Alternative pre-mRNA processing regulates cell-type specific expression of the <Emphasis Type="Italic">IL4l1</Emphasis> and <Emphasis Type="Italic">NUP62</Emphasis> genes

Background  

Given the complexity of higher organisms, the number of genes encoded by their genomes is surprisingly small. Tissue specific regulation of expression and splicing are major factors enhancing the number of the encoded products. Commonly these mechanisms are intragenic and affect only one gene.     

Poxvirus protein N1L targets the I-kappaB kinase complex, inhibits signaling to NF-kappaB by the tumor necrosis factor superfamily of receptors, and inhibits NF-kappaB and IRF3 signaling by toll-like receptors

Poxviruses encode proteins that suppress host immune responses, including secreted decoy receptors for pro-inflammatory cytokines such as interleukin-1 (IL-1) and the vaccinia virus proteins A46R and A52R that inhibit intracellular signaling by members of the IL-1 receptor (IL-1R) and Toll-like receptor (TLR) family. In vivo, the TLRs mediate the innate immune response by serving as pathogen recognition receptors, whose oligomerized intracellular Toll/IL-1 receptor (TIR) domains can initiate innate immune signaling. A family of TIR domain-containing adapter molecules transduces signals from engaged receptors that ultimately activate NF-kappaB and/or interferon regulatory factor 3 (IRF3) to induce pro-inflammatory cytokines. Data base searches detected a significant similarity between the N1L protein of vaccinia virus and A52R, a poxvirus inhibitor of TIR signaling. Compared with other poxvirus virulence factors, the poxvirus N1L protein strongly affects virulence in vivo; however, the precise target of N1L was previously unknown. Here we show that N1L suppresses NF-kappaB activation following engagement of Toll/IL-1 receptors, tumor necrosis factor receptors, and lymphotoxin receptors. N1L inhibited receptor-, adapter-, TRAF-, and IKK-alpha and IKK-beta-dependent signaling to NF-kappaB. N1L associated with several components of the multisubunit I-kappaB kinase complex, most strongly associating with the kinase, TANK-binding kinase 1 (TBK1). Together these findings are consistent with the hypothesis that N1L disrupts signaling to NF-kappaB by Toll/IL-1Rs and TNF superfamily receptors by targeting the IKK complex for inhibition. Furthermore, N1L inhibited IRF3 signaling, which is also regulated by TBK1. These studies define a role for N1L as an immunomodulator of innate immunity by targeting components of NF-kappaB and IRF3 signaling pathways.     

Active listening for spatial orientation in a complex auditory scene

To successfully negotiate a complex environment, an animal must control the timing of motor behaviors in coordination with dynamic sensory information. Here, we report on adaptive temporal control of vocal–motor behavior in an echolocating bat, Eptesicus fuscus, as it captured tethered insects close to background vegetation. Recordings of the bat's sonar vocalizations were synchronized with high-speed video images that were used to reconstruct the bat's three-dimensional flight path and the positions of target and vegetation. When the bat encountered the difficult task of taking insects as close as 10–20 cm from the vegetation, its behavior changed significantly from that under open room conditions. Its success rate decreased by about 50%, its time to initiate interception increased by a factor of ten, and its high repetition rate “terminal buzz” decreased in duration by a factor of three. Under all conditions, the bat produced prominent sonar “strobe groups,” clusters of echolocation pulses with stable intervals. In the final stages of insect capture, the bat produced strobe groups at a higher incidence when the insect was positioned near clutter. Strobe groups occurred at all phases of the wingbeat (and inferred respiration) cycle, challenging the hypothesis of strict synchronization between respiration and sound production in echolocating bats. The results of this study provide a clear demonstration of temporal vocal–motor control that directly impacts the signals used for perception.     

Spatial Differentiation in the Characterisation of Photochemical Ozone Formation: The EDIP2003 Methodology

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DOI: http://dx.doi.org/10.1065/lca2006.04.014

Background, Aims and Scope

In the life cycle of a product, emissions take place at many different locations. The location of the source and its surrounding conditions influence the fate of the emitted pollutant and the subsequent exposure it causes. This source of variation is normally neglected in Life Cycle Impact Assessment (LCIA), although it is well known that the impacts predicted by site-generic LCIA in some cases differ significantly from the actual impacts. Environmental impacts of photochemical ozone (ground-level ozone) depend on parameters with a considerable geographical variability (like emission patterns and population densities). A spatially differentiated characterisation model thus seems relevant.

