Comparative serum glycoproteomics using lectin selected sialic acid glycoproteins with mass spectrometric analysis: application to pancreatic cancer serum

A strategy is developed in this study for identifying sialylated glycoprotein markers in human cancer serum. This method consists of three steps: lectin affinity selection, a liquid separation and characterization of the glycoprotein markers using mass spectrometry. In this work, we use three different lectins (Wheat Germ Agglutinin, (WGA) Elderberry lectin,(SNA), Maackia amurensis lectin, (MAL)) to extract sialylated glycoproteins from normal and cancer serum. Twelve highly abundant proteins are depleted from the serum using an IgY-12 antibody column. The use of the different lectin columns allows one to monitor the distribution of alpha(2,3) and alpha(2,6) linkage type sialylation in cancer serum vs that in normal samples. Extracted glycoproteins are fractionated using NPS-RP-HPLC followed by SDS-PAGE. Target glycoproteins are characterized further using mass spectrometry to elucidate the carbohydrate structure and glycosylation site. We applied this approach to the analysis of sialylated glycoproteins in pancreatic cancer serum. Approximately 130 sialylated glycoproteins are identified using microLC-MS/MS. Sialylated plasma protease C1 inhibitor is identified to be down-regulated in cancer serum. Changes in glycosylation sites in cancer serum are also observed by glycopeptide mapping using microLC-ESI-TOF-MS where the N83 glycosylation of alpha1-antitrypsin is down regulated. In addition, the glycan structures of the altered proteins are assigned using MALDI-QIT-MS. This strategy offers the ability to quantitatively analyze changes in glycoprotein abundance and detect the extent of glycosylation alteration as well as the carbohydrate structure that correlate with cancer.     

Genome-wide copy number analysis of single cells

Copy number variation (CNV) is increasingly recognized as an important contributor to phenotypic variation in health and disease. Most methods for determining CNV rely on admixtures of cells in which information regarding genetic heterogeneity is lost. Here we present a protocol that allows for the genome-wide copy number analysis of single nuclei isolated from mixed populations of cells. Single-nucleus sequencing (SNS), combines flow sorting of single nuclei on the basis of DNA content and whole-genome amplification (WGA); this is followed by next-generation sequencing to quantize genomic intervals in a genome-wide manner. Multiplexing of single cells is discussed. In addition, we outline informatic approaches that correct for biases inherent in the WGA procedure and allow for accurate determination of copy number profiles. All together, the protocol takes ～3 d from flow cytometry to sequence-ready DNA libraries.     

The critical role of IL-1 receptor-associated kinase 4-mediated NF-κB activation in modified low-density lipoprotein-induced inflammatory gene expression and atherosclerosis

Exciting discoveries related to IL-1R/TLR signaling in the development of atherosclerosis plaque have triggered intense interest in the molecular mechanisms by which innate immune signaling modulates the onset and development of atherosclerosis. Previous studies have clearly shown the definitive role of proinflammatory cytokine IL-1 in the development of atherosclerosis. Recent studies have provided direct evidence supporting a link between innate immunity and atherogenesis. Although it is still controversial about whether infectious pathogens contribute to cardiovascular diseases, direct genetic evidence indicates the importance of IL-1R/TLR signaling in atherogenesis. In this study, we examined the role of IL-1R-associated kinase 4 (IRAK4) kinase activity in modified low-density lipoprotein (LDL)-mediated signaling using bone marrow-derived macrophage as well as an in vivo model of atherosclerosis. First, we found that the IRAK4 kinase activity was required for modified LDL-induced NF-κB activation and expression of a subset of proinflammatory genes but not for the activation of MAPKs in bone marrow-derived macrophage. IRAK4 kinase-inactive knockin (IRAK4KI) mice were bred onto ApoE(-/-) mice to generate IRAK4KI/ApoE(-/-) mice. Importantly, the aortic sinus lesion formation was impaired in IRAK4KI/ApoE(-/-) mice compared with that in ApoE(-/-) mice. Furthermore, proinflammatory cytokine production was reduced in the aortic sinus region of IRAK4KI/ApoE(-/-) mice compared with that in ApoE(-/-) mice. Taken together, our results indicate that the IRAK4 kinase plays an important role in modified LDL-mediated signaling and the development of atherosclerosis, suggesting that pharmacological inhibition of IRAK4 kinase activity might be a feasible approach in the development of antiatherosclerosis drugs.     

