Chain topology has a profound impact on the flow behavior of single macromolecules. For circular polymers, the absence of free ends results in a unique chain architecture compared to linear or branched chains, thereby generating distinct molecular dynamics. Here, we report the direct observation of circular DNA dynamics in transient and steady flows for molecular sizes spanning the range of 25.0−114.8 kilobase pairs (kbp). Our results show that the longest relaxation times of the rings follow a power-law scaling relation with molecular weight that differs from that of linear chains. Also, relative to their linear counterparts, circular DNA molecules show a shifted coil-to-stretch transition and less diverse "molecular individualism" behavior as evidenced by their conformational stretching pathways. These results show the impact of chain topology on dynamics and reveal commonalities in the steady state behavior of circular and linear DNA that extends beyond chain architecture.

Dickeya dadantii is a plant-pathogenic enterobacterium responsible for the soft rot disease of many plants of economic importance. We present here the sequence of strain 3937, a strain widely used as a model system for research on the molecular biology and pathogenicity of this group of bacteria. Dickeya dadantii, formerly Erwinia chrysanthemi (11), is the causative agent of soft rot disease in a wide range of plant species, including many economically important crops (10). Soft rot results from the maceration of plant tissues following degradation of pectin, the major component of primary cell walls (7). D. dadantii is a devastating opportunistic pathogen in storage organs and fleshy tissues, particularly when compromised by bruising, excess water, low oxygen levels, or high temperatures. D. dadantii is also associated with systemic infections, vascular disorders, foliar necroses, and latent infections in growing plants. We sequenced and annotated the complete genome of Dickeya dadantii strain 3937, a strain widely used as a model system for research on the molecular biology and pathogenicity of this group of bacteria. Two whole-genome shotgun libraries were prepared with plasmid pHOS2 with target insert sizes of 2 to 3 kb and 10 to 12 kb. We collected approximately 67,000 dual-end sequences, 67% from small-insert clones and 33% from the larger insert library. Sequences were assembled into contigs using the Celera assembler (9), and this assembly was transferred to SeqMan II (Lasergene) for finishing. Primer walking was employed to close gaps covered by clones available from the shotgun libraries. The remaining gaps were closed by sequencing PCR products generated using primers designed from the ends of assembled and ordered contigs. PCR products spanning each rRNA operon were sequenced separately to resolve sequence differences between copies. We used Glimmer 2.0 (3) for initial prediction of protein coding regions. We added, deleted, and revised endpoints of genes based on comparisons to other genomes, genes, and proteins in the NCBI databases. tRNA sequences were identified using tRNAscan-SE (8) with additional examination to identify specific tRNAs not distinguishable by their anticodons alone. rRNA genes were identified by comparison to other enterobacterial sequences using

We have measured the dynamics of completely monodisperse (PDI = 1.0) ultrahigh-molecular-weight linear lambda (λ) DNA solutions as a function of concentration. Due to the very high molecular weight of the DNA, M n = M w > 30 million g/mol, we were able to study the dynamic properties of well-entangled systems even in very dilute (low-concentration) conditions. We report the linear rheology by conducting dynamic oscillatory measurements well into the entanglement regime (11 < C* < 90), where C* is the overlap concentration. The tests are reported in good solvent conditions. Upon comparing our results with previously reported data in the literature by Teixeira et al. [Macromolecules 2007, 40 (7), 2461−2476 and reproducing their data, we can confirm their measurements to have been conducted in the nonlinear regime. This leads to the conclusion that the lambda DNA exhibits extreme strain sensitivity in the observed dynamics, and this induces the earlier onset of nonlinearity as the angular frequency decreases. The time−concentration superposition (TCS) was found to be valid in the terminal zone, which permitted the evaluation of ∼9 decades of dynamics in the mastercurve. The concentration dependence of the time− concentration shift factors (vertical and horizontal) was found to be in good agreement with the plateau moduli and the crossover frequency scaling. A concentration dependence of plateau modulus G N 0 ∼ C 2.29 is obtained from the dynamic tests. The plateau modulus scaling is consistent with the blob model for entangled polymer solutions. The terminal relaxation time shows a change like the unentangled-to-entangled crossover in synthetic polymer solutions from τ d ∼ C 1.1 and τ d ∼ C 3.53 at around 1 mg/mL (24C*). A very high concentration dependence of the zero-shear viscosity, η 0 ∼ C 5.5 , is estimated for the high-concentration samples. We interpret the concentration-dependent scaling to be in an entangled regime observed only in very high molecular weight solutions at sufficiently high concentrations. A Likhtman−McLeish model was used to fit the LVE with the constraint release parameter, c ν , fixed at 1 and 10. The Likhtman−McLeish model does not seem to capture all of the physical processes in the dynamics, and a good fit was not obtained, particularly for the higher-concentration samples though the fit quality improved with the greater constraint release parameter magnitude. Entanglement density predicted by the Likhtman−McLeish model scaled linearly with the entanglement density calculated by the blob model for solutions. The entangled dynamics is possibly nonreptative as reptation or its derivative models do not predict the observed strong nonlinearity and the high susceptibility of the system to strain.

