Interlaboratory Comparison of Six Real-Time PCR Assays for Detection of Bovine Leukemia Virus Proviral DNA.

Quantitative real-time PCR (qPCR) is increasingly being used for the detection of bovine leukemia virus (BLV) proviral DNA. Nevertheless, quality control for the validation and standardization of such tests is currently lacking. Therefore, the present study was initiated by three Office International des Epizooties (OIE) reference laboratories and three collaborating laboratories to measure the interlaboratory variability of six already developed and available BLV qPCR assays. For that purpose, an international panel of 58 DNA samples reflecting the dynamic range of the majority of the assays was distributed to six testing centers. Based on qualitative results, the overall agreement among all six laboratories was moderate. However, significant variability in the measurement of the BLV proviral DNA copy number was observed among different laboratories. Quantitative PCR assays, even when performed by experienced staff, can yield large variability in BLV proviral DNA copy numbers without harmonization. Further standardization of different factors (i.e., utilization of unified protocols and unique calibrators) should increase interlaboratory agreement.

Identification of serotype-specific T cell responses to highly conserved regions of the dengue viruses.

Determining previous infecting dengue virus (DENV) serotypes has been difficult due to highly cross-reactive immune responses from previous DENV infections. Determining the correlates of serotype-specific immune responses would be crucial in understanding dengue transmission in the community and would also help to determine the correlates of protective immune responses. Therefore, we set out to define highly conserved, serotype-specific regions of the DENVs. Serotype-specific and highly conserved regions of the four DENV serotypes were identified using Basic Local Alignment Search Tool (BLAST) searches and custom perl scripts. Using ex-vivo and cultured enzyme-linked immunospot (ELISPOT) assays, we identified serotype-specific T cell epitopes within the four DENV serotypes in healthy adult donors from Sri Lanka. We identified T cell responses to 19 regions of the four DENV serotypes. Six peptides were from the NS2A region and four peptides were from the NS4A region. All immune donors responded to peptides of at least two DENV serotypes, suggesting that heterologous infection is common in Sri Lanka. Eight of 20 individuals responded to at least two peptides of DENV-4, despite this serotype not being implicated previously in any of the epidemics in Sri Lanka. The use of these regions to determine past and current infecting DENV serotypes will be of value to characterize further the dynamics of silent dengue transmission in the community. In addition, these T cell responses to these regions could be used to characterize DENV serotype-specific immune responses and thus possibly help us to understand the immune correlates of a protective immune response.

Multidisciplinary team management of tracheostomy procedures in neurocritical care patients: our experience over 17 years in a quaternary centre.

OBJECTIVE: Tracheostomy in the neurocritical care population is associated with poorer outcomes. This study hypothesised that a multidisciplinary approach to tracheostomy care can improve outcomes. METHODS: This study was a prospective longitudinal study of all tracheostomised patients in the neurocritical care units of a quaternary centre over 17 years. All patients were managed by a tracheostomy team with a constant core membership of an intensive care consultant, speech and language therapist, and physiotherapist with consultant ENT input. RESULTS: A total of 51 per cent of patients were decannulated in hospital at an average of 48 (neuromedical) and 57.6 (neurosurgical) days. Of the 42 per cent of patients transferred to another facility with a tracheostomy tube in situ, 37.5 per cent were at an advanced stage of tracheostomy weaning. Complication rates were low at 4.8 per cent with no tracheostomy associated mortalities. CONCLUSION: A multidisciplinary approach can enable good outcomes in the neurocritical care population. Consistency of care spanning the step-down from critical to ward-level care is crucial to improving outcomes.

Marine resource abundance drove pre-agricultural population increase in Stone Age Scandinavia.

How climate and ecology affect key cultural transformations remains debated in the context of long-term socio-cultural development because of spatially and temporally disjunct climate and archaeological records. The introduction of agriculture triggered a major population increase across Europe. However, in Southern Scandinavia it was preceded by ~500 years of sustained population growth. Here we show that this growth was driven by long-term enhanced marine production conditioned by the Holocene Thermal Maximum, a time of elevated temperature, sea level and salinity across coastal waters. We identify two periods of increased marine production across trophic levels (P1 7600-7100 and P2 6400-5900 cal. yr BP) that coincide with markedly increased mollusc collection and accumulation of shell middens, indicating greater marine resource availability. Between ~7600-5900 BP, intense exploitation of a warmer, more productive marine environment by Mesolithic hunter-gatherers drove cultural development, including maritime technological innovation, and from ca. 6400-5900 BP, underpinned a ~four-fold human population growth.

