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Background: Predicting and explaining species occurrence using environmental characteristics is essential for nature conservation and management. Species distribution models consider species occurrence as the dependent variable and environmental conditions as the independent variables. Suitable conditions are estimated based on a sample of species observations, where one assumes that the underlying environmental conditions are known. This is not always the case, as environmental variables at broad spatial scales are regularly extrapolated from point-referenced data. However, treating the predicted environmental conditions as accurate surveys of independent variables at a specific point does not take into account their uncertainty. Methods: We present a joint hierarchical Bayesian model where models for the environmental variables, rather than a set of predicted values, are input to the species distribution model. All models are fitted together based only on point-referenced observations, which results in a correct propagation of uncertainty. We use 50 plant species representative of the Dutch flora in natural areas with 8 soil condition predictors taken during field visits in the Netherlands as a case study. We compare the proposed model to the standard approach by studying the difference in associations, predicted maps, and cross-validated accuracy. Findings: We find that there are differences between the two approaches in the estimated association between soil conditions and species occurrence (correlation 0.64-0.84), but the predicted maps are quite similar (correlation 0.82-1.00). The differences are more pronounced in the rarer species. The cross-validated accuracy is substantially better for 5 species out of the 50, and the species can also help to predict the soil characteristics. The estimated associations tend to have a smaller magnitude with more certainty. Conclusion: These findings suggests that the standard model is often sufficient for prediction, but effort should be taken to develop models which take the uncertainty in the independent variables into account for interpretation. [ABSTRACT FROM AUTHOR]

Serological assays for bovine tuberculosis diagnosis require the use of multiple Mycobacterium bovis specific antigens to ensure the detection of infected animals. In the present study, identification and selection process of antigens, based on data from published proteomic studies and involving the use of bioinformatics tools and an immuno-screening step, was firstly performed for identifying novel antigens that elicit an antibody response in M. bovis infection. Based on this approach, a panel of 10 M. bovis antigens [with known relevance (MPB70, MPB83, MPB70/83, and ESAT6/CFP10) and novel (Mb1961c, Mb1301c, Mb3871, Mb1403, Mb0592, and PE25/PPE41)] were constructed and thenused to develop a new multiplexed serological assay based on Luminex technology. The performance of the Luminex-bTB immunoassay was evaluated using sera from cattle with known tuberculosis status. Among the proteins whose ability to detect bovine tuberculosis was evaluated for the first time, PE25/PPE41 and Mb1403, but not Mb3871, showed good detection capacity. Following multiple antigen combination, the final Luminex-bTB immunoassay included seven antigens (MPB70, MPB83, MPB70/83, ESAT6/CFP10, PE25/PPE41, Mb1403, and Mb0592) and showed better global performance than the immunoassay using the four usual antigens (MPB70, MPB70/83, MPB83 and ESAT6/CFP10). The specificity and sensitivity values were, respectively, of 97.6% and 42.8% when the cut-off of two-positive antigens was used to classify samples as positive. With the use of the more-restrictive criterion of three-positive antigens, the specificity increased to 99.2% but the sensitivity decreased to 23.9%. The analysis of antigen profiles generated with the Luminex-bTB immunoassay showed that mainly serodominant proteins were recognized in samples from infected cattle. The detection of Mb1961c and Mb1301c appeared to be associated with presumed false-positive results. Moreover, sera from cattle originating from bTB-outbreaks but having inconclusive or negative skin test results were identified as positive by the Luminex-bTB immunoassay and showed an antigen pattern associated with M. bovis infection. The Luminex-bTB immunoassay including seven antigens may be useful as adjunct test for the detection of M. bovis–infected herds, and different cut-offs could be applied according to the bovine tuberculosis epidemiological context. [ABSTRACT FROM AUTHOR]

Video monitoring is a rapidly evolving tool in aquatic ecological research because of its non-destructive ability to assess fish assemblages. Nevertheless, methodological considerations of video monitoring techniques are often overlooked, especially in more complex sampling designs, causing inefficient data collection, processing, and interpretation. In this study, we discuss how video transect sampling designs could be assessed and how the inter-observer variability, design errors and sampling variability should be quantified and accounted for. The study took place in the coastal areas of the Galapagos archipelago and consisted of a hierarchical repeated-observations sampling design with multiple observers. Although observer bias was negligible for the assessment of fish assemblage structure, diversity and counts of individual species, sampling variability caused by simple counting/detection errors, observer effects and instantaneous fish displacement was often important. Especially for the counts of individual species, sampling variability most often exceeded the variability of the transects and sites. An extensive part of the variability in the fish assemblage structure was explained by the different transects (13%), suggesting that a sufficiently high number of transects is required to account for the within-location variability. Longer transect lengths allowed a better representation of the fish assemblages as sampling variability decreased by 33% if transect length was increased from 10 to 50 meters. However, to increase precision, including more repeats was typically more efficient than using longer transect lengths. The results confirm the suitability of the technique to study reef fish assemblages, but also highlight the importance of a sound methodological assessment since different biological responses and sampling designs are associated with different levels of sampling variability, precision and ecological relevance. Therefore, besides the direct usefulness of the results, the procedures to establish them may be just as valuable for researchers aiming to optimize their own sampling technique and design. [ABSTRACT FROM AUTHOR]

Oxidative stress and lipotoxicity effects on pancreatic β cells play a major role in the pathogenesis of type 2 diabetes (T2D). Flavonoids and antioxidants are under study for their cytoprotective effects and antidiabetic potential. In this study, we aimed to compare the protective effect of the Rooibos components aspalathin, isoorientin, 3-hydroxyphloretin (3-OH) and green Rooibos extract (GRT) itself, and exendin-4 and N-acetylcysteine (NAC) as reference molecules, against lipotoxicity and oxidative stress. The insulin-producing β cell line INS1E was exposed to hydrogen peroxide or streptozotocin (STZ) to induce oxidative stress, and palmitate to induce lipotoxicity. Cell viability was assessed by a MTS cell viability assay. Antioxidant response and antiapoptotic gene expression was performed by qRT-PCR. Glucose transporter 2 (GLUT 2) transporter inhibition was assessed through 2-NBDG uptake. GRT and the flavonoids aspalathin and 3-hydroxyphloretin offered significant protection against oxidative stress and lipotoxicity. GRT downregulated expression of pro-apoptotic genes Txnip and Ddit3. The flavonoids aspalathin and 3-hydroxyphloretin also downregulated these genes and in addition upregulated expression of antioxidant response genes Hmox1, Nqo1 and Sod1. Isoorientin gave no cytoprotection. Cytoprotection by Rooibos components was significantly higher than by NAC or exendin-4. Rooibos components strongly protect INS1E β cells against diabetogenic stress. Cytoprotection was associated with the upregulation of antioxidant response genes of the NRF2/KEAP1 pathway or suppression of the TXN system. The Rooibos molecules offered better protection against these insults than exendin-4 and NAC, making them interesting candidates as β cell cytoprotectants for therapeutic or nutraceutical applications. [ABSTRACT FROM AUTHOR]

While shifts to high-intensity land cover have caused overwhelming biodiversity loss, it remains unclear how important natural land cover is to the occurrence, and thus the conservation, of different species groups. We used over 4 million plant species' observations to evaluate the conservation importance of natural land cover by its association with the occurrence probability of 1 122 native and 403 exotic plant species at 1 km resolution by species distribution models. We found that 74.9% of native species, 83.9% of the threatened species and 77.1% rare species preferred landscapes with over 50% natural land cover, while these landscapes only accounted for 15.6% of all grids. Most species preferred natural areas with a mixture of forest and open areas rather than areas with completely open or forested nature. Compared to native species, exotic species preferred areas with lower natural land cover and the cover of natural open area, but they both preferred extremely high and low cover of natural forest area. Threatened and rare species preferred higher natural land cover, either cover of natural forest area or cover of natural open area than not threatened and common species, but rare species were also more likely to occur in landscapes with 0–25% cover of natural open area. Although more natural land cover in a landscape will not automatically result in more native species, because there is often a non-linear increase in species occurrence probability when going from 0% to 100% natural land cover, for conserving purposes, over 80% natural land cover should be kept in landscapes for conserving threatened and very rare species, and 60% natural land cover is the best for conserving common native species. Our results stress the importance of natural areas for plant species' conservation. It also informs improvements to species conservation by increasing habitat diversity. [ABSTRACT FROM AUTHOR]

