The Lung Microbiome in Moderate and Severe Chronic Obstructive Pulmonary Disease

Chronic obstructive pulmonary disease (COPD) is an inflammatory disorder characterized by incompletely reversible airflow obstruction. Bacterial infection of the lower respiratory tract contributes to approximately 50% of COPD exacerbations. Even during periods of stable lung function, the lung harbors a community of bacteria, termed the microbiome. The role of the lung microbiome in the pathogenesis of COPD remains unknown. The COPD lung microbiome, like the healthy lung microbiome, appears to reflect microaspiration of oral microflora. Here we describe the COPD lung microbiome of 22 patients with Moderate or Severe COPD compared to 10 healthy control patients. The composition of the lung microbiomes was determined using 454 pyrosequencing of 16S rDNA found in bronchoalveolar lavage fluid. Sequences were analyzed using mothur, Ribosomal Database Project, Fast UniFrac, and Metastats. Our results showed a significant increase in microbial diversity with the development of COPD. The main phyla in all samples were Actinobacteria, Firmicutes, and Proteobacteria. Principal coordinate analyses demonstrated separation of control and COPD samples, but samples did not cluster based on disease severity. However, samples did cluster based on the use of inhaled corticosteroids and inhaled bronchodilators. Metastats analyses demonstrated an increased abundance of several oral bacteria in COPD samples.     

Dyselectrolytemia in Chronic Obstructive Pulmonary Diseases with acute exacerbation

Chronic Obstructive Pulmonary Disease (COPD) is one of the leading causes of mortality and morbidity world wide. Due to lack of awareness about the precipitating factors and predictors of prognosis, cases of acute exacerbation of COPD often suffer the fatal outcomes. In our study we assessed the levels of serum sodium and potassium in subjects with acute episodes of COPD and their healthy controls. We found a significantly low level of serum sodium (133± 6.86 meq/lit) and potassium (3.39 ± 0.96 meq/L)) in subjects with acute exacerbation of COPD than their healthy counterparts [sodium-142 ± 2.28 meq/L and potassium- 4.52 ± 0.02 meq/L (p <0.05)]. Therefore, our study findings suggest that, serum sodium and potassium levels may get deranged in subjects with acute exacerbations of COPD which should be routinely checked for to avoid fatal outcomes.     

Bio-Energy Retains Its Mitigation Potential Under Elevated CO2

Background

If biofuels are to be a viable substitute for fossil fuels, it is essential that they retain their potential to mitigate climate change under future atmospheric conditions. Elevated atmospheric CO₂ concentration [CO₂] stimulates plant biomass production; however, the beneficial effects of increased production may be offset by higher energy costs in crop management.

Methodology/Main Findings

We maintained full size poplar short rotation coppice (SRC) systems under both current ambient and future elevated [CO₂] (550 ppm) and estimated their net energy and greenhouse gas balance. We show that a poplar SRC system is energy efficient and produces more energy than required for coppice management. Even more, elevated [CO₂] will increase the net energy production and greenhouse gas balance of a SRC system with 18%. Managing the trees in shorter rotation cycles (i.e., 2 year cycles instead of 3 year cycles) will further enhance the benefits from elevated [CO₂] on both the net energy and greenhouse gas balance.

Conclusions/Significance

Adapting coppice management to the future atmospheric [CO₂] is necessary to fully benefit from the climate mitigation potential of bio-energy systems. Further, a future increase in potential biomass production due to elevated [CO₂] outweighs the increased production costs resulting in a northward extension of the area where SRC is greenhouse gas neutral. Currently, the main part of the European terrestrial carbon sink is found in forest biomass and attributed to harvesting less than the annual growth in wood. Because SRC is intensively managed, with a higher turnover in wood production than conventional forest, northward expansion of SRC is likely to erode the European terrestrial carbon sink.     

The Regulatory Role of Reticulons in Neurodegeneration: Insights Underpinning Therapeutic Potential for Neurodegenerative Diseases

Cellular and Molecular Neurobiology - In the last few decades, cytoplasmic organellar dysfunction, such as that of the endoplasmic reticulum (ER), has created a new area of research interest...     

