Characterisation of silent and active genes for a variable large protein of Borrelia recurrentis

BACKGROUND: We report the characterisation of the variable large protein (vlp) gene expressed by clinical isolate A1 of Borrelia recurrentis; the agent of the life-threatening disease louse-borne relapsing fever. METHODS: The major vlp protein of this isolate was characterised and a DNA probe created. Use of this together with standard molecular methods was used to determine the location of the vlp1(B. recurrentis A1) gene in both this and other isolates. RESULTS: This isolate was found to carry silent and expressed copies of the vlp1(B. recurrentis A1) gene on plasmids of 54 kbp and 24 kbp respectively, whereas a different isolate, A17, had only the silent vlp1(B. recurrentis A17) on a 54 kbp plasmid. Silent and expressed vlp1 have identical mature protein coding regions but have different 5' regions, both containing different potential lipoprotein leader sequences. Only one form of vlp1 is transcribed in the A1 isolate of B. recurrentis, yet both 5' upstream sequences of this vlp1 gene possess features of bacterial promoters. CONCLUSION: Taken together these results suggest that antigenic variation in B. recurrentis may result from recombination of variable large and small protein genes at the junction between lipoprotein leader sequence and mature protein coding region. However, this hypothetical model needs to be validated by further identification of expressed and silent variant protein genes in other B. recurrentis isolates

High-Resolution Positional Tracking for Long-Term Analysis of Drosophila Sleep and Locomotion Using the “Tracker” Program

Drosophila melanogaster has been used for decades in the study of circadian behavior, and more recently has become a popular model for the study of sleep. The classic method for monitoring fly activity involves counting the number of infrared beam crosses in individual small glass tubes. Incident recording methods such as this can measure gross locomotor activity, but they are unable to provide details about where the fly is located in space and do not detect small movements (i.e. anything less than half the enclosure size), which could lead to an overestimation of sleep and an inaccurate report of the behavior of the fly. This is especially problematic if the fly is awake, but is not moving distances that span the enclosure. Similarly, locomotor deficiencies could be incorrectly classified as sleep phenotypes. To address these issues, we have developed a locomotor tracking technique (the “Tracker” program) that records the exact location of a fly in real time. This allows for the detection of very small movements at any location within the tube. In addition to circadian locomotor activity, we are able to collect other information, such as distance, speed, food proximity, place preference, and multiple additional parameters that relate to sleep structure. Direct comparisons of incident recording and our motion tracking application using wild type and locomotor-deficient (CASK-β null) flies show that the increased temporal resolution in the data from the Tracker program can greatly affect the interpretation of the state of the fly. This is especially evident when a particular condition or genotype has strong effects on the behavior, and can provide a wealth of information previously unavailable to the investigator. The interaction of sleep with other behaviors can also be assessed directly in many cases with this method

Regional Endothermy in a Coral Reef Fish?

Although a few pelagic species exhibit regional endothermy, most fish are regarded as ectotherms. However, we document significant regional endothermy in a benthic reef fish. Individual steephead parrotfish, Chlorurus microrhinos (Labridae, formerly Scaridae) were tagged and their internal temperatures were monitored for a 24 h period using active acoustic telemetry. At night, on the reef, C. microrhinos were found to maintain a consistent average peritoneal cavity temperature 0.16±0.005°C (SE) warmer than ambient. Diurnal internal temperatures were highly variable for individuals monitored on the reef, while in tank-based trials, peritoneal cavity temperatures tracked environmental temperatures. The mechanisms responsible for a departure of the peritoneal cavity temperature from environmental temperature occurred in C. microrhinos are not yet understood. However, the diet and behavior of the species suggests that heat in the peritoneal cavity may result primarily from endogenous thermogenesis coupled with physiological heat retention mechanisms. The presence of limited endothermy in C. microrhinos indicates that a degree of uncertainty may exist in the manner that reef fish respond to their thermal environment. At the very least, they do not always appear to respond to environmental temperatures as neutral thermal vessels and do display limited, but significant, visceral warming