This study is the first in the world to investigate the expected impact of the COVID-19 crisis on career outcomes and career aspirations. To this end, high-quality survey research with a relevant sample of Flemish (Belgian) employees was conducted. About 21% of them fear losing their jobs due to the crisis—14% are concerned that they will even lose their jobs in the near future. In addition, 26% expect to miss out on promotions that they would have received had the COVID-19 crisis not occurred. This fear of a negative impact is higher in vulnerable groups, such migrants. In addition, we observe that many respondents believe they will look at the labour market differently and will have different work-related priorities in the future. In this respect, more than half of the respondents indicate that they have attached more importance to working conditions and work-life balance since the COVID-19 crisis. [ABSTRACT FROM AUTHOR]

This research contributes to the limited literature concerning the determinants of loneliness at work, as well as to the literature on psychological outcomes associated with temporary work. More specifically, we are adding to the literature by exploring whether there is an association between working temporarily and loneliness at work and whether loneliness at work partly explains the association between working temporarily and job satisfaction. To this end, we analyse—by means of a mediation model—a unique sample of Flemish employees in the private sector. We find that employees with a temporary contract experience more loneliness at work as opposed to employees with a permanent contract. In addition, we discover that loneliness at work mediates the association between working temporarily and job satisfaction. [ABSTRACT FROM AUTHOR]

Dispersal is an important life-history trait. In marine meiofauna, and particularly in nematodes, dispersal is generally considered to be mainly passive, i.e. through transport with water currents and bedload transport. Because nematodes have no larval dispersal stage and have a poor swimming ability, their per capita dispersal capacity is expected to be limited. Nevertheless, many marine nematode genera and even species have near-cosmopolitan distributions, and at much smaller spatial scales, can rapidly colonise new habitat patches. Here we demonstrate that certain marine nematodes, like the morphospecies Litoditis marina, can live inside macroalgal structures such as receptacula and–to a lesser extent–floating bladders, which may allow them to raft over large distances with drifting macroalgae. We also demonstrate for the first time that these nematodes can colonize new habitat patches, such as newly deposited macroalgal wrack in the intertidal, not only through seawater but also through air. Our experimental set-up demonstrates that this aerial transport is probably the result of hitchhiking on vectors such as insects, which visit, and move between, the patches of deposited algae. Transport by wind, which has been observed for terrestrial nematodes and freshwater zooplankton, could not be demonstrated. These results can be important for our understanding of both large-scale geographic distribution patterns and of the small-scale colonization dynamics of habitat patches by marine nematodes. [ABSTRACT FROM AUTHOR]

Background: Building on the recent finding that chronic pain patients with impaired functioning of the descending nociceptive inhibitory system (DNIS) present lower resting heart rate variability (HRV), this study aims to investigate the impact of Spinal Cord Stimulation (SCS) on HRV in patients with Failed Back Surgery Syndrome (FBSS). More precisely, we hypothesize that SCS influences the DNIS, with increased parasympathetic tone as a consequence, as measurable by HRV analysis. Methods: Twenty-two patients diagnosed with FBSS and treated with SCS participated in this study. HRV was measured with a 2-lead ECG registration tool during on and off states of SCS. HRV analysis for time, frequency, time-frequency and nonlinear domain parameters was based on a 5-minute recording segment. Results: The mean heart rate and low frequency power were significantly lower when SCS was activated. HRV, absolute and normalized high frequency power significantly increased during SCS compared to without SCS. The ratio of low frequency/high frequency ratios, as parameter for global sympathetic-parasympathetic equilibrium, significantly decreased when SCS was activated. Conclusions: When SCS is switched off, patients with FBSS present relatively stronger sympathetic tone and weaker parasympathetic activity. Activation of the SCS, possibly via stimulation of the DNIS, restores this disbalance of autonomic activity. [ABSTRACT FROM AUTHOR]

Agents living in volatile environments must be able to detect changes in contingencies while refraining to adapt to unexpected events that are caused by noise. In Reinforcement Learning (RL) frameworks, this requires learning rates that adapt to past reliability of the model. The observation that behavioural flexibility in animals tends to decrease following prolonged training in stable environment provides experimental evidence for such adaptive learning rates. However, in classical RL models, learning rate is either fixed or scheduled and can thus not adapt dynamically to environmental changes. Here, we propose a new Bayesian learning model, using variational inference, that achieves adaptive change detection by the use of Stabilized Forgetting, updating its current belief based on a mixture of fixed, initial priors and previous posterior beliefs. The weight given to these two sources is optimized alongside the other parameters, allowing the model to adapt dynamically to changes in environmental volatility and to unexpected observations. This approach is used to implement the “critic” of an actor-critic RL model, while the actor samples the resulting value distributions to choose which action to undertake. We show that our model can emulate different adaptation strategies to contingency changes, depending on its prior assumptions of environmental stability, and that model parameters can be fit to real data with high accuracy. The model also exhibits trade-offs between flexibility and computational costs that mirror those observed in real data. Overall, the proposed method provides a general framework to study learning flexibility and decision making in RL contexts. [ABSTRACT FROM AUTHOR]

The use of music and specifically tempo-matched music has been shown to affect running performance. But can we maximize the synchronization of movements to music and does maximum synchronization influence kinematics and motivation? In this study, we explore the effect of different types of music-to-movement alignment strategies on phase coherence, cadence and motivation. These strategies were compared to a control condition where the music tempo was deliberately not aligned to the running cadence. Results show that without relative phase alignment, a negative mean asynchrony (NMA) of footfall timings with respect to the beats is obtained. This means that footfalls occurred slightly before the beat and that beats were anticipated. Convergence towards this NMA or preferred relative phase angle was facilitated when the first music beat of a new song started close to the step, which means that entrainment occurred. The results also show that using tempo and phase alignment, the relative phase can be manipulated or forced in a certain angle with a high degree of accuracy. Ensuring negative angles larger than NMA (step before beat) results in increased motivation and decreasing cadence. Running in NMA or preferred relative phase angles results in a null effect on cadence. Ensuring a positive phase angle with respect to NMA results in higher motivation and higher cadence. None of the manipulations resulted in change in perceived exhaustion or a change in velocity. Results also indicate that gender plays an important role when using forced phase algorithms: effects were more pronounced for the female population than for the male population. The implementation of the proposed alignment strategies and control of beat timing while running opens possibilities optimizing the individual running cadence and motivation. [ABSTRACT FROM AUTHOR]

Coexistence of highly similar species is at odds with ecological theory of competition; coexistence, then, requires stabilizing mechanisms such as differences in ecological niche. In the bacterivore nematode Litoditis marina species complex, which occurs associated with macro-algae, four cryptic lineages (Pm I-IV) co-occur in the field along the south-western coast and estuaries of The Netherlands. Here we investigate the temporal and/or spatial niche differentiation in their natural environment using a qPCR-based detection and relative quantification method. We collected different algal species (i.e. two Fucus species and Ulva sp.) and separated algal structures (i.e. receptacula, thalli, non-fertile tips and bladders) at different sampling months and times (i.e. twice per sampling month), to examine differences in microhabitat use between coexisting L. marina species. Results demonstrate that the cryptic species composition varied among different algal species and algal structures, which was also subject to temporal shifts. Pm I dominated on Fucus spp., Pm II showed dominance on Ulva sp., while Pm III overall had the lowest frequencies. Microhabitat partitioning was most pronounced between the two cryptic species which had similar microbiomes (Pm I and Pm II), and less so between the two species which had significantly different microbiomes (Pm I and Pm III), suggesting that species which share the same microhabitats may avoid competition through resource partitioning. The interplay of microhabitat differentiation and temporal dynamics among the cryptic species of L. marina implies that there is a complex interaction between biotic components and abiotic factors which contributes to their coexistence in the field. [ABSTRACT FROM AUTHOR]

