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1.  Changes of the human gut microbiome induced by a fermented milk product 
Scientific Reports  2014;4:6328.
The gut microbiota (GM) consists of resident commensals and transient microbes conveyed by the diet but little is known about the role of the latter on GM homeostasis. Here we show, by a conjunction of quantitative metagenomics, in silico genome reconstruction and metabolic modeling, that consumption of a fermented milk product containing dairy starters and Bifidobacterium animalis potentiates colonic short chain fatty acids production and decreases abundance of a pathobiont Bilophila wadsworthia compared to a milk product in subjects with irritable bowel syndrome (IBS, n = 28). The GM changes parallel improvement of IBS state, suggesting a role of the fermented milk bacteria in gut homeostasis. Our data challenge the view that microbes ingested with food have little impact on the human GM functioning and rather provide support for beneficial health effects.
doi:10.1038/srep06328
PMCID: PMC4160712  PMID: 25209713
2.  The double-helix point spread function enables precise and accurate measurement of 3D single-molecule localization and orientation 
Single-molecule-based super-resolution fluorescence microscopy has recently been developed to surpass the diffraction limit by roughly an order of magnitude. These methods depend on the ability to precisely and accurately measure the position of a single-molecule emitter, typically by fitting its emission pattern to a symmetric estimator (e.g. centroid or 2D Gaussian). However, single-molecule emission patterns are not isotropic, and depend highly on the orientation of the molecule’s transition dipole moment, as well as its z-position. Failure to account for this fact can result in localization errors on the order of tens of nm for in-focus images, and ~50–200 nm for molecules at modest defocus. The latter range becomes especially important for three-dimensional (3D) single-molecule super-resolution techniques, which typically employ depths-of-field of up to ~2 μm. To address this issue we report the simultaneous measurement of precise and accurate 3D single-molecule position and 3D dipole orientation using the Double-Helix Point Spread Function (DH-PSF) microscope. We are thus able to significantly improve dipole-induced position errors, reducing standard deviations in lateral localization from ~2x worse than photon-limited precision (48 nm vs. 25 nm) to within 5 nm of photon-limited precision. Furthermore, by averaging many estimations of orientation we are able to improve from a lateral standard deviation of 116 nm (~4x worse than the precision, 28 nm) to 34 nm (within 6 nm).
doi:10.1117/12.2001671
PMCID: PMC4013112  PMID: 24817798
super resolution; fluorescence microscopy; three-dimensional microscopy; single molecule; dipole orientation; mislocalization; polarization microscopy
3.  Deer Browsing Delays Succession by Altering Aboveground Vegetation and Belowground Seed Banks 
PLoS ONE  2014;9(3):e91155.
Soil seed bank composition is important to the recovery of natural and semi-natural areas from disturbance and serves as a safeguard against environmental catastrophe. White-tailed deer (Odocoileus virginianus) populations have increased dramatically in eastern North America over the past century and can have strong impacts on aboveground vegetation, but their impacts on seed bank dynamics are less known. To document the long-term effects of deer browsing on plant successional dynamics, we studied the impacts of deer on both aboveground vegetation and seed bank composition in plant communities following agricultural abandonment. In 2005, we established six 15×15 m fenced enclosures and paired open plots in recently fallowed agricultural fields near Ithaca, NY, USA. In late October of each of six years (2005–2010), we collected soil from each plot and conducted seed germination cycles in a greenhouse to document seed bank composition. These data were compared to measurements of aboveground plant cover (2005–2008) and tree density (2005–2012). The impacts of deer browsing on aboveground vegetation were severe and immediate, resulting in significantly more bare soil, reduced plant biomass, reduced recruitment of woody species, and relatively fewer native species. These impacts persisted throughout the experiment. The impacts of browsing were even stronger on seed bank dynamics. Browsing resulted in significantly decreased overall species richness (but higher diversity), reduced seed bank abundance, relatively more short-lived species (annuals and biennials), and fewer native species. Both seed bank richness and the relative abundance of annuals/biennials were mirrored in the aboveground vegetation. Thus, deer browsing has long-term and potentially reinforcing impacts on secondary succession, slowing succession by selectively consuming native perennials and woody species and favoring the persistence of short-lived, introduced species that continually recruit from an altered seed bank.
