A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins

Bacteriocins are peptide-derived molecules produced by bacteria, whose recently-discovered functions include virulence factors and signalling molecules as well as their better known roles as antibiotics. To date, close to five hundred bacteriocins have been identified and classified. Recent discoveries have shown that bacteriocins are highly diverse and widely distributed among bacterial species. Given the heterogeneity of bacteriocin compounds, many tools struggle with identifying novel bacteriocins due to their vast sequence and structural diversity. Many bacteriocins undergo post-translational processing or modifications necessary for the biosynthesis of the final mature form. Enzymatic modification of bacteriocins as well as their export is achieved by proteins whose genes are often located in a discrete gene cluster proximal to the bacteriocin precursor gene, referred to as \textit{context genes} in this study. Although bacteriocins themselves are structurally diverse, context genes have been shown to be largely conserved across unrelated species. Using this knowledge, we set out to identify new candidates for context genes which may clarify how bacteriocins are synthesized, and identify new candidates for bacteriocins that bear no sequence similarity to known toxins. To achieve these goals, we have developed a software tool, Bacteriocin Operon and gene block Associator (BOA) that can identify homologous bacteriocin associated gene clusters and predict novel ones. We discover that several phyla have a strong preference for bactericon genes, suggesting distinct functions for this group of molecules. Availability: https://github.com/idoerg/BOAComment: Accepted for publication in BMC Bioinformatic

Taxonomic revision transferring species in Kuklospora to Acaulospora (Glomeromycota) and a description of Acaulospora colliculosa sp. nov. from field collected spores

In a phylogenetic study of arbuscular mycorrhizal fungal species in Acaulospora (Acaulosporaceae, Glomeromycota) we discovered that species classified in genus Kuklospora, a supposed sister clade of Acaulospora, did not partition as a monophyletic clade. Species in these two genera can be distinguished only by the position of the spore relative to a precursor structure, the sporiferous saccule, as either within (entrophosporoid) or laterally (acaulosporoid) on the saccule subtending hypha. Subsequent spore differentiation follows identical patterns and organization. Molecular phylogeny reconstructed from nrLSU gene sequences, together with developmental data, support the hypothesis that the entrophosporoid mode of spore formation evolved many times and thus represents a convergent trait of little phylogenetic significance. Therefore genus Kuklospora is rejected as a valid monophyletic group and it is integrated taxonomically into genus Acaulospora. Thus Acaulospora colombiana and Acaulospora kentinensis are erected as new combinations (formerly Kuklospora colombiana and Kuklospora kentinensis). Mode of spore formation is demoted from a genus-specific character to one that is included with other traits to define Acaulospora species. In addition we describe a new AM fungal species, Acaulospora colliculosa (Acaulosporaceae), that originated from a tallgrass prairie in North America. Field-collected spores of A. colliculosa are small (<100 μm diam), hyaline or subhyaline to pale yellow and form via entrophosporoid development based on structure and organization of cicatrices and attached hyphae. Each spore consists of a bilayered spore wall and two bilayered inner walls. A germination orb likely forms after the completion of spore development to initiate germination, but this structure was not observed. A character distinguishing A. colliculosa from other Acaulospora species is hyaline to subhyaline hemispherical protuberances on the surface of the outer spore wall layer. A phylogeny reconstructed from partial nrLSU gene sequences unambiguously placed A. colliculosa in the Acaulospora clade

Acaulospora colossica sp. nov. from an old field in North Carolina and morphological comparisons with similar species, A. laevis and A. koskei

A new arbuscular mycorrhizal fungal species, Acaulospora colossica, (Glomales, Acaulosporaceae) is described, and its distribution and seasonality discussed. Spores of A. colossica develop from saccules that empty their contents in the developing spores. Spore wall structure consists of 3 layers, all originating from the subtending hyphae. The two inner layers are laminated. The outermost spore wall layer is typically sloughed off before the spores mature. Two inner walls arise sequentially. Both inner walls are comprised of two layers. The outer layer of the innermost wall is beaded. Acaulospora colossica is described from a population in Durham, North Carolina. Its name refers to the relatively large size of the spores. Finally, the morphology of the new species A. colossica is compared and contrasted to two closely related species A. laevis and A. koskei

Analytical Assessment of the Reciprocating Feed System

A preliminary analysis tool has been created in Microsoft Excel to determine deliverable payload mass, total system mass, and performance of spacecraft systems using various types of propellant feed systems. These mass estimates are conducted by inserting into the user interface the basic mission parameters (e.g., thrust, burn time, specific impulse, mixture ratio, etc.), system architecture (e.g., propulsion system type and characteristics, propellants, pressurization system type, etc.), and design properties (e.g., material properties, safety factors, etc.). Different propellant feed and pressurization systems are available for comparison in the program. This gives the user the ability to compare conventional pressure fed, reciprocating feed system (RFS), autogenous pressurization thrust augmentation (APTA RFS), and turbopump systems with the deliverable payload, inert mass, and total system mass being the primary comparison metrics. Analyses of several types of missions and spacecraft were conducted and it was found that the RFS offers a performance improvement, especially in terms of delivered payload, over conventional pressure fed systems. Furthermore, it is competitive with a turbopump system at low to moderate chamber pressures, up to approximately 1,500 psi. Various example cases estimating the system mass and deliverable payload of several types of spacecraft are presented that illustrate the potential system performance advantages of the RFS. In addition, a reliability assessment of the RFS was conducted, comparing it to simplified conventional pressure fed and turbopump systems, based on MIL-STD 756B; these results showed that the RFS offers higher reliability, and thus substantially longer periods between system refurbishment, than turbopump systems, and is competitive with conventional pressure fed systems. This is primarily the result of the intrinsic RFS fail-operational capability with three run tanks, since the system can operate with just two run tanks