Systemic and Pulmonary Vascular Remodelling in Chronic Obstructive Pulmonary Disease

BackgroundChronic Obstructive Pulmonary Disease (COPD) is associated with subclinical systemic atherosclerosis and pulmonary vascular remodelling characterized by intimal hyperplasia and luminal narrowing. We aimed to determine differences in the intimal thickening of systemic and pulmonary arteries in COPD subjects and smokers. Secondary aims include comparisons with a non-smokers group; determining the clinical variables associated with systemic and pulmonary intimal thickening, and the correlations between systemic and pulmonary remodelling changes.MethodsAll consecutive subjects undergoing lung resection were included and divided into 3 groups: 1) COPD, 2) smokers, and 3) non-smokers. Sections of the 5th intercostal artery and muscular pulmonary arteries were measured by histo-morphometry. Four parameters of intimal thickening were evaluated: 1) percentage of intimal area (%IA), 2) percentage of luminal narrowing, 3) intimal thickness index, and 4) intima-to-media ratio.ResultsIn the adjusted analysis, the systemic arteries of COPD subjects showed greater intimal thickening (%IA) than those of smokers (15.6±1.5% vs. 14.2±1.6%, p = 0.038). In the pulmonary arteries, significant differences were observed for %IA between the 2 groups (37.3±2.2% vs. 29.3±2.3%, p = 0.016). Among clinical factors, metabolic syndrome, gender and COPD status were associated with the systemic intimal thickening, while only COPD status was associated with pulmonary intimal thickening. A correlation between the %IA of the systemic and pulmonary arteries was observed (Spearman’s rho = 0.46, p = 0.008).ConclusionsGreater intimal thickening in systemic and pulmonary arteries is observed in COPD patients than in smokers. There is a correlation between systemic and pulmonary vascular remodelling in the overall population.     

Minireview: Insights into anti-interferon-γ autoantibodies

The association between the presence of anti-interferon-γ autoantibodies and the onset of immunodeficiency with intracellular infections has been clearly established. No standard regimen to control the production of these pathogenic autoantibodies, apart from antimicrobial therapy to eliminate infections, contributes to the medical burden of this syndrome, which sometimes has a fatal outcome. In this review, we summarize the findings on anti-interferon-γ autoantibodies to facilitate further research and to provide guidance for treatment strategies.     

Periodontal Disease and Risk of Chronic Obstructive Pulmonary Disease: A Meta-Analysis of Observational Studies

Background

Many epidemiological studies have found a positive association between periodontal disease (PD) and risk of chronic obstructive pulmonary disease (COPD), but this association is varied and even contradictory among studies. We performed a meta-analysis to ascertain the relationship between PD and COPD.

Methods

PubMed and Embase database were searched up to January 10, 2012, for relevant observational studies on the association between PD and risk of COPD. Data from the studies selected were extracted and analyzed independently by two authors. The meta-analysis was performed using the Comprehensive Meta-Analysis software.

Results

Fourteen observational studies (one nested case-control, eight case-control, and five cross-sectional) involving 3,988 COPD patients were yielded. Based on random-effects meta-analysis, a significant association between PD and COPD was identified (odds ratio = 2.08, 95% confidence interval = 1.48–2.91; P<0.001), with sensitivity analysis showing that the result was robust. Subgroups analyses according to study design, ethnicity, assessment of PD/COPD, and adjusted/unadjusted odds ratios also revealed a significant association. Publication bias was detected.

Conclusions

Based on current evidence, PD is a significant and independent risk factor of COPD. However, whether a causal relationships exists remains unclear. Morever, we suggest performing randomized controlled trails to explore whether periodontal interventions are beneficial in regulating COPD pathogenesis and progression.     

Genetic Characterization and Role in Virulence of the Ribonucleotide Reductases of Streptococcus sanguinis

Streptococcus sanguinis is a cause of infective endocarditis and has been shown to require a manganese transporter called SsaB for virulence and O₂ tolerance. Like certain other pathogens, S. sanguinis possesses aerobic class Ib (NrdEF) and anaerobic class III (NrdDG) ribonucleotide reductases (RNRs) that perform the essential function of reducing ribonucleotides to deoxyribonucleotides. The accompanying paper (Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., and Stubbe, J. (2014) J. Biol. Chem. 289, 6259–6272) indicates that in the presence of O₂, the S. sanguinis class Ib RNR self-assembles an essential diferric-tyrosyl radical (Fe^III₂-Y^•) in vitro, whereas assembly of a dimanganese-tyrosyl radical (Mn^III₂-Y^•) cofactor requires NrdI, and Mn^III₂-Y^• is more active than Fe^III₂-Y^• with the endogenous reducing system of NrdH and thioredoxin reductase (TrxR1). In this study, we have shown that deletion of either nrdHEKF or nrdI completely abolishes virulence in an animal model of endocarditis, whereas nrdD mutation has no effect. The nrdHEKF, nrdI, and trxR1 mutants fail to grow aerobically, whereas anaerobic growth requires nrdD. The nrdJ gene encoding an O₂-independent adenosylcobalamin-cofactored RNR was introduced into the nrdHEKF, nrdI, and trxR1 mutants. Growth of the nrdHEKF and nrdI mutants in the presence of O₂ was partially restored. The combined results suggest that Mn^III₂-Y^•-cofactored NrdF is required for growth under aerobic conditions and in animals. This could explain in part why manganese is necessary for virulence and O₂ tolerance in many bacterial pathogens possessing a class Ib RNR and suggests NrdF and NrdI may serve as promising new antimicrobial targets.     

