Factors influencing lysis time stochasticity in bacteriophage λ

<p>Abstract</p> <p>Background</p> <p>Despite identical genotypes and seemingly uniform environments, stochastic gene expression and other dynamic intracellular processes can produce considerable phenotypic diversity within clonal microbes. One trait that provides a good model to explore the molecular basis of stochastic variation is the timing of host lysis by bacteriophage (phage).</p> <p>Results</p> <p>Individual lysis events of thermally-inducible λ lysogens were observed using a temperature-controlled perfusion chamber mounted on an inverted microscope. Both mean lysis time (MLT) and its associated standard deviation (SD) were estimated. Using the SD as a measure of lysis time stochasticity, we showed that lysogenic cells in controlled environments varied widely in lysis times, and that the level of lysis time stochasticity depended on allelic variation in the holin sequence, late promoter (<it>p</it>_<it>R</it><it>'</it>) activity, and host growth rate. In general, the MLT was positively correlated with the SD. Both lower <it>p</it>_<it>R</it><it>' </it>activities and lower host growth rates resulted in larger SDs. Results from premature lysis, induced by adding KCN at different time points after lysogen induction, showed a negative correlation between the timing of KCN addition and lysis time stochasticity.</p> <p>Conclusions</p> <p>Taken together with results published by others, we conclude that a large fraction of λ lysis time stochasticity is the result of random events following the expression and diffusion of the holin protein. Consequently, factors influencing the timing of reaching critical holin concentrations in the cell membrane, such as holin production rate, strongly influence the mean lysis time and the lysis time stochasticity.</p

A freight transport demand, energy and emission model with technological choices. ESRI Working Paper 669 June 2020.

Reducing energy consumption and emissions from freight transport plays an important role in climate change mitigation. However, there remains a need for enhanced policymaking and research to explore a low carbon future of freight transport. This research establishes a freight transport model to simulate transport demand (tonne kilometre), energy consumption and emissions. The model incorporates macroeconomic factors, policy indicators, technological characteristics, detailed profiles of the vehicle stock and travel distances, and behavioural parameters with discrete based choices. This model is applied to the freight transport sector in Ireland with scenarios running out to 2050. The results show that overall freight transport demand increases substantially from 2015 to 2050. Economy-wide climate policies (i.e. carbon tax) and high fuel prices result in modest reductions in energy consumption and CO2 emissions in freight transport, compared to a baseline. Sectoral measures, such as European CO2 emission performance standards, that aim to improve new vehicle fuel efficiency/emission rates can potentially lead to significant reductions, but such measures face a lag in greening the goods vehicle stock in the short/mid term, and uncertainties in policy compliance and technical barriers in the long run. Notably, in spite of few commercially mature vehicle technologies, adoption of biofuel and alternative freight vehicles are expected to bring additional reductions in future energy consumption and emissions. In all, for a transition to a low carbon future for freight transport, a comprehensive and dynamic policy agenda should be developed to promote low or zero emission vehicles, especially for heavy goods vehicles

GN&C Engineering Best Practices for Human-Rated Spacecraft Systems

The NASA Engineering and Safety Center (NESC) recently completed an in-depth assessment to identify a comprehensive set of engineering considerations for the Design, Development, Test and Evaluation (DDT&E) of safe and reliable human-rated spacecraft systems. Reliability subject matter experts, discipline experts, and systems engineering experts were brought together to synthesize the current "best practices" both at the spacecraft system and subsystems levels. The objective of this paper is to summarize, for the larger Community of Practice, the initial set of Guidance, Navigation and Control (GN&C) engineering Best Practices as identified by this NESC assessment process

Viral Ecology and the Maintenance of Novel Host Use

Viruses can occasionally emerge by infecting new host species. However, the early phases of emergence can hinge upon ecological sustainability of the virus population, which is a product of both within‐host population growth and between‐host transmission. Insufficient growth or transmission can force virus extinction before the latter phases of emergence, where genetic adaptations that improve host use may occur. We examined the early phase of emergence by studying the population dynamics of RNA phages in replicated laboratory environments containing native and novel host bacteria. To predict the breadth of transmission rates allowing viral persistence on each species, we developed a simple model based on in vitro data for phage growth rate over a range of initial population densities on both hosts. Validation of these predictions using serial passage experiments revealed a range of transmission rates for which the native host was a source and the novel host was a sink. In this critical range of transmission rates, periodic exposure to the native host was sufficient for the maintenance of the viral population on the novel host. We argue that this effect should facilitate adaptation by the virus to utilize the novel host—often crucial in subsequent phases of emergence

