A streamlined approach to high-throughput proteomics

Proteomics has rapidly become an important tool for life science research, allowing the integrated analysis of global protein expression from a single experiment. To accommodate the complexity and dynamic nature of any proteome, researchers must use a combination of disparate protein biochemistry techniques, often a highly involved and time-consuming process. Whilst highly sophisticated, individual technologies for each step in studying a proteome are available, true high-throughput proteomics that provides a high degree of reproducibility and sensitivity has been difficult to achieve. The development of high-throughput proteomic platforms, encompassing all aspects of proteome analysis and integrated with genomics and bioinformatics technology, therefore represents a crucial step for the advancement of proteomics research. ProteomIQ™ (Proteome Systems) is the first fully integrated, start-to-finish proteomics platform to enter the market. Sample preparation and tracking, centralized data acquisition and instrument control, and direct interfacing with genomics and bioinformatics databases are combined into a single suite of integrated hardware and software tools, facilitating high reproducibility and rapid turnaround times. This review will highlight some features of ProteomIQ, with particular emphasis on the analysis of proteins separated by 2D polyacrylamide gel electrophoresis. © 2005 Future Drugs Ltd

EPO-receptor is present in mouse C2C12 and human primary skeletal muscle cells but EPO does not influence myogenesis.

Abstract The role and regulation of the pleiotropic cytokine erythropoietin (EPO) in skeletal muscle are controversial. EPO exerts its effects by binding its specific receptor (EPO-R), which activates intracellular signaling and gene transcription in response to internal and external stress signals. EPO is suggested to play a direct role in myogenesis via the EPO-R, but several studies have questioned the effect of EPO treatment in muscle in vitro and in vivo. The lack of certainty surrounding the use of nonspecific EPO-R antibodies contributes to the ambiguity of the field. Our study demonstrates that the EPO-R gene and protein are expressed at each stage of mouse C2C12 and human skeletal muscle cell proliferation and differentiation and validates a specific antibody for the detection of the EPO-R protein. However, in our experimental conditions, EPO treatment had no effect on mouse C2C12 and human muscle cell proliferation, differentiation, protein synthesis or EPO-R expression. While an increase in Akt and MAPK phosphorylation was observed, we demonstrate that this effect resulted from the stress caused by changing medium and not from EPO treatment. We therefore suggest that skeletal muscle EPO-R might be present in a nonfunctional form, or too lowly expressed to play a role in muscle cell function

The Angstrom Project: a microlensing survey of the structure and composition of the bulge of the Andromeda galaxy

The Andromeda Galaxy Stellar Robotic Microlensing Project (The Angstrom Project) aims to use stellar microlensing events to trace the structure and composition of the inner regions of the Andromeda Galaxy (M31). We present microlensing rate and timescale predictions and spatial distributions for stellar and sub-stellar lens populations in combined disk and barred bulge models of M31. We show that at least half of the stellar microlenses in and around the bulge are expected to have characteristic durations between 1 and 10 days, rising to as much as 80% for brown-dwarf dominated mass functions. These short-duration events are mostly missed by current microlensing surveys that are looking for Macho candidates in the M31 dark matter halo. Our models predict that an intensive monitoring survey programme such as Angstrom, which will be able to detect events of durations upwards of a day, could detect around 30 events per season within ~5 arcminutes of the M31 centre, due to ordinary low-mass stars and remnants. This yield increases to more than 60 events for brown-dwarf dominated mass functions. The overall number of events and their average duration are sensitive diagnostics of the bulge mass, in particular the contribution of low-mass stars and brown dwarfs. The combination of an inclined disk, an offset bar-like bulge, and differences in the bulge and disk luminosity functions results in a four-way asymmetry in the number of events expected in each quadrant defined by the M31 disk axes. The asymmetry is sensitive to the bar prolongation, orientation and mass.Comment: 9 pages, submitted to MNRA

Insight Into the Formation of the Milky Way Through Cold Halo Substructure. II. The Elemental Abundances of ECHOS