Germplasm Modification and Its Potential for Finding New Sources of Resistance to Diseases

In vitro procedures are playing a major role in plant breeding. Embryo rescue, either through the culture of excised embryos derived from incompatible crosses or by means of ovule culture, has been a standard procedure for the introgression of genes conferring disease resistance into economically important plants. Somatic hybridization (i.e., protoplast fusion) has also been demonstrated to have some potential in obtaining hybrids that result from very wide interspecific and intergeneric crosses. Wide crosses have also been achieved by means of in vitro pollination of excised ovaries or ovules. Tissue culture-induced variability in regenerated plant (i.e., somaclonal variation) appears to be an effective way of obtaining undirected genetic change that can enhance disease resistance and yield and alter the growth habit of crops that are normally propagated vegetatively (e.g., potato) or by seed (e.g., tomato). In the near future, the isolation and sequencing of genes that confer resistance to specific plant pathogens will be possible, and transfer of this information between species will become a reality.     

Review: Peroxisome Proliferator-Activated Receptor-γ and Its Role in the Development and Treatment of Diabetes

Since its identification as the receptor for antidiabetic thiazolidinedione drugs, peroxisome proliferator-activated receptor-γ (PPARγ) has been the focus of pharmaceutical drug discovery programs directed toward finding better drugs for the treatment of diabetes, as well as the object of basic research aimed at understanding its role in the regulation of metabolism. We now understand a great deal about the crucial role that PPARγ plays in adipocyte differentiation and development, and are rapidly gaining knowledge about the role of the receptor in the regulation of metabolism. However, many crucial aspects of the molecular mechanism by which modulation of PPARγ activity affects insulin resistance and glucose homeostasis are still not clearly understood. Here the authors review the current status of PPARγ research, with an emphasis on its role in the causes and treatment of type 2 diabetes.     

In Vitro Interactions of Extracellular Histones with LDL Suggest a Potential Pro-Atherogenic Role

Background

Nuclear histones have previously been shown to aggregate LDL in vitro, suggestive of a possible pro-atherogenic role. Recent studies indicate that histones are released during acute inflammation, and therefore might interact with circulating lipoproteins in vivo. In view of the associative link between inflammation and cardiovascular disease, the behaviour of histones was investigated using in vitro models of LDL retention and foam cell formation.

Methodology/Principal Findings

Heparin agarose beads were used as a model of a matrix rich in sulphated glycosaminoglycans, to which histones bind strongly. Histone-modified beads were observed to pull down more LDL from solution than untreated beads, indicating that histones can function as bridging molecules, enhancing LDL retention. Furthermore, addition of heparin inhibited histone-induced aggregation of LDL. To model foam cell formation, murine RAW 264.7 macrophages were incubated for 24 h in the presence of LDL, histones, LDL plus histones or vehicle control. Cells incubated with LDL in the presence of histones accumulated significantly more intracellular lipid than with LDL or histone alone.

Conclusions/Significance

These results are consistent with a potential pro-atherogenic role for extracellular histones, which should be investigated further.     