Objective: Successfully stopping or reducing treatment for patients with rheumatoid arthritis (RA) in low disease activity (LDA) may improve cost-effectiveness of care. We evaluated the multi-biomarker disease activity (MBDA) score as a predictor of disease relapse after discontinuation of TNF inhibitor (TNFi) treatment. Methods: 439 RA patients who were randomized to stop TNFi treatment in the POET study were analyzed post-hoc. Three indicators of disease relapse were assessed over 12 months: 1) restarting TNFi treatment, 2) escalation of any DMARD therapy and 3) physician-reported flare. MBDA score was assessed at baseline. Associations between MBDA score and disease relapse were examined using univariate analysis and multivariate logistic regression. Results: At baseline, 50.1%, 35.3% and 14.6% of patients had low (<30), moderate (30−44) or high (>44) MBDA scores. Within 12 months, 49.9% of patients had restarted TNFi medication, 59.0% had escalation of any DMARD and 57.2% had ≥1 physician-reported flare. MBDA score was associated with each indicator of relapse. At least one indicator of relapse was observed in 59.5%, 68.4% and 81.3% of patients with low, moderate or high MBDA scores, respectively (P = 0.004). Adjusted for baseline DAS28-ESR, disease duration, BMI and erosions, high MBDA scores were associated with increased risk for restarting TNFi treatment (OR = 1.85, 95% CI 1.00–3.40), DMARD escalation (OR = 1.99, 95% CI 1.01–3.94) and physician-reported flare (OR = 2.00, 95% 1.06–3.77). Conclusion: For RA patients with stable LDA who stopped TNFi, a high baseline MBDA score was independently predictive of disease relapse within 12 months. The MBDA score may be useful for identifying patients at risk of relapse after TNFi discontinuation. [ABSTRACT FROM AUTHOR]

Background: Methotrexate (MTX) is widely used as disease modifying treatment for psoriasis and psoriatic arthritis (PsA). Rheumatological and dermatological guidelines to prevent MTX-induced adverse events diverge in the number and frequency of blood tests. These differences are not based on evidence indicating a higher risk for patients with psoriasis compared to PsA or rheumatic arthritis (RA). This raises the question if multiple testing increases safety, or results in false positive signals potentially leading to early withdrawal of an effective treatment. Objective: Compare the effects of MTX monitoring strategies by rheumatologists and dermatologists regarding drug survival, reasons for withdrawal and safety. Methods: Retrospective follow-up of all patients diagnosed with psoriasis by dermatologists or PsA by rheumatologists. Included were consecutive patients who started methotrexate (MTX) between 2006 and 2012 and had a scheduled follow-up by dermatologist or rheumatologist. Exclusions were: drug not started after the first prescription or incomplete availability of lab data. Data were extracted from electronic records: start and stop dates and dosing of MTX; treatment with folic acid and dose; reasons for withdrawal of MTX; numbers of blood sampling and types of laboratory tests performed for MTX safety; number of abnormal tests; occurrence of any serious adverse event (SAE). Results: 190 Psoriasis and 196 PsA patients starting methotrexate (MTX) were included. Age and sex were comparable. PsA patients used higher initial and maximum doses of MTX and folic acid, but psoriasis patients had a higher frequency of abnormal laboratory results (0.14 vs 0.03 per treatment month, p<0.001), resulting in a striking difference in withdrawal of MTX for abnormal liver enzymes (15.8% vs 3.6%, p<0.001). In PsA patients MTX was withdrawn less frequently for ineffectiveness (15.8 vs 24.2%, p<0.05) leading to longer drug survival in the first course of treatment (37.4±30 vs 18.8±19.1 months). Repeated courses of MTX were more often prescribed by rheumatologists than by dermatologists. There were no significant differences in the occurrence of SAE (psoriasis 0.0041 vs PsA 0.0038 per treatment month) or death (1.6% vs 2.0%) between these groups. Hospital admissions related to infection were recorded in 6 (3.1%) PsA vs 4 (2.1%) psoriasis patients. Conclusion: Strict monitoring by dermatologists resulted in more abnormal findings, which reduced drug survival of MTX. The limited monitoring strategy by rheumatologists was not associated with more SAEs. Further research in other populations is needed to confirm whether reduced intensity of monitoring can optimize the use of MTX with sufficient long-term safety. [ABSTRACT FROM AUTHOR]

The article presents opinions of authors on guidelines for the use of morpholino in zebrafish. Topics discussed include zebrafish as a powerful model to study vertebrate development and disease, morpholino (MO) antisense oligomers as a tool of choice for gene knockdown in a range of models, and reverse genetics to study gene function in zebrafish.

The aim was to examine the effects of recumbency and anaesthesia on distribution of ventilation in beagle dogs using Electrical Impedance Tomography (EIT). Nine healthy beagle dogs, aging 3.7±1.7 (mean±SD) years and weighing 16.3±1.6 kg, received a series of treatments in a fixed order on a single occasion. Conscious dogs were positioned in right lateral recumbency (RLR) and equipped with 32 EIT electrodes around the thorax. Following five minutes of equilibration, two minutes of EIT recordings were made in each recumbency in the following order: RLR, dorsal (DR), left (LLR) and sternal (SR). The dogs were then positioned in RLR, premedicated (medetomidine 0.01, midazolam 0.1, butorphanol 0.1 mg kg-1 iv) and pre-oxygenated. Fifteen minutes later anaesthesia was induced with 1 mg kg-1 propofol iv and maintained with propofol infusion (0.1–0.2 mg kg-1 minute-1 iv). After induction, the animals were intubated and allowed to breathe spontaneously (FIO2 = 1). Recordings of EIT were performed again in four recumbencies similarly to conscious state. Centre of ventilation (COV) and global inhomogeneity (GI) index were calculated from the functional EIT images. Repeated-measures ANOVA and Bonferroni tests were used for statistical analysis (p < 0.05). None of the variables changed in the conscious state. During anaesthesia left-to-right COV increased from 46.8±2.8% in DR to 49.8±2.9% in SR indicating a right shift, and ventral-to-dorsal COV increased from 49.8±1.7% in DR to 51.8±1.1% in LLR indicating a dorsal shift in distribution of ventilation. Recumbency affected distribution of ventilation in anaesthetized but not in conscious dogs. This can be related to loss of respiratory muscle tone (e.g. diaphragm) and changes in thoracic shape. Changing position of thoraco-abdominal organs under the EIT belt should be considered as alternative explanation of these findings. [ABSTRACT FROM AUTHOR]

Avipoxvirus (APV) is a fairly common virus affecting birds that causes morbidity and mortality in wild and captive birds. We studied the prevalence of pox-like lesions and genetic diversity of APV in house sparrows (Passer domesticus) in natural, agricultural and urban areas in southern Spain in 2013 and 2014 and in central Spain for 8 months (2012–2013). Overall, 3.2% of 2,341 house sparrows visually examined in southern Spain had cutaneous lesions consistent with avian pox. A similar prevalence (3%) was found in 338 birds from central Spain. Prevalence was higher in hatch-year birds than in adults. We did not detect any clear spatial or temporal patterns of APV distribution. Molecular analyses of poxvirus-like lesions revealed that 63% of the samples were positive. Molecular and phylogenetic analyses of 29 DNA sequences from the fpv167 gene, detected two strains belonging to the canarypox clade (subclades B1 and B2) previously found in Spain. One of them appears predominant in Iberia and North Africa and shares 70% similarity to fowlpox and canarypox virus. This APV strain has been identified in a limited number of species in the Iberian Peninsula, Morocco and Hungary. The second one has a global distribution and has been found in numerous wild bird species around the world. To our knowledge, this represents the largest study of avian poxvirus disease in the broadly distributed house sparrow and strongly supports the findings that Avipox prevalence in this species in South and central Spain is moderate and the genetic diversity low. [ABSTRACT FROM AUTHOR]