We determine the average metallicities of the elements of cold halo substructure (ECHOS) that we previously identified in the inner halo of the Milky Way within 17.5 kpc of the Sun. As a population, we find that stars kinematically associated with ECHOS are chemically distinct from the background kinematically smooth inner halo stellar population along the same Sloan Extension for Galactic Understanding and Exploration (SEGUE) line of sight. ECHOS are systematically more iron-rich, but less alpha-enhanced than the kinematically-smooth component of the inner halo. ECHOS are also chemically distinct from other Milky Way components: more iron-poor than typical thick-disk stars and both more iron-poor and alpha-enhanced than typical thin-disk stars. In addition, the radial velocity dispersion distribution of ECHOS extends beyond sigma ~ 20 km s^-1. Globular clusters are unlikely ECHOS progenitors, as ECHOS have large velocity dispersions and are found in a region of the Galaxy in which iron-rich globular clusters are very rare. Likewise, the chemical composition of stars in ECHOS do not match predictions for stars formed in the Milky Way and subsequently scattered into the inner halo. Dwarf spheroidal (dSph) galaxies are possible ECHOS progenitors, and if ECHOS are formed through the tidal disruption of one or more dSph galaxies, the typical ECHOS [Fe/H] ~ -1.0 and radial velocity dispersion sigma ~ 20 km s^-1 implies a dSph with M_tot >~ 10^9 M_Sun. Our observations confirm the predictions of theoretical models of Milky Way halo formation that suggest that prominent substructures are likely to be metal-rich, and our result implies that the most likely metallicity for a recently accreted star currently in the inner halo is [Fe/H] ~ -1.0.Comment: 31 pages and 16 figures, and 3 tables in emulateapj format; accepted for publication in ApJ. Full tables can be extracted from TeX sourc

Effects of Grassland Management Practices on Ant Functional Groups in Central North America

Tallgrass prairies of central North America have experienced disturbances including fire and grazing for millennia. Little is known about the effects of these disturbances on prairie ants, even though ants are thought to play major roles in ecosystem maintenance. We implemented three management treatments on remnant and restored grassland tracts in the central U.S., and compared the effects of treatment on abundance of ant functional groups. Management treatments were: (1) patch-burn graze—rotational burning of three spatially distinct patches within a fenced tract, and growing-season cattle grazing; (2) graze-and-burn—burning entire tract every 3 years, and growing-season cattle grazing, and (3) burn-only—burning entire tract every 3 years, but no cattle grazing. Ant species were classified into one of four functional groups. Opportunist ants and the dominant ant species, Formica montana, were more abundant in burn-only tracts than tracts managed with either of the grazing treatments. Generalists were more abundant in graze-and-burn tracts than in burn-only tracts. Abundance of F. montana was negatively associated with pre-treatment time since fire, whereas generalist ant abundance was positively associated. F. montanawere more abundant in restored tracts than remnants, whereas the opposite was true for subdominants and opportunists. In summary, abundance of the dominant F. montana increased in response to intense disturbances that were followed by quick recovery of plant biomass. Generalist ant abundance decreased in response to those disturbances, which we attribute to the effects of competitive dominance of F. montana upon the generalists

Preoperative aerobic fitness and perioperative outcomes in patients undergoing cystectomy before and after implementation of a national lockdown

Abstract Background Lower fitness is a predictor of adverse outcomes after radical cystectomy. Lockdown measures during the COVID-19 pandemic affected daily physical activity. We hypothesised that lockdown during the pandemic was associated with a reduction in preoperative aerobic fitness and an increase in postoperative complications in patients undergoing radical cystectomy. Methods We reviewed routine preoperative cardiopulmonary exercise testing (CPET) data collected prior to the pandemic (September 2018 to March 2020) and after lockdown (March 2020 to July 2021) in patients undergoing radical cystectomy. Differences in CPET variables, Postoperative Morbidity Survey (POMS) data, and length of hospital stay were compared. Results We identified 267 patients (85 pre-lockdown and 83 during lockdown) who underwent CPET and radical cystectomy. Patients undergoing radical cystectomy throughout lockdown had lower ventilatory anaerobic threshold (9.0 [7.9–10.9] vs 10.3 [9.1–12.3] ml kg−1 min−1; P=0.0002), peak oxygen uptake (15.5 [12.9–19.1] vs 17.5 [14.4–21.0] ml kg−1 min−1; P=0.015), and higher ventilatory equivalents for carbon dioxide (34.7 [31.4–38.5] vs 33.4 [30.5–36.5]; P=0.030) compared with pre-lockdown. Changes were more pronounced in males and those aged >65 yr. Patients undergoing radical cystectomy throughout lockdown had a higher proportion of day 5 POMS-defined morbidity (89% vs 75%, odds ratio [OR] 2.698, 95% confidence interval [CI] 1.143–6.653; P=0.019), specifically related to pulmonary complications (30% vs 13%, OR 2.900, 95% CI 1.368–6.194; P=0.007) and pain (27% vs 9%, OR 3.471, 95% CI 1.427–7.960; P=0.004), compared with pre-lockdown on univariate analysis. Conclusions Lockdown measures in response to the COVID-19 pandemic were associated with a reduction in fitness and an increase in postoperative morbidity among patients undergoing radical cystectomy

Utilization, retention and bio-efficacy studies of PermaNet® in selected villages in Buie and Fentalie districts of Ethiopia