Pulmonary Aspergillosis and Aflatoxins in Chronic Lung Diseases

Recent studies have clearly defined the vaginopathic Candida albicans strains that cause severe vulvovaginal candidiasis (VVC). Therefore, genotyping C. albicans isolates may predict the success of and assist in choosing the appropriate antifungal therapy. The purpose of this study was to compare the genotypes of C. albicans isolates causing VVC with those found in asymptomatic healthy pregnant and non-pregnant women in Adana, Turkey, as well as the antifungal susceptibility profiles of these isolates. A total of 216 independent C. albicans isolates were genotyped by allelic combination based on the microsatellite marker analysis of one such microsatellite, present in the promoter region of the elongation factor 3-encoding gene (CEF3) of C. albicans. The susceptibility testing profiles of all of the isolates against five antifungals and boric acid were obtained retrospectively from our laboratory records. We identified 20 genotypes on the basis of different allelic combinations at the CEF3 locus with a discriminatory power of 0.85. Genotypes 136–144 and 126–135 were present in 50 % of the isolates. No differences existed in the genotypic profiles of fungal isolates between pregnant and non-pregnant women. Remarkably, we did not find a single vaginopathic genotype. All of the isolates were susceptible to amphotericin B and 5-fluorocytosine, and the fluconazole and ketoconazole resistance rates were 0.9 and 3.7 %, respectively. Therefore, we did not find any correlation between genotype, severity of VVC, and antifungal resistance (P > 0.05). Even so, additional molecular data may provide new insights into the management of VVC.     

lac Repressor Is an Antivirulence Factor of Salmonella enterica: Its Role in the Evolution of Virulence in Salmonella

The genus Salmonella includes many pathogens of great medical and veterinary importance. Bacteria belonging to this genus are very closely related to those belonging to the genus Escherichia. lacZYA operon and lacI are present in Escherichia coli, but not in Salmonella enterica. It has been proposed that Salmonella has lost lacZYA operon and lacI during evolution. In this study, we have investigated the physiological and evolutionary significance of the absence of lacI in Salmonella enterica. Using murine model of typhoid fever, we show that the expression of LacI causes a remarkable reduction in the virulence of Salmonella enterica. LacI also suppresses the ability of Salmonella enterica to proliferate inside murine macrophages. Microarray analysis revealed that LacI interferes with the expression of virulence genes of Salmonella pathogenicity island 2. This effect was confirmed by RT-PCR and Western blot analysis. Interestingly, we found that SBG0326 of Salmonella bongori is homologous to lacI of Escherichia coli. Salmonella bongori is the only other species of the genus Salmonella and it lacks the virulence genes of Salmonella pathogenicity island 2. Overall, our results demonstrate that LacI is an antivirulence factor of Salmonella enterica and suggest that absence of lacI has facilitated the acquisition of virulence genes of Salmonella pathogenicity island 2 in Salmonella enterica making it a successful systemic pathogen.     

Antibiotic Production by Myxobacteria Plays a Role in Predation

Myxobacteria are predatory and are prolific producers of secondary metabolites. Here, we tested a hypothesized role that secondary metabolite antibiotics function as weapons in predation. To test this, a Myxococcus xanthus Δta1 mutant, blocked in antibiotic TA (myxovirescin) production, was constructed. This TA⁻ mutant was defective in producing a zone of inhibition (ZOI) against Escherichia coli. This shows that TA is the major M. xanthus-diffusible antibacterial agent against E. coli. Correspondingly, the TA⁻ mutant was defective in E. coli killing. Separately, an engineered E. coli strain resistant to TA was shown to be resistant toward predation. Exogenous addition of spectinomycin, a bacteriostatic antibiotic, rescued the predation defect of the TA⁻ mutant. In contrast, against Micrococcus luteus the TA⁻ mutant exhibited no defect in ZOI or killing. Thus, TA plays a selective role on prey species. To extend these studies to other myxobacteria, the role of antibiotic corallopyronin production in predation was tested and also found to be required for Corallococcus coralloides killing on E. coli. Next, a role of TA production in myxobacterial fitness was assessed by measuring swarm expansion. Here, the TA⁻ mutant had a specific swarm rate reduction on prey lawns, and thus reduced fitness, compared to an isogenic TA⁺ strain. Based on these observations, we conclude that myxobacterial antibiotic production can function as a predatory weapon. To our knowledge, this is the first report to directly show a link between secondary metabolite production and predation.     

Indacaterol for Chronic Obstructive Pulmonary Disease: Systematic Review and Meta-Analysis

Background

Inhaled bronchodilators are the first-line therapy for COPD. Indacaterol is a novel addition to existing long-acting bronchodilators.

Objectives

Systematic review of randomized controlled trials (RCT) on efficacy and safety of indacaterol as compared: 1) with placebo at different dosages, 2) with existing bronchodilators; (3) as add-on treatment to tiotropium.

