WormBase 2014: new views of curated biology.

WormBase (http://www.wormbase.org/) is a highly curated resource dedicated to supporting research using the model organism Caenorhabditis elegans. With an electronic history predating the World Wide Web, WormBase contains information ranging from the sequence and phenotype of individual alleles to genome-wide studies generated using next-generation sequencing technologies. In recent years, we have expanded the contents to include data on additional nematodes of agricultural and medical significance, bringing the knowledge of C. elegans to bear on these systems and providing support for underserved research communities. Manual curation of the primary literature remains a central focus of the WormBase project, providing users with reliable, up-to-date and highly cross-linked information. In this update, we describe efforts to organize the original atomized and highly contextualized curated data into integrated syntheses of discrete biological topics. Next, we discuss our experiences coping with the vast increase in available genome sequences made possible through next-generation sequencing platforms. Finally, we describe some of the features and tools of the new WormBase Web site that help users better find and explore data of interest.

InterMOD: integrated data and tools for the unification of model organism research.

Model organisms are widely used for understanding basic biology, and have significantly contributed to the study of human disease. In recent years, genomic analysis has provided extensive evidence of widespread conservation of gene sequence and function amongst eukaryotes, allowing insights from model organisms to help decipher gene function in a wider range of species. The InterMOD consortium is developing an infrastructure based around the InterMine data warehouse system to integrate genomic and functional data from a number of key model organisms, leading the way to improved cross-species research. So far including budding yeast, nematode worm, fruit fly, zebrafish, rat and mouse, the project has set up data warehouses, synchronized data models, and created analysis tools and links between data from different species. The project unites a number of major model organism databases, improving both the consistency and accessibility of comparative research, to the benefit of the wider scientific community.

Are there distinct neural representations of object and limb dynamics?

In recent studies of human motor learning, subjects learned to move the arm while grasping a robotic device that applied novel patterns of forces to the hand. Here, we examined the generality of force field learning. We tested the idea that contextual cues associated with grasping a novel object promote the acquisition and use of a distinct internal model, associated with that object. Subjects learned to produce point-to-point arm movements to targets in a horizontal plane while grasping a robotic linkage that applied either a velocity-dependent counter-clockwise or clockwise force field to the hand. Following adaptation, subjects let go of the robot and were asked to generate the same movements in free space. Small but reliable after-effects were observed during the first eight movements in free space, however, these after-effects were significantly smaller than those observed for control subjects who moved the robot in a null field. No reduction in retention was observed when subjects subsequently returned to the force field after moving in free space. In contrast, controls who reached with the robot in a NF showed much poorer retention when returning to a force field. These findings are consistent with the idea that contextual cues associated with grasping a novel object may promote the acquisition of a distinct internal model of the dynamics of the object, separate from internal models used to control limb dynamics alone.

Susceptibilities of Yersinia pestis strains to 12 antimicrobial agents.

Ninety-two strains of Yersinia pestis recovered over a 21-year period were evaluated for susceptibility to traditional and newer antimicrobial agents. In vitro resistance was noted only against rifampin and imipenem (approximately 20% of strains). The most active compounds (MIC at which 90% of the isolates tested are inhibited) against Y. pestis were cefixime, ceftriaxone, trimethoprim-sulfamethoxazole, and trovafloxacin.

Ideological influence in U.S. health policy: catalysts or impediments?

Although pronouncements of the ¿health care crisis¿ have been made for thirty years, in many ways the fundamental underpinnings of the U.S. health care system have changed very little. However, calls for health care reform have progressed through four distinct phases. From before the 1965 passage of the Medicare and Medicaid programs until about 1972, the primary issue was expanding access to care. From 1972 through 1976, health care reform proposals experienced a transition period. From 1976 until about 1992, cost containment became the dominant theme. Since 1992 there has been a renewed emphasis on improving access to care. But Americans have mixed feelings about health care reform. On the one hand, Americans want improved access to care, increased efficiency, and high quality care. On the other hand, Americans are leery of higher taxes and expanding the government's role in health care decision-making. In the final analysis, it is ultimately politics which governs the form of health care reform by effecting compromises between what is ideologically desirable and what is economically plausible.

