The Influence of Radiographic Phenotype and Smoking Status on Peripheral Blood Biomarker Patterns in Chronic Obstructive Pulmonary Disease

Background

Chronic obstructive pulmonary disease (COPD) is characterized by both airway remodeling and parenchymal destruction. The identification of unique biomarker patterns associated with airway dominant versus parenchymal dominant patterns would support the existence of unique phenotypes representing independent biologic processes. A cross-sectional study was performed to examine the association of serum biomarkers with radiographic airway and parenchymal phenotypes of COPD.

Methodology/Principal Findings

Serum from 234 subjects enrolled in a CT screening cohort was analyzed for 33 cytokines and growth factors using a multiplex protein array. The association of serum markers with forced expiratory volume in one second percent predicted (FEV1%) and quantitative CT measurements of airway thickening and emphysema was assessed with and without stratification for current smoking status. Significant associations were found with several serum inflammatory proteins and measurements of FEV1%, airway thickening, and parenchymal emphysema independent of smoking status. The association of select analytes with airway thickening and emphysema was independent of FEV1%. Furthermore, the relationship between other inflammatory markers and measurements of physiologic obstruction or airway thickening was dependent on current smoking status.

Conclusions/Significance

Airway and parenchymal phenotypes of COPD are associated with unique systemic serum biomarker profiles. Serum biomarker patterns may provide a more precise classification of the COPD syndrome, provide insights into disease pathogenesis and identify targets for novel patient-specific biological therapies.     

BtubA-BtubB Heterodimer Is an Essential Intermediate in Protofilament Assembly

Background

BtubA and BtubB are two tubulin-like genes found in the bacterium Prosthecobacter. Our work and a previous crystal structure suggest that BtubB corresponds to α−tubulin and BtubA to β−tubulin. A 1∶1 mixture of the two proteins assembles into tubulin-like protofilaments, which further aggregate into pairs and bundles. The proteins also form a BtubA/B heterodimer, which appears to be a repeating subunit in the protofilament.

Methodology/Principal Findings

We have designed point mutations to disrupt the longitudinal interfaces bonding subunits into protofilaments. The mutants are in two classes, within dimers and between dimers. We have characterized one mutant of each class for BtubA and BtubB. When mixed 1∶1 with a wild type partner, none of the mutants were capable of assembly. An excess of between-dimer mutants could depolymerize preformed wild type polymers, while within-dimer mutants had no activity.

Conclusions

An essential first step in assembly of BtubA + BtubB is formation of a heterodimer. An excess of between-dimer mutants depolymerize wild type BtubA/B by sequestering the partner wild type subunit into inactive dimers. Within-dimer mutants cannot form dimers and have no activity.     

Detection of a colonizing, aquatic, non-indigenous species

Detecting the presence of rare species has interested ecologists and conservation biologists for many years. A particularly daunting application of this problem pertains to the detection of non-indigenous species (NIS) as they colonize new ecosystems. Ethical issues prevent experimental additions of NIS to most natural systems to explore the relationship between sampling intensity and the detection probability of a colonizing NIS. Here we examine this question using a recently introduced water flea, Cercopagis pengoi , in Lake Ontario. The species has biphasic population development, with sexually-produced 'spring morphs' developing prior to parthenogenetically-produced 'typical' morphs. Thus, this biphasic morphology allows distinction between new colonists (spring morphs) from subsequent generations. We repeatedly sampled Hamilton Harbour, Lake Ontario for the presence of both spring and typical morphs. Probability of detection was positively related to both the number of samples taken and animal density in the lake; however, even highly intensive sampling (100 samples) failed to detect the species in early spring when densities were very low. Spatial variation was greatest when densities of Cercopagis were intermediate to low. Sub-sampling, which increased space between adjacent samples, significantly decreased the number of samples required to reach greater, calculated detection probabilities on these dates. Typical sampling protocols for zooplankton have a low probability (< 0.2) of detecting the species unless population density is high. Results of this study suggest that early detection of colonizing, aquatic NIS may be optimized through use of a risk-based sampling design, combined with high sampling intensity in areas deemed most vulnerable to invasion, rather than less intensive sampling at a wider array of sites.     