Studies on the role of B lymphocytes in atherosclerosis development, have yielded contradictory results. Whereas B lymphocyte-deficiency aggravates atherosclerosis in mice; depletion of mature B lymphocytes reduces atherosclerosis. These observations led to the notion that distinct B lymphocyte subsets have different roles. B1a lymphocytes exert an atheroprotective effect, which has been attributed to secretion of IgM, which can be deposited in atherosclerotic lesions thereby reducing necrotic core formation. Tumor necrosis factor (TNF)-family member ‘A Proliferation-Inducing Ligand’ (APRIL, also known as TNFSF13) was previously shown to increase serum IgM levels in a murine model. In this study, we investigated the effect of APRIL overexpression on advanced lesion formation and composition, IgM production and B cell phenotype. We crossed APRIL transgenic (APRIL-Tg) mice with ApoE knockout (ApoE-/-) mice. After a 12-week Western Type Diet, ApoE-/-APRIL-Tg mice and ApoE-/- littermates showed similar increases in body weight and lipid levels. Histologic evaluation showed no differences in lesion size, stage or necrotic area. However, smooth muscle cell (α-actin stain) content was increased in ApoE-/-APRIL-Tg mice, implying more stable lesions. In addition, increases in both plaque IgM deposition and plasma IgM levels were found in ApoE-/-APRIL-Tg mice compared with ApoE-/- mice. Flow cytometry revealed a concomitant increase in peritoneal B1a lymphocytes in ApoE-/-APRIL-Tg mice. This study shows that ApoE-/-APRIL-Tg mice have increased oxLDL-specific serum IgM levels, potentially mediated via an increase in B1a lymphocytes. Although no differences in lesion size were found, transgenic ApoE-/-APRIL-Tg mice do show potential plaque stabilizing features in advanced atherosclerotic lesions. [ABSTRACT FROM AUTHOR]

The expressive features of music can influence the velocity of walking. So far, studies used instructed (and intended) synchronization. But is this velocity effect still present with non-instructed (spontaneous) synchronization? To figure that out, participants were instructed to walk in their own comfort tempo on an indoor track, first in silence and then with tempo-matched music. We compared velocities of silence and music conditions. The results show that some music has an activating influence, increasing velocity and motivation, while other music has a relaxing influence, decreasing velocity and motivation. The influence of musical expression on the velocity of self-paced walking can be predicted with a regression model using only three sonic features explaining 56% of the variance. Phase-coherence between footfall and beat did not contribute to the velocity effect, due to its implied fixed pacing. The findings suggest that the velocity effect depends on vigor entrainment that influences both stride length and pacing. Our findings are relevant for preventing injuries, for gait improvement in walking rehabilitation, and for improving performance in sports activities. [ABSTRACT FROM AUTHOR]

The planar cell polarity (PCP) pathway is a cell-contact mediated mechanism for transmitting polarity information between neighboring cells. PCP “core components” (Vangl, Fz, Pk, Dsh, and Celsr) are essential for a number of cell migratory events including the posterior migration of facial branchiomotor neurons (FBMNs) in the plane of the hindbrain neuroepithelium in zebrafish and mice. While the mechanism by which PCP signaling polarizes static epithelial cells is well understood, how PCP signaling controls highly dynamic processes like neuronal migration remains an important outstanding question given that PCP components have been implicated in a range of directed cell movements, particularly during vertebrate development. Here, by systematically disrupting PCP signaling in a rhombomere-restricted manner we show that PCP signaling is required both within FBMNs and the hindbrain rhombomere 4 environment at the time when they initiate their migration. Correspondingly, we demonstrate planar polarized localization of PCP core components Vangl2 and Fzd3a in the hindbrain neuroepithelium, and transient localization of Vangl2 at the tips of retracting FBMN filopodia. Using high-resolution timelapse imaging of FBMNs in genetic chimeras we uncover opposing cell-autonomous and non-cell-autonomous functions for Fzd3a and Vangl2 in regulating FBMN protrusive activity. Within FBMNs, Fzd3a is required to stabilize filopodia while Vangl2 has an antagonistic, destabilizing role. However, in the migratory environment Fzd3a acts to destabilize FBMN filopodia while Vangl2 has a stabilizing role. Together, our findings suggest a model in which PCP signaling between the planar polarized neuroepithelial environment and FBMNs directs migration by the selective stabilization of FBMN filopodia. [ABSTRACT FROM AUTHOR]

Ciliopathies are a group of human disorders caused by dysfunction of primary cilia, ubiquitous microtubule-based organelles involved in transduction of extra-cellular signals to the cell. This function requires the concentration of receptors and channels in the ciliary membrane, which is achieved by complex trafficking mechanisms, in part controlled by the small GTPase RAB8, and by sorting at the transition zone located at the entrance of the ciliary compartment. Mutations in the transition zone gene CC2D2A cause the related Joubert and Meckel syndromes, two typical ciliopathies characterized by central nervous system malformations, and result in loss of ciliary localization of multiple proteins in various models. The precise mechanisms by which CC2D2A and other transition zone proteins control protein entrance into the cilium and how they are linked to vesicular trafficking of incoming cargo remain largely unknown. In this work, we identify the centrosomal protein NINL as a physical interaction partner of CC2D2A. NINL partially co-localizes with CC2D2A at the base of cilia and ninl knockdown in zebrafish leads to photoreceptor outer segment loss, mislocalization of opsins and vesicle accumulation, similar to cc2d2a-/- phenotypes. Moreover, partial ninl knockdown in cc2d2a-/- embryos enhances the retinal phenotype of the mutants, indicating a genetic interaction in vivo, for which an illustration is found in patients from a Joubert Syndrome cohort. Similar to zebrafish cc2d2a mutants, ninl morphants display altered Rab8a localization. Further exploration of the NINL-associated interactome identifies MICAL3, a protein known to interact with Rab8 and to play an important role in vesicle docking and fusion. Together, these data support a model where CC2D2A associates with NINL to provide a docking point for cilia-directed cargo vesicles, suggesting a mechanism by which transition zone proteins can control the protein content of the ciliary compartment. [ABSTRACT FROM AUTHOR]

In addition to an increase in mean temperature, climate change models predict decreasing amplitudes of daily temperature fluctuations. In temperate regions, where daily and seasonal fluctuations are prominent, such decreases in daily temperature fluctuations can have a pronounced effect on the fitness of species and on the outcome of species interactions. In this study, the effect of a temperature regime with daily fluctuations versus a constant temperature on the fitness and interspecific interactions of three cryptic species of the marine nematode species complex of Litoditis marina (Pm I, Pm III and Pm IV) were investigated. In a lab experiment, different combinations of species (monospecific treatment: Pm I and Pm IV and Pm III alone; two-species treatment: Pm I + Pm IV; three-species treatment: Pm I + Pm IV + Pm III) were subjected to two different temperature regimes: one constant and one fluctuating temperature. Our results showed that fluctuating temperature had minor or no effects on the population fitness of the three species in monocultures. In contrast, interspecific interactions clearly influenced the fitness of all three species, both positively and negatively. Temperature regime did have a substantial effect on the interactions between the species. In the two-species treatment, temperature regime altered the interaction from a sort of mutualism to commensalism. In addition, the strength of the interspecific interactions changed depending on the temperature regime in the three-species treatment. This experiment confirms that interactions between the species can change depending on the abiotic environment; these results show that it is important to incorporate the effect of fluctuations on interspecific interactions to predict the effect of climate change on biodiversity. [ABSTRACT FROM AUTHOR]

Studies of CO ligand binding revealed that two protein states with different ligand affinities exist in the protoglobin from Methanosarcina acetivorans (in MaPgb*, residue Cys(E20)101 was mutated to Ser). The switch between the two states occurs upon the ligation of MaPgb*. In this work, site-directed mutagenesis was used to explore the role of selected amino acids in ligand sensing and stabilization and in affecting the equilibrium between the “more reactive” and “less reactive” conformational states of MaPgb*. A combination of experimental data obtained from electronic and resonance Raman absorption spectra, CO ligand-binding kinetics, and X-ray crystallography was employed. Three amino acids were assigned a critical role: Trp(60)B9, Tyr(61)B10, and Phe(93)E11. Trp(60)B9 and Tyr(61)B10 are involved in ligand stabilization in the distal heme pocket; the strength of their interaction was reflected by the spectra of the CO-ligated MaPgb* and by the CO dissociation rate constants. In contrast, Phe(93)E11 is a key player in sensing the heme-bound ligand and promotes the rotation of the Trp(60)B9 side chain, thus favoring ligand stabilization. Although the structural bases of the fast CO binding rate constant of MaPgb* are still unclear, Trp(60)B9, Tyr(61)B10, and Phe(93)E11 play a role in regulating heme/ligand affinity. [ABSTRACT FROM AUTHOR]

