Genomic analysis of 48 paenibacillus larvae bacteriophages

Indexación: Scopus.Funding: Research at UNLV was funded by National Institute of General Medical Sciences grant GM103440 (NV INBRE), the UNLV School of Life Sciences, and the UNLV College of Sciences. E.C.-N. was funded by CONICYT-FONDECYT de iniciación en la investigación 11160905. Research at BYU was funded by the BYU Microbiology & Molecular Biology Department, and private donations through LDS Philanthropies.The antibiotic-resistant bacterium Paenibacillus larvae is the causative agent of American foulbrood (AFB), currently the most destructive bacterial disease in honeybees. Phages that infect P. larvae were isolated as early as the 1950s, but it is only in recent years that P. larvae phage genomes have been sequenced and annotated. In this study we analyze the genomes of all 48 currently sequenced P. larvae phage genomes and classify them into four clusters and a singleton. The majority of P. larvae phage genomes are in the 38–45 kbp range and use the cohesive ends (cos) DNA-packaging strategy, while a minority have genomes in the 50–55 kbp range that use the direct terminal repeat (DTR) DNA-packaging strategy. The DTR phages form a distinct cluster, while the cos phages form three clusters and a singleton. Putative functions were identified for about half of all phage proteins. Structural and assembly proteins are located at the front of the genome and tend to be conserved within clusters, whereas regulatory and replication proteins are located in the middle and rear of the genome and are not conserved, even within clusters. All P. larvae phage genomes contain a conserved N-acetylmuramoyl-L-alanine amidase that serves as an endolysin. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.https://www.mdpi.com/1999-4915/10/7/37

Estimation of effective vaccination rate for pertussis in New Zealand as a case study

In some cases vaccination is unreliable. For example vaccination against pertussis has comparatively high level of primary and secondary failures. To evaluate efficiency of vaccination we introduce the idea of effective vaccination rate and suggest an approach to estimate it. We consider pertussis in New Zealand as a case study. The results indicate that the level of immunity failure for pertussis is considerably higher than was anticipated

A spinor approach to Walker geometry

A four-dimensional Walker geometry is a four-dimensional manifold M with a neutral metric g and a parallel distribution of totally null two-planes. This distribution has a natural characterization as a projective spinor field subject to a certain constraint. Spinors therefore provide a natural tool for studying Walker geometry, which we exploit to draw together several themes in recent explicit studies of Walker geometry and in other work of Dunajski (2002) and Plebanski (1975) in which Walker geometry is implicit. In addition to studying local Walker geometry, we address a global question raised by the use of spinors.Comment: 41 pages. Typos which persisted into published version corrected, notably at (2.15

Effect of 'loss of function' mutation in SER in wine yeast: fermentation outcomes in co-inoculation with non-Saccharomyces

Published: 20 April 2022In wine fermentation, improved wine complexity and sensorial properties can arise from the use of non-Saccharomyces yeast. Generally less alcohol tolerant, such strains often do not finish fermentation, therefore requiring a second inoculation with the more robust Saccharomyces cerevisiae, usually added on Day 3. This sequential approach affords non-Saccharomyces time to make an impact before being overtaken by S. cerevisiae. However, two inoculations are inconvenient; therefore the identification of a slow growing S. cerevisiae strain that can be used in a single co-inoculation with the non-Saccharomyces yeast is highly attractive. In this study we investigated the use of the naturally occurring ‘loss of function’ SER1 variant, identified in a Sake yeast, for the purposes of carrying out co-inoculated wine fermentations. The SER1-232(G > C; G78R) change was introduced into the commonly used wine strain, EC1118, via CRISPR/Cas9 editing. In a chemically defined grape juice medium, the SER1(G78R) mutant grew and fermented more slowly and increased acetic acid, succinic acid and glycerol concentrations. Simultaneous inoculation with the slower-growing mutant with a Metschnikowia pulcherrima or Lachancea thermotolerans strain in sterile Sauvignon blanc juice resulted in differences in sensorial compounds, most likely derived from the presence of non-Saccharomyces yeasts. The EC1118 SER1 (G78R) mutant completed fermentation with M. pulcherrima, MP2, and in fact improved the viability of MP2 compared to when it was used as a monoculture. The SER1 (G78R) mutant also promoted both the growth of the SO2-sensitive L. thermotolerans strain, Viniflora® Concerto™, in a juice high in SO2 and its subsequent dominance during fermentation. In co-fermentations with wild-type EC1118, the Concerto™ population was substantially reduced with no significant changes in wine properties. This research adds to our understanding of the use of a novel slow-growing S. cerevisiae yeast in wine fermentations co-inoculated with non-Saccharomyces strains.Tom A. Lang, Michelle E. Walker, Paul K. Boss and Vladimir Jirane