Mercury loading within the Selenga River basin and Lake Baikal, Siberia.

Mercury (Hg) loading in Lake Baikal, a UNESCO world heritage site, is growing and poses a serious health concern to the lake's ecosystem due to the ability of Hg to transform into a toxic form, known as methylmercury (MeHg). Monitoring of Hg into Lake Baikal is spatially and temporally sparse, highlighting the need for insights into historic Hg loading. This study reports measurements of Hg concentrations from water collected in August 2013 and 2014 from across Lake Baikal and its main inflow, the Selenga River basin (Russia, Mongolia). We also report historic Hg contamination using sediment cores taken from the south and north basins of Lake Baikal, and a shallow lake in the Selenga Delta. Field measurements from August 2013 and 2014 show high Hg concentrations in the Selenga Delta and river waters, in comparison to pelagic lake waters. Sediment cores from Lake Baikal show that Hg enrichment commenced first in the south basin in the late-19th century, and then in the north basin in the mid-20th century. Hg flux was also 20-fold greater in the south basin compared to the north basin sediments. Hg enrichment was greatest in the Selenga Delta shallow lake (Enrichment Ratio (ER) = 2.3 in 1994 CE), with enrichment occurring in the mid-to late-20th century. Local sources of Hg are predominantly from gold mining along the Selenga River, which have been expanding over the last few decades. More recently, another source is atmospheric deposition from industrial activity in Asia, due to rapid economic growth across the region since the 1980s. As Hg can bioaccumulate and biomagnify through trophic levels to Baikal's top consumer, the world's only truly freshwater seal (Pusa sibirica), it is vital that Hg input at Lake Baikal and within its catchment is monitored and controlled.

Neither interleukin-4 receptor alpha expression on CD4+ T cells, or macrophages and neutrophils is required for protective immunity to Trichinella spiralis.

The T helper type 2 (Th2) mediated expulsion of the gastrointestinal nematode Trichinella spiralis requires interleukin-4 receptor alpha (IL-4Ralpha) expression on both bone-marrow-derived and non-bone-marrow-derived cells. To more definitively investigate the role of IL-4/IL-13 responsiveness in the development of protective immunity to T. spiralis, cell-specific IL-4Ralpha signalling on CD4(+) T cells (Lck(cre) IL-4Ralpha(-/flox)) and macrophages/neutrophils (LysM(cre) IL-4Ralpha(-/flox)) was analysed on the BALB/c background. Infection of wild-type and control IL-4Ralpha(-/flox) mice induced a Th2-type immune response with elevated IL-4 cytokine production, parasite-specific immunoglobulin G1 (IgG1), total IgE, intestinal mastocytosis and enteropathy. In contrast, global IL-4Ralpha-deficient BALB/c mice showed reduced worm expulsion, antibody production, intestinal mastocytosis and gut pathology. BALB/c mice generated with cell-specific deletion of IL-4Ralpha on CD4(+) T lymphocytes or macrophages/neutrophils, controlled gastrointestinal helminth infection by eliciting a protective immune response comparable to that observed with wild-type and IL-4Ralpha(-/flox) controls. Together, this shows that the development of host protective Th2 responses accompanied by parasite loss is independent of IL-4Ralpha expression on CD4(+) T cells and macrophages/neutrophils.

Ankylosing spondylitis monocytes show upregulation of proteins involved in inflammation and the ubiquitin proteasome pathway.