Floral neighborhood influences pollinator assemblages and effective pollination in a native plant

Pollinators represent an important intermediary by which different plant species can influence each other’s reproductive fitness. Floral neighbors can modify the quantity of pollinator visits to a focal species but may also influence the composition of visitor assemblages that plants receive leading to potential changes in the average effectiveness of floral visits. We explored how the heterospecific floral neighborhood (abundance of native and non-native heterospecific plants within 2 m × 2 m) affects pollinator visitation and composition of pollinator assemblages for a native plant, Phacelia parryi. The relative effectiveness of different insect visitors was also assessed to interpret the potential effects on plant fitness of shifts in pollinator assemblage composition. Although the common non-native Brassica nigra did not have a significant effect on overall pollinator visitation rate to P. parryi, the proportion of flower visits that were made by native pollinators increased with increasing abundance of heterospecific plant species in the floral neighborhood other than B. nigra. Furthermore, native pollinators deposited twice as many P. parryi pollen grains per visit as did the nonnative Apis mellifera, and visits by native bees also resulted in more seeds than visits by A. mellifera. These results indicate that the floral neighborhood can influence the composition of pollinator assemblages that visit a native plant and that changes in local flower communities have the potential to affect plant reproductive success through shifts in these assemblages towards less effective pollinators.     

Disequilibrium,Adaptation, and the Norse Settlement of Greenland

There is increasing evidence to suggest that arctic cultures and ecosystems have followed non-linear responses to climate change. Norse Scandinavian farmers introduced agriculture to sub-arctic Greenland in the late tenth century, creating synanthropic landscapes and utilising seasonally abundant marine and terrestrial resources. Using a niche-construction framework and data from recent survey work, studies of diet, and regional-scale climate proxies we examine the potential mismatch between this imported agricultural niche and the constraints of the environment from the tenth to the fifteenth centuries. We argue that landscape modification conformed the Norse to a Scandinavian style of agriculture throughout settlement, structuring and limiting the efficacy of seasonal hunting strategies. Recent climate data provide evidence of sustained cooling from the mid thirteenth century and climate variation from the early fifteenth century. Archaeological evidence suggests that the Norse made incremental adjustments to the changing sub-arctic environment, but were limited by cultural adaptations made in past environments.     

Temporal dynamics of late-night photic stimulation of the human circadian timing system

The light-dark cycle is the primary synchronizing factor that keeps the internal circadian pacemaker appropriately aligned with the environmental 24-h day. Although it is known that ocular light exposure can effectively shift the human circadian pacemaker and do so in an intensity-dependent manner, the curve that describes the relationship between light intensity and pacemaker response has not been fully characterized for light exposure in the late biological night. We exposed subjects to 3 consecutive days of 5 h of experimental light, centered 1.5 h after the timing of the fitted minimum of core body temperature, and show that such light can phase advance shift the human circadian pacemaker in an intensity-dependent manner, with a logistic model best describing the relationship between light intensity and phase shift. A similar sigmoidal relationship is also observed between light intensity and the suppression of plasma melatonin concentrations that occurs during the experimental light exposure. As with a simpler, 1-day light exposure during the early biological night, our data indicate that the human circadian pacemaker is highly sensitive even to typical room light intensities during the late biological night, with approximately 100 lux evoking half of the effects observed with light 10 times as bright.     