Identifying the Independent Inertial Parameter Space of Robot Manipulators

This paper presents a new approach to the problem of finding the minimum number of inertial parameters of robot manipulator dynamic equations of motion. Based upon the energy difference equation, it is equally applica ble to serial link manipulators as well as graph structured manipulators. The method is conceptually simple, compu tationally efficient, and easy to implement. In particular, the manipulator kinematics and the joint positions and velocities are the only inputs to the algorithm. Applica tions to a serial link and a graph structured manipulator are illustrated.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/67982/2/10.1177_027836499101000606.pd

Disposition kinetics and urinary excretion of ciprofloxacin in goats following single intravenous administration

We evaluated the pharmacokinetics of ciprofloxacin in serum (n = 6) and urine (n = 4) in goats following a single intravenous administration of 4 mg/kg body weight. The serum concentration-time curves of ciprofloxacin were best fitted by a two-compartment open model. The drug was detected in goat serum up to 12 h. The elimination rate constant (β) and elimination half-life (t1/2β) were 0.446 ± 0.04 h-1 and 1.630 ± 0.17 h, respectively. The apparent volume of distribution at steady state (Vdss) was 2.012 ± 0.37 l/kg and the total body clearance (ClB) was 16.27 ± 1.87 ml/min/kg. Urinary recovery of ciprofloxacin was 29.70% ± 10.34% of the administered dose within 36 h post administration. In vitro serum protein binding was 41% ± 13.10%. Thus, a single daily intravenous dose of 4 mg/kg is sufficient to maintain effective levels in serum and for 36 h in urine, allowing treatment of systemic, Gram-negative bacterial infections and urinary tract infections by most pathogens

The ZEPLIN II dark matter detector: data acquisition system and data reduction

ZEPLIN-II is a two-phase (liquid/gas) xenon dark matter detector searching for WIMP-nucleon interactions. In this paper we describe the data acquisition system used to record the data from ZEPLIN-II and the reduction procedures which parameterise the data for subsequent analysis.Comment: 11 pages, 10 figure

Quantitative importance of staminodes for female reproductive success in Parnassia palustris under contrasting environmental conditions.

The five sterile stamens, or staminodes, in Parnassia palustris act both as false and as true nectaries. They attract pollinators with their conspicuous, but non-rewarding tips, and also produce nectar at the base. We removed staminodes experimentally and compared pollinator visitation rate and duration and seed set in flowers with and without staminodes in two different populations. We also examined the relative importance of the staminode size to other plant traits. Finally, we bagged, emasculated, and supplementary cross-pollinated flowers to determine the pollination strategy and whether reproduction was limited by pollen availability. Flowers in both populations were highly dependent on pollinator visitation for maximum seed set. In one population pollinators primarily cross-pollinated flowers, whereas in the other the pollinators facilitated self-pollination. The staminodes caused increased pollinator visitation rate and duration to flowers in both populations. The staminodes increased female reproductive success, but only when pollen availability constrained female reproduction. Simple linear regression indicated a strong selection on staminode size, multiple regression suggested that selection on staminode size was mainly caused by correlation with other traits that affected female fitness. [ABSTRACT FROM AUTHOR

Can forest management based on natural disturbances maintain ecological resilience?

Given the increasingly global stresses on forests, many ecologists argue that managers must maintain ecological resilience: the capacity of ecosystems to absorb disturbances without undergoing fundamental change. In this review we ask: Can the emerging paradigm of natural-disturbance-based management (NDBM) maintain ecological resilience in managed forests? Applying resilience theory requires careful articulation of the ecosystem state under consideration, the disturbances and stresses that affect the persistence of possible alternative states, and the spatial and temporal scales of management relevance. Implementing NDBM while maintaining resilience means recognizing that (i) biodiversity is important for long-term ecosystem persistence, (ii) natural disturbances play a critical role as a generator of structural and compositional heterogeneity at multiple scales, and (iii) traditional management tends to produce forests more homogeneous than those disturbed naturally and increases the likelihood of unexpected catastrophic change by constraining variation of key environmental processes. NDBM may maintain resilience if silvicultural strategies retain the structures and processes that perpetuate desired states while reducing those that enhance resilience of undesirable states. Such strategies require an understanding of harvesting impacts on slow ecosystem processes, such as seed-bank or nutrient dynamics, which in the long term can lead to ecological surprises by altering the forest's capacity to reorganize after disturbance