Methods

and Results. The European RAINS model is applied for calculation of site-dependent characterisation factors for Non-Methane Volatile Organic Compounds (NMVOCs) and nitrogen oxides (NOx) for 41 countries or regions within Europe, and compatible characterisation factors for carbon monoxide (CO) are developed based on expert judgement. These factors are presented for three emission years (1990, 1995 and 2010), and they address human health impacts and vegetation impacts in two separate impacts categories, derived from AOT40 and AOT60 values respectively. Compatible site-generic characterisation factors for NMVOC, NOx, CO and methane (CH4) are calculated as emission-weighted European averages to be applied on emissions for which the location is unknown. The site-generic and site-dependent characterisation factors are part of the EDIP2003 LCIA methodology. The factors are applied in a specific case study, and it is demonstrated how the inclusion of spatial differentiation may alter the results of the photochemical ozone characterisation of life cycle impact assessment.

Discussion

and Conclusions. Compared to traditional midpoint characterisation modelling, this novel approach is spatially resolved and comprises a larger part of the cause-effect chain including exposure assessment and exceeding of threshold values. This positions it closer to endpoint modelling and makes the results easier to interpret. In addition, the developed model allows inclusion of the contributions from NOx, which are ne- glected when applying the traditional approaches based on Photochemical Ozone Creation Potentials (POCPs). The variation in site-dependent characterisation factors is far larger than the variation in POCP factors. It thus seems more important to represent the spatially determined variation in exposure than the difference in POCP among the substances.

     

Protein-protein and protein-RNA contacts both contribute to the 15.5K-mediated assembly of the U4/U6 snRNP and the box C/D snoRNPs

The k-turn-binding protein 15.5K is unique in that it is essential for the hierarchical assembly of three RNP complexes distinct in both composition and function, namely, the U4/U6 snRNP, the box C/D snoRNP, and the RNP complex assembled on the U3 box B/C motif. 15.5K interacts with the cognate RNAs via an induced fit mechanism, which results in the folding of the surrounding RNA to create a binding site(s) for the RNP-specific proteins. However, it is possible that 15.5K also mediates RNP formation via protein-protein interactions with the complex-specific proteins. To investigate this possibility, we created a series of 15.5K mutations in which the surface properties of the protein had been changed. We assessed their ability to support the formation of the three distinct RNP complexes and found that the formation of each RNP requires a distinct set of regions on the surface of 15.5K. This implies that protein-protein contacts are essential for RNP formation in each complex. Further supporting this idea, direct protein-protein interaction could be observed between hU3-55K and 15.5K. In conclusion, our data suggest that the formation of each RNP involves the direct recognition of specific elements in both 15.5K protein and the specific RNA.     

Opisthorchis viverrini: identification of a glycine-tyrosine rich eggshell protein and its potential as a diagnostic tool for human opisthorchiasis

A cDNA encoding a novel eggshell protein (OvESP) with high-glycine (49.2%) and -tyrosine (27.8%) content was cloned from the human liver fluke Opisthorchis viverrini. In the adult parasite, the RNA products of the OvESP gene are limited to the vitelline follicles. They have a size of 800 nucleotides and are already present in 2-week-old juveniles. Immune sera of hamsters, experimentally infected, and humans, naturally infected with O. viverrini, detect bacterially expressed recombinant OvESP (rOvESP). A rabbit anti-rOvESP antiserum only reacts with the shells of intrauterine eggs in tissue sections of the parasite. Comparison of rOvESP with the parasite's excretion/secretion products as diagnostic tools for human opisthorchiasis shows a higher sensitivity (0.82-0.48) and specificity (0.97-0.91) of the recombinant protein in the ELISA technique. But the observed weak cross-reactivity of immune sera from mice infected with Schistosoma mansoni, Schistosoma mekongi, and Fasciola gigantica in Western blots of rOvESP indicates that the diagnostic quality of this protein might be compromised if infections by other trematodes are present.     

The structure of PknB in complex with mitoxantrone, an ATP-competitive inhibitor, suggests a mode of protein kinase regulation in mycobacteria

Mycobacterium tuberculosis PknB is an essential receptor-like protein kinase involved in cell growth control. Here, we demonstrate that mitoxantrone, an anthraquinone derivative used in cancer therapy, is a PknB inhibitor capable of preventing mycobacterial growth. The structure of the complex reveals that mitoxantrone partially occupies the adenine-binding pocket in PknB, providing a framework for the design of compounds with potential therapeutic applications. PknB crystallizes as a 'back-to-back' homodimer identical to those observed in other structures of PknB in complex with ATP analogs. This organization resembles that of the RNA-dependent protein kinase PKR, suggesting a mechanism for kinase activation in mycobacteria.     

Identification by families of pediatric adverse events and near misses overlooked by health care providers

Background:

Identifying adverse events and near misses is essential to improving safety in the health care system. Patients are capable of reliably identifying and reporting adverse events. The effect of a patient safety reporting system used by families of pediatric inpatients on reporting of adverse events by health care providers has not previously been investigated.