Background: Symptom research across conditions has historically focused on single symptoms, and the burden of multiple symptoms and their interactions has been relatively neglected especially in people living with HIV. Symptom cluster studies are required to set priorities in treatment planning, and to lessen the total symptom burden. This study aimed to identify and compare symptom clusters among people living with HIV attending five palliative care facilities in two sub-Saharan African countries. Methods: Data from cross-sectional self-report of seven-day symptom prevalence on the 32-item Memorial Symptom Assessment Scale-Short Form were used. A hierarchical cluster analysis was conducted using Ward’s method applying squared Euclidean Distance as the similarity measure to determine the clusters. Contingency tables, X2 tests and ANOVA were used to compare the clusters by patient specific characteristics and distress scores. Results: Among the sample (N=217) the mean age was 36.5 (SD 9.0), 73.2% were female, and 49.1% were on antiretroviral therapy (ART). The cluster analysis produced five symptom clusters identified as: 1) dermatological; 2) generalised anxiety and elimination; 3) social and image; 4) persistently present; and 5) a gastrointestinal-related symptom cluster. The patients in the first three symptom clusters reported the highest physical and psychological distress scores. Patient characteristics varied significantly across the five clusters by functional status (worst functional physical status in cluster one, p<0.001); being on ART (highest proportions for clusters two and three, p=0.012); global distress (F=26.8, p<0.001), physical distress (F=36.3, p<0.001) and psychological distress subscale (F=21.8, p<0.001) (all subscales worst for cluster one, best for cluster four). Conclusions: The greatest burden is associated with cluster one, and should be prioritised in clinical management. Further symptom cluster research in people living with HIV with longitudinally collected symptom data to test cluster stability and identify common symptom trajectories is recommended. [ABSTRACT FROM AUTHOR]

Exotosin (EXT) proteins are involved in the chain elongation step of heparan sulfate (HS) biosynthesis, which is intricately involved in organ development. Loss of function mutations (LOF) in EXT1 and EXT2 result in hereditary exostoses (HME). Interestingly, HS plays a role in pancreas development and beta-cell function, and genetic variations in EXT2 are associated with an increased risk for type 2 diabetes mellitus. We hypothesized that loss of function of EXT1 or EXT2 in subjects with hereditary multiple exostoses (HME) affects pancreatic insulin secretion capacity and development. We performed an oral glucose tolerance test (OGTT) followed by hyperglycemic clamps to investigate first-phase glucose-stimulated insulin secretion (GSIS) in HME patients and age and gender matched non-affected relatives. Pancreas volume was assessed with magnetic resonance imaging (MRI). OGTT did not reveal significant differences in glucose disposal, but there was a markedly lower GSIS in HME subjects during hyperglycemic clamp (iAUC HME: 0.72 [0.46–1.16] vs. controls 1.53 [0.69–3.36] nmol·l−1·min−1, p<0.05). Maximal insulin response following arginine challenge was also significantly attenuated (iAUC HME: 7.14 [4.22–10.5] vs. controls 10.2 [7.91–12.70] nmol·l−1·min−1 p<0.05), indicative of an impaired beta-cell reserve. MRI revealed a significantly smaller pancreatic volume in HME subjects (HME: 72.0±15.8 vs. controls 96.5±26.0 cm3 p = 0.04). In conclusion, loss of function of EXT proteins may affect beta-cell mass and insulin secretion capacity in humans, and render subjects at a higher risk of developing type 2 diabetes when exposed to environmental risk factors. [ABSTRACT FROM AUTHOR]

Primary Immunodeficiencies (PID) are genetically inherited disorders characterized by defects of the immune system, leading to increased susceptibility to infection. Due to the variety of clinical symptoms and the complexity of current diagnostic procedures, accurate diagnosis of PID is often difficult in daily clinical practice. Thanks to the advent of “next generation” sequencing technologies and target enrichment methods, the development of multiplex diagnostic assays is now possible. In this study, we applied a selector-based target enrichment assay to detect disease-causing mutations in 179 known PID genes. The usefulness of this assay for molecular diagnosis of PID was investigated by sequencing DNA from 33 patients, 18 of which had at least one known causal mutation at the onset of the experiment. We were able to identify the disease causing mutations in 60% of the investigated patients, indicating that the majority of PID cases could be resolved using a targeted sequencing approach. Causal mutations identified in the unknown patient samples were located in STAT3, IGLL1, RNF168 and PGM3. Based on our results, we propose a stepwise approach for PID diagnostics, involving targeted resequencing, followed by whole transcriptome and/or whole genome sequencing if causative variants are not found in the targeted exons. [ABSTRACT FROM AUTHOR]

In this study we explore how music can entrain human walkers to synchronise to the musical beat without being instructed to do so. For this, we use an interactive music player, called D-Jogger, that senses the user's walking tempo and phase. D-Jogger aligns the music by manipulating the timing difference between beats and footfalls. Experiments are reported that led to the development and optimisation of four alignment strategies. The first strategy matched the music's tempo continuously to the runner's pace. The second strategy matched the music's tempo at the beginning of a song to the runner's pace, keeping the tempo constant for the remainder of the song. The third alignment starts a song in perfect phase synchrony and continues to adjust the tempo to match the runner's pace. The fourth and last strategy additionally adjusts the phase of the music so each beat matches a footfall. The first two strategies resulted in a minor increase of steps in phase synchrony with the main beat when compared to a random playlist, the last two strategies resulted in a strong increase in synchronised steps. These results may be explained in terms of phase-error correction mechanisms and motor prediction schemes. Finding the phase-lock is difficult due to fluctuations in the interaction, whereas strategies that automatically align the phase between movement and music solve the problem of finding the phase-locking. Moreover, the data show that once the phase-lock is found, alignment can be easily maintained, suggesting that less entrainment effort is needed to keep the phase-lock, than to find the phase-lock. The different alignment strategies of D-Jogger can be applied in different domains such as sports, physical rehabilitation and assistive technologies for movement performance. [ABSTRACT FROM AUTHOR]

The discovery of morphologically very similar but genetically distinct species complicates a proper understanding of the link between biodiversity and ecosystem functioning. Cryptic species have been frequently observed to co-occur and are thus expected to be ecological equivalent. The marine nematode Halomonhystera disjuncta contains five cryptic species (GD1-5) that co-occur in the Westerschelde estuary. In this study, we investigated the effect of three abiotic factors (salinity, temperature and sulphide) on life-history traits of three cryptic H. disjuncta species (GD1-3). Our results show that temperature had the most profound influence on all life-cycle parameters compared to a smaller effect of salinity. Life-history traits of closely related cryptic species were differentially affected by temperature, salinity and presence of sulphides which shows that cryptic H. disjuncta species are not ecologically equivalent. Our results further revealed that GD1 had the highest tolerance to a combination of sulphides, high salinities and low temperatures. The close phylogenetic position of GD1 to Halomonhystera hermesi, the dominant species in sulphidic sediments of the Håkon Mosby mud volcano (Barent Sea, 1280 m depth), indicates that both species share a recent common ancestor. Differential life-history responses to environmental changes among cryptic species may have crucial consequences for our perception on ecosystem functioning and coexistence of cryptic species. [ABSTRACT FROM AUTHOR]

Objective: To calibrate the Dutch-Flemish version of the PROMIS physical function (PF) item bank in patients with rheumatoid arthritis (RA) and to evaluate cross-cultural measurement equivalence with US general population and RA data. Methods: Data were collected from RA patients enrolled in the Dutch DREAM registry. An incomplete longitudinal anchored design was used where patients completed all 121 items of the item bank over the course of three waves of data collection. Item responses were fit to a generalized partial credit model adapted for longitudinal data and the item parameters were examined for differential item functioning (DIF) across country, age, and sex. Results: In total, 690 patients participated in the study at time point 1 (T2, N = 489; T3, N = 311). The item bank could be successfully fitted to a generalized partial credit model, with the number of misfitting items falling within acceptable limits. Seven items demonstrated DIF for sex, while 5 items showed DIF for age in the Dutch RA sample. Twenty-five (20%) items were flagged for cross-cultural DIF compared to the US general population. However, the impact of observed DIF on total physical function estimates was negligible. Discussion: The results of this study showed that the PROMIS PF item bank adequately fit a unidimensional IRT model which provides support for applications that require invariant estimates of physical function, such as computer adaptive testing and targeted short forms. More studies are needed to further investigate the cross-cultural applicability of the US-based PROMIS calibration and standardized metric. [ABSTRACT FROM AUTHOR]

