Identification of a Novel Recycling Sequence in the C-tail of FPR2/ALX Receptor: Association with Cell Protection from Apoptosis

Formyl-peptide receptor type 2 (FPR2; also called ALX because it is the receptor for lipoxin A4) sustains a variety of biological responses relevant to the development and control of inflammation, yet the cellular regulation of this G-protein-coupled receptor remains unexplored. Here we report that, in response to peptide agonist activation, FPR2/ALX undergoes β-arrestin-mediated endocytosis followed by rapid recycling to the plasma membrane. We identify a transplantable recycling sequence that is both necessary and sufficient for efficient receptor recycling. Furthermore, removal of this C-terminal recycling sequence alters the endocytic fate of FPR2/ALX and evokes pro-apoptotic effects in response to agonist activation. This study demonstrates the importance of endocytic recycling in the anti-apoptotic properties of FPR2/ALX and identifies the molecular determinant required for modulation of this process fundamental for the control of inflammation.

IMP: Imperial Metagenomics Pipeline for high-throughput sequence data

We have developed an in-house pipeline for the processing and analyses of sequence data generated during Illumina technology-based metagenomic studies of the human gut microbiota. Each component of the pipeline has been selected following comparative analysis of available tools; however, the modular nature of software facilitates replacement of any individual component with an alternative should a better tool become available in due course. The pipeline consists of quality analysis and trimming followed by taxonomic filtering of sequence data allowing reads associated with samples to be binned according to whether they represent human, prokaryotic (bacterial/archaeal), viral, parasite, fungal or plant DNA. Viral, parasite, fungal and plant DNA can be assigned to species level on a presence/absence basis, allowing – for example – identification of dietary intake of plant-based foodstuffs and their derivatives. Prokaryotic DNA is subject to taxonomic and functional analyses, with assignment to taxonomic hierarchies (kingdom, class, order, family, genus, species, strain/subspecies) and abundance determination. After de novo assembly of sequence reads, genes within samples are predicted and used to build a non-redundant catalogue of genes. From this catalogue, per-sample gene abundance can be determined after normalization of data based on gene length. Functional annotation of genes is achieved through mapping of gene clusters against KEGG proteins, and InterProScan. The pipeline is undergoing validation using the human faecal metagenomic data of Qin et al. (2014, Nature 513, 59–64). Outputs from the pipeline allow development of tools for the integration of metagenomic and metabolomic data, moving metagenomic studies beyond determination of gene richness and representation towards microbial-metabolite mapping. There is scope to improve the outputs from viral, parasite, fungal and plant DNA analyses, depending on the depth of sequencing associated with samples. The pipeline can easily be adapted for the analyses of environmental and non-human animal samples, and for use with data generated via non-Illumina sequencing platforms.

A physical packing sequence algorithm for the container loading problem with static mechanical equilibrium conditions

The container loading problem (CLP) is a combinatorial optimization problem for the spatial arrangement of cargo inside containers so as to maximize the usage of space. The algorithms for this problem are of limited practical applicability if real-world constraints are not considered, one of the most important of which is deemed to be stability. This paper addresses static stability, as opposed to dynamic stability, looking at the stability of the cargo during container loading. This paper proposes two algorithms. The first is a static stability algorithm based on static mechanical equilibrium conditions that can be used as a stability evaluation function embedded in CLP algorithms (e.g. constructive heuristics, metaheuristics). The second proposed algorithm is a physical packing sequence algorithm that, given a container loading arrangement, generates the actual sequence by which each box is placed inside the container, considering static stability and loading operation efficiency constraints.

Product quality judgments in a two-sequence cue environment

Previous research demonstrated that the sequence of informational cues and the level of distraction have an impact on the judgment of a product’s quality. This study investigates the influence of the force behind the processing of these cues, working memory (WM). The results indicate that without distraction, consumers with low and high WM capacity (WMC) equally base their product evaluation on the first sequential cue. In the presence of a distractor, however, low WM individuals are no longer able to recall the initial cue, and thus derive their product judgment from the final cue. Moreover, evidence of intercultural differences in the perception of product related cues, and their aptitude for signaling a favorable product quality is provided.

