Waterloo Research

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The Calmodulin-binding, short linear motif, NSCaTE is conserved in L-type channel ancestors of vertebrate Cav1.2 and Cav1.3 channels
(Public Library of Science, 2013-04-23) Taiakina, Valentina; Boone, Adrienne N.; Fux, Julia; Senatore, Adriano; Weber-Adrian, Danielle; Guillemette, J. Guy; Spafford, J. David
NSCaTE is a short linear motif of (xWxxx(I or L)xxxx), composed of residues with a high helix-forming propensity within a mostly disordered N-terminus that is conserved in L-type calcium channels from protostome invertebrates to humans. NSCaTE is an optional, lower affinity and calcium-sensitive binding site for calmodulin (CaM) which competes for CaM binding with a more ancient, C-terminal IQ domain on L-type channels. CaM bound to N- and C- terminal tails serve as dual detectors to changing intracellular Ca2+ concentrations, promoting calcium-dependent inactivation of L-type calcium channels. NSCaTE is absent in some arthropod species, and is also lacking in vertebrate L-type isoforms, Cav1.1 and Cav1.4 channels. The pervasiveness of a methionine just downstream from NSCaTE suggests that L-type channels could generate alternative N-termini lacking NSCaTE through the choice of translational start sites. Long N-terminus with an NSCaTE motif in L-type calcium channel homolog LCav1 from pond snail Lymnaea stagnalis has a faster calcium-dependent inactivation than a shortened N-termini lacking NSCaTE. NSCaTE effects are present in low concentrations of internal buffer (0.5 mM EGTA), but disappears in high buffer conditions (10 mM EGTA). Snail and mammalian NSCaTE have an alpha-helical propensity upon binding Ca2+-CaM and can saturate both CaM N-terminal and C-terminal domains in the absence of a competing IQ motif. NSCaTE evolved in ancestors of the first animals with internal organs for promoting a more rapid, calcium-sensitive inactivation of L-type channels.
Short-latency afferent inhibition modulation during finger movement
(Public Library of Science, 2013-04-04) Asmussen, Michael J.; Jacobs, Mark F.; Lee, Kevin G. H.; Zapallow, Christopher M.; Nelson, Aimee J.
When somatosensory input via electrical stimulation of a peripheral nerve precedes a transcranial magnetic stimulation (TMS) pulse over the primary motor cortex (M1) the corticospinal output is substantially reduced, a phenomenon known as short-latency afferent inhibition (SAI). The present study investigated SAI during rest and during pre-movement, phasic and tonic components of movement. Participants were required to perform an index finger flexion reaction time task in response to an auditory cue. In a series of experiments, SAI was evoked from the mixed, median nerve at the wrist or the cutaneous, digital nerve stimulation of the index finger. To assess the spinal versus cortical origin of movement-related modulation of SAI, F-wave amplitudes were measured during rest and the three movement components. Results indicated that SAI was reduced during all movement components compared to rest, an effect that occurred for both nerves stimulated. Pre-movement SAI reduction was primarily attributed to reduced cortical inhibition, while increased spinal excitability additionally contributed to reduced SAI during tonic and phasic components of movement. SAI was differentially modulated across movement components with mixed but not cutaneous nerve stimulation. These findings reveal that SAI is reduced during movement and this reduction begins as early as the preparation to move. Further, these data suggest that the degree of SAI reduction during movement may be specific to the volume and/or composition of afferent input carried by each nerve.