Methods

We searched 13 electronic databases, including MEDLINE, EMBASE and CENTRAL, and contacted the manufacturer for unpublished data. Primary outcome was mean FEV1 change at 12^th week, secondary outcomes included changes in SGRQ, TDI and BODE index at 6 months, exacerbation at 1 year, and worsening of symptoms.

Results

Twelve eligible RCTs of moderate risk of bias included data from 10,977 patients. Compared to placebo, indacaterol improved FEV1 by a weighted mean difference (WMD) of 0.16 L (95%CI: 0.15, 0.18 L, p<0.001), homogeneously above the minimally important difference of 0.10 L. It offered clinically relevant improvement in all secondary outcomes except exacerbation. Magnitude of benefit did not differ significantly by dosage, but one treatment related death was reported at 300 ug. Efficacy of Indacaterol was similar to formoterol and salmeterol (FEV1 WMD = 0.04L, 95%CI: 0.01L, 0.07 L, p = 0.02); and tiotropium (FEV1 WMD = 0.01L, 95%CI: −0.01, 0.03L, p = 0.61). The use of indacaterol on top of tiotropium yielded additional improvement on FEV1 (WMD = 0.07 L, 95%CI: 0.05L, 0.10 L, p<0.001).

Conclusion

Indacaterol is safe and beneficial for patients with COPD at dosage ≤150 ug. It may serve as a good alternative to existing bronchodilators, or as an add-on to tiotropium for unresponsive patients. Use of higher dosage requires further justification.     

Helicobacter pylori's Unconventional Role in Health and Disease

The discovery of a bacterium, Helicobacter pylori, that is resident in the human stomach and causes chronic disease (peptic ulcer and gastric cancer) was radical on many levels. Whereas the mouth and the colon were both known to host a large number of microorganisms, collectively referred to as the microbiome, the stomach was thought to be a virtual Sahara desert for microbes because of its high acidity. We now know that H. pylori is one of many species of bacteria that live in the stomach, although H. pylori seems to dominate this community. H. pylori does not behave as a classical bacterial pathogen: disease is not solely mediated by production of toxins, although certain H. pylori genes, including those that encode exotoxins, increase the risk of disease development. Instead, disease seems to result from a complex interaction between the bacterium, the host, and the environment. Furthermore, H. pylori was the first bacterium observed to behave as a carcinogen. The innate and adaptive immune defenses of the host, combined with factors in the environment of the stomach, apparently drive a continuously high rate of genomic variation in H. pylori. Studies of this genetic diversity in strains isolated from various locations across the globe show that H. pylori has coevolved with humans throughout our history. This long association has given rise not only to disease, but also to possible protective effects, particularly with respect to diseases of the esophagus. Given this complex relationship with human health, eradication of H. pylori in nonsymptomatic individuals may not be the best course of action. The story of H. pylori teaches us to look more deeply at our resident microbiome and the complexity of its interactions, both in this complex population and within our own tissues, to gain a better understanding of health and disease.Common wisdom circa 1980 suggested that the stomach, with its low pH, was a sterile environment. Then, endoscopy of the stomach became common and, in 1984, pathologist Robin Warren and gastroenterologist Barry Marshall saw an extracellular, curved bacillus, often in dense sheets, lining the stomach epithelium of patients with gastritis (inflammation of the stomach) and ulcer disease [1]. Soon, the medical community understood that the gram-negative bacterium Helicobacter pylori, not stress, is the major cause of stomach inflammation, which, in some infected individuals, precedes peptic ulcer disease (10%–20%), distal gastric adenocarcinoma (1%–2%), and gastric mucosal-associated lymphoid tissue (MALT) lymphoma (<1%) [2]–[5]. Thus, H. pylori gained distinction as the only known bacterial carcinogen [6]. It is believed that half of the world''s population is infected with H. pylori; however, the burden of disease falls disproportionately on less-developed countries. The incidence of infection in developed countries has fallen dramatically, for unknown reasons, with a corresponding decrease in gastric cancer [7]. This public health success is tempered by the recent demonstration of an inverse relationship between H. pylori infection and esophageal adenocarcinoma, Barrett''s esophagus, and reflux esophagitis [8]. H. pylori has been with humans since our earliest days, thus it is not surprising that its relationship is that of both a commensal bacterium and a pathogen, causing some diseases and possibly protecting against others. In addition, it is genetically diverse, likely as a result of constant exposure to both environmental and immunological selection, suggesting that genetic diversification is a strategy for long-term colonization.