Results of a collaborative study of the EDNAP group regarding mitochondrial DNA heteroplasmy and segregation in hair shafts.

A collaborative exercise was carried out by the European DNA Profiling Group (EDNAP) in order to evaluate the distribution of mitochondrial DNA (mtDNA) heteroplasmy amongst the hairs of an individual who displays point heteroplasmy in blood and buccal cells. A second aim of the exercise was to study reproducibility of mtDNA sequencing of hairs between laboratories using differing chemistries, further to the first mtDNA reproducibility study carried out by the EDNAP group. Laboratories were asked to type 2 sections from each of 10 hairs, such that each hair was typed by at least two laboratories. Ten laboratories participated in the study, and a total of 55 hairs were typed. The results showed that the C/T point heteroplasmy observed in blood and buccal cells at position 16234 segregated differentially between hairs, such that some hairs showed only C, others only T and the remainder, C/T heteroplasmy at varying ratios. Additionally, differential segregation of heteroplasmic variants was confirmed in independent extracts at positions 16093 and the poly(C) tract at 302-309, whilst a complete A-G transition was confirmed at position 16129 in one hair. Heteroplasmy was observed at position 16195 on both strands of a single extract from one hair segment, but was not observed in the extracts from any other segment of the same hair. Similarly, heteroplasmy at position 16304 was observed on both strands of a single extract from one hair. Additional variants at positions 73, 249 and the HVII poly(C) region were reported by one laboratory; as these were not confirmed in independent extracts, the possibility of contamination cannot be excluded. Additionally, the electrophoresis and detection equipment used by this laboratory was different to those of the other laboratories, and the discrepancies at position 249 and the HVII poly(C) region appear to be due to reading errors that may be associated with this technology. The results, and their implications for forensic mtDNA typing, are discussed in the light of the biology of hair formation.

Are there two species of Pygmy Shrews (Sorex)? Revisiting the question using DNA sequence data

Pygmy Shrews in North America have variously been considered to be one species (Sorex hoyi) or two species (S. hoyi and S. thompsoni). Currently, only S. hoyi is recognized. In this study, we examine mitochondrial DNA sequence data for the cytochrome b gene to evaluate the level of differentiation and phylogeographic relationships among eleven samples of Pygmy Shrews from across Canada. Pygmy Shrews from eastern Canada (i.e., Ontario, Quebec, New Brunswick, Nova Scotia, and Prince Edward Island) are distinct from Pygmy Shrews from western Canada (Alberta, Yukon) and Alaska. The average level of sequence divergence between these clades (3.3%) falls within the range of values for other recognized pairs of sister species of shrews. A molecular clock based on third position transversion substitutions suggests that these two lineages diverged between 0.44 and 1.67 million years ago. These molecular phylogenetic data. combined with a reinterpretation of previously published morphological data, are suggestive of separate species status for S. hoyi and S. thompsoni as has been previously argued by others. Further analysis of specimens from geographically intermediate areas (e.g., Manitoba. northern Ontario) is required to determine if there is secondary contact and/or introgression between these two putative species.

Representation of motor habit in a sequence of repetitive reach and grasp movements performed by macaque monkeys: evidence for a contribution of the dorsolateral prefrontal cortex.

In the context of an autologous cell transplantation study, a unilateral biopsy of cortical tissue was surgically performed from the right dorsolateral prefrontal cortex (dlPFC) in two intact adult macaque monkeys (dlPFC lesioned group), together with the implantation of a chronic chamber providing access to the left motor cortex. Three other monkeys were subjected to the same chronic chamber implantation, but without dlPFC biopsy (control group). All monkeys were initially trained to perform sequential manual dexterity tasks, requiring precision grip. The motor performance and the prehension's sequence (temporal order to grasp pellets from different spatial locations) were analysed for each hand. Following the surgery, transient and moderate deficits of manual dexterity per se occurred in both groups, indicating that they were not due to the dlPFC lesion (most likely related to the recording chamber implantation and/or general anaesthesia/medication). In contrast, changes of motor habit were observed for the sequential order of grasping in the two monkeys with dlPFC lesion only. The changes were more prominent in the monkey subjected to the largest lesion, supporting the notion of a specific effect of the dlPFC lesion on the motor habit of the monkeys. These observations are reminiscent of previous studies using conditional tasks with delay that have proposed a specialization of the dlPFC for visuo-spatial working memory, except that this is in a different context of "free-will", non-conditional manual dexterity task, without a component of working memory.