Modulation of morphogenesis by Egfr during dorsal closure in Drosophila
(Public Library of Science, 2013-04-08) Shen, Weiping; Chen, Xi; Cormier, Olga; Cheng, David Chung-Pei; Reed, Bruce; Harden, Nicholas
During Drosophila embryogenesis the process of dorsal closure (DC) results in continuity of the embryonic epidermis, and DC is well recognized as a model system for the analysis of epithelial morphogenesis as well as wound healing. During DC the flanking lateral epidermal sheets stretch, align, and fuse along the dorsal midline, thereby sealing a hole in the epidermis occupied by an extra-embryonic tissue known as the amnioserosa (AS). Successful DC requires the regulation of cell shape change via actomyosin contractility in both the epidermis and the AS, and this involves bidirectional communication between these two tissues. We previously demonstrated that transcriptional regulation of myosin from the zipper (zip) locus in both the epidermis and the AS involves the expression of Ack family tyrosine kinases in the AS in conjunction with Dpp secreted from the epidermis. A major function of Ack in other species, however, involves the negative regulation of Egfr. We have, therefore, asked what role Egfr might play in the regulation of DC. Our studies demonstrate that Egfr is required to negatively regulate epidermal expression of dpp during DC. Interestingly, we also find that Egfr signaling in the AS is required to repress zip expression in both the AS and the epidermis, and this may be generally restrictive to the progression of morphogenesis in these tissues. Consistent with this theme of restricting morphogenesis, it has previously been shown that programmed cell death of the AS is essential for proper DC, and we show that Egfr signaling also functions to inhibit or delay AS programmed cell death. Finally, we present evidence that Ack regulates zip expression by promoting the endocytosis of Egfr in the AS. We propose that the general role of Egfr signaling during DC is that of a braking mechanism on the overall progression of DC.
The complete genome sequence of the plant growth-promoting bacterium Pseudomonas sp. UW4
(Public Library of Science, 2013-03-13) Duan, Jin; Jiang, Wei; Cheng, Zhenyu; Heikkila, John J.; Glick, Bernard R.
The plant growth-promoting bacterium (PGPB) Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 genome contains a single circular chromosome that is 6,183,388 bp with a 60.05% G+C content. The bacterial genome contains 5,423 predicted protein-coding sequences that occupy 87.2% of the genome. Nineteen genomic islands (GIs) were predicted and thirty one complete putative insertion sequences were identified. Genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, acetoin synthesis, and phosphate solubilization were determined. Moreover, genes that contribute to the environmental fitness of UW4 were also observed including genes responsible for heavy metal resistance such as nickel, copper, cadmium, zinc, molybdate, cobalt, arsenate, and chromate. Whole-genome comparison with other completely sequenced Pseudomonas strains and phylogeny of four concatenated “housekeeping” genes (16S rRNA, gyrB, rpoB and rpoD) of 128 Pseudomonas strains revealed that UW4 belongs to the fluorescens group, jessenii subgroup.
Enzyme-synthesized highly branched maltodextrins have slow glucose generation at the mucosal a-glucosidase level and are slowly digestible in vivo
(Public Library of Science, 2013-04-02) Lee, Byung-Hoo; Yan, Like; Phillips, Robert J.; Reuhs, Bradley L.; Jones, Kyra; Rose, David R.; Nichols, Buford L.; Quezada-Calcillo, Roberto; Yoo, Sang-Ho; Hamaker, Bruce R.
For digestion of starch in humans, α-amylase first hydrolyzes starch molecules to produce α-limit dextrins, followed by complete hydrolysis to glucose by the mucosal α-glucosidases in the small intestine. It is known that α-1,6 linkages in starch are hydrolyzed at a lower rate than are α-1,4 linkages. Here, to create designed slowly digestible carbohydrates, the structure of waxy corn starch (WCS) was modified using a known branching enzyme alone (BE) and an in combination with β-amylase (BA) to increase further the α-1,6 branching ratio. The digestibility of the enzymatically synthesized products was investigated using α-amylase and four recombinant mammalian mucosal α-glucosidases. Enzyme-modified products (BE-WCS and BEBA-WCS) had increased percentage of α-1,6 linkages (WCS: 5.3%, BE-WCS: 7.1%, and BEBA-WCS: 12.9%), decreased weight-average molecular weight (WCS: 1.73×108 Da, BE-WCS: 2.76×105 Da, and BEBA-WCS 1.62×105 Da), and changes in linear chain distributions (WCS: 21.6, BE-WCS: 16.9, BEBA-WCS: 12.2 DPw). Hydrolysis by human pancreatic α-amylase resulted in an increase in the amount of branched α-limit dextrin from 26.8% (WCS) to 56.8% (BEBA-WCS). The α-amylolyzed samples were hydrolyzed by the individual α-glucosidases (100 U) and glucogenesis decreased with all as the branching ratio increased. This is the first report showing that hydrolysis rate of the mammalian mucosal α-glucosidases is limited by the amount of branched α-limit dextrin. When enzyme-treated materials were gavaged to rats, the level of postprandial blood glucose at 60 min from BEBA-WCS was significantly higher than for WCS or BE-WCS. Thus, highly branched glucan structures modified by BE and BA had a comparably slow digesting property both in vitro and in vivo. Such highly branched α-glucans show promise as a food ingredient to control postprandial glucose levels and to attain extended glucose release.