doi:10.1371/journal.pone.0091155
PMCID: PMC3946751  PMID: 24608258
4.  Mitochondrial donation by stem cells: potential for novel therapeutics 
Molecular Cytogenetics  2014;7(Suppl 1):I59.
doi:10.1186/1755-8166-7-S1-I59
PMCID: PMC4043827  PMID: 24940382
6.  A systematic approach to interpretation of heterogeneous lung attenuation on computed tomography of the chest 
Computed tomography (CT) chest is widely used as an adjunct to clinical examination and pulmonary function tests in the evaluation of unexplained dyspnoea. In such patients, heterogeneous lung attenuation is a common finding on CT. Heterogeneous lungs can be caused by varying regional aeration, varying regional perfusion, and ground glass opacities (GGO) representing airspace or interstitial pathology. It does not serve the referring clinicians or the patients well if the radiology report simply mentions the heterogeneity of the lungs without due analysis of the cause of heterogeneity and a meaningful differential diagnosis. Therefore, it is imperative for the radiologist and the treating pulmonologist to have an in-depth understanding of the pathogenesis of pulmonary heterogeneity. This, in conjunction with clinical data, can narrow the differential diagnosis or, at times, lead to specific diagnoses. The purpose of this review is to familiarize readers with the CT representation of heterogeneities in aeration and perfusion of the lung, relate patterns of GGO to underlying pathology, and provide illustrative case studies highlighting the radiological approach to heterogeneous lungs.
doi:10.4103/0970-2113.120610
PMCID: PMC3841691  PMID: 24339492
Ground glass opacity; heterogeneous lungs; heterogeneous lung attenuation; mosaic attenuation; mosaic perfusion
7.  Insulin and the Lung: Connecting Asthma and Metabolic Syndrome 
Journal of Allergy  2013;2013:627384.
Obesity, metabolic syndrome, and asthma are all rapidly increasing globally. Substantial emerging evidence suggests that these three conditions are epidemiologically and mechanistically linked. Since the link between obesity and asthma appears to extend beyond mechanical pulmonary disadvantage, molecular understanding is necessary. Insulin resistance is a strong, independent risk factor for asthma development, but it is unknown whether a direct effect of insulin on the lung is involved. This review summarizes current knowledge regarding the effect of insulin on cellular components of the lung and highlights the molecular consequences of insulin-related metabolic signaling cascades that could adversely affect lung structure and function. Examples include airway smooth muscle proliferation and contractility and regulatory signaling networks that are associated with asthma. These aspects of insulin signaling provide mechanistic insight into the clinical evidence for the links between obesity, metabolic syndrome, and airway diseases, setting the stage for novel therapeutic avenues targeting these conditions.
doi:10.1155/2013/627384
PMCID: PMC3800560  PMID: 24204385
8.  Ultrastructural Changes of Airway in Murine Models of Allergy and Diet-Induced Metabolic Syndrome 
ISRN Allergy  2013;2013:261297.
Studying ultrastructural changes could reveal novel pathophysiology of obese-asthmatic condition as existing concepts in asthma pathogenesis are based on the histological changes of the diseased airway. While asthma is defined in functional terms, the potential of electron microscopy (EM) in providing cellular and subcellular detail is underutilized. With this view, we have performed transmission EM in the lungs from allergic mice that show key features of asthma and high-fat- or high-fructose-fed mice that mimicked metabolic syndrome to illustrate the ultrastructural changes. The primary focus was epithelial injury and metaplasia, which are cardinal features of asthma and initiate airway remodeling. EM findings of the allergically inflamed mouse lungs correlate with known features of human asthma such as increased mitochondria in airway smooth muscle, platelet activation and subepithelial myofibroblasts. Interestingly, we found a clear and unambiguous evidence to suggest that ciliated cells can become goblet cells using immunoelectron microscopy. Additionally, we show for the first time the stressed mitochondria in the bronchial epithelia of high-fat- or high-fructose-fed mice even without allergen exposure. These results may stimulate interest in using EM in understanding novel pathological mechanisms for different subtypes of asthma including obese asthma.
doi:10.1155/2013/261297
PMCID: PMC3782840  PMID: 24106613
9.  Integrating Health Care Delivery and Data Collection in Rural India Using a Rapidly Deployable eHealth Center 
PLoS Medicine  2013;10(6):e1001468.