Large Deletions in the pAtC58 Megaplasmid of Agrobacterium tumefaciens Can Confer Reduced Carriage Cost and Increased Expression of Virulence Genes

The accessory plasmid pAtC58 of the common laboratory strain of Agrobacterium tumefaciens confers numerous catabolic functions and has been proposed to play a role in virulence. Genomic sequencing of evolved laboratory strains of A. tumefaciens revealed the presence of multiple deletion events in the At plasmid, with reductions in plasmid size ranging from 25% to 30% (115–194 kb). Flanking both ends of the sites of these deletions is a short-nucleotide repeat sequence that is in a single copy in the deleted plasmids, characteristic of a phage- or transposon-mediated deletion event. This repeat sequence is widespread throughout the C58 genome, but concentrated on the At plasmid, suggesting its frequency to be nonrandom. In this study, we assess the prevalence of the larger of these deletions in multiple C58 derivatives and characterize its functional significance. We find that in addition to elevating virulence gene expression, this deletion is associated with a significantly reduced carriage cost to the cell. These observations are a clear demonstration of the dynamic nature of the bacterial genome and suggest a mechanism for genetic plasticity of these costly but otherwise stable plasmids. Additionally, this phenomenon could be the basis for some of the dramatic recombination events so ubiquitous within and among megaplasmids

Vitamin D supplementation does not improve human skeletal muscle contractile properties in insufficient young males

Vitamin D may be a regulator of skeletal muscle function, although human trials investigating this hypothesis are limited to predominantly elderly populations. We aimed to assess the effect of oral vitamin D3 in healthy young males upon skeletal muscle function

US Army in the Iraq War Volume 2 Surge and Withdrawal

https://press.armywarcollege.edu/monographs/1932/thumbnail.jp

The U.S. Army in the Iraq War – Volume 1: Invasion – Insurgency – Civil War, 2003-2006

The Iraq War has been the costliest U.S. conflict since the Vietnam War. To date, few official studies have been conducted to review what happened, why it happened, and what lessons should be drawn. The U.S. Army in the Iraq War is the Army\u27s initial operational level analysis of this conflict, written in narrative format, with assessments and lessons embedded throughout the work. This study reviews the conflict from a Landpower perspective and includes the contributions of coalition allies, the U.S. Marine Corps, and special operations forces. Presented principally from the point of view of the commanders in Baghdad, the narrative examines the interaction of the operational and strategic levels, as well as the creation of theater level strategy and its implementation at the tactical level. Volume 1 begins in the truce tent at Safwan Airfield in southern Iraq at the end of Operation DESERT STORM and briefly examines actions by U.S. and Iraqi forces during the interwar years. The narrative continues by examining the road to war, the initially successful invasion, and the rise of Iraqi insurgent groups before exploring the country\u27s slide toward civil war. This volume concludes with a review of the decision by the George W. Bush administration to “surge” additional forces to Iraq, placing the conduct of the “surge” and its aftermath in the second volume. This study was constructed over a span of 4 years and relied on nearly 30,000 pages of handpicked declassified documents, hundreds of hours of original interviews, and thousands of hours of previously unavailable interviews. Original interviews conducted by the team included President George W. Bush, Secretary of State Condoleezza Rice, Secretaries of Defense Leon Panetta and Robert Gates, Chairmen of the Joint Chiefs of Staff, and every theater commander for the war, among many others. With its release, this publication, The U.S. Army in the Iraq War, represents the U.S. Government\u27s longest and most detailed study of the Iraq conflict thus far.https://digitalcommons.usmalibrary.org/books/1018/thumbnail.jp

Facile access to functionalized chiral secondary benzylic boronic esters via catalytic asymmetric hydroboration

Allylic and homoallylic phosphonates bearing an aryl or heteroaryl substituent at the γ- or δ-position undergo rhodium-catalyzed asymmetric hydroboration by pinacolborane to give functionalized chiral secondary benzylic boronic esters in yields up to 86% and enantiomer ratios up to 99 : 1. Compared to minimally-functionalized terminal and 1,1-disubstituted vinyl arenes, there are relatively few reports of efficient catalytic asymmetric hydroboration (CAHB) of more highly functionalized internal alkenes. Phosphonate substrates bearing a variety of common heterocyclic ring systems, including furan, indole, pyrrole and thiophene derivatives, as well as those bearing basic nitrogen substituents (e.g., morpholine and pyrazine) are tolerated, although donor substituents positioned in close proximity of the alkene can influence the course of the reaction. Stereoisomeric (E)- and (Z)-substrates afford the same major enantiomer of the borated product. Deuterium-labelling studies reveal that rapid (Z)- to (E)-alkene isomerization accounts for the observed (E/Z)-stereoconvergence during CAHB. The synthetic utility of the chiral boronic ester products is illustrated by stereospecific C–B bond transformations including stereoretentive electrophile promoted 1,2-B-to-C migrations, stereoinvertive SE2 reactions of boron-ate complexes with electrophiles, and stereoretentive palladium- and rhodium-catalyzed cross-coupling protocols