Cu2+ Affects Amyloid-β (1–42) Aggregation by Increasing Peptide-Peptide Binding Forces
(Public Library of Science, 2013-03-11) Hane, Francis; Tran, Gary; Attwood, Simon J.; Leonenko, Zoya
The link between metals, Alzheimer's disease (AD) and its implicated protein, amyloid-β (Aβ), is complex and highly studied. AD is believed to occur as a result of the misfolding and aggregation of Aβ. The dyshomeostasis of metal ions and their propensity to interact with Aβ has also been implicated in AD. In this work, we use single molecule atomic force spectroscopy to measure the rupture force required to dissociate two Aβ (1–42) peptides in the presence of copper ions, Cu2+. In addition, we use atomic force microscopy to resolve the aggregation of Aβ formed. Previous research has shown that metal ions decrease the lag time associated with Aβ aggregation. We show that with the addition of copper ions the unbinding force increases notably. This suggests that the reduction of lag time associated with Aβ aggregation occurs on a single molecule level as a result of an increase in binding forces during the very initial interactions between two Aβ peptides. We attribute these results to copper ions acting as a bridge between the two peptide molecules, increasing the stability of the peptide-peptide complex.
Evaluting primers for profiling anaerobic ammonia oxidizing bacteria within freshwater environments
(Public Library of Science, 2013-03-07) Sonthiphand, Puntipar; Neufeld, Josh D.
Anaerobic ammonia oxidizing (anammox) bacteria play an important role in transforming ammonium to nitrogen gas and contribute to fixed nitrogen losses in freshwater environments. Understanding the diversity and abundance of anammox bacteria requires reliable molecular tools, and these are not yet well established for these important Planctomycetes. To help validate PCR primers for the detection of anammox bacteria within freshwater ecosystems, we analyzed representative positive controls and selected samples from Grand River and groundwater sites, both from Ontario, Canada. The objectives of this study were to identify a suitable anammox denaturing gradient gel electrophoresis (DGGE) fingerprint method by using GC-clamp modifications to existing primers, and to verify the specificity of anammox-specific primers used for DGGE, cloning and qPCR methods. Six primer combinations were tested from four published primer sets (i.e. A438f/A684r, Amx368f/Amx820r, An7f/An1388r, and Pla46/1392r) for both direct and nested PCR amplifications. All PCR products were run subsequently on DGGE gels to compare the resulting patterns. Two anammox-specific primer combinations were also used to generate clone libraries and quantify anammox bacterial 16S rRNA genes with qPCR. The primer set A438f/A684r was highly specific to anammox bacteria, provided reliable DGGE fingerprints and generated a high proportion of anammox-related clones. A second primer set (Amx368f/Amx820r) was anammox specific, based on clone library analysis, but PCR products from different candidate species of anammox bacteria resolved poorly using DGGE analysis. Both DGGE and cloning results revealed that Ca. Brocadia and an uncharacterized anammox bacterial cluster represented the majority of anammox bacteria found in Grand River sediment and groundwater samples, respectively. Together, our results demonstrate that although Amx368f/Amx820r was useful for anammox-specific qPCR and clone library analysis, A438f/A684r was the most suitable primer set for multiple molecular assessments of anammox bacteria in freshwater environments.
Active video games and health indicators in children and youth: A systematic review
(Public Library of Science, 2013-06-14) LeBlanc, Allana G.; Chaput, Jean-Philippe; McFarlane, Allison; Colley, Rachel C.; Thivel, David; Biddle, Stuart J. H.; Maddison, Ralph; Leatherdale, Scott T.; Tremblay, Mark S.