James Sullivan and the Birth of Massachusetts Republicanism

Thesis advisor: Alan RogersThe following narrative traces the political lives of James Sullivan, Christopher Gore, Rufus King and John Quincy Adams, four Massachusetts men who were actively involved in the creation of state and national policy during the formative years of the new republic. Their years of public service bridged the critical period between the Revolution and the period of Democratic- Republican dominance. Because they knew each other so well, corresponded with one another on a regular basis, and held so many different state and national government posts, their lives provide an ideal vehicle to explore and better understand the changes that were taking place in post-Revolutionary Massachusetts. Their stories help trace the evolution of Massachusetts from a Federalist stronghold into a legitimate multi-party state firmly committed to the national union. The primary figure in this study is Sullivan, the oldest of the four men, who was the state's highest ranking Republican leader during much of the Federalist Era. A staunch opponent of the Federalist assumption that government should be in the hands of the natural gentry and ruling class, he spent his adult life promoting equal access to power. After serving as a member of the Massachusetts Provincial Congress from 1774 to 1776, Sullivan was an active participant in the creation of the new state government. He later served as attorney general for seventeen years, from 1790 to 1807, through several Federalist administrations and served as a member of state legislature for many years. He also was a member of the Supreme Judicial Court and, in the final years of his life, governor of the Commonwealth. Because he participated in or observed firsthand the most significant political events of his day, his words also help trace, as few others could, the gradual transformation of Massachusetts from a one party state to a multi-party state. His election as governor in 1807 was clear evidence of the growing strength of the Republican Party in Massachusetts and of the extent to which the emerging national consensus had grown. Christopher Gore, whose stature and perspective were more deeply rooted in the colonial past, stood in stark personal as well as political contrast to Sullivan. As a conservative Federalist who often served as spokesman for his party during this period, Gore was a major player in the Massachusetts legal community and government between the American Revolution and early years of the nineteenth century. He stubbornly adhered to the aristocratic belief that the government should only be managed by the propertied class and traditional ruling elite. Where Sullivan was a sentimental moralist who hated everything British, Gore was the stern and unyielding spokesman for the merchant class who seemingly admired everything British. Where Sullivan's father had emigrated from Ireland, the victim of oppressive Penal Laws, Gore's father was a Tory, who fled Boston with the British in March 1776. Though Gore himself supported the Revolution, he was never able to shed, or indeed temper, his attachment to Great Britain in later years. As perhaps the most passionate defender of everything British in the years after the Revolution, Gore's habits and customs reflected the old deferential order and embodied everything Sullivan opposed. Despite their personal and political differences, Sullivan and Gore shared a close personal friend. Rufus King was a longtime confidant of both men, corresponding with each of them over many years. Though King's habits and background were more similar to those of Gore than Sullivan, he was less rooted in the colonial past than his conservative friend. Though an ardent Federalist, he was respected by men on both sides of the political aisle and served not only as a bridge between the two parties, but as a bridge between the two branches of his own party. It is because he enjoyed such a close personal relationship with Sullivan and Gore, and corresponded with both men on a regular basis, that King provides a unique vehicle to explore the differences between the two parties during this critical period in Massachusetts political history. The fourth subject of this study is John Quincy Adams. The fiercely independent one-time Federalist, who, though born many years after Gore, King, and Sullivan, became active in politics at a very young age and crossed political paths with all three men on a regular basis. Although born a member of the second generation of political leaders, Quincy Adams identified with the first generation of Revolutionary leaders. He matured early and took part in every critical debate that took place after the ratification of the Constitution. From the beginning, Quincy Adams charted an independent course and played a critical role in the growth of the Republican Party. John Quincy Adams is particularly relevant to this study because his political transformation reflected the change in attitude that was taking place in Massachusetts and the country in the early years of the nineteenth century. He represented a commitment to the interests of union over sectional concerns. A strong and independent unionist throughout his life, Quincy Adams eventually came to represent a new global nationalism. In many respects, Quincy Adams was the `transition man' in post- Revolutionary America. The son of a colonial who was very much a product of the deferential society of the eighteenth century, young Adams came to embrace the principle of majority rule. His elevation to the highest political posts in the country marked the final stage in America's transition from colony to union to nation. James Sullivan, Christopher Gore and Rufus King each played significant roles in the establishment of constitutional government in Massachusetts and in the United States. Though he was considered a member of the so-called Hancock faction, a group viewed as primarily anti-Constitutionalist, Sullivan was an independent thinker. He would call for greater legal safeguards for the benefit of the more vulnerable and for the end of the practice of multiple office holding which had long been a tool of the ruling elite to maintain power and influence.   A vocal proponent of the national government before King, Gore and Hancock, Sullivan had long recognized the importance of strengthening the central government. His embrace of participatory government and of law aimed at protecting all classes of people naturally appealed to a wider audience would continue to contribute to the democratization of Massachusetts politics. With a new national government in place and a new political era begun, Sullivan, King, Gore, and soon Quincy Adams, were uniquely positioned to play significant, if competing, roles in the coming struggle. This narrative differs from other secondary works on post-colonial Massachusetts in several respects. Firstly, the significant role played by Sullivan in the growth of Republicanism in Massachusetts has been largely overlooked by historians. His persistent calls for equal access to power stood in stark contrast to the views of the Federalists who dominated Massachusetts government in the years after the American Revolution. His active participation in regional politics both during and after the Revolution helped the people of Massachusetts in their transition from colony to state. Furthermore, he was one of the first Massachusetts political leaders to insist on placing the new central government on a sound financial footing. Indeed, his call for a strengthened and sufficiently financed national government predated the efforts of Massachusetts Federalists, including King and Gore. He was, I contend, one of the first political leaders of either party to be considered a true `nationalist.' While Quincy Adams' support for Jefferson's Embargo and his conversion to Republicanism have been well documented, this work explores the link between Sullivan and Quincy Adams, and details the critically important role they played in the national debate over how to respond to British aggression towards American shipping and American sailors. Though Gordon Wood and other historians point to the Embargo as the single biggest failure of Jefferson and his Republican supporters, I contend the opposite is true. The Embargo highlighted the central difference between the two parties, and though it provided Federalists with a temporary victory, it also sowed the seeds of their defeat. The Embargo enabled men like Sullivan and Quincy Adams to clarify one of the central issues of the post-Revolutionary period, ... national honor. Though Paul Goodman correctly points out that Republicanism tapped into the growing sense of nationalism in the country, I carry the discussion further and detail the growing disconnect between the Federalist Party and the American people. Quincy Adams, in particular, articulated the need to announce to the world that the United States would not submit to foreign aggression. Furthermore, his call for a stronger and expanded union, even if it meant a loss of power and prestige for Massachusetts, would soon strike a chord with a growing majority of Americans. Quincy Adams personified the shift in the national mood and represented a new national perspective. When John Quincy Adams left the Federalist Party, many Americans left with him.Thesis (PhD) — Boston College, 2011.Submitted to: Boston College. Graduate School of Arts and Sciences.Discipline: History