Anurag Agrawal and colleagues describe their experience of setting up a readily deployable cargo container-based health center in rural India.
Please see later in the article for the Editors' Summary
doi:10.1371/journal.pmed.1001468
PMCID: PMC3692411  PMID: 23825182
10.  Genome-wide analysis reveals downregulation of miR-379/miR-656 cluster in human cancers 
Biology Direct  2013;8:10.
Background
MicroRNAs (miRNAs) are non-uniformly distributed in genomes and ~30% of the miRNAs in the human genome are clustered. In this study we have focused on the imprinted miRNA cluster miR-379/miR-656 on 14q32.31 (hereafter C14) to test their coordinated function. We have analyzed expression profile of >1000 human miRNAs in >1400 samples representing seven different human tissue types obtained from cancer patients along with matched and unmatched controls.
Results
We found 68% of the miRNAs in this cluster to be significantly downregulated in glioblastoma multiforme (GBM), 61% downregulated in kidney renal clear cell carcinoma (KIRC), 46% in breast invasive carcinoma (BRCA) and 14% in ovarian serous cystadenocarcinoma (OV). On a genome-wide scale C14 miRNAs accounted for 12-30% of the total downregulated miRNAs in different cancers. Pathway enrichment for the predicted targets of C14 miRNA was significant for cancer pathways, especially Glioma (p< 3.77x10-6, FDR<0.005). The observed downregulation was confirmed in GBM patients by real-time PCR, where 79% of C14 miRNAs (34/43) showed downregulation. In GBM samples, hypermethylation at C14 locus (p<0.003) and downregulation of MEF2, a crucial transcription factor for the cluster was observed which likely contribute to the observed downregulation of the entire miRNA cluster.
Conclusion
We provide compelling evidence that the entire C14 miRNA cluster is a tumor suppressor locus involved in multiple cancers, especially in GBM, and points toward a general mechanism of coordinated function for clustered miRNAs.
Reviewers
Reviewed by: Prof. Gregory J Goodall and Dr. Alexander Max Burroughs
doi:10.1186/1745-6150-8-10
PMCID: PMC3680324  PMID: 23618224
MiRNAs; Cluster; GBM; DLK1-DIO3; MEF2; Tumor Suppressor; Cancer
11.  12/15-lipoxygenase expressed in non-epithelial cells causes airway epithelial injury in asthma 
Scientific Reports  2013;3:1540.
The mechanisms underlying asthmatic airway epithelial injury are not clear. 12/15-lipoxygenase (an ortholog of human 15-LOX-1), which is induced by IL-13, is associated with mitochondrial degradation in reticulocytes at physiological conditions. In this study, we showed that 12/15-LOX expressed in nonepithelial cells caused epithelial injury in asthma pathogenesis. While 12/15-LOX overexpression or IL-13 administration to naïve mice showed airway epithelial injury, 12/15-LOX knockout/knockdown in allergic mice reduced airway epithelial injury. The constitutive expression of 15-LOX-1 in bronchial epithelia of normal human lungs further indicated that epithelial 15-LOX-1 may not cause epithelial injury. 12/15-LOX expression is increased in various inflammatory cells in allergic mice. Though non-epithelial cells such as macrophages or fibroblasts released 12/15-LOX metabolites upon IL-13 induction, bronchial epithelia didn't release. Further 12-S-HETE, arachidonic acid metabolite of 12/15-LOX leads to epithelial injury. These findings suggested 12/15-LOX expressed in non-epithelial cells such as macrophages and fibroblasts leads to bronchial epithelial injury.
