Querying the public databases for sequences using complex keywords contained in the feature lines

Background  

High throughput technologies often require the retrieval of large data sets of sequences. Retrieval of EMBL or GenBank entries using keywords is easy using tools such as ACNUC, Entrez or SRS, but has some limitations, in particular when querying with complex keywords.     

Determination of strongly overlapping signaling activity from microarray data

Background

The Tissue Microarray (TMA) facilitates high-throughput analysis of hundreds of tissue specimens simultaneously. However, bottlenecks in the storage and manipulation of the data generated from TMA reviews have become apparent. A number of software applications have been developed to assist in image and data management; however no solution currently facilitates the easy online review, scoring and subsequent storage of images and data associated with TMA experimentation.

Results

This paper describes the design, development and validation of the Virtual Tissue Matrix (VTM). Through an intuitive HTML driven user interface, the VTM provides digital/virtual slide based images of each TMA core and a means to record observations on each TMA spot. Data generated from a TMA review is stored in an associated relational database, which facilitates the use of flexible scoring forms. The system allows multiple users to record their interpretation of each TMA spot for any parameters assessed. Images generated for the VTM were captured using a standard background lighting intensity and corrective algorithms were applied to each image to eliminate any background lighting hue inconsistencies or vignetting. Validation of the VTM involved examination of inter-and intra-observer variability between microscope and digital TMA reviews. Six bladder TMAs were immunohistochemically stained for E-Cadherin, β-Catenin and PhosphoMet and were assessed by two reviewers for the amount of core and tumour present, the amount and intensity of membrane, cytoplasmic and nuclear staining.

Conclusion

Results show that digital VTM images are representative of the original tissue viewed with a microscope. There were equivalent levels of inter-and intra-observer agreement for five out of the eight parameters assessed. Results also suggest that digital reviews may correct potential problems experienced when reviewing TMAs using a microscope, for example, removal of background lighting variance and tint, and potential disorientation of the reviewer, which may have resulted in the discrepancies evident in the remaining three parameters.     

Development of a new bicistronic retroviral vector with strong IRES activity

Background  

Internal Ribosome Entry Site (IRES)-based bicistronic vectors are important tools in today's cell biology. Among applications, the expression of two proteins under the control of a unique promoter permits the monitoring of expression of a protein whose biological function is being investigated through the observation of an easily detectable tracer, such as Green Fluorescent Protein (GFP). However, analysis of published results making use of bicistronic vectors indicates that the efficiency of the IRES-controlled expression can vary widely from one vector to another, despite their apparent identical IRES sequences. We investigated the molecular basis for these discrepancies.     

Epratuzumab (humanised anti-CD22 antibody) in primary Sjögren's syndrome: an open-label phase I/II study

This open-label, phase I/II study investigated the safety and efficacy of epratuzumab, a humanised anti-CD22 monoclonal antibody, in the treatment of patients with active primary Sj?gren's syndrome (pSS). Sixteen Caucasian patients (14 females/2 males, 33-72 years) were to receive 4 infusions of 360 mg/m2 epratuzumab once every 2 weeks, with 6 months of follow-up. A composite endpoint involving the Schirmer-I test, unstimulated whole salivary flow, fatigue, erythrocyte sedimentation rate (ESR), and immunoglobulin G (IgG) was devised to provide a clinically meaningful assessment of response, defined as a > or = 20% improvement in at least two of the aforementioned parameters, with > or = 20% reduction in ESR and/or IgG considered as a single combined criterion. Fourteen patients received all infusions without significant reactions, 1 patient received 3, and another was discontinued due to a mild acute reaction after receiving a partial infusion. Three patients showed moderately elevated levels of Human anti-human (epratuzumab) antibody not associated with clinical manifestations. B-cell levels had mean reductions of 54% and 39% at 6 and 18 weeks, respectively, but T-cell levels, immunoglobulins, and routine safety laboratory tests did not change significantly. Fifty-three percent achieved a clinical response (at > or = 20% improvement level) at 6 weeks, with 53%, 47%, and 67% responding at 10, 18, and 32 weeks, respectively. Approximately 40%-50% responded at the > or = 30% level, while 10%-45% responded at the > or = 50% level for 10-32 weeks. Additionally, statistically significant improvements were observed in fatigue, and patient and physician global assessments. Further, we determined that pSS patients have a CD22 over-expression in their peripheral B cells, which was downregulated by epratuzumab for at least 12 weeks after the therapy. Thus, epratuzumab appears to be a promising therapy in active pSS, suggesting that further studies be conducted.     