Glass-immobilized glycated-trypsin: A novel modified trypsin that is remarkably thermostable

Porcine trypsin was glycated with glucose and covalently immobilized through its carboxyl groups onto aminated glass beads to produce porcine immobilized glycated-trypsin (IGT). On incubation at 60 °C and pH 8, IGT retained its full activity for 8 h and 50% of its activity after 24 h. In comparison, under the same conditions porcine native trypsin lost 80% of its activity in 2 h and was completely inactivated in less than 4 h. The rate of autolysis of porcine glycated-trypsin at 37 °C was 40% that of native trypsin and with IGT there was no significant autolysis, even at elevated temperatures as high as 60 °C. Glycation significantly increased the stability of trypsin and immobilization also significantly increased the stability of trypsin. The remarkable thermostability of IGT is attributed to a synergistic effect when these two modifications are combined. Tryptic fragmentation of denatured proteins with IGT can be performed at 60 °C for shorter digestion times and with smaller amounts of enzyme than normally employed to achieve complete digestion with soluble forms of trypsin. Prior denaturation of proteins for tryptic digestion is not required with IGT as in situ denaturation and digestion can be achieved simultaneously at 60 °C with an enzyme:protein mass ratio as low as 1:1000.     

Plant invaders and their novel natural enemies: who is naïve?

Introduced exotic species encounter a wide range of non‐coevolved enemies and competitors in their new range. Evolutionary novelty is a key aspect of these interactions, but who benefits from novelty: the exotic species or their new antagonists? Paradoxically, the novelty argument has been used to explain both the release from and the suppression by natural enemies. We argue that this paradox can be solved by considering underlying interaction mechanisms. Using plant defenses as a model, we argue that mismatches between plant and enemy interaction traits can enhance plant invasiveness in the case of toxin‐based defenses, whereas invasiveness is counteracted by mismatches in recognition‐based defenses and selective foraging of generalist herbivores on plants with rare toxins. We propose that a mechanistic understanding of ecological mismatches can help to explain and predict when evolutionary novelty will enhance or suppress exotic plant invasiveness. This knowledge may also enhance our understanding of plant abundance following range expansion, or during species replacements along successional stages.     

Mitochondrial Malate Dehydrogenase Lowers Leaf Respiration and Alters Photorespiration and Plant Growth in Arabidopsis

