Thesis (Ph. D.)--Cornell University, May, 2008. / Vita. Includes bibliographical references (leaves 162-177).

Background: Genetic recombination is a driving force in genome evolution. Among viruses it has a dual role. For genomes with higher fitness, it maintains genome integrity in the face of high mutation rates. Conversely, for genomes with lower fitness, it provides immediate access to sequence space that cannot be reached by mutation alone. Understanding how recombination impacts the cohesion and dissolution of individual whole genomes within viral sequence space is poorly understood across double-stranded DNA bacteriophages (a.k.a phages) due to the challenges of obtaining appropriately scaled genomic datasets. Results: Here we explore the role of recombination in both maintaining and differentiating whole genomes of 142 wild double-stranded DNA marine cyanophages. Phylogenomic analysis across the 51 core genes revealed ten lineages, six of which were well represented. These phylogenomic lineages represent discrete genotypic populations based on comparisons of intra-and inter-lineage shared gene content, genome-wide average nucleotide identity, as well as detected gaps in the distribution of pairwise differences between genomes. McDonald-Kreitman selection tests identified putative niche-differentiating genes under positive selection that differed across the six well-represented genotypic populations and that may have driven initial divergence. Concurrent with patterns of recombination of discrete populations, recombination analyses of both genic and intergenic regions largely revealed decreased genetic exchange across individual genomes between relative to within populations. Conclusions: These findings suggest that discrete double-stranded DNA marine cyanophage populations occur in nature and are maintained by patterns of recombination akin to those observed in bacteria, archaea and in sexual eukaryotes.

Thesis (Ph. D.)--Cornell University, May, 2008. / Vita. Includes bibliographical references (leaves 125-133).

Background: Cacao swollen shoot virus (CSSV), Cacao swollen shoot CD virus (CSSCDV), and Cacao swollen shoot Togo A virus (CSSTAV) cause cacao swollen shoot disease (CSSD) in West Africa. During 2000-2003, leaf and shoot-swelling symptoms and rapid tree death were observed in cacao in Cote d'Ivoire and Ghana. Molecular tests showed positive infection in only similar to 50-60% of symptomatic trees, suggesting the possible emergence of an unknown badnavirus. Methods: The DNA virome was determined from symptomatic cacao samples using Illumina-Hi Seq, and sequence accuracy was verified by Sanger sequencing. The resultant 14, and seven previously known, full-length badnaviral genomic and RT-RNase H sequences were analyzed by pairwise distance analysis to resolve species relationships, and by Maximum likelihood (ML) to reconstruct phylogenetic relationships. The viral coding and non-coding sequences, genome organization, and predicted conserved protein domains (CPDs) were identified and characterized at the species level. Results: The 21 CSSD-badnaviral genomes and RT-RNase H sequences shared 70-100% and 72-100% identity, respectively. The RT-RNase H analysis predicted four species, based on an >= 80% species cutoff. The ML genome sequence tree resolved three well-supported clades, with >= 70% bootstrap, whereas, the RT-RNase H phylogeny was poorly resolved, however, both trees grouped CSSD isolates within one large clade, including the newly discovered Cacao red vein virus (CRVV) proposed species. The genome arrangement of the four species consists of four, five, or six predicted open reading frames (ORFs), and the CPDs have similar architectures. By comparison, two New World cacao-infecting badnaviruses encode four ORFs, and harbor CPDs like the West African species. Conclusions: Three previously recognized West African cacao-infecting badnaviral species were identified, and a fourth, previously unidentified species, CRVV, is described for the first time. The CRVV is a suspect causal agent of the rapid decline phenotype, however Koch's Postulates have not been proven. To reconcile viral evolutionary with epidemiology considerations, more detailed information about CSSD-genomic variability is essential. Also, the functional basis for the multiple genome arrangements and subtly distinct CPD architectures among cacao-infecting badnaviruses is poorly understood. New knowledge about functional relationships may help explain the diverse symptomatologies observed in affected cacao trees.

No description available.

