A Tangled Web: Origins of Reproductive Parasitism

While typically a flea parasite and opportunistic human pathogen, the presence of Rickettsia felis (strain LSU-Lb) in the non-blood- feeding, parthenogenetically reproducing booklouse, Liposcelis bostrychophila, provides a system to ascertain factors governing not only host transitions but also obligate reproductive parasitism (RP). Analysis of plasmid pLbAR, unique to R. felis str. LSU-Lb, revealed a toxin–antitoxin module with similar features to prophage-encoded toxin–antitoxin modules utilized by parasitic Wolbachia strains to induce another form of RP, cytoplasmic incompatibility, in their arthropod hosts. Curiously, multiple deubiquitinase and nuclease domains of the large (3,841 aa) pLbAR toxin, as well the entire antitoxin, facilitated the detection of an assortment of related proteins from diverse intracellular bacteria, including other reproductive parasites. Our description of these remarkable components of the intracellular mobilome, including their presence in certain arthropod genomes, lends insight on the evolution of RP, while invigo- rating research on parasite-mediated biocontrol of arthropod-borne viral and bacterial pathogens

Building the Holocene clinothem in the Gulf of Papua: An ocean circulation study

This paper investigates the role that tidal and wind-driven flows and buoyant river plumes play in the development of the Holocene clinothem in the Gulf of Papua. Time series data from bottom tripods and a mooring were obtained at four locations near the mouth of the Fly River during portions of 2003 and 2004. Flows in the Gulf of Papua during calendar year 2003 were hindcast every 3 h using the Navy Coastal Ocean Model (NCOM) with boundary conditions from the Navy Atmospheric Prediction System, the east Asian seas implementation of NCOM, and the OTIS Tidal Inversion System. Results show that tidal flows on the modern clinoform are strong and are landward and seaward directed. Peak spring tidal velocities can provide the shear stresses necessary to keep sediment up to sand size in motion as the wind-driven and baroclinic currents distribute it from the river mouths across and along the shelf in two circulation states. During the monsoon season, the clinoform topset is swept by a seaward surface flow and landward bottom flow, reflecting river plumes and coastal upwelling. Seaward, this structure evolves into a SW directed surface current over the clinothem foreset with accompanying landward directed near-bed currents that trend obliquely up the foreset to the WSW over much of the clinothem. During the trade wind season, the inner and outer topset are swept by NE directed, contour-parallel surface currents, underneath which lie obliquely landward near-bed currents. These modeled flows and complex gyres in shallow water coupled with wave- and current-supported gravity flows or river floods can explain the form, internal clinoform shapes, and mineralogy of the modern Gulf of Papua clinothem

Stable task information from an unstable neural population

Over days and weeks, neural activity representing an animal’s position and movement in sensorimotor cortex has been found to continually reconfigure or ‘drift’ during repeated trials of learned tasks, with no obvious change in behavior. This challenges classical theories, which assume stable engrams underlie stable behavior. However, it is not known whether this drift occurs systematically, allowing downstream circuits to extract consistent information. Analyzing long-term calcium imaging recordings from posterior parietal cortex in mice (Mus musculus), we show that drift is systematically constrained far above chance, facilitating a linear weighted readout of behavioral variables. However, a significant component of drift continually degrades a fixed readout, implying that drift is not confined to a null coding space. We calculate the amount of plasticity required to compensate drift independently of any learning rule, and find that this is within physiologically achievable bounds. We demonstrate that a simple, biologically plausible local learning rule can achieve these bounds, accurately decoding behavior over many days

The promise and peril of intensive-site-based ecological research: insights from the Hubbard Brook ecosystem study

Abstract. Ecological research is increasingly concentrated at particular locations or sites. This trend reflects a variety of advantages of intensive, site-based research, but also raises important questions about the nature of such spatially delimited research: how well does site based research represent broader areas, and does it constrain scientific discovery?We provide an overview of these issues with a particular focus on one prominent intensive research site: the Hubbard Brook Experimental Forest (HBEF), New Hampshire, USA. Among the key features of intensive sites are: long-term, archived data sets that provide a context for new discoveries and the elucidation of ecological mechanisms; the capacity to constrain inputs and parameters, and to validate models of complex ecological processes; and the intellectual cross-fertilization among disciplines in ecological and environmental sciences. The feasibility of scaling up ecological observations from intensive sites depends upon both the phenomenon of interest and the characteristics of the site. An evaluation of deviation metrics for the HBEF illustrates that, in some respects, including sensitivity and recovery of streams and trees from acid deposition, this site is representative of the Northern Forest region, of which HBEF is a part. However, the mountainous terrain and lack of significant agricultural legacy make the HBEF among the least disturbed sites in the Northern Forest region. Its relatively cool, wet climate contributes to high stream flow compared to other sites. These similarities and differences between the HBEF and the region can profoundly influence ecological patterns and processes and potentially limit the generality of observations at this and other intensive sites. Indeed, the difficulty of scaling up may be greatest for ecological phenomena that are sensitive to historical disturbance and that exhibit the greatest spatiotemporal variation, such as denitrification in soils and the dynamics of bird communities. Our research shows that end member sites for some processes often provide important insights into the behavior of inherently heterogeneous ecological processes. In the current era of rapid environmental and biological change, key ecological responses at intensive sites will reflect both specific local drivers and regional trends