The diaphragm is the main inspiratory muscle and the main indicator of diaphragmatic contractility is the trans-diaphragmatic pressure (Pdi). The aim of this clinical study was to determine the effect of four different anaesthetic protocols on Pdi in anaesthetized healthy dogs. Eighty client-owned dogs were recruited in this clinical study. All the animals received dexmedetomidine and morphine as premedication and propofol for induction. Anaesthesia was maintained with one of four protocols: isoflurane (I), isoflurane with CRI of propofol (IP), isoflurane with CRI of fentanyl (IF), and isoflurane with CRI of ketamine (IK). When the surgical plane of anaesthesia was achieved, two balloon catheters were inserted, one into the stomach and one into the mid-third of the oesophagus for Pdi measurement. Pdi value was the highest in groups I (14.9±4.7 mmHg) and IK (15.2±3.5 mmHg) and the lowest in groups IP (12.2±3.2 mmHg) and IF (12.0±5.9 mmHg). There was a statistically significant difference (p = 0.029) between groups IK and IF. PE’CO2 was statistically significantly higher (p<0.0005) in group IF (7.7±0.8 kPa) than in group IK (6.5±0.7 kPa). Isoflurane alone or isoflurane with ketamine for the maintenance of anaesthesia seem to better preserve the respiratory function and the diaphragmatic contractility than isoflurane with either propofol or fentanyl in dogs. Therefore, the use of isoflurane or isoflurane with ketamine may be of benefit when animals with respiratory problems have to be anaesthetized. [ABSTRACT FROM AUTHOR]

Biodiversity has diminished over the past decades with climate change being among the main responsible factors. One consequence of climate change is the increase in sea surface temperature, which, together with long exposure periods in intertidal areas, may exceed the tolerance level of benthic organisms. Benthic communities may suffer structural changes due to the loss of species or functional groups, putting ecological services at risk. In sandy beaches, free-living marine nematodes usually are the most abundant and diverse group of intertidal meiofauna, playing an important role in the benthic food web. While apparently many functionally similar nematode species co-exist temporally and spatially, experimental results on selected bacterivore species suggest no functional overlap, but rather an idiosyncratic contribution to ecosystem functioning. However, we hypothesize that functional redundancy is more likely to observe when taking into account the entire diversity of natural assemblages. We conducted a microcosm experiment with two natural communities to assess their stress response to elevated temperature. The two communities differed in diversity (high [HD] vs. low [LD]) and environmental origin (harsh vs. moderate conditions). We assessed their stress resistance to the experimental treatment in terms of species and diversity changes, and their function in terms of abundance, biomass, and trophic diversity. According to the Insurance Hypothesis, we hypothesized that the HD community would cope better with the stressful treatment due to species functional overlap, whereas the LD community functioning would benefit from species better adapted to harsh conditions. Our results indicate no evidence of functional redundancy in the studied nematofaunal communities. The species loss was more prominent and size specific in the HD; large predators and omnivores were lost, which may have important consequences for the benthic food web. Yet, we found evidence for alternative diversity–ecosystem functioning relationships, such as the Rivets and the Idiosyncrasy Model. [ABSTRACT FROM AUTHOR]

Protoglobin from Methanosarcina acetivorans C2A (MaPgb), a strictly anaerobic methanogenic Archaea, is a dimeric haem-protein whose biological role is still unknown. As other globins, protoglobin can bind O2, CO and NO reversibly in vitro, but it displays specific functional and structural properties within members of the hemoglobin superfamily. CO binding to and dissociation from the haem occurs through biphasic kinetics, which arise from binding to (and dissociation from) two distinct tertiary states in a ligation-dependent equilibrium. From the structural viewpoint, protoglobin-specific loops and a N-terminal extension of 20 residues completely bury the haem within the protein matrix. Thus, access of small ligand molecules to the haem is granted by two apolar tunnels, not common to other globins, which reach the haem distal site from locations at the B/G and B/E helix interfaces. Here, the roles played by residues Trp(60)B9, Tyr(61)B10 and Phe(93)E11 in ligand recognition and stabilization are analyzed, through crystallographic investigations on the ferric protein and on selected mutants. Specifically, protein structures are reported for protoglobin complexes with cyanide, with azide (also in the presence of Xenon), and with more bulky ligands, such as imidazole and nicotinamide. Values of the rate constant for cyanide dissociation from ferric MaPgb-cyanide complexes have been correlated to hydrogen bonds provided by Trp(60)B9 and Tyr(61)B10 that stabilize the haem-Fe(III)-bound cyanide. We show that protoglobin can strikingly reshape, in a ligand-dependent way, the haem distal site, where Phe(93)E11 acts as ligand sensor and controls accessibility to the haem through the tunnel system by modifying the conformation of Trp(60)B9. [ABSTRACT FROM AUTHOR]

Polyomaviruses are a family of small non-enveloped DNA viruses that encode oncogenes and have been associated, to greater or lesser extent, with human disease and cancer. Currently, twelve polyomaviruses are known to circulate within the human population. To further examine the diversity of human polyomaviruses, we have utilized a combinatorial approach comprised of initial degenerate primer-based PCR identification and phylogenetic analysis of nonhuman primate (NHP) polyomavirus species, followed by polyomavirus-specific serological analysis of human sera. Using this approach we identified twenty novel NHP polyomaviruses: nine in great apes (six in chimpanzees, two in gorillas and one in orangutan), five in Old World monkeys and six in New World monkeys. Phylogenetic analysis indicated that only four of the nine chimpanzee polyomaviruses (six novel and three previously identified) had known close human counterparts. To determine whether the remaining chimpanzee polyomaviruses had potential human counterparts, the major viral capsid proteins (VP1) of four chimpanzee polyomaviruses were expressed in E. coli for use as antigens in enzyme-linked immunoassay (ELISA). Human serum/plasma samples from both Côte d'Ivoire and Germany showed frequent seropositivity for the four viruses. Antibody pre-adsorption-based ELISA excluded the possibility that reactivities resulted from binding to known human polyomaviruses. Together, these results support the existence of additional polyomaviruses circulating within the human population that are genetically and serologically related to existing chimpanzee polyomaviruses. [ABSTRACT FROM AUTHOR]

Polyomaviruses are small, non-enveloped viruses with a circular double-stranded DNA genome. Using a generic polyomavirus PCR targeting the VP1 major structural protein gene, a novel polyomavirus was initially identified in resected human liver tissue and provisionally named Human Polyomavirus 12 (HPyV12). Its 5033 bp genome is predicted to encode large and small T antigens and the 3 structural proteins VP1, VP2 and VP3. Phylogenetic analyses did not reveal a close relationship to any known human or animal polyomavirus. Investigation of organs, body fluids and excretions of diseased individuals and healthy subjects with both HPyV12-specific nested PCR and quantitative real-time PCR revealed additional virus-positive samples of resected liver, cecum and rectum tissues and a positive fecal sample. A capsomer-based IgG ELISA was established using the major capsid protein VP1 of HPyV12. Seroprevalences of 23% and 17%, respectively, were determined in sera from healthy adults and adolescents and a pediatric group of children. These data indicate that the virus naturally infects humans and that primary infection may already occur in childhood. [ABSTRACT FROM AUTHOR]

