Design, Validation and Annotation of Transcriptome-Wide Oligonucleotide Probes for the Oligochaete Annelid Eisenia fetida

High density oligonucleotide probe arrays have increasingly become an important tool in genomics studies. In organisms with incomplete genome sequence, one strategy for oligo probe design is to reduce the number of unique probes that target every non-redundant transcript through bioinformatic analysis and experimental testing. Here we adopted this strategy in making oligo probes for the earthworm Eisenia fetida, a species for which we have sequenced transcriptome-scale expressed sequence tags (ESTs). Our objectives were to identify unique transcripts as targets, to select an optimal and non-redundant oligo probe for each of these target ESTs, and to annotate the selected target sequences. We developed a streamlined and easy-to-follow approach to the design, validation and annotation of species-specific array probes. Four 244K-formatted oligo arrays were designed using eArray and were hybridized to a pooled E. fetida cRNA sample. We identified 63,541 probes with unsaturated signal intensities consistently above the background level. Target transcripts of these probes were annotated using several sequence alignment algorithms. Significant hits were obtained for 37,439 (59%) probed targets. We validated and made publicly available 63.5K oligo probes so the earthworm research community can use them to pursue ecological, toxicological, and other functional genomics questions. Our approach is efficient, cost-effective and robust because it (1) does not require a major genomics core facility; (2) allows new probes to be easily added and old probes modified or eliminated when new sequence information becomes available, (3) is not bioinformatics-intensive upfront but does provide opportunities for more in-depth annotation of biological functions for target genes; and (4) if desired, EST orthologs to the UniGene clusters of a reference genome can be identified and selected in order to improve the target gene specificity of designed probes. This approach is particularly applicable to organisms with a wealth of EST sequences but unfinished genome

Antiinflammatory Therapy with Canakinumab for Atherosclerotic Disease

Background: Experimental and clinical data suggest that reducing inflammation without affecting lipid levels may reduce the risk of cardiovascular disease. Yet, the inflammatory hypothesis of atherothrombosis has remained unproved. Methods: We conducted a randomized, double-blind trial of canakinumab, a therapeutic monoclonal antibody targeting interleukin-1β, involving 10,061 patients with previous myocardial infarction and a high-sensitivity C-reactive protein level of 2 mg or more per liter. The trial compared three doses of canakinumab (50 mg, 150 mg, and 300 mg, administered subcutaneously every 3 months) with placebo. The primary efficacy end point was nonfatal myocardial infarction, nonfatal stroke, or cardiovascular death. RESULTS: At 48 months, the median reduction from baseline in the high-sensitivity C-reactive protein level was 26 percentage points greater in the group that received the 50-mg dose of canakinumab, 37 percentage points greater in the 150-mg group, and 41 percentage points greater in the 300-mg group than in the placebo group. Canakinumab did not reduce lipid levels from baseline. At a median follow-up of 3.7 years, the incidence rate for the primary end point was 4.50 events per 100 person-years in the placebo group, 4.11 events per 100 person-years in the 50-mg group, 3.86 events per 100 person-years in the 150-mg group, and 3.90 events per 100 person-years in the 300-mg group. The hazard ratios as compared with placebo were as follows: in the 50-mg group, 0.93 (95% confidence interval [CI], 0.80 to 1.07; P = 0.30); in the 150-mg group, 0.85 (95% CI, 0.74 to 0.98; P = 0.021); and in the 300-mg group, 0.86 (95% CI, 0.75 to 0.99; P = 0.031). The 150-mg dose, but not the other doses, met the prespecified multiplicity-adjusted threshold for statistical significance for the primary end point and the secondary end point that additionally included hospitalization for unstable angina that led to urgent revascularization (hazard ratio vs. placebo, 0.83; 95% CI, 0.73 to 0.95; P = 0.005). Canakinumab was associated with a higher incidence of fatal infection than was placebo. There was no significant difference in all-cause mortality (hazard ratio for all canakinumab doses vs. placebo, 0.94; 95% CI, 0.83 to 1.06; P = 0.31). Conclusions: Antiinflammatory therapy targeting the interleukin-1β innate immunity pathway with canakinumab at a dose of 150 mg every 3 months led to a significantly lower rate of recurrent cardiovascular events than placebo, independent of lipid-level lowering. (Funded by Novartis; CANTOS ClinicalTrials.gov number, NCT01327846.

Further evidence for the development of photic-zone euxinic conditions during Mesozoic oceanic anoxic events

Periods in Earth history characterized by extensive organic carbon deposition, so-called oceanic anoxic events (OAEs), are the subject of considerable scrutiny. Insight into the extent of anoxic conditions in the water column has been provided by the reported occurrence of derivatives of isorenieratene, a carotenoid found only in green sulphur bacteria and thus indicative of photic-zone euxinia (i.e. a water column containing free H2S), in North Atlantic deep-sea sediments deposited during the Cenomanian-Turonian boundary OAE2 (Bonarelli Event). In this study, we have used the distributions of chlorophyll and bacteriochlorophyll degradation products, maleimides (1-H-pyrrole-2,5-diones) and high molecular weight porphyrins, to examine further the Cenomanian-Turonian boundary OAE2 as well as other OAEs of the early Toarcian (Posidonienschiefer Event) and early Aptian (Selli Event). In particular, methyl isobutyl (Me,i-Bu) maleimide, on structural grounds, appears to be diagnostic of green sulphur bacteria. This compound occurs in five of seven examined marls that record the early Toarcian OAE (Marche-Umbria, Italy), further expanding the geographical range of Toarcian sediments where evidence for photic-zone euxinic conditions has been found. Me,i-Bu maleimide occurs in three of six black shales spanning the Livello Selli (Marche-Umbria, Italy), the type locality for the Aptian OAE1a, providing the first evidence for photic-zone euxinic conditions during this event. With respect to the Cenomanian-Turonian OAE, maleimide evidence for photic-zone euxinic conditions was found in all the North Atlantic sites investigated including those characterized by relatively organic-lean sediments, several Tethyan sites and one site off western Australia. These data indicate that euxinic conditions were common in the water column during Mesozoic oceanic anoxic events

Characterising wireless sensor motes for space applications

This paper is concerned with application of standard wireless COTS protocols to space. Suitability of commercially available wireless sensor mote kits for communication inside and between satellites is investigated Spacecraft applications of motes are being considered and a set of requirements are identified Selected mote kits are tested under various scenarios complying with spacecraft testing procedures. The paper details the results of the carried out functional, EMC/I, vibration, thermal and radiation tests

Characterising wireless sensor motes for space applications

This paper is concerned with application of standard wireless COTS protocols to space. Suitability of commercially available wireless sensor mote kits for communication inside and between satellites is investigated Spacecraft applications of motes are being considered and a set of requirements are identified Selected mote kits are tested under various scenarios complying with spacecraft testing procedures. The paper details the results of the carried out functional, EMC/I, vibration, thermal and radiation tests