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Recent research has underscored the immense diversity and key biogeochemical roles of large DNA viruses in the ocean. Although they are important constituents of marine ecosystems, it is sometimes difficult to detect these viruses due to their large size and complex genomes. This is true for "jumbo" bacteriophages, which have genome sizes >200 kbp and large capsids reaching up to 0.45 µm in diameter. In this study, we sought to assess the genomic diversity and distribution of these bacteriophages in the ocean by generating and analyzing jumbo phage genomes from metagenomes. We recover 85 marine jumbo phages that ranged in size from 201 to 498 kilobases, and we examine their genetic similarities and biogeography together with a reference database of marine jumbo phage genomes. By analyzing Tara Oceans metagenomic data, we show that although most jumbo phages can be detected in a range of different size fractions, 17 of our bins tend to be found in those greater than 0.22 µm, potentially due to their large size. Our network-based analysis of gene-sharing patterns reveals that jumbo bacteriophages belong to five genome clusters that are typified by diverse replication strategies, genomic repertoires, and potential host ranges. Our analysis of jumbo phage distributions in the ocean reveals that depth is a major factor shaping their biogeography, with some phage genome clusters occurring preferentially in either surface or mesopelagic waters, respectively. Taken together, our findings indicate that jumbo phages are widespread community members in the ocean with complex genomic repertoires and ecological impacts that warrant further targeted investigation.

The bacteriophages have been explored at a huge scale as a model system for their applications in many biological-related fields. Jumbo phages with a large genome size from 200 to 500 kbp were not previously assigned a great value, and characterized by complex structures coupled with large virions with a wide variety of hosts. The origin of most of the jumbo phages was not well understood; however, many other prominent features have been discovered recently. In the current review, we strive to unearth the most advanced characteristics of jumbo phages, particularly their significance and structural organization that holds immense value to the viral life cycle. The unique characteristics of jumbo phages are the basis of variations in different types of phages concerning their organization at the genomic level, virion structure, evolution, and progeny propagation. The presence of tRNA and additional translation-related genes along with chaperonin genes mark the ability of these phages for being independent of host molecular machinery enabling them to have wide host options. A large number of jumbo phages have been isolated from various sources through advanced standard screening methods. The current review has summarized the available data on jumbo phages and discussed the genome orientation of jumbo phages, translational machinery, diversity and evolution of jumbo phages. In the studies conducted, jumbo phages possessed special additional genes that helps to reduce the dependence of jumbo phages on their hosts. Furthermore, their genomes might have evolved from smaller genome phages.

Tailed bacteriophages with genomes larger than 200 kbp are classified as Jumbo phages, and are rarely isolated by conventional methods. These phages are designated "jumbo" owing to their most notable features of a large phage virion and large genome size. However, in addition to these, jumbo phages also exhibit several novel characteristics that have not been observed for phages with smaller genomes, which differentiate jumbo phages in terms of genome organization, virion structure, progeny propagation, and evolution. In this review, we summarize available reports on jumbo phages and discuss the differences between jumbo phages and small-genome phages. We also discuss data suggesting that jumbo phages might have evolved from phages with smaller genomes by acquiring additional functional genes, and that these additional genes reduce the dependence of the jumbo phages on the host bacteria.

Uncemented jumbo cups are commonly used for acetabular revision because they are technically straightforward to implant and provide good intermediate-term results. Understanding long-term survival is particularly important because this method is common and because jumbo cups do not provide notable bone stock restoration. The purpose of the present study was to determine the twenty-year results of jumbo cup use during revision total hip arthroplasty. In the original publication, we reported on eighty-nine patients who underwent revision with an uncemented jumbo cup with a single design (Harris-Galante) prior to 1993. The Harris Hip Score (HHS), radiographic results, and Kaplan-Meier survivorship curves were evaluated. Mean follow-up was twenty years. The mean postoperative HHS was 71 compared with 56 preoperatively (p=0.001). A total of five jumbo cups were revised for aseptic loosening; one, for infection; and one, for recurrent dislocation. Eight liners were revised with retention of the metal acetabular component: six during femoral component revision, one for wear, and one for recurrent dislocations. Twenty-year survivorship was 88% free from aseptic loosening of the metal acetabular component, 85% free from aseptic loosening or radiographic evidence of definite loosening of the metal acetabular component, and 83% free from revision of the metal acetabular component for any reason. The twenty-year results of revision with uncemented jumbo acetabular components demonstrated acceptable clinical outcomes and radiographic stability. These results justify the use of jumbo cups as a common method of acetabular revision.