Basal and antigen-induced exposure of the proline-rich sequence in CD3ε.

The CD3ε cytoplasmic tail contains a conserved proline-rich sequence (PRS) that influences TCR-CD3 expression and signaling. Although the PRS can bind the SH3.1 domain of the cytosolic adapter Nck, whether the PRS is constitutively available for Nck binding or instead represents a cryptic motif that is exposed via conformational change upon TCR-CD3 engagement (CD3Δc) is currently unresolved. Furthermore, the extent to which a cis-acting CD3ε basic amino acid-rich stretch (BRS), with its unique phosphoinositide-binding capability, might impact PRS accessibility is not clear. In this study, we found that freshly harvested primary thymocytes expressed low to moderate basal levels of Nck-accessible PRS ("open-CD3"), although most TCR-CD3 complexes were inaccessible to Nck ("closed-CD3"). Ag presentation in vivo induced open-CD3, accounting for half of the basal level found in thymocytes from MHC(+) mice. Additional stimulation with either anti-CD3 Abs or peptide-MHC ligands further elevated open-CD3 above basal levels, consistent with a model wherein antigenic engagement induces maximum PRS exposure. We also found that the open-CD3 conformation induced by APCs outlasted the time of ligand occupancy, marking receptors that had been engaged. Finally, CD3ε BRS-phosphoinositide interactions played no role in either adoption of the initial closed-CD3 conformation or induction of open-CD3 by Ab stimulation. Thus, a basal level of open-CD3 is succeeded by a higher, induced level upon TCR-CD3 engagement, involving CD3Δc and prolonged accessibility of the CD3ε PRS to Nck.

Spatially selective implementation of the adiabatic T2 prep sequence for magnetic resonance angiography of the coronary arteries.

In coronary magnetic resonance angiography, a magnetization-preparation scheme for T2 -weighting (T2 Prep) is widely used to enhance contrast between the coronary blood-pool and the myocardium. This prepulse is commonly applied without spatial selection to minimize flow sensitivity, but the nonselective implementation results in a reduced magnetization of the in-flowing blood and a related penalty in signal-to-noise ratio. It is hypothesized that a spatially selective T2 Prep would leave the magnetization of blood outside the T2 Prep volume unaffected and thereby lower the signal-to-noise ratio penalty. To test this hypothesis, a spatially selective T2 Prep was implemented where the user could freely adjust angulation and position of the T2 Prep slab to avoid covering the ventricular blood-pool and saturating the in-flowing spins. A time gap of 150 ms was further added between the T2 Prep and other prepulses to allow for in-flow of a larger volume of unsaturated spins. Consistent with numerical simulation, the spatially selective T2 Prep increased in vivo human coronary artery signal-to-noise ratio (42.3 ± 2.9 vs. 31.4 ± 2.2, n = 22, P < 0.0001) and contrast-to-noise-ratio (18.6 ± 1.5 vs. 13.9 ± 1.2, P = 0.009) as compared to those of the nonselective T2 Prep. Additionally, a segmental analysis demonstrated that the spatially selective T2 Prep was most beneficial in proximal and mid segments where the in-flowing blood volume was largest compared to the distal segments. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.