Objective of this study was to examine the impact of executive function (EF) on mathematical and attention problems in very preterm (gestational age ≤ 30 weeks) children. Participants were 200 very preterm (mean age 8.2 ± 2.5 years) and 230 term children (mean age 8.3 ± 2.3 years) without severe disabilities, born between 1996 and 2004. EFs assessed included verbal fluency, verbal working memory, visuospatial span, planning, and impulse control. Mathematics was assessed with the Dutch Pupil Monitoring System and parents and teachers rated attention problems using standardized behavior questionnaires. The impact of EF was calculated over and above processing speed indices and IQ. Interactions with group (very preterm versus term birth status) were examined. Analyses were conducted separately for two subsamples: children in preschool and children in primary school. Very preterm children performed poorer on tests for mathematics and had more parent and teacher rated attention problems than term controls (ßs>.11, Ps<.01). IQ contributed unique variance to mathematics in preschool and in primary school (ßs>.16, Ps<.007). A significant interaction of group with IQ (ß = −. 24, P = .02) showed that IQ contributed unique variance to attention problems as rated by teachers, but that effects were stronger for very preterm than for term infants. Over and above IQ, EF contributed unique variance to mathematics in primary school (ß = .13, P<.001), to parent rated inattention in preschool and in primary school (ßs>−.16, Ps<.04), and to teacher rated inattention in primary school (ß = −.19; ß = .19, Ps<.009). In conclusion, impaired EF is, over and above impaired IQ, an important predictor for poor mathematics and attention problems following very preterm birth. [ABSTRACT FROM AUTHOR]

Cytoglobin (Cygb) was recently discovered in the human genome and localized in different tissues. It was suggested to play tissue-specific protective roles, spanning from scavenging of reactive oxygen species in neurons to supplying oxygen to enzymes in fibroblasts. To shed light on the functioning of such versatile machinery, we have studied the processes supporting transport of gaseous heme ligands in Cygb. Carbon monoxide rebinding shows a complex kinetic pattern with several distinct reaction intermediates, reflecting rebinding from temporary docking sites, second order recombination, and formation (and dissociation) of a bis-histidyl heme hexacoordinated reaction intermediate. Ligand exit to the solvent occurs through distinct pathways, some of which exploit temporary docking sites. The remarkable change in energetic barriers, linked to heme bis-histidyl hexacoordination by HisE7, may be responsible for active regulation of the flux of reactants and products to and from the reaction site on the distal side of the heme. A substantial change in both protein dynamics and inner cavities is observed upon transition from the CO-liganded to the pentacoordinated and bis-histidyl hexacoordinated species, which could be exploited as a signalling state. These findings are consistent with the expected versatility of the molecular activity of this protein. [ABSTRACT FROM AUTHOR]

The genomic revolution in oncology will entail mutational analyses of vast numbers of patient-matched tumor and normal tissue samples. This has meant an increased risk of patient sample mix up due to manual handling. Therefore, scalable genotyping and sample identification procedures are essential to pathology biobanks. We have developed an efficient alternative to traditional genotyping methods suited for automated analysis. By targeting 53 prevalent deletions and insertions found in human populations with fluorescent multiplex ligation dependent genome amplification, followed by separation in a capillary sequencer, a peak spectrum is obtained that can be automatically analyzed. 24 tumor-normal patient samples were successfully matched using this method. The potential use of the developed assay for forensic applications is discussed. [ABSTRACT FROM AUTHOR]

Globins occur in all kingdoms of life where they fulfill a wide variety of functions. In the past they used to be primarily characterized as oxygen transport/storage proteins, but since the discovery of new members of the globin family like neuroglobin and cytoglobin, more diverse and complex functions have been assigned to this heterogeneous family. Here we propose a function for a membrane-bound globin of C. elegans, GLB-26. This globin was predicted to be myristoylated at its N-terminus, a post-translational modification only recently described in the globin family. In vivo, this globin is found in the membrane of the head mesodermal cell and in the tail stomato-intestinal and anal depressor muscle cells. Since GLB-26 is almost directly oxidized when exposed to oxygen, we postulate a possible function as electron transfer protein. Phenotypical studies show that GLB-26 takes part in regulating the length of the defecation cycle in C. elegans under oxidative stress conditions. [ABSTRACT FROM AUTHOR]

The Antarctic icefish Chaenocephalus aceratus lacks the globins common to most vertebrates, hemoglobin and myoglobin, but has retained neuroglobin in the brain. This conserved globin has been cloned, over-expressed and purified. To highlight similarities and differences, the structural features of the neuroglobin of this colourless-blooded fish were compared with those of the well characterised human neuroglobin as well as with the neuroglobin from the retina of the red blooded, hemoglobin and myoglobin-containing, closely related Antarctic notothenioid Dissostichus mawsoni. A detailed structural and functional analysis of the two Antarctic fish neuroglobins was carried out by UV-visible and Resonance Raman spectroscopies, molecular dynamics simulations and laser-flash photolysis. Similar to the human protein, Antarctic fish neuroglobins can reversibly bind oxygen and CO in the Fe2+ form, and show six-coordination by distal His in the absence of exogenous ligands. A very large and structured internal cavity, with discrete docking sites, was identified in the modelled three-dimensional structures of the Antarctic neuroglobins. Estimate of the free-energy barriers from laser-flash photolysis and Implicit Ligand Sampling showed that the cavities are accessible from the solvent in both proteins. Comparison of structural and functional properties suggests that the two Antarctic fish neuroglobins most likely preserved and possibly improved the function recently proposed for human neuroglobin in ligand multichemistry. Despite subtle differences, the adaptation of Antarctic fish neuroglobins does not seem to parallel the dramatic adaptation of the oxygen carrying globins, hemoglobin and myoglobin, in the same organisms. [ABSTRACT FROM AUTHOR]

Co-occurrence of closely related species may be achieved in environments with fluctuating dynamics, where competitively inferior species can avoid competition through dispersal. Here we present an experiment in which we compared active dispersal abilities (time until first dispersal, number and gender of dispersive adults, and nematode densities at time of dispersal) in Litoditis marina, a common bacterivorous nematode species complex comprising four often co-occurring cryptic species, Pm I, II, III, and IV, as a function of salinity and food distribution. The experiment was conducted in microcosms consisting of an inoculation plate, connection tube, and dispersal plate. Results show species-specific dispersal abilities with Pm I dispersing almost one week later than Pm III. The number of dispersive adults at time of first dispersal was species-specific, with one dispersive female in Pm I and Pm III and a higher, gender-balanced, number in Pm II and Pm IV. Food distribution affected dispersal: in absence of food in the inoculation plate, all species dispersed after ca four days. When food was available Pm I dispersed later, and at the same time and densities irrespective of food conditions in the dispersal plate (food vs no food), suggesting density-dependent dispersal. Pm III dispersed faster and at a lower population density. Salinity affected dispersal, with slower dispersal at higher salinity. These results suggest that active dispersal in Litoditis marina is common, density-dependent, and with species, gender- and environment-specific dispersal abilities. These differences can lead to differential responses under suboptimal conditions and may help to explain temporary coexistence at local scales. [ABSTRACT FROM AUTHOR]