Batrachochytrium dendrobatidis is a fungal pathogen of amphibians that is increasingly implicated as a major cause of large-scale mortalities of amphibian species worldwide. Previous studies indicate that motile zoospores of B. dendrobatidis colonize the keratinized tissues of susceptible amphibians. Infections spread to adults and cause destruction of epidermal tissue. In an effort to understand how the chytrid cues into its host we developed an assay to study chemotaxis in the fungus. Here we show that zoospores exhibit positive movement toward a variety of attractants including sugars, proteins and amino acids. These observations suggest that the chytrid can respond to nutritional cues, including those of host origin. Implications of these observations to amphibian susceptibility to infection and chytrid virulence are discussed.

Trauma patients (TPs) are highly susceptible to infections, which often lead to sepsis. Among the numerous causative agents, Pseudomonas aeruginosa is especially important, as P. aeruginosa sepsis is often fatal. Understanding the mechanism of its pathogenesis in bloodstream infections is imperative; however, this mechanism has not been previously described. To examine the effect of trauma-induced changes in blood on the expression of P. aeruginosa genes, we grew strain UCBPP-PA14 (PA14) in blood samples from eight TPs and seven healthy volunteers (HVs). Compared with its growth in blood from HVs, the growth of PA14 in blood from TPs significantly altered the expression of 285 genes. Genes whose expression was significantly increased were related to carbon metabolism, especially malonate utilization and mannitol uptake, and efflux of heavy metals. Genes whose expression was significantly reduced included genes of the type VI secretion system, genes related to uptake and metabolism of amino acids, and genes related to biosynthesis and transport of the siderophores pyoverdine and pyochelin. These results suggest that during systemic infection in trauma patients, and to adapt to the trauma-induced changes in blood, P. aeruginosa adjusts positively and negatively the expression of numerous genes related to carbon metabolism and virulence, respectively. IMPORTANCE While a considerable body of knowledge regarding sepsis in trauma patients is available, the potential influence of trauma-induced changes in the blood of these patients on the pathogenesis of Pseudomonas aeruginosa is basically an unexplored area. Rather than using standard laboratory media, we grew P. aeruginosa in whole blood from either healthy volunteers or trauma patients. The specific changes in the P. aeruginosa transcriptome in response to growth in blood from trauma patients reflect the adaptation of this organism to the bloodstream environment. This knowledge is vital for understanding the strategies this pathogen uses to adapt and survive within the host during systemic infection. Such information will help researchers and clinicians to develop new approaches for treatment of sepsis caused by P. aeruginosa in trauma patients, especially in terms of recognizing the effects of specific therapies (e.g., iron, zinc, or mannitol) on the organism. Further, this information can most likely be extrapolated to all patients with P. aeruginosa septicemia.