The Complete Genome Sequence of the Emerging Pathogen Mycobacterium haemophilum Explains Its Unique Culture Requirements

Mycobacterium haemophilum is an emerging pathogen associated with a variety of clinical syndromes, most commonly skin infections in immunocompromised individuals. M. haemophilum exhibits a unique requirement for iron supplementation to support its growth in culture, but the basis for this property and how it may shape pathogenesis is unclear. Using a combination of Illumina, PacBio, and Sanger sequencing, the complete genome sequence of M. haemophilum was determined. Guided by this sequence, experiments were performed to define the basis for the unique growth requirements of M. haemophilum. We found that M. haemophilum, unlike many other mycobacteria, is unable to synthesize iron-binding siderophores known as mycobactins or to utilize ferri-mycobactins to support growth. These differences correlate with the absence of genes associated with mycobactin synthesis, secretion, and uptake. In agreement with the ability of heme to promote growth, we identified genes encoding heme uptake machinery. Consistent with its propensity to infect the skin, we show at the whole-genome level the genetic closeness of M. haemophilumwith Mycobacterium leprae, an organism which cannot be cultivated in vitro, and we identify genes uniquely shared by these organisms. Finally, we identify means to express foreign genes in M. haemophilum. These data explain the unique culture requirements for this important pathogen, provide a foundation upon which the genome sequence can be exploited to improve diagnostics and therapeutics, and suggest use of M. haemophilum as a tool to elucidate functions of genes shared with M. leprae. IMPORTANCE Mycobacterium haemophilum is an emerging pathogen with an unknown natural reservoir that exhibits unique requirements for iron supplementation to grow in vitro. Understanding the basis for this iron requirement is important because it is fundamental to isolation of the organism from clinical samples and environmental sources. Defining the molecular basis for M. haemophilium\u27s growth requirements will also shed new light on mycobacterial strategies to acquire iron and can be exploited to define how differences in such strategies influence pathogenesis. Here, through a combination of sequencing and experimental approaches, we explain the basis for the iron requirement. We further demonstrate the genetic closeness of M. haemophilum and Mycobacterium leprae, the causative agent of leprosy which cannot be cultured in vitro, and we demonstrate methods to genetically manipulate M. haemophilum. These findings pave the way for the use of M. haemophilum as a model to elucidate functions of genes shared with M. leprae

Estimated prevalence of exposure to occupational carcinogens in Australia (2011-2012)

Background and objectives: Although past studies of workplace exposures have contributed greatly to our understanding of carcinogens, significant knowledge gaps still exist with regard to the actual extent of exposure among current workers, with no routinely collected population-based data being available in most countries. This study, the Australian Work Exposures Study (AWES), aimed to investigate the current prevalence of occupational exposure to carcinogens. Methods: A random sample of men and women aged between 18 and 65, who were currently in paid employment, were invited to participate in a telephone interview collecting information about their current job and various demographic factors. Interviews were conducted using a web-based application (OccIDEAS). OccIDEAS uses the expert exposure method in which participants are asked about their job tasks and predefined algorithms are used to automatically assign exposures. Responses were obtained from 5023 eligible Australian residents, resulting in an overall response rate of 53%. Results: 1879 respondents (37.6%) were assessed as being exposed to at least one occupational carcinogen in their current job. Extrapolation of these figures to the Australian working population suggested 3.6 million (40.3%) current workers could be exposed to carcinogens in their workplace. Exposure prevalence was highest among farmers, drivers, miners and transport workers, as well as men and those residing in regional areas. Conclusions: This study demonstrates a practical, web-based approach to collecting population information on occupational exposure to carcinogens and documents the high prevalence of current exposure to occupational carcinogens in the general population