doi:10.1038/srep01540
PMCID: PMC3607899  PMID: 23528921
12.  Oviposition strategy as a means of local adaptation to plant defence in native and invasive populations of the viburnum leaf beetle 
Herbivores have been hypothesized to adapt locally to variation in plant defences and such adaptation could facilitate novel associations in the context of biological invasions. Here, we show that in the native range of the viburnum leaf beetle (VLB, Pyrrhalta viburni), two populations of geographically isolated hosts—Viburnum opulus and Viburnum tinus—have divergent defences against VLB oviposition: negative versus positive density-dependent egg-crushing wound responses, respectively. Populations of beetles coexisting with each host show an adaptive behavioural response: aggregative versus non-aggregative oviposition on V. opulus and V. tinus, respectively. In parallel, we show that in North America, where VLB is invasive, defences of three novel hosts are negatively density-dependent, and beetles' oviposition behaviour is aggregative. Thus, local adaptation to plant defences has the potential to facilitate the invasion of herbivores onto novel hosts.
doi:10.1098/rspb.2011.1294
PMCID: PMC3259924  PMID: 21849322
insect oviposition strategy; invasion ecology; adaptive deme hypothesis; Chrysomelidae; plant–insect interactions; plant defence theory
13.  Lung cancer biomarkers: State of the art 
Lung cancer is one of the deadliest cancers worldwide, with the highest incidence and mortality amongst all cancers. While the prognosis of lung cancer is generally grim, with 5-year survival rates of only 15%, there is hope, and evidence, that early detection of lung cancer can reduce mortality. Today, only computed tomography screening has shown to lead to early detection and reduction in mortality, but is limited by being anatomic in nature, unable to differentiate between inflammatory and neoplastic pathways, and therefore, susceptible to false positives. There is increasing interest in biomarkers for lung cancer, especially those that predict metastatic risk. Some biomarkers like DNA mutations and epigenetic changes potentially require tissue from the at-risk site; some like serum proteins and miRNAs are minimally invasive, but may not be specific to the lung. In comparison, emerging biomarkers from exhaled breath, like volatile organic compounds (VOC), and exhaled breath condensate, e.g., small molecules and nucleic acids, have the potential to combine the best of both. This mini review is intended to provide an overview of the field, briefly discussing the potential of what is known and highlighting the exciting recent developments, particularly with miRNAs and VOCs.
doi:10.4103/1477-3163.107958
PMCID: PMC3622361  PMID: 23599685
Exhaled breath; lung cancer; miRNA; volatile organic compounds
14.  Linoleic acid metabolite drives severe asthma by causing airway epithelial injury 
Scientific Reports  2013;3:1349.
Airway epithelial injury is the hallmark of various respiratory diseases, but its mechanisms remain poorly understood. While 13-S-hydroxyoctadecadienoic acid (13-S-HODE) is produced in high concentration during mitochondrial degradation in reticulocytes little is known about its role in asthma pathogenesis. Here, we show that extracellular 13-S-HODE induces mitochondrial dysfunction and airway epithelial apoptosis. This is associated with features of severe airway obstruction, lung remodeling, increase in epithelial stress related proinflammatory cytokines and drastic airway neutrophilia in mouse. Further, 13-S-HODE induced features are attenuated by inhibiting Transient Receptor Potential Cation Channel, Vanilloid-type 1 (TRPV1) both in mouse model and human bronchial epithelial cells. These findings are relevant to human asthma, as 13-S-HODE levels are increased in human asthmatic airways. Blocking of 13-S-HODE activity or disruption of TRPV1 activity attenuated airway injury and asthma mimicking features in murine allergic airway inflammation. These findings indicate that 13-S-HODE induces mitochondrial dysfunction and airway epithelial injury.
doi:10.1038/srep01349
PMCID: PMC3583002  PMID: 23443229
15.  Regulation of NF-κB Activation through a Novel PI-3K-Independent and PKA/Akt-Dependent Pathway in Human Umbilical Vein Endothelial Cells 
PLoS ONE  2012;7(10):e46528.