Prokaryotic viruses with DNA genome longer than 200 kb are collectively referred to as "jumbo phages". Some representatives of this phylogenetically diverse group encode two DNA-dependent RNA polymerases (RNAPs)-a virion RNAP and a non-virion RNAP. In contrast to most other phage-encoded RNAPs, the jumbo phage RNAPs are multisubunit enzymes related to RNAPs of cellular organisms. Unlike all previously characterized multisubunit enzymes, jumbo phage RNAPs lack the universally conserved alpha subunits required for enzyme assembly. The mechanism of promoter recognition is also different from those used by cellular enzymes. For example, the AR9 phage non-virion RNAP requires uracils in its promoter and is able to initiate promoter-specific transcription from single-stranded DNA. Jumbo phages encoding multisubunit RNAPs likely have a common ancestor allowing making them a separate subgroup within the very diverse group of jumbo phages. In this review, we describe transcriptional strategies used by RNAP-encoding jumbo phages and describe the properties of characterized jumbo phage RNAPs.

Since their discovery more than 100 years ago, the viruses that infect bacteria (bacteriophages) have been widely studied as model systems. Largely overlooked, however, have been "jumbo phages," with genome sizes ranging from 200 to 500 kbp. Jumbo phages generally have large virions with complex structures and a broad host spectrum. While the majority of jumbo phage genes are poorly functionally characterized, recent work has discovered many unique biological features, including a conserved tubulin homolog that coordinates a proteinaceous nucleus-like compartment that houses and segregates phage DNA. The tubulin spindle displays dynamic instability and centers the phage nucleus within the bacterial host during phage infection for optimal reproduction. The shell provides robust physical protection for the enclosed phage genomes against attack from DNA-targeting bacterial immune systems, thereby endowing jumbo phages with broad resistance. In this review, we focus on the current knowledge of the cytoskeletal elements and the specialized nuclear compartment derived from jumbo phages, and we highlight their importance in facilitating spatial and temporal organization over the viral life cycle. Additionally, we discuss the evolutionary relationships between jumbo phages and eukaryotic viruses, as well as the therapeutic potential and drawbacks of jumbo phages as antimicrobial agents in phage therapy.

The jumbo squid Dosidicus gigas plays an important role in marine food webs both as predator and prey. We investigated the ontogenetic and spatiotemporal variability of the diet composition of jumbo squid in the northern Humboldt Current system. For that purpose we applied several statistical methods to an extensive dataset of 3,618 jumbo squid non empty stomachs collected off Peru from 2004 to 2011. A total of 55 prey taxa was identified that we aggregated into eleven groups. Our results evidenced a large variability in prey composition as already observed in other systems. However, our data do not support the hypothesis that jumbo squids select the most abundant or energetic taxon in a prey assemblage, neglecting the other available prey. Indeed, multinomial model predictions showed that stomach fullness increased with the number of prey taxa, while most stomachs with low contents contained one or two prey taxa only. Our results therefore question the common hypothesis that predators seek locally dense aggregations of monospecific prey. In addition D. gigas consumes very few anchovy Engraulis ringens in Peru, whereas a tremendous biomass of anchovy is potentially available. It seems that D. gigas cannot reach the oxygen unsaturated waters very close to the coast, where the bulk of anchovy occurs. Indeed, even if jumbo squid can forage in hypoxic deep waters during the day, surface normoxic waters are then required to recover its maintenance respiration (or energy?). Oxygen concentration could thus limit the co-occurrence of both species and then preclude predator-prey interactions. Finally we propose a conceptual model illustrating the opportunistic foraging behaviour of jumbo squid impacted by ontogenetic migration and potentially constrained by oxygen saturation in surface waters.