Food web complexity and stability across habitat connectivity gradients

The effects of habitat connectivity on food webs have been studied both empirically and theoretically, yet the question of whether empirical results support theoretical predictions for any food web metric other than species richness has received little attention. Our synthesis brings together theory and empirical evidence for how habitat connectivity affects both food web stability and complexity. Food web stability is often predicted to be greatest at intermediate levels of connectivity, representing a compromise between the stabilizing effects of dispersal via rescue effects and prey switching, and the destabilizing effects of dispersal via regional synchronization of population dynamics. Empirical studies of food web stability generally support both this pattern and underlying mechanisms. Food chain length has been predicted to have both increasing and unimodal relationships with connectivity as a result of predators being constrained by the patch occupancy of their prey. Although both patterns have been documented empirically, the underlying mechanisms may differ from those predicted by models. In terms of other measures of food web complexity, habitat connectivity has been empirically found to generally increase link density but either reduce or have no effect on connectance, whereas a unimodal relationship is expected. In general, there is growing concordance between empirical patterns and theoretical predictions for some effects of habitat connectivity on food webs, but many predictions remain to be tested over a full connectivity gradient, and empirical metrics of complexity are rarely modeled. Closing these gaps will allow a deeper understanding of how natural and anthropogenic changes in connectivity can affect real food webs.     

Occupancy modeling of <Emphasis Type="Italic">Parnassius clodius</Emphasis> butterfly populations in Grand Teton National Park,Wyoming

Estimating occupancy patterns and identifying vegetation characteristics that influence the presence of butterfly species are essential approaches needed for determining how habitat changes may affect butterfly populations in the future. The montane butterfly species, Parnassius clodius, was investigated to identify patterns of occupancy relating to habitat variables in Grand Teton National Park and Bridger-Teton National Forest, Wyoming, United States. A series of presence–absence surveys were conducted in 2013 in 41 mesic to xeric montane meadows that were considered suitable habitat for P. clodius during their flight season (June–July) to estimate occupancy (ψ) and detection probability (p). According to the null constant parameter model, P. clodius had high occupancy of ψ?=?0.78?±?0.07 SE and detection probability of p?=?0.75?±?0.04 SE. In models testing covariates, the most important habitat indicator for the occupancy of P. clodius was a strong negative association with big sagebrush (Artemisia tridentata; β = ??21.39?±?21.10 SE) and lupine (Lupinus spp.; β?=???20.03?±?21.24 SE). While P. clodius was found at a high proportion of meadows surveyed, the presence of A. tridentata may limit their distribution within montane meadows at a landscape scale because A. tridentata dominates a large percentage of the montane meadows in our study area. Future climate scenarios predicted for high elevations globally could cause habitat shifts and put populations of P. clodius and similar non-migratory butterfly populations at risk.     

Agrin Regulation of ��3 Sodium-Potassium ATPase Activity Modulates Cardiac Myocyte Contraction