Improving Short DNA Sequence Alignment with Parallel Computing

Variations in different types of genomes have been found to be responsible for a large degree of physical diversity such as appearance and susceptibility to disease. Identification of genomic variations is difficult and can be facilitated through computational analysis of DNA sequences. Newly available technologies are able to sequence billions of DNA base pairs relatively quickly. These sequences can be used to identify variations within their specific genome but must be mapped to a reference sequence first. In order to align these sequences to a reference sequence, we require mapping algorithms that make use of approximate string matching and string indexing methods. To date, few mapping algorithms have been tailored to handle the massive amounts of output generated by newly available sequencing technologies. In otrder to handle this large amount of data, we modified the popular mapping software BWA to run in parallel using OpenMPI. Parallel BWA matches the efficiency of multithreaded BWA functions while providing efficient parallelism for BWA functions that do not currently support multithreading. Parallel BWA shows significant wall time speedup in comparison to multithreaded BWA on high-performance computing clusters, and will thus facilitate the analysis of genome sequencing data.

THE ASSOCIATION OF SEQUENCE OF HIRING PRACTICE AND BIOPHYSICAL COMPONENTS IN SCREENING PROBATIONARY FIREFIGHTERS

Variation in hiring procedures occurs within fire service human resource departments. In this study, City 1 and City 2 applicants were required to pass their biophysical assessments prior to being hired as firefighters at the beginning and end of the screening process, respectively. City 1 applicants demonstrated significantly lower resting heart rate (RHR), resting diastolic blood pressure (RDBP), body fat% (BF) and higher z-scores for BF, trunk flexibility (TF) and overall clinical assessment (p<0.05). Regression analysis found that age and conducting the biophysical assessment at the end of the screening process explained poorer biophysical assessment results in BF% (R2=21%), BF z-score (R2=22%), TF z-score (R2=10%) and overall clinical assessment z-score (R2=7%). Each of RHR (OR=1.06, CI=1.01-1.10), RDBP (OR=1.05, CI=1.00-1.11) and BF% (OR=1.20, CI=1.07-1.37) increased the odds of being a City 2 firefighter (p<0.05). Biophysical screening at the end of the hiring process may result in the hiring of a less healthy firefighter.

Complete Genome Sequence of Erwinia amylovora Bacteriophage

The complete genome of an Erwinia amylovora bacteriophage, vB_EamM_Ea35-70 (Ea35-70), is 271,084 bp, encodes 318 putative proteins, and contains one tRNA. Comparative analysis with other Myoviridae genomes suggests that Ea35-70 is related to the Phikzlikevirus genus within the family Myoviridae, since 26% of Ea35-70 proteins share homology to proteins in Pseudomonas phage φKZ.

AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis

Affiliation: Département de biochimie, Faculté de médecine, Université de Montréal

Foraminiferal and Pteropod Records in the Late Quaternary Sequence off Northern Kerala and Their Oceanographic and Climatic Significance

In the present investigation, an attempt is made to study late Quaternary foraminiferal and pteropod records of the shelf of northern Kerala and to evaluate their potentiality in paleocenographic and paleoclimatic reconstruction. The study gives details of sediment cores, general characteristics of foraminifera and pteropod species recorded from the examined samples and their systematic classification, spatial distribution of Recent foraminifera and pteropods and their response to varying bathymetry, nature of substrate, organic matter content in sediment and hydrography across the shelf. An attempt is also made to establish an integrated chronostratigraphy for the examined core sections. An effort is also made to identify microfaunal criteria useful in biostratigraphic division in shallow marine core sections. An attempt is made to infer various factors responsible for the change in microfaunal assemblage. Reconstruction of sea level changes during the last 36,000 years was attempted based on the pteropod record. The study reveals a bathymetric control on benthic/planktic (BF/PF) foraminiferal and pteropods/planktic foraminiferal (Pt/PF) abundance ratio. Bathymetric distribution pattern of BF/PF ratio is opposite to the (Pt/PF) ratio with decreasing trend of former from the shore across the shelf. Quantitative benthic foraminiferal record in the surficial sediments reveals a positive correlation between the diversity and bathymetry. R-mode cluster analysis performed on 30n significant Recent benthic foraminiferal, determines three major assemblage.