Malate dehydrogenase (MDH) catalyzes a reversible NAD⁺-dependent-dehydrogenase reaction involved in central metabolism and redox homeostasis between organelle compartments. To explore the role of mitochondrial MDH (mMDH) in Arabidopsis (Arabidopsis thaliana), knockout single and double mutants for the highly expressed mMDH1 and lower expressed mMDH2 isoforms were constructed and analyzed. A mmdh1mmdh2 mutant has no detectable mMDH activity but is viable, albeit small and slow growing. Quantitative proteome analysis of mitochondria shows changes in other mitochondrial NAD-linked dehydrogenases, indicating a reorganization of such enzymes in the mitochondrial matrix. The slow-growing mmdh1mmdh2 mutant has elevated leaf respiration rate in the dark and light, without loss of photosynthetic capacity, suggesting that mMDH normally uses NADH to reduce oxaloacetate to malate, which is then exported to the cytosol, rather than to drive mitochondrial respiration. Increased respiratory rate in leaves can account in part for the low net CO₂ assimilation and slow growth rate of mmdh1mmdh2. Loss of mMDH also affects photorespiration, as evidenced by a lower postillumination burst, alterations in CO₂ assimilation/intercellular CO₂ curves at low CO₂, and the light-dependent elevated concentration of photorespiratory metabolites. Complementation of mmdh1mmdh2 with an mMDH cDNA recovered mMDH activity, suppressed respiratory rate, ameliorated changes to photorespiration, and increased plant growth. A previously established inverse correlation between mMDH and ascorbate content in tomato (Solanum lycopersicum) has been consolidated in Arabidopsis and may potentially be linked to decreased galactonolactone dehydrogenase content in mitochondria in the mutant. Overall, a central yet complex role for mMDH emerges in the partitioning of carbon and energy in leaves, providing new directions for bioengineering of plant growth rate and a new insight into the molecular mechanisms linking respiration and photosynthesis in plants.Plant tissues contain multiple isoforms of malate dehydrogenase (l-malate-NAD-oxidoreductase [MDH]; EC 1.1.1.37) that catalyze the interconversion of malate and oxaloacetate (OAA) coupled to reduction or oxidation of the NAD pool. These isoforms are encoded by separate genes in plants and have been shown to possess distinct kinetic properties as well as subcellular targeting and physiological functions (Gietl, 1992). While the MDH reaction is reversible, it strongly favors the reduction of OAA. The direction of the reaction in vivo depends on substrate/product ratios and the NAD redox state, and it can vary even in the same tissue due to prevailing physiological conditions. Isoforms operate in mitochondria, chloroplasts, peroxisomes, and the cytosol, but due to the ready transport and utilization of malate and OAA and the availability of NAD, this reaction can cooperate across compartments and is the basis for malate/OAA shuttling of reducing equivalents in many different metabolic schemes of plant cellular function (Krömer, 1995). It is clear, however, that the exchange through the membranes is strictly controlled, since large redox differences in NAD(H) pools exist between compartments (Igamberdiev and Gardeström, 2003).The mitochondrial MDH (mMDH) is thought to operate in at least three different pathways in plants. First, it is a classical tricarboxylic acid (TCA) cycle enzyme that oxidizes the malate product from the fumarase reaction to OAA for the citrate synthase-dependent condensation with acetyl-CoA to form citrate. Second, it is considered to operate in the reverse direction during the conversion of Gly to Ser by reducing OAA to malate and providing a supply of NAD⁺ for Gly decarboxylase (Journet et al., 1981). Third, in a more specialized pathway in C4 plants, it provides a supply of CO₂ for fixation in bundle sheath chloroplasts by reducing OAA (generated from Asp transported from mesophyll cells) into malate that is then decarboxylated by NAD-malic enzyme (NAD-ME) to CO₂ and pyruvate (Hatch and Osmond, 1976). Plant mitochondria can support TCA cycle activity with malate as the sole substrate due to MDH and NAD-ME, both ubiquitous in plants (Palmer, 1984). OAA is readily transported both into and out of isolated plant mitochondria (Douce and Bonner, 1972), in contrast to mammalian mitochondria, which are essentially impermeable to this organic acid.While these three mMDH schemes and metabolic schemes for other MDH isoforms are plausible, widely accepted, and consistent with a range of biochemical studies, the depletion, removal, and overexpression of specific MDH isoforms in plants have led to surprising insights into MDH roles in vivo. For example, the peroxisomal MDH (PMDH) was until recently generally considered to be involved in the synthesis of NADH for hydroxypyruvate reduction in the photorespiratory cycle and for the oxidation of NADH generated during β-oxidation of fatty acids, but its potential role in the oxidation of malate in the glyoxylate cycle was unclear. However, studies of the double knockout of PMDH in Arabidopsis (Arabidopsis thaliana) showed that while PMDH is essential for β-oxidation, its removal does not impair glyoxylate cycle activity (Pracharoenwattana et al., 2007) and has only a limited impact on hydroxypyruvate reduction (Cousins et al., 2008).Changes in mMDH have been reported both through the study of spontaneous mutants and the expression of antisense constructs. Spontaneous null mutants of mMDH1 in soybean (Glycine max) are linked to a yellow foliage phenotype and are associated with the removal of two of the three mMDH isoforms (Imsande et al., 2001). Expression of an antisense fragment of mMDH in tomato (Solanum lycopersicum), driven by the 35S promoter, lowered mMDH protein in mitochondria, decreased total cellular MDH by approximately 60%, but had a positive impact on photosynthetic activity, CO₂ assimilation rate, and total plant dry matter in long-day-grown plants (Nunes-Nesi et al., 2005). A range of carbohydrates also accumulated in the tomato antisense plants, as did redox-related compounds such as ascorbate. The increase in ascorbate content may be linked to the enhancement of photosynthesis, as ascorbate feeding to leaves can also increase photosynthetic performance (Nunes-Nesi et al., 2005). This link is not absolute, however, given that short-day-grown antisense tomato plants had stunted growth, which was potentially due to impaired photosynthesis, but still had elevated levels of ascorbate due to a higher ratio of reduction of the ascorbate pool compared with the wild type (Nunes-Nesi et al., 2008). Analysis of roots from these antisense tomato plants revealed a negative impact of mMDH loss, leading to a lower root dry weight and lower root respiratory rate (van der Merwe et al., 2009). This implies a distinct impact of mMDH loss on roots and shoots. Overexpression of cytosolic MDH led to a 4-fold elevation of root organic acids in alfalfa (Medicago sativa) plants and high rates of organic acid exudation that increased aluminum tolerance through metal chelation in the soil (Tesfaye et al., 2001). These studies imply that there is a complex form of functional redundancy between MDH isoforms in different compartments, allowing MDH in separate locations to maintain specific pathways via malate/OAA shuttling, or that a range of redox requirements that have been linked to MDH in accepted metabolic schemes are incorrect and other reactions couple NAD/NADH pool homeostasis. In addition, these studies clearly show that changes in the amount of MDH isoforms can alter metabolic flux into a range of organic acids and have far-reaching effects on plant growth and development.To better understand the importance of the mMDH and to determine if plants are viable without any mMDH isoforms due either to the role of NAD-ME and/or malate/OAA shuttling to other compartments, we have constructed and analyzed mMDH mutants in Arabidopsis. A major and a minor MDH isoform exist in Arabidopsis mitochondria, evidenced by differing levels of gene expression and differing protein abundance (Lee et al., 2008). We hypothesized that if mMDH works in concert with other MDH isoforms and is responsible for the reduction of OAA to malate for export from the mitochondrion, then if we remove mMDH, not only would the loss of extramitochondrial malate and the slowing of Gly decarboxylation limit photorespiratory carbon flux, but oxidation of NADH remaining in the mitochondrion could lead to elevated leaf respiration and alteration in plant growth. We found that not only did mutants have low photorespiratory flux, but they also increased respiration and had slow growth due to lowered net CO₂ assimilation. The previously established correlation between mMDH abundance, photosynthetic performance, and foliar ascorbate levels was also investigated. Elevated levels of the metabolite were found in Arabidopsis, consolidating the work done in tomato (Nunes-Nesi et al., 2005). Proteomic analyses, followed by immunodetection studies, unearthed altered abundance of the terminal enzyme of the ascorbate biosynthetic pathway, galactono-1,4-lactone dehydrogenase (GLDH), as a mechanistic element in the phenomenon linked directly to mitochondrial function.     