Drugs that inhibit Na,K-ATPases, such as digoxin and ouabain, alter cardiac myocyte contractility. We recently demonstrated that agrin, a protein first identified at the vertebrate neuromuscular junction, binds to and regulates the activity of α3 subunit-containing isoforms of the Na,K-ATPase in the mammalian brain. Both agrin and the α3 Na,K-ATPase are expressed in heart, but their potential for interaction and effect on cardiac myocyte function was unknown. Here we show that agrin binds to the α3 subunit of the Na,K-ATPase in cardiac myocyte membranes, inducing tyrosine phosphorylation and inhibiting activity of the pump. Agrin also triggers a rapid increase in cytoplasmic Na⁺ in cardiac myocytes, suggesting a role in cardiac myocyte function. Consistent with this hypothesis, spontaneous contraction frequencies of cultured cardiac myocytes prepared from mice in which agrin expression is blocked by mutation of the Agrn gene are significantly higher than in the wild type. The Agrn mutant phenotype is rescued by acute treatment with recombinant agrin. Furthermore, exposure of wild type myocytes to an agrin antagonist phenocopies the Agrn mutation. These data demonstrate that the basal frequency of myocyte contraction depends on endogenous agrin-α3 Na,K-ATPase interaction and suggest that agrin modulation of the α3 Na,K-ATPase is important in regulating heart function.Na,K-ATPases, or sodium pumps, are integral membrane enzymes found in all animal cells. Using energy from the hydrolysis of ATP they transport three Na⁺ ions out of the cell for every two K⁺ ions into the cell, resulting in a transmembrane chemical gradient that is reflected in the resting membrane potential and used to drive a variety of secondary transport processes. Each Na,K-ATPase is a heterodimer consisting of an α- and β-subunit. The α-subunit is the catalytic subunit and contains the binding sites for Na⁺ and K⁺. The β-subunit is required for pump function and targeting of the α-subunit to the plasma membrane. Four α- and three β-subunit genes have been identified. All combinations of α- and β-subunits form functional pumps, but developmental, cellular, and subcellular differences in expression suggest functional adaptation of the different isoforms (1).Na,K-ATPases play a central role in regulating the contractile activity of cardiac muscle (2). They are directly responsible for the Na⁺ gradient required for propagation of action potentials that initiate myocyte contraction. Moreover, because of the dependence of the Na⁺/Ca²⁺ exchanger (NCX)³ on the Na⁺ gradient as the source of counterions for transport of Ca²⁺ out of the cell, they play a critical role in Ca²⁺ homeostasis and excitation-contraction coupling. For example, inhibition of Na,K-ATPases by digoxin, ouabain, or other cardiac glycoside results in a decline of the Na⁺ gradient, reducing NCX activity and Ca²⁺ efflux. The inotropic effects of cardiac glycosides result from uptake of this “excess” cytoplasmic Ca²⁺ into the sarcoplasmic reticulum, raising the level of Ca²⁺ in intracellular stores, which, when released during excitation, enhances muscle contraction (3).In light of the importance of Na,K-ATPases for cardiac muscle function, it is not surprising that mechanisms have evolved to regulate their activity. Na,K-ATPases are susceptible to phosphorylation by either cAMP-dependent protein kinase or protein kinase C, and neurotransmitter- and peptide hormone-dependent activation of these cytoplasmic kinases have been shown to regulate pump activity (4). Other molecules exert their effects through direct interaction with the Na,K-ATPase. For example, phospholemman, a member of the FXYD family of membrane proteins expressed in heart, is tightly associated with the Na,K-ATPase and inhibits its function (5–7). Phosphorylation of phospholemman by either protein kinase C or cAMP-dependent protein kinase, however, relieves inhibition thereby restoring the activity of the pump (8, 9). Endogenous ouabain-like compounds have also been implicated in regulating Na,K-ATPase activity (10). Ouabain, or closely related molecules, is synthesized by the adrenal gland and hypothalamus, and increased circulating levels of these compounds observed in patients with congestive heart failure has been suggested as an adaptive response to improve heart function (11). Recent studies in the central nervous system have identified the protein agrin as a new endogenous ligand that regulates Na,K-ATPase function through interaction with its extracellular domains (12).Agrin was first identified as an extracellular matrix protein at the neuromuscular junction where, by signaling through a muscle-specific receptor tyrosine kinase called MuSK, it mediates the motor neuron-induced accumulation of acetylcholine receptors in the postsynaptic muscle fiber membrane (13). Agrin is also expressed in other tissues (14–16), but its function outside of the neuromuscular junction has been less well understood. Recently, however, we showed that agrin plays a role in regulating excitability of central nervous system neurons by binding to and inhibiting the activity of the α3 subunit-containing isoform of the Na,K-ATPase (12). Although both agrin (14, 16) and the α3 Na,K-ATPase (17) are expressed in heart, their potential interaction has not been explored. Here we show that the frequency of cardiac myocyte contraction is modulated by agrin regulation of α3 Na,K-ATPase activity.