Methods:

Between Nov. 1, 2008, and Nov. 30, 2009, families of children discharged from a single ward of British Columbia’s Children’s Hospital were asked to respond to a questionnaire about adverse events and near misses during the hospital stay. Rates of reporting by health care providers for this period were compared with rates for the previous year. Family reports for specific incidents were matched with reports by health care providers to determine overlap.

Results:

A total of 544 familes responded to the questionnaire. The estimated absolute increase in reports by health care providers per 100 admissions was 0.5% (95% confidence interval −1.8% to 2.7%). A total of 321 events were identified in 201 of the 544 family reports. Of these, 153 (48%) were determined to represent legitimate patient safety concerns. Only 8 (2.5%) of the adverse events reported by families were also reported by health care providers.

Interpretation:

The introduction of a family-based system for reporting adverse events involving pediatric inpatients, administered at the time of discharge, did not change rates of reporting of adverse events and near misses by health care providers. Most reports submitted by families were not duplicated in the reporting system for health care providers, which suggests that families and staff members view safety-related events differently. However, almost half of the family reports represented legitimate patient safety concerns. Families appeared capable of providing valuable information for improving the safety of pediatric inpatients.It has been estimated that adverse events occur in about 1% of children treated in hospital and that, on average, 60% of these events are preventable.¹ To increase institutional awareness of adverse events, hospitals have implemented systems to encourage health care providers to report adverse events.² The reporting of adverse events can be improved by making electronic systems for reporting readily accessible³ and by ensuring a “just culture,” which includes nonpunitive reporting policies.⁴ However, adverse events reported by health care providers account for only a small fraction of total adverse events as determined by chart review.⁵ Time pressures to treat patients, fear of punishment, lack of belief in the benefit of reporting and differing opinions of what defines a reportable event contribute to low reporting rates.⁶ However, patients and their families are readily available, keen and motivated observers who may not be subject to these reporting barriers. Family members are capable of observing and reporting adverse events in a variety of clinical settings.⁷ It is known that the interpretation of safety events and the threshold for reporting differ among health care disciplines and individual health care providers.⁶ However, it is not clear how families of pediatric patients interpret safety-related events or what their threshold would be for reporting events.The purpose of this study was to test whether the introduction of an adverse event reporting system for use by families of pediatric patients at the time of discharge from a surgical ward would significantly change the rate of reporting of adverse events by health care providers. We also evaluated the types of events that families reported, the relevance of these events with respect to patient safety, families’ desires for anonymous reporting and families’ assessments of institutional responses to reported events. We anticipated that health care providers’ reporting rates would rise with the introduction of the family reporting system, on the assumption that greater attention would be paid to reporting safety-related events on the ward. We also anticipated that families would provide useful information about safety-related events, at least some of the time. In particular, we thought that facilitating communication from the patient’s family directly to the study institution’s Quality, Safety and Outcome Improvement Department would allow more opportunities to improve safety through changes in practice.     

Discordant patterns of nuclear and mitochondrial introgression in Iberian populations of the European common frog (Rana temporaria)

Amphibians often show complex histories of intraspecific and interspecific genetic introgression, which might differ in mitochondrial and nuclear genes. In our study of the genetic differentiation of the European common frog, Rana temporaria (159 specimens from 23 populations were analyzed for 24 presumptive allozyme loci; 82 specimens were sequenced for a 540-bp fragment of the mitochondrial 16S rRNA gene), multilocus correspondence analysis (CA) and Bayesian assignment tests of the nuclear data were concordant in identifying 2 population groups corresponding to 1) the Pyrenees in the east and 2) the Galicia and Asturias regions in the west, the latter corresponding to the subspecies R. temporaria parvipalmata. Geographically intermediate populations were genetically intermediate in the allozyme CA and, less clearly in the Bayesian assignment, with mitochondrial haplotypes exclusively belonging to the parvipalmata group. This indicates different degrees of introgression in the mitochondrial and nuclear genomes. Although Pyrenean high-altitude populations are morphologically distinct from low-altitude populations, these 2 groups were not separate clusters in any analysis. This suggests that the morphological differences may be due to fast adaptation to elevational gradients, likely under maintenance of gene flow, and that the underlying genetic changes are not detectable by the analyzed markers. We argue that a parsimonious explanation for the observed pattern along the east-west axis in northern Spain may be competition between invading and resident populations, with no need to invoke selection. However, in order to conclusively rule out selective processes, additional and finer scale data are required to test for asymmetric mating preference/behaviour, sex-biased gene flow, or sex-biased survival of potential hybrids.