The transcription factor NF-κB regulates numerous inflammatory diseases, and proteins involved in the NF-κB-activating signaling pathway are important therapeutic targets. In human umbilical vein endothelial cells (HUVECs), TNF-α-induced IκBα degradation and p65/RelA phosphorylation regulate NF-κB activation. These are mediated by IKKs (IκB kinases) viz. IKKα, β and γ which receive activating signals from upstream kinases such as Akt. Akt is known to be positively regulated by PI-3K (phosphoinositide-3-kinase) and differentially regulated via Protein kinase A (PKA) in various cell types. However, the involvement of PKA/Akt cross talk in regulating NF-κB in HUVECs has not been explored yet. Here, we examined the involvement of PKA/Akt cross-talk in HUVECs using a novel compound, 2-methyl-pyran-4-one-3-O-β-D-2′,3′,4′,6′-tetra-O-acetyl glucopyranoside (MPTAG). We observed that MPTAG does not directly inhibit IKK-β but prevents TNF-α-induced activation of IKK-β by blocking its association with Akt and thereby inhibits NF-κB activation. Interestingly, our results also revealed that inhibitory effect of MPTAG on Akt and NF-κB activation was unaffected by wortmannin, and was completely abolished by H-89 treatment in these cells. Thus, MPTAG-mediated inhibition of TNF-α-induced Akt activation was independent of PI-3K and dependent on PKA. Most importantly, MPTAG restores the otherwise repressed activity of PKA and inhibits the TNF-α-induced Akt phosphorylation at both Thr308 and Ser473 residues. Thus, we demonstrate for the first time the involvement of PKA/Akt cross talk in NF-κB activation in HUVECs. Also, MPTAG could be useful as a lead molecule for developing potent therapeutic molecules for diseases where NF-κB activation plays a key role.
doi:10.1371/journal.pone.0046528
PMCID: PMC3465347  PMID: 23071583
18.  Munc18b is an essential gene in mice whose expression is limiting for secretion by airway epithelial and mast cells 
Biochemical Journal  2012;446(Pt 3):383-394.
Airway mucin secretion and MC (mast cell) degranulation must be tightly controlled for homoeostasis of the lungs and immune system respectively. We found the exocytic protein Munc18b to be highly expressed in mouse airway epithelial cells and MCs, and localized to the apical pole of airway secretory cells. To address its functions, we created a mouse with a severely hypomorphic Munc18b allele such that protein expression in heterozygotes was reduced by ~50%. Homozygous mutant mice were not viable, but heterozygotes showed a ~50% reduction in stimulated release of mucin from epithelial cells and granule contents from MCs. The defect in MCs affected only regulated secretion and not constitutive or transporter-mediated secretion. The severity of passive cutaneous anaphylaxis was also reduced by ~50%, showing that reduction of Munc18b expression results in an attenuation of physiological responses dependent on MC degranulation. The Munc18b promoter is controlled by INR (initiator), Sp1 (specificity protein 1), Ets, CRE (cAMP-response element), GRE (glucocorticoid-response element), GATA and E-box elements in airway epithelial cells; however, protein levels did not change during mucous metaplasia induced by allergic inflammation. Taken together, the results of the present study identify Munc18b as an essential gene that is a limiting component of the exocytic machinery of epithelial cells and MCs.
doi:10.1042/BJ20120057
PMCID: PMC3430001  PMID: 22694344
exocytosis; mast cell; mucin; mucus; Munc18; secretion; AB-PAS, Alcian Blue/periodic acid/Schiff reagent; bHLH, basic helix–loop–helix; CCSP, Clara cell secretory protein; Clca3, chloride channel, calcium-activated, family member 3; CRE, cAMP-response element; DNP, 2,4-dinitrophenol; FBS, fetal bovine serum; FcϵRIα, high-affinity IgE receptor, α subunit; FRT, flippase recognition target; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GRE, glucocorticoid-response element; HA, haemagglutinin; HSA, human serum albumin; HRP, horseradish peroxidase; IL-3, interleukin-3; INR, initiator; ISH, in situ hybridization; MC, mast cell; mBMMC, mouse bone-marrow-derived MC; mClca3, mouse Clca3; MFI, mean fluorescent intensity; mtCC, mouse transformed Clara cell; NK, natural killer; OCT, optimal cutting temperature compound; PAFS, periodic acid/fluorescent Schiff reagent; PBST, PBS containing 0.05% Tween 20; PGD2, prostaglandin D2; PGK, phosphoglucokinase; SCF, stem cell factor; SM, Sec1/Munc18; SNAP, soluble N-ethylmaleimide-sensitive factor-attachment protein; SNARE, SNAP receptor; Stxbp2, syntaxin-binding protein 2; TK, thymidine kinase; TNFα, tumour necrosis factor α; WT, wild-type; YFP, yellow fluorescent protein
19.  Ants defend aphids against lethal disease 
Biology Letters  2009;6(2):205-208.