OBJECTIVES: To determine if peripheral blood monocytes from patients with ankylosing spondylitis (AS) differed in protein expression compared to rheumatoid arthritis (RA) and healthy controls (HC). METHODS: Monocyte protein expression was characterised by 2D gel electrophoresis and by label-free quantitative expression profiling, using nano-ultra performance liquid chromatography coupled to electrospray ionisation mass spectrometry (ESI-MS(E), where (E) refers to low/high collision energy switching). Data sets were analysed using the Waters expression profiling system and Ingenuity pathway analysis (IPA). RESULTS: Two-dimensional gel electrophoresis showed upregulation of proteasomal constituents in AS monocytes, including the beta subunit of proteasome activator (PA)28. Monocyte expression profiling and IPA showed that significant changes in protein expression within the ubiquitin proteasome pathway (UPP) were restricted to AS monocytes. Statistically significant differences in protein expression involving the leucocyte extravasation, vascular endothelial growth factor, integrin and Toll-like receptor signalling pathways were seen in AS and RA monocytes compared to healthy controls. No evidence of upregulation of proteins involved in the endoplasmic reticulum stress response pathway was found in either AS or RA monocytes. Finally, the PA28 complex was shown to increase the generation of human leucocyte antigen (HLA)-B27 antigenic epitopes by the proteasome in vitro. CONCLUSIONS: Our proteomic analyses support the hypothesis that monocytes play an important role in the pathogenesis of AS and RA, and further suggest a specific role in AS for the UPP. Quantitative proteomic expression profiling constitutes a powerful new tool for rheumatology research.

Functional alpha 1-protease inhibitor in the lower respiratory tract of cigarette smokers is not decreased.

Cigarette smoking is the major risk factor for the development of pulmonary emphysema, a disorder that may result from an imbalance between the elastase and antielastase levels in the lungs. Decreased functional alpha 1-protease inhibitor, an inhibitor of neutrophil elastase, might render smokers susceptible to elastase-catalyzed destruction of pulmonary elastic fibers and the development of emphysema. Binding and inactivation of isotopically labeled porcine pancreatic elastase and human neutrophil elastase by alpha 1-protease inhibitor were measured in fluid obtained by bronchoalveolar lavage of volunteers. The inhibition of elastase-catalyzed solubilization of elastin and a tripeptide substrate were also determined. The mean level of functional alpha 1-protease inhibitor in the bronchoalveolar lavage fluid of smokers was found to be equal to or greater than that of nonsmokers, contradicting reports by other investigators. Increased elastase derived from pulmonary neutrophils, rather than decreased functional alpha 1-protease inhibitor, appears to be the main factor in the genesis of emphysema in smokers.

Incursion of Schmallenberg virus into Great Britain in 2011 and emergence of variant sequences in 2016.

Schmallenberg virus (SBV) is a vector-borne orthobunyavirus in the family Bunyaviridae, first identified in Germany before rapidly spreading throughout Europe. To investigate the events surrounding the incursion of this virus into Great Britain (GB) and its subsequent spread, archived sheep serum samples from an unrelated field survey in 2011 were analysed for the presence of SBV specific antibodies, to determine the earliest date of seroconversion. This serological study, along with analysis of the spatial spread of the sources of samples submitted for SBV analysis after January 2012, suggests that SBV entered GB on more than one occasion and in more than one location. Phylogenetic analysis of SBV sequences from 2012 ovine samples, from a variety of counties and dates, demonstrated a non-linear evolution of the virus, i.e. there was no distinct clustering between host species, geographical locations or during the outbreak. This also supports the notion of multiple viruses entering GB, rather than a single virus incursion. Premature termination signals were present in several non-structural putative protein sequences. One SBV sequence exhibited large deletions in the M segment of the genome. After the first outbreak in 2011-2012, interest in SBV in GB waned and continuous surveillance was not upheld. The re-emergence of SBV in 2016 has raised renewed concern and ended speculation that SBV might have been eradicated permanently from GB. When SBV sequences from 2012 were compared with those from the re-emergence in 2016-2017, a second distinct clade of SBV was identified that separates recent strains from those observed during the first outbreak.

Historical atmospheric pollution trends in Southeast Asia inferred from lake sediment records.