Background Active video games (AVGs) have gained interest as a way to increase physical activity in children and youth. The effect of AVGs on acute energy expenditure (EE) has previously been reported; however, the influence of AVGs on other health-related lifestyle indicators remains unclear. Objective This systematic review aimed to explain the relationship between AVGs and nine health and behavioural indicators in the pediatric population (aged 0-17 years). Data sources Online databases (MEDLINE, EMBASE, psycINFO, SPORTDiscus and Cochrane Central Database) and personal libraries were searched and content experts were consulted for additional material. Data selection Included articles were required to have a measure of AVG and at least one relevant health or behaviour indicator: EE (both habitual and acute), adherence and appeal (i.e., participation and enjoyment), opportunity cost (both time and financial considerations, and adverse events), adiposity, cardiometabolic health, energy intake, adaptation (effects of continued play), learning and rehabilitation, and video game evolution (i.e., sustainability of AVG technology). Results 51 unique studies, represented in 52 articles were included in the review. Data were available from 1992 participants, aged 3–17 years, from 8 countries, and published from 2006–2012. Overall, AVGs are associated with acute increases in EE, but effects on habitual physical activity are not clear. Further, AVGs show promise when used for learning and rehabilitation within special populations. Evidence related to other indicators was limited and inconclusive. Conclusions Controlled studies show that AVGs acutely increase light- to moderate-intensity physical activity; however, the findings about if or how AVG lead to increases in habitual physical activity or decreases in sedentary behaviour are less clear. Although AVGs may elicit some health benefits in special populations, there is not sufficient evidence to recommend AVGs as a means of increasing daily physical activity.
Investigating the link between molecular subtypes of glioblastoma, epithelial-mesenchymal transition, and CD133 cell surface protein
(Public Library of Science, 2013-05-29) Zarkoob, Hadi; Taube, Joseph H.; Singh, Sheila K.; Mani, Sendurai A.; Kohandel, Mohammad
In this manuscript, we use genetic data to provide a three-faceted analysis on the links between molecular subclasses of glioblastoma, epithelial-to-mesenchymal transition (EMT) and CD133 cell surface protein. The contribution of this paper is three-fold: First, we use a newly identified signature for epithelial-to-mesenchymal transition in human mammary epithelial cells, and demonstrate that genes in this signature have significant overlap with genes differentially expressed in all known GBM subtypes. However, the overlap between genes up regulated in the mesenchymal subtype of GBM and in the EMT signature was more significant than other GBM subtypes. Second, we provide evidence that there is a negative correlation between the genetic signature of EMT and that of CD133 cell surface protein, a putative marker for neural stem cells. Third, we study the correlation between GBM molecular subtypes and the genetic signature of CD133 cell surface protein. We demonstrate that the mesenchymal and neural subtypes of GBM have the strongest correlations with the CD133 genetic signature. While the mesenchymal subtype of GBM displays similarity with the signatures of both EMT and CD133, it also exhibits some differences with each of these signatures that are partly due to the fact that the signatures of EMT and CD133 are inversely related to each other. Taken together these data shed light on the role of the mesenchymal transition and neural stem cells, and their mutual interaction, in molecular subtypes of glioblastoma multiforme.
Developing a vulnerability mapping methodology: Applying the water-associated disease index to dengue in Malaysia
(Public Library of Science, 2013-05-08) Dickin, Sarah K.; Schuster-Wallace, Corinne J.; Elliott, Susan J.
The Water-associated Disease Index (WADI) was developed to identify and visualize vulnerability to different water-associated diseases by integrating a range of social and biophysical determinants in map format. In this study vulnerability is used to encompass conditions of exposure, susceptibility, and differential coping capacity to a water-associated health hazard. By assessing these conditions, the tool is designed to provide stakeholders with an integrated and long-term understanding of subnational vulnerabilities to water-associated disease and contribute to intervention strategies to reduce the burden of illness. The objective of this paper is to describe and validate the WADI tool by applying it to dengue. A systemic ecohealth framework that considers links between people, the environment and health was applied to identify secondary datasets, populating the index with components including climate conditions, land cover, education status and water use practices. Data were aggregated to create composite indicators of exposure and of susceptibility in a Geographic Information System (GIS). These indicators were weighted by their contribution to dengue vulnerability, and the output consisted of an overall index visualized in map format. The WADI was validated in this Malaysia case study, demonstrating a significant association with dengue rates at a sub-national level, and illustrating a range of factors that drive vulnerability to the disease within the country. The index output indicated high vulnerability to dengue in urban areas, especially in the capital Kuala Lumpur and surrounding region. However, in other regions, vulnerability to dengue varied throughout the year due to the influence of seasonal climate conditions, such as monsoon patterns. The WADI tool complements early warning models for water-associated disease by providing upstream information for planning prevention and control approaches, which increasingly require a comprehensive and geographically broad understanding of vulnerability for implementation.