Social insects defend their own colonies and some species also protect their mutualist partners. In mutualisms with aphids, ants typically feed on honeydew produced by aphids and, in turn guard and shelter aphid colonies from insect natural enemies. Here we report that Formica podzolica ants tending milkweed aphids, Aphis asclepiadis, protect aphid colonies from lethal fungal infections caused by an obligate aphid pathogen, Pandora neoaphidis. In field experiments, bodies of fungal-killed aphids were quickly removed from ant-tended aphid colonies. Ant workers were also able to detect infective conidia on the cuticle of living aphids and responded by either removing or grooming these aphids. Our results extend the long-standing view of ants as mutualists and protectors of aphids by demonstrating focused sanitizing and quarantining behaviour that may lead to reduced disease transmission in aphid colonies.
doi:10.1098/rsbl.2009.0743
PMCID: PMC2865061  PMID: 19923138
ant–aphid interactions; social insects; behaviour; mutualism; entomopathogenic fungi; common milkweed (Asclepias syriaca)
20.  Re-evaluating the costs and limits of adaptive phenotypic plasticity 
When the optimal phenotype differs among environments, adaptive phenotypic plasticity can evolve unless constraints impede such evolution. Costs and limits of plasticity have been proposed as important constraints on the evolution of plasticity, yet confusion exists over their distinction. We attempt to clarify these concepts by reviewing their categorization and measurement, highlighting how costs and limits are defined in different currencies (and may describe the same phenomenon). Conclusions from studies that measure the costs of plasticity have been equivocal, but we caution that these conclusions may be premature owing to a potentially common correlation between environment-specific trait values and the magnitude of trait plasticities (i.e. multi-collinearity) that results in imprecise and/or biased estimates of the costs. Meanwhile, our understanding of the limits of plasticity, and how they may be underlain by the costs of plasticity, is still in its infancy. Based on our re-evaluation of these constraints, we discuss areas for future research.
doi:10.1098/rspb.2009.1355
PMCID: PMC2842679  PMID: 19846457
adaptation; canalization; constraint; cost of defence; homeostasis; phenotypic stability
21.  Physical Properties of Intact Proteins May Predict Allergenicity or Lack Thereof 
PLoS ONE  2009;4(7):e6273.
Background
Predicting the allergenicity of proteins is challenging. We considered the possibility that the properties of the intact protein that may alter the likelihood of being taken up by antigen presenting cells, may be useful adjuncts in predicting allergens and non-allergens in silico. It has been shown that negatively charged acidic proteins are preferentially processed by dendritic cells.
Methodology
Datasets (aeroallergen, food-allergen and non-allergen) for in-silico study were obtained from public databases. Isoelectric point (pI), net charge, and electrostatic potential (EP) were calculated from the protein sequence (for pI and net charge) or predicted structure (for EP).
Result
Allergens and non allergens differed significantly in pI, net charge, and EP (p<0.0001). Cluster analysis based on these parameters resulted in well defined clusters. Non-allergens were characterized by neutral to basic pI (mean±SE, 7.6±0.16) and positive charge. In contrast allergens were acidic (5.7±0.15) and negatively charged. Surface electrostatic potentials calculated from predicted structures were mostly negative for allergens and mostly positive for non-allergens. The classification accuracy for non-allergens was superior to that for allergens. Thus neutral to basic pI, positive charge, and positive electrostatic potentials characterize non-allergens, and seem rare in allergens (p<0.0001). It may be possible to predict reduced likelihood of allergenicity in such proteins, but this needs to be prospectively validated.
doi:10.1371/journal.pone.0006273
PMCID: PMC2707619  PMID: 19609445

Results 1-21 (21)