Fossil fuel combustion leads to increased levels of air pollution, which negatively affects human health as well as the environment. Documented data for Southeast Asia (SEA) show a strong increase in fossil fuel consumption since 1980, but information on coal and oil combustion before 1980 is not widely available. Spheroidal carbonaceous particles (SCPs) and heavy metals, such as mercury (Hg), are emitted as by-products of fossil fuel combustion and may accumulate in sediments following atmospheric fallout. Here we use sediment SCP and Hg records from several freshwater lentic ecosystems in SEA (Malaysia, Philippines, Singapore) to reconstruct long-term, region-wide variations in levels of these two key atmospheric pollution indicators. The age-depth models of Philippine sediment cores do not reach back far enough to date first SCP presence, but single SCP occurrences are first observed between 1925 and 1950 for a Malaysian site. Increasing SCP flux is observed at our sites from 1960 onward, although individual sites show minor differences in trends. SCP fluxes show a general decline after 2000 at each of our study sites. While the records show broadly similar temporal trends across SEA, absolute SCP fluxes differ between sites, with a record from Malaysia showing SCP fluxes that are two orders of magnitude lower than records from the Philippines. Similar trends in records from China and Japan represent the emergence of atmospheric pollution as a broadly-based inter-region environmental problem during the 20th century. Hg fluxes were relatively stable from the second half of the 20th century onward. As catchment soils are also contaminated with atmospheric Hg, future soil erosion can be expected to lead to enhanced Hg flux into surface waters.

Characterisation of a major phytoplankton bloom in the River Thames (UK) using flow cytometry and high performance liquid chromatography.

Recent river studies have observed rapid phytoplankton dynamics, driven by diurnal cycling and short-term responses to storm events, highlighting the need to adopt new high-frequency characterisation methods to understand these complex ecological systems. This study utilised two such analytical methods; pigment analysis by high performance liquid chromatography (HPLC) and cell counting by flow cytometry (FCM), alongside traditional chlorophyll spectrophotometry and light microscopy screening, to characterise the major phytoplankton bloom of 2015 in the River Thames, UK. All analytical techniques observed a rapid increase in chlorophyll a concentration and cell abundances from March to early June, caused primarily by a diatom bloom. Light microscopy identified a shift from pennate to centric diatoms during this period. The initial diatom bloom coincided with increased HPLC peridinin concentrations, indicating the presence of dinoflagellates which were likely to be consuming the diatom population. The diatom bloom declined rapidly in early June, coinciding with a storm event. There were low chlorophyll a concentrations (by both HPLC and spectrophotometric methods) throughout July and August, implying low biomass and phytoplankton activity. However, FCM revealed high abundances of pico-chlorophytes and cyanobacteria through July and August, showing that phytoplankton communities remain active and abundant throughout the summer period. In combination, these techniques are able to simultaneously characterise a wider range of phytoplankton groups, with greater certainty, and provide improved understanding of phytoplankton functioning (e.g. production of UV inhibiting pigments by cyanobacteria in response to high light levels) and ecological status (through examination of pigment degradation products). Combined HPLC and FCM analyses offer rapid and cost-effective characterisation of phytoplankton communities at appropriate timescales. This will allow a more-targeted use of light microscopy to capture phytoplankton peaks or to investigate periods of rapid community succession. This will lead to greater system understanding of phytoplankton succession in response to biogeochemical drivers.

Iron sequestration by macrophages decreases the potential for extracellular hydroxyl radical formation.

Alveolar macrophages (AM) from smokers contain a much higher quantity of intracellular iron than AM from nonsmokers. Since some forms of iron will catalyze the formation of hydroxyl radical (.OH) from superoxide and hydrogen peroxide, the ability of AM derived from smokers and nonsmokers to generate .OH was assessed. No detectable .OH was produced by AM from either source, suggesting that iron sequestration by AM may limit the potential for .OH-mediated lung injury. Consistent with this hypothesis, the ability of bronchoalveolar lavage fluid (BAL) from smokers and nonsmokers to act as an .OH catalyst decreased after exposure to AM. We found that, like AM, human monocyte-derived macrophages (MDM) have the ability to acquire large quantities of iron from small low molecular weight iron chelates as well as decrease the ability of BAL to act as a .OH catalyst. When MDM or AM were exposed to the iron chelates or BAL they were then able to generate .OH after phorbol myristate acetate stimulation. However, when acutely iron-loaded or BAL-exposed MDM were placed in culture, their ability to produce .OH decreased with time to the level of non-iron-exposed controls. This process correlated with iron translocation from the plasma membrane to the cytosol as well as a 3-9-fold increase in cellular ferritin. No increase in antioxidant enzyme levels or induction of the heat shock response was observed. Iron sequestration by macrophages may protect nearby cells from exposure to potentially cytotoxic iron-catalyzed oxidants such as .OH.