Project Hummingbird: Recovery of a Rocket Using Autorotation

Project Hummingbird is an undergraduate research project with the goal of launching and recovering a sounding rocket using a rotor-recovery system that will safely guide the rocket to landing. It aims to demonstrate an alternative approach to current methods of booster recovery that would, like the other techniques, reduce the cost per launch, but would also require a less complex system and far less fuel. The system is designed to launch with an internally stored rotor-hub and externally folded rotor-blades. At apogee, the rocket will orient itself nose up and deploy the rotor blades. The rotor-blades will auto-rotate and slow the rocket’s descent. An onboard flight computer will control the guidance and descent of the rocket to the ground. Proving such a system involves a series of small-scale model tests to gain an understanding of rotor-blades’ ability to produce lift in unpowered flight. Project members are currently constructing a small-scale model for drop testing in order to gain an understanding of auto-rotational performance at varying speeds and pitch angles, as well as a full-scale rocket for validating all planned and emergency deployment systems. Once the small scale testing is complete and the full-scale rocket has been proven out, conditions for the full-scale autorotation will be selected and full scale tests will be performed. Upon successful landing using autorotation, guidance systems will be developed. The project aims to perform a demonstration flight at the 2019 Spaceport America Cup

Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns

Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortment-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments’ geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different tree spaces from each other and from the rest of the genome. By contrast, segments 10 and 11 (NSP4 and NSP5/6) occupied nearly indistinguishable tree spaces, suggesting strong co-segregation. Host-species barriers appeared to vary by segment, with segment 9 (VP7) presenting the weakest association with host species. Bayesian Skyride plots were generated for each segment to compare relative genetic diversity among segments over time. All segments showed a dramatic decrease in diversity around 2007 coinciding with the introduction of RVA vaccines. To assess selection pressures, codon adaptation indices and relative codon deoptimization indices were calculated with respect to different host genomes. Codon usage varied by segment with segment 11 (NSP5) exhibiting significantly higher adaptation to host genomes. Furthermore, RVA codon usage patterns appeared optimized for expression in humans and birds relative to the other hosts examined, suggesting that translational efficiency is not a barrier in RVA zoonosis