Could sensory mechanisms be a core factor that underlies freezing of gait in Parkinson's disease?
(Public Library of Science, 2013-05-08) Martens, Kaylena A. Ehgoetz; Pieruccini-Faria, Frederico; Almeida, Quincy J.
The main objective of this study was to determine how manipulating the amount of sensory information available about the body and surrounding environment influenced freezing of gait (FOG), while walking through a doorway. It was hypothesized that the more limited the sensory information, the greater the occurrence of freezing of gait. Nineteen patients with Parkinsoǹs disease who experience freezing of gait (PD-FOG) walked through a doorway or into open space in complete darkness. The three doorway conditions included: (i) FRAME (DARK) – walking through the remembered door frame; (ii) FRAME - walking through the door with the door frame illuminated; (iii) FRAME+BODY - walking through the door (both the door and the limbs illuminated). Additionally, two conditions of walking away from the doorway included: (iv) NO FRAME (DARK) - walking into open space; (v) NO FRAME+BODY - walking into open space with the limbs illuminated, to evaluate whether perception (or fear) of the doorway might account for FOG behaviour. Key outcome measures included: the number of freezing of gait episodes recorded, total duration of freezing of gait, and the percentage of time spent frozen. Significantly more freezing of gait episodes occurred when participants walked toward the doorway in complete darkness compared to walking into open space (p<0.05). Similar to previous studies, velocity (p<0.001) and step length (p<0.0001) significantly decreased when walking through the door in complete darkness, compared to all other conditions. Significant increases in step width variability were also identified but only when walking into open space (p<0.005). These results support the notion that sensory deficits may have a profound impact on freezing of gait that need to be carefully considered.
Evaluating the effectiveness of France's indoor smoke-free law 1 year and 5 years after implementation: Findings from the ITC France survey
(Public Library of Science, 2013-06-21) Fong, Geoffrey T.; Craig, Lorraine V.; Guignard, Romain; Nagelhout, Gera E.; Tait, Megan K.; Driezen, Pete; Kennedy, Ryan David; Boudreau, Christian; Wilquin, Jean-Louis; Deutsch, Antoine; Beck, Francois
France implemented a comprehensive smoke-free law in two phases: Phase 1 (February 2007) banned smoking in workplaces, shopping centres, airports, train stations, hospitals, and schools; Phase 2 (January 2008) banned smoking in hospitality venues (bars, restaurants, hotels, casinos, nightclubs). This paper evaluates France’s smoke-free law based on the International Tobacco Control Policy Evaluation Project in France (the ITC France Project), which conducted a cohort survey of approximately 1,500 smokers and 500 non-smokers before the implementation of the laws (Wave 1) and two waves after the implementation (Waves 2 and 3). Results show that the smoke-free law led to a very significant and near-total elimination of observed smoking in key venues such as bars (from 94–97% to 4%) and restaurants (from 60–71% to 2–3%) at Wave 2, which was sustained four years later (6–8% in bars; 1–2% in restaurants). The reduction in self-reported smoking by smoking respondents was nearly identical to the effects shown in observed smoking. Observed smoking in workplaces declined significantly after the law (from 41–48% to 18–20%), which continued to decline at Wave 3 (to 14–15%). Support for the smoke-free laws increased significantly after their implementation and continued to increase at Wave 3 (p<.001 among smokers for bars and restaurants; p<.001 among smokers and p = .003 for non-smokers for workplaces). The findings demonstrate that smoke-free policies that are implemented in ways consistent with the Guidelines for Article 8 of the WHO Framework Convention on Tobacco Control (WHO FCTC) lead to substantial and sustained reductions in indoor smoking while also leading to high levels of support by the public. Moreover, contrary to arguments by opponents of smoke-free laws, smoking in the home did not increase after the law was implemented and prevalence of smoke-free homes among smokers increased from 23.2% before the law to 37.2% 5 years after the law.