Application of a diagnosis-based clinical decision guide in patients with neck pain

<p>Abstract</p> <p>Background</p> <p>Neck pain (NP) is a common cause of disability. Accurate and efficacious methods of diagnosis and treatment have been elusive. A diagnosis-based clinical decision guide (DBCDG; previously referred to as a diagnosis-based clinical decision rule) has been proposed which attempts to provide the clinician with a systematic, evidence-based guide in applying the biopsychosocial model of care. The approach is based on three questions of diagnosis. The purpose of this study is to present the prevalence of findings using the DBCDG in consecutive patients with NP.</p> <p>Methods</p> <p>Demographic, diagnostic and baseline outcome measure data were gathered on a cohort of NP patients examined by one of three examiners trained in the application of the DBCDG.</p> <p>Results</p> <p>Data were gathered on 95 patients. Signs of visceral disease or potentially serious illness were found in 1%. Centralization signs were found in 27%, segmental pain provocation signs were found in 69% and radicular signs were found in 19%. Clinically relevant myofascial signs were found in 22%. Dynamic instability was found in 40%, oculomotor dysfunction in 11.6%, fear beliefs in 31.6%, central pain hypersensitivity in 4%, passive coping in 5% and depression in 2%.</p> <p>Conclusion</p> <p>The DBCDG can be applied in a busy private practice environment. Further studies are needed to investigate clinically relevant means to identify central pain hypersensitivity, oculomotor dysfunction, poor coping and depression, correlations and patterns among the diagnostic components of the DBCDG as well as inter-examiner reliability, validity and efficacy of treatment based on the DBCDG.</p

Analysis of a donor gene region for a variant surface glycoprotein and its expression site in African trypanosomes

African trypanosomes evade the immune response of their mammalian hosts by sequentially expressing genes for different variant surface glycoproteins (VSGs) from telomere-linked VSG expression sites. In the Trypanosoma brucei clone whose genome is being sequenced (GUTat 10.1), we show that the expressed VSG (VSG 10.1) is duplicated from a silent donor VSG located at another telomere-linked site. We have determined two 130 kb sequences representing the VSG 10.1 donor and expression sites. The telomere-linked donor VSG 10.1 resembles metacyclic VSG expression sites, and is preceded by a cluster of 35 or more tandem housekeeping genes, all of which are transcribed away from the telomere. The 45 kb telomere-linked VSG 10.1 expression site contains a promoter followed by seven expression site-associated genes (ESAGs), three pseudo ESAGs, two pseudo VSGs and VSG 10.1. The 80 kb preceding the expression site has few, if any, functional ORFs, but contains 50 bp repeats, INGI retrotransposon-like elements, and novel 4–12 kb repeats found near other telomeres. This analysis provides the first look over a 130 kb range of a telomere-linked donor VSG and its corresponding telomere-linked VSG expression site and forms the basis for studies on antigenic variation in the context of a completely sequenced genome

ABSTRACT Slotted Priorities: Supporting Real-Time Computing Within General-Purpose Operating Systems

Recent advances in network technologies, processor capabilities, and micro-computer system hardware, coupled with the explosive growth of the Internet and on-line data access, have created new demands on personal computer operating systems and hardware. In large part, these demands are for the ability to acquire, manipulate, display, and store multimedia data. The computational processes that successfully acquire and display multimedia data necessarily have deadlines. That is, the computation must be complete before a speci ed point in time. Currently, no general-purpose operating systems support such real-time processes. We have developed a software architecture, called slotted priorities, that de nes a way to add support for real-time computation to existing general-purpose operating sys-tems for uniprocessor machine architectures. The slotted priorities architecture shares the resources of a computing system between a general-purpose operating system and a real-time kernel. Software components called executives manage how an instance of a resource is shared. Executives ensure that the RTK can gain ac-cess to the resource at precise times. The resulting operating system will be abl