Prophylactic Bacteriophage Administration More Effective than Post-infection Administration in Reducing Salmonella enterica serovar Enteritidis Shedding in Quail

Infections caused by Salmonella bacteria, often through poultry products, are a serious public health issue. Because of drawbacks associated with antibiotic prophylaxis, alternative treatments are sought. Bacterial viruses (bacteriophages) may provide an effective alternative, but concerns remain with respect to bacteriophage stability and effectiveness. To this end, we assessed the stability of a novel bacteriophage isolated from poultry excreta, siphovirus PSE, and its effectiveness in reducing Salmonella enterica serovar Enteritidis colonization in vitro and in vivo. Moreover, we sought to determine how the timing (prophylactic or therapeutic) and route (oral gavage or vent lip) of PSE administration impacted its effectiveness. Here we report that significant quantities of viable PSE bacteriophages were recovered following exposure to high and low pH, high temperatures, and bile salts, testifying to its ability to survive extreme conditions. In addition, we found that ileal lactic acid bacteria and Streptococcus spp. counts increased, but colibacilli and total aerobe counts decreased, in quail receiving phage PSE through both oral gavage and vent lip routes. In other experiments, we assessed the efficiency of PSE administration, in both prophylactic and therapeutic contexts, via either oral gavage or vent lip administration, on S. Enteritidis colonization of quail cecal tonsils. Our results demonstrate that administration of PSE as a preventive agent could reduce the S. Enteritidis colonization more effectively than post-challenge administration. Furthermore, oral administration of PSE phage is a more effective prophylactic tool for reduction of S. Enteritidis shedding in poultry than is vent lip administration

Evolutionary interpretations of mycobacteriophage biodiversity and host-range through the analysis of codon usage bias

In an genomics course sponsored by the Howard Hughes Medical Institute (HHMI), undergraduate students have isolated and sequenced the genomes of more than 1,150 mycobacteriophages, creating the largest database of sequenced bacteriophages able to infect a single host, Mycobacterium smegmatis, a soil bacterium. Genomic analysis indicates that these mycobacteriophages can be grouped into 26 clusters based on genetic similarity. These clusters span a continuum of genetic diversity, with extensive genomic mosaicism among phages in different clusters. However, little is known regarding the primary hosts of these mycobacteriophages in their natural habitats, nor of their broader host ranges. As such, it is possible that the primary host of many newly isolated mycobacteriophages is not M. smegmatis, but instead a range of closely related bacterial species. However, determining mycobacteriophage host range presents difficulties associated with mycobacterial cultivability, pathogenicity and growth. Another way to gain insight into mycobacteriophage host range and ecology is through bioinformatic analysis of their genomic sequences. To this end, we examined the correlations between the codon usage biases of 199 different mycobacteriophages and those of several fully sequenced mycobacterial species in order to gain insight into the natural host range of these mycobacteriophages. We find that UPGMA clustering tends to match, but not consistently, clustering by shared nucleotide sequence identify. In addition, analysis of GC content, tRNA usage and correlations between mycobacteriophage and mycobacterial codon usage bias suggests that the preferred host of many clustered mycobacteriophages is not M. smegmatis but other, as yet unknown, members of the mycobacteria complex or closely allied bacterial species

Factors influencing lysis time stochasticity in bacteriophage l

Background Despite identical genotypes and seemingly uniform environments, stochastic gene expression and other dynamic intracellular processes can produce considerable phenotypic diversity within clonal microbes. One trait that provides a good model to explore the molecular basis of stochastic variation is the timing of host lysis by bacteriophage (phage). Results Individual lysis events of thermally-inducible l lysogens were observed using a temperature-controlled perfusion chamber mounted on an inverted microscope. Both mean lysis time (MLT) and its associated standard deviation (SD) were estimated. Using the SD as a measure of lysis time stochasticity, we showed that lysogenic cells in controlled environments varied widely in lysis times, and that the level of lysis time stochasticity depended on allelic variation in the holin sequence, late promoter (pR\u27) activity, and host growth rate. In general, the MLT was positively correlated with the SD. Both lower pR\u27 activities and lower host growth rates resulted in larger SDs. Results from premature lysis, induced by adding KCN at different time points after lysogen induction, showed a negative correlation between the timing of KCN addition and lysis time stochasticity. Conclusions Taken together with results published by others, we conclude that a large fraction of l lysis time stochasticity is the result of random events following the expression and diffusion of the holin protein. Consequently, factors influencing the timing of reaching critical holin concentrations in the cell membrane, such as holin production rate, strongly influence the mean lysis time and the lysis time stochasticity