La reconnaissance spécifique du génome viral et son encapsidation est une étape cruciale pour l’assemblage de particules virales. Chez SPP1, comme chez d’autres bactériophages à queue, le moteur moléculaire qui encapside le génome viral est composé de la terminase, une enzyme hétéro-oligomérique qui possède une activité ATPasique et nucléasique, et de la protéine portale, un oligomère cyclique par lequel l’ADN viral est transloqué. Dans un grand nombre de ses virus, l’encapsidation de l’ADN est initiée par la reconnaissance et le clivage d’une séquence spécifique nommée « pac ». C’est un évènement qui se produit une seule fois au début d’une série de cycles d’encapsidation processive à partir d’un concatémère issu de la réplication du génome du phage. La région pac de SPP1 contient deux séquences (pacL et pacR) où TerS (gp1) se lie entourant la région (pacC) où TerL (gp2) coupe l’ADN de SPP1.Ici, nous montrons qu’une région de la séquence pacL et qu’un motif polyadénine de pacR agissent ensemble pour promouvoir le clivage en pacC. La dégénération de la région pacC n’a pas montré d’effet sur que le clivage endonucléolytique qui a lieu à une position bien définie de pacC avec une précision de ~6 pb. Des études avec des phages proches de SPP1 ont montré une conservation dans la position du clivage, malgré des variations dans pacC, pacR ou dans la distance entre pacL et pacC. Les données sont compatibles avec un modèle dans lequel TerS interagit spécifiquement avec la région pacL, sur laquelle le multimère cyclique TerS doit s’enrouler, et le motif polyadénine de la région pacR. Le complexe nucléoprotéique résultant va créer un contexte structural qui permet de recruter et positionner le domaine nucléase de TerL pour une coupure très précise sur pacC sans spécificité de séquence. / The specific recognition of the viral genome and its packaging is a critical step in viral particle assembly. In SPP1, as in many tailed bacteriophages, the macromolecular motor that encapsidates viral DNA is composed of terminase, a hetero-oligomeric enzyme possessing ATPase and nuclease activities, and of portal protein, a cyclic oligomer through which DNA is translocated. In a large number of these viruses, DNA packaging is initiated by recognition and cleavage of a specific sequence pac. This event occurs once at the beginning of a series of processive encapsidation events along a substrate concatemer of replicated phage genomes. The SPP1 pac region has two sequences where TerS (gp1) binds (pacL and pacR) flanking the segment where TerL (gp2) cleaves the SPP1 DNA (pacC). Here we show that a sequence segment of pacL and a poly-adenine motif in pacR act together to promote cleavage at pacC. Extensive degeneration of pacC sequence has no detectable effect in pac cleavage. The endonucleolytic cut occurs at a defined position with a precision of ~6 bp. Studies with SPP1-related phages show conservation of the cut position, irrespectively of sequence variation in pacC, in pacR or changes in pacL-pacC distance. The data is compatible with a model in which TerS interacts specifically with a region of pacL that probably wraps around the TerS cyclical multimer, and a poly-A tract in pacR. The resulting nucleoprotein complex architecture positions TerL for accurate cleavage at pacC without specific sequence requirement.

Glioblastoma multiforme (GBM) is a deadly grade IV brain tumor characterized by a heterogeneous population of cells that are drug resistant, aggressive, and infiltrative. The current standard of care, which has not changed in over a decade, only provides GBM patients with 12-14 months survival post diagnosis. We asked if the addition of a novel endoplasmic reticulum (ER) stress inducing agent, JLK1486, to the standard chemotherapy, temozolomide (TMZ), which induces DNA double strand breaks (DSBs), would enhance TMZ’s efficacy. Because GBMs rely on the ER to mitigate their hypoxic environment and DNA repair to fix TMZ induced DSBs, we reasoned that DSBs occurring during heightened ER stress would be deleterious. Treatment of GBM cells with TMZ+JLK1486 decreased cell viability and increased cell death due to apoptosis. We found that TMZ+JLK1486 prolonged ER stress induction, as indicated by elevated ER stress marker BiP, ATF4, and CHOP, while sustaining activation of the DNA damage response pathway. This combination produced unresolved DNA DSBs due to RAD51 reduction, a key DNA repair factor. The combination of TMZ+JLK1486 is a potential novel therapeutic combination and suggests an inverse relationship between ER stress and DNA repair pathways.