Body mass and clutch size may modulate prolactin and corticosterone levels in eiders

Altered body condition, increased incubation costs, and egg loss are important proximate factors modulating bird parental behavior, since they inform the adult about its remaining chances of survival or about the expected current reproductive success. Hormonal changes should reflect internal or external stimuli, since corticosterone levels (inducing nest abandonment) are known to increase while body condition deteriorates, and prolactin levels (stimulating incubation) decrease following egg predation. However, in a capital incubator that based its investment on available body reserves and naturally lost about half of its body mass during incubation, corticosterone should be maintained at a low threshold to avoid protein mobilization for energy supply. This study focused on the regulation of corticosterone and prolactin release in such birds during incubation, when facing egg manipulation (control, reduced, or increased) or a stressful event. Blood samples were taken before and after clutch manipulation and at hatching. Corticosterone levels were determined before and after 30 min of captivity. Female eiders exhibited a high hypothalamic-pituitary-adrenal sensitivity, plasma concentration of corticosterone being increased by four- to fivefold following 30 min of captivity. The adrenocortical response was not modified by body mass loss but was higher in birds for which clutch size was increased. In the same way, females did not show different prolactin levels among the experimental groups. However, when incubation started, prolactin levels were correlated to body mass, suggesting that nest attendance is programmed in relation to the female initial body condition. Moreover, due to an artifactual impact of bird manipulation, increased baseline corticosterone was associated with a prolactin decrease in the control group. These data suggest that, in eiders, body mass and clutch size modification can modulate prolactin and corticosterone levels, which cross-regulate each other in order to finely control incubation behavior.     

HIV controllers: how these patients control viral replication?

Some patients infected by the HIV are called HIV controllers because viral replication remains undectectable during a prolonged period of time in the absence of any antiretroviral treatment. This state could be considered as a ??functional cure?? in these virally infected patients. Understanding mechanisms underlying this prolonged control of viral replication is key to the development of future vaccinal strategies. French ANRS is exploiting a cohort of HIV controllers since several years, and immunological analysis of these patients has yielded some mechanistic clues that this review will discuss. A striking feature is the very efficient and polyfunctional CD8 T cell response of these patients, which exhibits a high avidity against the gag protein of the virus. Other parameters and questions are studied?: the role of HLA B57, overrepresented in this cohort?; how HIV controllers who do not express a very robust CD8 response control the viral replication?? The long term follow up of these patients will also give important informations on their -immunological, viral and clinical evolution.     

Toll-like receptor 8: the awkward TLR

Toll-like receptors (TLR) sense a variety of microbial products and play an important role in the mounting of innate and adaptive immune responses. TLR1 to TLR9 are common in mice and humans and recognize similar ligands in both species, with the exception of TLR8. Human TLR7 and TLR8 and mouse TLR7 detect viral single-stranded RNA and imidazoquinoline compounds, while mouse TLR8 not. Based on this discrepancy, for long time it was believed that mouse TLR8 is not functional and as a consequence the contribution of TLR8 to innate immunity remained poorly understood. Our recent studies revealed an important role for TLR8 in the regulation of TLR7-mediated autoimmunity in the mouse. This review illustrates our current understanding regarding the function of TLR8 and its potential for future clinical use for the treatment and/or prevention of various pathological conditions.     

The diversity of aging models

Most of the signalling pathways involved in aging regulation have been recently found well conserved at various levels throughout the evolution. Taking this into account, a diversity of model organisms, including worms, rodents, and lemurs as well, allows to address different questions: how to understand the interactions between genetic and environmental factors while challenging theories of aging, to preserve hearing integrity, to fight against senescence of neural stem cells, or to explore brain fitness from gene expression to cognitive and social behavior? Here are the main issues that can be considered, stressing the complementarities of the models. The differentiation of aging physiological aspects from those induced by age-related pathologies will also be specified. By emphasizing recent ability of technologies to promote new aging insights, we discuss towards a better understanding of mechanisms governing aging.