Wabusk of the Omushkegouk: Cree-Polar Bear (Ursus maritimus) Interactions in Northern Ontario

In order to understand wabusk (polar bear, Ursus maritimus) behaviours and interactions with people in the Hudson Bay lowlands of northern Ontario we conducted this collaborative study of Cree kiskayndamowin/knowledge. Our findings reveal that Cree knowledge supports previously published information on polar bears, while adding further contextual findings: that male polar bears travel greater distances into the muskeg than previously recorded; that wabusk prey on amisk (beaver, Castor canadensis); that wabusk interact with muskwa (black bears, Ursus americanus); and that human-polar bear interactions occur in this region of northern Canada. Bearing in mind that Cree knowledge has been recognized in wildlife management strategies (i.e., for beaver, caribou and moose) elsewhere in Canada, this particular body of information is timely, especially since polar bears are considered threatened under the Ontario Endangered Species Act, and the province is developing a recovery strategy for the Southern Hudson Bay polar bear population. The federal government is also contemplating listing polar bears in Canada as a “species of special concern” under the Species at Risk Act (SARA). While it is unclear as to how these decisions will impact the Cree-polar interactions, the listing of polar bears by both governments, but especially the provincial government of Ontario, must recognize treaty and Aboriginal rights, acknowledge its duties to consult and properly accommodate Aboriginal people’s views, incorporate Cree kiskayndamowin/knowledge of wabusk, and re-examine the proposed Wabusk Co-Management Agreement draft developed by the Ontario Ministry of Natural Resources (OMNR) and Coastal Cree First Nations of Northern Ontario in 1994. The article provides recommendations that highlight how the Northern Cree First Nations, through the development of the Recovery Strategy for Polar Bear in Ontario, can become engaged in the management of wabusk in Ontario and throughout Canada.     

Elucidating mechanisms of solvent toxicity in ethanologenic Escherichia coli

Ethanol toxicity and its effect on ethanol production by the recombinant ethanologenic Escherichia coli strain KO11 were investigated in batch and continuous fermentation. During batch growth, ethanol produced by KO11 reduced both the specific cell growth rate (µ) and the cell yield (Y_X/S). The extent of inhibition increased with the production of both acetate and lactate. Subsequent accumulation of these metabolites and ethanol resulted in cessation of cell growth, redirection of metabolism to reduce ethanol production, and increased requirements for cell maintenance. These effects were found to depend on both the glycolytic flux and the flux from pyruvate to ethanol. Pyruvate decarboxylase (Pdc) and alcohol dehydrogenase (Adh) activities measured during the batch fermentation suggested that decreased ethanol production resulted from enzyme inhibition rather than down‐regulation of genes in the ethanol‐producing pathway. Ethanol was added in continuous fermentation to provide an ethanol concentration of either 17 or 27 g/L, triggering sustained oscillations in the cell growth rate. Cell concentrations oscillated in‐phase with ethanol and acetate concentrations. The amplitude of oscillations depended on the concentration of ethanol in the fermentor. Through multiple oscillatory cycles, the yield (Y_P/S) and concentration of ethanol decreased, while production of acetate increased. These results suggest that KO11 favorably adapted to improve growth by synthesizing more ATP though acetate production, and recycling NADH by producing more lactate and less ethanol. Implications of these results for strategies to improve ethanol production are described. Biotechnol. Bioeng. 2010;106: 721–730. © 2010 Wiley Periodicals, Inc.