The weight of a guilty conscience: Subjective body weight as an embodiment of guilt
(Public Library of Science, 2013-07-31) Day, Martin V.; Bobocel, D. Ramona
Guilt is an important social and moral emotion. In addition to feeling unpleasant, guilt is metaphorically described as a "weight on one's conscience." Evidence from the field of embodied cognition suggests that abstract metaphors may be grounded in bodily experiences, but no prior research has examined the embodiment of guilt. Across four studies we examine whether i) unethical acts increase subjective experiences of weight, ii) feelings of guilt explain this effect, and iii) whether there are consequences of the weight of guilt. Studies 1-3 demonstrated that unethical acts led to more subjective body weight compared to control conditions. Studies 2 and 3 indicated that heightened feelings of guilt mediated the effect, whereas other negative emotions did not. Study 4 demonstrated a perceptual consequence. Specifically, an induction of guilt affected the perceived effort necessary to complete tasks that were physical in nature, compared to minimally physical tasks.
Neuregulin unregulates microglial α7 nicotinic acetylcholine receptor expression in immortalized cell lines: Implications for regulating neuroinflammation
(Public Library of Science, 2013-07-30) Mencel, Malwina; Nash, Michelle; Jacobson, Christian
Neuregulin, previously known as ARIA, is a signaling protein involved in cell survival, synaptic plasticity, cell communication and differentiation. Neuregulin has also been described as a potent inducer of acetylcholine receptor transcription in muscle and although both neuregulin and acetylcholine have been individually described to have neuroprotective roles, their relationship in the cholinergic anti-inflammatory pathway of the brain has not been examined. Using three cell lines, BV-2, EOC-20 and RAW 264.7, we investigated the role that neuregulin signaling through the Erb family of tyrosine kinases may play in the anti-inflammatory process mediated by the α7 nicotinic acetylcholine receptors. Here we show that ErbB4 is expressed in all of our cell lines and is phosphorylated upon treatment with neuregulin. Neuregulin treatment further increases the expression of α7 nicotinic acetylcholine receptors in the microglial lines tested. Given the central role of α7 nicotinic acetylcholine receptors in regulating system inflammation we analyzed the expression of several pro-inflammatory cytokines in our system. Using ELISAs for TNF-α and IL-6 we show that treatment with NRG can produce a nearly a 33% decrease in the levels of tumor necrosis factor-α secreted by activated microglia and a nearly 88% decrease in IL-6. Given these results we propose a neuroprotective role for neuregulin wherein it modulates the expression of TNF-α and thus inflammation in the CNS via the upregulation of α7 nicotinic acetylcholine receptor expression in microglia in vitro. We suggest that the disregulation of neuregulin expression may be pivotal in neurological disorders characterized by inflammation.
ATP Consumption by Sarcoplasmic Reticulum Ca2+ Pumps Accounts for 40-50% of Resting Metabolic Rate in Mouse Fast and Slow Twitch Skeletal Muscle
(Public Library of Science, 2013-07-01) Smith, Ian Curtis; Bombardier, Eric; Vigna, Chris; Tupling, A. Russell
The main purpose of this study was to directly quantify the relative contribution of Ca2+ cycling to resting metabolic rate in mouse fast (extensor digitorum longus, EDL) and slow (soleus) twitch skeletal muscle. Resting oxygen consumption of isolated muscles (VO2, µL/g wet weight/s) measured polarographically at 30°C was ~20% higher (P<0.05) in soleus (0.326 ± 0.022) than in EDL (0.261 ± 0.020). In order to quantify the specific contribution of Ca2+ cycling to resting metabolic rate, the concentration of MgCl2 in the bath was increased to 10 mM to block Ca2+ release through the ryanodine receptor, thus eliminating a major source of Ca2+ leak from the sarcoplasmic reticulum (SR), and thereby indirectly inhibiting the activity of the sarco(endo) plasmic reticulum Ca2+-ATPases (SERCAs). The relative (%) reduction in muscle VO2 in response to 10 mM MgCl2 was similar between soleus (48.0±3.7) and EDL (42.4±3.2). Using a different approach, we attempted to directly inhibit SERCA ATPase activity in stretched EDL and soleus muscles (1.42x optimum length) using the specific SERCA inhibitor cyclopiazonic acid (CPA, up to 160 µM), but were unsuccessful in removing the energetic cost of Ca2+ cycling in resting isolated muscles. The results of the MgCl2 experiments indicate that ATP consumption by SERCAs is responsible for 40–50% of resting metabolic rate in both mouse fast- and slow-twitch muscles at 30°C, or 12–15% of whole body resting VO2. Thus, SERCA pumps in skeletal muscle could represent an important control point for energy balance regulation and a potential target for metabolic alterations to oppose obesity.