Vitamin A deficiency increases airway resistance following C-fiber stimulation.

Vitamin A deficiency (VAD) remains an important problem in the developing world where environmental air pollution is increasing. Because the coincidence of these factors could increase the prevalence of asthma in these regions, airway reactivity to methacholine (MCh), capsaicin, and sulfur dioxide was studied in VAD rats. The impedance to a small volume oscillation was analyzed to determine airway resistance (R(aw)) and lung elastance (H). VAD rats demonstrated larger increases in R(aw) and H after the administration of methacholine, and in R(aw) after administration of capsaicin or sulfur dioxide. The muscarinic receptor-2 (M2R) selective antagonist AFDX-116 enhanced the effect of capsaicin in vitamin A sufficient (VAS) but not VAD rats and retinoic acid-administration partially restored this enhancement. These data indicate that diminished auto-inhibitory muscarinic receptor-2 function contributed to this increased airway responsiveness to pulmonary C-fiber stimulation in VAD rats. If children with VAD also have diminished M2R function, they may be more prone to develop asthma, particularly in the presence of environmental co-factors such as sulfur dioxide.

Vitamin A deficiency alters pulmonary parenchymal collagen and tissue mechanics.

The mechanical properties of the pulmonary parenchyma are strongly influenced by the collagen and elastic fibers that course through the alveolar interstitium and interconnect the bronchovascular bundles. Vitamin A deficiency (VAD) produces effacement and remodeling of the alveolar architecture, resulting in alternating areas of alveolar dilatation and collapse. To better understand the mechanical consequences and reversibility of this remodeling process, we have examined how the remodeling of collagen and elastic fibers correlates with the mechanical properties of the lung parenchyma in VAD rats. An oscillatory impulse was applied at different levels of stress on the fiber network and the tissue damping (G), elastance (H), hysteresivity (G/H, eta) were analyzed. At a supra-physiological functional residual capacity, the lung parenchyma of VAD rats exhibited a lower G and H than Vitamin A sufficient (VAS) rats, which was accompanied by a significant decrease in the quantity of parenchymal collagen and collagen fibers. Retinoic acid (RA) administration restored the parenchymal collagen and mechanical properties.

A comparative study of inner membrane enzymes and transport systems in mitochondria from R3230AC mammary tumor and normal rat mammary gland.

Mitochondria from a rat mammary tumor (R3230AC) have been compared with mitochondria from pregnant and lactating rat mammary glands, with particular attention paid to inner membrane enzymes and Transport proteins. In the tumor the mitochondrial adenosine triphosphatase was not activated by 2,4-dinitrophenol, in contrast to the mammary mitochondria from lactating or pregnant rats. Translocation of adenosine diphosphate across the inner membrane was found to be more rapid in the tumor by virtue of lovered Km adenosine diphosphate and raised Vmax. Transport of phosphate and dicarboxylic acids occurred at similar rates in all three types of mitochondria. The inner membrane proteins were also examined directly by sodium dodecyl sulfate/polyacrylamide gel electrophoresis and some differences are noted. These results, although they indicate subtle differences between the inner mitochondrial membranes of tumor as compared with those of pregnant or lactating rat mammary glands, cannot form the basis of an explanation for enhanced glucose utilization and aerobic lactic acid production in this tumor.

Changes in the cell surface protein composition of human alveolar macrophages induced by smoking.