Elastic properties of carbon nanotubes (CNT), boron nitride nanotubes (BNNT), double stranded DNA (dsDNA), paranemic-juxtapose crossover (PX-JX) DNA and dendrimer bound DNA are discussed in this thesis. Structural phase transitions of nucleic acids induced by external force, carbon nanotubes and graphene substrate are also studied extensively. Electrostatic interactions have a strong effect on the elastic properties of BNNTs due to large partial atomic charges on boron and nitrogen atoms. We have computed Young’s modulus (Y ) and shear modulus (G) of BNNT and CNT as a function of the nanotube radius and partial atomic charges on boron and nitrogen atoms using molecular mechanics calculation. Our calculation shows that Young’s modulus of BNNTs increases with increase in magnitude of the partial atomic charges on B and N atoms and can be larger than the Young’s modulus of CNTs of same radius. Shear modulus, on the other hand depends weakly on the magnitude of partial atomic charges and is always less than the shear modulus of the CNT. The values obtained for Young’s modulus and shear modulus are in excellent agreement with the available experimental results. We also study the elasticity of dsDNA using equilibrium fluctuation methods as well as nonequilibrium stretching simulations. The results obtained from both methods quantitatively agree with each other. The end-to-end length distribution P(ρ) and angle distribution P(θ) of the dsDNA has a Gaussian form which gives stretch modulus (γ1) to be 708 pN and persistence length (Lp) to be 42 nm, respectively. When dsDNA is stretched along its helix axis, it undergoes a large conformational change and elongates about 1.7 times its initial contour length at a critical force. Applying a force perpendicular to the DNA helix axis, dsDNA gets unzipped and separated into two single-stranded DNA (ssDNA). DNA unzipping is a fundamental process in DNA replication. As the force at one end of the DNA is increased the DNA starts melting above a critical force depending on the pulling direction. The critical force fm , at which dsDNA melts completely decreases as the temperature of the system is increased. The melting force in the case of unzipping is smaller compared to the melting force when the dsDNA is pulled along the helical axis. In the case of melting through unzipping, the double-strand separation has jumps which correspond to the different energy minima arising due to sequence of different base-pairs. Similar force-extension curve has also been observed when crossover DNA molecules are stretched along the helix axis. In the presence of mono-valent Na+ counterions, we find that the stretch modulus (γ1 ) of the paranemic crossover (PX) and its topoisomer juxtapose (JX) DNA structure is significantly higher (30 %) compared to normal B-DNA of the same sequence and length. When the DNA motif is surrounded by a solvent of divalent Mg2+ counterions, we find an enhanced rigidity compared to in Na+ environment due to the electrostatic screening effects arising from the divalent nature of Mg2+ counterions. This is the first direct determination of the mechanical strength of these crossover motifs which can be useful for the design of suitable DNA motifs for DNA based nanostructures and nanomechanical devices with improved structural rigidity. Negatively charged DNA can be compacted by positively charged dendrimer and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. When the dsDNA is compacted by dendrimer, the stretch modulus, γ1 and persistence length, Lp decreases dramatically due to backbone charge neutralization of dsDNA by dendrimer. We also study the effect of CNT and graphene substrate on the elastic as well as adsorption properties of small interfering RNA (siRNA) and dsDNA. Our results show that siRNA strongly binds to CNT and graphene surface via unzipping its base-pairs and the propensity of unzipping increases with the increase in the diameter of the CNTs and is maximum on graphene. The unzipping and subsequent wrapping events are initiated and driven by van der Waals interactions between the aromatic rings of siRNA nucleobases and the CNT/graphene surface. However, dsDNA of the same sequence undergoes much less unzipping and wrapping on the CNT/graphene due to smaller interaction energy of thymidine of dsDNA with the CNT/graphene compared to that of uridine of siRNA. Unzipping probability distributions fitted to single exponential function give unzipping time (τ) of the order of few nanoseconds which decrease exponentially with temperature. From the temperature variation of unzipping time we estimate the free energy barrier to unzipping. We have also investigated the binding of siRNA to CNT by translocating siRNA inside CNT and find that siRNA spontaneously translocates inside CNT of various diameters and chiralities. Free en- ergy profiles show that siRNA gains free energy while translocating inside CNT and the barrier for siRNA exit from CNT ranges from 40 to 110 kcal/mol depending on CNT chirality and salt concentration. The translocation time τ decreases with the increase of CNT diameter having a critical diameter of 24 A for the translocation. After the optimal binding of siRNA to CNT/graphene, the complex is very stable which can serve as siRNA delivery agent for biomedical applications. Since siRNA has to undergo unwinding process in the presence of RNA-induced silencing complex, our proposed delivery mechanism by single wall CNT possesses potential advantages in achieving RNA interference (RNAi).

DNA double-strand break (DSB) repair is essential for maintenance of genome stability. However, the compaction of the eukaryotic genome into chromatin creates an inherent barrier to any DNA-mediated event, such as during DNA repair. This demands that there be mechanisms to modify the chromatin structure and thus access DNA. Recent work has implicated a host of chromatin regulators in the DNA damage response and several functional roles have been defined. Yet the mechanisms that control their recruitment to DNA lesions, and their relationship with concurrent histone modifications, remain unclear. We find that efficient DSB recruitment of many yeast chromatin regulators is cell-cycle dependent. Furthering this, we find recruitment of the INO80, SWR-C, NuA4, SWI/SNF, and RSC enzymes is inhibited by the non-homologous end joining machinery, and that their recruitment is controlled by early steps of homologous recombination. Strikingly, we find no significant role for H2A.X phosphorylation (γH2AX) in the recruitment of chromatin regulators, but rather that their recruitment coincides with reduced levels of γH2AX. We go on to determine the chromatin remodeling enzyme Fun30 functions in histone dynamics surround a DSB, but does not significantly affect γH2AX dynamics. Additionally, we describe a conserved functional interaction among the chromatin remodeling enzyme, SWI/SNF, the NuA4 and Gcn5 histone acetyltransferases, and phosphorylation of histone H2A.X. Specifically, we find that the NuA4 and Gcn5 enzymes are both required for the robust recruitment of SWI/SNF to a DSB, which in turn promotes the phosphorylation of H2A.X.

No description available.