Numerical modeling of interstitial fluid flow coupled wiht blood flow through a remodeled solid tumor microvascular network
(Public Library of Science, 2013-06-26) Soltani, M.; Chen, P.
Modeling of interstitial fluid flow involves processes such as fluid diffusion, convective transport in extracellular matrix, and extravasation from blood vessels. To date, majority of microvascular flow modeling has been done at different levels and scales mostly on simple tumor shapes with their capillaries. However, with our proposed numerical model, more complex and realistic tumor shapes and capillary networks can be studied. Both blood flow through a capillary network, which is induced by a solid tumor, and fluid flow in tumor’s surrounding tissue are formulated. First, governing equations of angiogenesis are implemented to specify the different domains for the network and interstitium. Then, governing equations for flow modeling are introduced for different domains. The conservation laws for mass and momentum (including continuity equation, Darcy’s law for tissue, and simplified Navier–Stokes equation for blood flow through capillaries) are used for simulating interstitial and intravascular flows and Starling’s law is used for closing this system of equations and coupling the intravascular and extravascular flows. This is the first study of flow modeling in solid tumors to naturalistically couple intravascular and extravascular flow through a network. This network is generated by sprouting angiogenesis and consisting of one parent vessel connected to the network while taking into account the non-continuous behavior of blood, adaptability of capillary diameter to hemodynamics and metabolic stimuli, non-Newtonian blood flow, and phase separation of blood flow in capillary bifurcation. The incorporation of the outlined components beyond the previous models provides a more realistic prediction of interstitial fluid flow pattern in solid tumors and surrounding tissues. Results predict higher interstitial pressure, almost two times, for realistic model compared to the simplified model.
Serum immune-related proteins are differentially expressed during hibernation in the American Black Bear
(Public Library of Science, 2013-06-25) Chow, Brian A.; Donahue, Seth W.; Vaughan, Michael R.; McConkey, Brendan; Vijayan, Mathilakath M.
Hibernation is an adaptation to conserve energy in the face of extreme environmental conditions and low food availability that has risen in several animal phyla. This phenomenon is characterized by reduced metabolic rate (∼25% of the active basal metabolic rate in hibernating bears) and energy demand, while other physiological adjustments are far from clear. The profiling of the serum proteome of the American black bear (Ursus americanus) may reveal specific proteins that are differentially modulated by hibernation, and provide insight into the remarkable physiological adaptations that characterize ursid hibernation. In this study, we used differential gel electrophoresis (DIGE) analysis, liquid chromatography coupled to tandem mass spectrometry, and subsequent MASCOT analysis of the mass spectra to identify candidate proteins that are differentially expressed during hibernation in captive black bears. Seventy serum proteins were identified as changing by ±1.5 fold or more, out of which 34 proteins increased expression during hibernation. The majority of identified proteins are involved in immune system processes. These included α2-macroglobulin, complement components C1s and C4, immunoglobulin μ and J chains, clusterin, haptoglobin, C4b binding protein, kininogen 1, α2-HS-glycoprotein, and apoplipoproteins A-I and A-IV. Differential expression of a subset of these proteins identified by proteomic analysis was also confirmed by immunodetection. We propose that the observed serum protein changes contribute to the maintenance of the hibernation phenotype and health, including increased capacities for bone maintenance and wound healing during hibernation in bears.
Bacterial communities associated with culex mosquito larvae and two emergent aquatic plants of bioremediation importance
(Public Library of Science, 2013-08-15) Duguma, Dagne; Pugman-Jones, Paul; Kaufman, Michael G.; Hall, Michael W.; Neufeld, Josh D.; Stouthamer, Richard; Walton, William E.