The cell surface proteins of human alveolar macrophages obtained from nonsmokers have been compared to those of alveolar macrophages obtained from smokers. Proteins of nonsmokers' alveolar macrophages surface labeled with 125I differed from those of smokers' alveolar macrophages, as shown by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Three major radiolabeled proteins with molecular weights of 183,000, 80,000, and 30,000 were identified in fresh smokers' cells. The major radiolabeled protein of nonsmokers' macrophages had an apparent molecular weight of approximately 183,000. Affinity chromatography suggested the Mr 183,000 protein is a mannose receptor. In contrast, the molecular weight of the major radiolabeled protein of smokers' alveolar macrophages was approximately 30,000; the Mr 183,000 protein was less prominent. When nonsmokers' alveolar macrophages were cultured in vitro before 125I labeling, the cell surface protein pattern changed to resemble that of smokers' alveolar macrophages; the Mr 183,000 protein could no longer be detected on the cell surface, whereas a Mr 80,000 protein was increased in quantity and a new Mr 30,000 protein was detected. Nonadherent macrophages showed similar changes in their surface-labeled proteins but also contained a new prominently labeled Mr 70,000 protein. Limited proteolysis peptide mapping with five different enzymes did not reveal any evidence of homology among the Mr 183,000, 80,000, 70,000, and 30,000 proteins. The differences in cell surface protein composition between alveolar macrophages of smokers and nonsmokers may reflect their functional capabilities or their state of "activation" and may be mechanistically important in the development of various pulmonary diseases seen in smokers including cancer. These results also demonstrate that major changes in the surface proteins of the human alveolar macrophage plasma membrane can occur rapidly following manipulation.

Bacterial production of carbapenems and clavams: evolution of beta-lactam antibiotic pathways.

Research into two of the four classes of naturally produced beta-lactams--the clavams and carbapenems--has started to throw light upon their biochemical pathways and underlying genetics. Interesting similarities between these two classes, from their joint discovery to an apparently common beta-lactam ring-forming enzyme, are now being revealed.

Analysis of bacterial carbapenem antibiotic production genes reveals a novel ß-lactam biosynthesis pathway.

Carbapenems are ß-lactam antibiotics which have an increasing utility in chemotherapy, particularly for nosocomial, multidrug-resistant infections. Strain GS101 of the bacterial phytopathogen, Erwinia carotovora, makes the simple ß-lactam antibiotic, 1-carbapen-2-em-3-carboxylic acid. We have mapped and sequenced the Erwinia genes encoding carbapenem production and have cloned these genes into Escherichia coli where we have reconstituted, for the first time, functional expression of the ß-lactam in a heterologous host. The carbapenem synthesis gene products are unrelated to enzymes involved in the synthesis of the so-called sulphur-containing ß-lactams, namely penicillins, cephamycins and cephalosporins. However, two of the carbapenem biosynthesis genes, carA and carC, encode proteins which show significant homology with proteins encoded by the Streptomycesclavuligerus gene cluster responsible for the production of the ß-lactamase inhibitor, clavulanic acid. These homologies, and some similarities in genetic organization between the clusters, suggest an evolutionary relatedness between some of the genes encoding production of the antibiotic and the ß-lactamase inhibitor. Our observations are consistent with the evolution of a second major biosynthetic route to the production of ß-lactam-ring-containing antibiotics.

Defining robustness protocols: a method to include and evaluate robustness in clinical plans.

We aim to define a site-specific robustness protocol to be used during the clinical plan evaluation process. Plan robustness of 16 skull base IMPT plans to systematic range and random set-up errors have been retrospectively and systematically analysed. This was determined by calculating the error-bar dose distribution (ebDD) for all the plans and by defining some metrics used to define protocols aiding the plan assessment. Additionally, an example of how to clinically use the defined robustness database is given whereby a plan with sub-optimal brainstem robustness was identified. The advantage of using different beam arrangements to improve the plan robustness was analysed. Using the ebDD it was found range errors had a smaller effect on dose distribution than the corresponding set-up error in a single fraction, and that organs at risk were most robust to the range errors, whereas the target was more robust to set-up errors. A database was created to aid planners in terms of plan robustness aims in these volumes. This resulted in the definition of site-specific robustness protocols. The use of robustness constraints allowed for the identification of a specific patient that may have benefited from a treatment of greater individuality. A new beam arrangement showed to be preferential when balancing conformality and robustness for this case. The ebDD and error-bar volume histogram proved effective in analysing plan robustness. The process of retrospective analysis could be used to establish site-specific robustness planning protocols in proton therapy. These protocols allow the planner to determine plans that, although delivering a dosimetrically adequate dose distribution, have resulted in sub-optimal robustness to these uncertainties. For these cases the use of different beam start conditions may improve the plan robustness to set-up and range uncertainties.