<p>Abstract</p> <p>Background</p> <p>Malaria remains a major public health problem in Ethiopia. Pyrethroid-treated mosquito nets are one of the major tools available for the prevention and control of malaria transmission. PermaNet^®is a long-lasting insecticide-treated net (LLIN) recommended by WHO for malaria control.</p> <p>Objective</p> <p>The objective of the study was to assess utilization and retention of PermaNet^®nets distributed for malaria control in Buie and Fentalie districts and monitor the bio-efficacy of the nets using the WHO cone bioassay test procedures.</p> <p>Methods</p> <p>A cross sectional study was carried out by interviewing household heads or their representative in Buie and Fentalie districts. The two districts were selected based on a priori knowledge of variations on ethnic background and housing construction. Clusters of houses were chosen within each of the study villages for selection of households. 20 households that had received one or more PermaNet^®nets were chosen randomly from the clusters in each village. A total of eight used PermaNet^®nets were collected for the bio-efficacy test. The bio-efficacy of PermaNet^®nets was monitored according to the standard WHO procedures using a susceptible colony of <it>Anopheles arabiensis </it>to deltamethrin.</p> <p>Results</p> <p>A total of 119 household heads were interviewed during the study. The retention rate of nets that were distributed in 2005 and 2006 season was 72%. A total of 62.2% of the interviewees claimed children under five years of age slept under LLIN, while only 50.7% of the nets were observed to be hanged inside houses when used as a proxy indicator of usage of LLIN. For the bio-efficacy test the mean knock-down was 94% and 100%, while the mean mortality rate observed after 24 hr holding period was 72.2% and 67% for Buie and Fentalie districts respectively.</p> <p>Conclusion</p> <p>The study revealed a moderately high retention of PermaNet^®in the study villages and effectiveness of the nets when tested according to the standard WHO procedure.</p

Physical and land-cover variables influence ant functional groups and species diversity along elevational gradients

Of particular importance in shaping species assemblages is the spatial heterogeneity of the environment. The aim of our study was to investigate the influence of spatial heterogeneity and environmental complexity on the distribution of ant functional groups and species diversity along altitudinal gradients in a temperate ecosystem (Pyrenees Mountains). During three summers, we sampled 20 sites distributed across two Pyrenean valleys ranging in altitude from 1,009 to 2,339 m by using pitfall traps and hand collection. The environment around each sampling points was characterized by using both physical and land-cover variables. We then used a self-organizing map algorithm (SOM, neural network) to detect and characterize the relationship between the spatial distribution of ant functional groups, species diversity, and the variables measured. The use of SOM allowed us to reduce the apparent complexity of the environment to five clusters that highlighted two main gradients: an altitudinal gradient and a gradient of environmental closure. The composition of ant functional groups and species diversity changed along both of these gradients and was differently affected by environmental variables. The SOM also allowed us to validate the contours of most ant functional groups by highlighting the response of these groups to the environmental and land-cover variables

A VAMP7/Vti1a SNARE complex distinguishes a non-conventional traffic route to the cell surface used by KChIP1 and Kv4 potassium channels

The KChIPs (K+ channel-interacting proteins) are EF hand-containing proteins required for the traffic of channel-forming Kv4 K+ subunits to the plasma membrane. KChIP1 is targeted, through N-terminal myristoylation, to intracellular vesicles that appear to be trafficking intermediates from the ER (endoplasmic reticulum) to the Golgi but differ from those underlying conventional ER–Golgi traffic. To define KChIP1 vesicles and the traffic pathway followed by Kv4/KChIP1 traffic, we examined their relationship to potential SNARE (soluble N-ethylmaleimide-sensitive fusion protein-attachment protein receptor) proteins mediating the trafficking step. To distinguish Kv4/KChIP1 from conventional constitutive traffic, we compared it to the traffic of the VSVG (vesicular-stomatitis virus G-protein). Expression of KChIP with single or triple EF hand mutations quantitatively inhibited Kv4/KChIP1 traffic to the cell surface but had no effect on VSVG traffic. KChIP1-expressing vesicles co-localized with the SNARE proteins Vti1a and VAMP7 (vesicle-associated membrane protein 7), but not with the components of two other ER–Golgi SNARE complexes. siRNA (small interfering RNA)-mediated knockdown of Vti1a or VAMP7 inhibited Kv4/KChIP1traffic to the plasma membrane in HeLa and Neuro2A cells. Vti1a and VAMP7 siRNA had no effect on VSVG traffic or that of Kv4.2 when stimulated by KChIP2, a KChIP with different intrinsic membrane targeting compared with KChIP1. The present results suggest that a SNARE complex containing VAMP7 and Vti1a defines a novel traffic pathway to the cell surface in both neuronal and non-neuronal cells