Complications associated with maxillary nerve block anaesthesia via the greater palatine canal.

This paper documents the type, frequency and duration of complications associated with regional anaesthesia of the maxillary nerve via the greater palatine canal in a series of 101 patients treated in the Oral Surgery Department, United Dental Hospital of Sydney.

Association of an important Neisseria species, Neisseria elongata subsp. nitroreducens, with bacteremia, endocarditis, and osteomyelitis.

We retrospectively analyzed epidemiologic information associated with 22 cultures of Neisseria elongata subsp. nitroreducens (formerly CDC group M-6) submitted to the Microbial Diseases Laboratory, California Department of Health Services, Berkeley, over a 16-year period. The most common illnesses noted with this bacterium were endocarditis, bacteremia, and osteomyelitis. Risk factors associated with N. elongata subsp. nitroreducens infection included dental manipulations and/or a previous history of endocarditis, valve damage, or rheumatic heart disease.

Preliminary studies on the use of carbon substrate utilization patterns for identification of Brucella species.

A commercial system (Biolog, Hayward, CA) that uses reduction of an indicator dye to determine the oxidation of 95 different carbon substrates contained in a defined minimal medium was tested with 35 isolates of Brucella spp. to determine if the system could be used in place of respirometric methods to identify species. Of 95 substrates contained in this system, three were oxidized by all the Brucella strains tested, 48 were oxidized by none of the strains tested, and 44 were oxidized differentially. Brucella melitensis, B. abortus, and B. suis could be distinguished from each other on the basis of their oxidation reactions in seven in these substrates; epidemiologically related strains could not be unambiguously differentiated. This carbon substrate utilization method may prove to be a useful alternative to respirometry as a means to identify strains of Brucella spp. to species level, provided that personnel are protected from exposure to this highly infectious agent.

Maxillary nerve block anaesthesia via the greater palatine canal: a modified technique and case reports.

A modification of the technique of maxillary nerve block (via the greater palatine canal) is discussed. This technique has been employed in the Exodontia and Oral Surgery Clinics of the United Dental Hospital of Sydney for more than 40 years. Clinical experience in that time has shown that once the greater palatine canal has been negotiated successfully, the palatal canal approach to the maxillary nerve is safe and reliable. The value of being able to anaesthetize the maxillary nerve and its branches is illustrated by the presentation of two clinical cases where local anaesthesia was achieved and the extractions performed in patients who would otherwise have required a general anaesthetic for the procedures.

Surface properties and ultrastructure of Edwardsiella species.

Twenty-two strains of Edwardsiella representing the three currently recognized species were evaluated for surface characteristics and ultrastructural morphology. All isolates tested possessed a high surface cell charge as detected by DEAE-cellulose chromatography; surface hydrophobicity was variable and strain but not species dependent. Two major types of adhesins detected by hemagglutination assays were identified: one was inhibited by D-mannose (mannose-sensitive hemagglutinin) and found on all three species, and a second was not inhibited by D-mannose (mannose-resistant hemagglutinin) and was principally associated with Edwardsiella tarda. The results of physiologic and ultrastructural studies suggest that both hemagglutinins are afimbrial adhesin proteins. The results of these studies suggest that there are a number of distinct surface and ultrastructural properties associated with each of the three Edwardsiella species.

Porphyrin test as an alternative to benzidine test for detecting cytochromes in catalase-negative gram-positive cocci.

A total of 66 strains of gram-positive cocci, including 21 catalase-negative members of the family Streptococcaceae and strains of Stomatococcus mucilaginosus, were investigated for the ability to produce porphobilinogen and porphyrin from delta-aminolevulinic acid as an alternative to the benzidine test for detecting the presence of cytochromes. Production of porphobilinogen correlated 100% with membership in the family Micrococcaceae.