Stomach contents and carbon (C) and nitrogen (N) stable isotope analysis were used to evaluate trophic relationships of jumbo squid, Dosidicus gigas . Buccal masses, beaks and stomach contents of large and medium maturing-sized jumbo squid and muscle from its main prey, the myctophid Benthosema panamense , were collected in the Gulf of California, Mexico during 1996, 1997 and 1999. Both the quantified C and N-isotope ratios in muscle, and stomach content analysis revealed that larger-sized maturing squid showed a higher trophic position than medium-sized individuals. However, a discrepancy between stomach contents versus stable isotope analyses was found in evaluating trophic relationships. Simple dilution models as a function of growth were used to estimate the C and N renewal dietary shift for jumbo squid. Estimates of the initial C and N pools in D. gigas with an initial age of 70 days and 210 days indicated isotopic shifts of 32% after a threefold biomass increase and 25% after a fourfold biomass increase, respectively. Additionally, beak samples of jumbo squid were evaluated as an alternative tissue to estimate squid trophic position using stable isotopes. The results showed a significant correlation between stable isotope ratios from muscle and beak samples. Muscle isotope values were higher than beak by 1% and 4% for δ 13 C and δ 15 N respectively. A test with jumbo squid beaks collected from a stomach of a stranded sperm whale confirmed the viability of this method.

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 333:291-302 (2007) - doi:10.3354/meps333291 Diving behavior of sperm whales in relation to behavior of a major prey species, the jumbo squid, in the Gulf of California, Mexico R. W. Davis1,*, N. Jaquet2, D. Gendron3, U. Markaida4, G. Bazzino5, W. Gilly6 1Texas A&M University, 5007 Avenue U, Galveston, Texas 77551, USA 2Center for Coastal Studies, 115 Bradford Street, Provincetown, Massachusetts 02657, USA 3Centro Interdisciplinario de Ciencias Marinas, Instituto Politécnico Nacional (CICIMAR-IPN), A. P. 592, La Paz, Baja California Sur 23000, Mexico 4Departamento de Aprovechamiento y Manejo de Recursos Acuáticos, El Colegio de la Frontera Sur, Calle 10 No. 246, Col. Centro, 24000 Campeche, Mexico 5Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Mar Bermejo No. 195, Col. Playa Palo de Santa Rita, A. P. 592, La Paz, Baja California Sur 23000, Mexico 6Hopkins Marine Station, Oceanview Boulevard, Stanford University, Pacific Grove, California 93950, USA *Email: davisr@tamug.edu ABSTRACT: Sperm whales occur worldwide and feed largely on meso- and bathypelagic squid, but little is known about the behavioral ecology of this predator and its prey. In the Gulf of California, sperm whales are thought to feed on the abundant jumbo (Humboldt) squid, an ecologically and commercially important species. In this study, we attached satellite-linked dive recorders to 5 sperm whales and pop-up archival transmitting tags to 3 jumbo squid in the same area and time period in order to record their diving behavior and movements. Most (91%) deep dives by whales ranged from 100 to 500 m (average 418 ± 216.0 m) and lasted 15 to 35 min (average 27 ± 9.1 min). During daytime hours, jumbo squid spent about 75% of the time in the 200 to 400 m depth range, and sperm whales showed a similar dive-depth preference. The vertical distribution pattern of squid changed during the night, with squid spending about half the time at depths of <200 m and the remainder at 200 to 400 m. Although the whales shifted their nighttime diving to somewhat shallower depths, about 75% of dives remained in the 200 to 400 m depth range. Analysis of squid nighttime diving behavior, based on archival time-series data, showed that excursions into warm surface waters were often terminated by deep dives to typical daytime depths, after which the squid appeared to be relatively quiescent. Diving behavior by whales is thus consistent with the idea that they feed on jumbo squid at depth during the day, and we suggest that deep nighttime foraging may target squid that are recovering from stress after recent surface activity and are therefore more susceptible to predation. KEY WORDS: Physeter macrocephalus · Dosidicus gigas · Diving behavior · Satellite telemeters · Movements · Predator · Prey · Gulf of California Full text in pdf format PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 333. Online publication date: March 12, 2007 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2007 Inter-Research.

Run-time code generation is a well-known technique for improving the efficiency of programs by exploiting dynamic information. Unfortunately, the difficulty of constructing run-time code-generators has hampered their widespread use. We describe Jumbo, a tool for easily creating run-time code generators for Java. Jumbo is a compiler for a two-level version of Java, where programs can contain quoted code fragments. The Jumbo API allows the code fragments to be combined at run-time and then executed. We illustrate Jumbo with several examples that show significant speed-ups over similar code written in plain Java, and argue further that Jumbo is a generalized software component system.