scale evaluation of gene expression variation among Caenorhabditis elegans lines that have diverged from a common ancestor allows for the analysis of a novel class of biological networks – evolutionary gene coexpression networks. Comparative analysis of these evolutionary networks has the potential to uncover the effects of natural selection in shaping coexpression network topologies since C. elegans mutation accumulation (MA) lines evolve essentially free from the effects of natural selection, whereas natural isolate (NI) populations are subject to selective constraints. Results. We compared evolutionary gene coexpression networks for C. elegans MA lines versus NI populations to evaluate the role that natural selection plays in shaping the evolution of network topologies. MA and NI evolutionary gene coexpression networks were found to have very similar global topological properties as measured by a number of network topological parameters. Observed MA and NI networks show node degree distributions and average values for node degree, clustering coefficient, path length, eccentricity and betweeness that are statistically indistinguishable from one another yet highly distinct from randomly simulated networks. On the other hand, at the local level the MA and NI coexpression networks are highly divergent; pairs of genes coexpressed in the MA versus NI lines are almost entirely different as are the connectivity and clustering properties of individual genes. Conclusion. It appears that selective forces shape how local patterns of coexpression change over time but do not control the global topology of C. elegans evolutionary gene coexpression networks. These results have implications for the evolutionary significance of global network topologies, which are known to be conserved across disparate complex systems.
Identification and characterization of a peptide toxin inhibitor of ClC-2 chloride channels

(Georgia Institute of Technology, 2008-11-05) Thompson, Christopher Hal

ClC proteins encompass a large protein family consisting of both voltage-dependent chloride channels and chloride/proton exchangers that are found in both eukaryotes and prokaryotes. These proteins mediate Cl- flux across the plasma membrane or intracellular membranes of many cell types including neurons, epithelial cells, and skeletal muscle in mammals. Mutations in genes encoding these channels also contribute to several human diseases. The mechanism of ion conduction through ClC proteins is becoming better defined, largely due to the availability of a crystal structure of a bacterial ClC transporter. Because crystal structures only capture a snapshot a protein in a single conformation, however, the large conformational changes associated with channel opening and closing have remained largely undefined. In the cation channel field, ion conduction and conformational changes that occur during channel gating have been studied using peptide toxin inhibitors isolated from animal venoms. However, only one peptide toxin inhibitor of a chloride channel of known molecular identity has ever been identified. Georgia anion toxin 1 (GaTx1), inhibits the CFTR chloride channel, which is unrelated to ClC proteins on the levels of both three dimensional structure and primary sequence. Here, we describe the characterization of the inhibitory activity of Leiurus quinquestriatus hebraeus scorpion venom against the ClC-2 chloride channel. We found that the venom from this scorpion contains a peptide component that is capable of inhibiting the ClC-2 chloride channel. This component was isolated using standard chromatography techniques, and found that the active component is a 3.2 kDa peptide composed of 29 amino acids. We showed that the active toxin, Georgia anion toxin 2 (GaTx2), interacts with ClC-2 with an affinity in the picomolar range, and appears to slow channel opening. Finally, GaTx2 is not capable of inhibiting other members of the ClC protein family, other major chloride channels, or voltage-gated potassium channels. This toxin will provide a new tool for structure/function studies of ClC-2, and will hopefully serve as only the first toxin inhibitor available for this protein family.
Hypermutability of Damaged Single-Strand DNA Formed at Double-Strand Breaks and Uncapped Telomeres in Yeast Saccharomyces cerevisiae

(Georgia Institute of Technology, 2008-11) Yang, Yong ; Sterling, Joan ; Storici, Francesca ; Resnick, Michael A. ; Gordenin, Dmitry A.

The major DNA repair pathways operate on damage in double-strand DNA because they use the intact strand as a template after damage removal. Therefore, lesions in transient single-strand stretches of chromosomal DNA are expected to be especially threatening to genome stability. To test this hypothesis, we designed systems in budding yeast that could generate many kilobases of persistent single-strand DNA next to double-strand breaks or uncapped telomeres. The systems allowed controlled restoration to the double-strand state after applying DNA damage. We found that lesions induced by UV-light and methyl methanesulfonate can be tolerated in long single-strand regions and are hypermutagenic. The hypermutability required PCNA monoubiquitination and was largely attributable to translesion synthesis by the error-prone DNA polymerase f. In support of multiple lesions in single-strand DNA being a source of hypermutability, analysis of the UVinduced mutants revealed strong strand-specific bias and unexpectedly high frequency of alleles with widely separated multiple mutations scattered over several kilobases. Hypermutability and multiple mutations associated with lesions in transient stretches of long single-strand DNA may be a source of carcinogenesis and provide selective advantage in adaptive evolution.