Microbes are important for mosquito nutrition, growth, reproduction and control. In this study, we examined bacterial communities associated with larval mosquitoes and their habitats. Specifically, we characterized bacterial communities associated with late larval instars of the western encephalitis mosquito (Culex tarsalis), the submerged portions of two emergent macrophytes (California bulrush, Schoenoplectus californicus and alkali bulrush, Schoenoplectus maritimus), and the associated water columns to investigate potential differential use of resources by mosquitoes in different wetland habitats. Using next-generation sequence data from 16S rRNA gene hypervariable regions, the alpha diversity of mosquito gut microbial communities did not differ between pond mesocosms containing distinct monotypic plants. Proteobacteria, dominated by the genus Thorsellia (Enterobacteriaceae), was the most abundant phylum recovered from C. tarsalis larvae. Approximately 49% of bacterial OTUs found in larval mosquitoes were identical to OTUs recovered from the water column and submerged portions of the two bulrushes. Plant and water samples were similar to one another, both being dominated by Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria and Verrucomicrobia phyla. Overall, the bacterial communities within C. tarsalis larvae were conserved and did not change across sampling dates and between two distinct plant habitats. Although Thorsellia spp. dominated mosquito gut communities, overlap of mosquito gut, plant and water-column OTUs likely reveal the effects of larval feeding. Future research will investigate the role of the key indicator groups of bacteria across the different developmental stages of this mosquito species.
Assessment of heavy metal contamination in the surrounding soils and surface sediments in Xiawangang River, Qingshuitang District
(Public Library of Science, 2013-08-08) Jiang, Min; Zeng, Guangming; Zhang, Chang; Ma, Xiaoying; Chen, Ming; Zhang, Jiachao; Lu, Lunhui; Yu, Qian; Hu, Langping; Liu, Lifeng
Xiawanggang River region is considered to be one of the most polluted areas in China due to its huge amount discharge of pollutants and accumulation for years. As it is one branch of Xiang River and the area downstream is Changsha city, the capital of Hunan Province, the ecological niche of Xiawangang River is very important. The pollution treatment in this area was emphasized in the Twelfth Five-Year Plan of Chinese government for Xiang River Water Environmental Pollution Control. In order to assess the heavy metal pollution and provide the base information in this region for The Twelfth Five-Year Plan, contents and fractions of four heavy metals (Cd, Cu, Pb and Zn) covering both sediments and soils were analyzed to study their contamination state. Three different indexes were applied to assess the pollution extent. The results showed this area was severely polluted by the four heavy metals, and the total concentrations exceeded the Chinese environmental quality standard for soil, grade III, especially for Cd. Moreover, Cd, rated as being in high risk, had a high mobility as its great contents of exchangeable and carbonates fractions in spite of its relative low content. Regression analysis revealed clay could well explain the regression equation for Cd, Cu and Zn while pH and sand could significantly interpret the regression equation for Pb. Moreover, there was a significant correlation between Non-residual fraction and Igeo for all the four metals. Correlation analysis showed four metals maybe had similar pollution sources.
Metagenomic guilt by association: An operonic perspective
(Public Library of Science, 2013-08-06) Vey, Gregory
Next-generation sequencing projects continue to drive a vast accumulation of metagenomic sequence data. Given the growth rate of this data, automated approaches to functional annotation are indispensable and a cornerstone heuristic of many computational protocols is the concept of guilt by association. The guilt by association paradigm has been heavily exploited by genomic context methods that offer functional predictions that are complementary to homology-based annotations, thereby offering a means to extend functional annotation. In particular, operon methods that exploit co-directional intergenic distances can provide homology-free functional annotation through the transfer of functions among co-operonic genes, under the assumption that guilt by association is indeed applicable. Although guilt by association is a well-accepted annotative device, its applicability to metagenomic functional annotation has not been definitively demonstrated. Here a large-scale assessment of metagenomic guilt by association is undertaken where functional associations are predicted on the basis of co-directional intergenic distances. Specifically, functional annotations are compared within pairs of adjacent co-directional genes, as well as operons of various lengths (i.e. number of member genes), in order to reveal new information about annotative cohesion versus operon length. The results suggests that co-directional gene pairs offer reduced confidence for metagenomic guilt by association due to difficulty in resolving the existence of functional associations when intergenic distance is the sole predictor of pairwise gene interactions. However, metagenomic operons, particularly those with substantial lengths, appear to be capable of providing a superior basis for metagenomic guilt by association due to increased annotative stability. The need for improved recognition of metagenomic operons is discussed, as well as the limitations of the present work.

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