Background: Clear therapeutic guidelines for HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) are missing due to the lack of randomized double-blind controlled clinical trials. Moderate yet similar clinical benefit has been demonstrated for IFN-α and high-dose ascorbic acid (AA) monotherapy in a large open clinical trial. However, there is a lack of in vivo and in vitro studies exploring and comparing the effects of high-dose AA and IFN-α treatment in the context of HAM/TSP. Therefore, we performed the first comparative analysis of the ex vivo and in vitro molecular and cellular mechanisms of action of IFN-α and high-dose AA in HAM/TSP. Principal Findings: Through thymidine incorporation and quantification of Th1/Th2/Th17 cytokines, we demonstrate that high-dose AA displays differential and superior antiproliferative and immunomodulatory effects over IFN-α in HAM/TSP PBMCs ex vivo. In addition, high-dose AA, but not IFN-α, induced cell death in both HAM/TSP PBMCs and HTLV-1-infected T-cell lines MT-2 and MT-4. Microarray data combined with pathway analysis of MT-2 cells revealed AA-induced regulation of genes associated with cell death, including miR-155. Since miR-155 has recently been demonstrated to up-regulate IFN-γ, this microRNA might represent a novel therapeutic target in HAM/TSP, as recently demonstrated in multiple sclerosis, another neuroinflammatory disease. On the other hand, IFN-α selectively up-regulated antiviral and immune-related genes. Conclusions: In comparison to IFN-α, high-dose AA treatment has superior ex vivo and in vitro cell death-inducing, antiproliferative and immunomodulatory anti-HTLV-1 effects. Differential pathway activation by both drugs opens up avenues for targeted treatment in specific patient subsets. Author Summary: HAM/TSP is a chronic and disabling neuroinflammatory disease, for which clinical management is mostly empirical and symptomatic rather than evidence-based, due to the lack of biomarkers and controlled clinical trials. Although similar clinical benefit has been demonstrated for IFN-α and high-dose ascorbic acid (vitamin C) in one major open clinical trial with 200 patients, their cellular and molecular mechanisms of action remain unexplored in HAM/TSP. We demonstrate that high-dose ascorbic acid strongly inhibits lymphoproliferation of HAM/TSP mononuclear cells in ex vivo cultures, in contrast to IFN-α. Furthermore, high-dose ascorbic acid, but not IFN-α, significantly decreased ex vivo TNF-α and IFN-γ pro-inflammatory cytokine levels in supernatant of mononuclear cells from HAM/TSP patients. In addition, ascorbic acid, but not IFN-α, induced cell death in HTLV-1-infected T-cell lines, which was confirmed by gene expression profiling, revealing cell death-associated pathways activated by high-dose ascorbic acid, including miR-155. This microRNA has previously been shown up-regulated in HTLV-1-infected cells, as well as in blood and brain samples of multiple sclerosis patients, another neuroinflammatory disease. In addition, miR-155 has also been reported to up-regulate IFN-γ production in human natural killer cells, thus linking both cell death and cytokine signaling pathways, rendering it a potential therapeutic target in neuroinflammatory disorders. Thus, our findings reveal molecular mechanisms of action as well as candidate biomarkers for high-dose ascorbic acid therapy and provide a rational basis, rather than an empirical basis, for its use in HAM/TSP treatment. [ABSTRACT FROM AUTHOR]

The pancreaticobiliary ductal system connects the liver and pancreas to the intestine. It is composed of the hepatopancreatic ductal (HPD) system as well as the intrahepatic biliary ducts and the intrapancreatic ducts. Despite its physiological importance, the development of the pancreaticobiliary ductal system remains poorly understood. The SRY-related transcription factor SOX9 is expressed in the mammalian pancreaticobiliary ductal system, but the perinatal lethality of Sox9 heterozygous mice makes loss-of-function analyses challenging. We turned to the zebrafish to assess the role of SOX9 in pancreaticobiliary ductal system development. We first show that zebrafish sox9b recapitulates the expression pattern of mouse Sox9 in the pancreaticobiliary ductal system and use a nonsense allele of sox9b, sox9bfh313, to dissect its function in the morphogenesis of this structure. Strikingly, sox9bfh313 homozygous mutants survive to adulthood and exhibit cholestasis associated with hepatic and pancreatic duct proliferation, cyst formation, and fibrosis. Analysis of sox9bfh313 mutant embryos and larvae reveals that the HPD cells appear to mis-differentiate towards hepatic and/or pancreatic fates, resulting in a dysmorphic structure. The intrahepatic biliary cells are specified but fail to assemble into a functional network. Similarly, intrapancreatic duct formation is severely impaired in sox9bfh313 mutants, while the embryonic endocrine and acinar compartments appear unaffected. The defects in the intrahepatic and intrapancreatic ducts of sox9bfh313 mutants worsen during larval and juvenile stages, prompting the adult phenotype. We further show that Sox9b interacts with Notch signaling to regulate intrahepatic biliary network formation: sox9b expression is positively regulated by Notch signaling, while Sox9b function is required to maintain Notch signaling in the intrahepatic biliary cells. Together, these data reveal key roles for SOX9 in the morphogenesis of the pancreaticobiliary ductal system, and they cast human Sox9 as a candidate gene for pancreaticobiliary duct malformation-related pathologies. [ABSTRACT FROM AUTHOR]

Protoglobin from Methanosarcina acetivorans (MaPgb) is a dimeric globin with peculiar structural properties such as a completely buried haem and two orthogonal tunnels connecting the distal cavity to the solvent. CO binding to and dissociation from MaPgb occur through a biphasic kinetics. We show that the heterogenous kinetics arises from binding to (and dissociation from) two tertiary conformations in ligation-dependent equilibrium. Ligation favours the species with high binding rate (and low dissociation rate). The equilibrium is shifted towards the species with low binding (and high dissociation) rates for the unliganded molecules. A quantitative model is proposed to describe the observed carbonylation kinetics. [ABSTRACT FROM AUTHOR]

Background: All globins belong to one of three families: the F (flavohemoglobin) and S (sensor) families that exhibit the canonical 3/3 α-helical fold, and the T (truncated 3/3 fold) globins characterized by a shortened 2/2 α-helical fold. All eukaryote 3/3 hemoglobins are related to the bacterial single domain F globins. It is known that Fungi contain flavohemoglobins and single domain S globins. Our aims are to provide a census of fungal globins and to examine their relationships to bacterial globins. Results: Examination of 165 genomes revealed that globins are present in >90% of Ascomycota and ∼60% of Basidiomycota genomes. The S globins occur in Blastocladiomycota and Chytridiomycota in addition to the phyla that have FHbs. Unexpectedly, group 1 T globins were found in one Blastocladiomycota and one Chytridiomycota genome. Phylogenetic analyses were carried out on the fungal globins, alone and aligned with representative bacterial globins. The Saccharomycetes and Sordariomycetes with two FHbs form two widely divergent clusters separated by the remaining fungal sequences. One of the Saccharomycete groups represents a new subfamily of FHbs, comprising a previously unknown N-terminal and a FHb missing the C-terminal moiety of its reductase domain. The two Saccharomycete groups also form two clusters in the presence of bacterial FHbs; the surrounding bacterial sequences are dominated by Proteobacteria and Bacilli (Firmicutes). The remaining fungal FHbs cluster with Proteobacteria and Actinobacteria. The Sgbs cluster separately from their bacterial counterparts, except for the intercalation of two Planctomycetes and a Proteobacterium between the Fungi incertae sedis and the Blastocladiomycota and Chytridiomycota. Conclusion: Our results are compatible with a model of globin evolution put forward earlier, which proposed that eukaryote F, S and T globins originated via horizontal gene transfer of their bacterial counterparts to the eukaryote ancestor, resulting from the endosymbiotic events responsible for the origin of mitochondria and chloroplasts. [ABSTRACT FROM AUTHOR]

Background: The human polyomavirus BK (BKV) infects humans worldwide and establishes a persistent infection in the kidney. The BK virus genome encodes three regulatory proteins, large and small tumor-antigen and the agnoprotein, as well as the capsid proteins VP1 to VP3. Agnoprotein is conserved among BKV, JC virus (JCV) and SV40, and agnoprotein-deficient mutants reveal reduced viral propagation. Studies with JCV and SV40 indicate that their agnoproteins may be involved in transcription, replication and/or nuclear and cellular release of the virus. However, the exact function(s) of agnoprotein of BK virus remains elusive. Principal Findings: As a strategy of exploring the functions of BKV agnoprotein, we decided to look for cellular interaction partners for the viral protein. Several partners were identified by yeast two-hybrid assay, among them α-SNAP which is involved in disassembly of vesicles during secretion. BKV agnoprotein and α-SNAP were found to partially co-localize in cells, and a complex consisting of agnoprotein and α-SNAP could be co-immunoprecipitated from cells ectopically expressing the proteins as well as from BKV-transfected cells. The N-terminal part of the agnoprotein was sufficient for the interaction with α-SNAP. Finally, we could show that BKV agnoprotein negatively interferes with secretion of VSVG-EGFP reporter suggesting that agnoprotein may modulate exocytosis. Conclusions: We have identified the first cellular interaction partner for BKV agnoprotein. The most N-terminal part of BKV agnoprotein is involved in the interaction with α-SNAP. Presence of BKV agnoprotein negatively interferes with secretion of VSVG-EGFP reporter. [ABSTRACT FROM AUTHOR]