PATRIC, the bacterial bioinformatics database and analysis resource

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issu

The Australian Work Exposures Study: Prevalence of Occupational Exposure to Formaldehyde

INTRODUCTION: The aims of this study were to produce a population-based estimate of the prevalence of work-related exposure to formaldehyde, to identify the main circumstances of exposure and to describe the use of workplace control measures designed to decrease those exposures. METHODS: The analysis used data from the Australian Workplace Exposures Study, a nationwide telephone survey, which investigated the current prevalence and exposure circumstances of work-related exposure to 38 known or suspected carcinogens, including formaldehyde, among Australian workers aged 18-65 years. Using the web-based tool OccIDEAS, semi-quantitative information was collected about exposures in the current job held by the respondent. Questions were addressed primarily at tasks undertaken rather than about self-reported exposures. RESULTS: Of the 4993 included respondents, 124 (2.5%) were identified as probably being exposed to formaldehyde in the course of their work [extrapolated to 2.6% of the Australian working population-265 000 (95% confidence interval 221 000-316 000) workers]. Most (87.1%) were male. About half worked in technical and trades occupations. In terms of industry, about half worked in the construction industry. The main circumstances of exposure were working with particle board or plywood typically through carpentry work, building maintenance, or sanding prior to painting; with the more common of other exposures circumstances being firefighters involved in fighting fires, fire overhaul, and clean-up or back-burning; and health workers using formaldehyde when sterilizing equipment or in a pathology laboratory setting. The use of control measures was inconsistent. CONCLUSION: Workers are exposed to formaldehyde in many different occupational circumstances. Information on the exposure circumstances can be used to support decisions on appropriate priorities for intervention and control of occupational exposure to formaldehyde, and estimates of burden of cancer arising from occupational exposure to formaldehyde

Ad-CD40L mobilizes CD4 T cells for the treatment of brainstem tumors

Diffuse Midline Glioma, formerly Diffuse Intrinsic Pontine Glioma (DIPG), is the deadliest pediatric brainstem tumor with median survival of less than one year. Here, we investigated 1) whether direct delivery of adenovirus expressing CD40L (Ad-CD40L) to brainstem tumors would induce immune-mediated tumor clearance and, 2) if so, whether therapy would be associated with a manageable toxicity due to immune-mediated inflammation in the brainstem. Methods Syngeneic gliomas in the brainstems of immune competent mice were treated with Ad-CD40L and survival, toxicity and immune profiles determined. A clinically translatable vector, whose replication would be tightly restricted to tumor cells, rAd-Δ24-CD40L, was tested in human patient-derived Diffuse Midline Gliomas and immunocompetent models. Results Expression of Ad-CD40L restricted to brainstem gliomas by pre-infection induced complete rejection, associated with immune cell infiltration, of which CD4+ T cells were critical for therapy. Direct intra-tumoral injection of Ad-CD40L into established brainstem tumors improved survival and induced some complete cures but with some acute toxicity. RNA-seq analysis showed that Ad-CD40L therapy induced neuroinflammatory immune responses associated with IL-6, IL-1β and TNF-α. Therefore, to generate a vector whose replication, and transgene expression, would be tightly restricted to tumor cells, we constructed rAd-Δ24-CD40L, the backbone of which has already entered clinical trials for Diffuse Midline Glioma. Direct intra-tumoral injection of rAd-Δ24-CD40L, with systemic blockade of IL-6 and IL-1β, generated significant numbers of cures with readily manageable toxicity. Conclusions Virus-mediated delivery of CD40L has the potential to be effective in treating Diffuse Midline Gliomas without obligatory neuroinflammation-associated toxicity

Progress report no. 1

Statement of responsibility on title-page reads: Editors: I.A. Forbes, M.J. Driscoll, D.D. Lanning, I. Kaplan, N.C. Rasmussen; Contributors: S.A. Ali, S.T. Brewer, D.K. Choi, F.M. Clikeman, W.R. Corcoran, M.J. Driscoll, I.A. Forbes, C.W. Forsberg, S.L. Ho, C.S. Kang, I. Kaplan, J.L. Klucar, D.D. Lanning, T.C. Leung, E.L. McFarland P.G. Mertens, N.R. Ortiz, A. Pant, N.A. Passman, N.C. Rasmussen, M.K. Sheaffer, D.A. Shupe, G.E. Sullivan, A.T. Supple, J.W. Synan, C.P. Tzanos, W.J. Westlake"MIT-4105-3."Includes bibliographical referencesProgress report; June 30, 1970U.S. Atomic Energy Commission contracts: AT(30-1)410